--- 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: 0.12841253791708795 name: Cosine Accuracy@1 - type: cosine_accuracy@3 value: 0.29322548028311424 name: Cosine Accuracy@3 - type: cosine_accuracy@5 value: 0.416582406471183 name: Cosine Accuracy@5 - type: cosine_accuracy@10 value: 0.6476238624873609 name: Cosine Accuracy@10 - type: cosine_precision@1 value: 0.12841253791708795 name: Cosine Precision@1 - type: cosine_precision@3 value: 0.09774182676103807 name: Cosine Precision@3 - type: cosine_precision@5 value: 0.0833164812942366 name: Cosine Precision@5 - type: cosine_precision@10 value: 0.06476238624873609 name: Cosine Precision@10 - type: cosine_recall@1 value: 0.12841253791708795 name: Cosine Recall@1 - type: cosine_recall@3 value: 0.29322548028311424 name: Cosine Recall@3 - type: cosine_recall@5 value: 0.416582406471183 name: Cosine Recall@5 - type: cosine_recall@10 value: 0.6476238624873609 name: Cosine Recall@10 - type: cosine_ndcg@10 value: 0.3461514728879504 name: Cosine Ndcg@10 - type: cosine_mrr@10 value: 0.2550883127096472 name: Cosine Mrr@10 - type: cosine_map@100 value: 0.27654953235702057 name: Cosine Map@100 - type: cosine_accuracy@1 value: 0.12891809908998988 name: Cosine Accuracy@1 - type: cosine_accuracy@3 value: 0.30940343781597573 name: Cosine Accuracy@3 - type: cosine_accuracy@5 value: 0.4398382204246714 name: Cosine Accuracy@5 - type: cosine_accuracy@10 value: 0.6926188068756319 name: Cosine Accuracy@10 - type: cosine_precision@1 value: 0.12891809908998988 name: Cosine Precision@1 - type: cosine_precision@3 value: 0.10313447927199192 name: Cosine Precision@3 - type: cosine_precision@5 value: 0.08796764408493427 name: Cosine Precision@5 - type: cosine_precision@10 value: 0.0692618806875632 name: Cosine Precision@10 - type: cosine_recall@1 value: 0.12891809908998988 name: Cosine Recall@1 - type: cosine_recall@3 value: 0.30940343781597573 name: Cosine Recall@3 - type: cosine_recall@5 value: 0.4398382204246714 name: Cosine Recall@5 - type: cosine_recall@10 value: 0.6926188068756319 name: Cosine Recall@10 - type: cosine_ndcg@10 value: 0.36461949198838806 name: Cosine Ndcg@10 - type: cosine_mrr@10 value: 0.2654840146371995 name: Cosine Mrr@10 - type: cosine_map@100 value: 0.2837399475240014 name: Cosine Map@100 - type: cosine_accuracy@1 value: 0.12740141557128412 name: Cosine Accuracy@1 - type: cosine_accuracy@3 value: 0.29221435793731043 name: Cosine Accuracy@3 - type: cosine_accuracy@5 value: 0.41304347826086957 name: Cosine Accuracy@5 - type: cosine_accuracy@10 value: 0.6354903943377148 name: Cosine Accuracy@10 - type: cosine_precision@1 value: 0.12740141557128412 name: Cosine Precision@1 - type: cosine_precision@3 value: 0.09740478597910346 name: Cosine Precision@3 - type: cosine_precision@5 value: 0.08260869565217391 name: Cosine Precision@5 - type: cosine_precision@10 value: 0.06354903943377148 name: Cosine Precision@10 - type: cosine_recall@1 value: 0.12740141557128412 name: Cosine Recall@1 - type: cosine_recall@3 value: 0.29221435793731043 name: Cosine Recall@3 - type: cosine_recall@5 value: 0.41304347826086957 name: Cosine Recall@5 - type: cosine_recall@10 value: 0.6354903943377148 name: Cosine Recall@10 - type: cosine_ndcg@10 value: 0.34256937669879595 name: Cosine Ndcg@10 - type: cosine_mrr@10 value: 0.2537997335772863 name: Cosine Mrr@10 - type: cosine_map@100 value: 0.27475648035535954 name: Cosine Map@100 - type: cosine_accuracy@1 value: 0.179474216380182 name: Cosine Accuracy@1 - type: cosine_accuracy@3 value: 0.43073811931243683 name: Cosine Accuracy@3 - type: cosine_accuracy@5 value: 0.6061678463094035 name: Cosine Accuracy@5 - type: cosine_accuracy@10 value: 0.8473205257836198 name: Cosine Accuracy@10 - type: cosine_precision@1 value: 0.179474216380182 name: Cosine Precision@1 - type: cosine_precision@3 value: 0.1435793731041456 name: Cosine Precision@3 - type: cosine_precision@5 value: 0.12123356926188068 name: Cosine Precision@5 - type: cosine_precision@10 value: 0.08473205257836199 name: Cosine Precision@10 - type: cosine_recall@1 value: 0.179474216380182 name: Cosine Recall@1 - type: cosine_recall@3 value: 0.43073811931243683 name: Cosine Recall@3 - type: cosine_recall@5 value: 0.6061678463094035 name: Cosine Recall@5 - type: cosine_recall@10 value: 0.8473205257836198 name: Cosine Recall@10 - type: cosine_ndcg@10 value: 0.4739618595288823 name: Cosine Ndcg@10 - type: cosine_mrr@10 value: 0.3588527372526363 name: Cosine Mrr@10 - type: cosine_map@100 value: 0.3682285718046807 name: Cosine Map@100 --- # SentenceTransformer based on allenai/specter2_base This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [allenai/specter2_base](https://huggingface.co/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](https://huggingface.co/allenai/specter2_base) - **Maximum Sequence Length:** 512 tokens - **Output Dimensionality:** 768 dimensions - **Similarity Function:** Cosine Similarity ### Model Sources - **Documentation:** [Sentence Transformers Documentation](https://sbert.net) - **Repository:** [Sentence Transformers on GitHub](https://github.com/UKPLab/sentence-transformers) - **Hugging Face:** [Sentence Transformers on Hugging Face](https://huggingface.co/models?library=sentence-transformers) ### 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: ```bash pip install -U sentence-transformers ``` Then you can load this model and run inference. ```python from sentence_transformers import SentenceTransformer # Download from the 🤗 Hub model = SentenceTransformer("jagadeesh/zeiss-re-1757443344") # 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, 0.6498, 0.6498], # [0.6498, 1.0000, 1.0000], # [0.6498, 1.0000, 1.0000]]) ``` ## Evaluation ### Metrics #### Information Retrieval * Dataset: `ir-eval` * Evaluated with [InformationRetrievalEvaluator](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator) | Metric | Value | |:--------------------|:-----------| | cosine_accuracy@1 | 0.1284 | | cosine_accuracy@3 | 0.2932 | | cosine_accuracy@5 | 0.4166 | | cosine_accuracy@10 | 0.6476 | | cosine_precision@1 | 0.1284 | | cosine_precision@3 | 0.0977 | | cosine_precision@5 | 0.0833 | | cosine_precision@10 | 0.0648 | | cosine_recall@1 | 0.1284 | | cosine_recall@3 | 0.2932 | | cosine_recall@5 | 0.4166 | | cosine_recall@10 | 0.6476 | | **cosine_ndcg@10** | **0.3462** | | cosine_mrr@10 | 0.2551 | | cosine_map@100 | 0.2765 | #### Information Retrieval * Dataset: `ir-eval` * Evaluated with [InformationRetrievalEvaluator](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator) | Metric | Value | |:--------------------|:-----------| | cosine_accuracy@1 | 0.1289 | | cosine_accuracy@3 | 0.3094 | | cosine_accuracy@5 | 0.4398 | | cosine_accuracy@10 | 0.6926 | | cosine_precision@1 | 0.1289 | | cosine_precision@3 | 0.1031 | | cosine_precision@5 | 0.088 | | cosine_precision@10 | 0.0693 | | cosine_recall@1 | 0.1289 | | cosine_recall@3 | 0.3094 | | cosine_recall@5 | 0.4398 | | cosine_recall@10 | 0.6926 | | **cosine_ndcg@10** | **0.3646** | | cosine_mrr@10 | 0.2655 | | cosine_map@100 | 0.2837 | #### Information Retrieval * Dataset: `ir-eval` * Evaluated with [InformationRetrievalEvaluator](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator) | Metric | Value | |:--------------------|:-----------| | cosine_accuracy@1 | 0.1274 | | cosine_accuracy@3 | 0.2922 | | cosine_accuracy@5 | 0.413 | | cosine_accuracy@10 | 0.6355 | | cosine_precision@1 | 0.1274 | | cosine_precision@3 | 0.0974 | | cosine_precision@5 | 0.0826 | | cosine_precision@10 | 0.0635 | | cosine_recall@1 | 0.1274 | | cosine_recall@3 | 0.2922 | | cosine_recall@5 | 0.413 | | cosine_recall@10 | 0.6355 | | **cosine_ndcg@10** | **0.3426** | | cosine_mrr@10 | 0.2538 | | cosine_map@100 | 0.2748 | #### Information Retrieval * Dataset: `ir-eval` * Evaluated with [InformationRetrievalEvaluator](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator) | Metric | Value | |:--------------------|:----------| | cosine_accuracy@1 | 0.1795 | | cosine_accuracy@3 | 0.4307 | | cosine_accuracy@5 | 0.6062 | | cosine_accuracy@10 | 0.8473 | | cosine_precision@1 | 0.1795 | | cosine_precision@3 | 0.1436 | | cosine_precision@5 | 0.1212 | | cosine_precision@10 | 0.0847 | | cosine_recall@1 | 0.1795 | | cosine_recall@3 | 0.4307 | | cosine_recall@5 | 0.6062 | | cosine_recall@10 | 0.8473 | | **cosine_ndcg@10** | **0.474** | | cosine_mrr@10 | 0.3589 | | cosine_map@100 | 0.3682 | ## 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 | | | * 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](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters: ```json { "scale": 20.0, "similarity_fct": "cos_sim", "gather_across_devices": false } ``` ### Training Hyperparameters #### Non-Default Hyperparameters - `eval_strategy`: steps - `per_device_train_batch_size`: 64 - `per_device_eval_batch_size`: 64 - `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`: 64 - `per_device_eval_batch_size`: 64 - `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`: 5e-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 | |:------:|:----:|:-------------:|:----------------------:| | -1 | -1 | - | 0.1872 | | 0.0898 | 100 | 2.488 | 0.2632 | | 0.1797 | 200 | 2.321 | 0.3059 | | 0.2695 | 300 | 2.0777 | 0.3453 | | 0.3594 | 400 | 1.8331 | 0.3041 | | 0.4492 | 500 | 1.7476 | 0.2957 | | 0.5391 | 600 | 1.636 | 0.3263 | | 0.6289 | 700 | 1.6187 | 0.3007 | | 0.7188 | 800 | 1.4823 | 0.3403 | | 0.8086 | 900 | 1.3278 | 0.2555 | | 0.8985 | 1000 | 1.3049 | 0.2055 | | 0.9883 | 1100 | 1.2643 | 0.2498 | | 1.0782 | 1200 | 2.0728 | 0.3045 | | 1.1680 | 1300 | 2.0786 | 0.3186 | | 1.2579 | 1400 | 1.949 | 0.3343 | | 1.3477 | 1500 | 1.7133 | 0.3402 | | 1.4376 | 1600 | 1.6963 | 0.2970 | | 1.5274 | 1700 | 1.5702 | 0.2728 | | 1.6173 | 1800 | 1.5279 | 0.2667 | | 1.7071 | 1900 | 1.3978 | 0.2342 | | 1.7969 | 2000 | 1.2756 | 0.2354 | | 1.8868 | 2100 | 1.1746 | 0.2236 | | 1.9766 | 2200 | 1.2698 | 0.2443 | | 2.0665 | 2300 | 1.8099 | 0.3395 | | 2.1563 | 2400 | 1.8809 | 0.3456 | | 2.2462 | 2500 | 1.826 | 0.3316 | | 2.3360 | 2600 | 1.5636 | 0.3375 | | 2.4259 | 2700 | 1.529 | 0.2894 | | 2.5157 | 2800 | 1.4501 | 0.2816 | | 2.6056 | 2900 | 1.3876 | 0.2782 | | 2.6954 | 3000 | 1.3273 | 0.2772 | | 2.7853 | 3100 | 1.1583 | 0.2810 | | 2.8751 | 3200 | 1.1515 | 0.2856 | | 2.9650 | 3300 | 1.1539 | 0.2849 | | 3.0548 | 3400 | 1.5729 | 0.3380 | | 3.1447 | 3500 | 1.6835 | 0.3462 | | 3.2345 | 3600 | 1.5857 | 0.3533 | | 3.3243 | 3700 | 1.4443 | 0.3462 | | -1 | -1 | - | 0.3661 | | 0.0898 | 100 | 1.7025 | 0.3527 | | 0.1797 | 200 | 1.6829 | 0.3600 | | 0.2695 | 300 | 1.6242 | 0.3649 | | 0.3594 | 400 | 1.5047 | 0.3614 | | 0.4492 | 500 | 1.4711 | 0.3793 | | 0.5391 | 600 | 1.4528 | 0.3646 | | -1 | -1 | - | 0.3183 | | 0.3584 | 100 | 1.823 | 0.3093 | | 0.7168 | 200 | 1.8014 | 0.3297 | | 1.0753 | 300 | 1.8726 | 0.3504 | | 1.4337 | 400 | 1.7708 | 0.3233 | | 1.7921 | 500 | 1.5537 | 0.3210 | | 2.1505 | 600 | 1.6994 | 0.3996 | | 2.5090 | 700 | 1.3569 | 0.3240 | | 2.8674 | 800 | 1.369 | 0.3325 | | 3.2258 | 900 | 1.3097 | 0.4251 | | 3.5842 | 1000 | 1.1224 | 0.3971 | | 3.9427 | 1100 | 1.2093 | 0.4377 | | 4.3011 | 1200 | 1.012 | 0.4723 | | 4.6595 | 1300 | 1.0207 | 0.4740 | ### 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 ```bibtex @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 ```bibtex @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} } ```