gebhart/patrepeval huggingface dataset:
A Subset of CD4+ T Cells Expressing Early Activation Antigen CD69 in Murine Lupus: Possible Abnormal Regulatory Role for Cytokine Imbalance (1998)

Systemic lupus erythematosus (SLE), which spontaneously develops in (NZB (New Zealand Black) x NZW (New Zealand White)) F1 mice, is strictly dependent on CD4+ T cells. We found that in these mice with overt SLE, CD4+ T cells expressing CD69 molecules, an early activation Ag, are dramatically increased in peripheral lymphoid tissues and inflammatory infiltrates in the kidney and lung, but not in peripheral blood, while CD8+ and NK1.1+ T cells were virtually CD69-. Various adhesion molecules, including LFA-1, ICAM-1, CD43, CD44, P-selectin, and E-selectin, were up-regulated. Analysis of the TCR repertoire showed no skewed TCR Vbeta usage. Studies on in vitro cytokine production of spleen cells on TCR cross-linking indicated that compared with findings in young mice, the aged mice showed severely impaired production of IL-2, IL-3, and IL-4, whereas the levels of IL-10 and IFN-gamma remained relatively intact. FACS-sorted CD69-CD4+ T cells from aged mice produced substantial amounts of these cytokines, including IL-2, IL-3, and IL-4, whereas CD69+CD4+ T cells were poor producers. Intriguingly, when cocultured, CD69+CD4+ T cells significantly inhibited the production of IL-2 by CD69-CD4+ T cells. IL-2 production by spleen cells from young mice was also markedly inhibited in the presence of CD69+CD4+ T cells obtained from aged mice. We propose that CD69+CD4+ T cells that are continuously activated by self peptides bound to MHC class II molecules in (NZB x NZW)F1 mice may be involved in the pathogenesis of SLE through abnormal regulatory effects on cytokine balance.
Identification of a Hepatic Factor Capable of Supporting Hepatitis C Virus Replication in a Nonpermissive Cell Line (2001)

Although hepatitis C virus E2 protein can bind to human cells by interacting with a putative viral receptor, CD81, the interaction alone is not sufficient to establish permissiveness for hepatitis C virus infection. Using an Epstein-Barr virus-based extrachromosomal replication system, we have screened through a human liver cDNA library and successfully identified a cDNA capable of supporting hepatitis C virus replication in an otherwise nonpermissive cell line. This cDNA encodes a protein exhibiting homology to a group of proteins derived from various evolutionarily distant species, including Oryza sativa submergence-induced protein 2A. The mRNAs encoding this factor are heterogeneous at the 5' ends and are ubiquitously expressed in multiple tissues, albeit in a very small amount. The longest mRNA contains an in-frame and upstream initiation codon and codes for a larger protein. This 5'-extended form of mRNA was detected in hepatocellular carcinoma, but not in normal liver tissue. Immunofluorescence analysis demonstrated that the hepatic factor was distributed evenly in cells, but occasionally formed aggregations in the peri- or intranuclear areas. In summary, we have identified a hepatic factor capable of supporting hepatitis C virus replication in an otherwise nonpermissive cell line. This factor belongs to a previously uncharacterized protein family. The physiological function of this protein awaits further study.
Multilabel Random Walker Image Segmentation Using Prior Models (2005)

The recently introduced random walker segmentation algorithm by Grady and Funka-Lea (2004) has been shown to have desirable theoretical properties and to perform well on a wide variety of images in practice. However, this algorithm requires user-specified labels and produces a segmentation where each segment is connected to a labeled pixel. We show that incorporation of a nonparametric probability density model allows for an extended random walkers algorithm that can locate disconnected objects and does not require user-specified labels. Finally, we show that this formulation leads to a deep connection with the popular graph cuts method by Boykov et al. (2001) and Wu and Leahy (1993).
Extending the scope of the Checkpoint‐on‐Failure protocol for forward recovery in standard MPI (2013)

SUMMARY Most predictions of exascale machines picture billion ways parallelism, encompassing not only millions of cores but also tens of thousands of nodes. Even considering extremely optimistic advances in hardware reliability, probabilistic amplification entails that failures will be unavoidable. Consequently, software fault tolerance is paramount to maintain future scientific productivity. Two major problems hinder ubiquitous adoption of fault tolerance techniques: (i) traditional checkpoint‐based approaches incur a steep overhead on failure free operations and (ii) the dominant programming paradigm for parallel applications (the message passing interface (MPI) Standard) offers extremely limited support of software‐level fault tolerance approaches. In this paper, we present an approach that relies exclusively on the features of a high quality implementation, as defined by the current MPI Standard, to enable advanced forward recovery techniques, without incurring the overhead of customary periodic checkpointing. With our approach, when failure strikes, applications regain control to make a checkpoint before quitting execution. This checkpoint is in reaction to the failure occurrence rather than periodic. This checkpoint is reloaded in a new MPI application, which restores a sane environment for the forward, application‐based recovery technique to repair the failure‐damaged dataset. The validity and performance of this approach are evaluated on large‐scale systems, using the QR factorization as an example. Published 2013. This article is a US Government work and is in the public domain in the USA.
CircumVent thermal cycle sequencing and alternative manual and automated DNA sequencing protocols using the highly thermostable VentR (exo-) DNA polymerase. (1992)

CircumVent thermal cycle and standard DNA sequencing protocols utilizing the cloned and highly thermostable VentR (exo-) DNA polymerase are described. The thermal cycle sequencing procedures are advantageous because they allow fast and simple semiautomation of the sequencing reaction; make possible the direct DNA sequencing of PCR products, bacterial colonies and phage plaques; require only femtomoles of template DNA; eliminate the requirement of an independent primer annealing step; remove the requirement of denatured plasmids for sequencing double-stranded templates; and use a highly thermostable DNA polymerase for sequencing through potential recalcitrant secondary structure domains and large linear double-stranded DNA templates such as lambda derivatives. More standard methods of DNA sequencing (i.e., a one-step protocol and a labeling-termination protocol) are also presented. For each protocol, alternatives for choice of label and method of labeling are presented, including the use of 5' biotinylated primers for chemiluminescent DNA sequencing and fluorinated primers for automated sequencing using the BaseStation Automated DNA Sequencer.
Limited combinatorial repertoire of gamma delta T-cell receptors expressed by T-cell acute lymphoblastic leukemias. (1991)

Detailed analysis of the rearrangement and expression of T-cell receptor gamma (TcR-gamma) and TcR-delta genes was performed in ten TcR-gamma delta+ T-cell acute lymphoblastic leukemias (T-ALL). In nine T-ALL the TcR-gamma genes were rearranged on both alleles, whereas in the tenth leukemia one allele was rearranged and the other was in germline configuration. Twelve out of the 19 rearranged alleles contained rearrangements of the J gamma 2.3 gene segment, five of which were to the V gamma 8 gene segment and three to the V gamma 3 gene segment. This implies that the combinatorial repertoire of the rearranged TcR-gamma gene is restricted due to the preferential usage of several V gamma and J gamma gene segments. The TcR-delta genes were rearranged on both alleles in nine T-ALL, whereas in the tenth leukemia one allele was rearranged and the other deleted. The combinatorial repertoire of the TcR-delta genes was homogeneous, as in all ten T-ALL at least one allele contained a V delta 1-J delta 1 rearrangement. In at least nine of the ten T-ALL the V delta 1-J delta 1 allele coded for the expressed TcR-delta chain, as was supported by reactivity with the anti-V delta 1-J delta 1 (delta TCS1) antibody in all T-ALL tested. As the total repertoire of the TcR molecules is not only dependent on combinations of gene segments, but also on the size and diversity of the junctional regions, we studied the V delta 1-J delta 1 junctional regions using the polymerase chain reaction (PCR) technique. These PCR analyses showed that the size of the V delta 1-J delta 1 junctional regions differed markedly (up to approximately 30 bases or more) between the leukemias. Therefore we conclude that the combinatorial repertoire of TcR-delta S+ T-ALL is limited, especially due to the homogeneous TcR-gamma gene rearrangements, but that the junctional repertoire of the TcR-delta genes seems to be extensive.
Study in the Terpene Series. X. Isomerization Accompanying Hydrogenolysis of Alcohols (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudy in the Terpene Series. X. Isomerization Accompanying Hydrogenolysis of AlcoholsV. N. Ipatieff, W. W. Thompson, and Herman PinesCite this: J. Am. Chem. Soc. 1951, 73, 2, 553–555Publication Date (Print):February 1, 1951Publication History Published online1 May 2002Published inissue 1 February 1951https://pubs.acs.org/doi/10.1021/ja01146a013https://doi.org/10.1021/ja01146a013research-articleACS PublicationsRequest reuse permissionsArticle Views150Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Identification of an internal cis-element essential for the human Li transcription and a nuclear factor(s) binding to the element (1992)

L1 (LINE-1) is a long interspersed repetitive sequence derived from a retrotransposon. Transfection studies using the CAT gene as a reporter demonstrated that the first 155bp in the human L1 sequence contains an element(s) responsible for the promoter activity in HeLa cells. The transcription was shown to initiate at the first nucleotide of the L1 sequence in the transgene. Three prominent nuclear protein binding sites were found in the 5' region of the L1 sequence by DNaseI footprint analysis. One of the binding sites, designated as site A located at +3 to +26, was shown to be essential for the L1 transcription because the mutation at the site A caused almost complete loss of the promoter activity. A sequence AAGATGGCC at +11 to +19 in the site A was defined as a target core element for the protein binding. The site A-binding protein (designated TFL1-A) was found in various types of cells including an embryonic teratocarcinoma cell line. These results indicate that an internal short element located at the very 5' terminal of L1 sequence and the nuclear factor binding to the element play a crucial role in the transcription of human L1.
Protocols in Human Molecular Genetics (1991)

Extraordinary advances have been made in the field of human molecular genetics during the past five years. The ability to amplify a specific region ofDNA a millionfold in a few hours using the polymerase chain reaction has led to the rapid identification of mutations in human disease and of DNA sequence polymorphisms on every human chro- some. DNA fragments of up to 1 megabase in length can now be resolved by pulsed-field gel electrophoresis to create long-range physical maps of important regions of the genome, and can be cloned in the form of yeast artificial chromosomes. The discovery of highly variable "minisatellite" DNA sequences has led to the development of DNA fingerprinting. The application of these techniques to the study of the human genome has culminated in major advances such as the cloning of the cystic fibrosis gene, the construction of genetic linkage maps of each human chro- some, the mapping of many genes responsible for human inherited d- orders, genetic fingerprinting of forensic specimens, and the detection of mutations involved in the development of human tumors. Although many of the new techniques in molecular genetics can be learned relatively easily, it is often difficult for a researcher to obtain all of the relevant information necessary for getting up a technique and applying it successfully. The information available in the research lite- ture often lacks the depth of description that the new user requires
Histone variants and histone modifications: A structural perspective (2001)

In this review, we briefly analyze the current state of knowledge on histone variants and their posttranslational modifications. We place special emphasis on the description of the structural component(s) defining and determining their functional role. The information available indicates that this histone "variability" may operate at different levels: short-range "local" or long-range "global", with different functional implications. Recent work on this topic emphasizes an earlier notion that suggests that, in many instances, the functional response to histone variability is possibly the result of a synergistic structural effect.
Effects of processing variables on the magnetic properties of melt-processed YBa2Cu3O (1997)

Samples of YBa2Cu3Ox (Y123) with excess Y2BaCuO5 (Y211) in the molar ratio of 5:1 (Y123/Y211) were processed using the SLMG (‘solid-liquid melt growth’) technique. The effects of precursor particle size, thermal pretreatment, and substrate choice were examined. Particle size was shown to accelerate degradation of the BaCuO2 precursor. Thermal pretreatment resulted in reduction of porosity in the samples and hence improved magnetic properties. Contamination by carbon and magnesium from the substrates was also examined and eliminated by using BaZrO3 substrates.
Dynamics and Free Energy of Polymers Partitioning into a Nanoscale Pore (1996)

Membrane-bound proteinaceous nanoscale pores allow us to simultaneously observe the thermodynamic and kinetic properties of differently sized polymers within their confines. We determine the dynamic partitioning of poly(ethylene glycol) (PEG) into the pore formed by Staphylococcus aureus α-toxin and evaluate the free energy of polymer confinement by measuring polymer-induced changes to the pore's ionic conductance. The free energy deduced from the partition coefficient has a sharper dependence on polymer length (or weight) than scaling theory predicts. Moreover, the polymer-induced conductance fluctuations show a striking nonmonotonic dependence on the polymer molecular weight. The movement of polymer inside the pore is characterized by a diffusion coefficient that is orders of magnitude smaller than that for polymer in the bulk aqueous solution, which suggests that PEG has an attractive interaction with the pore. Using an ad-hoc approach, we show that a simple molecular weight-dependent modification of the polymer's diffusion coefficient accounts for these results, but only qualitatively. Given that PEG associates with hydrophobic regions in proteins, we also conclude that, contrary to the conventional view of ion channels, the aqueous cavity of the α-toxin pore's interior is, to some extent, hydrophobic.
Mesoporous Materials for Drug Delivery (2007)

Research on mesoporous materials for biomedical purposes has experienced an outstanding increase during recent years. Since 2001, when MCM-41 was first proposed as drug-delivery system, silica-based materials, such as SBA-15 or MCM-48, and some metal-organic frameworks have been discussed as drug carriers and controlled-release systems. Mesoporous materials are intended for both systemic-delivery systems and implantable local-delivery devices. The latter application provides very promising possibilities in the field of bone-tissue repair because of the excellent behavior of these materials as bioceramics. This Minireview deals with the advances in this field by the control of the textural parameters, surface functionalization, and the synthesis of sophisticated stimuli-response systems.
Comparative analysis ofCandidabiofilm quantitation assays (2011)

Candida grows on devices producing treatment resistant biofilms. A key tool for the study of biofilms includes an accurate assessment of viable cell growth. This study systematically tested seven techniques, among which the XTT assay provided the most reproducible, accurate, and efficient method for the quantitative estimation of C. albicans biofilms.
Unpowered resonant wireless sensor nets for structural health monitoring (2008)

The primary objective of this work is the development of low-cost, wireless, unpowered, resonant sensor nets that can be used to monitor large areas in civil infrastructure systems. A critical new area of research relates to the coupling of individual sensors into a net to produce collective, crystal-like behavior, allowing large area coverage with high sensitivity to damage. We are investigating such collective phenomena in arrays of passive resonant sensors. The goal is to provide information about corrosion (or some other ldquotargetrdquo) anywhere within the sensor array. An electronic structural surveillance (ESS) net is formed from an array of inductively coupled, resonant sensors, such as those developed in our previous work. Here we present results showing the collective behavior of such a system that should lead to both larger areal coverage and more sensitive detection of small defects.
Integrated Pest Management (IPM) of the Caribbean Crazy Ant, Nylanderia (=Paratrechina) pubens (Forel) (2011)

Incidents of Caribbean crazy ant infestations are on the rise! These highly active ants are annoying to residents and pets. And, they can cause short circuits and power outages if they infest electrical equipment. Learn how to identify and apply the principles of integrated pest management (IPM) to deal with these difficult pests in this 4-page fact sheet written by Dawn Calibeo and Faith Oi and published by the UF Department of Entomology and Nematology, July 2011. ENY-2006/IN889: Integrated Pest Management (IPM) of the Tawny Crazy Ant, Nylanderia fulva (Mayr) (ufl.edu)
Projective depth: A geometric invariant for 3D reconstruction from two perspective/orthographic views and for visual recognition (2002)

The author addresses the problems of reconstructing 3-D space in a projective framework from two views and of artificially generating novel views of the scene from two given views. It is shown that with the correspondences coming from four non-coplanar points in the scene and the corresponding epipoles, it is possible to define and reconstruct a projective invariant, referred to as projective depth, that can be used later to reconstruct the projective or affine structure of the scene or directly to generate novel views of the scene. The derivation has the advantage that the viewing transformation matrix need not be recovered in the course of computations. >
Bacterial Characteristics in Relation to Clinical Source of Escherichia coli Isolates from Women with Acute Cystitis or Pyelonephritis and Uninfected Women (2005)

Characteristics differentiating Escherichia coli strains that cause cystitis or pyelonephritis from fecal E. coli remain incompletely defined, particularly among adult women in the United States. Accordingly, phylogenetic group, O antigens, and virulence factors (VFs) were analyzed among 329 E. coli isolates from the mid-to-late 1990s from women in the United States with acute pyelonephritis (n = 170), cystitis (n = 83), or no infection (fecal; n = 76). Compared with fecal and cystitis isolates, pyelonephritis isolates exhibited a greater prevalence of phylogenetic group B2, most virulence-associated O antigens, and most VFs and had higher VF scores. In contrast, cystitis and fecal isolates differed minimally. By stepwise multivariable logistic regression, significant (P < or = 0.015) predictors of cystitis and/or pyelonephritis (versus fecal) included afa/dra (Dr-binding adhesins), ibeA (invasion of brain endothelium), iha (putative adhesin-siderophore), malX (pathogenicity island marker), the O75 antigen, papEF (P fimbriae), papG allele II (P adhesin variant), group B2, and sfa/foc (S and F1C fimbriae). However, virulence profiles overlapped considerably among source groups and varied greatly within each group. E. coli "clonal group A" (CGA) and the O2:K5/K7:H1 and O75:K+ clonal groups were significantly associated with cystitis and/or pyelonephritis. These findings identify potential vaccine targets, suggest that urovirulence is multiply determined, and confirm the urovirulence of specific E. coli clonal groups, including recently recognized CGA.
Recombinant Subunits of Mammalian Elongation Factor 1 Expressed in Escherichia coli (1997)

The first step in elongation requires two different activities; elongation factor (EF)-1alpha transfers aminoacyl-tRNA to the ribosome and is released upon hydrolysis of GTP, EF-1betagammadelta catalyzes exchange of GDP on EF-1alpha with GTP. To analyze the role of the individual subunits of EF-1 in elongation, the cDNAs for the beta, gamma, and delta subunits of EF-1 from rabbit were cloned, and proteins of 225, 437, and 280 amino acids, respectively, were expressed in Escherichia coli. The purified recombinant beta subunit migrates as a dimer and the gamma subunit as a trimer upon gel filtration, whereas the delta subunit forms a large aggregate. Complexes of betagamma, gammadelta and betagammadelta were formed by self-association and eluted with a molecular mass of approximately 160, 530, and 670 kDa, respectively; no interaction was observed between beta and delta. The activity of the recombinant subunits was determined with native EF-1alpha by measuring stimulation of the rate of elongation by poly(U)-directed polyphenylalanine synthesis. Recombinant beta and delta alone stimulated the rate of elongation by 10-fold, with a ratio of 5alpha:2beta or delta. The betagammadelta complex stimulated EF-1alpha activity up to 10-fold with a ratio of 20alpha to 1betagammadelta. Phosphorylation of the beta and delta subunits alone or in betagammadelta by protein kinase CKII had no effect on the rate of elongation.
α‐Heteroatom‐Substituted Alkanamides (2006)

Abstract For Abstract see ChemInform Abstract in Full Text.
1932 (2014)

Abstract In these diary entries written between June and December 1932, Hollywood screenwriter Charles Brackett reveals that he was “impelled” to keep a diary after reading the Civil War diaries of his great uncle, William Corliss (1854–1915). Brackett says the best he can offer in substitution for the war is the Depression. He also talks about his interview with producer Jed Harris about his play, Present Laughter; his travel (by car) to Stockbridge to spend the day with his wife, Elizabeth; the suicide of Smith Reynolds, the bridegroom of blues singer Libby Holman; his weekend stay at the farmhouse of George and Beatrice Kaufman in Manhasset, Long Island; the relationship between Alexander Woollcott and Charles Lederer; and the telephone call from Otto Liveright telling Brackett about a new Hollywood offer; and his meeting with George Cukor and Constance Bennett.