gebhart/patrepeval huggingface dataset:
Molecular cloning of alcohol dehydrogenase genes of the yeast Pichia stipitis and identification of the fermentative ADH (1998)

Two Pichia stipitis ADH genes (PsADH1 and PsADH2) were isolated by complementation of a Saccharomyces cerevisiae Adh−-mutant. The genes enabled the transformants to grow in the presence of antimycin A on glucose, to use ethanol as sole carbon source and made them sensitive to allylalcohol. The sequences of the genes showed similarities of 70–77% to sequences of ADH genes of Candida albicans, Kluyveromyces lactis, K. marxianus, and S. cerevisiae and about 60% homology to those of Schizosaccharomyces pombe and Aspergillus flavus. Southern hybridization experiments suggested that P. stipitis has only these two ADH genes. Both genes are located on the largest chromosome of P. stipitis. PsADH2 encodes for the ADH activity that is responsible for ethanol formation at oxygen limitation. The gene is regulated at the transcriptional level. Moreover, also in cells grown on ethanol, only PsADH2 transcript was found. PsADH1 transcript was detected under aerobic conditions on fermentable carbon sources. The sequences have been deposited in the EMBL database under the accession numbers Y13238 (PsADH1) and Y13397 (PsADH2). © 1998 John Wiley & Sons, Ltd.
Sequence and structural elements that contribute to efficient encephalomyocarditis virus RNA translation (1992)

The nucleotide sequence of the 5' nontranslated region of encephalomyocarditis virus (EMCV-Rueckert) was determined, and a consensus RNA structural model for this sequence (850 bases) and three other poly(C)-containing cardioviruses (mengovirus, EMCV-B, and EMCV-D) was created through reiterative use of a minimum-free-energy folding algorithm. The RNA elements within this region which contribute to translation of EMCV proteins were mapped in cell-free reactions programmed with cDNA-derived RNA transcripts. The data provide evidence that stem-loop motifs I, J and K, formed by viral bases 451 to 785, are important components of cap-independent translation. In contrast to other reports, a minimal role for stem-loop H (bases 406 to 444) in translational activity is indicated. Small 5' nontranslated region fragments (bases 667 to 797) containing the J and K motifs proved strong competitive inhibitors when added to cell-free reactions programmed with exogenous capped or uncapped mRNAs. The putative sequestering of required translational factors by this segment clearly contributes to translational activity, but also suggests a possible competitive mechanism for the down regulation of host protein synthesis during viral infection.
Reliable messages and connection establishment (1993)

Distributed Systems: Architecture and Implementation, edited by Sape Mullender, Addison-Wesley, 1993. It contains a careful and complete treatment of protocols for ensuring that a message is delivered at most once, and that if there are no serious failures it is delivered exactly once and its delivery is properly acknowledged.
A monoclonal antibody recognizing human cancers with amplification/overexpression of the human epidermal growth factor receptor (2003)

Epidermal growth factor receptor (EGFR) has attracted considerable attention as a target for cancer therapy. Wild-type (wt)EGFR is amplified/overexpressed in a number of tumor types, and several mutant forms of the coding gene have been found, with DeltaEGFR, a deletion mutation lacking exons 2-7 of the external domain, being the most common and particularly associated with glioblastoma. We generated monoclonal antibodies (mAbs) against NR6(DeltaEGFR) (mouse fibroblast line NR6 transfected with DeltaEGFR). mAb 806 with selective reactivity for NR6(DeltaEGFR) in mixed hemadsorption assays, fluorescence-activated cell sorting, Western blot, and immunohistochemistry was analyzed in detail and compared with mAbs 528 (anti-wtEGFR) and DH8.3 (anti-DeltaEGFR). In xenograft tumors and molecularly pretyped glioblastomas, the reactivity pattern was as follows: 528 reactive with amplified and nonamplified wtEGFR; DH8.3 reactive with DeltaEGFR; and 806 reactive with amplified/overexpressed wtEGFR (with or without DeltaEGFR). In normal tissues, 528 but not DH8.3 or 806 was widely reactive with many organs, e.g., liver expressing high EGFR levels. In glioblastoma and non-CNS tumor panels, 806 was reactive with a high proportion of glioblastomas and a substantial number of epithelial cancers of lung and of head and neck. DH8.3 reactivity was restricted to DeltaEGFR-positive glioblastoma. Thus, 806 represents a category of mAbs that recognizes tumors with EGFR amplification/overexpression but not normal tissues or tumors with normal EGFR levels. Our study also indicates that DeltaEGFR is restricted to glioblastoma, in contrast to other reports that this mutation is found in tumors outside the brain.
Identification and Characterization of a PDZ Protein That Interacts with Activin Type II Receptors (2000)

We have identified a mouse PDZ protein that interacts with the activin type IIA receptor (ActRIIA), which we named activin receptor-interacting protein 1 (ARIP1). By using yeast two-hybrid screening, we isolated a cDNA clone of ARIP1 from a mouse brain cDNA library. We detected two forms of ARIP1, ARIP1-long and ARIP1-short, which may be produced by alternative splicing. ARIP1-long had one guanylate kinase domain in the NH(2)-terminal region, followed by two WW domains and five PDZ domains (PDZ1-5). ARIP1-short had a deletion in the NH(2)-terminal region and lacked the guanylate kinase domain. Both forms interacted with ActRIIA through PDZ5. The COOH-terminal residues of ActRIIA (ESSL) agree with a PDZ-binding consensus motif, and ARIP1 recognized the consensus sequence. ARIP1 interacts specifically with ActRIIA among the receptors for the transforming growth factor beta family. Interestingly, ARIP1 also interacted with Smad3, which is an activin/transforming growth factor beta intracellular signaling molecule. The mRNA of ARIP1 was more abundant in the brain than in other tissues. Overexpression of ARIP1 controls activin-induced and Smad3-induced transcription in activin-responsive cell lines. These findings suggest that ARIP1 has a significant role in assembling activin signaling molecules at specific subcellular sites and in regulating signal transduction in neuronal cells.
Isolation of a Streptococcus pyogenes gene locus that directs hyaluronan biosynthesis in acapsular mutants and in heterologous bacteria (1993)

A contiguous 3-kilobase pair region of DNA was isolated from Group A Streptococcus pyogenes (GAS) that can direct hyaluronic acid (HA) capsule biosynthesis in acapsular mutants as well as heterologous bacteria. The DNA was identified by transposon 916 insertional mutagenesis and subcloned into a plasmid shuttle vector. Mutant acapsular GAS or Enterococcus faecalis containing this plasmid, but not vector alone, displayed a mucoid phenotype on agar plates, possessed a capsule as seen by light microscopy, and produced HA in quantities comparable with wild-type GAS. The polysaccharide was shown to be authentic HA based on its recognition by a specific proteoglycan and its degradation by Streptomyces hyaluronate lyase. Escherichia coli with the complementing plasmid also produced HA but at only 10% of the level made by the above cells. E. coli minicell analysis showed that two proteins, 42 and 45 kDa, are expressed by the functional DNA insert. Deletion analysis of the insert in the minicells revealed that the 42-kDa protein is essential for HA production. This is the first demonstration of reconstitution of HA capsule biosynthesis in vivo.
Glycerol-Based Bicontinuous Cubic Lyotropic Liquid Crystal Monomer System for the Fabrication of Thin-Film Membranes with Uniform Nanopores (2012)

ADVERTISEMENT RETURN TO ISSUECommunicationNEXTADDITION / CORRECTIONThis article has been corrected. View the notice.Glycerol-Based Bicontinuous Cubic Lyotropic Liquid Crystal Monomer System for the Fabrication of Thin-Film Membranes with Uniform NanoporesBlaine M. Carter†, Brian R. Wiesenauer‡, Evan S. Hatakeyama†, John L. Barton§, Richard D. Noble*†, and Douglas L. Gin*†‡View Author Information† ‡ †Department of Chemical & Biological Engineering, and ‡Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado 80309, United States§ Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States*E-mail: [email protected]; [email protected]Cite this: Chem. Mater. 2012, 24, 21, 4005–4007Publication Date (Web):October 30, 2012Publication History Received28 June 2012Revised18 October 2012Published online30 October 2012Published inissue 13 November 2012https://pubs.acs.org/doi/10.1021/cm302027shttps://doi.org/10.1021/cm302027srapid-communicationACS PublicationsCopyright © 2012 American Chemical SocietyRequest reuse permissionsArticle Views3078Altmetric-Citations75LEARN 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:Alcohols,Layers,Membranes,Monomers,Solvents Get e-Alerts
A Discovery Resource of Rare Copy Number Variations in Individuals with Autism Spectrum Disorder (2012)

The identification of rare inherited and de novo copy number variations (CNVs) in human subjects has proven a productive approach to highlight risk genes for autism spectrum disorder (ASD). A variety of microarrays are available to detect CNVs, including single-nucleotide polymorphism (SNP) arrays and comparative genomic hybridization (CGH) arrays. Here, we examine a cohort of 696 unrelated ASD cases using a high-resolution one-million feature CGH microarray, the majority of which were previously genotyped with SNP arrays. Our objective was to discover new CNVs in ASD cases that were not detected by SNP microarray analysis and to delineate novel ASD risk loci via combined analysis of CGH and SNP array data sets on the ASD cohort and CGH data on an additional 1000 control samples. Of the 615 ASD cases analyzed on both SNP and CGH arrays, we found that 13,572 of 21,346 (64%) of the CNVs were exclusively detected by the CGH array. Several of the CGH-specific CNVs are rare in population frequency and impact previously reported ASD genes (e.g., NRXN1, GRM8, DPYD), as well as novel ASD candidate genes (e.g., CIB2, DAPP1, SAE1), and all were inherited except for a de novo CNV in the GPHN gene. A functional enrichment test of gene-sets in ASD cases over controls revealed nucleotide metabolism as a potential novel pathway involved in ASD, which includes several candidate genes for follow-up (e.g., DPYD, UPB1, UPP1, TYMP). Finally, this extensively phenotyped and genotyped ASD clinical cohort serves as an invaluable resource for the next step of genome sequencing for complete genetic variation detection.
Transient B-Cell Depletion Combined With Apoptotic Donor Splenocytes Induces Xeno-Specific T- and B-Cell Tolerance to Islet Xenografts (2013)

Peritransplant infusion of apoptotic donor splenocytes cross-linked with ethylene carbodiimide (ECDI-SPs) has been demonstrated to effectively induce allogeneic donor-specific tolerance. The objective of the current study is to determine the effectiveness and additional requirements for tolerance induction for xenogeneic islet transplantation using donor ECDI-SPs. In a rat-to-mouse xenogeneic islet transplant model, we show that rat ECDI-SPs alone significantly prolonged islet xenograft survival but failed to induce tolerance. In contrast to allogeneic donor ECDI-SPs, xenogeneic donor ECDI-SPs induced production of xenodonor-specific antibodies partially responsible for the eventual islet xenograft rejection. Consequently, depletion of B cells prior to infusions of rat ECDI-SPs effectively prevented such antibody production and led to the indefinite survival of rat islet xenografts. In addition to controlling antibody responses, transient B-cell depletion combined with ECDI-SPs synergistically suppressed xenodonor-specific T-cell priming as well as memory T-cell generation. Reciprocally, after initial depletion, the recovered B cells in long-term tolerized mice exhibited xenodonor-specific hyporesponsiveness. We conclude that transient B-cell depletion combined with donor ECDI-SPs is a robust strategy for induction of xenodonor-specific T- and B-cell tolerance. This combinatorial therapy may be a promising strategy for tolerance induction for clinical xenogeneic islet transplantation.
DNA damage-inducible transcripts in mammalian cells. (1988)

Hybridization subtraction at low ratios of RNA to cDNA was used to enrich for the cDNA of transcripts increased in Chinese hamster cells after UV irradiation. Forty-nine different cDNA clones were isolated. Most coded for nonabundant transcripts rapidly induced 2- to 10-fold after UV irradiation. Only 2 of the 20 cDNA clones sequenced matched known sequences (metallothionein I and II). The predicted amino acid sequence of one cDNA had two localized areas of homology with the rat helix-destabilizing protein. These areas of homology were at the two DNA-binding sites of this nucleic acid single-strand-binding protein. The induced transcripts were separated into two general classes. Class I transcripts were induced by UV radiation and not by the alkylating agent methyl methanesulfonate. Class II transcripts were induced by UV radiation and by methyl methanesulfonate. Many class II transcripts were induced also by H2O2 and various alkylating agents but not by heat shock, phorbol 12-tetradecanoate 13-acetate, or DNA-damaging agents which do not produce high levels of base damage. Since many of the cDNA clones coded for transcripts which were induced rapidly and only by certain types of DNA-damaging agents, their induction is likely a specific response to such damage rather than a general response to cell injury.
Experimental Auralization of Car Audio Installations (1996)

Wide-frequency-range auralization, such as needed for car audio, cannot be accomplished using currently available software for architectural acoustics modeling, since these are optimized for large rooms. This is due to the limitations of geometrical acoustics, which forms the basis for these programs. The possibilities of using other models for predicting the binaural room impulse responses for low frequencies have been studied. Finite-element and boundary-element models are being used at low frequencies, in conjunction with an augmented geometrical acoustics model for high frequencies to facilitate wide-frequency range auralization of, for example, car audio installations. Different binaural approaches to low-frequency modeling are described. The signal processing for joining the results from low- and high-frequency modeling is described in detail. Results from preliminary listening tests are discussed.
Four Highly Oxygenated Isopimarane-Type Diterpenes of Orthosiphon stamineus (2002)

Four highly oxygenated isopimarane-type diterpenes, named orthosiphols O, P and Q and nororthosiphonolide A, have been isolated from the aerial parts of Orthosiphon stamineus from Myanmar, together with three known diterpenes, orthosiphols D and E and orthosiphonone A. Their structures were determined on the basis of extensive spectral analysis. All the isolated compounds displayed mild antiproliferative activities against highly liver metastatic colon 26-L5 carcinoma and human HT-1080 fibrosarcoma cell lines.
An integrated map of genetic variation from 1,092 human genomes (2020)

SummaryThrough characterising the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help understand the genetic contribution to disease. We describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methodologies to integrate information across multiple algorithms and diverse data sources we provide a validated haplotype map of 38 million SNPs, 1.4 million indels and over 14 thousand larger deletions. We show that individuals from different populations carry different profiles of rare and common variants and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways and that each individual harbours hundreds of rare non-coding variants at conserved sites, such as transcription-factor-motif disrupting changes. This resource, which captures up to 98% of accessible SNPs at a frequency of 1% in populations of medical genetics focus, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.
Treating anxiety in patients with alcoholism. (1995)

The clinical management of patients who present with anxiety syndromes combined with alcohol abuse or dependence is reviewed. A critical step is to make the differential diagnosis between alcohol-induced anxiety (principally alcohol withdrawal) and anxiety disorders per se. Interview and examination techniques useful in making this differential are presented. Clinical management of and pharmacotherapy for alcohol withdrawal are outlined. Anxiety disorders that can be comorbid with alcoholism include panic disorder, social phobia, obsessive compulsive disorder, generalized anxiety disorder, and posttraumatic stress disorder. Psychotherapeutic and pharmacotherapeutic measures for each of these in the setting of alcoholism are suggested, and various possible interrelationships between anxiety disorders and alcoholism are considered. Although anxiety disorders may contribute to the underlying etiology of alcoholism in some cases, alcohol abuse tends to take on a life of its own. Treatment of an anxiety disorder can rarely, if ever, be expected to cure alcoholism. Therefore, the need to institute simultaneous treatment aimed at establishing and maintaining sobriety is emphasized. Research on anxiety disorders and alcoholism is as yet inadequate to fully answer many clinical questions about their relationship and their appropriate diagnosis and management. More research is needed in this area.
SM3B NICMOS Focus Check (2002)

We report determinations of the NICMOS foci following cool down of the NICMOS detectors after installation and activation of the NICMOS Cooling System (NCS). A focus sweep in all three cameras executed on May 3, 2002 (program ID: 8977). Visual inspection of the data indicated that a small amount of coma had been introduced since January 1999. Phase retrieval (STScI) and encircled energy (University of Arizona) measurements were used to determine the best focus positions. The results of the two methods compared quite favorably with each other. Adjustments to the current Pupil Alignment Mechanism (PAM) positions were implemented on May 9, 2002 for Camera 1 & 2 (PAM1 & PAM2). No focus adjustments were implemented for Camera 3 (PAM3) or for the Camera 2 coronagraphic focus (PAMC). Adjustment of the intermediate focus position between Camera 1 & 2 (PAMI) will be managed starting during week 2002.133 by SMS.
A New Reddening Law for M4 (2012)

We have used a combination of broad-band near-infrared and optical Johnson-Cousins photometry to study the dust properties in the line of sight to the Galactic globular cluster M4. We have investigated the reddening effects in terms of absolute strength and variation across the cluster field, as well as the form of the reddening law defined by the type of dust. Here, we determine the ratio of absolute to selective extinction (R_V) in the line of sight towards M4, which is known to be a useful indicator for the type of dust and therefore characterizes the applicable reddening law. Our method is independent of age assumptions and appears to be significantly more precise and accurate than previous approaches. We obtain A_V/E(B-V)=3.76\pm0.07 (random error) for the dust in the line of sight to M4 for our set of filters. With this value, the distance to M4 is found to be 1.80\pm0.05 kpc (random error). A reddening map for M4 has been created, which reveals a spatial differential reddening of delta E(B-V)&gt;0.2 mag across a field within 10' around the cluster centre and a total mean reddening of E(B-V)=0.37\pm0.01. In order to provide accurate zero points for the extinction coefficients of our photometric filters, we investigated the impact of stellar parameters such as temperature, surface gravity and metallicity on the extinction properties in different bandpasses. Using both synthetic ATLAS9 spectra and observed spectral energy distributions, we found similar sized effects for the range of temperature, surface gravity, and metallicity typical of globular cluster stars: each causes a change of about 3% in the necessary correction factor for each filter combination. From our calculations, we provide extinction zero points for Johnson-Cousins and 2MASS filters, spanning a wide range of stellar parameters and dust types, suited for accurate, object-specific extinction corrections.
Genomic Structure and Chromosomal Localization of Human Thioredoxin-Like Protein Gene (txl) (2000)

Human thioredoxin-like protein (txl) is a novel member of the expanding thioredoxin superfamily whose main characteristic is the presence, after the thioredoxin domain, of a C-terminal extension of 184 residues with no homology with any other protein in the databases. Txl is a cytosolic ubiquitously expressed protein and it has been copurified with a kinase of the STE20 family, which is proteolytically activated by caspases in apoptosis. However, no cellular function has yet been assigned to this protein. In the present study we report the genomic organization of the txl gene which encompasses approximately 36 kb organized in eight exons ranging from 96 bp to 303 bp. In contrast, intron sizes are much bigger ranging from 1.5 kb to 12 kb. Chromosomal localization of txl gene revealed that it maps at position 18q21, a region frequently affected in different human tumours. Furthermore, we have identified the putative homologues of txl in both Drosophila melanogaster and Caenorhabditis elegans that display much closer homology to the known thioredoxins than the human txl protein. Indeed, critical residues for optimal thioredoxin activity are present in both Drosophila and Caenorhabditis txl but absent in the human protein suggesting that txl might have evolved to carry out a function different from the general disulfide reductase typical of thioredoxins.
Iron-Catalyzed Negishi Coupling Toward an Effective Olefin Synthesis (2009)

A selective iron-catalyzed cross-coupling of alkyl halides with alkenylzinc reagents is described. Primary and secondary alkyl chlorides, bromides, and iodides take part in the reaction to give the corresponding olefins in good to excellent yields in a stereospecific manner. High functional group compatibility is also demonstrated by using combinations of substrates possessing rather reactive substituents.