gebhart/patrepeval huggingface dataset:
Adding Insult to Injury: Cochlear Nerve Degeneration after “Temporary” Noise-Induced Hearing Loss (2009)

Overexposure to intense sound can cause temporary or permanent hearing loss. Postexposure recovery of threshold sensitivity has been assumed to indicate reversal of damage to delicate mechano-sensory and neural structures of the inner ear and no persistent or delayed consequences for auditory function. Here, we show, using cochlear functional assays and confocal imaging of the inner ear in mouse, that acoustic overexposures causing moderate, but completely reversible, threshold elevation leave cochlear sensory cells intact, but cause acute loss of afferent nerve terminals and delayed degeneration of the cochlear nerve. Results suggest that noise-induced damage to the ear has progressive consequences that are considerably more widespread than are revealed by conventional threshold testing. This primary neurodegeneration should add to difficulties hearing in noisy environments, and could contribute to tinnitus, hyperacusis, and other perceptual anomalies commonly associated with inner ear damage.
Determination of fatty acid composition in seed oil of rapeseed (Brassica napus L.) by mutated alleles of the FAD3 desaturase genes (2011)

One of the goals in oilseed rape programs is to develop genotypes producing oil with low linolenic acid content (C18:3, ≤3%). Low linolenic mutant lines of canola rapeseed were obtained via chemical mutagenesis at the Plant Breeding and Acclimatization Institute - NRI, in Poznan, Poland, and allele-specific SNP markers were designed for monitoring of two statistically important single nucleotide polymorphisms detected by SNaPshot analysis in two FAD3 desaturase genes, BnaA.FAD3 and BnaC.FAD3, respectively. Strong negative correlation between the presence of mutant alleles of the genes and linolenic acid content was revealed by analysis of variance. In this paper we present detailed characteristics of the markers by estimation of the additive and dominance effects of the FAD3 genes with respect to particular fatty acid content in seed oil, as well as by calculation of the phenotypic variation of seed oil fatty acid composition accounted by particular allele-specific marker. The obtained percentage of variation in fatty acid composition was considerable only for linolenic acid content and equaled 35.6% for BnaA.FAD3 and 39.3% for BnaC.FAD3, whereas the total percentage of variation in linolenic acid content was 53.2% when accounted for mutations in both genes simultaneously. Our results revealed high specificity of the markers for effective monitoring of the wild-type and mutated alleles of the Brassica napus FAD3 desaturase genes in the low linolenic mutant recombinants in breeding programs.
Transcriptional repression by Oshox1, a novel homeodomain leucine zipper protein from rice (1997)

This paper describes the characterization of Oshox1, a cDNA clone from rice encoding a member of the homeodomain-leucine zipper (HD-Zip) class of putative transcription factors. Oshox1 maps to chromosome 10 and belongs to a family of related rice genes. Two-hybrid assays showed that Oshox1 protein can homodimerize, but can also form heterodimers with an Arabidopsis HD-Zip protein. This suggests that protein-protein interactions may also occur between different HD-Zip proteins in rice, which would provide enormous versatility for generating specific gene-control mechanisms. Oshox1 mRNA could be detected in various rice tissues at different developmental stages, with highest levels in embryos, shoots of seedlings, and leaves of mature plants. Transgenic expression of Oshox1 in Arabidopsis retarded growth and affected leaf size and shape, indicative of a role as developmental regulator. In vitro and in vivo DNA-binding studies revealed that Oshox1 interacts with the pseudopalindromic sequence CAAT(C/G)ATTG, confirming that the protein represents a transcription factor. Oshox1 was found to repress reporter gene activity in rice suspension cells, most likely by a mechanism of active transcriptional repression. Repression was strictly dependent on the presence of upstream Oshox1 binding sites in the reporter gene constructs and a function of the N-terminal region of Oshox1, preceding the homeodomain.
Galactose epimeraseless mutants of Salmonella typhimurium as live vaccines for calves. (1986)

The purpose of the study was to evaluate the safety and efficacy of a galactose epimeraseless mutant of Salmonella typhimurium administered as an oral vaccine to one week old calves and to investigate properties of galactose epimeraseless mutants which affect their virulence and immunogenicity. The galactose epimeraseless mutant S. typhimurium strain G30D caused diarrhea and fever in three calves to which it was administered orally at a dose of 10(10) organisms; all three calves died following challenge with virulent S. typhimurium ten days postvaccination. Mild illness developed in four calves vaccinated with a dose of 9 X 10(6) organisms and one of these calves survived challenge. Three unvaccinated calves died following challenge. The vaccine organism persisted in tissues and was shed for a prolonged period by calves which received 10(10) organisms. Studies of characteristics of galactose epimeraseless mutants of S. typhimurium showed that, in the presence of galactose, there is selection for secondary mutants which are galactose resistant. The studies indicate that galactose epimeraseless mutants of S. typhimurium are not good candidate live vaccine organisms for use in calves.
The G Protein-coupled Receptor GPR30 Mediates c-fos Up-regulation by 17β-Estradiol and Phytoestrogens in Breast Cancer Cells (2004)

A growing body of evidence concerning estrogen effects cannot be explained by the classic model of hormone action, which involves the binding to estrogen receptors (ERs) alpha and ERbeta and the interaction of the steroid-receptor complex with specific DNA sequences associated with target genes. Using c-fos proto-oncogene expression as an early molecular sensor of estrogen action in ERalpha-positive MCF7 and ER-negative SKBR3 breast cancer cells, we have discovered that 17beta-estradiol (E2), and the two major phytoestrogens, genistein and quercetin, stimulate c-fos expression through ERalpha as well as through an ER-independent manner via the G protein-coupled receptor homologue GPR30. The c-fos response is repressed in GPR30-expressing SKBR3 cells transfected with an antisense oligonucleotide against GPR30 and reconstituted in GPR30-deficient MDA-MB 231 and BT-20 breast cancer cells transfected with a GPR30 expression vector. GPR30-dependent activation of ERK1/2 by E2 and phytoestrogens occurs via a Gbetagamma-associated pertussis toxin-sensitive pathway that requires both Src-related and EGF receptor tyrosine kinase activities. The ability of E2 and phytoestrogens to regulate the expression of growth-related genes such as c-fos even in the absence of ER has interesting implications for understanding breast cancer progression.
Mass and Charge Measurements on Heavy Ions (2017)

The relationship between mass and charge has been a crucial topic in mass spectrometry (MS) because the mass itself is typically evaluated based on the <i>m</i>/<i>z</i> ratio. Despite the fact that this measurement is indirect, a precise mass can be obtained from the <i>m</i>/<i>z</i> value with a high <i>m</i>/<i>z</i> resolution up to 10<sup>5</sup> for samples in the low mass and low charge region under 10,000 Da and 20 <i>e</i>, respectively. However, the target of MS has recently been expanded to the very heavy region of Mega or Giga Da, which includes large particles and biocomplexes, with very large and widely distributed charge from kilo to Mega range. In this region, it is necessary to evaluate charge and mass simultaneously. Recent studies for simultaneous mass and charge observation and related phenomena are discussed in this review.
Cooperative autonomous platoon maneuvers on highways (2013)

This paper presents an approach for formulating dynamic cooperative maneuvers for platoons of autonomous vehicles. Each member of a platoon is represented by a dynamic model and has a set of tactical and operational controllers in the form of hierarchical event-chains and low-level longitudinal/latitudinal controllers. These models and controllers are incorporated in simulation environments and demonstrate the ability for platoons to cooperatively maneuver around each other and other hazards. Multiple vehicles in convoys drive autonomously down a two-lane roadway and are simulated to ensure a safe and cooperative operation taking into account a raft of widely varying requirements that exist in a public transport environments. A set of concepts such as event conditions, sub-chaining and limited progression are introduced and used to promote responsive maneuver patterns. Results from a multiple convoy simulation validate the strategy presented.
Heterologous reconstitution in yeast of the polyunsaturated fatty acid biosynthetic pathway (2000)

A Caenorhabditis elegans ORF encoding the presumptive condensing enzyme activity of a fatty acid elongase has been characterized functionally by heterologous expression in yeast. This ORF (F56H11. 4) shows low similarity to Saccharomyces cerevisiae genes involved in fatty acid elongation. The substrate specificity of the C. elegans enzyme indicated a preference for Delta(6)-desaturated C18 polyunsaturated fatty acids. Coexpression of this activity with fatty acid desaturases required for the synthesis of C20 polyunsaturated fatty acids resulted in the accumulation of arachidonic acid from linoleic acid and eicosapentaenoic acid from alpha-linolenic acid. These results demonstrate the reconstitution of the n-3 and n-6 polyunsaturated fatty acid biosynthetic pathways. The C. elegans ORF is likely to interact with endogenous components of a yeast elongation system, with the heterologous nematode condensing enzyme F56H11.4 causing a redirection of enzymatic activity toward polyunsaturated C18 fatty acid substrates.
Expression, Purification, and Biochemical Characterization of WbpP, a New UDP-GlcNAc C4 Epimerase from Pseudomonas aeruginosa Serotype O6 (2000)

B-band lipopolysaccharide is an important virulence factor of the opportunistic pathogen Pseudomonas aeruginosa. WbpP is an enzyme essential for B-band lipopolysaccharide production in serotype O6. Sequence analysis suggests that it is involved in the formation of N-acetylgalacturonic acid. To test this hypothesis, overexpression and biochemical characterization of WbpP were performed. By using spectrophotometric assays and capillary electrophoresis, we show that WbpP is a UDP-GlcNAc C4 epimerase. The K(m) for UDP-GlcNAc and UDP-GalNAc are 197 and 224 micrometer, respectively. At equilibrium, 70% of UDP-GalNAc is converted to UDP-GlcNAc, whereas the yield of the reverse reaction is only 30%. The enzyme can also catalyze the inter-conversion of non-acetylated substrates, although the efficiency of catalysis is significantly lower. Only 15 and 40% of UDP-Glc and UDP-Gal, respectively, are converted at equilibrium. WbpP contains tightly bound NAD(H) and does not require additional cofactors for activity. It exists as a dimer in its native state. This paper is the first report of expression and characterization of a C4 UDP-GlcNAc epimerase at the biochemical level. Moreover, the characterization of the enzymatic function of WbpP will help clarify ambiguous surface carbohydrate biosynthetic pathways in P. aeruginosa and other organisms where homologues of WbpP exist.
AVR1-CO39 Is a Predominant Locus Governing the Broad Avirulence of Magnaporthe oryzae 2539 on Cultivated Rice (Oryza sativa L.) (2010)

Magnaporthe oryzae 2539 was previously found to be avirulent to most rice cultivars and, therefore, was assumed to carry many avirulence (AVR) genes. However, only one AVR gene, AVR1-CO39, which corresponds to a resistance (R) gene Pi-CO39(t) in rice cv. CO39, has been found from 2539 thus far. In order to identify more AVR genes, we isolated 228 progeny strains from a cross between 2539 and Guy11, an M. oryzae strain with strong virulence on rice, and inoculated these strains onto 23 rice accessions (22 individual cultivars and a mixture of 14 cultivars) that are all resistant to 2539 but susceptible to Guy11. Unexpectedly, the experimental results indicated that the avirulence of 2539 on these rice cultivars appeared to be controlled only by the AVR1-CO39 locus. Consistent with this result, we further found that all except one of the rice cultivars were resistant to two transformed Guy11 strains carrying a 1.05-kb fragment containing the AVR1-CO39 gene from 2539. These results suggest that AVR1-CO39 is a predominant locus controlling the broad avirulence of 2539 on cultivated rice. Based on the results of this study and other previous studies, we infer that AVR1-CO39 is a species-wise rather than a cultivar-wise host-specific AVR locus of M. oryzae for rice.
Recent advances in the medical management of prostate cancer. (1996)

Prostate cancer is a 20th century seedling which, because of its attendant morbidity and mortality and the increased longevity of the population, is set to germinate into a substantial economic burden in the next millennium. Most patients with prostatic cancer present with either locally advanced or metastatic disease, for which palliative endocrine therapies are the first-line treatment. The increasingly sophisticated and selective hormonal methods available today, such as the longer-acting formulations of luteinizing hormone-releasing hormone (LH-RH) analogues and newer, better-tolerated, once-daily, non-steroidal anti-androgens, have increased the therapeutic options and improved patient quality of life. Maximum androgen blockade, combining medical or surgical castration with an anti-androgen, is an increasingly accepted therapy, and offers the greatest efficacy, particularly for patients with a lesser disease burden. The development of hormone-refractory tumours is still a problem in advanced prostate cancer, although elucidation of the mechanisms involved should offer many potentially fruitful avenues for new therapies.
Role of extracellular matrix assembly in interstitial transport in solid tumors. (2000)

The extracellular matrix (ECM) may contribute to the drug resistance of a solid tumor by preventing the penetration of therapeutic agents. We measured differences in interstitial resistance to macromolecule (IgG) motion in four tumor types and found an unexpected correspondence between transport resistance and the mechanical stiffness. The interstitial diffusion coefficient of IgG was measured in situ by fluorescence redistribution after photobleaching. Tissue elastic modulus and hydraulic conductivity were measured by confined compression of excised tissue. In apparent contradiction to an existing paradigm, these functional properties are correlated with total tissue content of collagen, not glycosaminoglycan. An extended collagen network was observed in the more penetration-resistant tumors. Collagenase treatment of the more penetration-resistant tumors significantly increased the IgG interstitial diffusion rate. We conclude that collagen influences the tissue resistance to macromolecule transport, possibly by binding and stabilizing the glycosaminoglycan component of the ECM. These findings suggest a new method to screen tumors for potential resistance to macromolecule-based therapy. Moreover, collagen and collagen-proteoglycan bonds are identified as potential targets of treatment to improve macromolecule delivery.
Fault-Tolerant Holonomic Quantum Computation (2009)

We explain how to combine holonomic quantum computation (HQC) with fault-tolerant quantum error correction. This establishes the scalability of HQC, putting it on equal footing with other models of computation, while retaining the inherent robustness the method derives from its geometric nature.
Differential expression of multiple fork head related genes during gastrulation and axial pattern formation in the mouse embryo (1993)

Four genes encoding fork-head-domain-containing proteins (FD genes) have been isolated from a mouse 8.5 days post coitum (p.c.) embryo cDNA library. Two are mouse homologues of rat HNF-3 beta and HNF-3 alpha. The other two are novel and have been named MF-1 and MF-2 (for mesoderm/mesenchyme fork head). Wholemount in situ hybridization of embryos between 6.5 and 9.5 days p. c. shows that each gene has a unique expression pattern. HNF-3 beta is expressed in the node, notochord, floor plate and gut, while HNF-3 alpha is mainly in the definitive endoderm and gut, but also in the floor plate of the midbrain. These results suggest that HNF-3 beta and HNF-3 alpha, in addition to their known functions as transcriptional activators in adult liver, play a role in body axis formation, neural tube patterning and definitive endoderm formation during gastrulation. MF-1 RNA is present in non-notochordal mesoderm, and in neural-crest-derived head mesenchyme, while MF-2 transcripts are found in the sclerotomes of the somites and in head mesenchyme, including that from neural crest. Studies on gastrulation stage embryos suggest that the early temporal and spatial patterns of HNF-3 beta, MF-1 and HNF-3 alpha correlate with populations of cells undergoing commitment to different developmental fates. A model is proposed linking FD gene expression with gastrulation events in the mouse.
Tumor necrosis factor induced adhesion molecule serum concentrations in Henoch-Schönlein purpura and pediatric systemic lupus erythematosus. (2000)

Our study provides additional evidence of a possible differential involvement of TNF and TNF induced adhesion molecules in the pathogenesis of tissue damage between pediatric SLE and HSP.
High‐Resolution Chromatin Profiling Using CUT&RUN (2019)

Abstract Determining the genomic location of DNA‐binding proteins is essential to understanding their function. Cleavage Under Targets and Release Using Nuclease (CUT&amp;RUN) is a powerful method for mapping protein‐DNA interactions at high resolution. In CUT&amp;RUN, a recombinant protein A–microccocal nuclease (pA‐MN) fusion is recruited by an antibody targeting the chromatin protein of interest; this can be done with either uncrosslinked or formaldehyde‐crosslinked cells. DNA fragments near sites of antibody binding are released from the insoluble bulk chromatin through endonucleolytic cleavage and used to build barcoded DNA‐sequencing libraries that can be sequenced in pools of at least 30. Therefore, CUT&amp;RUN provides an alternative to ChIP‐seq approaches for mapping chromatin proteins, which typically have relatively high signal‐to‐noise ratios, while using fewer cells and at a lower cost. Here, we describe the methods for performing CUT&amp;RUN, generating DNA‐sequencing libraries, and analyzing the resulting datasets. © 2019 by John Wiley &amp; Sons, Inc.
Acute and latent herpes simplex virus neurological disease in mice immunized with purified virus‐specific glycoproteins gB or gD (1985)

Groups of 5-week-old BALB/c mice were immunized intraperitoneally with approximately 10 micrograms of purified alum-precipitated glycoprotein gB or gD of either herpes simplex virus type 1 (HSV-1) or type 2 (HSV-2) origin. Control mice received injections of alum-precipitated 1% bovine serum albumin (BSA). Following a second immunization 4 weeks later, seroconversion was confirmed by demonstrating the presence of glycoprotein-specific antibody by immune precipitation. All animals were challenged with lethal doses of either HSV-1 or HSV-2 by footpad inoculation and assessed for acute virus-induced neurological disease and the development of ganglionic latency. Whereas 70% of control (BSA-immunized) HSV-1-infected animals developed ascending myelitis and died, 100% of mice immunized with either gB-1, gB-2, gD-1, or gD-2 antigens remained free of clinical illness and survived HSV-1 challenge. In contrast, gB-1-or gB-2-immunized mice were not protected against acute HSV-2-induced neurological disease and showed a mortality rate of 60-90% (equivalent to that seen in controls), although mean survival times were prolonged. However, significant protection against HSV-2 challenge was observed with gD-1 or gD-2 immunization. When sacral ganglia were removed from surviving mice 9-12 months after virus challenge, latent virus was detected in all gB- or gD-immunized animals, although the extent of latent infection was restricted. These results provide evidence that glycoprotein gD might be superior to glycoprotein gB as an immunogen for the control of acute HSV-1 and HSV-2 neurological disease in mice. However, neither glycoprotein prevents ganglionic latency, the source of virus for recurrent herpesvirus infections.
Biotin regulatory (bir) mutations of Escherichia coli (1980)

Most mutants selected for derepression of the biotin operon required elevated concentrations of biotin for growth. Mutant extracts were deficient in holoenzyme synthetase activity.
Polyglutamation of methotrexate. Is methotrexate a prodrug? (1985)

La polyglutamation est assuree par la folyl polyglutamyl synthetase. Leur etude decrit l'importance pharmacologique de la polyglutamation du methotrexate
A correlated topic model of Science (2018)

Topic models, such as latent Dirichlet allocation (LDA), can be useful tools for the statistical analysis of document collections and other discrete data. The LDA model assumes that the words of each document arise from a mixture of topics, each of which is a distribution over the vocabulary. A limitation of LDA is the inability to model topic correlation even though, for example, a document about genetics is more likely to also be about disease than X-ray astronomy. This limitation stems from the use of the Dirichlet distribution to model the variability among the topic proportions. In this paper we develop the correlated topic model (CTM), where the topic proportions exhibit correlation via the logistic normal distribution [J. Roy. Statist. Soc. Ser. B 44 (1982) 139–177]. We derive a fast variational inference algorithm for approximate posterior inference in this model, which is complicated by the fact that the logistic normal is not conjugate to the multinomial. We apply the CTM to the articles from Science published from 1990–1999, a data set that comprises 57M words. The CTM gives a better fit of the data than LDA, and we demonstrate its use as an exploratory tool of large document collections.