gebhart/patrepeval huggingface dataset:
A Role for iNOS in Fasting Hyperglycemia and Impaired Insulin Signaling in the Liver of Obese Diabetic Mice (2005)

Chronic inflammation has been postulated to play an important role in the pathogenesis of insulin resistance. Inducible nitric oxide synthase (iNOS) has been implicated in many human diseases associated with inflammation. iNOS deficiency was shown to prevent high-fat diet-induced insulin resistance in skeletal muscle but not in the liver. A role for iNOS in fasting hyperglycemia and hepatic insulin resistance, however, remains to be investigated in obesity-related diabetes. To address this issue, we examined the effects of a specific inhibitor for iNOS, L-NIL, in obese diabetic (ob/ob) mice. iNOS expression was increased in the liver of ob/ob mice compared with wild-type mice. Treatment with iNOS inhibitor reversed fasting hyperglycemia with concomitant amelioration of hyperinsulinemia and improved insulin sensitivity in ob/ob mice. iNOS inhibitor also increased the protein expression of insulin receptor substrate (IRS)-1 and -2 1.5- and 2-fold, respectively, and enhanced IRS-1- and IRS-2-mediated insulin signaling in the liver of ob/ob mice. Exposure to NO donor and ectopically expressed iNOS decreased the protein expression of IRS-1 and -2 in cultured hepatocytes. These results suggest that iNOS plays a role in fasting hyperglycemia and contributes to hepatic insulin resistance in ob/ob mice.
Embedding Entities and Relations for Learning and Inference in Knowledge Bases (2014)

Compared to black-box neural networks, logic rules express explicit knowledge, can provide human-understandable explanations for reasoning processes, and have found their wide application in knowledge graphs and other downstream tasks. As extracting rules manually from large knowledge graphs is labour-intensive and often infeasible, automated rule learning has recently attracted significant interest, and a number of approaches to rule learning for knowledge graphs have been proposed. This survey aims to provide a review of approaches and a classification of state-of-the-art systems for learning first-order logic rules over knowledge graphs. A comparative analysis of various approaches to rule learning is conducted based on rule language biases, underlying methods, and evaluation metrics. The approaches we consider include inductive logic programming (ILP)-based, statistical path generalisation, and neuro-symbolic methods. Moreover, we highlight important and promising application scenarios of rule learning, such as rule-based knowledge graph completion, fact checking, and applications in other research areas.
Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency (2015)

Fourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows were Bacteroidetes (49.42%), Firmicutes (39.32%), Proteobacteria (5.67%), and Tenericutes (2.17%), and the most abundant genera included Prevotella (40.15%), Butyrivibrio (2.38%), Ruminococcus (2.35%), Coprococcus (2.29%), and Succiniclasticum (2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles.
Induction of Cytokine Production from Human Monocytes Stimulated with Alginate (1991)

Alginates are polysaccharides with gel-forming properties composed of 1,4-linked beta-D-mannuronic acid (M), alpha-L-guluronic acid (G), and alternating (MG) blocks. Alginate can be used as a matrix for implanted cells in vivo. In this study, we have examined the ability of alginates and their components to stimulate human monocytes to produce tumor necrosis factor-alpha, interleukin-6, and interleukin-1. Alginates stimulated the monocytes to produce high levels of all three cytokines. Low G alginates were approximately 10 times more potent in inducing cytokine production compared with high G alginates. The M-blocks and the MG-blocks, but not the G-blocks, stimulated the cytokine production. The results demonstrate that the mannuronic acid residues are the active cytokine inducers in alginates.
The mRNA for the 23S rRNA methylase encoded by the ermE gene of Saccharopolyspora erythraea is translated in the absence of a conventional ribosome‐binding site (1994)

Transcriptional analysis of the ermE gene of Saccharopolyspora erythraea, which confers resistance to erythromycin by N6-dimethylation of 23S rRNA and which is expressed from two promoters, ermEp1 and ermEp2, revealed a complex regulatory region in which transcription is initiated in a divergent and overlapping manner. Two promoters (eryC1p1 and eryC1p2) were identified for the divergently transcribed erythromycin biosynthetic gene eryC1, which plays a role in the formation of desosamine or its attachment to the macrolide ring. Transcription from eryC1p2 starts at the same position as that of ermEp1, but on the opposite strand of the DNA helix, suggesting co-ordinate regulation of genes for erythromycin production and resistance. ermEp1 initiates transcription at, and one nucleotide before, the ermE translational start codon. Site-directed and deletion mutagenesis, combined with immunochemical analysis, demonstrated that the ermEp1 transcript is translated in the absence of a conventional ribosome-binding site to give rise to the full-length 23S rRNA methylase. Deletion of the -35 region of ermEp1 reduced, but did not abolish, promoter activity, reminiscent of the 'extended -10' class of bacterial promoters which, like ermEp1, possess TGN motifs immediately upstream of their -10 regions and which initiate transcription seven nucleotides downstream of the -10 region.
Class I MHC can present an endogenous peptide to cytotoxic T lymphocytes. (1989)

Since class I MHC glycoproteins may function by "screening and selecting" degraded proteins, we wished to determine whether very short peptides made within a cell were detected and bound by MHC, and presented for T cell perusal. We show that a 22 amino acid viral sequence containing a Db-restricted nonameric CTL epitope is sufficient to direct CTL recognition/lysis of H2b target cells. The mechanism of epitope presentation is by the "natural" endogenous route, and appears to direct lysis as effectively as wild-type virus infection, in which the epitope is part of a 236 residue glycoprotein.
Transfer of a protein binding epitope to a minimal designed peptide (1998)

Results from protein mutagenesis and x-ray crystallographic studies of the multidomain protein Vascular Cell Adhesion Molecule (VCAM) were used to design cyclic octapeptides that retain the critical structural and binding elements of the epitope of VCAM in the interaction with the integrin α4β1 (VLA-4). Changes in the activities of peptide analogues correlated with the relative activities of protein mutants of VCAM, and predicted the properties of two new mutants that bound α4β1 with improved affinity vs wild type protein. The nmr structures of two peptides revealed a high degree of similarity to the structure of the VCAM binding epitope. These results demonstrate that a compact binding epitope identified via protein structure–function studies may be transferred to a synthetically accessible small peptide with the key structure–activity relationships intact. © 1998 John Wiley & Sons, Inc. Biopoly 47: 265–275, 1998
OFDM subchannel space-combining transmission diversity for broadband wireless communication systems (2002)

This paper proposes a transmission diversity (TD) technique combined with orthogonal frequency division multiplex (OFDM) modulation to enhance packet-error-rate (PER) performance in microcell broadband wireless communication systems. The proposed TD technique selects the antenna with the anticipated better-channel conditions in a subchannel-by-subchannel manner at the access point (AP) based on the quality-measurement results of signals sent by the mobile terminal (MT). In the subsequent transmission timing from the AP to the MT, each antenna at the AP station transmits OFDM-modulated signals that only possess the selected subchannel components. On the MT side, the space-combined whole subchannel OFDM signal is received through the single antenna.
Acoustic microscopy by atomic force microscopy (1994)

We have constructed an atomic force microscope enabling one to image the topography of a sample, and to monitor simultaneously ultrasonic surface vibrations in the MHz range. For detection of the distribution of the ultrasonic vibration amplitude, a part of the position-sensing light beam reflected from the cantilever is directed to an external knife-edge detector. Acoustic images taken on the surface of a wafer show a lateral resolution of about 100 nm at an ultrasonic frequency of 20 MHz.
In Vitro Conversion of Estradiol-Receptor Protein to Its Nuclear Form: Dependence on Hormone and DNA (1972)

Early events in the action of 17-beta-estradiol can be studied in soluble extracts of rat uterus by exposure of the estradiol-receptor protein to a DNA-cellulose matrix. After complexing with [(3)H]estradiol, the 4S receptor protein binds to the DNA, and it can be eluted with buffer of high ionic strength as a more tightly binding, 5S form. This parallels the in vivo situation, where migration of the receptor to the nucleus follows addition of hormone and is concomitant with a similar increase in sedimentation rate to 5 S. In both cases, the formation of a 5S receptor requires the presence of 17-beta-estradiol. The rate at which 5S receptor forms is sensitive to extract concentration in a way that suggests that this receptor is a complex created by addition of a second subunit to the hormone-binding 4S component; physical studies on both in vivo and in vitro 5S receptors also support this view. These results are interpreted in terms of a model for action of estrogen in which the hormone potentiates binding of receptor to DNA, and in turn, the DNA-binding process triggers the cell response.
Temperature Dependence of Photoluminescence Decay Time of Ir(ppy)~3 (2004)

Theoretical calculation has been done on the decay time of photoluminescence of Ir(ppy) 3 dissolved in tetrahydrofuran and its temperature dependence at 1.2-300 K. Taking into account that the emitting triplet state consists of three zero-field splitting substates and taking into account one-phonon non-radiative transitions among these substates, the rate equations for the populations of these substates have been obtained. Three decay components are derived by solving not only the secular equation but also the rate equations, where the slow decay time shows decrease from 145 to 2μs with increasing temperature from 1.2 to 300 K. A good agreement has been obtained for the temperature dependence between the calculated slow decay time and the observed one.
Identification of Sialyltransferase 8B as a Generalized Susceptibility Gene for Psychotic and Mood Disorders on Chromosome 15q25-26 (2012)

We previously identified a significant bipolar spectrum disorder linkage peak on 15q25-26 using 35 extended families with a broad clinical phenotype, including bipolar disorder (types I and II), recurrent unipolar depression and schizoaffective disorder. However, the specific gene(s) contributing to this signal had not been identified. By a fine mapping association study in an Australian case-control cohort (n = 385), we find that the sialyltransferase 8B (ST8SIA2) gene, coding for an enzyme that glycosylates proteins involved in neuronal plasticity which has previously shown association to both schizophrenia and autism, is associated with increased risk to bipolar spectrum disorder. Nominal single point association was observed with SNPs in ST8SIA2 (rs4586379, P = 0.0043; rs2168351, P = 0.0045), and a specific risk haplotype was identified (frequency: bipolar vs controls = 0.41 vs 0.31; χ(2) = 6.46, P = 0.011, OR = 1.47). Over-representation of the specific risk haplotype was also observed in an Australian schizophrenia case-control cohort (n = 256) (χ(2) = 8.41, P = 0.004, OR = 1.82). Using GWAS data from the NIMH bipolar disorder (n = 2055) and NIMH schizophrenia (n = 2550) cohorts, the equivalent haplotype was significantly over-represented in bipolar disorder (χ(2) = 5.91, P = 0.015, OR = 1.29), with the same direction of effect in schizophrenia, albeit non-significant (χ(2) = 2.3, P = 0.129, OR = 1.09). We demonstrate marked down-regulation of ST8SIA2 gene expression across human brain development and show a significant haplotype×diagnosis effect on ST8SIA2 mRNA levels in adult cortex (ANOVA: F(1,87) = 6.031, P = 0.016). These findings suggest that variation the ST8SIA2 gene is associated with increased risk to mental illness, acting to restrict neuronal plasticity and disrupt early neuronal network formation, rendering the developing and adult brain more vulnerable to secondary genetic or environmental insults.
In vitro Transformation by Hepatitis B Virus DNA (1995)

There is strong epidemiological evidence that the hepatitis B virus (HBV) contributes to the development of hepatocellular carcinoma (HCC). In several immortalized cell lines, an in vitro transforming activity of HBV DNA and expression vectors for the viral protein X (HBx) has now been demonstrated. Furthermore, it appears as if still unknown parts of the HBV genome other than HBx contribute to the transforming activity of HBV DNA in vitro. Only one of several studies found that HBx-transgenic mouse lines develop HCC. A mouse line transgenic for the large surface protein of HBV develops HCC due to concomitant necroinflammatory infection. Growing evidence shows the importance of recombination of integrated viral DNA and cellular DNA for HCC development. A direct transforming potential of one of these viral integrates has been demonstrated. Chemical carcinogens are more effective in HBV-containing cell lines or transgenic mice.
Semiconducting Metal Oxide Based Sensors for Selective Gas Pollutant Detection (2009)

A review of some papers published in the last fifty years that focus on the semiconducting metal oxide (SMO) based sensors for the selective and sensitive detection of various environmental pollutants is presented.
Agreement between chromogenic in situ hybridisation (CISH) and FISH in the determination of HER2 status in breast cancer (2003)

Determination of the HER2/neu (HER2) status in breast carcinoma has become necessary for the selection of breast cancer patients for trastuzumab therapy. Amplification of the gene analysed by fluorescence in situ hybridisation (FISH) or overexpression of the protein determined by immunohistochemistry (IHC) are the two major methods to establish this status. A strong correlation has been previously demonstrated between these two methods. However, FISH is not always feasible in routine practice and weakly positive IHC tumours (2+) do not always correspond to a gene amplification. Our study was performed in order to evaluate the contribution of chromogenic in situ hybridisation (CISH), which enables detection of the gene copies through an immunoperoxidase reaction. CISH was performed in 79 breast carcinomas for which the HER2 status was previously determined by IHC and FISH. The results of IHC, FISH and CISH were compared for each tumour. CISH procedures were successful in 95% of our cases. Whatever the IHC results, we found a very good concordance (96%) between CISH and FISH. Our study confirms that CISH may be an alternative to FISH for the determination of the gene amplification status in 2+ tumours. Our results allow us to think that, in many laboratories, CISH may also be an excellent method to calibrate the IHC procedures or, as a quality control test, to check regularly that the IHC signal is in agreement with the gene status.
CTGF Mediates TGF-β–Induced Fibronectin Matrix Deposition by Upregulating Active α5β1 Integrin in Human Mesangial Cells (2003)

Excessive deposition of fibronectin in the glomerular mesangium in diabetic nephropathy (DN) is partly due to the induction of transforming growth factor-beta (TGF-beta) by high glucose. TGF-beta induces its downstream mediator connective tissue growth factor (CTGF), which stimulates fibronectin matrix synthesis, a process that requires the presence of alpha5beta1 integrin. Although TGF-beta has been shown to upregulate alpha5beta1 integrin expression in human mesangial cells (HMC), little is known about the effect of CTGF on levels of this receptor. This study tested whether CTGF modulates alpha5beta1 expression by HMC in culture and whether changes induced by TGF-beta are mediated through the induction of CTGF. FACS analysis showed that both TGF-beta and CTGF significantly increased cell-surface alpha5beta1 levels compared with basal conditions. RT-PCR indicated that the changes were at the level of transcription. Treatment of cells with TGF-beta and antisense CTGF oligonucleotides significantly reduced the TGF-beta-induced increases in alpha5beta1 levels. CTGF and TGF-beta also significantly increased levels of ligand-occupied cell-surface beta1 integrins and cell adhesion to fibronectin, the main alpha5beta1 substrate. Antisense CTGF significantly reduced the number of adherent cells from TGF-beta-stimulated cultures. Finally, alpha5beta1 blocking antibodies inhibited HMC fibronectin matrix deposition, confirming the importance of this receptor for this process. Taken together, these data provide evidence that CTGF controls alpha5beta1 expression by HMC in vitro. Alterations in alpha5beta1 levels induced by TGF-beta are mediated at least in part through the induction of CTGF, and specific targeting of either alpha5beta1 or CTGF could be useful in controlling excessive fibronectin matrix production in DN.
Cell Binding Sequences in Mouse Laminin α1 Chain (1998)

Laminin-1, a multifunctional glycoprotein of the basement membrane, consists of three different subunits, alpha1, beta1, and gamma1 chains. Previously, we used synthetic peptides to screen for biologically active sequences in the laminin alpha1 chain C-terminal globular domain (G domain) and identified several cell binding sequences (Nomizu, M., Kim, W. H., Yamamura, K., Utani, A., Song, S. Y., Otaka, A., Roller, P. P., Kleinman, H. K., and Yamada, Y. (1995) J. Biol. Chem. 270, 20583-20590). Here, we identify new cell binding sequences on the remainder of the laminin alpha1 chain by systematic peptide screening, using 208 overlapping synthetic peptides encompassing the central and N-terminal portions of the alpha1 chain. HT-1080 cell attachment activity to the peptides was evaluated using peptide-coated plastic substrates and peptide-conjugated Sepharose beads. Twenty five peptides showed cell attachment activities on either the peptide-coated plastic substrates and/or the peptide-conjugated Sepharose beads. A-13 (RQVFQVAYIIIKA) showed strongest cell attachment activity in both the assays. Cell attachment to 14 of the peptides was inhibited by heparin. EDTA and integrin antibodies inhibited cell adhesion to two of the peptides, A-13 and A-25, suggesting that these sites likely bind to integrins. These peptides inhibited cell attachment to laminin-1 but not to collagen I, suggesting these active sites are available on the intact molecule. Most of active sequences were localized on globular domains suggesting that these structures play a critical role in binding to cell-surface receptors.
High-Throughput Genotyping with Single Nucleotide Polymorphisms (2001)

To make large-scale association studies a reality, automated high-throughput methods for genotyping with single-nucleotide polymorphisms (SNPs) are needed. We describe PCR conditions that permit the use of the TaqMan or 5' nuclease allelic discrimination assay for typing large numbers of individuals with any SNP and computational methods that allow genotypes to be assigned automatically. To demonstrate the utility of these methods, we typed >1600 individuals for a G-to-T transversion that results in a glutamate-to-aspartate substitution at position 298 in the endothelial nitric oxide synthase gene, and a G/C polymorphism (newly identified in our laboratory) in intron 8 of the 11-beta hydroxylase gene. The genotyping method is accurate-we estimate an error rate of fewer than 1 in 2000 genotypes, rapid-with five 96-well PCR machines, one fluorescent reader, and no automated pipetting, over one thousand genotypes can be generated by one person in one day, and flexible-a new SNP can be tested for association in less than one week. Indeed, large-scale genotyping has been accomplished for 23 other SNPs in 13 different genes using this method. In addition, we identified three "pseudo-SNPs" (WIAF1161, WIAF2566, and WIAF335) that are probably a result of duplication.
Introduction (1992)

As we move into the last decade of the twentieth century, we are often reminded of how rapidly our world is changing. Yesterday's political, social, economic, and technological certainties seem frequently disrupted and reconfigured. While some changes, such as EC 1993, have been anticipated, others, such as the breakup of the U.S.S.R. have come mostly by surprise. Whether foreseeable or unforeseen, enormous changes are transforming our institutions and how we operate in them. In this context, the editors of this volume have elected to begin this book with a section on the HR function in transition. If our institutions are changing so dramatically, then acknowledging that change becomes a necessary starting point for all of our professional endeavors. Given that starting point, the editors have selected three articles that address the HR function in transition. These articles envision opportunities for effective HR practice in an unfamiliar world.
A Human Cytotoxic T-Lymphocyte Epitope and Its Agonist Epitope from the Nonvariable Number of Tandem Repeat Sequence of MUC-1 (2004)

In addition to the identification of novel MUC-1 epitopes outside the variable number of tandem repeat region, the studies reported here describe the first agonist epitope of MUC-1. The employment of this agonist epitope in peptide-, protein-, and vector-based vaccines may well aid in the development of effective vaccines for a range of human cancers.