gebhart/patrepeval huggingface dataset:
Computer Identification of Bacteria on the Basis of Their Antibiotic Susceptibility Patterns (1973)

A computer program utilizing a Baysean mathematical model was developed to identify bacteria solely on the basis of their antibiotic sensitivities. The model contains probability data on the antibiotic sensitivity patterns for 31 species of bacteria, which account for over 99% of all isolates submitted to our laboratory for testing. During a 4-month test period, antibiotic sensitivity data on 1,000 clinical isolates were processed by the program. The identification achieved by using the model was the same as that of the laboratory for over 86% of the isolates.
Quality of life of Hurler syndrome patients after successful hematopoietic stem cell transplantation (2017)

Hurler syndrome (HS) is a lysosomal storage disease characterized by multisystem morbidity and death in early childhood. Hematopoietic stem cell transplantation (HSCT) results in long-term survival, although with significant residual disease burden. How this residual disease affects the health-related quality of life is unknown. Therefore, we conducted a multicenter cohort study on functional and psychosocial health and compared the outcomes to normative data using the Child Health Questionnaire and Pediatric Outcomes Data Collection Instrument. Perception of care was evaluated by the Measure of Processes of Care questionnaire. Sixty-three HS patients receiving HSCT with at least 3 years of follow-up after HSCT were included. The influence of potential predictors was analyzed using linear regression analysis, and correlation analysis was performed using Spearman rank correlation. Functional health of transplanted HS patients was significantly diminished compared with normative data (median physical summary <i>z</i> score, -2.4 [range, -3.5 to -1.6]; median global functioning <i>z</i> score, -3.2 [range, -4.8 to -1.8]). Psychosocial health was comparable or only slightly reduced compared with healthy peers (median psychosocial summary <i>z</i> score, 0.15 [range, -0.7 to 0.8]). A higher obtained lysosomal enzyme level post-HSCT predicted for superior functional health. Overall, parents were satisfied with the care received. Functional health of transplanted HS patients appeared significantly more affected than psychosocial health. To improve functional health, the use of only noncarrier donors and striving to achieve full-donor chimerism, both resulting in higher enzyme levels, is advised. Assessing the health-related quality of life could play an important role in evaluating outcomes of HS patients receiving novel (cell) therapies, including autologous gene-transduced HSCT.
Ongoing efforts to generate "Tagged PDF" using pdfTEX (2009)

Abstract. Recently PDF has been accepted as a standard for production of electronic documents, as ISO 32000-1:2008, with an acronym of PDF/UA (for “Universal Accessibility”). The second draft ISO 32000-2:2009 is to include specifications for including MathML tagging of mathematical environments and expressions. This talk presents a report on work-in-progress, aimed at: (a) developing the primitive commands for pdfTEX needed to support the production of fully tagged PDF documents; (b) writing appropriate TEX and L ATEX macros to make effective use of the new primitives; (c) authoring changes to internal L ATEX structures to use these macros automatically at appropriate places within the existing code-base for L ATEX. This is work that is being undertaken together with Hàn Thê ´ Thành, author of pdfTEX [2], who has added some new primitive commands to an experimental version of this software tool.
Soluble ?-galactosyl-binding lectin (galectin) from toad ovary: Crystallographic studies of two protein-sugar complexes (2000)

Galectin-1, S-type beta-galactosyl-binding lectins present in vertebrate and invertebrate species, are dimeric proteins that participate in cellular adhesion, activation, growth regulation, and apoptosis. Two high-resolution crystal structures of B. arenarum galectin-1 in complex with two related carbohydrates, LacNAc and TDG, show that the topologically equivalent hydroxyl groups in the two disaccharides exhibit identical patterns of interaction with the protein. Groups that are not equivalent between the two sugars present in the second moiety of the disaccharide, interact differently with the protein, but use the same number and quality of interactions. The structures show additional protein-carbohydrate interactions not present in previously reported lectin-lactose complexes. These contacts provide an explanation for the enhanced affinity of galectin-1 for TDG and LacNAc relative to lactose. Galectins are in dimer-monomer equilibrium at physiological protein concentrations, suggesting that this equilibrium may be involved in organ-specific regulation of activity. Comparison of B. arenarum with other galectin-1 structures shows that among different galectins there are significant changes in accessible surface area buried upon dimer formation, providing a rationale for the variations observed in the free-energies of dimerization. The structure of the B. arenarum galectin-1 has a large cleft with a strong negative potential that connects the two binding sites at the surface of the protein. Such a striking characteristic suggests that this cleft is probably involved in interactions of the galectin with other intra or extra-cellular proteins. Proteins 2000;40:378-388.
Protein from petroleum (1972)

The first published report that hydrocarbons were subject to microbial degradation appears to be that of the Japanese botanist Miyoshi in 1895. He observed that certain alkanes were attacked by the fungus Botrytis Cinerea. The first reports of microbial oxidation of methane, the simplest alkane, were made about 10 years later by Kaserer (1905), and Sohngen (1905). According to the recent review of Quayle (1967), the ability to utilise hydrocarbons is widespread amongst micro‐organisms. The ability to grow on methane appears to be a more restricted property although Whittenbury, Phillips and Wilkinson (1970) have recently isolated more than 100 strains of methane utilising bacteria.
Chondroitin sulphate covalently cross‐links the three polypeptide chains of inter‐α‐trypsin inhibitor (1994)

Inter-alpha-trypsin inhibitor (ITI) is a tight complex of three different proteins: bikunin and two heavy chains H1 and H2. In order to demonstrate that the three chains are covalently linked by a chondroitin sulphate chain as previously proposed [Enghild, J. J., Salvesen, G., Hefta, S. A., Thogersen, I. B., Rutherford, S. and Pizzo, S. V. (1991) J. Biol. Chem. 266, 747-751], ITI was extensively digested with thermolysin and the glycosaminoglycan-containing fragment was isolated from the digest by ion-exchange chromatography. Its peptide structural determination and mass spectrometry analysis both provide evidence that the different peptide chains constituting ITI are associated by the new cross-link described as the protein-glycosaminoglycan-protein cross-link.
Towards Prioritizing GitHub Issues (2020)

The vast growth in usage of GitHub by developers to host their projects has led to extensive forking and open source contributions. These contributions occur in the form of issues that report bugs or pull requests to either fix bugs or add new features to the project. On the other hand, massive increase in the number of issues reported by developers and users is a major challenge for integrators, as the number of concurrent issues to be handled is much higher than the number of core contributors. While there exists prior work on prioritizing pull requests, in this paper we make an attempt towards prioritizing issues using machine learning techniques. We present the Issue Prioritizer, a tool to prioritize issues based on three criteria: issue lifetime, issue hotness and category of the issue. We see this work as an initial step towards supporting developers to handle large volumes of issues in projects.
An authentication scheme for fast handover between WiFi access points (2007)

In this paper, we propose an authentication scheme that is designed to reduce the authentication delay during a WiFi handover process. We observe that the largest part of the delay is due to the remote communications between the ac- cess point and the AAA server that authorizes the access to the net
Design and Optimization of a Cable Driven Upper Arm Exoskeleton (2009)

This paper outlines the design of a wearable upper arm exoskeleton that can be potentially used to assist and train arm movements of stroke survivors or subjects with weak musculature. In the last 10 years, a number of upper arm training devices have emerged. However, due to their size and weight, their use is restricted to clinics and research laboratories. Our proposed wearable exoskeleton builds upon our research experience in wire driven manipulators and design of rehabilitative systems. The exoskeleton consists of three main parts: (i) an inverted U-shaped cuff that rests on the shoulder, (ii) a cuff on the upper arm, and (iii) a cuff on the forearm. Six motors mounted on the shoulder cuff drive the cuffs on the upper arm and forearm with the use of cables. In order to assess the performance of this exoskeleton prior to use on humans, a laboratory test-bed has been developed where this exoskeleton is mounted on a model skeleton, instrumented with sensors to measure joint angles. This paper describes the design details of the exoskeleton and addresses the key issue of parameter optimization to achieve a useful workspace based on kinematic and kinetic models. The optimization results have also been motivated from activities of daily living.
The Preparation of Cyclopropene (1941)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Preparation of CyclopropeneMaurice J. SchlatterCite this: J. Am. Chem. Soc. 1941, 63, 6, 1733–1737Publication Date (Print):June 1, 1941Publication History Published online1 May 2002Published inissue 1 June 1941https://pubs.acs.org/doi/10.1021/ja01851a068https://doi.org/10.1021/ja01851a068research-articleACS PublicationsRequest reuse permissionsArticle Views571Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
An efficient signcryption scheme with shortened ciphertext (2010)

Signcryption is a novel cryptographic primitive that prove confidentiality and authenticity simultaneously. In bandwidth-constrained environments, the data mount of ciphertext is the crucial factor that holds back its broad application. While most of the known schemes based on discrete logarithm problem and RSA problem, have the low communication performance. Based on BLS signature scheme, an efficient signcryption scheme with shortened ciphertext is proposed in this paper. It is provable secure in random oracle model under GDH (Gap Diffie-Hellman) assumption. With the present secure parameters, the data rate of proposed scheme is 76%. With the long term secure parameters, the data rate is 73%. It has the highest communication performance in all of the known schemes.
Precursor Medications as a Source of Methamphetamine and/or Amphetamine Positive Drug Testing Results (2002)

Medical Review Officer interpretation of laboratory results is an important component of drug testing programs. The clinical evaluation of laboratory results to assess the possibility of appropriate medical use of a drug is a task with many different facets, depending on the drug class considered. This intercession prevents the reporting of positive results unless it is apparent that drugs were used illicitly. In addition to the commonly encountered prescribed drugs that yield positive drug testing results, other sources of positive results must be considered. This review describes a series of compounds referred to as "precursor" drugs that are metabolized by the body to amphetamine and/or methamphetamine. These compounds lead to positive results for amphetamines even though neither amphetamine nor methamphetamine were used, a possibility that must be considered in the review of laboratory results. Description of the drugs, their clinical indications, and results seen following administration are provided. This information allows for the informed evaluation of results with regard to the potential involvement of these drugs.
Passive demodulation of optical interferometric sensors (1982)

Two techniques for passive (no-feedback) demodulation of signals from a remote two-beam interferometric sensor are discussed. Termed "synthetic heterodyne" and "quadrature recombination," both methods are based on forced sinusoidal modulation of phase within the interferometer. If the phase modulation is generated by linearly proportional frequency modulation of the laser light source, then the interferometer, deployed by means of optical fibers, can be a completely passive remote sensor, and an array of identical sensors can be operated from one light source. The former technique, proposed by Cole, Danver, and Bucaro permits standard FM demodulation. The latter technique, proposed by Cable and Green, employs arithmetic operations that are appropriate to digital implementation. Constraints on application of the technique, especially frequency distribution and amplitude of phase noise (out-of-band) versus signal amplitude (in-band), are analyzed and an implementation is proposed that is consistent with Contemporary analog-to-digital conversion technology.
Combination therapy with lamivudine and HB vaccine on chronic hepatitis B (2007)

Combination therapy of LAM and HB vaccine is a safe and effective way to control HBV replication and prevent the development of BTH especially in patients with high viral load. However, further study is required in order to achieve the continuous suppression of HBV replication even after cessation of LAM.
Failure to eliminate a phosphorylated glucose analog leads to neutropenia in patients with G6PT and G6PC3 deficiency (2019)

Neutropenia represents an important problem in patients with genetic deficiency in either the glucose-6-phosphate transporter of the endoplasmic reticulum (G6PT/SLC37A4) or G6PC3, an endoplasmic reticulum phosphatase homologous to glucose-6-phosphatase. While affected granulocytes show reduced glucose utilization, the underlying mechanism is unknown and causal therapies are lacking. Using a combination of enzymological, cell-culture, and in vivo approaches, we demonstrate that G6PT and G6PC3 collaborate to destroy 1,5-anhydroglucitol-6-phosphate (1,5AG6P), a close structural analog of glucose-6-phosphate and an inhibitor of low-<i>K</i><sub>M</sub> hexokinases, which catalyze the first step in glycolysis in most tissues. We show that 1,5AG6P is made by phosphorylation of 1,5-anhydroglucitol, a compound normally present in human plasma, by side activities of ADP-glucokinase and low-<i>K</i><sub>M</sub> hexokinases. Granulocytes from patients deficient in G6PC3 or G6PT accumulate 1,5AG6P to concentrations (∼3 mM) that strongly inhibit hexokinase activity. In a model of G6PC3-deficient mouse neutrophils, physiological concentrations of 1,5-anhydroglucitol caused massive accumulation of 1,5AG6P, a decrease in glucose utilization, and cell death. Treating G6PC3-deficient mice with an inhibitor of the kidney glucose transporter SGLT2 to lower their blood level of 1,5-anhydroglucitol restored a normal neutrophil count, while administration of 1,5-anhydroglucitol had the opposite effect. In conclusion, we show that the neutropenia in patients with G6PC3 or G6PT mutations is a metabolite-repair deficiency, caused by a failure to eliminate the nonclassical metabolite 1,5AG6P.
Hardening COTS software with generic software wrappers (2003)

Numerous techniques exist to augment the security functionality of commercial off-the-shelf (COTS) applications and operating systems, making them more suitable for use in mission-critical systems. Although individually useful, as a group these techniques present difficulties to system developers because they are not based on a common framework which might simplify integration and promote portability and reuse. The paper presents techniques for developing Generic Software Wrappers-protected, non-bypassable kernel-resident software extensions for augmenting security without modification of COTS source. We describe the key elements of our work: our high-level Wrapper Definition Language (WDL), and our framework for configuring, activating, and managing wrappers. We also discuss code reuse, automatic management of extensions, a framework for system-building through composition, platform-independence, and our experiences with our Solaris and FreeBSD prototypes.
High tumour contamination of leukaphereses in patients with small cell carcinoma of the lung: a comparison of immunocytochemistry and RT-PCR (2001)

In small-cell lung carcinoma (SCLC) tumour cell contamination of leukaphereses is unknown. The present study was performed to define appropriate markers for reverse transcriptase polymerase chain reaction (RT-PCR), then to assess the contamination rate of leukaphereses and corresponding bone marrow samples. Immunocytochemistry (ICC) and RT-PCR methods were also compared. Among the 33 patients included, analyses were performed in 16 who had multiple leukaphereses and 17 who had only bone marrow. Leukapheresis products and bone marrow were analysed by ICC using several specific monoclonal antibodies against neural-cell adhesion molecule (N-CAM), epithelial glycoprotein (EGP-40) and cytokeratins (CK). Samples were also analyzed by RT-PCR for expression for N-CAM, synaptophysin, neuron-specific enolase, chromogranin, cytokeratin-18/-19, CEA, EGP-40, apomucin type 1 (MUC-1) and human endothelial cell-specific molecule (ESM-1). Using ICC staining, contaminating tumour cells were detected in 34% of leukaphereses (27% in patients with limited disease and 43% in those with extensive disease). N-CAM was the most reliable marker for detection of contamination. For RT-PCR, CK-19 and CEA were the only appropriate markers. Positive signal rate in leukaphereses increased to 78% (89% for patients with limited disease and 67% for extensive disease). In bone marrow, both techniques were in agreement whereas in leukaphereses, RT-PCR was better than ICC. A high rate of tumour cell contamination was demonstrated not only in bone marrow but also in leukaphereses from SCLC patients. The most appropriate technique was RT-PCR mainly in patients with limited disease.
Antioxidative Effect of Far-Infrared Radiation in Human (2013)

The antioxidative effect of far-infrared radiation (FIR) in human was evaluated by half maximal inhibitory concentration of blood against superoxide anions. All samples ranging from 18 to 30 years old were grouped into sympathetic, parasympathetic, sympathetic plus parasympathetic and the control group. The ability of antioxidation of blood from the subjects was measured with an ultraweak chemiluminescence analyzer. According to the results, the level of superoxide anions was decreased in sympathetic, parasympathetic, and sympathetic plus parasympathetic group, while that in the control group was increased. This suggested that the FIR radiation performed a significantly antioxidative effect by defending human from oxidative damage of superoxide anions in blood. This may probably be achieved by increasing SOD concentration and/or increasing heart rate variability. KeywordsFar-Infrared Radiation; Antioxidative Effect; Ultraweak Chemiluminescence Analyzer; Autonomic Nervous System; Superoxide Anions
Enhanced Escherichia coli invasion of human brain microvascular endothelial cells is associated with alterations in cytoskeleton induced by nicotine (2002)

Although epidemiological studies have shown that exposure to tobacco smoking significantly increases the risk of bacterial meningitis, heretofore the pathogenic effects of smoking on this disease have been poorly understood. In order to dissect this issue, we have investigated the effects of nicotine, the major component of tobacco, on E. coli invasion of human brain microvascular endothelial cells (HBMEC). Our studies showed that E. coli invasion of HBMEC was significantly enhanced by nicotine in a dose-dependent manner. The nicotine-mediated enhancement was associated with actin cytoskeleton rearrangement and morphological changes in the eukaryotic host cell that are essential for bacterial entry. The recombinant IbeA protein and alpha-bungarotoxin (a nicotinic acetylcholine receptor antagonist) were able to efficiently block the nicotine-mediated cellular effects, suggesting the involvement of the IbeA and nicotinic receptors. Blocking of phosphatidylinositol 3-kinase (PI3K) by LY294002 abolished the entry of E. coli in HBMECs treated with nicotine in a dose-dependent manner. Inhibition of PI3K was associated with decreased phosphorylation of Akt and actin cytoskeletal rearrangement. In contrast to PI3K, blockage of Rho kinase (ROCK) by Y27632 upregulated both nicotine- and E. coli-mediated cellular responses. Thus, this study provides experimental evidence for the first time that the major component of tobacco, nicotine, enhances meningitic E. coli invasion of HBMEC through modulation of cytoskeleton.
The Avian Coronavirus Infectious Bronchitis Virus Undergoes Direct Low-pH-Dependent Fusion Activation during Entry into Host Cells (2006)

Coronaviruses are the causative agents of respiratory disease in humans and animals, including severe acute respiratory syndrome. Fusion of coronaviruses is generally thought to occur at neutral pH, although there is also evidence for a role of acidic endosomes during entry of a variety of coronaviruses. Therefore, the molecular basis of coronavirus fusion during entry into host cells remains incompletely defined. Here, we examined coronavirus-cell fusion and entry employing the avian coronavirus infectious bronchitis virus (IBV). Virus entry into cells was inhibited by acidotropic bases and by other inhibitors of pH-dependent endocytosis. We carried out fluorescence-dequenching fusion assays of R18-labeled virions and show that for IBV, coronavirus-cell fusion occurs in a low-pH-dependent manner, with a half-maximal rate of fusion occurring at pH 5.5. Fusion was reduced, but still occurred, at lower temperatures (20 degrees C). We observed no effect of inhibitors of endosomal proteases on the fusion event. These data are the first direct measure of virus-cell fusion for any coronavirus and demonstrate that the coronavirus IBV employs a direct, low-pH-dependent virus-cell fusion activation reaction. We further show that IBV was not inactivated, and fusion was unaffected, by prior exposure to pH 5.0 buffer. Virions also showed evidence of reversible conformational changes in their surface proteins, indicating that aspects of the fusion reaction may be reversible in nature.
Prognostic and Predictive Blood-Based Biomarkers in Patients with Advanced Pancreatic Cancer: Results from CALGB80303 (Alliance) (2013)

This study identified strong prognostic markers for pancreatic cancer patients. Predictive marker analysis indicated that plasma levels of VEGF-D, Ang2, and SDF1 significantly predicted for benefit or lack of benefit from bevacizumab in this population.