gebhart/patrepeval huggingface dataset:
Vibrio cholerae O395 tcpA pilin gene sequence and comparison of predicted protein structural features to those of type 4 pilins (1990)

Vibrio cholerae O1 expresses a pilus that is coordinately regulated with cholera toxin production and hence termed TCP, for toxin-coregulated pilus. Insertion of Tn5 IS50L::phoA (TnphoA) into the major pilin subunit gene, tcpA, has previously been shown to render the strain avirulent as a result of its inability to colonize. One such insertion was isolated and used as a probe to screen for clones containing the intact tcpA gene. The DNA sequence of tcpA was determined by using the intact gene and several tcpA-phoA gene fusions. The deduced protein sequence agreed completely with that previously determined for the TcpA N terminus and with the size of the mature pilin protein. The reported homology with N-methylphenylalanine (type 4) pilins near the N terminus was extended and shown to include components of the atypical leader peptide as well as overall predicted structural similarities in other regions of the pilins. In contrast to the modified N-terminal phenylalanine residue found in all characterized type 4 pilins, the corresponding position in tcpA contains a Met codon, thus implying that the previously uncharacterized amino acid corresponding to the N-terminal position of the mature TcpA pilin is a modified form of methionine. Except for this difference, mature TcpA has the overall predicted structural motifs shared among type 4 pilins.
Identifying Key Regulatory Genes in the Whole Blood of Septic Patients to Monitor Underlying Immune Dysfunctions (2013)

There is currently no reliable tool available to measure immune dysfunction in septic patients in the clinical setting. This proof-of-concept study assesses the potential of gene expression profiling of whole blood as a tool to monitor immune dysfunction in critically ill septic patients. Whole-blood samples were collected daily for up to 5 days from patients admitted to the intensive care unit with sepsis. RNA isolated from whole-blood samples was assayed on Illumina HT-12 gene expression microarrays consisting of 48,804 probes. Microarray analysis identified 3,677 genes as differentially expressed across 5 days between septic patients and healthy controls. Of the 3,677 genes, biological pathway analysis identified 86 genes significantly downregulated in the sepsis patients were present in pathways relating to immune response. These 86 genes correspond to known immune pathways implicated in sepsis, including lymphocyte depletion, reduced T-lymphocyte activation, and deficient antigen presentation. Furthermore, expression levels of these genes correlated with clinical severity, with a significantly greater degree of downregulation found in nonsurvivors compared with survivors. The results show that whole-blood gene expression analysis can capture systemic immune dysfunctions in septic patients. Our study provides an experimental basis to support further study on the use of a gene expression-based assay, to assess immunosuppression, and to guide immunotherapy in future clinical trials.
Transgenic Tobacco Plants Overexpressing Chitinases of Fungal Origin Show Enhanced Resistance to Biotic and Abiotic Stress Agents (2006)

Genes encoding defense-related proteins have been used to alter the resistance of plants to pathogens and other environmental challenges, but no single fungal gene overexpression has produced broad-spectrum stress resistance in transgenic lines. We have generated transgenic tobacco (Nicotiana tabacum) lines that overexpress the endochitinases CHIT33 and CHIT42 from the mycoparasitic fungus Trichoderma harzianum and have evaluated their tolerance to biotic and abiotic stress. Both CHIT33 and CHIT42, individually, conferred broad resistance to fungal and bacterial pathogens, salinity, and heavy metals. Such broad-range protective effects came off with no obvious detrimental effect on the growth of tobacco plants.
Yeast transformation: a model system for the study of recombination. (1981)

DNA molecules that integrate into yeast chromosomes during yeast transformation do so by homologous recombination. We have studied the way in which circular and linear molecules recombine with homologous chromosomal sequences. We show that DNA ends are highly recombinogenic and interact directly with homologous sequences. Circular hybrid plasmids can integrate by a single reciprocal crossover, but only at a low frequency. Restriction enzyme digestion within a region homologous to yeast chromosomal DNA greatly enhances the efficiency of integration. Furthermore, if two restriction cuts are made within the same homologous sequence, thereby removing an internal segment of DNA, the resulting deleted-linear molecules are still able to transform at a high frequency. Surprisingly, the integration of these gapped-linear molecules results in replacement of the missing segment using chromosomal information. The final structure is identical to that obtained from integration of a circular molecule. The integration of linear and gapped-linear molecules, but not of circular molecules, is blocked by the rad52-1 mutation. Consideration of models for plasmid integration and gene conversion suggests that RAD52 may be involved in the DNA repair synthesis required for these processes. Implications of this work for the isolation of integrative transformants, fine-structure mapping, and the cloning of mutations are discussed.
Oligonucleotide probes specific for the genus Salmonella and for Salm. typhimurium (1995)

Synthetic oligonucleotides have been deduced and synthesized based on the sequence of a salmonella-specific polynucleotide probe. Two oligonucleotide probes, ST4 and ST15rev hybridized to 93 and 92 strains respectively out of 93 strains of Salmonella analysed. ST4, however, cross hybridized to one of the 28 strains of 16 genera of Enterobacteriaceae tested. Based on sequence alignment, in 16 strains of Salmonella, of a 114 base pair region, a Salm. typhimurium specific oligonucleotide probe, ST22, was identified. In colony hybridization, this probe detected all 47 strains of Salm. typhimurium analysed without hybridization to 94 strains of other Salmonella serotypes and to 26 strains of non-Salmonella bacteria.
Characterization of SAL605 negative resist at {lambda}=13 nm (1996)

We have characterized the response of the negative resist SAL605 in the extreme ultraviolet ({lambda}=13 nm). The sensitivity was found to be {approx}1 mJ/cm{sup 3} for all conditions studied. We have identified processing conditions leading to high ({gamma}{gt}4) contrast. The resist response was modeled using Prolith/2 and the development parameters were obtained from the exposure curves.
Heat Shock Protein 90-Dependent (Geldanamycin-Inhibited) Movement of the Glucocorticoid Receptor through the Cytoplasm to the Nucleus Requires Intact Cytoskeleton (1998)

We use here a chimera of the green fluorescent protein (GFP) and the glucocorticoid receptor (GR) to test the notion that the protein chaperone heat shock protein-90 (hsp90) is required for steroid-dependent translocation of the receptor through the cytoplasm along cytoskeletal tracks. The GFP-GR fusion protein undergoes steroid-mediated translocation from the cytoplasm to the nucleus, where it is transcriptionally active. Treatment of 3T3 cells containing steroid-bound GFP-GR with geldanamycin, a benzoquinone ansamycin that binds to hsp90 and disrupts its function, inhibits dexamethasone-dependent translocation from the cytoplasm to the nucleus. The t1/2 for translocation in the absence of geldanamycin is approximately 5 min, and the t1/2 in the presence of geldanamycin is approximately 45 min. In cells treated for 1 h with the cytoskeletal disrupting agents colcemid, cytochalasin D, and beta,beta'-iminodipropionitrile to completely disrupt the microtubule, microfilament, and intermediate filament networks, respectively, the GFP-GR still translocates rapidly to the nucleus in a strictly dexamethasone-dependent manner but translocation is no longer affected by geldanamycin. After withdrawal of the cytoskeletal disrupting agents for 3 h, normal cytoskeletal architecture is restored, and geldanamycin inhibition of dexamethasone-dependent GFP-GR translocation is restored. We suggest that in cells without an intact cytoskeletal system, the GFP-GR moves through the cytoplasm by diffusion. However, under physiological conditions in which the cytoskeleton is intact, diffusion is limited, and the GFP-GR utilizes a movement machinery that is dependent upon hsp90 chaperone activity. In contrast to the GR, GFP-STAT5B, a signaling protein that is not complexed with hsp90, undergoes GH-dependent translocation to the nucleus in a manner that is not dependent upon hsp90 chaperone activity.
The effects of fecl3 intercalation on the optical properties of multilayer epitaxial graphene (2012)

In this study we investigate the effects of intercalation of graphene with Iron III Chloride on the optical and electronic properties of the multilayer graphene. While both the optical properties and the electronic properties of graphene have been previously examined, a viable method of preserving the optical properties while enhancing the electrical properties has not yet been developed. Research has been conducted into the effects of other chemical dopants such as HNO3, but the demonstrated results do not yet provide the high transparency and low sheet resistance required in a TCE. The results from our studies suggest that the decrease in the absorption of the optical wavelengths is a result of the p-doping of the graphene that excludes low energy direct optical transitions. Optical absorption is shown to be both a function of thickness and intercalation staging, as are the electrical properties. The results indicate that intercalating graphene with Iron III Chloride may be a viable method to improve the electronic characteristics of graphene without losing the desired optical properties.
High and low anticoagulant activity heparins. Preparation in large scale and degree of complexation with antithrombin III. (1985)

Heparin was separated into fractions with high and low anticoagulant activities by selective barium precipitation, gel filtration and ion exchange chromatography methods. Enrichment in the anticoagulant activities were observed in fractions with high molecular weight or high degree of sulfation. The combination of selective barium precipitation and ion exchange chromatography led to the preparation of heparins with very high anticoagulant activities (300 IU/mg). These heparins have a high affinity for antithrombin III (greater than 80%) and were undistinguishable from those prepared by antithrombin III affinity chromatography regarding molecular weight, sulfate/hexosamine ratio, degree of binding to antithrombin III, electrofocusing pattern and anticoagulant activity. These methods allow now the preparation in industrial scale of heparins with high anticoagulant activities for in vivo studies.
Development and significance of nucleoside drug resistance in infection caused by the human immunodeficiency virus type 1. (1994)

Nucleoside antagonists of human immunodeficiency virus (HIV) reverse transcriptase (RT) activity have been commonly used in the therapy of HIV-associated disease. The prolonged use of such drugs has led to the development of HIV variants that display resistance against these compounds. HIV drug resistance has been documented clinically for each of the following nucleosides: 3'-azido-3'-deoxythymidine (AZT; zidovudine, ZDV), 2',3'-dideoxyinosine (ddI; didanosine), and 2',3'-dideoxycytidine (ddC; zalcitabine). In addition, resistance has been demonstrated against a series of non-nucleoside inhibitors of the viral RT. Several groups have documented that a series of point mutations within the HIV pol gene, that encodes the RT enzyme, is responsible for HIV drug resistance. Diminished sensitivity to anti-viral drugs results from both the selective pressure exerted by these compounds in individuals receiving prolonged therapy and the error-prone nature of the viral RT itself, thus permitting the outgrowth of mutated forms. Patients suffering from both disease progression and/or low CD4 counts are most likely to develop HIV drug resistance.
Campylobacter colitis in ranch mink in Ontario. (1986)

Outbreaks of colitis, where Campylobacter jejuni and Campylobacter coli were the only pathogens isolated occurred in weanling mink (Mustella vision) on two commercial mink ranches in Ontario. Lesions were restricted to the proximal colon and were characterized by multiple 1 mm focal or 1 mm linear erosions/ulcers in the region 2 cm distal to the ileal-colonic junction. Histological changes included thickening of the colonic mucosa, inflammatory cell infiltrate in the lamina propria and submucosa, cellular debris and inflammatory exudate within cryptal lumens and multiple areas of mucosal erosion/ulceration. Four C. jejuni negative mink were challenged with 5.1 X 10(9) colony forming units of C. jejuni by oral inoculation. Three of four experimentally infected mink developed diarrhea by day 4 postinfection with lesions grossly and microscopically similar to mink in the naturally occurring outbreak. Examination of lesions by transmission electron microscope failed to show evidence of C. jejuni invasion of intestinal epithelium. Feeding uncooked slaughterhouse chicken offal was the likely source of C. jejuni in the naturally occurring outbreaks.
SFK/FAK Signaling Attenuates Osimertinib Efficacy in Both Drug-Sensitive and Drug-Resistant Models of EGFR-Mutant Lung Cancer (2017)

Mutant-selective EGFR tyrosine kinase inhibitors (TKI), such as osimertinib, are active agents for the treatment of <i>EGFR</i>-mutant lung cancer. Specifically, these agents can overcome the effects of the T790M mutation, which mediates resistance to first- and second-generation EGFR TKI, and recent clinical trials have documented their efficacy in patients with <i>EGFR</i>-mutant lung cancer. Despite promising results, therapeutic efficacy is limited by the development of acquired resistance. Here we report that Src family kinases (SFK) and focal adhesion kinase (FAK) sustain AKT and MAPK pathway signaling under continuous EGFR inhibition in osimertinib-sensitive cells. Inhibiting either the MAPK pathway or the AKT pathway enhanced the effects of osimertinib. Combined SFK/FAK inhibition exhibited the most potent effects on growth inhibition, induction of apoptosis, and delay of acquired resistance. SFK family member <i>YES1</i> was amplified in osimertinib-resistant <i>EGFR</i>-mutant tumor cells, the effects of which were overcome by combined treatment with osimertinib and SFK inhibitors. In conclusion, our data suggest that the concomitant inhibition of both SFK/FAK and EGFR may be a promising therapeutic strategy for <i>EGFR</i>-mutant lung cancer. <i>Cancer Res; 77(11); 2990-3000. ©2017 AACR</i>.
New enhancers for the chemiluminescent peroxidase catalysed chemiluminescent oxidation of pyrogallol and purpurogallin (1995)

The effects of various boronate compounds, 4-biphenylboronic acid, 4-bromobenzene-boronic acid, trans-4-(3-propionic acid)phenylboronic acid and 4-iodophenylboronic acid, on the horseradish peroxidase (HRP) catalysed chemiluminescent oxidation of pyrogallol and purpurogallin by peroxide were investigated. trans-4-(3-Propionic acid)phenylboronic acid produced a 13.7-fold enhancement in the peak light emission from the chemiluminescent HRP catalysed pyrogallol reaction (detection limit for HRP < 1.25 fmol). At low enhancer concentration a single peak of light emission was observed and as the enhancer concentration increased the time to peak light emission became progressively longer. The chemiluminescence showed two peaks at higher concentrations (> 54.3 mumol/L) and the individual peak times depended upon the concentration of the enhancer. All of the boronates enhanced peak light emission in the chemiluminescent HRP catalysed purpurogallin reaction. 4-Biphenylboronic acid was the most effective and it enhanced peak light emission 314-fold. The practical detection limit for HRP (Type VIA) using this enhancer was 4.18 pmol (peak emission at 20 minutes). This compound also enhanced peak light emission 232-fold from a chemiluminescent HRP-purpurogallin reaction in which molecular oxygen replaced peroxide as the oxidant.
大米中黄曲霉毒素B 1 经灯光照射后的破坏情况 (1989)

（毫瓦/平方厘米）及36、40、42、49和60℃。据观察光强度在毒素的破坏率方面具有明显的效果,那就是随着光强和照射时间的增加而增加。为此,建立了一个评价光导致毒素降解的动态模式来说明包括两相第一级速率的作用原理。此模式证实了一些毒素比残留物更
Reaction of binuclear carboxylate complexes of molybdenum, rhenium, ruthenium, and rhodium with tert-butyl isocyanide: metal-metal bond cleavage vs. bond retention (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of binuclear carboxylate complexes of molybdenum, rhenium, ruthenium, and rhodium with tert-butyl isocyanide: metal-metal bond cleavage vs. bond retentionGregory S. Girolami and Richard A. AndersenCite this: Inorg. Chem. 1981, 20, 7, 2040–2044Publication Date (Print):July 1, 1981Publication History Published online1 May 2002Published inissue 1 July 1981https://pubs.acs.org/doi/10.1021/ic50221a022https://doi.org/10.1021/ic50221a022research-articleACS PublicationsRequest reuse permissionsArticle Views182Altmetric-Citations29LEARN 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
Subcutaneous Clostridial Infection in Broilers (1986)

A flock of 12,500 broilers 36 days of age experienced a sudden increase in mortality. Post-mortem lesions were emphysema, severe enteritis, and a serosanguineous fluid in the subcutaneous tissue of the breast and thighs; there was no evidence of a loss in the integrity of the skin. Clostridium perfringens and C. septicum were isolated from the affected subcutaneous tissue. Histopathological and serological examination indicated previous infection with infectious bursal disease virus. The subsequent immunosuppression and severe enteritis may have permitted the clostridia access to the circulatory system, with localization in the subcutaneous areas of the breast and thighs. Mortality returned to normal 48 hours after potassium penicillin G was administered via the drinking water.
Visualizing odorant receptor trafficking in living cells down to the single-molecule level (2006)

Despite the importance of trafficking for regulating G protein-coupled receptor signaling, for many members of the seven transmembrane helix protein family, such as odorant receptors, little is known about this process in live cells. Here, the complete life cycle of the human odorant receptor OR17-40 was directly monitored in living cells by ensemble and single-molecule imaging, using a double-labeling strategy. While the overall, intracellular trafficking of the receptor was visualized continuously by using a GFP tag, selective imaging of cell surface receptors was achieved by pulse-labeling an acyl carrier protein tag. We found that OR17-40 efficiently translocated to the plasma membrane only at low expression, whereas at higher biosynthesis the receptor accumulated in intracellular compartments. Receptors in the plasma membrane showed high turnover resulting from constitutive internalization along the clathrin pathway, even in the absence of ligand. Single-molecule microscopy allowed monitoring of the early, dynamic processes in odorant receptor signaling. Although mobile receptors initially diffused either freely or within domains of various sizes, binding of an agonist or an antagonist increased partitioning of receptors into small domains of approximately 190 nm, which likely are precursors of clathrin-coated pits. The binding of a ligand, therefore, resulted in modulation of the continuous, constitutive internalization. After endocytosis, receptors were directed to early endosomes for recycling. This unique mechanism of continuous internalization and recycling of OR17-40 might be instrumental in allowing rapid recovery of odor perception.
Androgen receptor action in hormone‐dependent and recurrent prostate cancer (2006)

The importance of androgens and androgen receptors (AR) in primary prostate cancer is well established. Metastatic disease is usually treated with some form of androgen ablation, which is effective for a limited amount of time. The role of AR in prostate cancers that recur despite androgen ablation therapy is less certain. Most of these tumors express prostate specific antigen (PSA), an androgen-regulated gene; moreover, AR is generally highly expressed in recurrent prostate cancer. We propose that AR continues to play a role in many of these tumors and that it is not only the levels of AR, ligands, and co-regulators, but also the changes in cell signaling that induce AR action in recurrent prostate cancer. These pathways are, therefore, potential therapeutic targets.
Zeitgeber Hierarchy in Humans: Resetting the Circadian Phase Positions of Blind People Using Melatonin (2003)

Four blind individuals who were thought to be entrained at an abnormal circadian phase position were reset to a more normal phase using exogenous melatonin administration. In one instance, circadian phase was shifted later. A fifth subject who was thought to be entrained was monitored over four years and eventually was shown to have a circadian period different from 24 h. These findings have implications for treating circadian phase abnormalities in the blind, for distinguishing between abnormally entrained and free-running blind individuals, and for informing the debate over zeitgeber hierarchy in humans.
Propant Free-Shear Dilation: An Emerging Techology for Exploiting Tight to Ultra-Tight Gas Resources (1998)

Abstract In recent years there has been a growing interest in applying proppant free fracturing technique to stimulate tight to ultra tight gas reservoirs. The permeability enhancement mechanism for proppant free fracture stimulation has, in the HDR geothermal industry, been long recognised as shear dilation induced by elevated fluid pressure. Passive micro seismic monitoring technique has been well established in the HDR geothermal industry for imaging growth and geometry of reservoirs created by proppant free stimulation. Both field evidence from seismic monitoring and 3D stochastic stimulation modelling show clearly the volumetric nature of the stimulated rock mass with the proppant free stimulation technology. The detailed reservoir geometry, however, is complex due to interaction of natural fractures and in-situ stress regimes, and may be controlled either by dominant fracture sets or in-situ stresses. There exists a threshold stimulation fluid pressure above which permeability of stimulated fractures increases rapidly with increase in fluid pressure. The threshold pressure is inversely related to the deviatoric stresses. In regions with strong deviatoric stresses such as in Central Australia, the threshold stimulation pressure is expected to be low. Thus, creation of a large volume of reservoir by relatively low stimulation pressure could make the proppant free stimulation a viable alternative to conventional massive hydraulic stimulation from both technical and economical stand point. P. 687