gebhart/patrepeval huggingface dataset:
N ‐Terminal myristoylation predictions by ensembles of neural networks (2004)

N-terminal myristoylation is a post-translational modification that causes the addition of a myristate to a glycine in the N-terminal end of the amino acid chain. This work presents neural network (NN) models that learn to discriminate myristoylated and nonmyristoylated proteins. Ensembles of 25 NNs and decision trees were trained on 390 positive sequences and 327 negative sequences. Experiments showed that NN ensembles were more accurate than decision tree ensembles. Our NN predictor evaluated by the leave-one-out procedure, obtained a false positive error rate equal to 2.1%. That was better than the PROSITE pattern for myristoylation for which the false positive error rate was 22.3%. On a recent version of Swiss-Prot (41.2), the NN ensemble predicted 876 myristoylated proteins, while 1150 proteins were predicted by the PROSITE pattern for myristoylation. Finally, compared to the well-known NMT predictor, the NN predictor gave similar results. Our tool is available under http://www.expasy.org/tools/myristoylator/myristoylator.html.
Scavenger Receptor, Class B, Type I-dependent Stimulation of Cholesterol Esterification by High Density Lipoproteins, Low Density Lipoproteins, and Nonlipoprotein Cholesterol (1998)

Scavenger receptor, class B, type I (SR-BI) is a cell surface glycoprotein that mediates selective uptake and efflux of sterols from high density lipoproteins (HDL) to cells. A Chinese hamster ovary cell line that is deficient in functional LDL receptors, but has high expression levels of recombinant SR-BI (ldlA7-SR-BI), was used to examine the effect of SR-BI on the trafficking of sterols between lipoproteins and cells. To monitor the fate of sterols transported by SR-BI into cells, we measured the incorporation of [14C]oleate into cholesterol esters by acyl-CoA:cholesteryl acyltransferase in the endoplasmic reticulum. We show that incubation of ldlA7-SRBI cells with either LDL or HDL resulted in an equally dramatic increase in the formation of [14C]oleate-labeled cholesterol esters. The lipoprotein-stimulated, SR-BI-dependent increase in cholesterol esterification was inhibited by chloroquine. The uptake of sterols and their incorporation into cholesterol esters by SR-BI from LDL was largely a selective process. The addition of free cholesterol to ldlA7-SRBI cells also stimulated cholesterol ester formation in a chloroquine-sensitive fashion. We also show that SR-BI mediates the efflux of endogenously synthesized sterols from the cell membrane. From these studies we conclude that, in the absence of the LDL receptor, overexpression of SR-BI can mediate significant transport of sterols between lipoproteins and the endoplasmic reticulum of cells.
Initial efficacy of anti-lymphocyte activation gene-3 (anti–LAG-3; BMS-986016) in combination with nivolumab (nivo) in pts with melanoma (MEL) previously treated with anti–PD-1/PD-L1 therapy. (2017)

9520 Background: Signaling via LAG-3 and other T-cell inhibitory receptors (eg, PD-1) can lead to T-cell dysfunction and tumor immune escape. Simultaneous blockade of LAG-3 + PD-1 may synergistically restore T-cell activation and enhance antitumor immunity. In a phase 1/2a study, BMS-986016 (IgG4 mAb targeting LAG-3) ± nivo (IgG4 mAb targeting PD-1) demonstrated tolerability, peripheral T-cell activation, and preliminary clinical activity (NCT01968109; Lipson E, et al. J Immunother Cancer. 2016;4[s1]:173 [P232]). Here we describe preliminary efficacy of BMS-986016 + nivo in pts with MEL whose disease progressed on/after prior anti–PD-1/PD-L1 therapy, along with updated safety from all dose expansion pts. Methods: Pts with MEL must have had prior anti–PD-1/PD-L1 (± anti–CTLA-4 or BRAF/MEK inhibitors) and progressive disease (PD). Pts received BMS-986016 80 mg + nivo 240 mg IV Q2W. Primary objectives were safety and objective response rate (ORR; complete [CR] + partial [PR] response), disease control rate (DCR; CR + uCR + PR + uPR + stable disease [SD] &gt; 12 wk), and duration of response (RECIST v1.1). Results: At data cutoff, 43 pts with MEL had been treated with BMS-986016 + nivo following PD on/after prior anti–PD-1/PD-L1 with known prior best responses of 1 CR, 9 PR, 12 SD, and 16 PD. Of the 43 pts, 30 (70%) also had prior anti–CTLA-4, 20 (47%) had ≥ 3 prior therapies, and 15 (35%) had BRAFmutations .In the 31 efficacy-evaluable pts to date, ORR was 16% (confirmed/unconfirmed) and DCR was 45% with benefit observed even in some pts refractory to prior anti–PD-1. Evaluations are ongoing for most pts, with median treatment duration of 10 wk for all 43 pts. Immunopathologic (eg, PD-1/PD-L1 and LAG-3 expression) and clinical characteristics of responders vs nonresponders will be presented. Any grade and grade 3/4 treatment-related AEs occurred in 46% and 9%, respectively, across all dose expansion pts (n = 129). Conclusion: Addition of BMS-986016 to nivolumab demonstrates encouraging initial efficacy in pts with MEL whose disease progressed on/after prior anti–PD-1/PD-L1 therapy, and a safety profile similar to nivolumab monotherapy. Clinical trial information: NCT01968109.
A role-based access control model and reference implementation within a corporate intranet (1999)

This paper describes NIST's enhanced RBAC model and our approach to designing and implementing RBAC features for networked Web servers. The RBAC model formalized in this paper is based on the properties that were first described in Ferraiolo and Kuhn [1992] and Ferraiolo et al. [1995], with adjustments resulting from experience gained by prototype implementations, market analysis, and observations made by Jansen [1988] and Hoffman [1996]. The implementation of RBAC for the Web (RBAC/Web) provides an alternative to the conventional means of administering and enforcing authorization policy on a server-by-server basis. RBAC/Web provides administrators with a means of managing authorization data at the enterprise level, in a manner consistent with the current set of laws, regulations, and practices.
The Adaptation of Existing Personal Inhalable Aerosol Samplers for Bioaerosol Sampling (1998)

Health-related monitoring of bioaerosol exposures in the workplace should ideally be carried out using size-selective personal samplers that separate the aerosol into biologically relevant size fractions and allow both quantification and identification of the microorganisms present in each fraction. As a first stage in the development of personal bioaerosol samplers a number of collection substrates were assessed for their ability to maintain the viability of the collected microorganisms, so that subsequent culturing and species identification may be carried out. The substrates were tested with bioaerosols of varying robustness, consisting of Saccharomyces cerevisiae cells, Escherichia coli cells, and Penicillium expansum spores, aerosolized under controlled environmental conditions. The survival of microorganisms on each test substrate, assessed on the basis of the culturable fractions of cells recovered, was compared with that of microorganisms collected in a reference glass cyclone sampler. These bioefficiency tests identified the substrate combinations with the potential to fulfill personal sampler design criteria. The substrates were then subjected to further development to evaluate and optimize their particle size selection characteristics. The outcome of this work is two prototype personal bioaerosol samplers in which size-selective substrates are adapted for use in existing designs of personal inhalable sampler. This offers an effective and low-cost solution to personal monitoring of bioaerosol exposures in the workplace.
Mouse CD20 expression and function (2003)

CD20 plays a role in human B cell proliferation and is an effective target for immunotherapy. In this study, mouse CD20 expression and biochemistry were assessed for the first time using a new panel of CD20-specific mAb, with CD20 function assessed using CD20-deficient (CD20(-/-)) mice. CD20 expression was B cell restricted and was initiated during late pre-B cell development. The frequency and density of CD20 expression increased during B cell maturation in the bone marrow, with a subpopulation of transitional IgM(hi) B cells expressing higher CD20 levels than the majority of mature recirculating B cells. Transitional T1 B cells in the spleen also expressed high CD20 levels, providing a useful new marker for this B cell subset. In CD20(-/-) mice, immature and mature B cell IgM expression was approximately 20-30% lower relative to B cells from wild-type littermates. In addition, CD19-induced intracellular calcium responses were significantly reduced in CD20(-/-) B cells, with a less dramatic effect on IgM-induced responses. These results reveal a role for CD20 in transmembrane Ca(2+) movement in mouse primary B cells that complements previous results obtained using human CD20 cDNA-transfected cell lines. Otherwise, B cell development, tissue localization, signal transduction, proliferation, T cell-dependent antibody responses and affinity maturation were normal in CD20(-/-) mice. Thus, mouse and human CD20 share similar patterns of expression and function. These studies thereby provide an animal model for studying CD20 function in vivo and the molecular mechanisms that influence anti-CD20 immunotherapy.
MALDI on a Chip:  Analysis of Arrays of Low-Femtomole to Subfemtomole Quantities of Synthetic Oligonucleotides and DNA Diagnostic Products Dispensed by a Piezoelectric Pipet (1997)

A piezoelectric pipet is used to dispense arrays of low-nanoliter aliquots of matrix and DNA into individual etched wells on <1 in.2 silicon chips prior to their semiautomated analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Spectrum acquisition is expedited relative to conventional “large-spot” MALDI since the resulting miniaturized samples are approximately the same size as the irradiation area of the ionization/desorption laser; thus, searching for crystal regions from which intense analyte signals may be obtained is not necessary. Using a linear TOF instrument designed for scanning high-density arrays of samples, mass spectra from as little as 0.2 fmol (45 nM) of a 36-mer DNA have been acquired from single miniature elements. Spot-to-spot reproducibility from microdispensed samples is superior to that using conventional pipets; in less than 6 min, spectra with high signal-to-noise ratios were acquired from 100 elements containing 8 fmol of a 25-mer. Low-nanoliter quantities of DNA diagnostic products generated in primer oligo base extension reactions from PCR templates were transferred to chips and analyzed by MALDI-TOF MS, giving accurate genotyping results for single base mutations and short tandem repeat polymorphisms (microsatellites). These procedures provide enabling capabilities for extremely accurate high-throughput DNA diagnostics and sequencing based on mass spectrometry.
High-Throughput High-Performance TDMA Through Pseudo-Orthogonal Carrier Interferometry Pulse Shaping (2004)

This letter provides a novel method for doubling throughput in time division multiple access (TDMA) systems. Specifically, with pseudo-orthogonal positioning of carrier interferometry pulse shapes, a TDMA system is designed to support twice as many real symbols in a slot, without increasing bandwidth or slot duration. With regard to performance, the doubling of throughput comes at the cost of only 1-2 dB performance degradations at probability of error of 10/sup -2/.
Recombinant bacillus Calmette–Guérin (BCG) vaccines expressing theMycobacterium tuberculosis30-kDa major secretory protein induce greater protective immunity against tuberculosis than conventional BCG vaccines in a highly susceptible animal model (2000)

Tuberculosis (TB) continues to ravage humanity, causing 2 million deaths per year. A vaccine against TB more potent than the current live vaccine, bacillus Calmette-Guérin (BCG), is desperately needed. Using two commercially available strains of BCG as host strains, BCG Connaught and Tice, we have constructed two recombinant BCG vaccines stably expressing and secreting the 30-kDa major secretory protein of Mycobacterium tuberculosis (M. tb.), the primary causative agent of TB. We have tested the efficacy of the two strains in the highly susceptible guinea pig model of pulmonary TB, a model noteworthy for its close resemblance to human TB. Animals immunized with the recombinant BCG vaccines and challenged by aerosol with a highly virulent strain of M. tb. had 0.5 logs fewer M. tb. bacilli in their lungs and 1 log fewer bacilli in their spleens on average than animals immunized with their parental conventional BCG vaccine counterparts. Statistically, these differences were highly significant. Paralleling these results, at necropsy, animals immunized with the recombinant BCG vaccines had fewer and smaller lesions in the lung, spleen, and liver and significantly less lung pathology than animals immunized with the parental BCG vaccines. The recombinant vaccines are the first vaccines against TB more potent than the current commercially available BCG vaccines, which were developed nearly a century ago.
NEONATAL RAT CARDIOMYOCYTES - A MODEL FOR THE STUDY OF MORPHOLOGICAL, BIOCHEMICAL AND ELECTROPHYSIOLOGICAL CHARACTERISTICS OF THE HEART (2001)

The neonatal rat cardiomyocyte model enables heart researchers to study and understand the morphological, biochemical and electrophysiological characteristics of the heart. This model offers a broad spectrum of experiments, such as studies of contraction, ischaemia, hypoxia and the toxicity of various compounds. This review examines the methodology for the isolation and cultivation of primary neonatal rat cardiomyocyte cultures, considers possible problems and pitfalls, and presents an optimized protocol for cardiomyocyte preparation.
The DAZL1 gene is expressed in human male and female embryonic gonads before meiosis (2000)

The human DAZL1 gene (known also as DAZH or DAZLA) is the autosomal homologue of the Y-chromosomal DAZ gene which has been found to be deleted in azoospermic males. Evidence suggests that the role of DAZL1 may not be restricted to spermatogenesis, but may include oogenesis as well. In order to study the function of human DAZL1 gene in the ovary, we observed its expression pattern during embryonic development. RNA in-situ hybridization showed that DAZL1 transcripts were localized to a subset of cells (somatic versus germ cells) in human embryonic ovary (23 weeks of gestation) and testis (21 weeks gestation). In the ovary, DAZL1 transcripts were found in oogonia and in oocytes and granulosa cells of primordial follicles. In the testis, DAZL1 transcripts were identified exclusively in the germ cells. Our results demonstrate high similarity between the human DAZL1 and the mouse Dazl1 gene expression patterns during embryonic development, suggesting that the human gene functions at the first phase of gametogenesis, just as in the mouse, where Dazl1 mutations cause male and female sterility.
对中国青年谈几点看法 美国生物化学家,1997年诺贝尔化学奖获得者 (2002)

你们这些正处在早期教育和职业选择的青年们。或许会对一位有幸获得诺贝尔奖的80岁老教授的某些思想产生兴趣.你们的祖国是一个伟大的国家,拥有灿烂的文化和杰出的人民.你们有能力为自己和他人建造举世瞩目的未来.我期望你们会这样做。并且要求你们这样做. 60年来,我所从
A Strategy To Estimate Unknown Viral Diversity in Mammals (2013)

Recent years have seen a dramatic increase in viral discovery efforts. However, most lack rigorous systematic design, which limits our ability to understand viral diversity and its ecological drivers and reduces their value to public health intervention. Here, we present a new framework for the discovery of novel viruses in wildlife and use it to make the first-ever estimate of the number of viruses that exist in a mammalian host. As pathogens continue to emerge from wildlife, this estimate allows us to put preliminary bounds around the potential size of the total zoonotic pool and facilitates a better understanding of where best to allocate resources for the subsequent discovery of global viral diversity.
All in-Focus View Synthesis from Under-Sampled Light Fields (2003)

Light field rendering (LFR) is a fundamental method for generating new views from a set of pre-acquired images. We use densely-aligned cameras for the process of acquiring the set of images. In most practical cases, the density of the aligned cameras is not high enough to synthesize appropriate views. This &amp;quot;under-sampling&amp;quot; condition causes focus-like effects in the synthesized views. This paper proposes a new method for solving this problem. First, a set of differently focused views is synthesized from the undersampled set of pre-acquired images. Then, an all in-focus view is generated from the set of differently focused views. This is based on a new focus measurement algorithm specialized for light field rendering and plenoptic sampling theory. Experimental results show the effectiveness of our approach.
Model for auditory localization (1976)

A mathematical model based on statistical decision theory has been devised to represent the human auditory localization task. The known localization cues have been represented as Gaussian random variables, so that their interaction in a given experiment can be analyzed (and predicted) along the lines of classical detection/estimation theory. We have applied this technique to most of the horizontal and vertical localization experiments reported in the literature during the past ten years, encompassing over 200 subjects and 20 000 trials. Using a nonlinear regression program we have been able to estimate the standard deviations of four of the auditory localization cues, allowing objective comparison of their relative accuracy. The resulting model provides a relatively good fit to the published results on 40 localization experiments. Subject Classification: [43]65.62, [43]65.58, [43]65.35.
Human Embryonic and Mesenchymal Stem Cells Express Different Nuclear Proteomes (2008)

Human embryonic stem cells (hESCs) are characterized by their immortality and pluripotency. Human mesenchymal stem cells (hMSC), on the other hand, have limited self-renewal and differentiation capabilities. The underlying molecular differences that account for this characteristic self-renewal and plasticity are, however, poorly understood. This study reports a nuclear proteomic analysis of human embryonic and bone marrow-derived mesenchymal stem cells. Our proteomic screen highlighted a 5-fold difference in the expression of Reptin52. We show, using two-dimensional difference gel electrophoresis (2-DIGE), western analysis, and quantitative reverse transcriptase polymerase chain reaction, that Reptin52 is more abundantly expressed in hESC than hMSC. Moreover, we observed differential expression of Pontin52 and beta-catenin-proteins known to interact with Reptin52. This difference in the expression of Reptin52 and Pontin52 (known regulators of beta-catenin) further supports a role for Wnt signaling in stem cell self-renewal and proliferation.
Acceleration of B-lymphoid tumorigenesis in E mu-myc transgenic mice by v-H-ras and v-raf but not v-abl. (1989)

Emu-myc transgenic mice constitutively express the c-myc oncogene from before birth, but their inexorable development of B-lymphoid tumors appears to require rare spontaneous alterations within B-lineage cells. To determine whether other oncogenes can cooperate with myc to induce B-lymphoid transformation, we infected neonatal Emu-myc mice and normal littermates with helper-free retroviruses bearing the v-H-ras, v-raf, or v-abl oncogene. The v-H-ras and the v-raf oncogene dramatically accelerated Emu-myc pre-B-lymphoma onset, whereas v-abl did not, despite the increased numbers of presumptive target pre-B cells in Emu-myc mice. These results imply that v-H-ras and v-raf synergize with deregulated myc expression to transform pre-B cells, while v-abl apparently does not.
Schottky barrier height and interface chemistry of annealed metal contacts to alpha 6H-SiC: Crystal face dependence (1993)

The electrical properties and interface chemistry of unannealed and annealed Ni, Ti, and Al contacts to both Si (0001) and C (0001̄) terminated faces of 6H-SiC are compared by using x-ray photoemission spectroscopy, current-voltage, and capacitance-voltage data. For annealing temperatures in the 400 to 600 °C range Ni and Ti contacts have significantly more dissociation of interface SiC and formation of reaction products for the C-face than the Si-face. The chemical reactivity of the Al contact was limited and equal for both faces. Stability of the Schottky barrier height with annealing, which has a wide variation according to metal and face, is not correlated with the degree of metal/6H-SiC interface chemical reactivity
NK Cells and Polymorphonuclear Neutrophils Are Both Critical for IL-2-Induced Pulmonary Vascular Leak Syndrome (2004)

The mechanism of IL-2-induced vascular leak syndrome (VLS) is still poorly understood. Cells of both innate and adaptive immune systems have been implicated, but no definitive conclusions have been reached concerning their respective roles. In this study we report a new mouse model of IL-2-induced pulmonary VLS used to obtain a detailed analysis of the early events (sequestration of polymorphonuclear neutrophils and bronchoconstriction) and late events (modifications in the cell and protein content of bronchoalveolar lavages, followed by edema) that characterize this lung injury. This model and knockout animals are used to reconsider the importance of the different leukocyte lineages in early and late events. Recombinase-activating gene 2(-/-) mice are used to demonstrate that adaptive lymphocytes, including NK T cells, are not required for pulmonary VLS induction. By contrast, results obtained with newly described recombinase-activating gene 2(-/-)/IL-15(-/-) mice indicate that NK cells play a key role in both early and late events. In parallel, polymorphonuclear neutrophil depletion is used to evaluate the contributions made by these cells to the late alterations occurring in the lung. Furthermore, when used in combination with inhibition of NO synthase, granulocyte depletion was completely effective in protecting mice from the late events of IL-2-induced pulmonary VLS. Together our results indicate that both NK and PMN cells play a central role in the late events of IL-2-induced VLS.
About the safety of stevioside used as a sweetener (2004)

Journal of Food, Agriculture & Environment, Vol.2 (3&4), August&December 2004safety aspects and risk assessment, and discussed the metabolism of oral stevioside in humans. The general conclusion of the symposium wasthat stevioside used as a sweetener is safe.It was also decided that the full texts of the lectures will be published as “Proceedings of the first symposium on the “Safety of Stevioside”available at Euprint, Parkbosstraat 3, 3001 Heverlee, Belgium. Email: info@euprint.be.
Expression of integrin alpha v beta 6 in rats with ventilator-induced lung injury and the attenuating effect of synthesized peptide S247. (2008)

Pretreatment with S247 attenuated VILI, suggesting pulmonary epithelial integrins are involved in its pathogenesis and agents such as S247 may be useful in treating it.
Review of Inman et al. “An Introduction to Forensic DNA Analysis” (1998)

Abstract The two qualified authors of this attractive, spiral-bound handbook have attempted to expand a previous publication and, simultaneously, to translate “science into English” (p.1). Novices are presented with a number of instructive presentations in both narrative and illustrative formats. Some chapters (e.g., Chapter 7) are succinct, accurate and especially helpful to a beginner. Some appendices and references provide the reader with ready information and means of learning more about specific subjects. The index appears complete and accurate. The illustrations and the paper on which they are printed are of high quality. Unfortunately, the authors have only partly succeeded in meeting their two objectives. I hope the next version of the work will address the issues cited below.