gebhart/patrepeval huggingface dataset:
Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform (2013)

Active global surveillance and characterization of influenza viruses are essential for better preparation against possible pandemic events. Obtaining comprehensive information about the influenza genome can improve our understanding of the evolution of influenza viruses and emergence of new strains, and improve the accuracy when designing preventive vaccines. This study investigated the use of deep sequencing by the next-generation sequencing (NGS) Illumina MiSeq Platform to obtain complete genome sequence information from influenza virus isolates. The influenza virus isolates were cultured from 6 respiratory acute clinical specimens collected in Thailand and Nepal. DNA libraries obtained from each viral isolate were mixed and all were sequenced simultaneously. Total information of 2.6 Gbases was obtained from a 455±14 K/mm2 density with 95.76% (8,571,655/8,950,724 clusters) of the clusters passing quality control (QC) filters. Approximately 93.7% of all sequences from Read1 and 83.5% from Read2 contained high quality sequences that were ≥Q30, a base calling QC score standard. Alignments analysis identified three seasonal influenza A H3N2 strains, one 2009 pandemic influenza A H1N1 strain and two influenza B strains. The nearly entire genomes of all six virus isolates yielded equal or greater than 600-fold sequence coverage depth. MiSeq Platform identified seasonal influenza A H3N2, 2009 pandemic influenza A H1N1and influenza B in the DNA library mixtures efficiently.
Using Transmission Line Outage Data to Estimate Cascading Failure Propagation in an Electric Power System (2008)

We study cascading transmission line outages recorded over nine years in an electric power system with approximately 200 lines. The average amount of propagation of the line outages is estimated from the data. The distribution of the total number of line outages is predicted from the propagation and the initial outages using a Galton-Watson branching process model of cascading failure.
Overexpressed A1 Adenosine Receptors Reduce Activation of Acetylcholine-Sensitive K+ Current by Native Muscarinic M2 Receptors in Rat Atrial Myocytes (2000)

Abstract—In adult rat atrial myocytes, muscarinic acetylcholine (ACh)-sensitive K+ current activated by a saturating concentration of adenosine (IK(ACh),(Ado)) via A1 receptors (A1Rs) amounts to only 30% of the current activated by a saturating concentration of ACh (IK(ACh),(ACh)) via muscarinic M2 receptors. The half-time of activation of IK(ACh),(Ado) on a rapid exposure to agonist was ≈4-fold longer than that of IK(ACh),(ACh). Furthermore, IK(ACh),(Ado) never showed fast desensitization. To study the importance of receptor density for A1R-IK(ACh),(Ado) signaling, adult atrial myocytes in vitro were transfected with cDNA encoding for rat brain A1R and enhanced green fluorescent protein (EGFP) as a reporter. Whole-cell current was measured on days 3 and 4 after transfection. Time-matched cells transfected with only the EGFP vector served as controls. In ≈30% of EGFP-positive cells (group I), the density of IK(ACh),(Ado) was increased by 72%, and its half-time of activation was reduced. Density and kineti...
Success Strategies Being Implemented in Fresh Milk Supply Chains (2003)

Deregulation of the Australian dairy industry, and ensuing supermarket strategies are transforming the fresh milk supply chains. Factors such as increasing consumer awareness, concerns about food safety and environment, innovation, supply chain integration and rationalisation of supply base are adding momentum to this transformation. Milk processors in response to changing market expectations are getting proactive in their relationship with retailers across all aspects of business, innovating to generate sufficient returns from proprietary brands and strategically orienting themselves to develop a mixed customer portfolio and appropriate management structures to service that portfolio. Milk producers are expanding businesses to achieve production and cost efficiencies and strengthening contractual relationships on input and output side for a greater security.
Caprine T‐Cell Receptor Variable β‐Chain (TCRVβ) Repertoire Analysis and Potential Applications in Cowdriosis Immune Response Studies<sup>a</sup> (1998)

Anchor polymerase chain reaction has been applied to the study of caprine TCR V beta-chain repertoire at the mRNA level in peripheral blood of a Saanen goat. Single stranded, g-tailed cDNA synthesized from total RNA was PCR-amplified using a sheep V beta constant region primer (3') and a poly(dC) anchor primer (5') at the variable region end of the TCR V beta-chain. The obtained amplicon was subsequently cloned into Bluescript plasmid vector. A total of 72 recombinant clones whereof 61 contained an insert of appropriate size were harvested. Up to now, the full length sequences of a total of 55 clones have been obtained. Nine clones were rearranged but not functional due to stop codons. Forty-five sequences were functionally rearranged and further analyzed. They were classified into 15 different V beta families on the basis of V-region sequence homology with their human counterpart. V beta families corresponding to the 9 published bovine families were represented in our library. This complexity enables us to develop V beta family-specific primers in order to study the TCR V beta repertoire of other goat breeds of interest, i.e., the Creole goat. There the TCR V beta repertoire analysis and kinetic study of the cowdriosis model will provide insight into the type of the immune response and the status of protection during the immunization process and challenge.
Selective Inhibition of KCa3.1 Channels Mediates Adenosine Regulation of the Motility of Human T Cells (2013)

Abstract Adenosine, a purine nucleoside, is present at high concentrations in tumors, where it contributes to the failure of immune cells to eliminate cancer cells. The mechanisms responsible for the immunosuppressive properties of adenosine are not fully understood. We tested the hypothesis that adenosine’s immunosuppressive functions in human T lymphocytes are in part mediated via modulation of ion channels. The activity of T lymphocytes relies on ion channels. KCa3.1 and Kv1.3 channels control cytokine release and, together with TRPM7, regulate T cell motility. Adenosine selectively inhibited KCa3.1, but not Kv1.3 and TRPM7, in activated human T cells. This effect of adenosine was mainly mediated by A2A receptors, as KCa3.1 inhibition was reversed by SCH58261 (selective A2A receptor antagonist), but not by MRS1754 (A2B receptor antagonist), and it was mimicked by the A2A receptor agonist CGS21680. Furthermore, it was mediated by the cAMP/protein kinase A isoform (PKAI) signaling pathway, as adenylyl-cyclase and PKAI inhibition prevented adenosine effect on KCa3.1. The functional implication of the effect of adenosine on KCa3.1 was determined by measuring T cell motility on ICAM-1 surfaces. Adenosine and CGS21680 inhibited T cell migration. Comparable effects were obtained by KCa3.1 blockade with TRAM-34. Furthermore, the effect of adenosine on cell migration was abolished by pre-exposure to TRAM-34. Additionally, adenosine suppresses IL-2 secretion via KCa3.1 inhibition. Our data indicate that adenosine inhibits KCa3.1 in human T cells via A2A receptor and PKAI, thereby resulting in decreased T cell motility and cytokine release. This mechanism is likely to contribute to decreased immune surveillance in solid tumors.
Is Fecal Microbiota Transplantation the Answer for Irritable Bowel Syndrome? A Single-Center Experience (2014)

1 Beth Israel Medical Center, New York City, New York, USA 2 Division of Gastroenterology, Montefiore Medical Center, New York City, New York, USA Correspondence: Lawrence J. Brandt, MD, MACG, Division of Gastroenterology, Montefiore Medical Center, 111 East 210th Street, Bronx, New York, New York 10467, USA. E-mail: [email protected]
Performance of the receivers of trellis-coded data signals transmitted through HF channels (1988)

Shows the results of investigation by computer simulation of several receiver structures for trellis-coded signals transmitted through an HF radio channel. It is well known that application of Ungerboeck codes jointly with PSK or QAM modulation and the soft-decision Viterbi algorithm results in 2-6 dB asymptotic gain depending on the applied code. However, it is worth investigating the effective gain over uncoded systems when deep selective fades and ISI occur and signal-to-noise ratio is low or moderate, as in HF channels. >
Identification, Characterization and Quantification of Process-Related and Degradation Impurities in Lisdexamfetamine Dimesylate: Identifiction of Two New Compounds (2018)

Twelve impurities (process-related and degradation) in lisdexamfetamine dimesylate (LDX), a central nervous system (CNS) stimulant drug, were first separated and quantified by high-performance liquid chromatography (HPLC) and then identified by liquid chromatography mass spectrometry (LC-MS). The structures of the twelve impurities were further confirmed and characterized by IR, HRMS and NMR analyses. Based on the characterization data, two previously unknown impurities formed during the process development and forced degradation were proposed to be (2<i>S</i>)-2,6-di-(lysyl)-amino-<i>N</i>-[(1<i>S</i>)-1-methyl-2-phenyl ethyl]hexanamide (Imp-H) and (2<i>S</i>)-2,6-diamino-<i>N</i>-[(1<i>S</i>)-1-methyl-2-(2-hydroxyphenyl)ethyl] hexanamide (Imp-M). Furthermore, these two compounds are new. Probable mechanisms for the formation of the twelve impurities were discussed based on the synthesis route of LDX. Superior separation was achieved on a YMC-Pack ODS-AQ S5 120A silica column (250 × 4.6 mm × 5 μm) using a gradient of a mixture of acetonitrile and 0.1% aqueous methanesulfonic acid solution. The HPLC method was optimized in order to separate, selectively detect, and quantify all the impurities. The full identification and characterization of these impurities should prove useful for quality control in the manufacture of lisdexamfetamine dimesylate.
Synthesis of High-Quality Graphene through Electrochemical Exfoliation of Graphite in Alkaline Electrolyte (2013)

Owing to wide variety of applications of graphene, high-quality and economical way of synthesizing graphene is highly desirable. In this study, we report a cost effective and simple approach to production of high-quality graphene. Here the synthesis route is based on electrochemical exfoliation of graphite. Instead of using strong acids (which oxidise and damage the geometrical topology of graphene), we have used alkaline solution (KOH dissolved in water) as electrolyte. TEM analysis shows that as prepared graphene has 1-4 layers and large lateral size (up to ~18 micrometer). Raman analysis shows a unique feature. The D peak which is invariably present in graphene is absent here. This suggests that disorder in the graphene sheets synthesized by the present method, is nearly absent. A tentative mechanism of electrochemical exfoliation in alkaline electrolyte is discussed and described.
Copy number evolution with weighted aberrations in cancer (2020)

Supplementary data are available at Bioinformatics online.
Preparation of Polyethylenimine‐Functionalized Graphene Oxide Composite and Its Application in Electrochemical Ammonia Sensors (2013)

Abstract In this study, branched polyethyleneimine (PEI) was covalently linked to carboxylic acid functionalized graphene (GO‐COOH) to form GO‐COOH/PEI composites. Transmission electron microscopy, Fourier transform infrared spectroscopy, Raman spectra and thermogravimetric analysis were used to characterize the obtained composites. Electrochemical measurements indicated that the modification of the composites on the electrode could efficiently enhance the voltammetric response, suggesting the potential application for making electrochemical sensors. Moreover, our results also indicated that the electrocatalytic oxidation of ammonia could be observed on the GO‐COOH/PEI composites modified glassy carbon electrode. Consequently, our observations demonstrated that GO‐COOH/PEI composites were excellent materials for electrochemical sensing.
Palladium-Catalyzed Direct Heck Arylation of Dual π-Deficient/π-Excessive Heteroaromatics. Synthesis of C-5 Arylated Imidazo[1,5-<i>a</i>]pyrazines (2008)

A general and efficient synthesis of 5-aryl imidazo[1,5- a]pyrazines by palladium-catalyzed coupling of the corresponding 8-substituted derivatives with aryl halides is described. The scope of this new reaction for the imidazo[1,5- a]pyrazine ring system was explored using three readily available 8-substituted precursors, X = NH2, NMe2, and OMe, as well as 8-aryl derivatives, X = Ar'. On the basis of these results as well as studies using a deuterated derivative, a Heck-like mechanism is proposed for this transformation.
14-3-3 Antagonizes Ras-Mediated Raf-1 Recruitment to the Plasma Membrane To Maintain Signaling Fidelity (2002)

We have investigated the role that S259 phosphorylation, S621 phosphorylation, and 14-3-3 binding play in regulating Raf-1 activity. We show that 14-3-3 binding, rather than Raf-1 phosphorylation, is required for the correct regulation of kinase activity. Phosphorylation of S621 is not required for activity, but 14-3-3 binding is essential. When 14-3-3 binding to conserved region 2 (CR2) was disrupted, Raf-1 basal kinase activity was elevated and it could be further activated by (V12,G37)Ras, (V23)TC21, and (V38)R-Ras. Disruption of 14-3-3 binding at CR2 did not recover binding of Raf-1 to (V12,G37)Ras but allowed more efficient recruitment of Raf-1 to the plasma membrane and stimulated its phosphorylation on S338. Finally, (V12)Ras, but not (V12,G37)Ras, displaced 14-3-3 from full-length Raf-1 and the Raf-1 bound to Ras. GTP was still phosphorylated on S259. Our data suggest that stable association of Raf-1 with the plasma membrane requires Ras-mediated displacement of 14-3-3 from CR2. Small G proteins that cannot displace 14-3-3 fail to recruit Raf-1 to the membrane efficiently and so fail to stimulate kinase activity.
Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer (2012)

Ovarian cancer is the fifth leading cause of cancer death for women in the U.S. and the seventh most fatal worldwide. Although ovarian cancer is notable for its initial sensitivity to platinum-based therapies, the vast majority of patients eventually develop recurrent cancer and succumb to increasingly platinum-resistant disease. Modern, targeted cancer drugs intervene in cell signaling, and identifying key disease mechanisms and pathways would greatly advance our treatment abilities. In order to shed light on the molecular diversity of ovarian cancer, we performed comprehensive transcriptional profiling on 129 advanced stage, high grade serous ovarian cancers. We implemented a, re-sampling based version of the ISIS class discovery algorithm (rISIS: robust ISIS) and applied it to the entire set of ovarian cancer transcriptional profiles. rISIS identified a previously undescribed patient stratification, further supported by micro-RNA expression profiles, and gene set enrichment analysis found strong biological support for the stratification by extracellular matrix, cell adhesion, and angiogenesis genes. The corresponding "angiogenesis signature" was validated in ten published independent ovarian cancer gene expression datasets and is significantly associated with overall survival. The subtypes we have defined are of potential translational interest as they may be relevant for identifying patients who may benefit from the addition of anti-angiogenic therapies that are now being tested in clinical trials.
Identification of widespread Helicobacter hepaticus infection in feces in commercial mouse colonies by culture and PCR assay (1995)

The identification of a new murine pathogen, Helicobacter hepaticus, and its association with chronic active hepatitis and liver tumors prompted an evaluation of the prevalence of H. hepaticus in commercially available mice. Of the 28 different strains or stocks, totaling 160 mice from four major commercial vendors, cultured for H. hepaticus, 100% of mice from two outbred strains from one vendor were infected with H. hepaticus, whereas 9 of 13 inbred mouse strains from another vendor were infected. This high prevalence of H. hepaticus established a need for a rapid and reproducible, noninvasive assay for the screening of colony-maintained mice being used for biomedical research. The culturing of fecal material by using 0.45-microns-pore- size filtration for H. hepaticus consistently yielded reproducible results but required extended periods of time. (1 to 3 weeks) to obtain a definitive answer. Although it is rapid, the use of a direct PCR-based detection assay with fecal specimens is restricted by inhibitory agents. to circumvent these inhibitory agents and to augment our H. hepaticus culture technique, we have developed a novel PCR system in which the bacteria are isolated from fecal material in the presence of polyvinylpyropyrollidone and lysed by treatment with Chelex 100. The PCR is performed with Tth polymerase supplemented with a polymerase enhancer. By this PCR method, 24 H. hepaticus culture-positive and 30 H. hepaticus culture-negative fecal samples were correctly identified. Moreover, two samples which were PCR positive and culture negative initially were positive by both methods upon retesting of fresh material. Southern blot hybridizations and sequencing of PCR products showed them to be H. hepaticus specific. A comparison of results obtained under identical conditions indicated a 100-fold increase in sensitivity with Tth polymerase over Taq polymerase. This PCR method can be used as a noninvasive means of rapidly screening large numbers of colony mice for H. hepaticus.
Replication control for distributed real-time database systems (2003)

An algorithm that integrates real-time scheduling with replication control is presented. The algorithm adopts a token-based scheme for replication control and attempts to balance the urgency of real-time transactions with the conflict resolution policies. In addition, the algorithm employs epsilon-serializability (ESR), a correctness criterion that is less stringent than conventional one-copy serializability. The algorithm is flexible and very practical, since no prior knowledge of data requirements or execution time of each transaction is required.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Automatic Music Genre Classification of Audio Signals with Machine Learning Approaches (2013)

Musical genre classification is put into context by explaining about the structures in music and how it is analyzed and perceived by humans.The increase of the music databases on the personal collection and the Internet has brought a great demand for music information retrieval, and especially automatic musical genre classification.In this research we focused on combining information from the audio signal than different sources.This paper presents a comprehensive machine learning approach to the problem of automatic musical genre classification using the audio signal.The proposed approach uses two feature vectors, Support vector machine classifier with polynomial kernel function and machine learning algorithms.More specifically, two feature sets for representing frequency domain, temporal domain, cepstral domain and modulation frequency domain audio features are proposed.Using our proposed features SVM act as strong base learner in AdaBoost, so its performance of the SVM classifier cannot improve using boosting method.The final genre classification is obtained from the set of individual results according to a weighting combination late fusion method and it outperformed the trained fusion method.Music genre classification accuracy of 78% and 81% is reported on the GTZAN dataset over the ten musical genres and the ISMIR2004 genre dataset over the six musical genres, respectively.We observed higher classification accuracies with the ensembles, than with the individual classifiers and improvements of the performances on the GTZAN and ISMIR2004 genre datasets are three percent on average.This ensemble approach show that it is possible to improve the classification accuracy by using different types of domain based audio features.
Algal Biomass Constituent Analysis: Method Uncertainties and Investigation of the Underlying Measuring Chemistries (2012)

Algal biomass compositional analysis data form the basis of a large number of techno-economic process analysis models that are used to investigate and compare different processes in algal biofuels production. However, the analytical methods used to generate these data are far from standardized. This work investigated the applicability of common methods for rapid chemical analysis of biomass samples with respect to accuracy and precision. This study measured lipids, protein, carbohydrates, ash, and moisture of a single algal biomass sample at 3 institutions by 8 independent researchers over 12 separate workdays. Results show statistically significant differences in the results from a given analytical method among laboratories but not between analysts at individual laboratories, suggesting consistent training is a critical issue for empirical analytical methods. Significantly different results from multiple lipid and protein measurements were found to be due to different measurement chemistries. We identified a set of compositional analysis procedures that are in best agreement with data obtained by more advanced analytical procedures. The methods described here and used for the round robin experiment do not require specialized instrumentation, and with detailed analytical documentation, the differences between laboratories can be markedly reduced.
Synthesis of 2-Alkynyl-Tellurophene Derivatives via Palladium-Catalyzed Cross-Coupling (2006)

We present herein our results on the palladium-catalyzed cross-coupling of 2-halotellurophene with several terminal alkynes to give the 2-alkynyl-tellurophene derivatives in excellent yields. The reaction proceeded cleanly under mild conditions and was performed with propargyl alcohols, propargyl amines, propiolate, as well as alkyl and aryl alkynes, in the presence of PdCl2(PPh3)2, Et3N, THF and CuI.
Map-based isolation of the leaf rust disease resistance gene <i>Lr10</i> from the hexaploid wheat ( <i>Triticum aestivum</i> L.) genome (2003)

More than 50 leaf rust resistance (Lr) genes against the fungal pathogen Puccinia triticina have been identified in the wheat gene pool, and a large number of them have been extensively used in breeding. Of the 50 Lr genes, all are known only from their phenotype and/or map position except for Lr21, which was cloned recently. For many years, the problems of molecular work in the large (1.6 x 10(10) bp), highly repetitive (80%), and hexaploid bread wheat (Triticum aestivum L.) genome have hampered map-based cloning. Here, we report the isolation of the Lr gene Lr10 from hexaploid wheat by using a combination of subgenome map-based cloning and haplotype studies in the genus Triticum. Lr10 is a single-copy gene on chromosome 1AS. It encodes a CC-NBS-LRR type of protein with an N-terminal domain, which is under diversifying selection. When overexpressed in transgenic wheat plants, Lr10 confers enhanced resistance to leaf rust. Lr10 has similarities to RPM1 in Arabidopsis thaliana and to resistance gene analogs in rice and barley, but is not closely related to other wheat Lr genes based on Southern analysis. We conclude that map-based cloning of genes of agronomic importance in hexaploid wheat is now feasible, opening perspectives for molecular bread wheat improvement trough transgenic strategies and diagnostic allele detection.