gebhart/patrepeval huggingface dataset:
Transgenic fish and aquaculture (1995)

Transgenic fish species can be routinely produced by transferring foreign DNA into developing embryos via microinjection or electroporation. This technology offers an excellent opportunity for modifying or improving the genetic traits of commercially important Fishes, mollusks, and crustaceans for aquaculture. Studies have shown that administration of recombinant fish or mammalian growth hormone (GH) to juvenile fish or oysters resulted in significant growth enhancement. Thus, it is possible to improve the growth rates of marine animals by manipulating GH or its gene. This paper reviews the results of studies to determine the efficacy of recombinant fish GH in improving the growth rates of fishes, mollusks, and crustaceans, and of gene transfer technology in producing fast-growing transgenic animals.
Low-temperature magnetron sputter-deposition, hardness, and electrical resistivity of amorphous and crystalline alumina thin films (2000)

Aluminum oxide films were grown by reactive magnetron sputtering. In order to maintain a stable deposition process and high deposition rate, a pulsed direct current bias was applied to the aluminum target and the substrate. An external solenoid was used to form a magnetic trap between the target and the substrate. The influence of substrate temperature, substrate bias, and the magnetic trap on film growth and properties was studied by different surface and thin-film analysis techniques and electrical measurements. Normally, amorphous alumina films were produced. However, under optimum process conditions, crystalline alumina films can be obtained at temperatures as low as 250 °C, with a hardness ∼20 GPa and excellent electrical insulating properties.
Crystal Structure of Prothrombin Reveals Conformational Flexibility and Mechanism of Activation (2013)

The zymogen prothrombin is composed of fragment 1 containing a Gla domain and kringle-1, fragment 2 containing kringle-2, and a protease domain containing A and B chains. The prothrombinase complex assembled on the surface of platelets converts prothrombin to thrombin by cleaving at Arg-271 and Arg-320. The three-dimensional architecture of prothrombin and the molecular basis of its activation remain elusive. Here we report the first x-ray crystal structure of prothrombin as a Gla-domainless construct carrying an Ala replacement of the catalytic Ser-525. Prothrombin features a conformation 80 Å long, with fragment 1 positioned at a 36° angle relative to the main axis of fragment 2 coaxial to the protease domain. High flexibility of the linker connecting the two kringles suggests multiple arrangements for kringle-1 relative to the rest of the prothrombin molecule. Luminescence resonance energy transfer measurements detect two distinct conformations of prothrombin in solution, in a 3:2 ratio, with the distance between the two kringles either fully extended (54 ± 2 Å) or partially collapsed (≤34 Å) as seen in the crystal structure. A molecular mechanism of prothrombin activation emerges from the structure. Of the two sites of cleavage, Arg-271 is located in a disordered region connecting kringle-2 to the A chain, but Arg-320 is well defined within the activation domain and is not accessible to proteolysis in solution. Burial of Arg-320 prevents prothrombin autoactivation and directs prothrombinase to cleave at Arg-271 first. Reversal of the local electrostatic potential then redirects prothrombinase toward Arg-320, leading to thrombin generation via the prethrombin-2 intermediate.
Polymerase chain reaction detection of nonviable bacterial pathogens (1993)

Polymerase chain reaction (PCR) methodologies for detection of pathogens in environmental samples are currently available. However, positive amplification products for any set of primers only signal that the appropriate target nucleic acid sequences were present in the sample. The presence of the amplification products does not imply that the target organisms were viable. Here we show that PCR will detect nonviable cells, as long as intact target nucleic acid sequences are available. In an environmental water sample, nucleic acids degraded quickly and were not detectable by PCR after 3 weeks even when stored at 4 degrees C. However, these data show that there is a window of opportunity for PCR analyses to result in false positives with respect to viable cells. We further show that care must be taken in the way samples are stored for future PCR amplifications and that filter sterilization of media is not acceptable for long-term preservation of samples for PCR.
Apolipoprotein (apo) E4 enhances HIV-1 cell entry in vitro , and the APOE ε4/ε4 genotype accelerates HIV disease progression (2008)

Originally recognized for their role in lipoprotein metabolism and cardiovascular disease, apolipoprotein (apo) E isoforms (apoE2, apoE3, and apoE4) have also been implicated to play a key role in several biological processes not directly related to their lipid transport function. For example, apoE4 contributes significantly to neurodegeneration in Alzheimer's disease. However, the role of apoE in infectious diseases is less well defined. Here, by examining a large cohort of HIV(+) European and African American subjects, we found that the APOE epsilon4/epsilon4 genotype is associated with an accelerated disease course and especially progression to death compared with the APOE epsilon3/epsilon3 genotype. However, an association between the epsilon4/epsilon4 genotype and HIV-associated dementia (HAD), a neurological condition with clinicopathological features similar to Alzheimer's disease, was not detected. Consistent with the genotype-phenotype relationships observed, compared with recombinant apoE3, apoE4 enhanced HIV fusion/cell entry of both R5 and X4 HIV strains in vitro. These findings establish apoE as a determinant of HIV-AIDS pathogenesis and raise the possibility that current efforts to convert apoE4 to an "apoE3-like" molecule to treat Alzheimer's disease might also have clinical applicability in HIV disease.
Unmasking the information encoded as structural motifs of viral RNA genomes: a potential antiviral target (2013)

RNA viruses show enormous capacity to evolve and adapt to new cellular and molecular contexts, a consequence of mutations arising from errors made by viral RNA-dependent RNA polymerase during replication. Sequence variation must occur, however, without compromising functions essential for the completion of the viral cycle. RNA viruses are safeguarded in this respect by their genome carrying conserved information that does not code only for proteins but also for the formation of structurally conserved RNA domains that directly perform these critical functions. Functional RNA domains can interact with other regions of the viral genome and/or proteins to direct viral translation, replication and encapsidation. They are therefore potential targets for novel therapeutic strategies. This review summarises our knowledge of the functional RNA domains of human RNA viruses and examines the achievements made in the design of antiviral compounds that interfere with their folding and therefore their function.
Identification of the Lymphocytic Choriomeningitis Virus (LCMV) Proteins Required To Rescue LCMV RNA Analogs into LCMV-Like Particles (2002)

We have used a reverse genetic approach to identify the viral proteins required for packaging and assembly of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV). Plasmids encoding individual LCMV proteins under the control of an RNA polymerase II promoter were cotransfected with a plasmid containing an LCMV minigenome (MG). Intracellular synthesis of the LCMV MG was driven by T7 RNA polymerase whose expression was also mediated by a Pol II promoter. The supernatant from transfected cells was passaged onto fresh cells that were subsequently infected with LCMV to provide the minimal viral trans-acting factors, NP and L, that are required for LCMV MG RNA replication and expression. Reconstitution of LCMV-specific packaging and passage was detected by expression of the chloramphenicol acetyl transferase (CAT) reporter gene present in the MG. NP and L did not direct detectable levels of MG passage. Addition of Z and GP resulted in high levels of passage of CAT activity, which could be prevented by LCMV neutralizing antibodies. Passage of LCMV MG was inhibited by omission of either GP or Z.
Examination of Racial Disparities in Childhood Asthma Management Practices (2008)

Objective: To analyze asthma management plan practices for children with asthma in the United States considering race and other demographic and person-level characteristics.\nMethods: Univariate/Bivariate/Multivariate analysis was performed to examine asthma management plan physician recommendations among children in the United States utilizing secondary data analysis of the 2002 and 2003 National Health Interview Survey.\nResults: The majority of the study participants reported not having an asthma management plan at (59.00%). In multivariate analysis using SAS callable SUDAAN, Whites were significantly more likely to have an asthma management plan (OR=1.66, p=.0031).\nConclusion: Findings from this study indicate that Black and Hispanic children with asthma are less likely to have an asthma management plan. Mandating all insurers to provide an asthma management plan to children with asthma may reduce the race-based inequities and requiring emergency room physicians to provide children with an asthma management plan may target those children that do not have a plan.
Performance Characteristics of a Quantitative TaqMan Hepatitis C Virus RNA Analyte-Specific Reagent (2004)

We determined the dynamic range, reproducibility, accuracy, genotype bias, and sensitivity of the TaqMan hepatitis C virus (HCV) analyte-specific reagent (ASR). Serum samples were processed using the MagNA Pure LC instrument and run on the COBAS TaqMan 48 analyzer. The performance characteristics of the ASR were also compared with those of the qualitative AMPLICOR and quantitative AMPLICOR MONITOR HCV tests. The ASR exhibited a >/=6-log(10) linear dynamic range and excellent reproducibility, with a mean coefficient of variation of 14%. HCV RNA concentration measured with the ASR agreed within an average of 0.42 log(10) (2.6-fold) of the labeled concentration with members of a standard reference panel. HCV genotypes 1 to 4 were amplified with similar efficiencies with the ASR. The ASR and AMPLICOR MONITOR viral load results were significantly correlated (r = 0.8898; P < 0.01), but the agreement was poor (mean difference, 0.45 +/- 0.35 log(10)) for 72 HCV RNA-positive clinical samples. However, 98.9% agreement between the ASR and qualitative AMPLICOR test results was found with 60 positive and 29 negative samples. Limiting-dilution experiments demonstrated that the limits of detection for ASR and AMPLICOR tests were 84 and 26 IU/ml, respectively. The performance characteristics of the TaqMan HCV ASR are appropriate for all clinical applications of HCV RNA testing.
[Protective effect of compound tongfu granule on intestinal mucosal barrier in patients with cirrhosis of decompensation stage]. (2008)

CTG can improve the intestinal barrier function, correct the intestinal bacteria disturbance, and significantly reduce the entero-derived endotoxemia in cirrhotic patients of decompensation stage.
Antitumor Monoclonal Antibodies Enhance Cross-Presentation of Cellular Antigens and the Generation of Myeloma-specific Killer T Cells by Dendritic Cells (2002)

The mechanism of antitumor effect of monoclonal antibodies (mAbs) is not fully understood. Here we show that coating myeloma cells with anti-syndecan-1 antibody promotes cross-presentation of cellular antigens by dendritic cells (DCs) to autologous T cells from healthy donors. The tumor cells treated with anti-syndecan-1 or isotype-matched control antibody were fed to HLA-mismatched monocyte-derived immature DCs. Tumor cell-loaded mature DCs induced a strong CD8(+) T cell response that was specific for the cancer-testis (C-T) antigens expressed in the tumor. The CD8(+) T cells killed peptide-pulsed targets, as well as myeloma tumor cells. Importantly, mAbs-coated tumor-loaded DCs were consistently superior to DCs loaded with peptides or dying cells for eliciting tumor-specific killer T cells. This enhanced cross-presentation was not due to enhanced tumor cell uptake or to DC maturation. When mixtures of NY-Eso-1-positive and -negative myeloma cells were captured by DCs, the anti-syndecan-1 antibody had to be on the NY-Eso-1-positive cells to elicit NY-Eso-1-specific response. Cross-presentation was inhibited by pretreatment of DCs with Fc gamma receptor blocking antibodies. Targeting of mAb-coated tumors to DCs may contribute to the efficacy of tumor-reactive mAb and offers a new strategy for immunotherapy.
The Vero cell-derived, inactivated, SA14-14-2 strain-based vaccine (Ixiaro) for prevention of Japanese encephalitis (2015)

With an estimated 68,000 cases each year, Japanese encephalitis (JE) is the leading cause of viral encephalitis in Asia. Vaccination against the disease is recommended for endemic populations and also for travelers at risk. Recently, a Vero cell-derived, inactivated, SA14-14-2 strain-based JE vaccine (JE-VC) became available for travelers from non-endemic regions, replacing the traditional mouse brain-derived vaccines. First licensed in 2009, JE-VC is currently available in Europe, the USA, Canada, Australia and several other countries. In 2013, the vaccine was approved by the European Medicines Agency and the US Food and Drug Administration for use in children. This review summarizes current data on the immunogenicity, safety and clinical use of JE-VC.
CRYSTAL AND MOLECULAR STRUCTURE OF 2-OXO-BIS(2-β-CHLOROETHYLAMINO)-4,6-DIMETHYL-1,3,2-OXAZAPHOSPHORINANE: AN ANALOGUE OF CYCLOPHOSPHAMIDE (1982)

Abstract The isomer of the title compound chosen for determination of its crystal and molecular structure by x-ray means has been found to possess an axial mustard group and an equatorial phosphoryl oxygen. This contrasts the phosphorus stereochemistry in cyclophosphamide in which these groups are interchanged. As a consequence of forcing the mustard group into the axial position in the title compound, the C2N plane of this moiety is positioned such that neither of the pendant ClCH2CH2 groups are under the ring. The rotomeric conformation of this group differs from that in cyclophosphamide wherein the mustard C2N plane is perpendicular to the OPN plane in the ring.
Asymmetric Aldol Reaction via a Dinuclear Zinc Catalyst:  α-Hydroxyketones as Donors (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAsymmetric Aldol Reaction via a Dinuclear Zinc Catalyst: α-Hydroxyketones as DonorsBarry M. Trost, Hisanaka Ito, and Elliad R. SilcoffView Author Information Department of Chemistry, Stanford University Stanford, California 94305-5080 Cite this: J. Am. Chem. Soc. 2001, 123, 14, 3367–3368Publication Date (Web):March 15, 2001Publication History Received6 November 2000Published online15 March 2001Published inissue 1 April 2001https://pubs.acs.org/doi/10.1021/ja003871hhttps://doi.org/10.1021/ja003871hrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views4735Altmetric-Citations291LEARN 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:Aldehydes,Aldol reactions,Catalysts,Selectivity,Stereoselectivity Get e-Alerts
Moderated statistical tests for assessing differences in tag abundance (2007)

Abstract Motivation: Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. They are sensitive technologies for measuring gene expression on a genomic scale, without the need for prior knowledge of the genome sequence. As the cost of sequencing DNA decreases, the number of DGE datasets is expected to grow dramatically. Various tests of differential expression have been proposed for replicated DGE data using binomial, Poisson, negative binomial or pseudo-likelihood (PL) models for the counts, but none of the these are usable when the number of replicates is very small. Results: We develop tests using the negative binomial distribution to model overdispersion relative to the Poisson, and use conditional weighted likelihood to moderate the level of overdispersion across genes. Not only is our strategy applicable even with the smallest number of libraries, but it also proves to be more powerful than previous strategies when more libraries are available. The methodology is equally applicable to other counting technologies, such as proteomic spectral counts. Availability: An R package can be accessed from http://bioinf.wehi.edu.au/resources/ Contact: smyth@wehi.edu.au Supplementary information: http://bioinf.wehi.edu.au/resources/
Targeting Dinitrophenol to Mitochondria: Limitations to the Development of a Self-limiting Mitochondrial Protonophore (2006)

The protonmotive force (Deltap) across the mitochondrial inner membrane drives ATP synthesis. In addition, the energy stored in Deltap can be dissipated by proton leak through the inner membrane, contributing to basal metabolic rate and thermogenesis. Increasing mitochondrial proton leak pharmacologically should decrease the efficiency of oxidative phosphorylation and counteract obesity by enabling fatty acids to be oxidised with decreased ATP production. While protonophores such as 2,4-dinitrophenol (DNP) increase mitochondrial proton leak and have been used to treat obesity, a slight increase in DNP concentration above the therapeutically effective dose disrupts mitochondrial function and leads to toxicity. Therefore we set out to develop a less toxic protonophore that would increase proton leak significantly at high Deltap but not at low Deltap. Our design concept for a potential self-limiting protonophore was to couple the DNP moiety to the lipophilic triphenylphosphonium (TPP) cation and this was achieved by the preparation of 3-(3,5-dinitro-4-hydroxyphenyl)propyltriphenylphosphonium methanesulfonate (MitoDNP). TPP cations accumulate within mitochondria driven by the membrane potential (Deltapsi), the predominant component of Deltap. Our hypothesis was that MitoDNP would accumulate in mitochondria at high Deltapsi where it would act as a protonophore, but that at lower Deltapsi the accumulation and uncoupling would be far less. We found that MitoDNP was extensively taken into mitochondria driven by Deltapsi. However MitoDNP did not uncouple mitochondria as judged by its inability to either increase respiration rate or decrease Deltapsi. Therefore MitoDNP did not act as a protonophore, probably because the efflux of deprotonated MitoDNP was inhibited.
SEPARATION OF THE LIGHT AND DARK REACTIONS IN ELECTRON TRANSFER DURING PHOTOSYNTHESIS (1963)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Red cell distribution width, haemoglobin A1c and incidence of diabetes mellitus (2014)

Low RDW is associated with increased incidence of DM independently of other risk factors. We propose that low RDW could be a surrogate marker of reduced RBC survival, with lower HbA1c due to shorter duration of glucose exposure. RDW is a biomarker that could improve risk assessment for individuals at risk of developing DM.
Suppression of Heating Rates in Cryogenic Surface-Electrode Ion Traps (2008)

Dense arrays of trapped ions provide one way of scaling up ion trap quantum information processing. However, miniaturization of ion traps is currently limited by sharply increasing motional state decoherence at sub-100 mum ion-electrode distances. We characterize heating rates in cryogenically cooled surface-electrode traps, with characteristic sizes in the 75 to 150 mum range. Upon cooling to 6 K, the measured rates are suppressed by 7 orders of magnitude, 2 orders of magnitude below previously published data of similarly sized traps operated at room temperature. The observed noise depends strongly on the fabrication process, which suggests further improvements are possible.
Thyroxine Promotes Association of Mitogen-activated Protein Kinase and Nuclear Thyroid Hormone Receptor (TR) and Causes Serine Phosphorylation of TR (2000)

Activated nongenomically by l-thyroxine (T(4)), mitogen-activated protein kinase (MAPK) complexed in 10-20 min with endogenous nuclear thyroid hormone receptor (TRbeta1 or TR) in nuclear fractions of 293T cells, resulting in serine phosphorylation of TR. Treatment of cells with the MAPK kinase inhibitor, PD 98059, prevented both T(4)-induced nuclear MAPK-TR co-immunoprecipitation and serine phosphorylation of TR. T(4) treatment caused dissociation of TR and SMRT (silencing mediator of retinoid and thyroid hormone receptor), an effect also inhibited by PD 98059 and presumptively a result of association of nuclear MAPK with TR. Transfection into CV-1 cells of TR gene constructs in which one or both zinc fingers in the TR DNA-binding domain were replaced with those from the glucocorticoid receptor localized the site of TR phosphorylation by T(4)-activated MAPK to a serine in the second zinc finger of the TR DNA-binding domain. In an in vitro cell- and hormone-free system, purified activated MAPK phosphorylated recombinant human TRbeta1 (). Thus, T(4) activates MAPK and causes MAPK-mediated serine phosphorylation of TRbeta1 and dissociation of TR and the co-repressor SMRT.
[p53 gene polymorphism with susceptibility to esophageal cancer and lung cancer in Chinese population]. (2003)

In the northern Chinese population, p53 Pro/Pro genotype is an independent risk factor for both esophageal cancer and lung cancer. The possible common genetic basis of the development of these two cancers is suggested by this study.
Intensive Care Society's APACHE II study in Britain and Ireland--I: Variations in case mix of adult admissions to general intensive care units and impact on outcome. (1993)

Comparing crude death rates in hospital between intensive care units may be misleading indicators of performance. The collection of data on case mix needs to be standardised and differences in case mix adjusted for when comparing outcome between different intensive care units.