PMID
int64 275k
40M
| DateCompleted
stringdate 1965-11-14 00:00:00
2025-02-28 00:00:00
⌀ | DateRevised
stringdate 2000-12-18 00:00:00
2025-02-28 00:00:00
| ISSN
stringlengths 9
9
⌀ | JournalTitle
stringlengths 2
239
| ArticleTitle
stringlengths 1
1.99k
⌀ | Authors
stringlengths 3
61.6k
⌀ | Language
stringclasses 47
values | Grants
stringlengths 11
10.6k
⌀ | PublicationTypes
stringlengths 4
259
| Chemicals
stringlengths 3
1.33k
⌀ | CitationSubset
stringclasses 2
values | ArticleIds
stringlengths 6
44.3k
| Abstract
stringlengths 1
16.7k
⌀ | MeshTerms
stringlengths 3
1.18k
⌀ | Keywords
stringlengths 1
17.2k
⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
22,705,752 | 2014-02-04 | 2018-12-02 | 1878-8769 | World neurosurgery | Intervertebral disc degeneration: genes hold the key. | Erwin W Mark, Fehlings Michael G | eng | null | Journal Article, Comment | null | IM | 22705752, S1878-8750(12)00630-4, 10.1016/j.wneu.2012.06.010 | null | Humans, Intervertebral Disc Degeneration | Aggrecan, Collagens, DDD, Degeneration, Degenerative disc disease, ECM, Extracellular matrix, Genetics, IL, IVD, Interleukin, Interleukins, Intervertebral disc, MMP, Matrix metalloproteinase, Matrix-degrading enzymes, NP, Nucleus pulposus, TNF, Tumor necrosis factor, Vitamin D receptor |
22,705,756 | 2014-02-04 | 2018-12-02 | 1878-8769 | World neurosurgery | A short history of neurosurgical localization. | De Ridder Dirk | eng | null | Journal Article, Comment | null | IM | 22705756, S1878-8750(12)00633-X, 10.1016/j.wneu.2012.06.013 | null | Humans, Movement Disorders, Neuroanatomy, Neurosurgery, Stereotaxic Techniques, Subthalamus | Behavioral disorders, Chronic pain, Epilepsy, Functional stereotaxy, Movement disorders, Subthalamus (ventral thalamus) |
22,705,753 | 2013-11-05 | 2018-12-02 | 1878-8769 | World neurosurgery | Brainstem cavernoma surgery: the state of the art. | Abla Adib A, Spetzler Robert F | eng | null | Journal Article, Comment | null | IM | 22705753, S1878-8750(12)00631-6, 10.1016/j.wneu.2012.06.011 | null | Endovascular Procedures, Female, Humans, Intracranial Arteriovenous Malformations, Male, Neurosurgical Procedures | Angioma, Brainstem, Cavernoma, Cavernous, MRI, Magnetic resonance imaging, Surgery |
22,705,758 | 2013-02-21 | 2018-12-02 | 1878-8769 | World neurosurgery | Outcomes after stereotactic radiosurgery and various adjuvant treatments for recurrent glioblastoma multiforme: a current literature review and comparison of multiple factors that impact outcome. | Murovic Judith A, Chang Steven D | eng | null | Journal Article, Comment | null | IM | 22705758, S1878-8750(12)00625-0, 10.1016/j.wneu.2012.06.005 | null | Brain Neoplasms, Female, Glioblastoma, Humans, Male, Neoplasm Recurrence, Local, Postoperative Complications, Radiosurgery | null |
22,705,755 | 2013-11-05 | 2018-12-02 | 1878-8769 | World neurosurgery | Interspinous distraction devices: too good to be true? Yes. | Krauss William E | eng | null | Journal Article, Comment | null | IM | 22705755, S1878-8750(12)00632-8, 10.1016/j.wneu.2012.06.012 | null | Equipment and Supplies, Female, Humans, Intermittent Claudication, Male, Spinal Stenosis | FDA, Interspinous device, NC/LS, Neurogenic claudication/lumbar stenosis, Neurogenic intermittent claudication, Spinal stenosis, U.S. Food and Drug Administration, X-STOP |
22,705,761 | 2013-01-24 | 2016-05-19 | 1878-8769 | World neurosurgery | Patient positioning: is it really a big deal? | Harrop James S | eng | null | Comment, Journal Article | null | null | 22705761, S1878-8750(12)00628-6, 10.1016/j.wneu.2012.06.008 | null | null | null |
22,705,754 | 2013-12-05 | 2018-12-02 | 1878-8769 | World neurosurgery | Chasing the Holy Grail of vestibular schwannoma management. | Link Michael J, Pollock Bruce E | eng | null | Journal Article, Comment | null | IM | 22705754, S1878-8750(12)00627-4, 10.1016/j.wneu.2012.06.007 | null | Cochlea, Female, Hearing Loss, Humans, Male, Neuroma, Acoustic, Postoperative Complications, Radiosurgery | CT, Cochlea, Computed tomography, GR, Gardner-Robertson, Hearing preservation, IAC, Internal auditory canal, Radiation, SRS, SRT, Stereotactic radiation therapy, Stereotactic radiosurgery, VS, Vestibular schwannoma |
22,705,762 | 2012-11-23 | 2012-07-16 | 1095-8630 | Journal of environmental management | Diagnostic reframing of intractable environmental problems: case of a contested multiparty public land-use conflict. | Asah Stanley T, Bengston David N, Wendt Keith, Nelson Kristen C | eng | null | Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705762, S0301-4797(12)00238-1, 10.1016/j.jenvman.2012.04.041 | Intractable conflicts are omnipresent in environmental management. These conflicts do not necessarily resist resolution but need to be fundamentally transformed in order to reach agreement. Reframing, a process that allows disputants to create new alternative understandings of the problem, is one way of transforming these conflicts. Cognitive and interactional reframing are the two major approaches to conflict transformation. These approaches have some drawbacks. Cognitive reframing does not guarantee commensurate consideration of all disputants' views about the problem. Interactional reframing is prone to inter-disputant influences that interfere with presenting the problems as accurately as they exist in disputants' minds. Inadequate consideration of other disputants' views and inter-disputant influences often lead to inaccurate problem identification and definition. This in turn leads to solving the wrong problem, enabling intractability to persist. Proper problem identification and definition requires commensurate consideration of all sides of the conflict while minimizing inter-disputant influences. From a problem diagnosis perspective, we show how Q methodology is used to reframe environmental problems, rendering them more tractable to analysis while minimizing the influence of who disputants are talking with, and without ignoring the perspectives of other disputants. Using a case of contentious All-Terrain Vehicle (ATV) use in a state-administered public land, conflicting parties reframed the problem by prioritizing issues, outlining areas and levels of consensus and disagreement, and revealing inherent unrecognized and/or unspoken agendas. The reframing process surprisingly revealed several areas of common ground in disputants' diagnosis of the problem, including lack of emphasis on environmental protection and uncoordinated management factions. Emergent frames were misaligned on some issues, such as the behaviors of ATV riders and the role of management, including political and economic influences on decision making. We discuss how the reframing process enhances tractability of multiparty environmental problems. We point to some limitations of Q methodology as a tool for the diagnostic reframing of such problems. | Consensus, Conservation of Natural Resources, Environment, Minnesota, Off-Road Motor Vehicles, Problem Solving, Recreation | null |
22,705,757 | 2013-06-18 | 2022-04-08 | 1878-8769 | World neurosurgery | Meningiomas and postoperative epilepsy: it is time for a randomized controlled clinical trial. | Tomasello Francesco | eng | null | Journal Article, Comment | null | IM | 22705757, S1878-8750(12)00624-9, 10.1016/j.wneu.2012.06.004 | null | Female, Humans, Male, Meningioma, Neurosurgical Procedures, Seizures, Supratentorial Neoplasms | null |
22,705,763 | 2012-11-23 | 2017-11-16 | 1095-8630 | Journal of environmental management | Responses of fungal and plant communities to partial humus removal in mid-boreal N-enriched forests. | Tarvainen Oili, Hamberg Leena, Ohenoja Esteri, Strömmer Rauni, Markkola Annamari | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Soil, Nitrogen | IM | 22705763, S0301-4797(12)00260-5, 10.1016/j.jenvman.2012.05.003 | Partial removal of the forest humus layer was performed in nitrogen-enriched urban Scots pine forest stands in the northern Finland in order to improve soil conditions for ectomycorrhizal (ECM) fungi, important symbionts of trees. Aboveground part of understory vegetation and the uppermost half of the humus layer were removed (REMOVAL treatment) from sample plots in six urban and eight rural reference forest sites at the beginning of the 2001 growing season. During the seasons 2001-2005, we inventoried sporocarp production of ECM and saprophytic fungi, and in 2003 the recovery of understory vegetation. The REMOVAL treatment resulted in a higher number of fruiting ECM species and sporocarps than controls at the rural, but not at urban sites. The sporocarp number of saprophytic fungi declined in the REMOVAL subplots at the urban sites. The recovery of bryophytes and lichens in the REMOVAL treatment was slow at both the urban and rural sites, whereas Vaccinium dwarf shrub cover, and herb and grass cover returned rapidly at the urban sites. We conclude that the partial vegetation and humus layer removal as a tool to promote the reproduction of ECM fungal species is limited in the boreal urban forests. | Bryophyta, Ecosystem, Finland, Lichens, Mycorrhizae, Nitrogen, Pinus sylvestris, Soil, Vaccinium | null |
22,705,766 | 2012-11-21 | 2012-07-23 | 1096-0279 | Protein expression and purification | Enhancement of alkaline phytase production in Pichia pastoris: influence of gene dosage, sequence optimization and expression temperature. | Yang Mimi, Johnson Steven C, Murthy Pushpalatha P N | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Recombinant Proteins, 6-Phytase | IM | 22705766, S1046-5928(12)00170-2, 10.1016/j.pep.2012.06.001 | Supplementation of animal feed with phytases has proven to be an effective strategy to alleviate phosphorous contamination of soil and water bodies. The inability of non-ruminant animals to digest phytates in corn and soybeans contributes to environmental contamination. Alkaline phytase from lily pollen (LlALP) exhibits unique catalytic and thermal stability properties that could be useful as a feed supplement. rLlALP2 was successfully expressed in Pichia pastoris; however, enzyme yields were modest (8-10 mg/L). In this paper, we describe our efforts to enhance rLlALP2 yield by investigating the influence of the following potential limiting factors: transgene copy number, codon bias, sequence optimization, and temperature during expression. Data presented indicate that increasing rLlAlp2 copy number was detrimental to heterologous expression, clones with one copy of wt-rLlAlp2 produced the highest activity, clones with two, four and seven or more copies produced 70%, 25% and 10% respectively, of enzyme activity implying that gene dosage is not limiting rLlALP2 yield. Use of a sequence-optimized rLlAlp2 increased the yield of the active enzyme by 25-50% in one/two copy clones, suggesting that translational efficiency is not a major bottleneck for rLlALP2 expression. Reducing the temperature during heterologous expression led to increases of 1.2-20-fold suggesting that protein folding and post-translational processes may be the dominant factors limiting rLlALP2 expression. Early knowledge of the transgene copy number allowed us to develop a more rational strategy for yield enhancement. Cumulatively, sequence optimization and temperature reduction led to the doubling of rLlALP2 enzyme activity in P. pastoris. | 6-Phytase, Amino Acid Sequence, Base Sequence, Cloning, Molecular, Gene Dosage, Gene Expression, Lilium, Molecular Sequence Data, Pichia, Plasmids, Recombinant Proteins, Sequence Alignment, Temperature | null |
22,705,764 | 2012-11-23 | 2012-07-16 | 1095-8630 | Journal of environmental management | Human disturbance of the Waitomo catchment, New Zealand. | van Beynen Philip E, Bialkowska-Jelinska Elzbieta | eng | null | Journal Article | null | IM | 22705764, S0301-4797(12)00235-6, 10.1016/j.jenvman.2012.04.038 | The karst disturbance index (KDI) consists of 31 environmental indicators categorized within the five broad categories of geomorphology, hydrology, atmosphere, biota, and culture. This article discusses the application of the KDI to the rural karst region of Waitomo, New Zealand. Previous applications of the KDI measured disturbance to urban areas as delineated by geo-political boundaries while this study used a physical boundary of a small karst catchment. Such an approach ensures greater environmental specificity of measured disturbance levels compared to those determined according to arbitrary, politically defined areas. The study included a comparison of a local resource manager and a visiting karst expert's determinations of disturbance levels for the catchment. Overall, the Waitomo catchment was found to be moderately disturbed. The only significant, direct disturbances were deforestation and erosion; however, these lead to the indirect disturbance of cave biota, water quality and accelerated sedimentation of the catchment's waterways. We have a high degree of confidence in the validity of these results due to the ability to assess all of the applicable indicators in the index, and the consistency of scoring by both individuals who applied the index. The benefit of applying the KDI at the catchment level is the greater accuracy measuring disturbance as opposed to applying the index within geo-political boundaries that incorporate both karst and non-karst terrains. With disturbance data for a highly specific area, the Waitomo resource managers have the improved ability to effectively identify, target, remediate, and manage human disturbance of the karst landscape. | Agriculture, Animals, Artifacts, Caves, Conservation of Natural Resources, Groundwater, Humans, New Zealand, Water Pollution, Water Supply | null |
22,705,765 | 2012-11-21 | 2013-11-21 | 1096-0279 | Protein expression and purification | Fractional factorial approach combining 4 Escherichia coli strains, 3 culture media, 3 expression temperatures and 5 N-terminal fusion tags for screening the soluble expression of recombinant proteins. | Noguère Christophe, Larsson Anna M, Guyot Jean-Christophe, Bignon Christophe | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Culture Media, His-His-His-His-His-His, Oligopeptides, Recombinant Proteins, Histidine | IM | 22705765, S1046-5928(12)00162-3, 10.1016/j.pep.2012.05.011 | Producing recombinant proteins in Escherichia coli (E. coli) is generally performed using a trial and error approach with the different expression variables being tested independently from each other. As a consequence, variable interactions are lost which makes the trial and error approach quite time-consuming. In this paper, we report how switching from a trial and error to a fractional factorial approach allows testing in less than 2 weeks four expression variables (E. coli strains, culture media, expression temperatures and N-terminal fusion tags) in a single experiment. The method, called "Fusion-InFFact", was validated using four test proteins. In all cases, Fusion-InFFact allowed finding conditions for expressing high yields of soluble proteins. The method was originally set-up for high throughput structural genomics programs, but can be used in any recombinant protein expression project. | Amino Acid Sequence, Cloning, Molecular, Culture Media, Escherichia coli, Gene Expression, Genetic Vectors, Genomics, Histidine, Molecular Sequence Data, Oligopeptides, Recombinant Proteins, Solubility, Temperature | null |
22,705,767 | 2012-09-25 | 2020-12-16 | 1941-3297 | Circulation. Heart failure | Exercise hemodynamics in patients with and without diastolic dysfunction and preserved ejection fraction after myocardial infarction. | Andersen Mads J, Ersbøll Mads, Bro-Jeppesen John, Gustafsson Finn, Hassager Christian, Køber Lars, Borlaug Barry A, Boesgaard Søren, Kjærgaard Jasper, Møller Jacob E | eng | null | Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705767, CIRCHEARTFAILURE.112.967919, 10.1161/CIRCHEARTFAILURE.112.967919 | Left ventricular diastolic dysfunction (DD) is common after myocardial infarction (MI) despite preservation of left ventricular ejection fraction, yet it remains unclear how or whether DD affects cardiac hemodynamics with stress. | Adult, Aged, Analysis of Variance, Cardiac Catheterization, Cardiac Output, Case-Control Studies, Chi-Square Distribution, Denmark, Diastole, Disease Progression, Echocardiography, Doppler, Exercise, Exercise Test, Female, Heart Failure, Hemodynamics, Humans, Male, Middle Aged, Myocardial Infarction, Prospective Studies, Stroke Volume, Ventricular Dysfunction, Left, Ventricular Function, Left, Ventricular Pressure | null |
22,705,768 | 2012-09-25 | 2012-11-15 | 1941-3297 | Circulation. Heart failure | Phosphoinositide 3-kinase p110α is a master regulator of exercise-induced cardioprotection and PI3K gene therapy rescues cardiac dysfunction. | Weeks Kate L, Gao Xiaoming, Du Xiao-Jun, Boey Esther J H, Matsumoto Aya, Bernardo Bianca C, Kiriazis Helen, Cemerlang Nelly, Tan Joon Win, Tham Yow Keat, Franke Thomas F, Qian Hongwei, Bogoyevitch Marie A, Woodcock Elizabeth A, Febbraio Mark A, Gregorevic Paul, McMullen Julie R | eng | null | Journal Article, Research Support, Non-U.S. Gov't | HSP70 Heat-Shock Proteins, 1-phosphatidylinositol 3-kinase p110 subunit, mouse, Class I Phosphatidylinositol 3-Kinases | IM | 22705768, CIRCHEARTFAILURE.112.966622, 10.1161/CIRCHEARTFAILURE.112.966622 | Numerous molecular and biochemical changes have been linked with the cardioprotective effects of exercise, including increases in antioxidant enzymes, heat shock proteins, and regulators of cardiac myocyte proliferation. However, a master regulator of exercise-induced protection has yet to be identified. Here, we assess whether phosphoinositide 3-kinase (PI3K) p110α is essential for mediating exercise-induced cardioprotection, and if so, whether its activation independent of exercise can restore function of the failing heart. | Animals, Class I Phosphatidylinositol 3-Kinases, Disease Models, Animal, Female, Gene Expression Regulation, Genetic Therapy, Genotype, HSP70 Heat-Shock Proteins, Heart Failure, Hypertrophy, Left Ventricular, Mice, Mice, Inbred BALB C, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Myocardial Contraction, Myocardium, Phenotype, Physical Exertion, Recovery of Function, Time Factors, Ventricular Function, Left, Ventricular Remodeling | null |
22,705,759 | 2013-12-05 | 2018-12-02 | 1878-8769 | World neurosurgery | Prognostic prediction of patients with poor-grade aneurysmal subarachnoid hemorrhage and additional intracerebral hemorrhage. | Zhu Wei, Mao Ying | eng | null | Journal Article, Comment | null | IM | 22705759, S1878-8750(12)00626-2, 10.1016/j.wneu.2012.06.006 | null | Aneurysm, Ruptured, Cerebral Hemorrhage, Female, Humans, Intracranial Aneurysm, Male, Middle Cerebral Artery | CT, Clip ligation, Computed tomography, ICH, Intracerebral hematoma, Intracerebral hemorrhage, MCA, Middle cerebral artery, Middle cerebral artery aneurysm, Neurosurgical procedures, Outcome, SAH, Subarachnoid hemorrhage, Surgical evacuation |
22,705,770 | 2012-10-26 | 2012-06-26 | 1364-548X | Chemical communications (Cambridge, England) | In situ UV-Vis DRS evidence of Cr2+ species oxidation by CO2. | Michorczyk Piotr, Ogonowski Jan | eng | null | Journal Article | null | null | 22705770, 10.1039/c2cc32056h | In situ UV-Vis DRS investigations have revealed that the Cr(2+) species, which dominate on the surface of a CO-reduced Cr/SBA-1 catalyst, can be oxidized by CO(2) at a wide range of temperatures. Such an oxidation is a multistep process proceeding probably via carboxylate intermediates. | null | null |
22,705,760 | 2013-06-18 | 2018-12-02 | 1878-8769 | World neurosurgery | Intramedullary spinal deposits: overview and perspective. | El-Fiki Mohamed | eng | null | Journal Article, Comment | null | IM | 22705760, S1878-8750(12)00629-8, 10.1016/j.wneu.2012.06.009 | null | Female, Humans, Male, Spinal Cord Neoplasms | null |
22,705,769 | 2012-09-25 | 2022-03-17 | 1941-3297 | Circulation. Heart failure | Agonist-induced hypertrophy and diastolic dysfunction are associated with selective reduction in glucose oxidation: a metabolic contribution to heart failure with normal ejection fraction. | Mori Jun, Basu Ratnadeep, McLean Brent A, Das Subhash K, Zhang Liyan, Patel Vaibhav B, Wagg Cory S, Kassiri Zamaneh, Lopaschuk Gary D, Oudit Gavin Y | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Angiotensin II Type 1 Receptor Blockers, E2F Transcription Factors, Pyruvate Dehydrogenase Acetyl-Transferring Kinase, Receptor, Angiotensin, Type 1, Receptors, Adrenergic, alpha, Retinoblastoma Protein, Angiotensin II, Phenylephrine, Protein Serine-Threonine Kinases, Cyclin-Dependent Kinases, Glucose | IM | 22705769, CIRCHEARTFAILURE.112.966705, 10.1161/CIRCHEARTFAILURE.112.966705 | Activation of the renin-angiotensin and sympathetic nervous systems may alter the cardiac energy substrate preference, thereby contributing to the progression of heart failure with normal ejection fraction. We assessed the qualitative and quantitative effects of angiotensin II (Ang II) and the α-adrenergic agonist, phenylephrine (PE), on cardiac energy metabolism in experimental models of hypertrophy and diastolic dysfunction and the role of the Ang II type 1 receptor. | Angiotensin II, Angiotensin II Type 1 Receptor Blockers, Animals, Cardiomegaly, Cyclin-Dependent Kinases, E2F Transcription Factors, Energy Metabolism, Glucose, Heart Failure, Male, Mice, Mice, Inbred C57BL, Myocardium, Oxidation-Reduction, Phenylephrine, Protein Serine-Threonine Kinases, Pyruvate Dehydrogenase Acetyl-Transferring Kinase, Receptor, Angiotensin, Type 1, Receptors, Adrenergic, alpha, Retinoblastoma Protein, Signal Transduction, Stroke Volume, Time Factors, Ultrasonography, Ventricular Function | null |
22,705,771 | 2013-01-15 | 2013-11-21 | 1873-6351 | Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association | Inhibitory effects of Zataria multiflora essential oil and its main components on nitric oxide and hydrogen peroxide production in glucose-stimulated human monocyte. | Kavoosi Gholamreza, Teixeira da Silva Jaime A | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Multienzyme Complexes, Oils, Volatile, Nitric Oxide, Hydrogen Peroxide, Nitric Oxide Synthase, NADH oxidase, NADH, NADPH Oxidoreductases, Glucose | IM | 22705771, S0278-6915(12)00416-4, 10.1016/j.fct.2012.06.002 | The inhibitory effects of Zataria multiflora essential oil on nitric oxide (NO) and hydrogen peroxide (H(2)O(2)) production were examined in human monocytes cultured in the presence of 20mM glucose. Z. multiflora essential oil was extracted by water-distillation and then analyzed by GC-MS. Carvacrol (29.2%), thymol (25.4%), p-cymene (11.2%), linalool (9.6%) and γ-terpinene (8%) were the main components detected in the essential oil. Cells cultured in the presence of 20mM glucose showed an increase in NO and H(2)O(2) production as well as NO synthase (NOS) and NADH oxidase (NOX) activities compared to cells cultured in the presence of 5mM glucose. Pretreatment with Z. multiflora essential oil, carvacrol and thymol reduced NO and H(2)O(2) production as well as NOS and NOX activities in those cells cultured in the presence of 20mM glucose. However, p-cymene, linalool and γ-terpinene did not show any such activities. Accordingly, it was concluded that Z. multiflora can reduce oxidative stress and can be used in the therapy of oxidative damage accompanying hyperglycemia and some inflammatory conditions. | Cells, Cultured, Gas Chromatography-Mass Spectrometry, Glucose, Humans, Hydrogen Peroxide, Lamiaceae, Monocytes, Multienzyme Complexes, NADH, NADPH Oxidoreductases, Nitric Oxide, Nitric Oxide Synthase, Oils, Volatile | null |
22,705,772 | 2013-01-15 | 2017-11-16 | 1873-6351 | Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association | Bergamottin is a competitive inhibitor of CYP1A1 and is antimutagenic in the Ames test. | Olguín-Reyes S, Camacho-Carranza R, Hernández-Ojeda S, Elinos-Baez M, Espinosa-Aguirre J J | eng | null | Journal Article | Antimutagenic Agents, Enzyme Inhibitors, Furocoumarins, Cytochrome P-450 CYP1A1, bergamottin | IM | 22705772, S0278-6915(12)00411-5, 10.1016/j.fct.2012.05.058 | Grapefruit juice (GJ) is a well known Cytochrome P450 (CYP) inhibitor; CYP3A is one of the most affected subfamily leading to anticarcinogenic and antimutagenic effects when GJ is administered to experimental animals in combination with mutagenic/carcinogenic agents metabolized by CYP3A. Bergamottin, naringin and dihydroxybergamottin are three main constituents contained within GJ and their inhibitory effect against CYP3A4 has been well documented. Reports suggest that CYP3A is not the only one affected but CYP1A and 2B are also affected by GJ. To explore this last possibility in depth we tested the in vitro capacity of bergamottin, naringin and dihydroxybergamottin to inhibit the activity of CYP1A and 2B subfamilies and found that bergamottin showed the strongest inhibitory effect and naringin showed no inhibition at all. Therefore, we decided to biochemically characterize the inhibitory properties of bergamottin. CYP1A1 Supersome® used in this study showed a Km(app)=0.0723 μM and a Vm(app)=6.141 μU/pmol with substrate ethoxyresorufin, and the biochemical characterization of bergamottin CYP1A1 inhibitory effect revealed that it is a competitive inhibitor with a Ki=10.703 nM. We also confirmed the antimutagenicity of this compound against the mutagenic effect of 3-methylcholanthrene and benzo[a]pyrene in the Ames test. | Animals, Antimutagenic Agents, Cytochrome P-450 CYP1A1, Enzyme Inhibitors, Furocoumarins, Male, Mutagenicity Tests, Rats, Rats, Wistar, Salmonella typhimurium | null |
22,705,773 | 2013-01-10 | 2012-07-24 | 1872-8308 | Behavioural processes | A few days of social separation affects yearling horses' response to emotional reactivity tests and enhances learning performance. | Lansade Léa, Neveux Claire, Levy Frédéric | eng | null | Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705773, S0376-6357(12)00138-6, 10.1016/j.beproc.2012.06.003 | Learning performance is influenced by emotional reactivity, low reactivity being generally beneficial. Previous experiments show that emotional reactivity can be modified after a period of social isolation. We hypothesized that eleven days of isolation would affect yearlings' emotional reactivity and improve their learning abilities. Twenty-five yearlings were divided into two groups: 12 were continuously isolated for 11 days (isolated) and 13 stayed together (control). During the period of isolation, all yearlings underwent two learning tasks: a habituation procedure in which a novel object was presented for 120 s every day, either when the horse was alone (isolated) or with conspecifics (control); an instrumental learning task in which the yearling had to walk forwards or backwards to obtain a food reward. At the end of the isolation period, animals performed tests to assess aspects of emotional reactivity: reactivity to novelty, to humans, to social separation, to suddenness and to sensory stimuli. Results showed that isolated yearlings habituated more to the novel object than controls and performed better in the instrumental task. Moreover, they were less reactive to novelty, to social separation and to suddenness than controls. Overall, these data suggest that the better performance of isolated yearlings could be explained by a decrease in their emotional reactivity. This article is part of a Special Issue entitled: insert SI title. | Age Factors, Animals, Conditioning, Operant, Emotions, Female, Habituation, Psychophysiologic, Horses, Male, Random Allocation, Social Isolation, Time Factors | null |
22,705,774 | 2012-12-04 | 2022-03-21 | 1538-9235 | Optometry and vision science : official publication of the American Academy of Optometry | High prevalence of myopia in an adult population, Shahroud, Iran. | Hashemi Hassan, Khabazkhoob Mehdi, Jafarzadehpur Ebrahim, Yekta Abbas Ali, Emamian Mohammad Hassan, Shariati Mohammad, Fotouhi Akbar | eng | null | Comparative Study, Journal Article, Multicenter Study, Research Support, Non-U.S. Gov't | null | IM | 22705774, 10.1097/OPX.0b013e31825e6554 | To determine the prevalence of myopia and hyperopia and the associated risk factors in the presbyopic age group of the population in Shahroud, Iran. | Adult, Age Distribution, Age Factors, Confidence Intervals, Female, Follow-Up Studies, Humans, Iran, Male, Middle Aged, Myopia, Odds Ratio, Refraction, Ocular, Retrospective Studies, Risk Factors | null |
22,705,775 | 2012-12-04 | 2012-06-26 | 1538-9235 | Optometry and vision science : official publication of the American Academy of Optometry | The Glenn A. Fry Award Lecture 2011: Peripheral optics of the human eye. | Atchison David A | eng | null | Journal Article, Research Support, Non-U.S. Gov't, Review | null | IM | 22705775, 10.1097/OPX.0b013e31825c3454 | There has been a low level of interest in peripheral aberrations and corresponding image quality for over 200 years. Most work have been concerned with the second-order aberrations of defocus and astigmatism that can be corrected with conventional lenses. Studies have found high levels of aberration, often amounting to several dioptres, even in eyes with only small central defocus and astigmatism. My investigations have contributed to understanding shape changes in the eye with increases in myopia, changes in eye optics with ageing, and how surgical interventions intended to correct central refractive errors have unintended effects on peripheral optics.My research group has measured peripheral second- and higher-order aberrations over a 42° horizontal × 32° vertical diameter visual field. There is substantial variation in individual aberrations with age and pathology. While the higher-order aberrations in the periphery are usually small compared with second-order aberrations, they can be substantial and change considerably after refractive surgery.The thrust of my research in the next few years is to understand more about the peripheral aberrations of the human eye, to measure visual performance in the periphery and determine whether this can be improved by adaptive optics correction, to use measurements of peripheral aberrations to learn more about the optics of the eye and in particular the gradient index structure of the lens, and to investigate ways of increasing the size of the field of good retinal image quality. | Aging, Humans, Lenses, Intraocular, Refraction, Ocular, Refractive Errors | null |
22,705,776 | 2012-12-04 | 2022-03-16 | 1538-9235 | Optometry and vision science : official publication of the American Academy of Optometry | Characteristics of astigmatism as a function of age in a Hong Kong clinical population. | Leung Tsz-Wing, Lam Andrew Kwok-Cheung, Deng Li, Kee Chea-Su | eng | null | Comparative Study, Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705776, 10.1097/OPX.0b013e31825da156 | To characterize astigmatism as a function of age in a Hong Kong clinical population. | Adolescent, Adult, Aged, Aged, 80 and over, Aging, Astigmatism, Child, Child, Preschool, Disease Progression, Female, Follow-Up Studies, Hong Kong, Humans, Male, Middle Aged, Population Surveillance, Prevalence, Prognosis, Refraction, Ocular, Retrospective Studies, Young Adult | null |
22,705,777 | 2012-12-04 | 2012-06-26 | 1538-9235 | Optometry and vision science : official publication of the American Academy of Optometry | Effect of age on components of peripheral ocular aberrations. | Mathur Ankit, Atchison David A, Tabernero Juan | eng | null | Comparative Study, Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705777, 10.1097/OPX.0b013e31825da172 | To investigate the effect of age on the contributions of the anterior cornea and internal components to ocular aberrations in the peripheral visual field. | Aberrometry, Adult, Aged, Aging, Astigmatism, Cornea, Corneal Topography, Follow-Up Studies, Humans, Middle Aged, Reference Values, Refraction, Ocular, Visual Fields, Young Adult | null |
22,705,778 | 2012-12-04 | 2022-03-17 | 1538-9235 | Optometry and vision science : official publication of the American Academy of Optometry | Peripheral refraction in myopic eyes after LASIK surgery. | Queirós António, Villa-Collar César, Jorge Jorge, Gutiérrez Angel Ramón, González-Méijome José Manuel | eng | null | Comparative Study, Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705778, 10.1097/OPX.0b013e31825ddf54 | To characterize the axial and off-axis refraction across the horizontal meridian of the visual field before and after myopic laser-assisted in situ keratomileusis (LASIK) surgery. This research took place at the Clinical Ophthalmologic-NovoVisión, Madrid, Spain. | Adult, Female, Follow-Up Studies, Humans, Keratomileusis, Laser In Situ, Male, Myopia, Postoperative Period, Prospective Studies, Refraction, Ocular, Treatment Outcome, Visual Fields, Young Adult | null |
22,705,779 | 2012-09-13 | 2012-06-18 | 0021-4884 | Arerugi = [Allergy] | [Allergic conjunctival diseases]. | Shoji Jun | jpn | null | Journal Article, Review | null | IM | 22705779, 061050587e | null | Conjunctivitis, Allergic, Humans, Practice Guidelines as Topic, Tears | null |
22,705,780 | 2012-09-13 | 2012-06-18 | 0021-4884 | Arerugi = [Allergy] | [Progress in food allergy diagnosis by antigen-specific IgE antibody measurement (application of probability curve and allergen component)]. | Komata Takatsugu, Ebisawa Motohiro | jpn | null | Case Reports, Journal Article, Review | Allergens, Antibodies, Immunoglobulin E | IM | 22705780, 061050599e | null | Adolescent, Allergens, Antibodies, Child, Child, Preschool, Food Hypersensitivity, Humans, Immunoglobulin E, Infant, Male, Probability | null |
22,705,781 | 2012-09-13 | 2012-06-18 | 0021-4884 | Arerugi = [Allergy] | [Allergic conjunctival diseases]. | Takamura Etsuko | jpn | null | Journal Article, Review | null | IM | 22705781, 061050608e | null | Conjunctivitis, Allergic, Humans | null |
22,705,782 | 2012-09-13 | 2012-06-18 | 0021-4884 | Arerugi = [Allergy] | [One point comment of "Japanese Guideline for the Diagnosis and Treatment of Allergic Disease 2010" (adult asthma)]. | Sagara Hironori | jpn | null | Journal Article | null | IM | 22705782, 061050614e | null | Adult, Aged, Asthma, Humans, Practice Guidelines as Topic | null |
22,705,783 | 2012-09-13 | 2012-06-18 | 0021-4884 | Arerugi = [Allergy] | [Thirty years since discovery of mast cell deficient mice]. | Kitamura Yukihiko | jpn | null | Historical Article, Journal Article | Stem Cell Factor | IM | 22705783, 061050620e | null | Allergy and Immunology, Animals, Gastrointestinal Stromal Tumors, History, 20th Century, Humans, Japan, Mast Cells, Mice, Mice, Mutant Strains, Stem Cell Factor | null |
22,705,784 | 2012-09-13 | 2012-06-18 | 0021-4884 | Arerugi = [Allergy] | [Reevaluation of allergen-immunotherapy]. | Nagata Makoto | jpn | null | Journal Article, Review | Allergens | IM | 22705784, 061050624e | null | Allergens, Bronchitis, Humans, Hypersensitivity, Immunotherapy, Rhinitis, Allergic, Perennial, Rhinitis, Allergic, Seasonal | null |
22,705,785 | 2012-09-13 | 2012-06-18 | 0021-4884 | Arerugi = [Allergy] | [Clinical effects of Lactobacillus acidophilus strain L-55-contained yogurt on symptoms of Japanese cedar pollen allergy]. | Kimura Goro, Akagi Hirofumi, Okada Chiharu, Hirano Atsushi, Amano Yoshimi, Ohmura Etsuko, Nakashige Yoshito, Sunada Yosuke, Fujii Yusuke, Nakamura Syoji, Soda Ryo, Takahashi Kiyoshi | jpn | null | Clinical Conference, English Abstract, Journal Article | null | IM | 22705785, 061050628e | It has been reported that oral administration of Lactobacillus acidophilus strain L-55 (L-55) suppressed nasal symptom and antigen-specific IgE induced by antigen challenge in mice. We investigated clinical effects of L-55-contained yogurt on symptoms and IgE production in the patients with Japanese cedar pollinosis. | Adult, Cryptomeria, Double-Blind Method, Female, Humans, Lactobacillus acidophilus, Male, Rhinitis, Allergic, Seasonal, Yogurt | null |
22,705,786 | 2012-09-13 | 2015-11-19 | 0021-4884 | Arerugi = [Allergy] | [The effects of great East Japan earthquake on patients with food allergy in Miyagi Prefecture]. | Minoura Takanori, Yanagida Noriyuki, Watanabe Youhei, Yamaoka Akiko, Miura Katsushi | jpn | null | English Abstract, Journal Article | null | IM | 22705786, 061050642e | Although many food-allergic children experienced the Great East Japan Earthquake, little was known about the effects of the disaster on them. | Child, Earthquakes, Food Hypersensitivity, Food Supply, Humans, Japan, Retrospective Studies, Surveys and Questionnaires | null |
22,705,787 | 2012-09-13 | 2012-06-18 | 0021-4884 | Arerugi = [Allergy] | [A case of oral allergy syndrome whose symptoms were dramatically improved after rush subcutaneous injection immunotherapy with pollen extracts of birch]. | Okamoto Yoshihisa, Kurihara Kazuyuki | jpn | null | Case Reports, English Abstract, Journal Article | Plant Extracts | IM | 22705787, 061050652e | We report a case of oral allergy syndrome, whose symptoms were dramatically improved after rush subcutaneous injection immunotherapy (SCIT) with pollen extracts of birch, ragweed and Japanese cedar. She was diagnosed as allergic rhinitis at 2 years old, and experienced oral allergy syndrome at 5 years old after eating cucumber. Then she had become allergic to wide range of fruits and vegetables. She was introduced to our department for the possible treatment for allergic rhinitis, and underwent rush SCIT at 15 years old. The symptom of single blind oral challenge test of apple up to 30 g, which had been positive before SCIT, turned to negative after the treatment. The threshold of apple measured by open oral challenge test increased from 3 g to more than 50 g. The symptoms to most fruits and vegetables were improved or disappeared. This suggests the possibility that SCIT of birch pollen can be a promising candidate as a radical treatment for pollen-food allergy syndrome. | Adolescent, Betula, Female, Food Hypersensitivity, Humans, Immunotherapy, Injections, Subcutaneous, Plant Extracts, Pollen | null |
22,705,788 | 2012-09-13 | 2023-01-06 | 1545-9985 | Nature structural & molecular biology | Structural basis for heteromeric assembly and perinuclear organization of keratin filaments. | Lee Chang-Hun, Kim Min-Sung, Chung Byung Min, Leahy Daniel J, Coulombe Pierre A | eng | Y1-GM-1104 (NIGMS NIH HHS, United States); T32 CA009110 (NCI NIH HHS, United States); Y1-CO-1020 (NCI NIH HHS, United States); R01 HD055545 (NICHD NIH HHS, United States); R01 AR042047 (NIAMS NIH HHS, United States); P30 CA006973 (NCI NIH HHS, United States); HD055545 (NICHD NIH HHS, United States); AR42047 (NIAMS NIH HHS, United States) | Journal Article, Research Support, N.I.H., Extramural, Research Support, U.S. Gov't, Non-P.H.S. | Disulfides, Keratins | IM | 22705788, nsmb.2330, 10.1038/nsmb.2330, PMC3864793, NIHMS441033, 15326189, 9763512, 416022, 20124702, 20176112, 17606637, 6186504, 17289402, 13013241, 15373777, 1383231, 15537907, 7686169, 21516532, 18033728, 15476822, 15189158, 17452350, 1948029, 2445593, 11889032, 27754618, 1717157, 7681879, 11973334, 1691189, 12057196, 7539810, 1694855, 6191871, 21144725, 6137189, 21378307, 19422834, 10064706, 7188712, 22235123, 11243787, 10430181, 11194897, 11517324, 16580748, 19651890, 15572765, 15767464, 15277542, 11901143, 9438837, 7630882, 14696367, 6186379, 17050693, 19587453, 16710422, 18342539, 11029054, 8689554, 6187996, 18428767 | There is as yet no high-resolution data regarding the structure and organization of keratin intermediate filaments, which are obligate heteropolymers providing vital mechanical support in epithelia. We report the crystal structure of interacting 2B regions from the central coiled-coil domains of keratins 5 and 14 (K5 and K14), expressed in progenitor keratinocytes of epidermis. The interface of the K5-K14 coiled-coil heterodimer has asymmetric salt bridges, hydrogen bonds and hydrophobic contacts, and its surface exhibits a notable charge polarization. A trans-dimer homotypic disulfide bond involving Cys367 in K14's stutter region occurs in the crystal and in skin keratinocytes, where it is concentrated in a keratin filament cage enveloping the nucleus. We show that K14-Cys367 impacts nuclear shape in cultured keratinocytes and that mouse epidermal keratinocytes lacking K14 show aberrations in nuclear structure, highlighting a new function for keratin filaments. | Amino Acid Sequence, Animals, Crystallography, X-Ray, Dimerization, Disulfides, Epidermolysis Bullosa Simplex, Humans, Keratinocytes, Keratins, Models, Molecular, Molecular Sequence Data, Sequence Homology, Amino Acid | null |
22,705,790 | 2012-09-13 | 2022-04-09 | 1545-9985 | Nature structural & molecular biology | Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo. | Taggart Allison J, DeSimone Alec M, Shih Janice S, Filloux Madeleine E, Fairbrother William G | eng | 8P30GM103410 (NIGMS NIH HHS, United States); T32 GM007601 (NIGMS NIH HHS, United States); P30 GM103410 (NIGMS NIH HHS, United States); R01 GM095612 (NIGMS NIH HHS, United States); R01GM095612-01 (NIGMS NIH HHS, United States) | Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S. | RNA Precursors, RNA, Messenger | IM | 22705790, nsmb.2327, 10.1038/nsmb.2327, PMC3465671, NIHMS395885, 3065622, 15215366, 19261174, 12824352, 20064465, 19289445, 15173120, 16507133, 12754702, 8336728, 21925391, 20601959, 22574288, 10487864, 10639124, 11238888, 19015125, 2812024, 19136955, 9115373 | We present the first large-scale identification of lariats-the transient branched introns that are released as a byproduct of pre-mRNA splicing. The locations of the branchpoints in these introns provide insight into the early steps of splicing. From this data set, we have developed a comprehensive model of 3' splice-site selection, identified new mechanisms of alternative splicing and mapped the distribution of splicing factors around branchpoints. | Humans, Introns, RNA Precursors, RNA, Messenger | null |
22,705,789 | 2012-09-13 | 2021-10-21 | 1545-9985 | Nature structural & molecular biology | Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef. | Jia Xiaofei, Singh Rajendra, Homann Stefanie, Yang Haitao, Guatelli John, Xiong Yong | eng | R01 AI097064 (NIAID NIH HHS, United States); AI038201 (NIAID NIH HHS, United States); P30 AI36214 (NIAID NIH HHS, United States); R21 AI038201 (NIAID NIH HHS, United States); R01 AI038201 (NIAID NIH HHS, United States); AI076040 (NIAID NIH HHS, United States); R21 AI076040 (NIAID NIH HHS, United States); P30 AI036214 (NIAID NIH HHS, United States); AI097064 (NIAID NIH HHS, United States) | Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't | Gene Products, nef | IM | 22705789, nsmb.2328, 10.1038/nsmb.2328, PMC3407041, NIHMS378380, 11092928, 9736718, 18155264, 15377783, 11463741, 18653452, 17681537, 18057255, 8681387, 16959901, 8612235, 17267500, 15299374, 18725938, 7678431, 15596859, 18073204, 14646132, 14566337, 9351809, 9761844, 15299926, 10366557, 8660525, 7481804, 9194185, 10403641, 7808489, 3118220, 9450757, 17189639, 18438604, 7975260, 15572765, 9586638, 21477083, 9812899, 15158672, 12486136, 20124702, 8500185, 8227126, 10814565, 20020046, 19129443, 9582271, 18094151, 10799608, 19696796, 15569716, 20603002, 14691137, 12527304, 9971776, 18156677 | The HIV-1 protein Nef inhibits antigen presentation by class I major histocompatibility complex (MHC-I). We determined the mechanism of this activity by solving the crystal structure of a protein complex comprising Nef, the MHC-I cytoplasmic domain (MHC-I CD) and the μ1 subunit of the clathrin adaptor protein complex 1. A ternary, cooperative interaction clamps the MHC-I CD into a narrow binding groove at the Nef-μ1 interface, which encompasses the cargo-recognition site of μ1 and the proline-rich strand of Nef. The Nef C terminus induces a previously unobserved conformational change in μ1, whereas the N terminus binds the Nef core to position it optimally for complex formation. Positively charged patches on μ1 recognize acidic clusters in Nef and MHC-I. The structure shows how Nef functions as a clathrin-associated sorting protein to alter the specificity of host membrane trafficking and enable viral evasion of adaptive immunity. | Adaptation, Physiological, Cell Line, Gene Products, nef, HIV-1, Humans, Immune Evasion, Models, Molecular, Protein Conformation, Static Electricity | null |
22,705,791 | 2012-09-13 | 2024-06-10 | 1545-9985 | Nature structural & molecular biology | Structure of Mre11-Nbs1 complex yields insights into ataxia-telangiectasia-like disease mutations and DNA damage signaling. | Schiller Christian B, Lammens Katja, Guerini Ilaria, Coordes Britta, Feldmann Heidi, Schlauderer Florian, Möckel Carolin, Schele Alexandra, Strässer Katja, Jackson Stephen P, Hopfner Karl-Peter | eng | 092096 (Wellcome Trust, United Kingdom); C6/A11226 (Cancer Research UK, United Kingdom); U19 AI083025 (NIAID NIH HHS, United States); 268536 (European Research Council, International); A11224 (Cancer Research UK, United Kingdom); U19AI83025 (NIAID NIH HHS, United States); 11224 (Cancer Research UK, United Kingdom) | Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't | Chromosomal Proteins, Non-Histone, Nbs1 protein, S pombe, Schizosaccharomyces pombe Proteins | IM | 22705791, nsmb.2323, 10.1038/nsmb.2323, PMC3392456, NIHMS377602, 10835381, 12944481, 20690856, 19633668, 18806779, 21511873, 20192759, 15964794, 15138496, 19151086, 20061370, 16622404, 18275380, 20811461, 11544181, 9755192, 20580718, 11371344, 15758953, 17965729, 17656141, 21937514, 21441914, 9590181, 15064416, 19732584, 15215455, 21102445, 16107854, 21329706, 19171781, 21035407, 15548595, 11850621, 17485521, 11741547, 19409520, 15790808, 15716496, 12846809, 18854158, 9000052, 19804755, 17429352, 20647759, 12152085, 18082599, 20620955, 21227757, 15279810, 10346816, 11877377, 11357144, 10612394, 9501103, 18805091, 9928492, 21458667, 18650924, 19804756, 21252998, 2184035, 7984417, 17674145, 22078559, 15574463 | The Mre11-Rad50-Nbs1 (MRN) complex tethers, processes and signals DNA double-strand breaks, promoting genomic stability. To understand the functional architecture of MRN, we determined the crystal structures of the Schizosaccharomyces pombe Mre11 dimeric catalytic domain alone and in complex with a fragment of Nbs1. Two Nbs1 subunits stretch around the outside of the nuclease domains of Mre11, with one subunit additionally bridging and locking the Mre11 dimer via a highly conserved asymmetrical binding motif. Our results show that Mre11 forms a flexible dimer and suggest that Nbs1 not only is a checkpoint adaptor but also functionally influences Mre11-Rad50. Clinical mutations in Mre11 are located along the Nbs1-interaction sites and weaken the Mre11-Nbs1 interaction. However, they differentially affect DNA repair and telomere maintenance in Saccharomyces cerevisiae, potentially providing insight into their different human disease pathologies. | Binding Sites, Chromosomal Proteins, Non-Histone, DNA Damage, Dimerization, Humans, Models, Molecular, Mutation, Protein Conformation, Schizosaccharomyces pombe Proteins, Signal Transduction | null |
22,705,792 | 2012-11-23 | 2021-10-21 | 1362-4962 | Nucleic acids research | Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data. | Ragan Chikako, Mowry Bryan J, Bauer Denis C | eng | null | Journal Article, Research Support, Non-U.S. Gov't | MicroRNAs, RNA Precursors, RNA, Small Interfering, RNA, Small Untranslated | IM | 22705792, gks505, 10.1093/nar/gks505, PMC3439898, 17446352, 16683026, 19908360, 20605486, 20823303, 21622957, 21976421, 20478827, 16751776, 19332473, 19451168, 15980563, 22094948, 20478825, 19261174, 17571346, 21911355, 18392026, 16751777, 16766680, 20801911, 21632744, 19908359, 20661255, 18948287, 16452114, 19821977, 21765801, 18583537, 16332711, 21854988, 16723972, 19944475, 20413612, 20110278, 19966272, 21037258 | Recent advances in RNA sequencing technology (RNA-Seq) enables comprehensive profiling of RNAs by producing millions of short sequence reads from size-fractionated RNA libraries. Although conventional tools for detecting and distinguishing non-coding RNAs (ncRNAs) from reference-genome data can be applied to sequence data, ncRNA detection can be improved by harnessing the full information content provided by this new technology. Here we present NorahDesk, the first unbiased and universally applicable method for small ncRNAs detection from RNA-Seq data. NorahDesk utilizes the coverage-distribution of small RNA sequence data as well as thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes. Using publicly available mouse sequence data from brain, skeletal muscle, testis and ovary, we evaluated our method with an emphasis on the performance for microRNAs (miRNAs) and piwi-interacting small RNA (piRNA). We compared our method with Dario and mirDeep2 and found that NorahDesk produces longer transcripts with higher read coverage. This feature makes it the first method particularly suitable for the prediction of both known and novel piRNAs. | Animals, High-Throughput Nucleotide Sequencing, Mice, MicroRNAs, Nucleic Acid Conformation, Nucleic Acid Hybridization, RNA Precursors, RNA, Small Interfering, RNA, Small Untranslated, Sequence Analysis, RNA, Software | null |
22,705,793 | 2012-12-28 | 2021-10-21 | 1362-4962 | Nucleic acids research | 'Shotgun DNA synthesis' for the high-throughput construction of large DNA molecules. | Kim Hwangbeom, Han Hyojun, Ahn Jinwoo, Lee Joongoo, Cho Namjin, Jang Hoon, Kim Hyoki, Kwon Sunghoon, Bang Duhee | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Penicillins, DNA | IM | 22705793, gks546, 10.1093/nar/gks546, PMC3467036, 20010598, 17439967, 22127863, 20981747, 20935651, 21113165, 20571086, 16056220, 2129535, 21237219, 18037891, 15616567, 21516083, 20693531, 20488990, 22209624, 15561997, 6221115, 18463615, 21113166, 19023044 | We developed a highly scalable 'shotgun' DNA synthesis technology by utilizing microchip oligonucleotides, shotgun assembly and next-generation sequencing technology. A pool of microchip oligonucleotides targeting a penicillin biosynthetic gene cluster were assembled into numerous random fragments, and tagged with 20 bp degenerate barcode primer pairs. An optimal set of error-free fragments were identified by high-throughput DNA sequencing, selectively amplified using the barcode sequences, and successfully assembled into the target gene cluster. | DNA, High-Throughput Nucleotide Sequencing, Oligonucleotide Array Sequence Analysis, Penicillins, Polymerase Chain Reaction, Synthetic Biology | null |
22,705,795 | 2012-11-23 | 2021-10-21 | 1362-4962 | Nucleic acids research | Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde. | Bohnuud Tanggis, Beglov Dmitri, Ngan Chi Ho, Zerbe Brandon, Hall David R, Brenke Ryan, Vajda Sandor, Frank-Kamenetskii Maxim D, Kozakov Dima | eng | P42 ES007381 (NIEHS NIH HHS, United States); R01 GM064700 (NIGMS NIH HHS, United States); GM064700 (NIGMS NIH HHS, United States) | Journal Article, Research Support, N.I.H., Extramural | DNA, B-Form, Formaldehyde, Cytosine, Nitrogen | IM | 22705795, gks519, 10.1093/nar/gks519, PMC3439909, 18383062, 14696386, 17394297, 21514356, 22092261, 10592235, 9630949, 22081012, 19911048, 5553329, 21686245, 235285, 19906722, 6877235, 1018321, 16500982, 20364130, 560859, 3037378, 21808046, 18508808, 19865164, 19444816, 21350476, 21270796, 11517324, 19176554, 235286, 9062927, 7053230, 3037381, 20373914, 4922326 | Formaldehyde has long been recognized as a hazardous environmental agent highly reactive with DNA. Recently, it has been realized that due to the activity of histone demethylation enzymes within the cell nucleus, formaldehyde is produced endogenously, in direct vicinity of genomic DNA. Should it lead to extensive DNA damage? We address this question with the aid of a computational mapping method, analogous to X-ray and nuclear magnetic resonance techniques for observing weakly specific interactions of small organic compounds with a macromolecule in order to establish important functional sites. We concentrate on the leading reaction of formaldehyde with free bases: hydroxymethylation of cytosine amino groups. Our results show that in B-DNA, cytosine amino groups are totally inaccessible for the formaldehyde attack. Then, we explore the effect of recently discovered transient flipping of Watson-Crick (WC) pairs into Hoogsteen (HG) pairs (HG breathing). Our results show that the HG base pair formation dramatically affects the accessibility for formaldehyde of cytosine amino nitrogens within WC base pairs adjacent to HG base pairs. The extensive literature on DNA interaction with formaldehyde is analyzed in light of the new findings. The obtained data emphasize the significance of DNA HG breathing. | Algorithms, Base Pairing, Binding Sites, Computational Biology, Cytosine, DNA, B-Form, Formaldehyde, Models, Molecular, Nitrogen | null |
22,705,794 | 2012-11-23 | 2021-10-21 | 1362-4962 | Nucleic acids research | CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus. | Junier Ivan, Dale Ryan K, Hou Chunhui, Képès François, Dean Ann | eng | KIA 15508 (PHS HHS, United States) | Journal Article, Research Support, N.I.H., Intramural, Research Support, Non-U.S. Gov't | CCCTC-Binding Factor, CTCF protein, human, Chromatin, Repressor Proteins, beta-Globins | IM | 22705794, gks536, 10.1093/nar/gks536, PMC3439919, 17033623, 19374771, 20436457, 12504019, 21685913, 19171905, 16954542, 20675721, 16951251, 21045820, 19458616, 18725929, 21358745, 20010836, 15694345, 19815776, 15489291, 19563753, 22001755, 19559093, 15273689, 21131981, 17913488, 16705039, 10618382, 17936653, 22010104, 15730849, 22169023, 16369547, 20570862, 18082606, 14517543, 21398517, 16645164, 19234129, 20133600, 19074263, 19752020, 22123989, 22198700, 20169181, 11121056, 9834246, 17280735, 22026390, 16815976, 22265598 | The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the three-dimensional folding of a 1 Mbp region of human chromosome 11 containing the β-globin genes by integrating looping interactions of the CCCTC-binding insulator protein CTCF determined comprehensively by chromosome conformation capture (3C) into a polymer model of chromatin. We find that CTCF-mediated cell type-specific interactions in erythroid cells are organized to favor contacts known to occur in vivo between the β-globin locus control region (LCR) and genes. In these cells, the modeled β-globin domain folds into a globule with the LCR and the active globin genes on the periphery. In contrast, in non-erythroid cells, the globule is less compact with few but dominant CTCF interactions driving the genes away from the LCR. This leads to a decrease in contact frequencies that can exceed 1000-fold depending on the stiffness of the chromatin and the exact position of the genes. Our findings show that an ensemble of CTCF contacts functionally affects spatial distances between control elements and target genes contributing to chromosomal organization required for transcription. | CCCTC-Binding Factor, Cell Line, Chromatin, Chromosomes, Human, Pair 11, Gene Expression Regulation, Genetic Loci, Genome, Human, Humans, K562 Cells, Locus Control Region, Repressor Proteins, Transcription, Genetic, beta-Globins | null |
22,705,796 | 2012-11-23 | 2021-10-21 | 1362-4962 | Nucleic acids research | Dual roles of the SUMO-interacting motif in the regulation of Srs2 sumoylation. | Kolesar Peter, Sarangi Prabha, Altmannova Veronika, Zhao Xiaolan, Krejci Lumir | eng | P30 CA008748 (NCI NIH HHS, United States); 076476 (Wellcome Trust, United Kingdom); GM080670 (NIGMS NIH HHS, United States) | Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't | Proliferating Cell Nuclear Antigen, SUMO-1 Protein, Saccharomyces cerevisiae Proteins, Siz2 protein, S cerevisiae, SRS2 protein, S cerevisiae, Ubiquitin-Protein Ligases, DNA Helicases, Siz1 protein, S cerevisiae, Lysine | IM | 22705796, gks484, 10.1093/nar/gks484, PMC3439891, 19136956, 16429130, 19325626, 383698, 2182387, 20096651, 17081985, 12354763, 18538659, 16322557, 19748359, 18000527, 18708356, 17591698, 16611731, 22921573, 15189146, 20195513, 17105346, 17077124, 15569683, 15931174, 3044923, 2693208, 12761287, 22153967, 11259410, 15738391, 15388847, 12748645, 17081986, 11154282, 15989970, 20371517, 12226657, 17452246, 9341106, 12475932, 11853669, 19745052, 15823533, 11572779, 15314145, 16524884, 19034694, 18658248, 12748644, 18691969, 12641448, 14622595, 9312010, 22382979, 19736316, 15959518, 18440969, 11577116, 19748360, 21518767, 11587849, 21743457, 22467216, 16344309, 21486569, 22285753, 9414323, 21459050, 19107407, 21984413, 19506039, 18166982 | The Srs2 DNA helicase of Saccharomyces cerevisiae affects recombination in multiple ways. Srs2 not only inhibits recombination at stalled replication forks but also promotes the synthesis-dependent strand annealing (SDSA) pathway of recombination. Both functions of Srs2 are regulated by sumoylation--sumoylated PCNA recruits Srs2 to the replication fork to disfavor recombination, and sumoylation of Srs2 can be inhibitory to SDSA in certain backgrounds. To understand Srs2 function, we characterize the mechanism of its sumoylation in vitro and in vivo. Our data show that Srs2 is sumoylated at three lysines, and its sumoylation is facilitated by the Siz SUMO ligases. We also show that Srs2 binds to SUMO via a C-terminal SUMO-interacting motif (SIM). The SIM region is required for Srs2 sumoylation, likely by binding to SUMO-charged Ubc9. Srs2's SIM also cooperates with an adjacent PCNA-specific interaction site in binding to sumoylated PCNA to ensure the specificity of the interaction. These two functions of Srs2's SIM exhibit a competitive relationship: sumoylation of Srs2 decreases the interaction between the SIM and SUMO-PCNA, and the SUMO-PCNA-SIM interaction disfavors Srs2 sumoylation. Our findings suggest a potential mechanism for the equilibrium of sumoylated and PCNA-bound pools of Srs2 in cells. | Amino Acid Sequence, DNA Helicases, Lysine, Molecular Sequence Data, Proliferating Cell Nuclear Antigen, Protein Interaction Domains and Motifs, SUMO-1 Protein, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Sumoylation, Ubiquitin-Protein Ligases | null |
22,705,799 | 2013-06-24 | 2023-02-02 | 1476-5365 | Bone marrow transplantation | Akinetic mutism-a serious complication to tacrolimus-based GVHD prophylaxis. | Najera J E, Alousi A, De Lima M, Ciurea S O | eng | null | Case Reports, Letter | Immunosuppressive Agents, Tacrolimus | IM | 22705799, bmt2012110, 10.1038/bmt.2012.110 | null | Akinetic Mutism, Drug Monitoring, Drug Therapy, Combination, Female, Graft vs Host Disease, Humans, Immunosuppressive Agents, Leukemia, Myeloid, Acute, Middle Aged, Neurotoxicity Syndromes, Nuclear Family, Stem Cell Transplantation, Tacrolimus, Treatment Outcome | null |
22,705,797 | 2012-11-23 | 2021-10-21 | 1362-4962 | Nucleic acids research | Prioritizing cancer-related key miRNA-target interactions by integrative genomics. | Xiao Yun, Guan Jinxia, Ping Yanyan, Xu Chaohan, Huang Teng, Zhao Hongying, Fan Huihui, Li Yiqun, Lv Yanling, Zhao Tingting, Dong Yucui, Ren Huan, Li Xia | eng | null | Journal Article, Research Support, Non-U.S. Gov't | 3' Untranslated Regions, MIRN155 microRNA, human, MicroRNAs, RNA, Messenger | IM | 22705797, gks538, 10.1093/nar/gks538, PMC3439920, 20927335, 21145484, 21245843, 20216554, 18923704, 18772890, 10592173, 21037258, 16166262, 21460854, 17923094, 19135886, 14993899, 18955434, 22384175, 19551852, 17612493, 16685651, 18187662, 20427544, 16615898, 16530703, 16757574, 21720365, 18710882, 20703300, 16680138, 15964265, 21423181, 16594986, 11752252, 15075390, 18988627, 20385818, 16141076, 16461460, 20071740, 10802651, 18927107, 8252621, 21515357, 8252622, 15118671, 21976726, 21835775, 19386588, 20054295, 18450484, 19450959, 16041695, 16549876, 12045153, 19167326, 18426918, 15372042, 21071411, 14695998, 18048652, 18455451, 20696049, 15657099, 19763153, 20495573, 17638813, 21143814, 22446039, 16641092, 19240133, 19074876, 19887047 | Accumulating evidence indicates that microRNAs (miRNAs) can function as oncogenes or tumor suppressor genes by controlling few key targets, which in turn contribute to the pathogenesis of cancer. The identification of cancer-related key miRNA-target interactions remains a challenge. We performed a systematic analysis of known cancer-related key interactions manually curated from published papers based on different aspects including sequence, expression and function. Known cancer-related key interactions show more miRNA binding sites (especially for 8mer binding sites), more reliable binding of miRNA to the target region, higher expression associations and broader functional coverage when compared to non-disease-related interactions. Through integrating these sequence, expression and function features, we proposed a bioinformatics approach termed PCmtI to prioritize cancer-related key interactions. Ten-fold cross-validation of our approach revealed that it can achieve an area under the receiver operating characteristic curve of 93.9%. Subsequent leave-one-miRNA-out cross-validation also demonstrated the performance of our approach. Using miR-155 as a case, we found that the top ranked interactions can account for most functions of miR-155. In addition, we further demonstrated the power of our approach by 23 recently identified cancer-related key interactions. The approach described here offers a new way for the discovery of novel cancer-related key miRNA-target interactions. | 3' Untranslated Regions, Binding Sites, Cell Line, Tumor, Genomics, Humans, MicroRNAs, Neoplasms, Protein Interaction Mapping, RNA, Messenger, Software | null |
22,705,798 | 2013-01-04 | 2024-06-10 | 1872-9096 | Antiviral research | The Syrian hamster model of hantavirus pulmonary syndrome. | Safronetz David, Ebihara Hideki, Feldmann Heinz, Hooper Jay W | eng | Y99 AI999999 (NIAID NIH HHS, United States); Z99 AI999999 (Intramural NIH HHS, United States) | Journal Article, Review | null | IM | 22705798, S0166-3542(12)00143-X, 10.1016/j.antiviral.2012.06.002, PMC3425723, NIHMS391107, 2573685, 20375360, 16485469, 21177802, 9618541, 9499807, 15494907, 18032485, 7887439, 17436235, 11217400, 10882580, 8627258, 12941899, 12408987, 11739712, 1381911, 11756112, 21775442, 10069952, 22194683, 21917979, 10973478, 21334343, 17054070, 21945215, 9684629, 22044619, 12163608, 2568827, 21672562, 11504409, 20113567, 12404153, 10196290, 2865331, 1359802, 6116436, 18606242, 18036672, 20463083, 18385367, 17251568, 10982372, 22248821, 11601912, 16965713, 16513381, 1972201, 19837289, 16950493, 11459009, 16483801, 18604199, 2861296, 9878011, 11502657, 21853152, 9866751, 3137914, 18093668, 19403663, 11304061, 2869089, 8121458, 21593160, 19038412, 16378630, 2869749, 12447754, 10544095, 22095538, 7901740, 21566265, 12363052, 15262501, 20810734, 6134678, 17475651, 8607269, 20846417, 15602208, 17875986, 22558299, 18716663, 18329474, 10723500, 19846530, 16793309, 18054395, 20455779, 21994770, 17878294 | Hantavirus pulmonary syndrome (HPS) is a relatively rare, but frequently fatal disease associated with New World hantaviruses, most commonly Sin Nombre and Andes viruses in North and South America, respectively. It is characterized by fever and the sudden, rapid onset of severe respiratory distress and cardiogenic shock, which can be fatal in up to 50% of cases. Currently there are no approved antiviral therapies or vaccines for the treatment or prevention of HPS. A major obstacle in the development of effective medical countermeasures against highly pathogenic agents like the hantaviruses is recapitulating the human disease as closely as possible in an appropriate and reliable animal model. To date, the only animal model that resembles HPS in humans is the Syrian hamster model. Following infection with Andes virus, hamsters develop HPS-like disease which faithfully mimics the human condition with respect to incubation period and pathophysiology of disease. Perhaps most importantly, the sudden and rapid onset of severe respiratory distress observed in humans also occurs in hamsters. The last several years has seen an increase in studies utilizing the Andes virus hamster model which have provided unique insight into HPS pathogenesis as well as potential therapeutic and vaccine strategies to treat and prevent HPS. The purpose of this article is to review the current understanding of HPS disease progression in Syrian hamsters and discuss the suitability of utilizing this model to evaluate potential medical countermeasures against HPS. | Animals, Cricetinae, Disease Models, Animal, Orthohantavirus, Hantavirus Pulmonary Syndrome, Humans, Mesocricetus | null |
22,705,801 | 2013-06-24 | 2022-12-07 | 1476-5365 | Bone marrow transplantation | Practice variation in physician referral for allogeneic hematopoietic cell transplantation. | Pidala J, Craig B M, Lee S J, Majhail N, Quinn G, Anasetti C | eng | P20 MD003375 (NIMHD NIH HHS, United States); P30 CA076292 (NCI NIH HHS, United States); P20 MD003375-02 (NIMHD NIH HHS, United States) | Journal Article, Research Support, N.I.H., Extramural | null | IM | 22705801, bmt201295, 10.1038/bmt.2012.95, PMC3549547, NIHMS433484, 20036337, 17075568, 15994282, 17448920, 15517006, 9368521, 19059878, 18768435, 17476142, 16707175, 20485378, 18978820, 19224849, 16145067, 11877268, 9215836, 12555212, 19074758, 14551294, 19822308, 19896078, 15484218, 20538804, 17443629, 12142775 | Hematological malignancy patients not referred by their primary hematologist/medical oncologist suffer disparate access to allogeneic hematopoietic cell transplantation (HCT). However, investigation into physician, system and patient factors relevant to this decision making is lacking. We surveyed a national randomized sample of practicing hematologists/medical oncologists identified through the AMA (American Medical Association) masterfile. A modified Dillman approach was utilized to encourage survey response. From 1200 surveyed, a total of 113 physicians responded. In all, 68% were male, 62% identified as White/non-Hispanic, 79% practiced in non-academic settings and 80% reported spending 75-100% of their professional effort in clinical care. Using clinical vignettes, we detected significantly increased odds for HCT non-referral according to age (age 60 vs 30, odds ratio (OR) 8.3, 95% confidence interval (CI): 5.9-11.7, P<0.0001), insurance coverage (no coverage vs coverage, OR 6.9, 95% CI: 5.2-9.1, P<0.0001) and race (African-American vs Caucasian, OR 2.4, 95% CI: 1.9-2.9, P<0.0001). Physician (perception of HCT risks), system (insurance coverage) and patient (age, social support and co-morbid illness) factors were strongly endorsed by respondents as important determinants of their HCT referral practices. These data speak to important factors relevant to HCT referral practices, and highlight several opportunities for education and intervention to reduce current disparities. | Adult, Black or African American, Age Factors, Comorbidity, Female, Health Care Surveys, Healthcare Disparities, Hematology, Hematopoietic Stem Cell Transplantation, Humans, Insurance Coverage, Insurance, Health, Leukemia, Male, Medical Oncology, Middle Aged, Myelodysplastic Syndromes, Practice Patterns, Physicians', Referral and Consultation, Social Support, Transplantation, Homologous, United States, White People, Workforce | null |
22,705,800 | 2013-06-24 | 2013-01-09 | 1476-5365 | Bone marrow transplantation | Allogeneic hematopoietic stem cell transplantation for intermediate cytogenetic risk AML in first CR. | Imahashi N, Suzuki R, Fukuda T, Kakihana K, Kanamori H, Eto T, Mori T, Kobayashi N, Iwato K, Sakura T, Ikegame K, Kurokawa M, Kondo T, Iida H, Sakamaki H, Tanaka J, Kawa K, Morishima Y, Atsuta Y, Miyamura K | eng | null | Comparative Study, Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705800, bmt201284, 10.1038/bmt.2012.84 | Allogeneic hematopoietic SCT (allo-HCT) from matched sibling donor (MSD) is recommended for younger patients with intermediate cytogenetic risk AML in first CR (CR1), whereas the role of alternative donor transplants in these patients is unknown. We retrospectively analyzed 605 patients with intermediate-risk AML, who received myeloablative allo-HCT in CR1. The 4-year OS for MSD (n=290) and matched unrelated donor (MUD; n=141) was 65% and 68% (P=0.50), respectively. In multivariate analysis, MUD had a similar risk of overall mortality as MSD (hazard ratio=0.90; 95% confidence interval, 0.62-1.30; P=0.58), whereas older age, female donor/male recipient (FDMR) combination, and requiring more than one course of induction chemotherapy to achieve CR1 were poor prognostic factors for OS. Thus, OS after MUD HCT with sex combinations other than FDMR was significantly higher than that after MSD HCT from female donors to male recipients (4-year OS 72% versus 55%, P=0.04). These results suggest that HCT, not only from MSD, but also from MUD, should be considered in younger patients with intermediate-risk AML in CR1, and that the donor-recipient sex combination is more important than the donor type in donor selection. | Adolescent, Adult, Age Factors, Blood Donors, Bone Marrow Transplantation, Chromosome Aberrations, Female, Follow-Up Studies, Genetic Predisposition to Disease, Hematopoietic Stem Cell Transplantation, Humans, Leukemia, Myeloid, Acute, Male, Middle Aged, Peripheral Blood Stem Cell Transplantation, Remission Induction, Retrospective Studies, Sex Characteristics, Siblings, Survival Analysis, Tissue Donors, Transplantation, Homologous, Young Adult | null |
22,705,803 | 2013-06-24 | 2018-12-02 | 1476-5365 | Bone marrow transplantation | Response to the article by Linnankivi et al., entitled 'Cerebroretinal microangiopathy with calcifications and cyst, Revesz syndrome and aplastic anemia'. | Asai D, Osone S, Imamura T, Sakaguchi H, Nishio N, Kuroda H, Kojima S, Hosoi H | eng | null | Letter, Comment | null | IM | 22705803, bmt2012108, 10.1038/bmt.2012.108 | null | Anemia, Aplastic, Bone Diseases, Metabolic, Humans, Male, Stem Cell Transplantation, Transplantation Conditioning | null |
22,705,802 | 2013-06-24 | 2017-11-16 | 1476-5365 | Bone marrow transplantation | Immediate and long-term somatic effects, and health-related quality of life of BM donation during early childhood. A single-center report in 210 pediatric donors. | van Walraven S M, Straathof L M, Switzer G E, Lankester A, Korthof E T, Brand A, Ball L M | eng | null | Journal Article | null | IM | 22705802, bmt2012102, 10.1038/bmt.2012.102 | Since 1968, when Leiden undertook the first successful European pediatric BM transplantation with a 7-year-old sibling donor, more than 300 young children have donated BM in our unit. We first retrospectively studied a cohort of 210 donors, younger than 13 years at donation, to survey procedures of donor eligibility and study immediate effects of BM donation. We then performed a long-term follow-up (FU) and health-related quality of life (HRQoL) study. Despite documentation of previous medical conditions, no child was declared unfit to donate. We found that iron deficiency anemia or low-iron stores in BM did not result in treatment or extended FU. Harvest volumes exceeded 15 mL/kg in 65% of donors, with more than half requiring allogeneic blood transfusions. Donors had no structured FU after their first post-donation control. In this study, 25% of donors reported at least one somatic complaint at long-term FU. Finally long-term HRQoL revealed high scores in most subdomains (representing a higher QoL), compared to norm groups. These results indicate the need for development of (inter)national guidelines for pediatric stem cell donor care management. | Anemia, Iron-Deficiency, Blood Transfusion, Bone Marrow Cells, Bone Marrow Transplantation, Child, Child Development, Child, Preschool, Cohort Studies, Directed Tissue Donation, Donor Selection, Follow-Up Studies, Humans, Infant, Medical Records, Netherlands, Practice Guidelines as Topic, Prospective Studies, Psychology, Child, Quality of Life, Retrospective Studies, Siblings, Tissue Donors, Transfusion Reaction | null |
22,705,804 | 2013-06-24 | 2016-11-25 | 1476-5365 | Bone marrow transplantation | Non-invasive transient elastography for the prediction of liver toxicity following hematopoietic SCT. | Auberger J, Graziadei I, Clausen J, Vogel W, Nachbaur D | eng | null | Letter | Myeloablative Agonists | IM | 22705804, bmt2012113, 10.1038/bmt.2012.113 | null | Adult, Aged, Austria, Chemical and Drug Induced Liver Injury, Cohort Studies, Disease Susceptibility, Elasticity Imaging Techniques, Fibrosis, Graft vs Host Disease, Hematopoietic Stem Cell Transplantation, Hepatic Insufficiency, Hepatic Veno-Occlusive Disease, Humans, Liver, Middle Aged, Myeloablative Agonists, Risk, Transplantation Conditioning, Whole-Body Irradiation, Young Adult | null |
22,705,805 | 2013-06-24 | 2018-12-02 | 1476-5365 | Bone marrow transplantation | Cerebroretinal microangiopathy with calcifications and cysts, Revesz syndrome and aplastic anemia. | Linnankivi T, Polvi A, Mäkitie O, Lehesjoki A-E, Kivelä T | eng | null | Letter, Comment | null | IM | 22705805, bmt2012107, 10.1038/bmt.2012.107 | null | Anemia, Aplastic, Bone Diseases, Metabolic, Humans, Male, Stem Cell Transplantation, Transplantation Conditioning | null |
22,705,806 | 2012-11-28 | 2021-12-03 | 1873-3492 | Clinica chimica acta; international journal of clinical chemistry | Serum soluble transferrin receptor concentrations in US preschool children and non-pregnant women of childbearing age from the National Health and Nutrition Examination Survey 2003-2010. | Mei Zuguo, Pfeiffer Christine M, Looker Anne C, Flores-Ayala Rafael C, Lacher David A, Mirel Lisa B, Grummer-Strawn Laurence M | eng | null | Journal Article | Receptors, Transferrin, Iron | IM | 22705806, S0009-8981(12)00302-6, 10.1016/j.cca.2012.05.022 | Serum soluble transferrin receptor (sTfR) is recommended as a sensitive and accurate measure of iron deficiency (ID) in populations when only a single indicator can be used. The lack of assay standardization and of representative data on the distribution of sTfR in at-risk populations currently limits its utility. | Adolescent, Adult, Anemia, Iron-Deficiency, Child, Child, Preschool, Female, Humans, Infant, Infant, Newborn, Iron, Iron Deficiencies, Male, Middle Aged, Nutrition Surveys, Parity, Predictive Value of Tests, Pregnancy, Racial Groups, Receptors, Transferrin, Reference Values, Solubility, United States | null |
22,705,807 | 2013-02-14 | 2014-11-20 | 1096-0929 | Toxicological sciences : an official journal of the Society of Toxicology | Using novel in vitro NociOcular assay based on TRPV1 channel activation for prediction of eye sting potential of baby shampoos. | Forsby Anna, Norman Kimberly G, El Andaloussi-Lilja Johanna, Lundqvist Jessica, Walczak Vincent, Curren Rodger, Martin Katharine, Tierney Neena K | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Hair Preparations, Irritants, TRPV Cation Channels, TRPV1 protein, human | IM | 22705807, kfs198, 10.1093/toxsci/kfs198 | The transient receptor potential vanilloid type 1 (TRPV1) channel is one of the most well-characterized pain-inducing receptors. The purpose of this study was to predict human eye stinging of 19 baby bath and shampoo formulations by studying TRPV1 activity, as measured by increase in intracellular free Ca(2+). The NociOcular test, a novel recombinant neuronal in vitro model with high expression of functional TRPV1 channels, was used to test formulations containing a variety of surfactants, preservatives, and fragrances. TRPV1-specific Ca(2+) influx was abolished when the TRPV1 channel antagonist capsazepine was applied to the cells prior to shampoo samples. The positive control, an adult shampoo that contains cocamide monoethanolamine (CMEA), a known stinging ingredient, was the most active sample tested in the NociOcular test. The negative control, a marketed baby shampoo, was negative in the NociOcular and human tests. Seven of the formulations induced stinging in the human test, and of those six were positive in the NociOcular test. Twelve formulations were classified as nonstinging in the human test, and of those ten were negative in the NociOcular test. There was no correlation between the clinical stinging results for the baby formulations and the data generated from other in vitro eye irritation assays (cytosensor microphysiometer, neutral red uptake, EpiOcular, transepithelial permeability). Our data support that the TRPV1 channel is a principal mediator of eye-stinging sensation induced by baby bath and shampoo formulations and that the NociOcular test may be a valuable in vitro tool to predict human eye-stinging sensation. | Cell Line, Tumor, Eye, Hair Preparations, Humans, In Vitro Techniques, Irritants, TRPV Cation Channels | null |
22,705,809 | 2013-03-27 | 2012-10-19 | 1096-0929 | Toxicological sciences : an official journal of the Society of Toxicology | Regulation of allergic responses to chemicals and drugs: possible roles of epigenetic mechanisms. | Moggs Jonathan G, Terranova Rémi, Kammüller Michael E, Chibout Salah-Dine, Chapman Victoria, Dearman Rebecca J, Kimber Ian | eng | null | Journal Article, Review | Allergens, Xenobiotics | IM | 22705809, kfs207, 10.1093/toxsci/kfs207 | There is increasing evidence that epigenetic regulation of gene expression plays a pivotal role in the orchestration of immune and allergic responses. Such regulatory mechanisms have potentially important implications for the acquisition of sensitization to chemical and drug allergens; and in determining the vigor, characteristics, and longevity of allergic responses. Importantly, the discovery of long-lasting epigenetic alterations in specific immunoregulatory genes provides a mechanistic basis for immune cell memory, and thereby the potential of chemical allergens to influence the subsequent orientation of the adaptive immune system. In this article, we consider the implications of epigenetic mechanisms for the development of sensitization to chemical and drug allergens and the form that allergic reactions will take. | Allergens, Drug Hypersensitivity, Epigenesis, Genetic, Gene Expression, Humans, Immune System, Immunization, Xenobiotics | null |
22,705,810 | 2012-12-28 | 2012-08-29 | 1095-8630 | Journal of environmental management | Robust optimization approach to regional wastewater system planning. | Zeferino João A, Cunha Maria C, Antunes António P | eng | null | Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705810, S0301-4797(12)00266-6, 10.1016/j.jenvman.2012.05.008 | Wastewater systems are subject to several sources of uncertainty. Different scenarios can occur in the future, depending on the behavior of a variety of demographic, economic, environmental, and technological variables. Robust optimization approaches are aimed at finding solutions that will perform well under any likely scenario. The planning decisions to be made about wastewater system planning involve two main issues: the setup and operation costs of sewer networks, treatment plants, and possible pump stations; and the water quality parameters to be met in the water body where the (treated) wastewater is discharged. The source of uncertainty considered in this article is the flow of the river that receives the wastewater generated in a given region. Three robust optimization models for regional wastewater system planning are proposed. The models are solved using a simulated annealing algorithm enhanced with a local improvement procedure. Their application is illustrated through a case study representing a real-world situation, with the results being compared and commented upon. | Algorithms, Models, Theoretical, Waste Disposal, Fluid | null |
22,705,808 | 2013-02-14 | 2021-10-21 | 1096-0929 | Toxicological sciences : an official journal of the Society of Toxicology | Expression, circulation, and excretion profile of microRNA-21, -155, and -18a following acute kidney injury. | Saikumar Janani, Hoffmann Dana, Kim Tae-Min, Gonzalez Victoria Ramirez, Zhang Qin, Goering Peter L, Brown Ronald P, Bijol Vanesa, Park Peter J, Waikar Sushrut S, Vaidya Vishal S | eng | R01 DK093574 (NIDDK NIH HHS, United States); R01 ES017543 (NIEHS NIH HHS, United States); ES017543 (NIEHS NIH HHS, United States) | Journal Article, Research Support, N.I.H., Extramural | Gentamicins, MIRN155 microRNA, human, MIRN18A microRNA, human, MIRN21 microRNA, human, MicroRNAs | IM | 22705808, kfs210, 10.1093/toxsci/kfs210, PMC3499041, 19696117, 19289365, 20651252, 22351564, 19745058, 18515182, 19646430, 19212447, 21197658, 15143321, 16495376, 22112502, 20458318, 22157656, 18954897, 19375957, 19641480, 19509361, 17463290, 21775484, 18270516, 20702592, 22302755, 18837928, 17968323, 19610612, 19758836, 21703910, 19246379, 18925646, 21412018, 14597658, 22113526, 19386588, 16199517, 21700819, 16177006, 21062749, 15944708, 22408260, 17214507, 21887224, 21975865, 15253693, 8618585, 18230805, 15372042, 18766170, 19289371, 19201770, 18346642, 17242365, 22344686, 21788439, 18713256, 21891774, 21487102, 16024602, 19289845, 18949056, 19181739, 18663219, 14744438, 6704974, 21980462 | MicroRNAs (miRNAs) are endogenous noncoding RNA molecules that are involved in post-transcriptional gene silencing. Using global miRNA expression profiling, we found miR-21, -155, and 18a to be highly upregulated in rat kidneys following tubular injury induced by ischemia/reperfusion (I/R) or gentamicin administration. Mir-21 and -155 also showed decreased expression patterns in blood and urinary supernatants in both models of kidney injury. Furthermore, urinary levels of miR-21 increased 1.2-fold in patients with clinical diagnosis of acute kidney injury (AKI) (n = 22) as compared with healthy volunteers (n = 25) (p < 0.05), and miR-155 decreased 1.5-fold in patients with AKI (p < 0.01). We identified 29 messenger RNA core targets of these 3 miRNAs using the context likelihood of relatedness algorithm and found these predicted gene targets to be highly enriched for genes associated with apoptosis or cell proliferation. Taken together, these results suggest that miRNA-21 and -155 could potentially serve as translational biomarkers for detection of AKI and may play a critical role in the pathogenesis of kidney injury and tissue repair process. | Acute Kidney Injury, Algorithms, Animals, Case-Control Studies, Gentamicins, Humans, MicroRNAs, Polymerase Chain Reaction, Rats, Rats, Wistar | null |
22,705,811 | 2012-12-28 | 2016-11-25 | 1095-8630 | Journal of environmental management | Improving public engagement in ICZM: a practical approach. | Areizaga J, Sanò M, Medina R, Juanes J | eng | null | Journal Article | null | IM | 22705811, S0301-4797(12)00263-0, 10.1016/j.jenvman.2012.05.006 | Stakeholder engagement is at the core of successful ICZM stories. This paper proposes a practical approach to set the basis for a wide and efficient stakeholder engagement process in ICZM which was tested in Cantabria, a Region in the north of Spain. The coastal system was modelled by defining three basic interacting components: coastal units, coastal activities and coastal stakeholders. This approach allowed the identification of a very clear set of relationships emerging from a survey of stakeholders and an assessment of coastal projects. This process was also useful to inform stakeholders about a new regional coastal strategy and to consider their opinion on coastal issues and public participation. From a very ill-defined situation, a clear relationship chart was defined and a spatial database implemented which conveys all the data gathered into a useful tool for coastal managers. | Community Participation, Conservation of Natural Resources, Ecosystem, Models, Theoretical, Spain | null |
22,705,812 | 2012-12-28 | 2012-08-29 | 1095-8630 | Journal of environmental management | Post-incident monitoring to evaluate environmental damage from shipping incidents: chemical and biological assessments. | Radović Jagoš R, Rial Diego, Lyons Brett P, Harman Christopher, Viñas Lucia, Beiras Ricardo, Readman James W, Thomas Kevin V, Bayona Josep M | eng | null | Journal Article, Research Support, Non-U.S. Gov't, Review | Water Pollutants, Chemical | IM | 22705812, S0301-4797(12)00239-3, 10.1016/j.jenvman.2012.04.042 | Oil and chemical spills in the marine environment are an issue of growing concern. Oil exploration and exploitation is moving from the continental shelf to deeper waters, and to northern latitudes where the risk of an oil spill is potentially greater and may affect pristine ecosystems. Moreover, a growing number of chemical products are transported by sea and maritime incidents of hazardous and noxious substances (HNS) are expected to increase. Consequently, it seems timely to review all of the experience gained from past spills to be able to cope with appropriate response and mitigation strategies to combat future incidents. Accordingly, this overview is focused on the dissemination of the most successful approaches to both detect and assess accidental releases using chemical as well as biological approaches for spills of either oil or HNS in the marine environment. Aerial surveillance, sampling techniques for water, suspended particles, sediments and biota are reviewed. Early warning bioassays and biomarkers to assess spills are also presented. Finally, research needs and gaps in knowledge are discussed. | Biological Assay, Environmental Monitoring, Petroleum Pollution, Ships, Water Pollutants, Chemical | null |
22,705,813 | 2012-08-13 | 2018-10-23 | 1756-1833 | BMJ (Clinical research ed.) | After repair of tracheo-oesophageal atresia. | Love Caroline, Morice Alyn H | eng | null | Journal Article | null | IM | 22705813, 10.1136/bmj.e3517 | null | Adult, Diagnosis, Differential, Esophageal Atresia, Female, Humans, Physicians, Tracheoesophageal Fistula | null |
22,705,814 | 2012-08-13 | 2022-03-30 | 1756-1833 | BMJ (Clinical research ed.) | Problems of stopping trials early. | Guyatt Gordon H, Briel Matthias, Glasziou Paul, Bassler Dirk, Montori Victor M | eng | null | Journal Article | Adrenergic beta-Antagonists, Insulin, Protein C | IM | 22705814, 10.1136/bmj.e3863 | null | Adrenergic beta-Antagonists, Clinical Trials Data Monitoring Committees, Critical Illness, Decision Making, Endpoint Determination, Ethics, Research, Humans, Insulin, Myocardial Infarction, Protein C, Randomized Controlled Trials as Topic, Research Design, Sepsis, Surgical Procedures, Operative, Time Factors, Treatment Outcome | null |
22,705,815 | 2012-08-13 | 2021-10-21 | 1756-1833 | BMJ (Clinical research ed.) | Aristolochic acid nephropathy. | Gökmen M Refik, Lord Graham M | eng | G1000758 (Medical Research Council, United Kingdom); MR/J006742/1 (Medical Research Council, United Kingdom) | Editorial | Aristolochic Acids, Carcinogens, Drugs, Chinese Herbal, aristolochic acid I | IM | 22705815, 10.1136/bmj.e4000 | null | Aristolochic Acids, Balkan Nephropathy, Carcinogens, Drugs, Chinese Herbal, Humans, Kidney Diseases, Risk Assessment | null |
22,705,816 | 2012-08-13 | 2018-10-23 | 1756-1833 | BMJ (Clinical research ed.) | Achieving Nicholson challenge requires fundamental rethink on NHS, conference hears. | Hawkes Nigel | eng | null | News | null | IM | 22705816, 10.1136/bmj.e4175 | null | Budgets, Cost Savings, Diffusion of Innovation, Efficiency, Organizational, Health Care Reform, Humans, Organizational Objectives, Politics, State Medicine, United Kingdom | null |
22,705,817 | 2012-08-13 | 2018-10-23 | 1756-1833 | BMJ (Clinical research ed.) | Europe plans to strengthen surveillance system for medical devices, MPs are told. | O'Dowd Adrian | eng | null | News | null | IM | 22705817, 10.1136/bmj.e4179 | null | Breast Implants, Equipment Safety, Equipment and Supplies, Europe, Humans, Legislation, Medical, Product Surveillance, Postmarketing, Quality Control | null |
22,705,819 | 2012-08-13 | 2018-10-23 | 1756-1833 | BMJ (Clinical research ed.) | Christian GP is given warning after expressing his religious beliefs to patient. | Dyer Clare | eng | null | News | null | IM | 22705819, 10.1136/bmj.e4192 | null | Christianity, Employee Discipline, England, Humans, Physician-Patient Relations, Physicians, Family, Religion | null |
22,705,818 | 2012-08-13 | 2021-12-03 | 1756-1833 | BMJ (Clinical research ed.) | Hungarian geneticists call for prosecution of firm that carried out tests to prove politician's racial origin. | Mayor Susan | eng | null | News | null | IM | 22705818, 10.1136/bmj.e4190 | null | Genetic Testing, Genome, Human, Humans, Hungary, Politics, Prejudice, Racial Groups, Societies, Medical | null |
22,705,820 | 2012-10-25 | 2016-11-25 | 1361-6560 | Physics in medicine and biology | A three-dimensional model-based partial volume correction strategy for gated cardiac mouse PET imaging. | Dumouchel Tyler, Thorn Stephanie, Kordos Myra, DaSilva Jean, Beanlands Rob S B, deKemp Robert A | eng | MIS-100935 (Canadian Institutes of Health Research, Canada); MOP-79311 (Canadian Institutes of Health Research, Canada) | Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705820, 10.1088/0031-9155/57/13/4309 | Quantification in cardiac mouse positron emission tomography (PET) imaging is limited by the imaging spatial resolution. Spillover of left ventricle (LV) myocardial activity into adjacent organs results in partial volume (PV) losses leading to underestimation of myocardial activity. A PV correction method was developed to restore accuracy of the activity distribution for FDG mouse imaging. The PV correction model was based on convolving an LV image estimate with a 3D point spread function. The LV model was described regionally by a five-parameter profile including myocardial, background and blood activities which were separated into three compartments by the endocardial radius and myocardium wall thickness. The PV correction was tested with digital simulations and a physical 3D mouse LV phantom. In vivo cardiac FDG mouse PET imaging was also performed. Following imaging, the mice were sacrificed and the tracer biodistribution in the LV and liver tissue was measured using a gamma-counter. The PV correction algorithm improved recovery from 50% to within 5% of the truth for the simulated and measured phantom data and image uniformity by 5-13%. The PV correction algorithm improved the mean myocardial LV recovery from 0.56 (0.54) to 1.13 (1.10) without (with) scatter and attenuation corrections. The mean image uniformity was improved from 26% (26%) to 17% (16%) without (with) scatter and attenuation corrections applied. Scatter and attenuation corrections were not observed to significantly impact PV-corrected myocardial recovery or image uniformity. Image-based PV correction algorithm can increase the accuracy of PET image activity and improve the uniformity of the activity distribution in normal mice. The algorithm may be applied using different tracers, in transgenic models that affect myocardial uptake, or in different species provided there is sufficient image quality and similar contrast between the myocardium and surrounding structures. | Algorithms, Animals, Cardiac-Gated Imaging Techniques, Electrocardiography, Heart Ventricles, Image Processing, Computer-Assisted, Mice, Models, Biological, Movement, Phantoms, Imaging, Positron-Emission Tomography | null |
22,705,823 | 2012-11-26 | 2022-03-11 | 1095-9513 | Molecular phylogenetics and evolution | Molecular phylogeny of the Robust clade (Faviidae, Mussidae, Merulinidae, and Pectiniidae): an Indian Ocean perspective. | Arrigoni Roberto, Stefani Fabrizio, Pichon Michel, Galli Paolo, Benzoni Francesca | eng | null | Journal Article | DNA, Mitochondrial, DNA, Ribosomal | IM | 22705823, S1055-7903(12)00214-X, 10.1016/j.ympev.2012.06.001 | Recent phylogenetic analyses have demonstrated the limits of traditional coral taxonomy based solely on skeletal morphology. In this phylogenetic context, Faviidae and Mussidae are ecologically dominant families comprising one third of scleractinian reef coral genera, but their phylogenies remain partially unresolved. Many of their taxa are scattered throughout most of the clades of the Robust group, and major systematic incongruences exist. Numerous genera and species remain unstudied, and the entire biogeographic area of the Indian Ocean remains largely unsampled. In this study, we analyzed a portion of the mitochondrial cytochrome c oxidase subunit 1 gene and a portion of ribosomal DNA for 14 genera and 27 species of the Faviidae and Mussidae collected from the Indian Ocean and New Caledonia and this is the first analysis of five of these species. For some taxa, newly discovered evolutionary relationships were detected, such as the evolutionary distinctiveness of Acanthastrea maxima, the genetic overlap of Parasimplastrea omanensis and Blastomussa merleti, and the peculiar position of Favites peresi in clade XVII together with Echinopora and Montastraea salebrosa. Moreover, numerous cases of intraspecific divergences between Indian Ocean and Pacific Ocean populations were detected. The most striking cases involve the genera Favites and Favia, and in particular Favites complanata, F. halicora, Favia favus, F. pallida, F. matthaii, and F. rotumana, but divergence also is evident in Blastomussa merleti, Cyphastrea serailia, and Echinopora gemmacea. High morphological variability characterizes most of these taxa, thus traditional skeletal characteristics, such as corallite arrangement, seem to be evolutionary misleading and are plagued by convergence. Our results indicate that the systematics of the Faviidae and the Mussidae is far from being resolved and that the inclusion of conspecific populations of different geographical origin represents an unavoidable step when redescribing the taxonomy and systematics of scleractinian corals. More molecular phylogenies are needed to define the evolutionary lineages that could be corroborated by known and newly discovered micromorphological characters. | Animals, Anthozoa, Biological Evolution, DNA, Mitochondrial, DNA, Ribosomal, Indian Ocean, Pacific Ocean, Phylogeny, Sequence Analysis, DNA | null |
22,705,824 | 2012-11-26 | 2025-01-03 | 1095-9513 | Molecular phylogenetics and evolution | Concordance analysis in mitogenomic phylogenetics. | Weisrock David W | eng | null | Journal Article, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S. | null | IM | 22705824, S1055-7903(12)00216-3, 10.1016/j.ympev.2012.06.003 | Here I advocate the utility of Bayesian concordance analysis as a mechanism for exploring the magnitude and source of phylogenetic signal in concatenated mitogenomic phylogenetic studies. While typically applied to the study of independently evolving gene trees, Bayesian concordance analysis can also be applied to linked, but individually analyzed, gene regions using a prior probability that reflects the expectation of similar phylogenetic reconstructions. For true branches in the mitogenomic tree, concordance factors should represent the number of gene regions that contain phylogenetic signal for a particular clade. As a demonstration of the application of Bayesian concordance analysis to empirical data, I analyzed two different salamander (Hynobiidae and Plethodontidae) mitogenomic data sets using a gene-based partitioning strategy. The results revealed many strongly supported clades in the concatenated trees that have high concordance factors, permitting the inference that these are robustly resolved through phylogenetic signal distributed across the mitogenome. In contrast, a number of strongly supported clades in the concatenated tree received low concordance factors, indicating that their reconstruction is either driven primarily by phylogenetic signal in a small number of gene regions, or that they are inconsistent reconstructions influenced by properties of the data that can produce inaccurate trees (e.g., compositional bias, selection, etc.). Exploration of the Bayesian joint posterior distribution of trees highlighted partitions that contribute phylogenetic information to similar clade reconstructions. This approach was particularly insightful in the hynobiid data, where different combinations of genes were identified that support alternative tree reconstructions. Concatenated analysis of these different subsets of genes highlighted through Bayesian concordance analysis produced strongly supported and contrasting trees, demonstrating the potential for inconsistency in concatenated mitogenomic phylogenetics. The overall results presented here suggest that Bayesian concordance analysis can serve as an effective exploration of the influence of different gene regions in mitogenomic (and other organellar genomic) phylogenetic studies. | Animals, Bayes Theorem, Genes, Mitochondrial, Genome, Mitochondrial, Genomics, Phylogeny, Sequence Analysis, DNA, Caudata | null |
22,705,825 | 2014-02-27 | 2013-09-09 | 1095-9513 | Molecular phylogenetics and evolution | Mitogenomic analyses from ancient DNA. | Paijmans Johanna L A, Gilbert M Thomas P, Hofreiter Michael | eng | null | Journal Article, Research Support, Non-U.S. Gov't, Review | DNA, Mitochondrial | IM | 22705825, S1055-7903(12)00215-1, 10.1016/j.ympev.2012.06.002 | The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences (mitogenomes). Such studies were initially limited to analyses of extant organisms, but developments in both DNA sequencing technologies and general methodological aspects related to working with degraded DNA have resulted in complete mitogenomes becoming increasingly popular for ancient DNA studies as well. To date, at least 124 partially or fully assembled mitogenomes from more than 20 species have been obtained, and, given the rapid progress in sequencing technology, this number is likely to dramatically increase in the future. The increased information content offered by analysing full mitogenomes has yielded major progress with regard to both the phylogenetic positions of extinct species, as well as resolving population genetics questions in both extinct and extant species. | Animals, DNA, Mitochondrial, Extinction, Biological, Genetics, Population, Genome, Mitochondrial, Nucleic Acid Hybridization, Phylogeny, Phylogeography, Sequence Analysis, DNA | Mitochondrial DNA, Museum specimens, Next Generation Sequencing, Phylogenetics, Phylogeography, Population genetics |
22,705,826 | 2012-10-11 | 2018-12-01 | 1879-0038 | Gene | MDR1 gene polymorphisms may be associated with Behçet's disease and its colchicum treatment response. | Rustemoglu Aydin, Gül Ülker, Gümüş-Akay Güvem, Gönül Müzeyyen, Yiğit Serbülent, Bozkurt Nihan, Karadağ Aynur, Pişkin Emine, Sunguroğlu Asuman, Kadıkıran Ahmet | eng | null | Journal Article | ABCB1 protein, human, ATP Binding Cassette Transporter, Subfamily B, ATP Binding Cassette Transporter, Subfamily B, Member 1, Tubulin Modulators, Colchicine | IM | 22705826, S0378-1119(12)00628-2, 10.1016/j.gene.2012.05.040 | Behçet's disease (BD) is a chronic multisystem disorder. Infectious agents, immune system mechanisms, and genetic factors are implicated in the etiopathogenesis of BD, which remains to be explained. The human MDR1 (ABCB1) gene encoder P-glycoprotein (P-gp) plays a key role in drug disposition, serves as a protective mechanism against xenobiotics, and provides additional protection for the brain, testis, and fetus. We investigated the genotype and haplotype distributions of three MDR1 gene polymorphisms (C1236T, G2677T/A, and C3435T) in 104 BD patients and 130 control subjects. The genotyping analysis was performed by using PCR-RFLP methods. No statistically significant differences were found for the genotypic and allelic distributions of three individual single nucleotide polymorphisms (SNPs) in the MDR1 gene between BD patients and control subjects in this study (p>0.05). However, combined genotype and haplotype frequencies have found statistically significant differences between BD and control subjects for some combinations (p<0.05). The CC-GG binary genotype for C1236T-G2677T/A loci couple in particular may have a high degree of predisposition to BD (p=0.009; OR, 3.03; 95% CI, 1.41-6.54). Furthermore, significant differences between colchicine-responsive and -nonresponsive groups were found. Genotypic and allelic distributions of C3435T and G2677T/A loci, as well as their genotype and haplotype combinations, were found to have statistically significant differences (p<0.05). The TT genotype for the C3435T locus (p=0.001; OR, 6.59; 95% CI, 1.86-23.30) and T allele (p=0.009; OR, 2.09; 95% CI, 1.18-3.70) plays a substantial role in the colchicine response. Our study showed that MDR1 genes and their polymorphisms may affect a patient's BD susceptibility and colchicine response. | ATP Binding Cassette Transporter, Subfamily B, ATP Binding Cassette Transporter, Subfamily B, Member 1, Adult, Behcet Syndrome, Colchicine, Colchicum, Female, Genetic Predisposition to Disease, Haplotypes, Humans, Male, Middle Aged, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Treatment Outcome, Tubulin Modulators | null |
22,705,827 | 2012-10-11 | 2013-11-21 | 1879-0038 | Gene | Transcription directed by human core promoters with a HomolD box sequence requires DDB1, RECQL and RNA polymerase II machinery. | Contreras-Levicoy Juan, Moreira-Ramos Sandra, Rojas Diego A, Urbina Fabiola, Maldonado Edio | eng | null | Journal Article, Research Support, Non-U.S. Gov't | DDB1 protein, human, DNA-Binding Proteins, RNA Polymerase II, RECQL protein, human, RecQ Helicases | IM | 22705827, S0378-1119(12)00678-6, 10.1016/j.gene.2012.05.059 | TATA box is the most studied core promoter element and has a well-described transcription mechanism. However, most metazoan promoters lack TATA box and contain other core promoter elements. One of such elements is HomolD box, which was first described in promoters of ribosomal protein genes in Schizosaccharomyces pombe, and studies performed in this model showed that transcription directed by HomolD box is dependent on RNAPII machinery, and the HomolD-binding protein was Rrn7, a component of RNAPI core factor. Nevertheless, the mechanisms that underlie HomolD-dependent transcription are still unknown. The purpose of this study is to determine the mechanism of transcription directed by human HomolD box. By stepwise purification through different ion exchange columns and affinity chromatography, we purified two proteins: DDB1 and RECQL (DNA damage-binding protein 1 and ATP-dependent DNA helicase Q1 respectively). These proteins showed specific HomolD-binding activity and were required for in vitro HomolD-directed transcription. Recombinant RECQL, but not DDB1, presented HomolD-binding activity in vitro. Both proteins bound to HomolD box in vivo, which could be explained because these proteins co-immunoprecipitated. Additionally, RNAPII machinery was also required to transcription. Collectively, these data suggest that HomolD-containing promoters require the RNAPII machinery and the proteins DDB1 and RECQL for an accurate transcription. | DNA-Binding Proteins, Gene Expression Regulation, HeLa Cells, Humans, Promoter Regions, Genetic, Protein Binding, RNA Polymerase II, RecQ Helicases, Transcription Initiation Site, Transcription, Genetic | null |
22,705,828 | 2012-10-11 | 2012-07-24 | 1879-0038 | Gene | Aldehyde oxidase 1 gene is regulated by Nrf2 pathway. | Maeda Kenichiro, Ohno Takashi, Igarashi Shizuka, Yoshimura Takaaki, Yamashiro Koji, Sakai Masaharu | eng | null | Journal Article | NF-E2-Related Factor 2, Nfe2l2 protein, rat, Aldehyde Oxidase, Aox1protein, rat | IM | 22705828, S0378-1119(12)00703-2, 10.1016/j.gene.2012.06.010 | Aldehyde oxidase is a member of the molybd-flavo enzyme family that catalyzes the hydroxylation of heterocycles and the oxidation of aldehydes into corresponding carboxylic acids. Aldehyde oxidase-1 (AOX1) is highly expressed in liver and is involved in the oxidation of a variety of aldehydes and nitrogenous heterocyclic compounds, including anti-cancer and immunosuppressive drugs. However, the physiological substrates of AOX1 have not been identified, and it was unknown how the expression of AOX1 is regulated. Here, we found that the AOX1 gene is regulated by the Nrf2 pathway. Two Nrf2 binding consensus elements (antioxidant responsive element, ARE) are located in the 5' upstream region of the rat AOX1 gene. Molecular analyses using reporter transfection analysis, EMSA, and ChIP analysis show that Nrf2 binds to and strongly activates the rat AOX1 gene. | Aldehyde Oxidase, Animals, Base Sequence, Cell Line, Tumor, Gene Expression Regulation, Enzymologic, Liver, Molecular Sequence Data, NF-E2-Related Factor 2, Protein Binding, Rats, Signal Transduction, Transcriptional Activation | null |
22,705,829 | 2013-07-08 | 2012-12-24 | 1873-1570 | Resuscitation | Quality of chest compressions performed by inexperienced rescuers in simulated cardiac arrest associated with pregnancy. | Kim Seunghwan, You Je Sung, Lee Hye Sun, Lee Jae Ho, Park Yoo Seok, Chung Sung Phil, Park Incheol | eng | null | Journal Article, Randomized Controlled Trial | null | IM | 22705829, S0300-9572(12)00298-5, 10.1016/j.resuscitation.2012.06.003 | We aimed to compare the quality of chest compressions performed by inexperienced rescuers in different positions, notably supine and at a 30° inclined lateral position, to ascertain whether high-quality chest compression is feasible on a pregnant subject in cardiac arrest. | Adult, Clinical Competence, Cross-Over Studies, Female, Heart Arrest, Heart Massage, Humans, Male, Manikins, Pregnancy, Pregnancy Complications, Cardiovascular, Prospective Studies, Students, Medical, Video Recording | null |
22,705,830 | 2013-01-28 | 2018-12-01 | 1873-1570 | Resuscitation | Bystander CPR: how to best increase the numbers. | Atkins Dianne L | eng | null | Editorial, Comment | null | IM | 22705830, S0300-9572(12)00307-3, 10.1016/j.resuscitation.2012.06.005 | null | Female, Humans, Male, Out-of-Hospital Cardiac Arrest, Resuscitation | null |
22,705,831 | 2013-07-08 | 2022-03-18 | 1873-1570 | Resuscitation | Current termination of resuscitation (TOR) guidelines predict neurologically favorable outcome in Japan. | Kajino Kentaro, Kitamura Tetsuhisa, Iwami Taku, Daya Mohamud, Ong Marcus Eng Hock, Hiraide Atsushi, Shimazu Takeshi, Kishi Masashi, Yamayoshi Shigeru | eng | null | Journal Article, Research Support, Non-U.S. Gov't | null | IM | 22705831, S0300-9572(12)00305-X, 10.1016/j.resuscitation.2012.05.027 | It is unclear whether the basic life support (BLS) and advanced life support (ALS) pre-hospital termination of resuscitation (TOR) rules developed in North America can be applied successfully to patients with out-of-hospital cardiac arrest (OHCA) in other countries. | Aged, Decision Support Techniques, Female, Humans, Japan, Male, Medical Futility, Practice Guidelines as Topic, Predictive Value of Tests, Registries, Resuscitation Orders, Sensitivity and Specificity | null |
22,705,832 | 2013-09-23 | 2013-03-07 | 1873-1570 | Resuscitation | Does the number of rescuers affect the survival rate from out-of-hospital cardiac arrests? Two or more rescuers are not always better than one. | Nishi Taiki, Maeda Tetsuo, Takase Keiko, Kamikura Takahiro, Tanaka Yoshio, Inaba Hideo | eng | null | Journal Article | null | IM | 22705832, S0300-9572(12)00304-8, 10.1016/j.resuscitation.2012.05.026 | An increased number of rescuers may improve the survival rate from out-of-hospital cardiac arrests (OHCAs). The majority of OHCAs occur at home and are handled by family members. | Aged, Aged, 80 and over, Emergency Medical Services, Emergency Medical Technicians, Female, Humans, Male, Middle Aged, Out-of-Hospital Cardiac Arrest, Prospective Studies, Survival Rate | null |
22,705,833 | 2013-07-08 | 2012-12-24 | 1873-1570 | Resuscitation | Medical emergencies in the imaging department of a university hospital: event and imaging characteristics. | van Tonder F C, Sutherland T, Smith R J, Chock J M E, Santamaria J D | eng | null | Journal Article | null | IM | 22705833, S0300-9572(12)00272-9, 10.1016/j.resuscitation.2012.05.020 | We aimed to describe the characteristics of medical emergencies that occurred in the medical imaging department (MID) of a university hospital in Melbourne, Australia. A database of 'Respond Medical Emergency Team (MET)' and 'Respond Blue' calls was retrospectively examined for the period June 2003 to November 2010 in relation to events that occurred in the MID. The hospital medical imaging database was also examined in relation to these events and, where necessary, patients' notes were reviewed. Ethics approval was granted by the hospital ethics review board. There were 124 medical emergency calls in the MID during the study period, 28% Respond Blue and 72% Respond MET. Of these 124 calls, 26% occurred outside of usual work hours and 12% involved cardiac arrest. The most common reasons for the emergency calls were seizures (14%) and altered conscious state (13%). Contrast anaphylaxis precipitated the emergency in 4% of cases. In 83% of cases the emergency calls were for patients attending the MID for diagnostic imaging, the remainder being for a procedure. Of the scheduled imaging techniques, 45% were for computed tomography. The scheduled imaging was abandoned due to the emergency in 12% of cases. When performed, imaging informed patient management in 34% of cases in diagnostic imaging and in all cases in the context of image-guided procedures. Medical emergency calls in the MID often occurred outside usual work hours and were attributed to a range of medical problems. The emergencies occurred in relation to all imaging techniques and imaging informed patient management in many cases. | Emergencies, Female, Hospitals, University, Humans, Male, Middle Aged, Patient Care Team, Radiology Department, Hospital, Retrospective Studies, Victoria | null |
22,705,834 | 2012-11-20 | 2018-12-01 | 1537-4505 | Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology | Transport augmentation through the blood-inner ear barriers of guinea pigs treated with 3-nitropropionic acid and patients with acute hearing loss, visualized with 3.0 T MRI: figure labeling clarification. | Zou Jing | eng | null | Journal Article, Comment, Published Erratum | Nitro Compounds, Propionates | IM | 22705834, 10.1097/MAO.0b013e3182544a56, 00129492-201207000-00001 | null | Animals, Ear, Inner, Female, Hearing Loss, Sensorineural, Humans, Nitro Compounds, Propionates | null |
22,705,835 | 2012-11-20 | 2015-11-19 | 1537-4505 | Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology | People with symptoms of Ménière's disease: the relationship between illness intrusiveness, illness uncertainty, dizziness handicap, and depression. | Arroll Megan, Dancey Christine P, Attree Elizabeth A, Smith Sharon, James Trevor | eng | null | Journal Article | null | IM | 22705835, 10.1097/MAO.0b013e3182536ac6, 00129492-201207000-00024 | The goal of this study was to assess the impact of dizziness handicap, illness intrusiveness (in relation to vertigo, tinnitus, and hearing problems), and illness uncertainty on depression in people with the symptoms of Ménière's disease. | Adult, Aged, Aged, 80 and over, Depression, Disability Evaluation, Dizziness, Female, Humans, Male, Meniere Disease, Middle Aged, Quality of Life, Self Report, Severity of Illness Index, Surveys and Questionnaires, Uncertainty | null |
22,705,838 | 2013-03-26 | 2022-04-08 | 2165-5987 | Bioengineered | Genetically attenuated Trypanosoma cruzi parasites as a potential vaccination tool. | Pérez Brandan Cecilia, Basombrío Miguel Ángel | eng | null | Journal Article | Protozoan Proteins, Protozoan Vaccines, Vaccines, Attenuated, Tetrahydrofolate Dehydrogenase | IM | 22705838, 20680, 10.4161/bioe.20680, PMC3476874, 8813691, 7479765, 20644616, 18367671, 2180768, 21693561, 18754700, 21687672, 17938222, 18263655, 21628516, 20363262, 19432966, 20537954, 20883728, 10383767, 15696374, 3111281, 21980474, 16879036, 16569451, 8352387, 8314840, 8381972, 18373245, 21893541, 21073906, 22180798, 11349059, 1651496, 9724634, 19838068, 17624327, 18425131, 19646853, 18557814, 17239886, 6804390, 12972544, 18468462 | Chagas disease is the clinical manifestation of the infection produced by the parasite Trypanosoma cruzi. Currently there is no vaccine to prevent this disease and the protection attained with vaccines containing non-replicating parasites is limited. Genetically attenuated trypanosomatid parasites can be obtained by deletion of selected genes. Gene deletion takes advantage of the fact that this parasite can undergo homologous recombination between endogenous and foreign DNA sequences artificially introduced in the cells. This approach facilitated the discovery of several unknown gene functions, as well as allowing us to speculate about the potential for genetically attenuated live organisms as experimental immunogens. Vaccination with live attenuated parasites has been used effectively in mice to reduce parasitemia and histological damage, and in dogs, to prevent vector-delivered infection in the field. However, the use of live parasites as immunogens is controversial due to the risk of reversion to a virulent phenotype. Herein, we present our results from experiments on genetic manipulation of two T. cruzi strains to produce parasites with impaired replication and infectivity, and using the mutation of the dhfr-ts gene as a safety device against reversion to virulence. | Animals, CD8-Positive T-Lymphocytes, Chagas Disease, Dogs, Gene Deletion, Genetic Engineering, Homologous Recombination, Mice, Mutation, Parasitemia, Protozoan Proteins, Protozoan Vaccines, Tetrahydrofolate Dehydrogenase, Trypanosoma cruzi, Vaccines, Attenuated, Virulence | null |
22,705,845 | 2013-04-08 | 2019-12-10 | 1873-2933 | Clinical biochemistry | Short-term (90 min) diagnostic performance for acute non-ST segment elevation myocardial infarction and 30-day prognostic evaluation of a novel third-generation high sensitivity troponin I assay. | Schreiber Donald H, Agbo Chioma, Wu Alan H B | eng | null | Comparative Study, Evaluation Study, Journal Article, Research Support, Non-U.S. Gov't | Troponin I | IM | 22705845, S0009-9120(12)00274-3, 10.1016/j.clinbiochem.2012.06.005 | We evaluated a third-generation high sensitivity "guidelines acceptable" troponin I assay (hs-cTnI) against a contemporary "clinically usable" troponin assay (cTnI). | Adult, Aged, Aged, 80 and over, Area Under Curve, Blood Chemical Analysis, Female, Humans, Male, Middle Aged, Myocardial Infarction, Prognosis, ROC Curve, Troponin I, Young Adult | null |
22,705,840 | 2013-03-26 | 2022-01-29 | 2165-5987 | Bioengineered | Progress toward the development of polyvalent vaccination strategies against multiple viral infections in chickens using herpesvirus of turkeys as vector. | Iqbal Munir | eng | BB/E01111X/1 (Biotechnology and Biological Sciences Research Council, United Kingdom); BBS/E/I/00001708 (Biotechnology and Biological Sciences Research Council, United Kingdom); BBS/E01111X/1 (Biotechnology and Biological Sciences Research Council, United Kingdom) | Comment, Journal Article, Research Support, Non-U.S. Gov't | null | null | 22705840, 20476, 10.4161/bioe.20476, PMC3476869, 12163258, 19523282, 20545911, 16528024, 19230164, 19768403, 19471864, 12885890, 9890037, 17126960, 19618629, 10708438, 11991992, 9890038, 19618616, 19618635, 19565020, 15542691, 18442853, 19026690, 19187788, 17494574, 10696444, 19573638, 8782342, 8980804, 21907750, 17050610 | Vaccination is the most cost effective strategy for the control and prevention of the plethora of viral diseases affecting poultry production. The major challenge for poultry vaccination is the design of vaccines that will protect against multiple pathogens via a single protective dose, delivered by mass vaccination. The Marek disease virus and the highly pathogenic avian influenza virus cause severe disease outbreaks in chickens. Vaccination with live herpesvirus of turkeys protects chickens from Marek disease and inactivated influenza viruses are used as antigens to protect chickens against influenza virus infections. We developed herpesvirus of turkeys (HVT) as a vaccine vector that can act as a dual vaccine against avian influenza and Marek disease. The HVT vector was developed using reverse genetics based on an infectious bacterial artificial chromosome (BAC) clone of HVT. The BAC carrying the HVT genome was genetically modified to express the haemagglutinin (HA) gene of a highly pathogenic H7N1 virus. The resultant recombinant BAC construct containing the modified HVT sequence was transfected into chicken embryo fibroblast (CEF) cells and HVT recombinants (rHVT-H7HA) harbouring the H7N1 HA were recovered. Analysis of cultured CEF cells infected with the rHVT-H7HA showed that HA was expressed and that the rescued rHVT-H7HA stocks were stable during several in vitro passages with no difference in growth kinetics compared with the parent HVT. Immunization of one-day-old chicks with rHVT-H7HA induced H7-specific antibodies and protected chickens challenged with homologous H7N1 virus against virus shedding, clinical disease and death. The rHVT-H7HA vaccine also induced strong and long-lasting antibody titers against H7HA in chickens that were vaccinated in ovo 3 d before hatching. This vaccine supports differentiation between infected and vaccinated animals (DIVA), because no influenza virus nucleoprotein-specific antibodies were detected in the rHVT-H7HA vaccinated birds. The rHVT-H7HA not only provided protection against a lethal challenge with highly pathogenic H7N1 virus but also against highly virulent Marek disease virus and can be used as a DIVA vaccine. | null | null |
22,705,839 | 2013-03-26 | 2021-10-21 | 2165-5987 | Bioengineered | Genetic bioaugmentation as an effective method for in situ bioremediation: functionality of catabolic plasmids following conjugal transfers. | Ikuma Kaoru, Gunsch Claudia K | eng | null | Journal Article, Research Support, U.S. Gov't, Non-P.H.S. | Soil Pollutants, Toluene, Carbon | IM | 22705839, 20551, 10.4161/bioe.20551, PMC3476876, 17905994, 8779592, 16138096, 9603843, 10851144, 3467347, 12849778, 16138098, 20506384, 12902542, 7993092, 24196251, 19442633, 19709279, 10515934, 97271, 22367613 | Genetic bioaugmentation is an in situ bioremediation method that stimulates horizontal transfer of catabolic plasmids between exogenous donor cells and indigenous bacteria to increase the biodegradation potential of contaminants. A critical outcome of genetic bioaugmentation is the expression of an active catabolic phenotype upon plasmid conjugation. Using a pWW0-derivative TOL plasmid, we showed that certain genetic characteristics of the recipient bacteria, including genomic guanine-cytosine (G + C) content and phylogeny, may limit the expression of the transferred catabolic pathway. However, such genetic limitations observed in transconjugants could be overcome by the presence of an additional carbon source. Glucose and Luria-Bertani broth were shown to enhance the toluene degradation rates of transconjugants; these enhancement effects were dependent on transconjugant genomic G + C contents. Based on these observations, thorough genetic characterization of the indigenous microbial community in the contaminated environment of interest may provide a predictive tool for assessing the success of genetic bioaugmentation. | Base Composition, Biodegradation, Environmental, Biotransformation, Carbon, Conjugation, Genetic, Escherichia coli, Gene Transfer, Horizontal, Genetic Engineering, Metagenome, Microbial Consortia, Phylogeny, Plasmids, Pseudomonas putida, Serratia marcescens, Soil Pollutants, Toluene | null |
22,705,846 | 2013-03-04 | 2021-10-21 | 1476-5403 | Cell death and differentiation | The TNF family member APRIL promotes colorectal tumorigenesis. | Lascano V, Zabalegui L F, Cameron K, Guadagnoli M, Jansen M, Burggraaf M, Versloot M, Rodermond H, van der Loos C, Carvalho-Pinto C E, Kalthoff H, Medema J P, Hahne M | eng | null | Journal Article, Research Support, Non-U.S. Gov't | RNA, Small Interfering, Tumor Necrosis Factor Ligand Superfamily Member 13 | IM | 22705846, cdd201268, 10.1038/cdd.2012.68, PMC3469063, 18362943, 16474316, 14729948, 19142624, 11591325, 15199544, 19141538, 14988498, 20303878, 17768131, 14502235, 10956646, 9743536, 7969362, 15851487, 11520463, 21677748, 15488762, 19466596, 19291294, 16793914, 20016944, 11509692, 10898980, 11104810, 20418870, 12070306, 2296722, 18718755, 18765800, 21289624, 20933088, 17570691, 18726990, 11509691, 20420949, 15846369, 17119122, 20003335, 10880535, 18371377 | The tumor necrosis factor (TNF) family member APRIL (A proliferation inducing ligand) is a disease promoter in B-cell malignancies. APRIL has also been associated with a wide range of solid malignancies, including colorectal cancer (CRC). As evidence for a supportive role of APRIL in solid tumor formation was still lacking, we studied the involvement of APRIL in CRC. We observed that ectopic APRIL expression exacerbates the number and size of adenomas in Apc(Min) mice and in a mouse model for colitis-associated colon carcinogenesis. Furthermore, knockdown of APRIL in primary spheroid cultures of colon cancer cells and both mouse and human CRC cell lines reduced tumor clonogenicity and in vivo outgrowth. Taken together, our data therefore indicate that both tumor-derived APRIL and APRIL produced by non-tumor cells is supportive in colorectal tumorigenesis. | Animals, Cell Transformation, Neoplastic, Colorectal Neoplasms, Disease Models, Animal, Humans, Lentivirus, Mice, Mice, Inbred C57BL, Mice, Nude, Mice, Transgenic, RNA Interference, RNA, Small Interfering, Tumor Cells, Cultured, Tumor Necrosis Factor Ligand Superfamily Member 13 | null |
22,705,841 | 2013-03-26 | 2021-10-21 | 2165-5987 | Bioengineered | PanDaTox: a tool for accelerated metabolic engineering. | Amitai Gil, Sorek Rotem | eng | R01 AI082376 (NIAID NIH HHS, United States); R01AI082376-01 (NIAID NIH HHS, United States) | Comment, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't | null | null | 22705841, 20431, 10.4161/bioe.20431, PMC3476872, 22314049, 16878333, 22300632, 17947550, 22135293, 18205292, 22357141, 16617034, 21822239, 18996194, 11230695, 21958462, 12778056, 21127247 | Metabolic engineering is often facilitated by cloning of genes encoding enzymes from various heterologous organisms into E. coli. Such engineering efforts are frequently hampered by foreign genes that are toxic to the E. coli host. We have developed PanDaTox (www.weizmann.ac.il/pandatox), a web-based resource that provides experimental toxicity information for more than 1.5 million genes from hundreds of different microbial genomes. The toxicity predictions, which were extensively experimentally verified, are based on serial cloning of genes into E. coli as part of the Sanger whole genome shotgun sequencing process. PanDaTox can accelerate metabolic engineering projects by allowing researchers to exclude toxic genes from the engineering plan and verify the clonability of selected genes before the actual metabolic engineering experiments are conducted. | null | null |
22,705,848 | 2013-03-04 | 2021-12-03 | 1476-5403 | Cell death and differentiation | DNA damage response by single-strand breaks in terminally differentiated muscle cells and the control of muscle integrity. | Fortini P, Ferretti C, Pascucci B, Narciso L, Pajalunga D, Puggioni E M R, Castino R, Isidoro C, Crescenzi M, Dogliotti E | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Cell Cycle Proteins, DNA-Binding Proteins, H2AX protein, mouse, Histones, Imidazoles, Piperazines, Tumor Suppressor Protein p53, Tumor Suppressor Proteins, nutlin 3, Vitamin K 3, Doxorubicin, ATM protein, human, Ataxia Telangiectasia Mutated Proteins, Atm protein, mouse, Protein Serine-Threonine Kinases | IM | 22705848, cdd201253, 10.1038/cdd.2012.53, PMC3469061, 15504905, 19005492, 8853900, 17060614, 21034966, 21757407, 19557000, 16973621, 17508921, 20965415, 17664158, 11025438, 20534341, 15175264, 19307704, 8698814, 15226436, 11431331, 18971944, 18626472, 17526518, 21316216, 19333375, 18834305, 20023421, 9407038, 19151707, 10931918, 20698753, 19866340, 17218959, 17940040, 10801407, 19571671, 19941876, 17353358, 20937380, 17875725, 21036674, 19007744 | DNA single-strand breaks (SSB) formation coordinates the myogenic program, and defects in SSB repair in post-mitotic cells have been associated with human diseases. However, the DNA damage response by SSB in terminally differentiated cells has not been explored yet. Here we show that mouse post-mitotic muscle cells accumulate SSB after alkylation damage, but they are extraordinarily resistant to the killing effects of a variety of SSB-inducers. We demonstrate that, upon SSB induction, phosphorylation of H2AX occurs in myotubes and is largely ataxia telangiectasia mutated (ATM)-dependent. However, the DNA damage signaling cascade downstream of ATM is defective as shown by lack of p53 increase and phosphorylation at serine 18 (human serine 15). The stabilization of p53 by nutlin-3 was ineffective in activating the cell death pathway, indicating that the resistance to SSB inducers is due to defective p53 downstream signaling. The induction of specific types of damage is required to activate the cell death program in myotubes. Besides the topoisomerase inhibitor doxorubicin known for its cardiotoxicity, we show that the mitochondria-specific inhibitor menadione is able to activate p53 and to kill effectively myotubes. Cell killing is p53-dependent as demonstrated by full protection of myotubes lacking p53, but there is a restriction of p53-activated genes. This new information may have important therapeutic implications in the prevention of muscle cell toxicity. | Animals, Apoptosis, Ataxia Telangiectasia Mutated Proteins, Cell Cycle Proteins, Cell Differentiation, DNA Breaks, Single-Stranded, DNA Damage, DNA Repair, DNA-Binding Proteins, Doxorubicin, Histones, Imidazoles, Mice, Muscle Fibers, Skeletal, Phosphorylation, Piperazines, Protein Serine-Threonine Kinases, Signal Transduction, Tumor Suppressor Protein p53, Tumor Suppressor Proteins, Vitamin K 3 | null |
22,705,847 | 2013-08-15 | 2021-10-21 | 1476-5403 | Cell death and differentiation | Selective autophagy in budding yeast. | Suzuki Kuninori | eng | null | Journal Article, Research Support, Non-U.S. Gov't, Review | null | IM | 22705847, cdd201273, 10.1038/cdd.2012.73, PMC3524628, 13679515, 8050581, 16027116, 14536056, 17382324, 21757540, 10888680, 8224160, 18287526, 18331717, 18391941, 20138172, 11309418, 22157017, 12479807, 9151668, 21801009, 15138258, 9412464, 18818209, 21343297, 20659891, 17295840, 11430817, 7593182, 11856375, 19061865, 8663607, 21169734, 7814324, 20508643, 16874024, 1478473, 19363139, 16874036, 14761979, 22123825, 15901835, 16874081, 9214379, 8601598, 21364763, 19793921, 17909521, 20943953, 15743910, 11689437, 12839986, 11487704, 12529432, 18701704, 22308029, 9296392, 21839922, 19619495, 22311637, 12479808, 19619494, 1400574, 20639194 | Autophagy is a bulk degradation system, widely conserved in eukaryotes. Upon starvation, autophagosomes enclose a portion of the cytoplasm and ultimately fuse with the vacuole. The contents of autophagosomes are degraded in the vacuole, and recycled to maintain the intracellular amino-acid pool required for protein synthesis and survival under starvation conditions. Previously, autophagy was thought to be an essentially nonselective pathway, but recent evidence suggests that autophagosomes carry selected cargoes. These studies have identified two categories of selective autophagy - one highly selective and dependent on autophagy-related 11 (Atg11); another, less selective, that is, independent of Atg11. The former, selective category comprises the Cvt pathway, mitophagy, pexophagy and piecemeal microautophagy of the nucleus; acetaldehyde dehydrogenase 6 degradation and ribophagy belong to the latter, less selective category. In this review, I focus on the mechanisms and the physiological roles of these selective types of autophagy. | Autophagy, Mitophagy, Saccharomycetales | null |
22,705,843 | 2013-03-26 | 2021-10-21 | 2165-5987 | Bioengineered | Ethanol production from lignocellulosic biomass by recombinant Escherichia coli strain FBR5. | Saha Badal, Cotta Michael A | eng | null | Journal Article, Review | Bacterial Proteins, lignocellulose, Ethanol, Lignin, Xylose, Arabinose, Alcohol Dehydrogenase, Pyruvate Decarboxylase, Glucose, Galactose | IM | 22705843, 19874, 10.4161/bioe.19874, PMC3476873, 8953729, 16680457, 2644194, 10849788, 16599561, 10514256, 11499918, 8669902, 3322191, 21234754, 15932261, 21968655, 20478373, 2059047, 20717665, 21983410, 12892470, 19874923, 15917615, 18588096, 13680206, 9025293, 17541520, 12698321 | Lignocellulosic biomass, upon pretreatment and enzymatic hydrolysis, generates a mixture of hexose and pentose sugars such as glucose, xylose, arabinose and galactose. While Escherichia coli utilizes all these sugars it lacks the ability to produce ethanol from them. Recombinant ethanologenic E. coli strains have been created with a goal to produce ethanol from both hexose and pentose sugars. Herein, we review the current state of the art on the production of ethanol from lignocellulosic hydrolyzates by an ethanologenic recombinant E. coli strain (FBR5). The bacterium is stable without antibiotics and can tolerate ethanol up to 50 gL(-1). It produces up to 45 g ethanol per L and has the potential to be used for industrial production of ethanol from lignocellulosic hydrolyzates. | Alcohol Dehydrogenase, Arabinose, Bacterial Proteins, Biomass, Bioreactors, Escherichia coli, Ethanol, Fermentation, Galactose, Glucose, Hydrolysis, Lignin, Metabolic Engineering, Mutation, Pyruvate Decarboxylase, Xylose, Zymomonas | null |
22,705,851 | 2013-04-17 | 2021-10-21 | 1476-5403 | Cell death and differentiation | Activation of OASIS family, ER stress transducers, is dependent on its stabilization. | Kondo S, Hino S-I, Saito A, Kanemoto S, Kawasaki N, Asada R, Izumi S, Iwamoto H, Oki M, Miyagi H, Kaneko M, Nomura Y, Urano F, Imaizumi K | eng | R01 DK067493 (NIDDK NIH HHS, United States) | Journal Article, Research Support, Non-U.S. Gov't | Basic-Leucine Zipper Transcription Factors, CREB3L1 protein, human, CREB3L2 protein, human, Cyclic AMP Response Element-Binding Protein, Nerve Tissue Proteins, RNA, Small Interfering, Ubiquitin, Collagen, SYVN1 protein, human, Ubiquitin-Protein Ligases, Proteasome Endopeptidase Complex | IM | 22705851, cdd201277, 10.1038/cdd.2012.77, PMC3504707, 20160352, 16417584, 21438114, 16469704, 15938716, 15845366, 14744430, 18212250, 21251164, 12110171, 9930704, 500673, 11780124, 20237263, 10958673, 19767743, 21415858, 17887918, 21454302, 10693756, 18344614, 12191470, 12111373, 17170702, 15260976, 16236796, 19767744, 17059562, 3421938, 15735697, 10619424, 18264092, 17178827, 17565364, 12975321, 12202038, 9228060, 15665855 | Endoplasmic reticulum (ER) stress transducers transduce signals from the ER to the cytoplasm and nucleus when unfolded proteins accumulate in the ER. BBF2 human homolog on chromosome 7 (BBF2H7) and old astrocyte specifically induced substance (OASIS), ER-resident transmembrane proteins, have recently been identified as novel ER stress transducers that have roles in chondrogenesis and osteogenesis, respectively. However, the molecular mechanisms that regulate the activation of BBF2H7 and OASIS under ER stress conditions remain unresolved. Here, we showed that BBF2H7 and OASIS are notably unstable proteins that are easily degraded via the ubiquitin-proteasome pathway under normal conditions. ER stress conditions enhanced the stability of BBF2H7 and OASIS, and promoted transcription of their target genes. HMG-CoA reductase degradation 1 (HRD1), an ER-resident E3 ubiquitin ligase, ubiquitinated BBF2H7 and OASIS under normal conditions, whereas ER stress conditions dissociated the interaction between HRD1 and BBF2H7 or OASIS. The stabilization of OASIS in Hrd1(-/-) cells enhanced the expression of collagen fibers during osteoblast differentiation, whereas a knockdown of OASIS in Hrd1(-/-) cells suppressed the production of collagen fibers. These findings suggest that ER stress stabilizes OASIS family members and this is a novel molecular mechanism for the activation of ER stress transducers. | Animals, Basic-Leucine Zipper Transcription Factors, Cell Differentiation, Cell Line, Collagen, Cyclic AMP Response Element-Binding Protein, Endoplasmic Reticulum Stress, HEK293 Cells, HeLa Cells, Humans, Mice, Nerve Tissue Proteins, Osteoblasts, Proteasome Endopeptidase Complex, RNA Interference, RNA, Small Interfering, Rats, Ubiquitin, Ubiquitin-Protein Ligases, Ubiquitination | null |
22,705,842 | 2013-03-26 | 2022-07-27 | 2165-5987 | Bioengineered | Constitutive expression of Botrytis aclada laccase in Pichia pastoris. | Kittl Roman, Gonaus Christoph, Pillei Christian, Haltrich Dietmar, Ludwig Roland | eng | W 1224 (Austrian Science Fund FWF, Austria) | Journal Article, Research Support, Non-U.S. Gov't | Fungal Proteins, Alcohol Oxidoreductases, alcohol oxidase, Laccase, Glyceraldehyde-3-Phosphate Dehydrogenases | IM | 22705842, 20037, 10.4161/bioe.20037, PMC3476866, 21094600, 22178779, 12898062, 9251203, 19780817, 16915640, 16630262, 12115407, 10640598, 17038162, 16574262, 11377762, 20178646, 21204882, 16472305, 18257236, 10712591, 12480904, 10898858, 15489201 | The heterologous expression of laccases is important for their large-scale production and genetic engineering--a prerequisite for industrial application. Pichia pastoris is the preferred expression host for fungal laccases. The recently cloned laccase from the ascomycete Botrytis aclada (BaLac) has been efficiently expressed in P. pastoris under the control of the inducible alcohol oxidase (AOX1) promoter. In this study, we compare these results to the constitutive expression in the same organism using the glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter. The results show that the amounts of BaLac produced with the GAP system (517 mgL(-1)) and the AOX1 system (495 mgL(-1)) are comparable. The constitutive expression is, however, faster, and the specific activity of BaLac in the culture supernatant is higher (41.3 Umg(-1) GAP, 14.2 Umg(-1) AOX1). In microtiter plates, the constitutive expression provides a clear advantage due to easy manipulation (simple medium, no methanol feeding) and fast enzyme production (high-throughput screening assays can already be performed after 48 h). | Alcohol Oxidoreductases, Bioreactors, Botrytis, Cloning, Molecular, Fermentation, Fungal Proteins, Gene Expression, Gene Expression Regulation, Fungal, Genetic Engineering, Glyceraldehyde-3-Phosphate Dehydrogenases, High-Throughput Screening Assays, Kinetics, Laccase, Pichia, Promoter Regions, Genetic | null |
22,705,844 | 2013-03-26 | 2021-10-21 | 2165-5987 | Bioengineered | Engineering bacteria to manufacture functionalized polyester beads. | Draper Jenny L, Rehm Bernd H | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Bacterial Proteins, Enzymes, Immobilized, Polyhydroxyalkanoates, Recombinant Fusion Proteins, Tuberculosis Vaccines, Acyltransferases, poly(3-hydroxyalkanoic acid) synthase | IM | 22705844, 19567, 10.4161/bioe.19567, PMC3476867, 20674365, 8704958, 18367283, 17263145, 21803888, 17420063, 16517622, 9914303, 15963662, 12177335, 16936052, 21261300, 16204482, 19837843, 21984246, 19397912, 22072720, 19275166, 21906264, 19581473, 11038522, 7603982, 20079678, 18088086, 19201981, 12954080, 17204164, 14580576, 19623359, 18941699, 18800192, 12924980, 15901706, 22170266, 20581859, 15883185, 20214931, 2087222, 18778091, 19465535 | The ability to generate tailor-made, functionalized polyester (polyhydroxyalkanoate, PHA) beads in bacteria by harnessing their natural carbon-storage granule production system is an exciting recent development. Proteins that naturally attach to the polyester granule core were rationally engineered to enable in vivo production of PHA beads which are applicable in bioseparation, protein purification, enzyme immobilization and diagnostics and which show advantageous properties toward the development of safe and efficient particulate vaccines. These beads are recombinantly produced as fully functional, insoluble polyester inclusions that can be easily separated from the cell. This simple one-step production of functionalized beads provides a tantalizing alternative to current commercial functional beads, for which proteins must be expressed, purified and then chemically attached to solid supports. The recent success in generating antigen-displaying PHA granules in the food-grade bacterium Lactococcus lactis capable of mediating protective immunity against Mycobacterium tuberculosis infection highlights the promise and flexibility of this new technology. | Acyltransferases, Animals, Bacterial Proteins, Cell Engineering, Chemical Fractionation, Cloning, Molecular, Cupriavidus necator, Enzymes, Immobilized, Escherichia coli, Humans, Inclusion Bodies, Lactococcus lactis, Mice, Molecular Imaging, Mycobacterium tuberculosis, Polyhydroxyalkanoates, Recombinant Fusion Proteins, Tuberculosis, Tuberculosis Vaccines | null |
22,705,849 | 2013-03-04 | 2022-03-18 | 1476-5403 | Cell death and differentiation | Differential regulation of DNA damage response activation between somatic and germline cells in Caenorhabditis elegans. | Vermezovic J, Stergiou L, Hengartner M O, d'Adda di Fagagna F | eng | GGP12059 (Telethon, Italy) | Journal Article, Research Support, Non-U.S. Gov't | Caenorhabditis elegans Proteins, Cell Cycle Proteins, DNA-Binding Proteins, Tumor Suppressor Proteins, Ataxia Telangiectasia Mutated Proteins, Protein Serine-Threonine Kinases | IM | 22705849, cdd201269, 10.1038/cdd.2012.69, PMC3469062, 16855104, 11747819, 16862143, 12529635, 18285803, 18082599, 12447382, 9501103, 18329363, 15707894, 19879883, 12828945, 17525332, 19506556, 1457827, 21979466, 10608806, 21151025, 16319925, 10716435, 11238374, 12445383, 16469927, 16049496, 2257628, 11557844, 10882129, 17347667, 15574327, 10646593, 12049741 | The germline of Caenorhabditis elegans is a well-established model for DNA damage response (DDR) studies. However, the molecular basis of the observed cell death resistance in the soma of these animals remains unknown. We established a set of techniques to study ionizing radiation-induced DNA damage generation and DDR activation in a whole intact worm. Our single-cell analyses reveal that, although germline and somatic cells show similar levels of inflicted DNA damage, somatic cells, differently from germline cells, do not activate the crucial apical DDR kinase ataxia-telengiectasia mutated (ATM). We also show that DDR signaling proteins are undetectable in all somatic cells and this is due to transcriptional repression. However, DNA repair genes are expressed and somatic cells retain the ability to efficiently repair DNA damage. Finally, we demonstrate that germline cells, when induced to transdifferentiate into somatic cells within the gonad, lose the ability to activate ATM. Overall, these observations provide a molecular mechanism for the known, but hitherto unexplained, resistance to DNA damage-induced cell death in C. elegans somatic cells. We propose that the observed lack of signaling and cell death but retention of DNA repair functions in the soma is a Caenorhabditis-specific evolutionary-selected strategy to cope with its lack of adult somatic stem cell pools and regenerative capacity. | Animals, Apoptosis, Ataxia Telangiectasia Mutated Proteins, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Cycle Proteins, DNA Damage, DNA Repair, DNA-Binding Proteins, Germ Cells, Protein Serine-Threonine Kinases, Radiation, Ionizing, Signal Transduction, Single-Cell Analysis, Tumor Suppressor Proteins | null |
22,705,852 | 2013-03-04 | 2022-04-08 | 1476-5403 | Cell death and differentiation | PERK is required at the ER-mitochondrial contact sites to convey apoptosis after ROS-based ER stress. | Verfaillie T, Rubio N, Garg A D, Bultynck G, Rizzuto R, Decuypere J-P, Piette J, Linehan C, Gupta S, Samali A, Agostinis P | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Reactive Oxygen Species, Transcription Factor CHOP, Thapsigargin, PERK kinase, eIF-2 Kinase | IM | 22705852, cdd201274, 10.1038/cdd.2012.74, PMC3469056, 19144519, 17952126, 21475307, 9862416, 16455754, 17979528, 20186508, 10643557, 20307213, 19917257, 21642428, 9930704, 18437163, 16352659, 19061639, 21245373, 8261400, 19052620, 18023214, 10318777, 20453876, 10087326, 21146562, 21364565, 22252128, 18426796, 20732741, 12667446, 21030605, 20665666, 21854214, 17765680, 16408030, 20930847, 14517290, 16214108, 15982187, 21617154, 15037201, 10882126 | Endoplasmic reticulum stress is emerging as an important modulator of different pathologies and as a mechanism contributing to cancer cell death in response to therapeutic agents. In several instances, oxidative stress and the onset of endoplasmic reticulum (ER) stress occur together; yet, the molecular events linking reactive oxygen species (ROS) to ER stress-mediated apoptosis are currently unknown. Here, we show that PERK (RNA-dependent protein kinase (PKR)-like ER kinase), a key ER stress sensor of the unfolded protein response, is uniquely enriched at the mitochondria-associated ER membranes (MAMs). PERK(-/-) cells display disturbed ER morphology and Ca(2+) signaling as well as significantly weaker ER-mitochondria contact sites. Re-expression of a kinase-dead PERK mutant but not the cytoplasmic deletion mutant of PERK in PERK(-/-) cells re-establishes ER-mitochondria juxtapositions and mitochondrial sensitization to ROS-mediated stress. In contrast to the canonical ER stressor thapsigargin, during ROS-mediated ER stress, PERK contributes to apoptosis twofold by sustaining the levels of pro-apoptotic C/EBP homologous protein (CHOP) and by facilitating the propagation of ROS signals between the ER and mitochondria through its tethering function. Hence, this study reveals an unprecedented role of PERK as a MAMs component required to maintain the ER-mitochondria juxtapositions and propel ROS-mediated mitochondrial apoptosis. Furthermore, it suggests that loss of PERK may cause defects in cell death sensitivity in pathological conditions linked to ROS-mediated ER stress. | Animals, Apoptosis, Calcium Signaling, Cell Line, Endoplasmic Reticulum Stress, HCT116 Cells, Humans, Light, Mice, Mitochondria, Mitochondrial Membranes, Reactive Oxygen Species, Thapsigargin, Transcription Factor CHOP, Unfolded Protein Response, eIF-2 Kinase | null |
22,705,850 | 2013-04-17 | 2021-10-21 | 1476-5403 | Cell death and differentiation | Disruption of the VDAC2-Bak interaction by Bcl-x(S) mediates efficient induction of apoptosis in melanoma cells. | Plötz M, Gillissen B, Hossini A M, Daniel P T, Eberle J | eng | null | Journal Article, Research Support, Non-U.S. Gov't | Myeloid Cell Leukemia Sequence 1 Protein, Proto-Oncogene Proteins c-bcl-2, RNA, Small Interfering, VDAC2 protein, human, Voltage-Dependent Anion Channel 2, bcl-2 Homologous Antagonist-Killer Protein, bcl-X Protein | IM | 22705850, cdd201271, 10.1038/cdd.2012.71, PMC3504705, 20705336, 21256112, 10822279, 22506026, 16474435, 17289999, 17115033, 14668794, 19390557, 16243507, 15694340, 17237344, 14572633, 12853473, 8358789, 20467424, 18025305, 10365962, 22056880, 11511312, 20159550, 19520842, 9531611, 16007125, 15861188, 12881569, 17406435, 20977303, 11095261, 11526448, 18054518, 11259441, 17417626, 17589543, 21720385, 19380879, 12655297, 18778689, 19095149 | The proapoptotic B-cell lymphoma (Bcl)-2 protein Bcl-x(S) encloses the Bcl-2 homology (BH) domains BH3 and BH4 and triggers apoptosis via the multidomain protein Bak, however, the mechanism remained elusive. For investigating Bcl-x(S) efficacy and pathways, an adenoviral vector was constructed with its cDNA under tetracycline-off control. Bcl-x(S) overexpression resulted in efficient apoptosis induction and caspase activation in melanoma cells. Indicative of mitochondrial apoptosis pathways, Bcl-x(S) translocated to the mitochondria, disrupted the mitochondrial membrane potential and induced release of cytochrome c, apoptosis-inducing factor and second mitochondria-derived activator of caspases. In melanoma cells, Bcl-x(S) resulted in significant Bak activation, and Bak knockdown as well as Bcl-x(L) overexpression abrogated Bcl-x(S)-induced apoptosis, whereas Mcl-1 (myeloid cell leukemia-1) knockdown resulted in a sensitization. With regard to the particular role of voltage-dependent anion channel 2 (VDAC2) for inhibition of Bak, we identified here a notable interaction between Bcl-x(S) and VDAC2 in melanoma cells, which was proven in reciprocal coimmunoprecipitation analyses. On the other hand, Bcl-x(S) showed no direct interaction with Bak, and its binding to VDAC2 appeared as also independent of Bak expression. Suggesting a new proapoptotic mechanism, Bcl-x(S) overexpression resulted in disruption of the VDAC2-Bak interaction leading to release of Bak. Further supporting this pathway, overexpression of VDAC2 strongly decreased apoptosis by Bcl-x(S). New proapoptotic pathways are of principle interest for overcoming apoptosis deficiency of melanoma cells. | Apoptosis, Cell Line, Tumor, HCT116 Cells, Humans, Melanoma, Myeloid Cell Leukemia Sequence 1 Protein, Protein Binding, Proto-Oncogene Proteins c-bcl-2, RNA Interference, RNA, Small Interfering, Voltage-Dependent Anion Channel 2, bcl-2 Homologous Antagonist-Killer Protein, bcl-X Protein | null |
22,705,853 | 2012-10-25 | 2012-06-20 | 1361-6560 | Physics in medicine and biology | Study of time reversibility/irreversibility of cardiovascular data: theoretical results and application to laser Doppler flowmetry and heart rate variability signals. | Humeau-Heurtier Anne, Mahé Guillaume, Chapeau-Blondeau François, Rousseau David, Abraham Pierre | eng | null | Journal Article | null | IM | 22705853, 10.1088/0031-9155/57/13/4335 | Time irreversibility can be qualitatively defined as the degree of a signal for temporal asymmetry. Recently, a time irreversibility characterization method based on entropies of positive and negative increments has been proposed for experimental signals and applied to heart rate variability (HRV) data (central cardiovascular system (CVS)). The results led to interesting information as a time asymmetry index was found different for young subjects and elderly people or heart disease patients. Nevertheless, similar analyses have not yet been conducted on laser Doppler flowmetry (LDF) signals (peripheral CVS). We first propose to further investigate the above-mentioned characterization method. Then, LDF signals, LDF signals reduced to samples acquired during ECG R peaks (LDF_R(ECG) signals) and HRV recorded simultaneously in healthy subjects are processed. Entropies of positive and negative increments for LDF signals show a nonmonotonic pattern: oscillations--more or less pronounced, depending on subjects--are found with a period matching the one of cardiac activity. However, such oscillations are not found with LDF_R(ECG) nor with HRV. Moreover, the asymmetry index for LDF is markedly different from the ones of LDF_R(ECG) and HRV. The cardiac activity may therefore play a dominant role in the time irreversibility properties of LDF signals. | Adult, Female, Heart Rate, Humans, Laser-Doppler Flowmetry, Male, Signal Processing, Computer-Assisted, Time Factors | null |
22,705,854 | 2013-01-23 | 2019-12-10 | 1095-8630 | Journal of environmental management | Effectiveness of vegetated filter strips in retention of Escherichia coli and Salmonella from swine manure slurry. | Cardoso Fatima, Shelton Daniel, Sadeghi Ali, Shirmohammadi Adel, Pachepsky Yakov, Dulaney Wayne | eng | null | Evaluation Study, Journal Article | Bromides, Manure, Soil, Soil Pollutants | IM | 22705854, S0301-4797(12)00270-8, 10.1016/j.jenvman.2012.05.012 | Vegetated filter strips (VFS) are commonly recommended as a best management practice to prevent manure-borne microorganisms from reaching surface water resources. However, relatively little is known about the efficacy of VFS in mitigating bacterial runoff from land-applied swine manure. A field lysimeter study was designed to evaluate the effect of surface soil hydrologic conditions and vegetation on the retention of swine manure-borne Escherichia coli and Salmonella under simulated rainfall conditions. Experimental plots (6.5 m × 3.9 m) were set on a 5% slope lysimeter with loamy topsoil, clay loam or loam subsoil and a controllable groundwater level. Three small flow-intercepting miniflumes were installed 4.5 m from the plot's top, while all remaining runoff was collected in a gutter at the bottom. Plots were divided into bare soil and grass vegetation and upper surface soil moisture before rainfall events was controlled by the subsurface groundwater level. Swine manure slurry inoculated with E. coli and Salmonella, and with added bromide tracer, was applied on the top of the plots and simultaneously initiated the simulated rainfall. Runoff was collected and analyzed every 5 min. No substantial differences between retention of E. coli and Salmonella were found. In initially wet soil surface conditions, there was limited infiltration both in bare and in vegetated plots; almost all bromide and about 30% of bacteria were recovered in runoff water. In initially dry soil surface conditions, there were substantial discrepancies between bare and vegetated plots. In bare plots, recoveries of runoff water, bromide and bacteria under dry conditions were comparable to wet conditions. However, in dry vegetated plots, from 50% to 75% of water was lost to infiltration, while bromide recoveries ranged from 14 to 36% and bacteria recovery was only 5%. Substantial intraplot heterogeneity was revealed by the data from miniflumes. GIS analysis of the plot microtopography showed that miniflumes located in the zones of flow convergence collected the majority of bacteria. Overall, the efficiency of VFS, with respect to the retention of swine manure bacteria, varied dramatically depending upon the hydrologic soil surface condition. Consequently, VFS recommendations should account for expected amounts of surface soil water saturation as well as the relative soil water storage capacity of the VFS. | Animals, Bromides, Ecosystem, Environmental Restoration and Remediation, Escherichia coli, Groundwater, Manure, Maryland, Plants, Rain, Salmonella typhimurium, Soil, Soil Microbiology, Soil Pollutants, Swine, Water Microbiology, Water Movements, Water Pollution, Chemical | null |
22,705,855 | 2013-01-23 | 2022-12-07 | 1095-8630 | Journal of environmental management | Foaming Scum Index (FSI)--a new tool for the assessment and characterisation of biological mediated activated sludge foams. | Fryer Martin, Gray N F | eng | null | Evaluation Study, Journal Article, Research Support, Non-U.S. Gov't | Waste Water | IM | 22705855, S0301-4797(12)00267-8, 10.1016/j.jenvman.2012.05.009 | The formation of thick stable brown foams within the activated sludge process has become a familiar operational problem. Despite much research having already been carried out into establishing the causes of activated sludge foaming there is still no general consensus on the mechanisms involved. Historically investigation into activated sludge foaming has involved either measuring, under aeration conditions, the propensity of mixed liquor samples to foam, or evaluating different physico-chemical properties of the sludge which have previously been linked to activated sludge foaming. Both approaches do not present a means to quantify the risk posed to the treatment plants once foams have started to develop on the surface of aeration basins and final clarifiers. The Foaming Scum Index (FSI) is designed to offer a means to quantify risk on the basis of different foam characteristics which can easily be measured. For example, foam stability, foam coverage, foam suspended solids content and biological composition. The FSI was developed by measuring foam samples taken from several different domestic and municipal wastewater treatment sites located in Greater Dublin area (South-East Ireland). Path analysis was used to predict co-dependencies among the different sets of variables following a number of separate hypotheses. The standardized beta coefficients (β) produced from the multivariate correlation analysis (providing a measure of the contribution of each variable in the structural equation model) was used to finalise the weighting of each parameter in the index accordingly. According to this principal, foam coverage exerted the greatest influence on the overall FSI (β = 0.33), whilst the filamentous bacterial composition in terms of the filament index of foam, provided the least (β = 0.03). From this work it is proposed that the index can be readily applied as a standard tool in the coordination of research into the phenomenon of activated sludge foaming. | Ireland, Multivariate Analysis, Waste Disposal, Fluid, Wastewater, Water Pollution, Chemical | null |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.