gebhart/patrepeval huggingface dataset:
Deep Learning for Drug-Induced Liver Injury (2015)

Drug-induced liver injury (DILI) has been the single most frequent cause of safety-related drug marketing withdrawals for the past 50 years. Recently, deep learning (DL) has been successfully applied in many fields due to its exceptional and automatic learning ability. In this study, DILI prediction models were developed using DL architectures, and the best model trained on 475 drugs predicted an external validation set of 198 drugs with an accuracy of 86.9%, sensitivity of 82.5%, specificity of 92.9%, and area under the curve of 0.955, which is better than the performance of previously described DILI prediction models. Furthermore, with deep analysis, we also identified important molecular features that are related to DILI. Such DL models could improve the prediction of DILI risk in humans. The DL DILI prediction models are freely available at http://www.repharma.cn/DILIserver/DILI_home.php.
Collective annotation of Wikipedia entities in web text (2009)

To take the first step beyond keyword-based search toward entity-based search, suitable token spans ("spots") on documents must be identified as references to real-world entities from an entity catalog. Several systems have been proposed to link spots on Web pages to entities in Wikipedia. They are largely based on local compatibility between the text around the spot and textual metadata associated with the entity. Two recent systems exploit inter-label dependencies, but in limited ways. We propose a general collective disambiguation approach. Our premise is that coherent documents refer to entities from one or a few related topics or domains. We give formulations for the trade-off between local spot-to-entity compatibility and measures of global coherence between entities. Optimizing the overall entity assignment is NP-hard. We investigate practical solutions based on local hill-climbing, rounding integer linear programs, and pre-clustering entities followed by local optimization within clusters. In experiments involving over a hundred manually-annotated Web pages and tens of thousands of spots, our approaches significantly outperform recently-proposed algorithms.
Wuyunanthus gen. nov., a flower of Celastraceae from the Palaeocene of north-east China (2001)

A flower assigned to Wuyunanthus hexapetalus gen. & sp. nov. has been collected from the Wuyun Formation of Palaeocene age, Jiayin County, Heilongjiang Province, north-east China. The flower is bisexual, actinomorphic, and 6-merous. There are six free valvate petals in a whorl inserted on the margin of a hexagonal disk, and six free stamens alternate with petals within it. The pistil consists of fused carpels. Ovary with an apical style is superior. The unique combination of characters of the fossil, such as stamens inside the thick and flattened disk surrounding the ovary and equal in number to the petals, is similar to that of Celastraceae. The fossil is assigned to Celastraceae but distinguished from other extant genera of the family by being 6-merous rather than 4- or 5-merous. It might represent an extinct and early type of Celastraceae. The presence of a disk might provide evidence for insect pollination in the early stages of Celastraceae evolution.
Cross-talk in Plant Hormone Signalling: What Arabidopsis Mutants Are Telling Us (2003)

Genetic screens have been extremely useful in identifying genes involved in hormone signal transduction. However, although these screens were originally designed to identify specific components involved in early hormone signalling, mutations in these genes often confer changes in sensitivity to more than one hormone at the whole-plant level. Moreover, a variety of hormone response genes has been identified through screens that were originally designed to uncover regulators of sugar metabolism. Together, these facts indicate that the linear representation of the hormone signalling pathways controlling a specific aspect of plant growth and development is not sufficient, and that hormones interact with each other and with a variety of developmental and metabolic signals. Following the advent of arabidopsis molecular genetics we are beginning to understand some of the mechanisms by which a hormone is transduced into a cellular response. In this Botanical Briefing we review a subset of genes in arabidopsis that influence hormonal cross-talk, with emphasis on the gibberellin, abscisic acid and ethylene pathways. In some cases it appears that modulation of hormone sensitivity can cause changes in the synthesis of an unrelated hormone, while in other cases a hormone response gene defines a node of interaction between two response pathways. It also appears that a variety of hormones may converge to regulate the turnover of important regulators involved in growth and development. Examples are cited of the recent use of suppressor and enhancer analysis to identify new nodes of interaction between these pathways.
In vitro degradation of natural insoluble lignin in aqueous media by the extracellular peroxidases ofPhanerochaete chrysosporium (1998)

The lignin peroxidases (LIP) and manganese peroxidases (MNP) of Phanerochaete chrysosporium catalyze a wide range of lignin depolymerization reactions with lignin models and synthetic lignins in solution. However, their ability to degrade insoluble natural lignin in aqueous media has not been demonstrated. Insoluble isolated poplar lignin similar to natural lignin was treated in vitro in aqueous media for 12 h with LIP, MNP, and both. Treatment with MNP alone slightly increased the solid mass and produced measurable amounts of lignin-derived 2,6-dimethoxyhydroquinone and 2-methoxyhydroquinone but did not appreciably decrease the total lignin content. Treatment with LIP alone did not decrease the mass but produced measurable amounts of lignin-derived p-hydroxybenzoic acid and slightly decreased the lignin content. Finally, treatment with LIP and MNP together decreased the solid mass by 11%, decreased the lignin content by 5%, and released low-concentration compounds with mass spectra containing the typical lignin-derived electron-impact fragments of mass 107, 137, 151, 167, and 181. These results suggest that MNP increases the effectiveness of LIP-mediated lignin degradation.
Visualization of Trna Movements on theEscherichia coli70s Ribosome during the Elongation Cycle (2000)

Three-dimensional cryomaps have been reconstructed for tRNA-ribosome complexes in pre- and posttranslocational states at 17-A resolution. The positions of tRNAs in the A and P sites in the pretranslocational complexes and in the P and E sites in the posttranslocational complexes have been determined. Of these, the P-site tRNA position is the same as seen earlier in the initiation-like fMet-tRNA(f)(Met)-ribosome complex, where it was visualized with high accuracy. Now, the positions of the A- and E-site tRNAs are determined with similar accuracy. The positions of the CCA end of the tRNAs at the A site are different before and after peptide bond formation. The relative positions of anticodons of P- and E-site tRNAs in the posttranslocational state are such that a codon-anticodon interaction at the E site appears feasible.
Role of type I and type II interferon responses in recovery from infection with an encephalitic flavivirus (2003)

We have investigated the contribution of the interferon (IFN)-alpha/beta system, IFN-gamma and nitric oxide to recovery from infection with Murray Valley encephalitis virus, using a mouse model for flaviviral encephalitis where a small dose of virus was administered to 6-week-old wild-type and gene knockout animals by the intravenous route. We show that a defect in the IFN-alpha/beta responses results in uncontrolled extraneural virus growth, rapid virus entry into the brain and 100 % mortality. In contrast, mice deficient in IFN-gamma or nitric oxide production display an only marginally increased susceptibility to infection with the neurotropic virus.
Immunohistochemical demonstration of interleukin-1 receptor antagonist protein and interleukin-1 in human lymphoid tissue and granulomas. (1992)

Human interleukin 1 receptor antagonist protein (IRAP) is a specific antagonist of interleukin 1 (IL-1) action in both in vitro and in vivo experimental models. Presently, the significance of this protein in human pathophysiology is unknown. In the present study, monoclonal antibodies against IRAP were prepared and used to demonstrate IRAP expression in human tissues, immunohistochemically. Specifically, this study focused on lymphoid tissues and granulomatous inflammatory reactions since IL-1 is believed to play roles in lymphocyte development and inflammation. In addition, these tissues were also stained for IL-1 beta to compare the expression of agonist and antagonist. These findings indicate that IRAP expression is largely limited to macrophages and their derivatives. Strong IRAP expression was observed in germinal center macrophages of lymph nodes, spleen, and tonsil. In contrast, IL-1 was marginally expressed in these organs. Granulomas associated with active M. tuberculosis infection, sarcoidosis and foreign bodies all contained strongly IRAP positive cells, which included macrophages, epithelioid cells and multinucleate giant cells. Unlike reactive lymphoid tissue, tuberculous and sarcoid granulomas also contained IL-1 positive cells which included macrophages and their derivatives, as well as some stromal cells. Foreign body lesions showed minimal IL-1 expression. Interestingly, granulomas in patients with acquired immunodeficiency disease (AIDS) associated with M. avium-intracellulare contained IRAP positive cells but were negative for IL-1 expression. Taken together, these findings suggest that IRAP takes part in both physiologic and pathologic reactions. Moreover, they provide a basis to design future studies to determine the precise contribution of IRAP to these reactions.
Cytotoxic and antiangiogenic activity of AW464 (NSC 706704), a novel thioredoxin inhibitor: an in vitro study (2005)

AW464 (NSC 706704) is a novel benzothiazole substituted quinol compound active against colon, renal and certain breast cancer cell lines. NCI COMPARE analysis indicates possible interaction with thioredoxin/thioredoxin reductase, which is upregulated under hypoxia. Through activity on HIF1alpha, VEGF levels are regulated and angiogenesis controlled. A thioredoxin inhibitor could therefore exhibit enhanced hypoxic toxicity and indirect antiangiogenic effects. In vitro experiments were performed on colorectal and breast cancer cell lines under both normoxic and hypoxic conditions and results compared against those obtained with normal cell lines, fibroblasts and keratinocytes. Antiangiogenic effects were studied using both large and microvessel cells. Indirect antiangiogenic effects (production of angiogenic growth factors) were studied via ELISA. We show that AW464 exerts antiproliferative effects on tumour cell lines as well as endothelial cells with an IC(50) of approximately 0.5 microM. Fibroblasts are however resistant. Proliferating, rather than quiescent, endothelial cells are sensitive to the drug indicating potential antiangiogenic rather than antivascular action. Endothelial differentiation is also inhibited in vitro. Hypoxia (1% O(2) for 48 h) sensitises colorectal cells to lower drug concentrations, and in HT29s greater inhibition of VEGF is observed under such conditions. In contrast, bFGF levels are unaffected, suggesting possible involvement of HIF1alpha. Thus, AW464 is a promising chemotherapeutic drug that may have enhanced potency under hypoxic conditions and also additional antiangiogenic activity.
Isolation and characterization of a class II α-mannosidase cDNA from lepidopteran insect cells (1997)

Lepidopteran insect cells are used routinely as hosts for foreign glycoprotein expression by recombinant baculoviruses, but the precise nature of their N-glycosylation pathway remains poorly defined. These cells clearly have processing glucosidases and mannosidases that can convert precursors to Man3GlcNAc2 structures and fucosyltransferases that can add fucose to the oligosaccharide core. However, their ability to extend these structures to produce complex side chains like those found in mammalian cells remains to be determined. To begin to examine this pathway at the molecular genetic level, we isolated and characterized a class II alpha-mannosidase (alpha-mannosidase II) cDNA from Sf9, a lepidopteran insect cell line. In mammalian cells, this enzyme catalyzes the committed step in the pathway converting N-linked carbohydrates to complex forms. Degenerate primers against conserved regions in known class II alpha-mannosidase protein sequences were used to generate an alpha-mannosidase II-specific PCR product from Sf9 cell DNA. Sequence information from this product was used to isolate a partial cDNA clone, the 5' end was isolated by ligation-anchored PCR, and the full length alpha-mannosidase II cDNA was assembled. This cDNA contained a long open reading frame predicted to encode an 1130 amino acid protein with 37% identity to human Golgi alpha-mannosidase II and with a type II membrane topology, a feature of all known Golgi processing enzymes. Southern blotting indicated that alpha-mannosidase II is a single copy gene in Sf9 cells. Other Lepidoptera had related alpha-mannosidase II genes, but there was variation among different genera, and the Sf9 alpha-mannosidase II cDNA did not cross-hybridize with DNA from animals outside Lepidoptera. Steady-state levels of alpha-mannosidase II RNA were low in uninfected Sf9 cells and even lower after baculovirus infection. The in vitro-translated Sf9 alpha-mannosidase II protein had the expected size and was translocated and N-glycosylated by microsomal membranes. Expression of the Sf9 alpha-mannosidase II cDNA in the baculovirus system produced large amounts of a protein with the expected size and swainsonine-sensitive alpha-mannosidase II activity towards an aryl-alpha-mannoside substrate. These results demonstrate that Sf9 cells encode and express an alpha-mannosidase II with properties similar to those of the mammalian enzyme.
Eosinophilic inflammation in COPD: prevalence and clinical characteristics (2014)

targeted treatment strategies directed towards specific biological pathways.
Hippocampectomy disrupts auditory trace fear conditioning and contextual fear conditioning in the rat (1999)

The hippocampus is believed to be an important structure for learning tasks that require temporal processing of information. The trace classical conditioning paradigm requires temporal processing because the conditioned stimulus (CS) and the unconditioned stimulus (US) are temporally separated by an empty trace interval. The present study sought to determine whether the hippocampus was necessary for rats to perform a classical trace fear conditioning task in which each of 10 trials consisted of an auditory tone CS (1 5-s duration) followed by an empty 30-s trace interval and then a fear-producing floor-shock US (0.5-s duration). Several weeks prior to training, animals were anesthetized and given aspiration lesions of the neocortex (NEO; n = 6), hippocampus and overlying neocortex (HIPP; n = 7), or no lesions at all (control; n = 6). Approximately 24 h after trace conditioning, NEO and control animals showed a significant decrease in movement to a CS-alone presentation that was indicative of a conditioned fear response. Animals in the HIPP group did not show conditioned fear responses to the CS alone, nor did a pseudoconditioning group (n = 7) that was trained with unpaired CSs and USs. Furthermore, all groups except the HIPP group showed conditioned fear responses to the original context in which they received shock USs. One week later, HIPP, NEO, and control animals received delay fear-conditioning trials with no trace interval separating the CS and US. Six of seven HIPP animals could perform the delay version, but none could perform the trace version. This result suggests that the trace fear task is a reliable and useful model for examining the neural mechanisms of hippocampally dependent learning.
Double data rate SYNCHRONOUS DRAMs in high performance applications (2002)

Double Data Rate Synchronous DRAMs are recently introduced SDRAM type products that can offer an evolutionary change with performance advantages for all Memory Systems. These advantages are based on a synchronous I/O interface and dual edge clock based data bus with improved internal architecture that enables faster data throughput rates. Architectural differences are discussed between various memory solutions and future trends in Synchronous DRAMs. The device functionality and timing are explained as compared with single data rate SDRAMs. Performance estimations are shown for present and future DDR SDRAM products when compared with traditional commodity type DRAMs or single edge clock SDRAMs.
Improving BER Performance of LDPC Codes based on Intermediate Decoding Results (2007)

The paper presents a novel approach to reduce the bit error rate (BER) in iterative belief propagation (BP) decoding of low density parity check (LDPC) codes. The behavior of the BP algorithm is first investigated as a function of number of decoder iterations, and it is shown that typical uncorrected error patterns can be classified into 3 categories: oscillating, nearly-constant, or random-like, with a predominance of oscillating patterns at high Signal-to-Noise (SNR) values. A proposed decoder modification is then introduced based on tracking the number of failed parity check equations in the intermediate decoding iterations, rather than relying on the final decoder output (after reaching the maximum number of iterations). Simulation results with a rate ¿ (1024,512) progressive edge-growth (PEG) LDPC code show that the proposed modification can decrease the BER by as much as 10-to-40%, particularly for high SNR values.
ERK1 and ERK2 mitogen-activated protein kinases affect Ras-dependent cell signaling differentially (2006)

These results reveal an unexpected interplay between ERK1 and ERK2 in transducing Ras-dependent cell signaling and proliferation. Whereas ERK2 seems to have a positive role in controlling normal and Ras-dependent cell proliferation, ERK1 probably affects the overall signaling output of the cell by antagonizing ERK2 activity.
Atopic eczema: its impact on the family and financial cost (1997)

Childhood atopic eczema has a profound impact on the social, personal, emotional, and financial perspectives of families.
New Terminology and Clarifications for Diffserv (2002)

This memo captures Diffserv working group agreements concerning new and improved terminology, and provides minor technical clarifications. It is intended to update RFC 2474, RFC 2475 and RFC 2597. When RFCs 2474 and 2597 advance on the standards track, and RFC 2475 is updated, it is intended that the revisions in this memo will be incorporated, and that this memo will be obsoleted by the new RFCs.
Human Natural Killer cell receptors: insights into their molecular function and structure (2003)

NK cells express receptors characterized by opposite functions that finely regulate their activities. Among inhibitory receptors, some are specific for different groups of MHC class I alleles, while others are still orphan receptors. On the contrary, various activating receptors are involved in the triggering of NK-mediated natural cytotoxicity. In general, their engagement induces human NK cells to kill target cells that are either HLA class I-negative or -deficient. Thus, the process of NK cell triggering mediated by Natural Cytotoxicity Receptors can be mainly considered as a non MHC-restricted mechanism. Here, a brief description of the molecular nature of these receptors, as well as, of their 3D-structures and of the implications for ligand recognition, is given.
EXPRESSION ANALYSIS OF Y CHROMOSOME GENES IN HUMAN PROSTATE CANCER (2001)

The differential expression of Y chromosome genes in prostate cancer, BPH tissue and prostate cancer cell lines indicates that they may have a role in prostate cancer.
Breathing abnormalities during sleep (1983)

• The purpose of this communication is to review obstructive and central breathing abnormalities that may occur during sleep, such as obstructive sleep apnea, and Cheyne-Stokes respiration. Emphasis is placed on noninvasive monitoring of the breathing pattern and intrapleural pressure swings by respiratory and surface inductive plethysmography, respectively, which establish the diagnosis of these abnormal breathing patterns. (<i>Arch Intern Med</i>1983;143:1221-1228)
Prevalence of Diabetes, Impaired Fasting Glucose, and Impaired Glucose Tolerance in U.S. Adults: The Third National Health and Nutrition Examination Survey, 1988–1994 (1998)

The high rates of abnormal fasting and postchallenge glucose found in NHANES III, together with the increasing frequency of obesity and sedentary lifestyles in the population, make it likely that diabetes will continue to be a major health problem in the U.S.
Antibiotics versus placebo for acute bacterial conjunctivitis (2006)

Acute bacterial conjunctivitis is frequently a self-limiting condition, but the use of antibiotics is associated with significantly improved rates of clinical and microbiological remission.
Identification of overexpression of orphan G protein-coupled receptor GPR49 in human colon and ovarian primary tumors (2006)

We used gene expression profiling to probe differences in transcriptional output between 15 panels of colon tumor and matched normal colon tissues. This analysis revealed that GPR49, an orphan G Protein-Coupled Receptor (GPCR) is overexpressed in 66% (10/15) colon tumors compared with normal colon tissues. Subsequent analysis of an additional 39 sets of matched normal and tumor colon tissues by real-time quantitative reverse transcriptase confirmed the upregulation of this receptor. The differential expression of GPR49 between normal and tumor tissue was significant (p > 0.001). GPR49 was upregulated in 25 of 39 (64%) colon primary tumor tissues. In addition to colon tumors, GPR49 was also found to be upregulated in 18 of 33 (53%) ovarian primary tumor tissues analyzed by RT-PCR. Moreover, the expression level of GPR49 in colon and ovarian tumors increased in more advanced tumors suggesting a role for the receptor in tumor progression. The selective overexpression of GPR49 in tumor tissues was further illustrated by specific immunohistochemical staining of colon and ovarian tumor tissues, a finding that correlates with the mRNA expression of the receptor. In addition, expression of GPR49 induced transformation in a ligand-dependent manner and Knockdown of GPR49 mRNA level induced apoptosis in colon tumor cells. These novel findings provide a foundation for further studies and suggest a potential role for GPR49 in tumorigenesis.
High Performance Computing in Structural Engineering (1998)

From the Publisher:
This book is about high-performance computing in structural engineering on supercomputers with vectorization and parallel processing capabilities. High-Performance Computing in Structural Engineering presents robust parallel-vector algorithms for analysis and optimization of large three-dimensional structures. The authors outline many step-by-step algorithms for the analysis and optimization of structures on shared-memory multiprocessor computers. By extension, the material in High-Performance Computing in Structural Engineering will also find applications in distributed computing on a cluster of workstations.