README.md

metadata

tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - dense
  - generated_from_trainer
  - dataset_size:17793
  - loss:MultipleNegativesRankingLoss
base_model: allenai/specter2_base
widget:
  - source_sentence: >-
      Achieving high cell transfection efficiency is essential for various cell
      types in numerous disease applications. However, the efficient
      introduction of genes into natural killer (NK) cells remains a challenge.
      In this study, we proposed a design strategy for delivering exogenous
      genes into the NK cell line, NK-92, using a modified non-viral gene
      transfection method. Calcium phosphate/DNA nanoparticles (pDNA-CaP NPs)
      were prepared using co-precipitation methods and combined with low-voltage
      pulse electroporation to facilitate NK-92 transfection. The results
      demonstrated that the developed pDNA-CaP NPs exhibited a uniform diameter
      of approximately 393.9 nm, a DNA entrapment efficiency of 65.8%, and a
      loading capacity of 15.9%. Furthermore, at three days post-transfection,
      both the transfection efficiency and cell viability of NK-92 were
      significantly improved compared to standalone plasmid DNA (pDNA)
      electroporation or solely relying on the endocytosis pathway of pDNA-CaP
      NPs. This study provides valuable insights into a novel approach that
      combines calcium phosphate nanoparticles with low-voltage electroporation
      for gene delivery into NK-92 cells, offering potential advancements in
      cell therapy.
    sentences:
      - >-
        ZEISS Airyscan is an advanced imaging technology that enhances
        traditional confocal microscopy by using a 32-channel detector to
        capture more light with higher resolution and sensitivity. Unlike
        standard confocal systems that rely on a single pinhole, Airyscan
        collects the entire Airy disk pattern and reconstructs images for
        super-resolution clarityâ down to 120 nm laterally. This results in
        significantly improved signal-to-noise ratio and reduced photodamage,
        making it ideal for detailed imaging of live cells and biological
        samples. It's compatible with ZEISS LSM systems like the LSM 880 and
        900, offering researchers a powerful tool for high-precision
        fluorescence microscopy
      - >-
        the zeiss lsm 900 with airyscan 2 is a compact confocal microscope
        designed for high-quality imaging and intelligent analysis of biological
        samples, supporting a wide range of research applications from resolving
        nanoscale structures to observing dynamic processes in living systems.
        its key technologies enable researchers to acquire detailed and
        quantitative data while maintaining sample integrity and maximizing
        experimental efficiency. key research and application areas: -
        super-resolution imaging: investigating the ultrastructure of biological
        specimens by achieving resolution beyond the diffraction limit (down to
        90 nm laterally) through airyscan 2 and joint deconvolution (jdcv). this
        allows for the detailed visualization of cellular and molecular
        architecture. - gentle live cell imaging: studying biological processes
        in living organisms with minimized phototoxicity and photobleaching due
        to optimized components and sensitive detectors. this facilitates
        long-term observation of cellular dynamics and molecular interactions
        without disturbing the sample. - fast multiplex imaging: acquiring data
        from multiple fluorescent labels or large fields of view rapidly using
        multiplex modes of airyscan 2, enabling the study of dynamic events and
        efficient screening of samples. - enhanced confocal imaging: improving
        the signal-to-noise ratio and resolution of standard confocal imaging
        through lsm plus, allowing for better data quality in multi-color and
        live cell experiments with minimal user interaction. - molecular
        dynamics analysis: determining molecular concentration, diffusion, and
        flow in living samples using the zeiss dynamics profiler, which
        leverages the unique capabilities of the airyscan 2 detector for
        advanced spatial cross-correlation analyses. this enables the study of
        molecular behavior in various biological contexts, including flow in
        microfluidic systems and blood vessels and asymmetric diffusion in
        cellular condensates. - automated and reproducible experiments:
        streamlining complex imaging workflows with zen microscopy software,
        including features like ai sample finder for rapid region of interest
        identification and smart setup for automated application of optimal
        imaging settings. the experiment designer module allows for the creation
        of sophisticated, repeatable imaging routines. - correlative microscopy:
        integrating data from different imaging modalities and sources using zen
        connect to provide a comprehensive understanding of the sample, from
        overview to high-resolution details, including the possibility of
        correlative cryo microscopy workflows. typical sample types: - cultured
        cells and cell lines: for studying subcellular structures, dynamics, and
        responses to stimuli. - tissues and tissue sections: to investigate
        cellular organization, protein localization, and interactions within a
        complex environment. - small model organisms and embryos: such as
        drosophila and zebrafish for in vivo studies of development, physiology,
        and disease. - organoids and 3d cell cultures: for studying tissue
        architecture and development in vitro. - plant samples: such as pollen
        grains, for investigating cellular structures. - samples requiring
        correlative microscopy: like yeast cells for cryo-em workflows. -
        microfluidic systems: for controlled studies of fluid dynamics and
        molecular flow. commonly performed tasks: - confocal laser scanning
        microscopy: obtaining high-resolution optical sections of samples to
        visualize internal structures and create 3d reconstructions. -
        super-resolution imaging with airyscan: resolving nanoscale details
        beyond the limits of conventional light microscopy. - live cell imaging:
        capturing time-lapse sequences of living samples to study dynamic
        biological processes. - multi-color fluorescence imaging: simultaneously
        detecting multiple fluorescent probes to study the co-localization and
        interactions of different molecules. - spectral imaging and unmixing:
        separating the signals of spectrally overlapping fluorophores for
        accurate multi-target analysis. - quantitative image analysis:
        extracting meaningful data from images, including measurements of
        intensity, area, distance, and co-localization, using tools within zen
        software and the bio apps toolkit. - automated sample identification and
        imaging: utilizing ai sample finder to quickly locate and image regions
        of interest on various sample carriers. - analysis of molecular
        dynamics: measuring parameters such as diffusion coefficients, flow
        speeds, and molecular concentrations using the dynamics profiler. -
        creating 3d and 4d visualizations: reconstructing volumetric datasets
        and generating animations to understand spatial and temporal
        relationships within samples. - correlating light and electron
        microscopy data: combining functional light microscopy data with
        ultrastructural details from electron microscopy. - performing bleaching
        experiments: such as frap, to study molecular mobility within cellular
        compartments (although frap is mentioned in the software features , no
        specific application examples are provided in the excerpts). - tiling
        and multi-position imaging: acquiring large datasets by automatically
        imaging and stitching together multiple adjacent fields of view or
        imaging multiple regions of interest.
      - >-
        the zeiss sigma family of field emission scanning electron microscopes
        (fe-sems) offers versatile solutions for high-quality imaging and
        advanced analytical microscopy across a multitude of scientific and
        industrial domains. these instruments are engineered for reliable,
        high-end nano-analysis, combining fe-sem technology with an intuitive
        user experience to enhance productivity. key research and application
        areas: - advancing materials science: facilitating the development and
        understanding of novel materials by enabling the investigation of micro-
        and nanoscale structures. this includes characterizing metals, alloys,
        polymers, catalysts, and coatings for various applications such as
        electronics and energy. - driving innovation in nanoscience and
        nanomaterials: providing capabilities for the analysis of nanoparticles,
        thin films, 2d materials (like graphene and mos2), and other
        nanostructures to understand their properties and potential
        applications. - supporting energy research: enabling the study of
        materials and devices relevant to energy storage and conversion, such as
        battery components, to improve their performance and longevity. -
        enabling life sciences investigations: allowing for the exploration of
        the ultrastructural details of biological samples, including cells,
        tissues, spores, and diatoms, often utilizing low voltage to minimize
        beam damage. - contributing to geosciences and natural resources:
        supporting the characterization of rocks, ores, and minerals for
        improved understanding, processing, and modeling in geology and related
        fields. - ensuring quality in industrial applications: serving as a
        vital tool for failure analysis of mechanical, optical, and electronic
        components, as well as for quality inspection of particles and materials
        to meet defined standards. typical sample types: - a wide variety of
        materials including metals, ceramics, polymers, composites, thin films,
        and coatings. - nanomaterials such as nanoparticles, nanotubes,
        nanowires, and 2d crystals. - biological specimens encompassing cells,
        tissues, bacteria, fungi (e.g., spores), and diatoms. - geological
        samples including rocks, minerals, ores, and thin sections. -
        particulates for quality inspection and technical cleanliness analysis.
        - non-conductive samples such as polymers, biological tissues, and
        ceramics, often analyzed without coating using variable pressure modes.
        - beam-sensitive samples like biological materials and some
        nanomaterials, which can be imaged at low voltages to prevent damage.
        commonly performed tasks: - high-resolution imaging of sample surfaces
        and internal structures, often at low accelerating voltages (e.g., 1 kv
        and below) to enhance resolution and contrast, especially on challenging
        samples. - material contrast imaging to visualize different phases or
        compositions within a sample using backscattered electron (bse)
        detectors. - elemental analysis and mapping using energy dispersive
        x-ray spectroscopy (eds) to determine the chemical composition and
        distribution of elements in a sample. - variable pressure (vp) imaging
        and analysis of non-conductive and outgassing samples without the need
        for conductive coatings, often utilizing nanovp lite mode to minimize
        the skirt effect and enhance image quality and analytical precision. -
        crystallographic orientation imaging using techniques like electron
        backscatter diffraction (ebsd) to study the microstructure of
        crystalline materials. - transmission imaging of thin samples using
        scanning transmission electron microscopy (stem) with dedicated
        detectors. - correlative microscopy by combining sem imaging with other
        techniques such as raman spectroscopy (rise microscopy) to gain
        complementary chemical and structural information. - automated workflows
        for imaging, analysis (e.g., particle analysis, non-metallic inclusion
        analysis), and in situ experiments to increase productivity and ensure
        reproducible results. - surface topography and 3d reconstruction using
        techniques like the annular bse detector (absd) and dedicated software
        to obtain quantitative information about the sample surface. - in situ
        experiments such as heating and tensile testing within the sem chamber
        to observe material behavior under controlled conditions. - failure
        analysis to investigate fractures, defects, and corrosion in various
        materials and components. - particle analysis for technical cleanliness
        and material characterization, including automated detection,
        measurement, counting, and classification of particles based on
        morphology and elemental composition. - quantitative mineralogy using
        automated sem and eds to classify mineral phases based on their chemical
        composition and provide detailed information on their properties.
  - source_sentence: >-
      Spinally projecting serotonergic neurons play a key role in controlling
      pain sensitivity and can either increase or decrease nociception depending
      on physiological context. It is currently unknown how serotonergic neurons
      mediate these opposing effects. Utilizing virus-based strategies and
      Tph2-Cre transgenic mice, we identified two anatomically separated
      populations of serotonergic hindbrain neurons located in the lateral
      paragigantocellularis (LPGi) and the medial hindbrain, which respectively
      innervate the superficial and deep spinal dorsal horn and have contrasting
      effects on sensory perception. Our tracing experiments revealed that
      serotonergic neurons of the LPGi were much more susceptible to
      transduction with spinally injected AAV2retro vectors than medial
      hindbrain serotonergic neurons. Taking advantage of this difference, we
      employed intersectional chemogenetic approaches to demonstrate that
      activation of the LPGi serotonergic projections decreases thermal
      sensitivity, whereas activation of medial serotonergic neurons increases
      sensitivity to mechanical von Frey stimulation. Together these results
      suggest that there are functionally distinct classes of serotonergic
      hindbrain neurons that differ in their anatomical location in the
      hindbrain, their postsynaptic targets in the spinal cord, and their impact
      on nociceptive sensitivity. The LPGi neurons that give rise to rather
      global and bilateral projections throughout the rostrocaudal extent of the
      spinal cord appear to be ideally poised to contribute to widespread
      systemic pain control.
    sentences:
      - >-
        the zeiss stemi 508 is an apochromatic stereo microscope with an 8:1
        zoom range, designed for high-contrast, color-accurate three-dimensional
        observation and documentation of diverse samples. its ergonomic design
        and robust mechanics support demanding applications in laboratory and
        industrial settings. key research and application areas: - biological
        research: suitable for observing the development and growth of model
        organisms like spider crabs, chicken, mouse, or zebrafish, including the
        evaluation, sorting, selection, or dissection of eggs, larvae, or
        embryos. it is also used in botany to observe changes in plant organs,
        diseases, and root development, in entomology for insect observation,
        documentation, and identification, in marine biology to study the life
        and reproduction of fish, and in parasitology for detecting and
        identifying the spread of parasites. the microscope is valuable for
        forensic analysis of ammunition parts, tool marks, documents, fibers,
        coatings, glass, textiles, or hair, and in art restoration for analyzing
        and conserving artworks layer by layer. - industrial inspection and
        quality control: applied in printed circuit board (pcb) inspection to
        check for contact quality, wiring, residues, and solder joint faults. it
        is also used in failure search and analysis to identify reasons for
        faulty circuits, in the diamond industry for quality evaluation and
        impurity detection, and in the assembly of small, high-precision
        components in medical devices, sensor manufacturing, and the clocks and
        watches industry. the microscope is also relevant for evaluating the
        surface quality in printing and engraving and for inspecting minted
        coins and medals. - geology and paleontology: used for collecting and
        investigating assemblages of fossil foraminifera to determine rock age.
        typical sample types: - biological specimens: eggs, larvae, embryos of
        various organisms, plant organs, insects, fish, parasites, tissues,
        hairs, fibers. - industrial components: printed circuit boards,
        electronic contacts, wiring, solder joints, metal parts, small
        mechanical components (e.g., in medical devices, sensors, watches),
        optical fibers, diamonds, paper, engravings, minted coins, medals. -
        forensic evidence: ammunition parts, tool marks, documents, fibers,
        coatings, glass, textiles, hair. - artworks: paintings, sculptures,
        various materials used in art. - geological samples: fossil
        foraminifera. - transparent and semi-transparent materials: may be
        analyzed using transmitted light techniques. commonly performed tasks: -
        detailed observation and examination: utilizing the 8:1 zoom to
        transition from large overviews (up to 122 mm object field) to high
        magnification (up to 50x with basic system, or 2x to 250x with
        interchangeable optics) for minute structural analysis. the apochromatic
        correction ensures distortion-free and color-fringe-free imaging. -
        three-dimensional viewing: leveraging the greenough stereoscopic design
        with twin body tubes inclined by 11deg to achieve a strong spatial
        impression and depth perception, essential for understanding sample
        morphology. the precise zoom adjustment maintains a well-balanced 3d
        impression for relaxed viewing. - specimen manipulation and preparation:
        the long working distances (up to 287 mm with specific optics) provide
        ample space for easy specimen handling, dissection, and manipulation
        using tools or micromanipulators. - illumination and contrast
        optimization: employing a variety of reflected and transmitted light
        techniques, including brightfield, darkfield, polarization, and oblique
        illumination, facilitated by interchangeable led illuminators (spot,
        double spot, segmentable ringlight) and fiber optic light sources. these
        techniques enhance the visibility of specific features like surface
        structures, defects, or internal details in diverse sample types. -
        image acquisition and documentation: integrating with zeiss axiocam
        cameras and other digital cameras via interchangeable camera adapters to
        capture high-resolution images and videos for documentation, archiving,
        and sharing. software like zen lite and labscope facilitates image
        processing and analysis. - ergonomic operation: maintaining a
        comfortable posture during extended use due to the low 35deg viewing
        angle. optional accessories like hand rests further enhance user
        comfort. - reproducible settings: utilizing the optional zoom click
        stops to easily reproduce magnification levels for consistent
        observation and documentation. the memory function in stand m led allows
        storing and recalling illumination settings. - customizable
        configurations: adapting the microscope to specific application needs by
        choosing from a wide range of stands, interchangeable optics (eyepieces
        and front optics), and illumination systems. various stages (gliding,
        tilting, rotating polarization) enable precise specimen positioning.
      - >-
        the zeiss lsm 990 is a versatile confocal microscope system offering a
        wide range of multimodal imaging options for advanced biological
        research. its capabilities extend beyond traditional confocal
        microscopy, enabling intricate investigations into cellular structures,
        molecular dynamics, and physiological processes in various biological
        samples. key research and application areas: - high-resolution imaging
        of biological structures: investigating subcellular details and
        resolving fine structures down to 90 nm using super-resolution
        techniques like airyscan. this allows for the detailed study of
        components like the synaptonemal complex and sperm flagella. - live cell
        imaging and dynamics: observing dynamic biological processes in living
        cells and organisms, including molecular dynamics, protein interactions,
        flow in microfluidic systems, and developmental processes. the system
        supports high-speed volume acquisition up to 80 volumes per second for
        capturing fast events like the beating of a zebrafish heart. - advanced
        spectral imaging and multiplexing: identifying and separating multiple
        fluorescent labels across a broad emission wavelength range (380 to 900
        nm), enabling the simultaneous study of over 10 labels in a single scan.
        this facilitates in-depth understanding of spatial biology through
        techniques like lambda scans and spectral unmixing. - deep tissue
        imaging: recovering information from deep within tissues, organoids, and
        spheroids using multiphoton excitation (690 - 1300 nm). this is crucial
        for studying complex biological systems in a more native context. -
        molecular dynamics and interaction studies: gaining insights into
        protein concentrations, movement, and interactions using techniques like
        fluorescence correlation spectroscopy (fcs) and spectral rics. the
        system also supports fluorescence lifetime imaging microscopy (flim) and
        fluorescence resonance energy transfer (fret) to investigate
        physiological parameters and molecular proximity. - volumetric imaging
        of living organisms: studying the dynamics of entire living organisms
        and tissues in 3d over time using lightfield 4d microscopy, capturing up
        to 80 volumes per second. this is beneficial for visualizing development
        and other dynamic processes in intact animals and organoids. -
        correlative microscopy: combining light microscopy with electron
        microscopy under cryogenic conditions to study cellular structures in a
        near-to-native state. - imaging of cleared samples: achieving increased
        optical penetration depth in cleared biological samples like brains,
        organoids, and spheroids, allowing for imaging up to 5.6 mm deep with
        specialized objectives. typical sample types: - live cells and cell
        cultures: including various cell lines and primary cells. - tissues and
        tissue sections: from various organs and organisms, both fixed and live.
        - whole organisms and embryos: such as zebrafish larvae and drosophila
        pupae. - organoids and spheroids: including 3d cell cultures and tissue
        models. - cleared biological samples: such as whole mouse brains, tissue
        sections, organoids, and spheroids rendered transparent for deep
        imaging. - microfluidic systems: for studying flow and molecular
        dynamics in controlled environments. - yeast cells: for advanced
        spectral multiplexing experiments. commonly performed tasks: - confocal
        microscopy: high-resolution optical sectioning of various samples. -
        super-resolution imaging: resolving structures beyond the diffraction
        limit down to 90 nm. - live imaging: capturing dynamic events in living
        samples over time. - volumetric imaging: acquiring 3d datasets of
        biological samples. - spectral imaging and unmixing: separating and
        analyzing the emission spectra of multiple fluorescent labels. -
        multiphoton microscopy: deep tissue imaging using longer excitation
        wavelengths. - fluorescence correlation spectroscopy (fcs) and spectral
        rics: investigating molecular concentrations, diffusion, and
        interactions. - fluorescence lifetime imaging microscopy (flim):
        analyzing fluorescence decay to gain information on molecular
        interactions and environmental parameters. - fluorescence resonance
        energy transfer (fret): studying protein interaction and distance. -
        fluorescence recovery after photobleaching (frap) and photomanipulation:
        investigating molecular and cellular dynamics through targeted laser
        manipulation. - image analysis and processing: utilizing software like
        zen and arivis pro for visualization, segmentation, tracking, and
        quantification of imaging data. - correlative light and electron
        microscopy (clem): combining light and electron microscopy data for
        comprehensive ultrastructural analysis. - imaging of cleared samples:
        deep imaging of transparent biological specimens for 3d structural
        analysis.
      - >-
        the zeiss lsm 910 is a compact confocal microscope designed for
        innovative imaging and smart analysis, enabling a broad spectrum of
        biological research applications. its core capabilities facilitate the
        detailed visualization and analysis of diverse biological specimens,
        ranging from subcellular structures to dynamic processes in living
        organisms. key research and application areas: - high-resolution
        structural imaging: achieving super-resolution down to 90 nm laterally
        using airyscan technology to resolve fine details of cellular and
        molecular structures. this enables the investigation of intricate
        biological organization. - live cell and high-speed imaging: capturing
        dynamic processes in living samples with high temporal resolution,
        including 4d imaging at up to 80 volumes per second using lightfield 4d.
        this allows for the study of rapid biological events such as zebrafish
        heartbeats and intracellular movements. - advanced spectral analysis:
        employing spectral flexibility with nanometer precision for multi-color
        imaging and efficient spectral unmixing of multiple fluorescent labels,
        facilitating the detailed study of spatial biology. - gentle imaging for
        sensitive samples: utilizing an efficient beam path and sensitive
        detectors (gaasp-pmts and ma-pmts) to achieve high signal-to-noise
        ratios while minimizing phototoxicity, crucial for long-term live cell
        imaging. - quantitative molecular dynamics studies: investigating
        molecular concentration, diffusion, and flow dynamics in living samples
        using the dynamics profiler based on airyscan. this allows for the
        analysis of molecular behavior in various biological contexts. - deep
        tissue imaging with clearing: integrating with clearing techniques and
        specialized objectives to significantly increase optical penetration
        depth in samples like brains, organoids, and tissues, enabling the
        visualization of structures in deeper layers. - correlative cryo
        microscopy: facilitating workflows that combine light and electron
        microscopy under cryogenic conditions to study cellular structures in a
        near-to-native state, bridging the gap between functional and
        ultrastructural information. typical sample types: - cells and cell
        cultures: including various cell lines for studying subcellular
        structures and dynamics. - tissues and tissue sections: allowing for the
        investigation of cellular organization and molecular distribution within
        complex environments. - organoids and spheroids: enabling the study of
        3d tissue models and their development using various imaging modalities,
        including high-speed volume acquisition. - whole organisms and embryos:
        such as zebrafish embryos, for observing developmental processes and
        physiological functions in vivo with high spatiotemporal resolution. -
        cleared biological samples: including whole brains, tissue sections,
        organoids, and spheroids made transparent to enable deep optical
        imaging. - microfluidic devices: for controlled studies of flow and
        molecular dynamics. - plant tissues: such as arabidopsis thaliana stems,
        for investigating protein behavior in response to environmental stimuli.
        commonly performed tasks: - confocal imaging: high-resolution optical
        sectioning to visualize specific planes within a sample and generate 3d
        reconstructions. - super-resolution microscopy: resolving structures
        beyond the diffraction limit to visualize nanoscale details of cellular
        components. - live cell imaging: capturing time-series data of living
        cells and organisms to study dynamic processes and cellular behaviors
        over time. - high-speed volumetric imaging: acquiring 3d datasets at
        rapid frame rates to visualize fast biological events in their entirety.
        - spectral imaging and unmixing: separating the contributions of
        multiple fluorescent probes based on their emission spectra to allow for
        simultaneous multi-target analysis. - fluorescence recovery after
        photobleaching (frap): investigating molecular mobility and dynamics
        within cellular compartments. - fluorescence correlation spectroscopy
        (fcs) and dynamics profiling: measuring molecular concentrations,
        diffusion coefficients, and flow velocities in living samples. - image
        processing and analysis: utilizing software tools like zen and arivis
        pro for image enhancement, quantification, segmentation, tracking, and
        3d visualization of complex datasets. - correlative light and electron
        microscopy (clem): combining light microscopy for functional
        identification with electron microscopy for ultrastructural details. -
        imaging of large volumes and tiled acquisitions: acquiring data from
        large samples or multiple regions of interest and stitching them
        together for comprehensive analysis. - automated imaging workflows:
        setting up and executing complex imaging experiments with automation
        features for reproducible data acquisition. - advanced image analysis
        using ai: employing artificial intelligence-assisted features for sample
        finding, setup optimization, and image analysis.
  - source_sentence: >-
      In Arabidopsis thaliana, the asymmetric cell division (ACD) of the zygote
      gives rise to the embryo proper and an extraembryonic suspensor,
      respectively. This process is controlled by the ERECTA-YODA-MPK3/6
      receptor kinase-MAP kinase-signaling pathway, which also orchestrates ACDs
      in the epidermis. In this context, the bHLH transcription factor ICE1/SCRM
      is negatively controlled by MPK3/6-directed phosphorylation. However, it
      is unknown whether this regulatory module is similarly involved in the
      zygotic ACD. We investigated the function of SCRM in zygote polarization
      by analyzing the effect of loss-of-function alleles and variants that
      cannot be phosphorylated by MPK3/6, protein accumulation, and target gene
      expression. Our results show that SCRM has a critical function in zygote
      polarization and acts in parallel with the known MPK3/6 target WRKY2 in
      activating WOX8. Our work further demonstrates that SCRM activity in the
      early embryo is positively controlled by MPK3/6-mediated phosphorylation.
      Therefore, the effect of MAP kinase-directed phosphorylation of the same
      target protein fundamentally differs between the embryo and the epidermis,
      shedding light on cell type-specific, differential gene regulation by
      common signaling pathways.
    sentences:
      - >-
        the zeiss evo family of scanning electron microscopes offers a modular
        and versatile platform for a wide range of scientific and industrial
        investigations, combining high-performance imaging and analysis with
        intuitive operation for users of varying experience levels. key research
        and application areas: - materials science: characterizing the
        morphology, structure, and composition of diverse materials, including
        metals, composites, polymers, ceramics, and coatings, for research and
        development. this includes investigating surface structures, fractures,
        inclusions, and grain boundaries. the evo supports advanced material
        analysis through techniques like energy dispersive spectroscopy (eds)
        and electron backscatter diffraction (ebsd). - life sciences: enabling
        the examination of biological specimens in their native or near-native
        hydrated states using variable and extended pressure modes. applications
        include imaging cells, tissues, plants, and microorganisms for
        structural and morphological studies. the system facilitates correlative
        light and electron microscopy for comprehensive biological
        investigations. - industrial quality assurance and failure analysis:
        providing solutions for routine inspection, quality control, and failure
        analysis across various industries. this includes cleanliness
        inspection, morphological and chemical analysis of particles, and the
        examination of electronic components. automated workflows and reporting
        tools enhance efficiency in industrial settings. - semiconductors and
        electronics: supporting the visual inspection and analysis of electronic
        components, integrated circuits, and mems devices. the evo's
        capabilities include high-contrast imaging of non-conductive
        semiconductor materials and cross-sectional failure analysis. - raw
        materials and earth sciences: facilitating the morphological,
        mineralogical, and compositional analysis of geological samples and raw
        chemicals. this includes imaging core samples and performing automated
        mineral analysis for resource characterization. - forensics: providing
        tools for the analysis of forensic evidence such as gunshot residue,
        paint, glass, fibers, and biological traces with minimal sample
        preparation. the system supports consistent imaging and high-throughput
        chemical analysis. typical sample types: - conductive materials: metals,
        alloys, and coated samples examined under high vacuum. - non-conductive
        materials: polymers, ceramics, composites, uncoated geological samples,
        and biological tissues imaged using variable pressure modes to
        neutralize charging. - hydrated and contaminated samples: biological
        specimens, wet materials, and uncleaned industrial parts imaged in
        extended pressure mode with water vapor to maintain their native state
        and prevent contamination of the electron column. - large and
        challenging samples: industrial parts and geological cores accommodated
        by various chamber sizes and stage options, with weight capacities up to
        5 kg and dimensions up to 300 mm wide and 210 mm high. - coated and
        uncoated samples: the evo offers imaging capabilities for both prepared
        and unprepared samples, catering to diverse analytical needs. commonly
        performed tasks: - high-resolution imaging: acquiring detailed images of
        sample surfaces and microstructures using secondary electrons (se) and
        backscattered electrons (bse) detectors in various vacuum modes. the
        lab6 emitter enhances resolution and contrast. - elemental analysis:
        determining the chemical composition of specimens using integrated
        energy dispersive spectroscopy (eds) systems. - automated workflows:
        implementing predefined or user-defined automated routines for image
        acquisition, particle analysis, and routine inspections, enhancing
        throughput and reproducibility. - variable pressure imaging:
        investigating non-conductive samples without coating by utilizing gas
        ionization to dissipate charge build-up. - extended pressure imaging:
        examining hydrated and sensitive samples in a water vapor environment to
        preserve their natural state and prevent artifacts. - correlative
        microscopy: combining data from the evo with light microscopes or other
        analytical techniques to gain multi-modal insights into samples. -
        particle analysis: automatically detecting, characterizing, and
        classifying particles based on morphology and chemical composition for
        applications in industrial cleanliness, material analysis, and
        environmental monitoring. - automated mineralogy: performing
        quantitative mineral analysis on geological samples for geometallurgy,
        ore characterization, and reservoir analysis. - beam deceleration
        imaging: enhancing surface sensitivity and reducing charging artifacts
        on delicate non-conductive samples by controlling the electron landing
        energy. - navigation and sample management: using navigation cameras and
        software tools to easily locate regions of interest and manage large
        sample arrays. - data management and reporting: utilizing software like
        zeiss zen core for image processing, analysis, data connectivity, and
        generating reports, including options for gxp compliance in regulated
        industries.
      - >-
        the zeiss crossbeam family of focused ion beam scanning electron
        microscopes (fib-sems) provides a powerful platform for high-throughput
        3d analysis and advanced sample preparation across diverse scientific
        and industrial fields. combining the high-resolution imaging of a field
        emission sem with the precise processing of a next-generation fib,
        crossbeam instruments enable intricate manipulation and detailed
        characterization of materials. key research and application areas: -
        high-resolution imaging and surface analysis: - applications: obtaining
        detailed 2d and 3d images of various samples, including conductive and
        non-conductive specimens. investigating surface details and material
        contrast. - sample types: a wide range of materials, including metals,
        ceramics, polymers, biological samples, and electronic components. -
        commonly performed tasks: high-resolution sem imaging at various
        accelerating voltages, including low voltage for surface sensitivity and
        beam-sensitive samples. utilizing inlens detectors (se and esb) for
        topographical and material contrast. imaging non-conductive samples
        using variable pressure or local charge compensation. large area
        mapping. surface sensitive imaging using tandem decel. - 3d volume
        analysis and tomography: - applications: reconstructing the 3d
        microstructure and composition of materials. morphological analysis of
        biological samples. correlative multi-scale, multi-modal imaging using
        atlas 5. - sample types: diverse materials requiring volumetric
        analysis, including solid oxide fuel cells, metallic alloys, biological
        tissues (cells, organisms, brain sections), and geological samples. -
        commonly performed tasks: serial sectioning using the fib for 3d
        reconstruction. automated tomography data acquisition. 3d eds and 3d
        ebsd analysis during tomography runs. precise and reliable results with
        leading isotropic voxel size. tracking voxel sizes and automated image
        quality control. - focused ion beam milling and nanofabrication: -
        applications: precise cross-sectioning to reveal subsurface information.
        preparation of specimens for further analysis (e.g., tem lamellae).
        nanopatterning and creation of micro/nanostructures. fast material
        removal for accessing buried structures. - sample types: wide variety of
        materials requiring targeted modification, including semiconductors,
        metals, ceramics, polymers, and biological samples. - commonly performed
        tasks: high-precision milling with the ion-sculptor fib column,
        minimizing sample damage. fast and precise material removal with high
        beam currents (up to 100 na). low voltage fib performance for delicate
        samples. automated milling of cross-sections and user-defined patterns.
        fastmill strategy for enhanced milling speed. utilizing a femtosecond
        laser for rapid ablation of large volumes to access deeply buried
        regions. - tem sample preparation: - applications: preparing
        high-quality, ultra-thin lamellae for transmission electron microscopy
        (tem) and scanning transmission electron microscopy (stem) analysis.
        preparing batches of tem lamellae automatically. - sample types: diverse
        materials requiring tem analysis, including semiconductors, metals,
        polymers, and biological tissues. - commonly performed tasks: guided,
        semi-automated tem lamella preparation workflows. automated chunk
        milling, in situ lift-out, and thinning. utilizing the low voltage
        performance of the ion-sculptor fib for high-quality lamellae with
        minimal amorphization. live monitoring of lamella thinning using sem.
        quantitative thickness determination with smartepd. preparation of
        ultra-thin lamellae using the x2-holder for challenging samples. fully
        automated tem preparation with crossbeam 550 samplefab. - advanced
        analytical techniques: - applications: analyzing the elemental and
        isotopic composition of surfaces. performing analytical mapping and
        depth profiling. correlating structural and chemical information. -
        sample types: various solid surfaces requiring detailed compositional
        analysis, including batteries, polymers, and semiconductors. - commonly
        performed tasks: time-of-flight secondary ion mass spectrometry
        (tof-sims) for parallel detection of atomic and molecular ions. 3d eds
        and ebsd analysis integrated with tomography. the zeiss crossbeam family
        offers modularity and customization options, including various
        detectors, gas injection systems (gis), manipulators, and software
        packages like atlas 5, enabling researchers to tailor the instrument to
        their specific application needs and achieve high-impact results. the
        gemini electron optics ensure excellent image quality and long-term
        stability, while the ion-sculptor fib column provides superior
        processing capabilities with minimal sample damage.
      - >-
        ZEISS Airyscan is an advanced imaging technology that enhances
        traditional confocal microscopy by using a 32-channel detector to
        capture more light with higher resolution and sensitivity. Unlike
        standard confocal systems that rely on a single pinhole, Airyscan
        collects the entire Airy disk pattern and reconstructs images for
        super-resolution clarityâ down to 120 nm laterally. This results in
        significantly improved signal-to-noise ratio and reduced photodamage,
        making it ideal for detailed imaging of live cells and biological
        samples. It's compatible with ZEISS LSM systems like the LSM 880 and
        900, offering researchers a powerful tool for high-precision
        fluorescence microscopy
  - source_sentence: >-
      The identity and source of flexible, semi-transparent, vascular-like
      components recovered from non-avian dinosaur bone are debated, because:
      (1) such preservation is not predicted by degradation models; (2)
      taphonomic mechanisms for this type of preservation are not well defined;
      and (3) although support for molecular endogeneity has been demonstrated
      in select specimens, comparable data are lacking on a broader scale. Here,
      we use a suite of micromorphological and molecular techniques to examine
      vessel-like material recovered from the skeletal remains of six non-avian
      dinosaurs, representing different taxa, depositional environments and
      geological ages, and we compare the data obtained from our analyses
      against vessels liberated from extant ostrich bone. The results of this
      in-depth, multi-faceted study present strong support for endogeneity of
      the fossil-derived vessels, although we also detect evidence of invasive
      microorganisms.
    sentences:
      - >-
        ZEISS ZEN is a comprehensive microscopy software platform designed to
        streamline the entire imaging workflow from acquisition to analysis and
        data management. It offers a modular structure with specialized toolkits
        for image acquisition, processing, and analysis, allowing users to
        tailor the software to their specific experimental needs. ZEN supports
        advanced features such as  smart microscopy with feedback experiments,
        GPU-powered 3D visualization, and machine learning-based image analysis,
        facilitating efficient handling of complex, multidimensional datasets.
        The software's intuitive interface ensures ease of use across various
        microscopy modalities, especially in light microscopy, making it
        suitable for both routine laboratory tasks and advanced research
        applications. 
      - >-
        ZEISS ZEN is a comprehensive microscopy software platform designed to
        streamline the entire imaging workflow from acquisition to analysis and
        data management. It offers a modular structure with specialized toolkits
        for image acquisition, processing, and analysis, allowing users to
        tailor the software to their specific experimental needs. ZEN supports
        advanced features such as  smart microscopy with feedback experiments,
        GPU-powered 3D visualization, and machine learning-based image analysis,
        facilitating efficient handling of complex, multidimensional datasets.
        The software's intuitive interface ensures ease of use across various
        microscopy modalities, especially in light microscopy, making it
        suitable for both routine laboratory tasks and advanced research
        applications. 
      - >-
        the zeiss lsm 910 is a compact confocal microscope designed for
        innovative imaging and smart analysis, enabling a broad spectrum of
        biological research applications. its core capabilities facilitate the
        detailed visualization and analysis of diverse biological specimens,
        ranging from subcellular structures to dynamic processes in living
        organisms. key research and application areas: - high-resolution
        structural imaging: achieving super-resolution down to 90 nm laterally
        using airyscan technology to resolve fine details of cellular and
        molecular structures. this enables the investigation of intricate
        biological organization. - live cell and high-speed imaging: capturing
        dynamic processes in living samples with high temporal resolution,
        including 4d imaging at up to 80 volumes per second using lightfield 4d.
        this allows for the study of rapid biological events such as zebrafish
        heartbeats and intracellular movements. - advanced spectral analysis:
        employing spectral flexibility with nanometer precision for multi-color
        imaging and efficient spectral unmixing of multiple fluorescent labels,
        facilitating the detailed study of spatial biology. - gentle imaging for
        sensitive samples: utilizing an efficient beam path and sensitive
        detectors (gaasp-pmts and ma-pmts) to achieve high signal-to-noise
        ratios while minimizing phototoxicity, crucial for long-term live cell
        imaging. - quantitative molecular dynamics studies: investigating
        molecular concentration, diffusion, and flow dynamics in living samples
        using the dynamics profiler based on airyscan. this allows for the
        analysis of molecular behavior in various biological contexts. - deep
        tissue imaging with clearing: integrating with clearing techniques and
        specialized objectives to significantly increase optical penetration
        depth in samples like brains, organoids, and tissues, enabling the
        visualization of structures in deeper layers. - correlative cryo
        microscopy: facilitating workflows that combine light and electron
        microscopy under cryogenic conditions to study cellular structures in a
        near-to-native state, bridging the gap between functional and
        ultrastructural information. typical sample types: - cells and cell
        cultures: including various cell lines for studying subcellular
        structures and dynamics. - tissues and tissue sections: allowing for the
        investigation of cellular organization and molecular distribution within
        complex environments. - organoids and spheroids: enabling the study of
        3d tissue models and their development using various imaging modalities,
        including high-speed volume acquisition. - whole organisms and embryos:
        such as zebrafish embryos, for observing developmental processes and
        physiological functions in vivo with high spatiotemporal resolution. -
        cleared biological samples: including whole brains, tissue sections,
        organoids, and spheroids made transparent to enable deep optical
        imaging. - microfluidic devices: for controlled studies of flow and
        molecular dynamics. - plant tissues: such as arabidopsis thaliana stems,
        for investigating protein behavior in response to environmental stimuli.
        commonly performed tasks: - confocal imaging: high-resolution optical
        sectioning to visualize specific planes within a sample and generate 3d
        reconstructions. - super-resolution microscopy: resolving structures
        beyond the diffraction limit to visualize nanoscale details of cellular
        components. - live cell imaging: capturing time-series data of living
        cells and organisms to study dynamic processes and cellular behaviors
        over time. - high-speed volumetric imaging: acquiring 3d datasets at
        rapid frame rates to visualize fast biological events in their entirety.
        - spectral imaging and unmixing: separating the contributions of
        multiple fluorescent probes based on their emission spectra to allow for
        simultaneous multi-target analysis. - fluorescence recovery after
        photobleaching (frap): investigating molecular mobility and dynamics
        within cellular compartments. - fluorescence correlation spectroscopy
        (fcs) and dynamics profiling: measuring molecular concentrations,
        diffusion coefficients, and flow velocities in living samples. - image
        processing and analysis: utilizing software tools like zen and arivis
        pro for image enhancement, quantification, segmentation, tracking, and
        3d visualization of complex datasets. - correlative light and electron
        microscopy (clem): combining light microscopy for functional
        identification with electron microscopy for ultrastructural details. -
        imaging of large volumes and tiled acquisitions: acquiring data from
        large samples or multiple regions of interest and stitching them
        together for comprehensive analysis. - automated imaging workflows:
        setting up and executing complex imaging experiments with automation
        features for reproducible data acquisition. - advanced image analysis
        using ai: employing artificial intelligence-assisted features for sample
        finding, setup optimization, and image analysis.
  - source_sentence: >-
      We previously demonstrated that neural stem/progenitor cells (NSPCs) were
      induced within and around the ischemic areas in a mouse model of ischemic
      stroke. These injury/ischemia-induced NSPCs (iNSPCs) differentiated to
      electrophysiologically functional neurons in vitro, indicating the
      presence of a self-repair system following injury. However, during the
      healing process after stroke, ischemic areas were gradually occupied by
      inflammatory cells, mainly microglial cells/macrophages (MGs/MΦs), and
      neurogenesis rarely occurred within and around the ischemic areas.
      Therefore, to achieve neural regeneration by utilizing endogenous iNSPCs,
      regulation of MGs/MΦs after an ischemic stroke might be necessary. To test
      this hypothesis, we used iNSPCs isolated from the ischemic areas after a
      stroke in our mouse model to investigate the role of MGs/MΦs in iNSPC
      regulation. In coculture experiments, we show that the presence of MGs/MΦs
      significantly reduces not only the proliferation but also the
      differentiation of iNSPCs toward neuronal cells, thereby preventing
      neurogenesis. These effects, however, are mitigated by MG/MΦ depletion
      using clodronate encapsulated in liposomes. Additionally, gene ontology
      analysis reveals that proliferation and neuronal differentiation are
      negatively regulated in iNSPCs cocultured with MGs/MΦs. These results
      indicate that MGs/MΦs negatively impact neurogenesis via iNSPCs,
      suggesting that the regulation of MGs/MΦs is essential to achieve
      iNSPC-based neural regeneration following an ischemic stroke.
    sentences:
      - >-
        ZEISS Airyscan is an advanced imaging technology that enhances
        traditional confocal microscopy by using a 32-channel detector to
        capture more light with higher resolution and sensitivity. Unlike
        standard confocal systems that rely on a single pinhole, Airyscan
        collects the entire Airy disk pattern and reconstructs images for
        super-resolution clarityâ down to 120 nm laterally. This results in
        significantly improved signal-to-noise ratio and reduced photodamage,
        making it ideal for detailed imaging of live cells and biological
        samples. It's compatible with ZEISS LSM systems like the LSM 880 and
        900, offering researchers a powerful tool for high-precision
        fluorescence microscopy
      - >-
        the zeiss geminisem family of field emission scanning electron
        microscopes (fesems) provides versatile solutions for advanced imaging
        and analysis across a wide range of scientific and industrial
        disciplines. these instruments are designed to meet the highest demands
        in sub-nanometer imaging, analytics, and sample flexibility. key
        research and application areas: - advancing nanoscience and
        nanomaterials: enabling the visualization, characterization, and
        manipulation of nanoscale structures and materials for applications in
        electronics, catalysis, sensing, and medicine. this includes analyzing
        the structure and integrity of nanoelectronic and photonic devices,
        imaging sensitive 2d materials, and investigating nanomagnetism and
        nanomechanics. - innovating energy materials: providing insights into
        the microstructure of materials and devices critical for batteries,
        solar cells, and fuel cells, aiding in the development of more efficient
        energy solutions. this encompasses microstructure and device evaluation,
        defect analysis, and the quantification of phases, pores, and fractures.
        - engineering next-generation materials: supporting the development and
        improvement of advanced alloys, composites, coatings, and additively
        manufactured parts by detailed characterization of their properties.
        this involves high-resolution imaging with superior contrast,
        metallography, fracture analysis, and in situ material behavior studies.
        - exploring bio-inspired materials, polymers, and catalysts:
        facilitating the design, optimization, and functional characterization
        of these often non-conductive and beam-sensitive materials for diverse
        applications. key tasks include surface evaluation, structural analysis,
        correlative multiscale characterization, and failure analysis. -
        ensuring industrial quality and reliability: serving as a crucial tool
        for failure analysis in mechanical, optical, and electronic components,
        helping to identify root causes and improve manufacturing processes. -
        driving innovation in electronics and semiconductors: addressing the
        increasing complexity of semiconductor devices by providing
        high-resolution imaging and analysis techniques essential for process
        control and failure analysis of nanoscale features. this includes
        construction analysis, passive voltage contrast imaging, and subsurface
        analysis. - unveiling the complexity of life sciences: enabling detailed
        characterization of biological samples, from ultrastructural
        investigations of cells and tissues to large-area imaging for
        statistical analysis in various fields like neuroscience, cell biology,
        and developmental biology. typical sample types: - a wide array of
        nanostructured materials, including nanoparticles, nanowires, thin
        films, and 2d materials. - components and materials used in energy
        storage and conversion, such as battery electrodes and separators, solar
        cell layers, and fuel cell membranes. - various engineering materials,
        including metals, alloys, ceramics, polymers, composites, and coatings,
        often analyzed in cross-section or after mechanical failure. -
        bio-inspired and soft materials, such as polymer scaffolds, biological
        tissues, and catalysts, often imaged without conductive coatings. -
        industrial components from diverse sectors, including electronics,
        mechanics, and optics, analyzed for defects, composition, and structural
        integrity. - semiconductor devices at various stages of fabrication,
        including transistors, interconnects, and integrated circuits. - a broad
        spectrum of biological samples, including cells, tissues, bacteria,
        viruses, and whole organisms, prepared using various techniques like
        fixation, staining, and embedding. commonly performed tasks: -
        high-resolution imaging to reveal nanoscale details of material surfaces
        and internal structures, often utilizing low accelerating voltages to
        minimize sample damage. - detailed surface characterization to
        understand topography, roughness, and the presence of specific features
        or defects. - compositional analysis using various detectors to identify
        and map different material phases and elemental distributions. -
        crystallographic investigations to determine grain orientations and
        crystalline structures within materials. - correlative microscopy by
        integrating data from multiple imaging modalities (e.g., light and
        electron microscopy) to obtain a more comprehensive understanding of
        samples. - automated large-area imaging and data acquisition to enable
        statistical analysis and the study of heterogeneous samples. -
        three-dimensional reconstruction of sample volumes using techniques like
        serial sectioning and tomography to visualize internal structures in
        detail. - in situ experimentation to observe dynamic processes and
        material behavior under controlled environmental conditions such as
        temperature changes, mechanical stress, or vacuum levels. - analysis of
        challenging samples, including non-conductive and beam-sensitive
        materials, using specialized modes like variable pressure to mitigate
        charging artifacts and beam damage. - failure analysis to identify the
        root causes of material and device malfunctions in industrial and
        research settings. - subsurface imaging and electronic property analysis
        of semiconductor devices to aid in design and failure diagnostics.
      - >-
        ZEISS Airyscan is an advanced imaging technology that enhances
        traditional confocal microscopy by using a 32-channel detector to
        capture more light with higher resolution and sensitivity. Unlike
        standard confocal systems that rely on a single pinhole, Airyscan
        collects the entire Airy disk pattern and reconstructs images for
        super-resolution clarityâ down to 120 nm laterally. This results in
        significantly improved signal-to-noise ratio and reduced photodamage,
        making it ideal for detailed imaging of live cells and biological
        samples. It's compatible with ZEISS LSM systems like the LSM 880 and
        900, offering researchers a powerful tool for high-precision
        fluorescence microscopy
pipeline_tag: sentence-similarity
library_name: sentence-transformers
metrics:
  - cosine_accuracy@1
  - cosine_accuracy@3
  - cosine_accuracy@5
  - cosine_accuracy@10
  - cosine_precision@1
  - cosine_precision@3
  - cosine_precision@5
  - cosine_precision@10
  - cosine_recall@1
  - cosine_recall@3
  - cosine_recall@5
  - cosine_recall@10
  - cosine_ndcg@10
  - cosine_mrr@10
  - cosine_map@100
model-index:
  - name: SentenceTransformer based on allenai/specter2_base
    results:
      - task:
          type: information-retrieval
          name: Information Retrieval
        dataset:
          name: ir eval
          type: ir-eval
        metrics:
          - type: cosine_accuracy@1
            value: 0
            name: Cosine Accuracy@1
          - type: cosine_accuracy@3
            value: 0
            name: Cosine Accuracy@3
          - type: cosine_accuracy@5
            value: 0
            name: Cosine Accuracy@5
          - type: cosine_accuracy@10
            value: 0
            name: Cosine Accuracy@10
          - type: cosine_precision@1
            value: 0
            name: Cosine Precision@1
          - type: cosine_precision@3
            value: 0
            name: Cosine Precision@3
          - type: cosine_precision@5
            value: 0
            name: Cosine Precision@5
          - type: cosine_precision@10
            value: 0
            name: Cosine Precision@10
          - type: cosine_recall@1
            value: 0
            name: Cosine Recall@1
          - type: cosine_recall@3
            value: 0
            name: Cosine Recall@3
          - type: cosine_recall@5
            value: 0
            name: Cosine Recall@5
          - type: cosine_recall@10
            value: 0
            name: Cosine Recall@10
          - type: cosine_ndcg@10
            value: 0
            name: Cosine Ndcg@10
          - type: cosine_mrr@10
            value: 0
            name: Cosine Mrr@10
          - type: cosine_map@100
            value: 0
            name: Cosine Map@100
          - type: cosine_accuracy@1
            value: 0.14206268958543983
            name: Cosine Accuracy@1
          - type: cosine_accuracy@3
            value: 0.31243680485338726
            name: Cosine Accuracy@3
          - type: cosine_accuracy@5
            value: 0.4524772497472194
            name: Cosine Accuracy@5
          - type: cosine_accuracy@10
            value: 0.6698685540950455
            name: Cosine Accuracy@10
          - type: cosine_precision@1
            value: 0.14206268958543983
            name: Cosine Precision@1
          - type: cosine_precision@3
            value: 0.10414560161779575
            name: Cosine Precision@3
          - type: cosine_precision@5
            value: 0.09049544994944388
            name: Cosine Precision@5
          - type: cosine_precision@10
            value: 0.06698685540950455
            name: Cosine Precision@10
          - type: cosine_recall@1
            value: 0.14206268958543983
            name: Cosine Recall@1
          - type: cosine_recall@3
            value: 0.31243680485338726
            name: Cosine Recall@3
          - type: cosine_recall@5
            value: 0.4524772497472194
            name: Cosine Recall@5
          - type: cosine_recall@10
            value: 0.6698685540950455
            name: Cosine Recall@10
          - type: cosine_ndcg@10
            value: 0.36473696593145394
            name: Cosine Ndcg@10
          - type: cosine_mrr@10
            value: 0.2722448922271969
            name: Cosine Mrr@10
          - type: cosine_map@100
            value: 0.29173778100425013
            name: Cosine Map@100

SentenceTransformer based on allenai/specter2_base

This is a sentence-transformers model finetuned from allenai/specter2_base. It maps sentences & paragraphs to a 768-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, text classification, clustering, and more.

Model Details

Model Description

• Model Type: Sentence Transformer
• Base model: allenai/specter2_base
• Maximum Sequence Length: 512 tokens
• Output Dimensionality: 768 dimensions
• Similarity Function: Cosine Similarity

Model Sources

• Documentation: Sentence Transformers Documentation
• Repository: Sentence Transformers on GitHub
• Hugging Face: Sentence Transformers on Hugging Face

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 512, 'do_lower_case': False, 'architecture': 'BertModel'})
  (1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
)

Usage

Direct Usage (Sentence Transformers)

First install the Sentence Transformers library:

pip install -U sentence-transformers

Then you can load this model and run inference.

from sentence_transformers import SentenceTransformer

# Download from the 🤗 Hub
model = SentenceTransformer("jagadeesh/zeiss-re-1757437055")
# Run inference
sentences = [
    'We previously demonstrated that neural stem/progenitor cells (NSPCs) were induced within and around the ischemic areas in a mouse model of ischemic stroke. These injury/ischemia-induced NSPCs (iNSPCs) differentiated to electrophysiologically functional neurons in vitro, indicating the presence of a self-repair system following injury. However, during the healing process after stroke, ischemic areas were gradually occupied by inflammatory cells, mainly microglial cells/macrophages (MGs/MΦs), and neurogenesis rarely occurred within and around the ischemic areas. Therefore, to achieve neural regeneration by utilizing endogenous iNSPCs, regulation of MGs/MΦs after an ischemic stroke might be necessary. To test this hypothesis, we used iNSPCs isolated from the ischemic areas after a stroke in our mouse model to investigate the role of MGs/MΦs in iNSPC regulation. In coculture experiments, we show that the presence of MGs/MΦs significantly reduces not only the proliferation but also the differentiation of iNSPCs toward neuronal cells, thereby preventing neurogenesis. These effects, however, are mitigated by MG/MΦ depletion using clodronate encapsulated in liposomes. Additionally, gene ontology analysis reveals that proliferation and neuronal differentiation are negatively regulated in iNSPCs cocultured with MGs/MΦs. These results indicate that MGs/MΦs negatively impact neurogenesis via iNSPCs, suggesting that the regulation of MGs/MΦs is essential to achieve iNSPC-based neural regeneration following an ischemic stroke.',
    "ZEISS Airyscan is an advanced imaging technology that enhances traditional confocal microscopy by using a 32-channel detector to capture more light with higher resolution and sensitivity. Unlike standard confocal systems that rely on a single pinhole, Airyscan collects the entire Airy disk pattern and reconstructs images for super-resolution clarityâ down to 120 nm laterally. This results in significantly improved signal-to-noise ratio and reduced photodamage, making it ideal for detailed imaging of live cells and biological samples. It's compatible with ZEISS LSM systems like the LSM 880 and 900, offering researchers a powerful tool for high-precision fluorescence microscopy",
    "ZEISS Airyscan is an advanced imaging technology that enhances traditional confocal microscopy by using a 32-channel detector to capture more light with higher resolution and sensitivity. Unlike standard confocal systems that rely on a single pinhole, Airyscan collects the entire Airy disk pattern and reconstructs images for super-resolution clarityâ down to 120 nm laterally. This results in significantly improved signal-to-noise ratio and reduced photodamage, making it ideal for detailed imaging of live cells and biological samples. It's compatible with ZEISS LSM systems like the LSM 880 and 900, offering researchers a powerful tool for high-precision fluorescence microscopy",
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 768]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities)
# tensor([[1.0000, 0.6165, 0.6165],
#         [0.6165, 1.0000, 1.0000],
#         [0.6165, 1.0000, 1.0000]])

Evaluation

Metrics

Information Retrieval

• Dataset: ir-eval
• Evaluated with InformationRetrievalEvaluator

Metric	Value
cosine_accuracy@1	0.0
cosine_accuracy@3	0.0
cosine_accuracy@5	0.0
cosine_accuracy@10	0.0
cosine_precision@1	0.0
cosine_precision@3	0.0
cosine_precision@5	0.0
cosine_precision@10	0.0
cosine_recall@1	0.0
cosine_recall@3	0.0
cosine_recall@5	0.0
cosine_recall@10	0.0
cosine_ndcg@10	0.0
cosine_mrr@10	0.0
cosine_map@100	0.0

Information Retrieval

• Dataset: ir-eval
• Evaluated with InformationRetrievalEvaluator

Metric	Value
cosine_accuracy@1	0.1421
cosine_accuracy@3	0.3124
cosine_accuracy@5	0.4525
cosine_accuracy@10	0.6699
cosine_precision@1	0.1421
cosine_precision@3	0.1041
cosine_precision@5	0.0905
cosine_precision@10	0.067
cosine_recall@1	0.1421
cosine_recall@3	0.3124
cosine_recall@5	0.4525
cosine_recall@10	0.6699
cosine_ndcg@10	0.3647
cosine_mrr@10	0.2722
cosine_map@100	0.2917

Training Details

Training Dataset

Unnamed Dataset

• Size: 17,793 training samples
• Columns: anchor and positive
• Approximate statistics based on the first 1000 samples:

  	anchor	positive
  type	string	string
  details	min: 2 tokens mean: 283.9 tokens max: 512 tokens	min: 91 tokens mean: 355.19 tokens max: 512 tokens

• Samples:

  anchor	positive
  Nutrition and resilience are linked, though it is not yet clear how diet confers stress resistance or the breadth of stressors that it can protect against. We have previously shown that transiently restricting an essential amino acid can protect Drosophila melanogaster against nicotine poisoning. Here, we sought to characterize the nature of this dietary-mediated protection and determine whether it was sex, amino acid and/or nicotine specific. When we compared between sexes, we found that isoleucine deprivation increases female, but not male, nicotine resistance. Surprisingly, we found that this protection afforded to females was not replicated by dietary protein restriction and was instead specific to individual amino acid restriction. To understand whether these beneficial effects of diet were specific to nicotine or were generalizable across stressors, we pre-treated flies with amino acid restriction diets and exposed them to other types of stress. We found that some of the diets th...	the zeiss stemi 508 is an apochromatic stereo microscope with an 8:1 zoom range, designed for high-contrast, color-accurate three-dimensional observation and documentation of diverse samples. its ergonomic design and robust mechanics support demanding applications in laboratory and industrial settings. key research and application areas: - biological research: suitable for observing the development and growth of model organisms like spider crabs, chicken, mouse, or zebrafish, including the evaluation, sorting, selection, or dissection of eggs, larvae, or embryos. it is also used in botany to observe changes in plant organs, diseases, and root development, in entomology for insect observation, documentation, and identification, in marine biology to study the life and reproduction of fish, and in parasitology for detecting and identifying the spread of parasites. the microscope is valuable for forensic analysis of ammunition parts, tool marks, documents, fibers, coatings, glass, textiles...
  The controlled supply of bioactive molecules is a subject of debate in animal nutrition. The release of bioactive molecules in the target organ, in this case the intestine, results in improved feed, as well as having a lower environmental impact. However, the degradation of bioactive molecules' in transit in the gastrointestinal passage is still an unresolved issue. This paper discusses the feasibility of a simple and cost-effective procedure to bypass the degradation problem. A solid/liquid adsorption procedure was applied, and the operating parameters (pH, reaction time, and LY initial concentration) were studied. Lysozyme is used in this work as a representative bioactive molecule, while Adsorbo ® , a commercial mixture of clay minerals and zeolites which meets current feed regulations, is used as the carrier. A maximum LY loading of 32 mg LY /g AD (LY(32)-AD) was obtained, with fixing pH in the range 7.5-8, initial LY content at 37.5 mg LY /g AD , and reaction time at 30 min. A ful...	the zeiss evo family of scanning electron microscopes offers a modular and versatile platform for a wide range of scientific and industrial investigations, combining high-performance imaging and analysis with intuitive operation for users of varying experience levels. key research and application areas: - materials science: characterizing the morphology, structure, and composition of diverse materials, including metals, composites, polymers, ceramics, and coatings, for research and development. this includes investigating surface structures, fractures, inclusions, and grain boundaries. the evo supports advanced material analysis through techniques like energy dispersive spectroscopy (eds) and electron backscatter diffraction (ebsd). - life sciences: enabling the examination of biological specimens in their native or near-native hydrated states using variable and extended pressure modes. applications include imaging cells, tissues, plants, and microorganisms for structural and morpholog...
  Amorphous potassium sodium niobate (KNN) films were synthesized at 300 °C through the radio frequency magnetron sputtering method and subsequently crystallized by post-annealing at 700 °C in various alkali element atmospheres (Na and K). The as-deposited film is notably deficient in alkali metal elements, particularly K, whereas the loss of alkali elements in the films can be replenished through annealing in an alkali element atmosphere. By adjusting the molar ratio of Na and K in the annealing atmosphere, the ratio of Na/K in the resultant film varied, consequently suggesting the efficiency of this method on composition regulation of KNN films. Meanwhile, we also found that the physical characteristics of the films also underwent differences with the change of an annealing atmosphere. The films annealed in a high Na atmosphere exhibit large dielectric losses with limited piezoelectric vibration behavior, while annealing in a high K atmosphere reduces the dielectric losses and enhances...	the zeiss sigma family of field emission scanning electron microscopes (fe-sems) offers versatile solutions for high-quality imaging and advanced analytical microscopy across a multitude of scientific and industrial domains. these instruments are engineered for reliable, high-end nano-analysis, combining fe-sem technology with an intuitive user experience to enhance productivity. key research and application areas: - advancing materials science: facilitating the development and understanding of novel materials by enabling the investigation of micro- and nanoscale structures. this includes characterizing metals, alloys, polymers, catalysts, and coatings for various applications such as electronics and energy. - driving innovation in nanoscience and nanomaterials: providing capabilities for the analysis of nanoparticles, thin films, 2d materials (like graphene and mos2), and other nanostructures to understand their properties and potential applications. - supporting energy research: enab...

• Loss: MultipleNegativesRankingLoss with these parameters:

  {
      "scale": 20.0,
      "similarity_fct": "cos_sim",
      "gather_across_devices": false
  }
  

Training Hyperparameters

Non-Default Hyperparameters

• eval_strategy: steps
• per_device_train_batch_size: 16
• per_device_eval_batch_size: 16
• learning_rate: 1e-05
• num_train_epochs: 5
• warmup_ratio: 0.1
• fp16: True
• batch_sampler: no_duplicates

All Hyperparameters

Click to expand

• overwrite_output_dir: False
• do_predict: False
• eval_strategy: steps
• prediction_loss_only: True
• per_device_train_batch_size: 16
• per_device_eval_batch_size: 16
• per_gpu_train_batch_size: None
• per_gpu_eval_batch_size: None
• gradient_accumulation_steps: 1
• eval_accumulation_steps: None
• torch_empty_cache_steps: None
• learning_rate: 1e-05
• weight_decay: 0.0
• adam_beta1: 0.9
• adam_beta2: 0.999
• adam_epsilon: 1e-08
• max_grad_norm: 1.0
• num_train_epochs: 5
• max_steps: -1
• lr_scheduler_type: linear
• lr_scheduler_kwargs: {}
• warmup_ratio: 0.1
• warmup_steps: 0
• log_level: passive
• log_level_replica: warning
• log_on_each_node: True
• logging_nan_inf_filter: True
• save_safetensors: True
• save_on_each_node: False
• save_only_model: False
• restore_callback_states_from_checkpoint: False
• no_cuda: False
• use_cpu: False
• use_mps_device: False
• seed: 42
• data_seed: None
• jit_mode_eval: False
• use_ipex: False
• bf16: False
• fp16: True
• fp16_opt_level: O1
• half_precision_backend: auto
• bf16_full_eval: False
• fp16_full_eval: False
• tf32: None
• local_rank: 0
• ddp_backend: None
• tpu_num_cores: None
• tpu_metrics_debug: False
• debug: []
• dataloader_drop_last: False
• dataloader_num_workers: 0
• dataloader_prefetch_factor: None
• past_index: -1
• disable_tqdm: False
• remove_unused_columns: True
• label_names: None
• load_best_model_at_end: False
• ignore_data_skip: False
• fsdp: []
• fsdp_min_num_params: 0
• fsdp_config: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}
• fsdp_transformer_layer_cls_to_wrap: None
• accelerator_config: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}
• parallelism_config: None
• deepspeed: None
• label_smoothing_factor: 0.0
• optim: adamw_torch_fused
• optim_args: None
• adafactor: False
• group_by_length: False
• length_column_name: length
• ddp_find_unused_parameters: None
• ddp_bucket_cap_mb: None
• ddp_broadcast_buffers: False
• dataloader_pin_memory: True
• dataloader_persistent_workers: False
• skip_memory_metrics: True
• use_legacy_prediction_loop: False
• push_to_hub: False
• resume_from_checkpoint: None
• hub_model_id: None
• hub_strategy: every_save
• hub_private_repo: None
• hub_always_push: False
• hub_revision: None
• gradient_checkpointing: False
• gradient_checkpointing_kwargs: None
• include_inputs_for_metrics: False
• include_for_metrics: []
• eval_do_concat_batches: True
• fp16_backend: auto
• push_to_hub_model_id: None
• push_to_hub_organization: None
• mp_parameters:
• auto_find_batch_size: False
• full_determinism: False
• torchdynamo: None
• ray_scope: last
• ddp_timeout: 1800
• torch_compile: False
• torch_compile_backend: None
• torch_compile_mode: None
• include_tokens_per_second: False
• include_num_input_tokens_seen: False
• neftune_noise_alpha: None
• optim_target_modules: None
• batch_eval_metrics: False
• eval_on_start: False
• use_liger_kernel: False
• liger_kernel_config: None
• eval_use_gather_object: False
• average_tokens_across_devices: False
• prompts: None
• batch_sampler: no_duplicates
• multi_dataset_batch_sampler: proportional
• router_mapping: {}
• learning_rate_mapping: {}

Training Logs

Epoch	Step	Training Loss	ir-eval_cosine_ndcg@10
0.0898	100	2.488	0.0
0.1797	200	2.321	0.0
0.2695	300	2.0777	0.0
0.3594	400	1.833	0.0
0.4492	500	1.7474	0.0
-1	-1	-	0.2969
0.0898	100	2.2378	0.3023
0.1797	200	2.1268	0.3196
0.2695	300	1.8964	0.3541
0.3594	400	1.6197	0.3123
0.4492	500	1.493	0.3086
0.5391	600	1.4507	0.3146
0.6289	700	1.6187	0.2985
0.7188	800	1.4818	0.3412
0.8086	900	1.3241	0.2945
0.8985	1000	1.3055	0.2161
0.9883	1100	1.2704	0.2712
1.0782	1200	2.009	0.3143
1.1680	1300	2.0103	0.3403
1.2579	1400	1.8953	0.3408
1.3477	1500	1.662	0.3409
1.4376	1600	1.656	0.3073
1.5274	1700	1.537	0.2792
1.6173	1800	1.4893	0.2730
1.7071	1900	1.3447	0.2537
1.7969	2000	1.2444	0.2496
1.8868	2100	1.1493	0.2314
1.9766	2200	1.26	0.2753
2.0665	2300	1.7302	0.3514
2.1563	2400	1.7719	0.3546
2.2462	2500	1.7208	0.3366
2.3360	2600	1.4715	0.3387
2.4259	2700	1.45	0.2974
2.5157	2800	1.3878	0.3084
2.6056	2900	1.3184	0.2915
2.6954	3000	1.2562	0.2917
2.7853	3100	1.119	0.2940
2.8751	3200	1.1307	0.2989
2.9650	3300	1.1421	0.3081
3.0548	3400	1.4917	0.3402
3.1447	3500	1.5628	0.3392
3.2345	3600	1.4621	0.3684
3.3243	3700	1.342	0.3601
3.4142	3800	1.3052	0.3222
3.5040	3900	1.2133	0.3566
3.5939	4000	1.248	0.3631
3.6837	4100	1.2261	0.3558
3.7736	4200	0.978	0.3428
3.8634	4300	0.9916	0.3545
3.9533	4400	1.0824	0.3492
4.0431	4500	1.2055	0.3418
4.1330	4600	1.404	0.3481
4.2228	4700	1.3775	0.3613
4.3127	4800	1.2128	0.3579
4.4025	4900	1.168	0.3625
4.4924	5000	1.1061	0.3600
4.5822	5100	1.1213	0.3658
4.6721	5200	1.0396	0.3603
4.7619	5300	0.9766	0.3702
4.8518	5400	0.9143	0.3618
4.9416	5500	0.9728	0.3647

Framework Versions

• Python: 3.11.11
• Sentence Transformers: 5.1.0
• Transformers: 4.56.1
• PyTorch: 2.8.0.dev20250319+cu128
• Accelerate: 1.10.1
• Datasets: 3.6.0
• Tokenizers: 0.22.0

Citation

BibTeX

Sentence Transformers

@inproceedings{reimers-2019-sentence-bert,
    title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
    author = "Reimers, Nils and Gurevych, Iryna",
    booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
    month = "11",
    year = "2019",
    publisher = "Association for Computational Linguistics",
    url = "https://arxiv.org/abs/1908.10084",
}

MultipleNegativesRankingLoss

@misc{henderson2017efficient,
    title={Efficient Natural Language Response Suggestion for Smart Reply},
    author={Matthew Henderson and Rami Al-Rfou and Brian Strope and Yun-hsuan Sung and Laszlo Lukacs and Ruiqi Guo and Sanjiv Kumar and Balint Miklos and Ray Kurzweil},
    year={2017},
    eprint={1705.00652},
    archivePrefix={arXiv},
    primaryClass={cs.CL}
}