gebhart/patrepeval huggingface dataset:
The 2019 novel coronavirus resource. (2020)

An ongoing outbreak of a novel coronavirus infection in Wuhan, China since December 2019 has led to 31,516 infected persons and 638 deaths across 25 countries (till 16:00 on February 7, 2020). The virus causing this pneumonia was then named as the 2019 novel coronavirus (2019-nCoV) by the World Health Organization. To promote the data sharing and make all relevant information of 2019-nCoV publicly available, we construct the 2019 Novel Coronavirus Resource (2019nCoVR, https://bigd.big.ac.cn/ncov). 2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the Global Initiative on Sharing All Influenza Data, National Center for Biotechnology Information, China National GeneBank, National Microbiology Data Center and China National Center for Bioinformation (CNCB)/National Genomics Data Center (NGDC). It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains. Moreover, by linking seamlessly with related databases in CNCB/NGDC, 2019nCoVR offers virus data submission and sharing services for raw sequence reads and assembled sequences. In this report, we provide comprehensive descriptions on data deposition, management, release and utility in 2019nCoVR, laying important foundations in aid of studies on virus classification and origin, genome variation and evolution, fast detection, drug development and pneumonia precision prevention and therapy.
MS for Identification of Single Nucleotide Polymorphisms and MS/MS for Discrimination of Isomeric PCR Products (2000)

ESI (electrospray ionization) MS and tandem mass spectrometry (MS/MS) were used for the analysis of single nucleotide polymorphisms (SNPs) and more complex genetic variations. Double-stranded (ds) PCR products were studied. PCR products of the proline [5'-x(G17)-x(C38)x-3'] and arginine variants [(5'-x(Gl7)-x(G38)x-3'] of the p53 gene are distinguished by an SNP (cytosine or guanine) and were discriminated using both quadrupole and quadrupole ion trap MS analysis. A 69 bp arginine mutant PCR product [5'-x(C17)-x(G38)x-3'] with a negating switch has the same mass as the proline variant but was readily distinguishable on ion trap MS/MS analysis; fragments containing the mutation site, but not the polymorphism, were identified. The 69 bp PCR products were restriction-enzyme-digested, to create 43 bp fragments. ESI quadrupole ion trap MS/MS analysis of the 43 bp product-ion spectra readily demonstrated both polymorphism and negating switch sites. MS and MS/MS are powerful and complementary techniques for analysis of DNA. MS can readily distinguish SNPs but MS/MS is required to differentiate isomeric PCR products (same nucleotide composition but different sequence).
Effect of Confinement on Proton Transport Mechanisms in Block Copolymer/Ionic Liquid Membranes (2012)

Nanostructured membranes containing structural and proton-conducting domains are of great interest for a wide range of applications requiring high conductivity coupled to high thermal stability. Understanding the effect of nanodomain confinement on proton-conducting properties in such materials is essential for designing new, improved membranes. This relationship has been investigated for a lamellae-forming mixture of poly(styrene-b-2-vinyl pyridine) (PS-b-P2VP) with ionic liquid composed of imidazole and bis(trifluoromethylsulfonyl)imide, where the ionic liquid selectively resides in the P2VP domains of the block copolymer. Quasi-elastic neutron scattering and NMR diffusion measurements reveal increased prevalence of a fast proton hopping transport mechanism, which we hypothesize is due to changes in the hydrogen bond structure of the ionic liquid under confinement. This, in combination with unique ion aggregation behavior, leads to a lower activation energy for macroscopic ion transport compared with that in a mixture of ionic liquid with P2VP homopolymer. The proton transference number in both samples is significantly higher than that in the neat ionic liquid, which could be taken advantage of for applications such as proton exchange membrane fuel cells and actuators. These results portend the rational design of nanostructured membranes having improved mechanical properties and conductivity.
Proteomics of human body fluids : principles, methods, and applications (2007)

PROTEOMICS OF HUMAN BODY FLUIDS: Principles, Methods, and Applications' EDITOR: VISITH THONGBOONKERD, MD, FRCPT Table of Contents Preface Part I: Principles of Proteomics Applied to Human Body Fluids 1. Proteomic Strategies for Analyzing Body Fluids Sung-Min Ahn Richard J. Simpson* 2. Sample Preparation of Body Fluids for Proteomics Analysis Natalia Govorukhina Rainer Bischoff* 3. Multiplexed Immunoassays for Protein Profiling in Human Body Fluids Silke Wittemann Dominic P. Eisinger Laurie L. Stephen Thomas O. Joos* 4. Deciphering the Hieroglyphics of Functional Proteomics Using Small Molecule Probes Wayne F. Patton* 5. Modification-Specific Proteomic Analysis of Glycoproteins in Human Body Fluids by Mass Spectrometry Jakob Bunkenborg Per Hagglund Ole N. Jensen* 6. Plasma Proteome Database Malabika Sarker G. Hanumanthu Akhilesh Pandey* 7. 2-D PAGE Databases for Proteins in Human Body Fluids Christine Hoogland* Khaled Mostaguir Jean-Charles Sanchez Denis F. Hochstrasser Ron D. Appel 8. Bioinformatics and Experimental Design for Biomarker Discovery Marc R. Wilkins* Sybille M. N. Hunt 9. Integrative Omics, Pharmacoproteomics and Human Body Fluids K. K. Jain* Part II: Proteomic Analysis of Specific Types of Human Body Fluids: Methods, Findings, Applications, Perspectives, and Future Directions 10. The Human Plasma Proteome Gilbert S. Omenn* Raji Menon Marcin Adamski Thomas Blackwell Brian B. Haab Weimin Gao David J. States 11. Proteomics of Human Urine Visith Thongboonkerd* Pedro R. Cutillas Robert J. Unwin Stefan Schaub Peter Nickerson Marion Haubitz Harald Mischak Dobrin Nedelkov Urban Kiernan Randall W. Nelson 12. Proteomics of Human Cerebrospinal Fluid Margareta Ramstrom Jonas Bergquist* 13. Proteomics of Pleural Effusion Joost Hegmans* Annabrita Hemmes Bart N. Lambrecht 14. Proteomics of Bronchoalveolar Lavage Fluid and Sputum Ruddy Wattiez* Olivier Michel Paul Falmagne 15. Proteomics of Sinusitis Nasal Lavage Fluid Begona Casado*,# Simona Viglio James N. Baraniuk 16. Proteomics of Human Saliva Francisco M. L. Amado* Rui M. P. Vitorino Maria J. C. Lobo Pedro M. D. N. Domingues 17. Proteomics of Human Pancreatic Juice Mads Gronborg Anirban Maitra Akhilesh Pandey* 18. Proteomics of Human Bile Troels Z. Kristiansen Anirban Maitra Akhilesh Pandey* 19. Proteomics of Amniotic Fluid David Crettaz Lynne Thadikkaran Denis Gallot Pierre-Alain Queloz Vincent Sapin Joel S. Rossier Patrick Hohlfled Jean-Daniel Tissot* 20. Proteomics of Human Milk Amedeo Conti* Maria G. Giuffrida Maria Cavaletto 21. Proteomics of Nipple Aspirate Fluid in Non-Lactating Women Edward R. Sauter* 22. Proteomics of Seminal Fluid Benjamin Solomon Mark W. Duncan* 23. Proteomics of Vitreous Fluid Atsushi Minamoto* Ken Yamane Tomoko Yokoyama 24. Proteomics of Human Dialysate and Ultrafiltrate Fluids Yielded by Renal Replacement Therapy Michael Walden Stefan Wittke Harald Mischak Raymond C. Vanholder For the European Uremic Toxin Work Group (EUTox)
Analysis of T cell reactivities to phosphorylcholine‐conjugated hen egg lysozyme in C57BL/6 mice: hapten‐conjugate specificity reflects an altered expression of a major carrier epitope (1991)

We have selected several different T cell hybridoma clones reactive to hen egg lysozyme (HEL) conjugated to phosphorylcholine (PC) after fusion of PC-HEL-primed C57BL/6 lymphocytes with BW5147 parent cells. These hybridoma clones preferentially recognize PC-HEL over unconjugated HEL, but not other carrier molecules conjugated with the same hapten. All the PC-HEL-reactive clones are similarly responsive to not only p-azobenzenearsonate (ABA)-conjugated HEL (ABA-HEL) but also to a variety of other diazotized hapten-HEL conjugates. However, these clones are not stimulated by fluoresceinated or dinitrophenylated HEL beyond the level of HEL carrier alone. Therefore, the type of hapten linkage (diazonium) to the carrier molecule appears to affect T cell recognition. The hybridoma clones apparently recognize the carrier molecule alone, although the level of stimulation is relatively low compared to that induced by either PC-HEL or ABA-HEL. Interestingly, HEL unfolded by S-carboxymethylation is capable of stimulating the hybridomas to a level comparable to that obtained with PC-HEL. T cell recognition of the unfolded HEL is independent of antigen processing, which is different from that of PC-HEL. The peptide sequence corresponding to the amino acids 81-93 of HEL appears to contain the epitope region for the hybridoma clones based on testing stimulation activity with synthetic peptides. Previously, the peptides including this region (81-96) have been reported as the determinant recognized by T cells derived from C57BL/6 mice after immunization with an HEL peptide (HEL 13-105) but not with native HEL. These results suggest that a hapten conjugation via diazonium linkage modifies antigen presentation and consequently the presentation of the major T cell epitopes similar to that of the HEL fragment.
Leukotrienes enhance the bactericidal activity of alveolar macrophages against Klebsiella pneumoniae through the activation of NADPH oxidase (2005)

Leukotrienes (LTs) are lipid mediators that participate in inflammatory diseases and innate immune function. We sought to investigate the importance of LTs in regulating the microbicidal activity of alveolar macrophages (AMs) and the molecular mechanisms by which this occurs. The role of LTs in enhancing AM microbicidal activity was evaluated pharmacologically and genetically using in vitro challenge with Klebsiella pneumoniae. Exogenous LTs increased AM microbicidal activity in a dose- and receptor-dependent manner, and endogenous production of LTs was necessary for optimal killing. Leukotriene B4 (LTB4) was more potent than cysteinyl LTs. An important role for nicotinamide adenine dinucleotide (NADPH) oxidase in LT-induced microbicidal activity was indicated by the fact that bacterial killing was abrogated by the NADPH oxidase inhibitor diphenyleneiodonium (DPI; 10 microM) and in AMs derived from gp91phox-deficient mice. By contrast, LT-induced microbicidal activity was independent of the generation of nitric oxide. LTs increased H2O2 production, and LTB4 was again the more potent agonist. Both classes of LTs elicited translocation of p47phox to the cell membrane, and LTB4 induced phosphorylation of p47phox in a manner dependent on protein kinase C-delta (PKC-delta) activity. In addition, the enhancement of microbicidal activity by LTs was also dependent on PKC-delta activity. Our results demonstrate that LTs, especially LTB4, enhanceAM microbicidal activity through the PKC-delta-dependent activation of NADPH oxidase.
Intratumoral Genomic Heterogeneity in Advanced Head and Neck Cancer Detected by Comparative Genomic Hybridization (2004)

We demonstrate a high individual variation of intratumoral genomic heterogeneity depending on the localization and selection of matched pairs. These findings are of specific importance in view of establishing prognostic markers.
Suppressing TGFβ Signaling in Regenerating Epithelia in an Inflammatory Microenvironment Is Sufficient to Cause Invasive Intestinal Cancer (2015)

Genetic alterations in the TGFβ signaling pathway in combination with oncogenic alterations lead to cancer development in the intestines. However, the mechanisms of TGFβ signaling suppression in malignant progression of intestinal tumors have not yet been fully understood. We have examined Apc(Δ716) Tgfbr2(ΔIEC) compound mutant mice that carry mutations in Apc and Tgfbr2 genes in the intestinal epithelial cells. We found inflammatory microenvironment only in the invasive intestinal adenocarcinomas but not in noninvasive benign polyps of the same mice. We thus treated simple Tgfbr2(ΔIEC) mice with dextran sodium sulfate (DSS) that causes ulcerative colitis. Importantly, these Tgfbr2(ΔIEC) mice developed invasive colon cancer associated with chronic inflammation. We also found that TGFβ signaling is suppressed in human colitis-associated colon cancer cells. In the mouse invasive tumors, macrophages infiltrated and expressed MT1-MMP, causing MMP2 activation. These results suggest that inflammatory microenvironment contributes to submucosal invasion of TGFβ signaling-repressed epithelial cells through activation of MMP2. We further found that regeneration was impaired in Tgfbr2(ΔIEC) mice for intestinal mucosa damaged by DSS treatment or X-ray irradiation, resulting in the expansion of undifferentiated epithelial cell population. Moreover, organoids of intestinal epithelial cells cultured from irradiated Tgfbr2(ΔIEC) mice formed "long crypts" in Matrigel, suggesting acquisition of an invasive phenotype into the extracellular matrix. These results, taken together, indicate that a simple genetic alteration in the TGFβ signaling pathway in the inflamed and regenerating intestinal mucosa can cause invasive intestinal tumors. Such a mechanism may play a role in the colon carcinogenesis associated with inflammatory bowel disease in humans.
B-Type Natriuretic Peptide: Endogenous Regulator of Myocardial Structure, Biomarker and Therapeutic Target (2009)

B-type natriuretic peptide (BNP), initially identified in brain tissues, is now recognized as a key cardiac hormone. Numerous studies over the last decade have demonstrated that both exogenous and endogenous BNP prevent left ventricular (LV) hypertrophy in experimental settings, largely via activation of particulate guanylyl cyclase (pGC)-coupled receptors. BNP represents somewhat of a paradox, in that upregulation of BNP expression is widely used as a diagnostic marker for LV hypertrophy, diastolic dysfunction and heart failure in the clinic. We and others have postulated that BNP serves as an endogenous brake on the LV myocardium, seeking to curb the runaway train of signaling pathways that drive the progression from LV hypertrophy though remodeling, heart failure and death. This review summarizes the mechanisms of BNP's antihypertrophic actions, the role for cyclic GMP-mediated inhibition of pro-hypertrophic signaling, and BNP's impact on LV function. The improved understanding of the mechanisms of BNP regulation of LV hypertrophy and function that has emerged from both the experimental and clinical experience with this peptide provides new insight into the potential that BNP pharmacotherapy still offers for patients with LV hypertrophy.
Free to Follow (2014)

Tibetan Buddhism prospers in northwest China’s Qinghai Province Since its introduction to the region in the seventh century,Buddhism has become deeply rooted in the culture of the local people of the Qinghai-Tibet Plateau,particularly among the Tibetan ethnic group.All practitioners and believers consider themselves followers of the teachings of the Buddha,Sakyamuni.Located mostly on the Qinghai-Tibet Plateau,Qinghai Province has an ethnic Tibetan population of more than 1.37 million.Religious activities in Qinghai are rich in their content and
Accumulation of fibronectin in the heart after myocardial infarction: a putative stimulator of adhesion and proliferation of adipose-derived stem cells (2008)

Stem cell therapy is a promising treatment after myocardial infarction (MI). A major problem in stem cell therapy, however, is that only a small proportion of stem cells applied to the heart can survive and differentiate into cardiomyocytes. We hypothesized that fibronectin in the heart after MI might positively affect stem cell adhesion and proliferation at the site of injury. Therefore, we investigated the kinetics of attachment and proliferation of adipose-tissue-derived stem cells (ASC) on fibronectin and analysed the time frame and localization of fibronectin accumulation in the human heart after MI. ASCs were seeded onto fibronectin-coated and uncoated culture wells. The numbers of adhering ASC were quantified after various incubation periods (5-30 min) by using DNA quantification assays. The proliferation of ASC was quantified after culturing ASC for various periods (0-9 days) by using DNA assays. Fibronectin accumulation after MI was quantified by immunohistochemical staining of heart sections from 35 patients, after different infarction periods (0-14 days old). We found that ASC attachment and proliferation on fibronectin-coated culture wells was significantly higher than on uncoated wells. Fibronectin deposition was significantly increased from 12 h to 14 days post-infarction, both in the infarction area and in the border-zone, compared with the uninfarcted heart. Our results suggest that a positive effect of fibronectin on stem cells in the heart can only be achieved when stem cell therapy is applied at least 12 h after MI, when the accumulation of fibronectin occurs in the infarcted heart.
Giant Room-Temperature Piezoresistance in a Metal-Silicon Hybrid Structure (2008)

Metal-semiconductor hybrids are artificially created structures presenting novel properties not exhibited by either of the component materials alone. Here we present a giant piezoresistance effect in a hybrid formed from silicon and aluminum. The maximum piezoresistive gage factor of 843, measured at room temperature, compares with a gage factor of -93 measured in the bulk homogeneous silicon. This piezoresistance boost is not due to the silicon-aluminum interface, but results from a stress induced anisotropy in the silicon conductivity that acts to switch current away from the highly conductive aluminum for uniaxial tensile strains. Its magnitude is shown, via the calculation of hybrid resistivity weighting functions, to depend only on the geometrical arrangement of the component parts of the hybrid.
Dietary Estrogens Act through Estrogen Receptor-Mediated Processes and Show No Antiestrogenicity in Cultured Breast Cancer Cells. (1994)

Dietary estrogens are believed to exert their estrogenic or antiestrogenic (chemopreventive) action in estrogen responsive cells by interacting with the estrogen receptor (ER). The present study was undertaken to evaluate a direct role of ER in estrogenic or antiestrogenic activities of three dietary estrogens (coumestrol, genistein and zearalenone). HeLa cells were transiently co-transfected with an expression vector for ER and an estrogen-responsive reporter gene construct. Coumestrol, genistein, and zearalenone all increased the activity of the reporter gene, only in the presence of the ER, and the activation was blocked with the ER antagonist ICI 164,384, demonstrating an ER-specific, agonist response. In addition, in MCF-7 cells, coumestrol and zearalenone increased the expression of the estrogen-responsive pS2 gene. Coumestrol and genistein inhibited the purified estrogen-specific 17ß-hydroxysteroid oxidoreductase enzyme and the conversion of estrone to 17ß-estradiol in T-47D cells, which contain this enzyme. However, they did not inhibit the estrone-induced proliferation of T-47D cells. In conclusion, coumestrol, genistein, and zearalenone are all potent estrogens in vitro, and they act through ER mediated mechanism. Our findings give no evidence to support the idea that these compounds act as antiestrogens through competition for the binding sites of ER or by inhibition of the conversion of estrone to 17ß-estradiol in breast cancer cells, since this effect was nullified by their agonist action on cell proliferation. Therefore, their suggested chemopreventive action in estrogen-related cancers must be mediated through other mechanisms.
Silicon waveguide infrared photodiodes with >35 GHz bandwidth and phototransistors with 50 AW-1 response (2009)

SOI CMOS compatible Si waveguide photodetectors are made responsive from 1100 to 1750 nm by Si+ implantation and annealing. Photodiodes have a bandwidth of >35 GHz, an internal quantum efficiency of 0.5 to 10 AW-1, and leakage currents of 0.5 nA to 0.5 microA. Phototransistors have an optical response of 50 AW-1 with a bandwidth of 0.2 GHz. These properties are related to carrier mobilities in the implanted Si waveguide. These detectors exhibit low optical absorption requiring lengths from <0.3 mm to 3 mm to absorb 50% of the incoming light. However, the high bandwidth, high quantum efficiency, low leakage current, and potentially high fabrication yields, make these devices very competitive when compared to other detector technologies.
Nutrition in the elderly (2002)

It is now well accepted that older persons experience a physiologic anorexia, the anorexia of aging, which is caused by alterations in hedonic qualities of food, fundal compliance, and increased leptin levels. Depression is the most common pathologic cause of weight loss in older persons. Older persons fail to recognize thirst and as such have an increased risk of dehydration. Alterations in brain membrane fatty acids can lead to cognitive impairment in older persons.
Improved PeT Molecules for Optically Sensing Voltage in Neurons (2015)

VoltageFluor (VF) dyes have the potential to measure voltage optically in excitable membranes with a combination of high spatial and temporal resolution essential to better characterize the voltage dynamics of large groups of excitable cells. VF dyes sense voltage with high speed and sensitivity using photoinduced electron transfer (PeT) through a conjugated molecular wire. We show that tuning the driving force for PeT (ΔGPeT + w) through systematic chemical substitution modulates voltage sensitivity, estimate (ΔGPeT + w) values from experimentally measured redox potentials, and validate the voltage sensitivities in patch-clamped HEK cells for 10 new VF dyes. VF2.1(OMe).H, with a 48% ΔF/F per 100 mV, shows approximately 2-fold improvement over previous dyes in HEK cells, dissociated rat cortical neurons, and medicinal leech ganglia. Additionally, VF2.1(OMe).H faithfully reports pharmacological effects and circuit activity in mouse olfactory bulb slices, thus opening a wide range of previously inaccessible applications for voltage-sensitive dyes.
Alternative Pathway of Complement in Children with Diarrhea-Associated Hemolytic Uremic Syndrome (2009)

Patients with acute-onset D+HUS manifest activation of the AP of complement that is temporally related to the onset of disease and that resolves within 1 mo. Therapies to inhibit the AP of complement may be useful in attenuating the severity of renal injury and extrarenal complications.
Your GAS experiment and the media or why does that other can get all of the publicity (1993)

NASA has flown almost 100 Get Away Special (GAS) cans. Only a few of them are remembered by the general public, including the 'snowflakes in space' from STS-6, 'ants in space' from STS-7, and CanDO from STS-57. Why do some GAS cans get all of the publicity, while others are barely mentioned in press conferences, press kits, and on NASA Select during the mission? How can you make sure your GAS can gets as much attention as the others on your flight? And why is it important for you to make sure the public finds out about your activities? Writer Philip Chien has covered the space program since 1983, and is a regular participant in GAS press conferences. This paper will use STS-57 as a case study showing why some GAS cans got more publicity than others. The paper will offer advice for upcoming GAS payloads and how to prepare your press kits and other handouts.