gebhart/patrepeval huggingface dataset:
Evaluation of Computational Models for Hemolysis Estimation (2005)

The potential for mechanical erythrocyte damage, or hemolysis, in heart valves and blood pumps has been estimated using computational fluid dynamics (CFD) analysis, combined with mathematical models of red cell damage mechanisms. To date, these prediction approaches have not been compared with each other in common benchmark cases, nor have they been evaluated in radically different flow geometries. In this study, four test devices, including a hemoresistometer, a spinning disk, a capillary tube, and a concentric cylinder viscometer were hemolysis tested and computationally simulated. A number of existing models were used to predict blood damage and these models were compared with each other and with actual measurement of hemolysis. The study indicates that the effectiveness of blood damage prediction from the existing models is similar and can potentially be improved with the consideration of a proposed repeated flow passage effect. It also indicates that the improved models can be used to more effectively predict blood damage in widely different situations.
Microwave-accelerated metal-enhanced fluorescence: application to detection of genomic and exosporium anthrax DNA in <30 seconds (2007)

We describe the ultra-fast and sensitive detection of the gene encoding the protective antigen of Bacillus anthracis the causative agent of anthrax. Our approach employs a highly novel platform technology, Microwave-Accelerated Metal-Enhanced Fluorescence (MAMEF), which combines the use of Metal-Enhanced Fluorescence to enhance assay sensitivity and focused microwave heating to spatially and kinetically accelerate DNA hybridization. Genomic and exosporium target DNA of Bacillus anthracis spores was detected within a minute in the nanograms per microliter concentration range using low-power focused microwave heating. The MAMEF technology was able to distinguish between B. anthracis and B. cereus, a non-virulent close relative. We believe that this study has set the stage and indeed provides an opportunity for the ultra-fast and specific detection of B. anthracis spores with minimal pre-processing steps using a relatively simple but cost-effective technology that could minimize casualties in the event of another anthrax attack.
Keto-Steroids, I Conversion of Diosgenin to 6 β-Methylpregn-4-ene-6 α,20-diol-3,16-dione (1982)

Abstract The reaction of diosgenin (1) with hydrogen peroxide/formic acid was investigated. As a result of this work, 5 α (25 R)-spirostane-3 β,5,6 β-triol (2) was prepared in 79% yield and 5 α-pregnane-3 β,5,6 β,16 β,20 α-pentol (3) in 80% yield. The pentol (3) was oxidised to 5 α-pregnane-3 β,5,10 β,20 α-tetrol-6-one (5) without forming its 16 β,20 α-isopropylidenedioxy derivative (4). Reaction of product 5 with CH 3 Mgl to give 6-methylpregnane derivative was unsuccessful. Therefore, product 7 was oxidatively degraded by H 2 O 2 /HCOOH to the 10-keto pregnane derivative (13) and its structure was proved through its transformation to 6 β-methylpregn-4-ene-6 α,20 α-diol-3,16-dione (15).
Cyclin G: a new mammalian cyclin with homology to fission yeast Cig1. (1993)

A new gene encoding a cyclin-like protein has been isolated from a rat fibroblast cDNA library by cross-hybridization with a mixture of c-src family proto-oncogene kinase domains as a probe. This putative cyclin, called cyclin G, contains a typical cyclin box at the N-terminus but no apparent 'destruction box' or 'PEST' sequence. Interestingly, in its C-terminus region, it has a sequence homologous with a tyrosine phosphorylation site of the epidermal growth factor receptor. Although this cyclin is phylogenetically related to HCS26 of Saccharomyces cerevisiae, it most resembles Cig1, a B-type cyclin, of Schizosaccharomyces pombe, which has been suggested to act at the G1/S phase of the cell cycle. Cyclin G mRNA is induced within 3 h after growth stimulation and remains elevated with no apparent cell cycle dependency, indicating its close association with growth stimuli but not with the cell cycle.
Cytolytic T cell granules. Isolation, structural, biochemical, and functional characterization. (1984)

The cytoplasmic, dense granules of cloned T cell lines were isolated and analyzed for their functional and biochemical properties. Isolated granules of approximately 90% homogeneity, in the presence of Ca, effect strong tumoricidal and hemolytic activity. Tumor cell lysis is complete in less than 30 min, with less than 2 micrograms granule protein corresponding to a killer/target ratio of 3-6:1 by assuming 50% yield for granule isolation. The granules contain a set of unique proteins, responsible for cytolytic activity and designated K1 to K6, in the molecular weight range of 14,000 to 75,000, as defined by sodium dodecyl sulfate (SDS) polyacrylamide slab gel analysis under reducing and nonreducing conditions. Cytolysis mediated by isolated granules is accompanied by the assembly of tubular complexes of 160 A (poly P1) and of approximately 70 A width (poly P2) that are inserted into membranes and form ultrastructural membrane lesions. As shown by immunofluorescence and by Percoll gradient fractionation, cytolytic granules are detected in cells of cytolytic T cell lineage and not in the T cell lymphomas E14 and S194. Poly perforin 1 assembled by CTLL-2 upon stimulation with concanavalin A (Con A) and phorbol myristate acetate (PMA) was isolated by detergent extraction and gel filtration. Poly P1 is composed of disulfide-linked subunits that, after reduction, co-migrate with certain granule proteins. The results are compatible with the hypothesis that the dense granules of cytolytic T cells contain cytolytic proteins that polymerize to disulfide-linked tubular poly perforins in a Ca-dependent reaction and may cause cytolysis by membrane insertion and transmembrane channel formation.
Neuromuscular Junction Formation Between Human Stem-Cell-Derived Motoneurons and Rat Skeletal Muscle in a Defined System (2010)

To date, the coculture of motoneurons (MNs) and skeletal muscle in a defined in vitro system has only been described in one study and that was between rat MNs and rat skeletal muscle. No in vitro studies have demonstrated human MN to rat muscle synapse formation, although numerous studies have attempted to implant human stem cells into rat models to determine if they could be of therapeutic use in disease or spinal injury models, although with little evidence of neuromuscular junction (NMJ) formation. In this report, MNs differentiated from human spinal cord stem cells, together with rat skeletal myotubes, were used to build a coculture system to demonstrate that NMJ formation between human MNs and rat skeletal muscles is possible. The culture was characterized by morphology, immunocytochemistry, and electrophysiology, while NMJ formation was demonstrated by immunocytochemistry and videography. This defined system provides a highly controlled reproducible model for studying the formation, regulation, maintenance, and repair of NMJs. The in vitro coculture system developed here will be an important model system to study NMJ development, the physiological and functional mechanism of synaptic transmission, and NMJ- or synapse-related disorders such as amyotrophic lateral sclerosis, as well as for drug screening and therapy design.
Strained Germanium quantum well pMOS FinFETs fabricated on in situ phosphorus-doped SiGe strain relaxed buffer layers using a replacement Fin process (2013)

Strained Ge p-channel FinFETs on Strain Relaxed SiGe are reported for the first time, demonstrating peak transconductance gm <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SAT</sub> of 1.3mS/μm at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DS</sub> =-0.5V and good short channel control down to 60nm gate length. Optimization of P-doping in the SiGe, optimized Si cap passivation thickness on the Ge, and improved gate wrap of the channel all improve device characteristics. The Ge FinFETs presented in this work outperform published relaxed Ge FinFET devices for the gm <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SAT</sub> /SS <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SAT</sub> benchmarking metric.
Novel approach for detection of isolated tumor cells in pulmonary vein using negative selection method: morphological classification and clinical implications☆☆☆ (2011)

The present method was useful to detect and enrich ITCs from the PV, and showed the clinical relevance of their morphology in lung cancer cases. The presence of ITC clusters may be a prognostic biomarker for patients with resected NSCLC.
A Brief History of Oligonucleotide Synthesis (2003)

Julian Barnes wrote A History of the World in 10 1/2 Chapters (). Oligonucleotides on this score warrant at most a comma, a literary augenblick, but lacking the skill of the aforementioned author and still using a broad brush, perhaps ten pages or so may suffice to paint the picture. This is an essay or perhaps commentary, not a review, so that the references regrettably do not do justice to the work of the chemists involved in oligonucleotide synthesis who have provided the single most important development in chemistry as applied to biology in the past 40 years. Where, without it, would molecular biology be today? The matter hardly bears thinking about. In a period during which synthetic organic chemistry has flourished, when more and more subtle reactions have been uncovered and applied to more and more complex structures none, or at most very few, of the great exponents have touched oligonucleotide synthesis. Why? That linearity breeds contempt, and having only four types of building blocks to deal with might have something to do with it. After all, the two major hurdles have been the development of protecting groups, their addition and removal, and phosphorylation, and, one should add, separation methods. Perhaps it was believed that this was intellectually limiting.
InterProScan: protein domains identifier (2005)

InterProScan [E. M. Zdobnov and R. Apweiler (2001) Bioinformatics, 17, 847-848] is a tool that combines different protein signature recognition methods from the InterPro [N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bradley, P. Bork, P. Bucher, L. Cerutti et al. (2005) Nucleic Acids Res., 33, D201-D205] consortium member databases into one resource. At the time of writing there are 10 distinct publicly available databases in the application. Protein as well as DNA sequences can be analysed. A web-based version is accessible for academic and commercial organizations from the EBI (http://www.ebi.ac.uk/InterProScan/). In addition, a standalone Perl version and a SOAP Web Service [J. Snell, D. Tidwell and P. Kulchenko (2001) Programming Web Services with SOAP, 1st edn. O'Reilly Publishers, Sebastopol, CA, http://www.w3.org/TR/soap/] are also available to the users. Various output formats are supported and include text tables, XML documents, as well as various graphs to help interpret the results.
Integrin activation by the lipid molecule 25-hydroxycholesterol induces a proinflammatory response (2019)

Integrins are components of cell-matrix adhesions, and function as scaffolds for various signal transduction pathways. So far no lipid ligand for integrin has been reported. Here we show that a lipid, oxysterol 25-hydroxycholesterol (25HC), directly binds to α5β1 and αvβ3 integrins to activate integrin-focal adhesion kinase (FAK) signaling. Treatment of macrophages and epithelial cells with 25HC results in an increase in activated αvβ3 integrin in podosome and focal adhesion matrix adhesion sites. Moreover, activation of pattern recognition receptor on macrophages induces secretion of 25HC, triggering integrin signaling and the production of proinflammatory cytokines such as TNF and IL-6. Thus, the lipid molecule 25HC is a physiologically relevant activator of integrins and is involved in positively regulating proinflammatory responses. Our data suggest that extracellular 25HC links innate immune inflammatory response with integrin signaling.
Conjugated‐Polymer‐Functionalized Graphene Oxide: Synthesis and Nonvolatile Rewritable Memory Effect (2010)

An ITO/TPAPAM-GO/Al memory device (see figure; ITO = indium tin oxide, TPAPAM-GO = graphene oxide covalently grafted with triphenylamine-based polyazomethine) exhibits typical bistable electrical switching and a nonvolatile rewritable memory effect with a turn-on voltage of −1.0 V and an ON/OFF-state current ratio of more than 103. Both ON and OFF state are stable under a constant voltage stress and survive up to 108 read cycles at a read voltage of −1.0 V.
Low-power, high-speed CMOS VLSI design (2003)

Ubiquitous computing is a next generation information technology where computers and communications will be scaled further, merged together, and materialized in consumer applications. Computers will be invisible behind broadband networks as servers, while terminals will come closer to us as wearable/implantable devices, more friendly devices with sophisticated human-computer interactions. IC chips will be implanted everywhere so that things can think and talk for distributed information processing. Key technologies here are low power, low cost, and good interfaces, especially for wireless data communications. Low-power, high-speed CMOS circuit techniques are presented in this paper, including low-voltage design with variable/multiple V/sub DD//V/sub TH/ control, embedded memory technology for reducing capacitance, and low-switching activity design.
Reverse Transcriptase Motifs in the Catalytic Subunit of Telomerase (1997)

Telomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes. Telomerase RNA components have been identified from many organisms, but no protein component has been demonstrated to catalyze telomeric DNA extension. Telomerase was purified from Euplotes aediculatus, a ciliated protozoan, and one of its proteins was partially sequenced by nanoelectrospray tandem mass spectrometry. Cloning and sequence analysis of the corresponding gene revealed that this 123-kilodalton protein (p123) contains reverse transcriptase motifs. A yeast (Saccharomyces cerevisiae) homolog was found and subsequently identified as EST2 (ever shorter telomeres), deletion of which had independently been shown to produce telomere defects. Introduction of single amino acid substitutions within the reverse transcriptase motifs of Est2 protein led to telomere shortening and senescence in yeast, indicating that these motifs are important for catalysis of telomere elongation in vivo. In vitro telomeric DNA extension occurred with extracts from wild-type yeast but not from est2 mutants or mutants deficient in telomerase RNA. Thus, the reverse transcriptase protein fold, previously known to be involved in retroviral replication and retrotransposition, is essential for normal chromosome telomere replication in diverse eukaryotes.
(S)-(−)-5-Ethynyl-3-(1-methyl-2-pyrroli- dinyl)pyridine Maleate (SIB-1508Y):  A Novel Anti-Parkinsonian Agent with Selectivity for Neuronal Nicotinic Acetylcholine Receptors (1996)

ADVERTISEMENT RETURN TO ISSUEPREVLetterNEXT(S)-(−)-5-Ethynyl-3-(1-methyl-2-pyrroli- dinyl)pyridine Maleate (SIB-1508Y): A Novel Anti-Parkinsonian Agent with Selectivity for Neuronal Nicotinic Acetylcholine ReceptorsNicholas D. P. Cosford, Leo Bleicher, Audrey Herbaut, J. Stuart McCallum, Jean-Michel Vernier, Heather Dawson, Jeffrey P. Whitten, Pamala Adams, Laura Chavez-Noriega, Lucia D. Correa, James H. Crona, Lorrence S. Mahaffy, Frederique Menzaghi, Tadimeti S. Rao, Richard Reid, Aida I. Sacaan, Emily Santori, Kenneth A. Stauderman, Kevin Whelan, G. Kenneth Lloyd, and Ian A. McDonaldView Author Information SIBIA Neurosciences Inc., 505 Coast Boulevard South, Suite 300, La Jolla, California 92037Cite this: J. Med. Chem. 1996, 39, 17, 3235–3237Publication Date (Web):August 16, 1996Publication History Received2 May 1996Published online16 August 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jm960328whttps://doi.org/10.1021/jm960328wrapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views919Altmetric-Citations73LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Agonists,Assays,Genetics,Receptors,Rodent models Get e-Alerts
Eukaryotic protein production in designed storage organelles (2009)

The Zera sequence provides an efficient and universal means to produce recombinant proteins by accumulation in ER-derived organelles. The remarkable cross-kingdom conservation of PB formation and their biophysical properties should have broad application in the manufacture of non-secreted recombinant proteins and suggests the existence of universal ER pathways for protein insulation.
[A signal generator using standard MIT-BIH arrhythmia database]. (2007)

This paper introduces the design of a device which combines the waves with notes from standard MIT-BIH Arrhythmia Database to generate a signal source. The device displays both waves and notes on LCD while the waves are being output, making things convenient for testing and observation. In addition, this generator includes some necessary test signals stated in our new National Industry Standard on Medical Instrumentation as well.
Using web-graph distance for relevance feedback in web search (2006)

We study the effect of user supplied relevance feedback in improving web search results. Rather than using query refinement or document similarity measures to rerank results, we show that the web-graph distance between two documents is a robust measure of their relative relevancy. We demonstrate how the use of this metric can improve the rankings of result URLs, even when the user only rates one document in the dataset. Our research suggests that such interactive systems can significantly improve search results.
High-stability 1.5 mu m external-cavity semiconductor lasers for phase-lock applications (1989)

Applications using phase-locked semiconductor lasers, such as homodyne detection, require lasers with narrow linewidth and high-frequency stability. The design and operating characteristics of two 1.5 mu m external-cavity semiconductor lasers built for such applications are described. The measured beat linewidth is 4 kHz, and the spectral density of relative frequency noise deviates significantly from the intrinsic white spectrum only at frequencies below 4 kHz. It is estimated that this frequency jitter will induce approximately 1.1 degrees RMS phase error in a second-order homodyne optical phase-lock loop that is optimized for the present beat linewidth.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Infectious Disease Genomics: Individual Variability, New Opportunities (2011)

A large number of novel genetic loci that are involved in susceptibility to common immune-related diseases, such as rheumatoid arthritis and inflammatory bowel disease, have been identified through genomewide association studies. This article discusses recent studies, challenges, and next steps in infectious disease genomics.
Regulatory T‐cell phenotype in association with large cell transformation of mycosis fungoides (2006)

Transformation of MF to high grade lymphoma may be associated with the adoption of a regulatory T-cell phenotype. FOXP3 expression may contribute to aggressive behavior of MF after large cell transformation via immune escape mechanism. The significance of this observation is limited by the low case number in this study.
Optogenetic probing of functional brain circuitry (2010)

Recently developed optogenetic technologies offer the promise of high-speed mapping of brain circuitry. Genetically targeted light-gated channels and pumps, such as channelrhodopsins and halorhodopsin, allow optical control of neuronal activity with high spatial and temporal resolution. Optogenetic probes of neuronal activity, such as Clomeleon and Mermaid, allow light to be used to monitor the activity of a genetically defined population of neurons. Combining these two complementary sets of optogenetic probes will make it possible to perform all-optical circuit mapping. Owing to the improved efficiency and higher speed of data acquisition, this hybrid approach should enable high-throughput mapping of brain circuitry.
Rain: A Workload Generation Toolkit for Cloud Computing Applications (2010)

Existing workload generation tools are not flexible enough to generate workloads that vary in three key dimensions relevant for making resource allocation decisions for Cloud Computing applications --- variations in the amount of load, variations in the mix of operations performed by clients (e.g. changes in reads vs. writes or customer usage-patterns) and variations in the popularity of the data accessed, i.e., data hotspots. In this paper we present Rain, a workload generation toolkit designed to address this lack of flexibility. Rain allows for the use of probability distributions as first class elements that describe variations in the three key dimensions of workload Its architecture supports multiple workload generation strategies (open-loop, closed loop and partly-open loop), easy extensibility via user-defined request generators targeting new systems/applications --- we demonstrate targeting the Olio Web 2.0 application. Rain also supports trace generation, which allows it to be used in conjunction with high-performance load-replay systems, e.g., httperf.