gebhart/patrepeval huggingface dataset:
Extensive Determination of Glycan Heterogeneity Reveals an Unusual Abundance of High Mannose Glycans in Enriched Plasma Membranes of Human Embryonic Stem Cells (2011)

Most cell membrane proteins are known or predicted to be glycosylated in eukaryotic organisms, where surface glycans are essential in many biological processes including cell development and differentiation. Nonetheless, the glycosylation on cell membranes remains not well characterized because of the lack of sensitive analytical methods. This study introduces a technique for the rapid profiling and quantitation of N- and O-glycans on cell membranes using membrane enrichment and nanoflow liquid chromatography/mass spectrometry of native structures. Using this new method, the glycome analysis of cell membranes isolated from human embryonic stem cells and somatic cell lines was performed. Human embryonic stem cells were found to have high levels of high mannose glycans, which contrasts with IMR-90 fibroblasts and a human normal breast cell line, where complex glycans are by far the most abundant and high mannose glycans are minor components. O-Glycosylation affects relatively minor components of cell surfaces. To verify the quantitation and localization of glycans on the human embryonic stem cell membranes, flow cytometry and immunocytochemistry were performed. Proteomics analyses were also performed and confirmed enrichment of plasma membrane proteins with some contamination from endoplasmic reticulum and other membranes. These findings suggest that high mannose glycans are the major component of cell surface glycosylation with even terminal glucoses. High mannose glycans are not commonly presented on the surfaces of mammalian cells or in serum yet may play important roles in stem cell biology. The results also mean that distinguishing stem cells from other mammalian cells may be facilitated by the major difference in the glycosylation of the cell membrane. The deep structural analysis enabled by this new method will enable future mechanistic studies on the biological significance of high mannose glycans on stem cell membranes and provide a general tool to examine cell surface glycosylation.
Supplementary Figure 6 from Enhanced Cancer Radiotherapy through Immunosuppressive Stromal Cell Destruction in Tumors (2023)

&lt;p&gt;PDF file - 1656K, Characterization of the distribution of CD11b+ myeloid cells and CD11b+ Gr-1+ MDSCs in tumor, spleen and DLN after radiation.&lt;/p&gt;
Digital Micromirror Devices: Principles and Applications in Imaging (2013)

A digital micromirror device (DMD) is an array of individually switchable mirrors that can be used in many advanced optical systems as a rapid spatial light modulator. With a DMD, several implementations of confocal microscopy, hyperspectral imaging, and fluorescence lifetime imaging can be realized. The DMD can also be used as a real-time optical processor for applications such as the programmable array microscope and compressive sensing. Advantages and disadvantages of the DMD for these applications as well as methods to overcome some of the limitations will be discussed in this article. Practical considerations when designing with the DMD and sample optical layouts of a completely DMD-based imaging system and one in which acousto-optic deflectors (AODs) are used in the illumination pathway are also provided.
Supplementary Table S2 from Bacterial-Driven Inflammation and Mutant <i>BRAF</i> Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy (2023)

&lt;p&gt;Differential methylation values for methylation-binding domain sequencing (MBDseq) for sham and ETBF-colonized normal epithelium and tumors from Min and BRAFV600ELgr5CreMin (BLM) colons.&lt;/p&gt;
Fluorination of MXene by Elemental F2 as Electrode Material for Lithium‐Ion Batteries (2019)

Abstract Invited for this month′s cover is the group of Dr. Sheng Dai at the University of Tennessee, Oak Ridge National Laboratory and Joint Institute for Advanced Materials. The image shows the transformation of 2D Mxene into novel 2D TiOF 2 via low temperature direct fluorination. The Full Paper itself is available at 10.1002/cssc.201900003 .
FactGraph: Evaluating Factuality in Summarization with Semantic Graph Representations (2022)

Despite recent improvements in abstractive summarization, most current approaches generate summaries that are not factually consistent with the source document, severely restricting their trust and usage in real-world applications. Recent works have shown promising improvements in factuality error identification using text or dependency arc entailments; however, they do not consider the entire semantic graph simultaneously. To this end, we propose FactGraph, a method that decomposes the document and the summary into structured meaning representations (MR), which are more suitable for factuality evaluation. MRs describe core semantic concepts and their relations, aggregating the main content in both document and summary in a canonical form, and reducing data sparsity. FactGraph encodes such graphs using a graph encoder augmented with structure-aware adapters to capture interactions among the concepts based on the graph connectivity, along with text representations using an adapter-based text encoder. Experiments on different benchmarks for evaluating factuality show that FactGraph outperforms previous approaches by up to 15%. Furthermore, FactGraph improves performance on identifying content verifiability errors and better captures subsentence-level factual inconsistencies.
Optically clearing tissue as an initial step for 3D imaging of core biopsies to diagnose pancreatic cancer (2014)

The pancreas is a deeply seated organ requiring endoscopically, or radiologically guided biopsies for tissue diagnosis. Current approaches include either fine needle aspiration biopsy (FNA) for cytologic evaluation, or core needle biopsies (CBs), which comprise of tissue cores (L = 1-2 cm, D = 0.4-2.0 mm) for examination by brightfield microscopy. Between procurement and visualization, biospecimens must be processed, sectioned and mounted on glass slides for 2D visualization. Optical information about the native tissue state can be lost with each procedural step and a pathologist cannot appreciate 3D organization from 2D observations of tissue sections 1-8 &mu;m in thickness. Therefore, how might histological disease assessment improve if entire, intact CBs could be imaged in both brightfield and 3D? CBs are mechanically delicate; therefore, a simple device was made to cut intact, simulated CBs (L = 1-2 cm, D = 0.2-0.8 mm) from porcine pancreas. After CBs were laid flat in a chamber, z-stack images at 20x and 40x were acquired through the sample with and without the application of an optical clearing agent (FocusClear&reg;). Intensity of transmitted light increased by 5-15x and islet structures unique to pancreas were clearly visualized 250-300 &mu;m beneath the tissue surface. CBs were then placed in index matching square capillary tubes filled with FocusClear&reg; and a standard optical clearing agent. Brightfield z-stack images were then acquired to present 3D visualization of the CB to the pathologist.
Developing a Framework to Establish a Life-Cycle Integrated Open Access Support System (2023)

본 연구는 오픈액세스를 기반으로 학술출판의 전주기를 지원하는 오픈액세스 통합 지원체제 구축을 위한 프레임워크를 개발하는 것을 목적으로 한다. 국가오픈액세스플랫폼 AccessON과 논문 투고심사시스템 같은 기존의 학술출판 지원 시스템을 분석하고, 학술단체의 편집위원장, 편집위원, 편집간사 등을 대상으로 한 설문을 통해 학술출판 전주기 지원을 위해 고려되어야 할 요소들을 도출하였다. 이를 기반으로 학술논문의 검색 및 활용, 투고, 심사 및 편집, 출판, 논문의 배포 및 모니터링에 이르는 학술출판의 각 단계를 지원하는 시스템과 주요 기능을 정의하는 전주기 오픈액세스 통합 지원체제 구축을 위한 프레임워크를 설계하였다. 설계한 프레임워크는 학술 커뮤니티 전문가들의 정량평가와 검토 절차를 거쳐 완성도를 제고하였다. 개발된 프레임워크를 토대로 중장기적으로 국내 학술단체의 지속가능한 오픈액세스 학술출판을 지원할 수 있을 것이다.
PEDESTRIAN SAFETY FOR THE ELDERLY: A STATE OF THE ART REVIEW (1983)

The study of pedestrian accidents among the elderly encompasses many areas of research. This review focuses on the relationship of the physical environment of accidents to human behavior. Only two aspects of driver behavior are considered - the relationship of driver and pedestrian during or immediately preceding pedestrian accidents and knowledge about driving behavior that can be directly applied to pedestrian problems. Statistical information that can be used to understand accident patterns has been included in the scope of the review in order to assess the importance of the problem and identify priority issues. Material on accident theory has been included in order to define the pedestrian accident phenomenon more clearly, to insure that no important factors would be omitted, and to obtain new insights that could be transferred from other areas of accident investigation to the specific problem of pedestrian accidents. The report is organized into the following sections: 1. Introduction, 2. Theoretical background, 3. Characteristics of pedestrian accidents, 4. Causes of pedestrian accidents, 5. Driver behavior related to pedestrian accidents, 6. Pedestrian behavior and accidents, 7. Human performance in old age, 8. Countermeasures, 9. Research methods, and 10. Annotated bibliography.
Forcing surface issues (1991)

The landscape spreads before you as rolling hills, punctuated by occasional pits and holes, and leads westerly to a precipitous cliff. This scene usually resides in holiday photographs but it is now appearing in the laboratory too in images from atomic force microscopes. The imaged hills are really atomic steps and terraces, the pits are random atomic vacancies, and the cliff is a screw dislocation. What allows us to draw this analogy between the large and small scales of nature? In part, it is the modern techniques of graphics visualisation of data; but increasingly, it is the stunning resolution of atomic and molecular features that this class of microscope can produce. The excitement of studying the physics and chemistry of surfaces with the force microscopes is enhanced by the knowledge that the instruments are still in their infancies.
Outpatient Initiation of Dialysis for AKI Requiring Dialysis Following Diagnosis of COVID-19 (2020)

Background: COVID-19 has been associated with the development of AKI, and the incidence of AKI-D may be as high as 3-5% in patients hospitalized with COVID-19. We examined the initiation of outpatient (OP) dialysis for AKI-D following a diagnosis of COVID-19. Methods: We identified patients who were diagnosed with COVID-19 prior to initiating OP dialysis for AKI-D in a Fresenius Medical Care North America (FMCNA) dialysis facility between March 30, 2020 and May 22, 2020. COVID-19 diagnosis was based on information provided at the time of referral or data collected within FMCNA. We assessed demographics, geographic location, and select initial outpatient lab values. We followed patients from initiation of OP dialysis until the earliest of recovery of kidney function, transition to ESKD, death, loss to follow-up (typically, transfer to another dialysis provider), or May 24, 2020, and estimated the cumulative incidence of these outcomes. Results: The cohort comprised 127 patients who were diagnosed with COVID-19 prior to initiating OP dialysis for AKI-D. Mean age was 56.3 ± 14.7 years and 64% were male. Initiation of OP dialysis for AKI-D was observed in regions with a known high incidence of COVID-19 disease (Figure). The median hemoglobin, platelet count and albumin at dialysis initiation were 8.9 g/dL, 271,000 per microliter, and 3.2 g/dL, respectively. During a median follow-up period of 19 days, 18 (14.2%) patients recovered kidney function, 2 (1.6%) transitioned to ESKD, and 2 (1.6%) died. Conclusions: In an approximate 7-week period, 127 adults started OP dialysis for AKI-D following a diagnosis of COVID-19. Unfortunately, information regarding the clinical course of COVID-19 preceding OP initiation of dialysis was not available and using information at the time of referral may have resulted in misclassification of COVID-19 disease. Nevertheless, these are important findings and warrant further study, especially with respect to long-term outcomes in this population. Funding: Commercial Support - Fresenius Medical Care
Soluble tumour necrosis factor receptors (sTNF-R) and HIV infection: correlation to CD8+ lymphocytes (1993)

The objective of this study was to determine sTNF-R, type I (p55) and type II (p75) in sera of HIV-infected male homosexuals and correlate them to T lymphocyte subpopulations and course of HIV infection. Serum samples were obtained from 39 HIV-1+ asymptomatic male homosexuals, 10 symptomatic (ARC and AIDS) male homosexuals and 44 HIV- non-homosexual healthy controls. sTNF-R levels were determined by ELISA with specific MoAbs and polyclonal antibodies to the sTNF-R proteins. sTNF-RI and II levels were significantly elevated in 72% and 74% respectively of HIV+ asymptomatic male homosexuals and in all of the symptomatic male homosexuals. In sequential studies a highly significant positive correlation was found between sTNF-RI and sTNF-RII (r = 0.8, P < 0.001) and between both sTNF-R and CD8+ lymphocyte counts (r = 0.6 and 0.92, respectively, P < 0.01-0.001) during the asymptomatic stage of the infection. All these correlations were lost, however, during the symptomatic phase of the disease. These results suggest that: (i) HIV infection is associated with elevation of sTNF-R serum levels; (ii) sTNF-R levels are strongly correlated to CD8+ lymphocytes during the asymptomatic stage of HIV infection.
Compartment-Specific Labeling of Bacterial Periplasmic Proteins by Peroxidase-Mediated Biotinylation (2018)

The study of the bacterial periplasm requires techniques with sufficient spatial resolution and sensitivity to resolve the components and processes within this subcellular compartment. Peroxidase-mediated biotinylation has enabled targeted labeling of proteins within subcellular compartments of mammalian cells. We investigated whether this methodology could be applied to the bacterial periplasm. In this study, we demonstrated that peroxidase-mediated biotinylation can be performed in mycobacteria and Escherichia coli. To eliminate detection artifacts from natively biotinylated mycobacterial proteins, we validated two alternative labeling substrates, tyramide azide and tyramide alkyne, which enable biotin-independent detection of labeled proteins. We also targeted peroxidase expression to the periplasm, resulting in compartment-specific labeling of periplasmic versus cytoplasmic proteins in mycobacteria. Finally, we showed that this method can be used to validate protein relocalization to the cytoplasm upon removal of a secretion signal. This novel application of peroxidase-mediated protein labeling will advance efforts to characterize the role of the periplasm in bacterial physiology and pathogenesis.
A neutron imaging detector from bundled lithium silicate glass fibers (2009)

Scientific applications of neutrons ranging from protein crystallography to non-destructive inspections require sensitive neutron detectors having a high spatial resolution that are able to discriminate against unwanted gamma ray events. To address this problem, 2 and 5 mm thick prototype detectors were fabricated as a bundled array of 120 ¿m diameter cerium activated lithium silicate glass fibers cast in a low-index epoxy resin that helps improve light transmission. Performance of this detector was determined from measured pulse height spectra of isotopic gamma-ray sources and a moderated 10 Ci Am/Li neutron source. Imaging experiments were also performed in a polychromatic neutron beam using an electron-multiplying CCD. 1.5 MeV of electron equivalent light output was determined from pulse height spectra of the bulk glass which is comparable to commercial glasses. Light output for neutron events in the 2 mm thick bundled array was about 50% lower than the bulk sample but gamma rays were similarly affected. The 5 mm thick sample exhibited poorer light output with some asymmetry in the neutron capture peak that is associated with light losses in the fiber bundle. The neutron detection efficiency of the 2 and 5 mm thick detectors was 68 and 98%, respectively. Both detectors successfully imaged patterns fashioned from cadmium neutron absorbers and indicate a spatial resolution of approximately 250 ¿m. These data demonstrate the feasibility of this approach and further studies are underway to improve overall light output and spatial resolution.
Generation of an induced pluripotent stem cells line, CSSi014-A 9407, carrying the variant c.479C>T in the human iduronate 2-sulfatase (hIDS) gene (2022)

Mucopolysaccharidosis type II (Hunter Syndrome) is a rare X-linked inherited lysosomal storage disorder presenting a wide genetic heterogeneity. It is due to pathogenic variants in the IDS gene, causing the deficit of the lysosomal hydrolase iduronate 2-sulfatase, degrading the glycosaminoglycans (GAGs) heparan- and dermatan-sulfate. Based on the presence/absence of neurocognitive signs, commonly two forms are recognized, the severe and the attenuate ones. Here we describe a line of induced pluripotent stem cells, generated from dermal fibroblasts, carrying the mutation c.479C>T, and obtained from a patient showing an attenuated phenotype. The line will be useful to study the disease neuropathogenesis.
Effects of Solvent-Salt Charge-Transfer Complexes on Oxidative Stability of Li-Ion Battery Electrolytes (2018)

Electrochemical stability windows of electrolytes largely determine the limitations of operating regimes and energy density of Li-ion batteries but the controlling degradation mechanisms are difficult to characterize and remain poorly understood. We investigate the oxidative decomposition mechanisms governing high voltage stability of multi-component organic electrolytes using computational techniques of quantum chemistry. The intrinsic oxidation potential is modeled using vertical ionization potentials (IP) of ensembles of anion-solvent clusters generated using molecular dynamics. In some cases, the IP of the solvent-anion complex is significantly lower than that of each individual component. This effect is found to originate from the oxidation-driven charge transfer complex formation between the anion and the solvent. We propose a simple model to quantitatively understand this phenomenon and validate it for 16 combinations of common anions (4,5-dicyano-2-(trifluoromethyl)imidazolium, bis-(trifluoromethane solfonimmide), tetrafluroborate, hexafluorophosphate) and solvents (dimethyl sulfoxide, dimethoxyethane, propylene carbonate, acetonitrile). This new understanding of the microscopic details of oxidation allows us to interpret trends in published experimental and computational results and to formulate design rules for rapidly assessing stability of electrolyte compositions.
[Chronic osteomylitis in the standard animal model on the tibia head of rabbits]. (1979)

The making of a standardized model of a chronic osteomyelitis is represented. The standardized cavity in the tibia head of 7 x 12 x 5 mm is attainable by trepanation. A plastic body was inserted in the cavity. The cavity was inoculated with staphylococcus aureus after 4 weeks. The model is suitable for the assessment of different therapy methods and for the clarification of other questions, because of the control possibility of healing by exact methods.
A three-dimensional stochastic wire-length distribution for variable separation of strata (2002)

A complete wire-length distribution for future three-dimensional, homogeneous gigascale integrated (GSI) architectures with variable vertical separation of strata is derived. Because stratal pitch was not found to impact the wire-length distribution significantly, bonded three-dimensional implementations which are technologically feasible can be used to obtain large increases in global clock frequencies. The longest interconnect can be reduced by 30% through the introduction of a single additional stratum. A 93% reduction in the length of the longest interconnect can be obtained through the optimal use of a three-dimensional architecture for a 100 nm ASIC, potentially leading to a 15.8 times increase in global clock frequency.
Enablement, Evaluation and Extension of a CDM ESD Verification Tool for IC Level (2021)

A complex IC design marginally passes CDM targets during qualification. Employing the verification tool ESRA initially reveals CDM-uncritical voltages. Detailed testing beyond the CDM target levels and an extended tool setup provide valuable findings: pin-specific CDM robustness, design improvements, and the need to treat particular on-chip conductors as inductive components during CDM.
Connectivity in the presence of shadowing in 802.11 ad hoc networks (2005)

Connectivity is an important property for QoS support in mobile ad hoc networks (MANETs). Recently, there has been a big effort in exploring the critical transmission range (CTR) analytically, based on different network models. While most of these studies rely on a geometric model and come up with asymptotic bounds, their significance regarding finite 802.11 based MANETs is unclear. In this paper, we investigate connectivity in MANETs from a layered perspective. We first point out how the transmission range affects the end-to-end connection probability in a log-normal shadowing model and compare the results to theoretical bounds and measurements in the path loss model. We then show how connectivity issues behave in 802.11 and IP based networks if the fading effect increases. The paper concludes with an analytical model for the link probability in log-normal shadowing environments as a function of the number of nodes, network area, transmission range, path loss exponent and shadowing deviation.
From Conception to Realization: An Historial Account of Graphene and Some Perspectives for Its Future (2010)

There has been an intense surge in interest in graphene during recent years. However, graphene-like materials derived from graphite oxide were reported in 1962, and related chemical modifications of graphite were described as early as 1840. In this detailed account of the fascinating development of the synthesis and characterization of graphene, we hope to demonstrate that the rich history of graphene chemistry laid the foundation for the exciting research that continues to this day. Important challenges remain, however; many with great technological relevance.
Bioinformatics for Diagnostics, Forensics, and Virulence Characterization and Detection (2005)

We summarize four of our group's high-risk/high-payoff research projects funded by the Intelligence Technology Innovation Center (ITIC) in conjunction with our DHS-funded pathogen informatics activities. These are (1) quantitative assessment of genomic sequencing needs to predict high quality DNA and protein signatures for detection, and comparison of draft versus finished sequences for diagnostic signature prediction; (2) development of forensic software to identify SNP and PCR-RFLP variations from a large number of viral pathogen sequences and optimization of the selection of markers for maximum discrimination of those sequences; (3) prediction of signatures for the detection of virulence, antibiotic resistance, and toxin genes and genetic engineering markers in bacteria; (4) bioinformatic characterization of virulence factors to rapidly screen genomic data for potential genes with similar functions and to elucidate potential health threats in novel organisms. The results of (1) are being used by policy makers to set national sequencing priorities. Analyses from (2) are being used in collaborations with the CDC to genotype and characterize many variola strains, and reports from these collaborations have been made to the President. We also determined SNPs for serotype and strain discrimination of 126 foot and mouth disease virus (FMDV) genomes. For (3), currently &gt;1000 probes have been predicted for the specific detection of &gt;4000 virulence, antibiotic resistance, and genetic engineering vector sequences, and we expect to complete the bioinformatic design of a comprehensive ''virulence detection chip'' by August 2005. Results of (4) will be a system to rapidly predict potential virulence pathways and phenotypes in organisms based on their genomic sequences.