gebhart/patrepeval huggingface dataset:
Efficient word-graph parsing and search with a stochastic context-free grammar (2002)

Word graphs provide a compact representation for the output of the acoustic decoder in a speech recogniser. This paper proposes an efficient algorithm for parsing the graph structure using a stochastic context-free grammar (SCFG). By parsing an entire graph in a single pass significant savings can be made over techniques that parse individual sentences, such as the common N-best strategy, or methods that parse paths through a graph. A backward Viterbi search is used to recover the parsed sentences from the graph. The full graph parsing algorithm is shown to be better than a heuristic search that parses only portions of the graph. On the resource management task a reduction in computation of 5 times over N-best is demonstrated. The integration of SCFG gives a reduction in recogniser word error rate of 9.8%.
Experimental investigation of self coherent optical OFDM systems using fabry-perot filters for carrier extraction (2010)

We experimentally demonstrate self coherent optical OFDM transmission with IQ demultiplexing employing a Fabry-Perot-tunable filter for the extraction of the optical carrier. The performance is investigated and compared to a conventional CO-OFDM.
The Angiographic Differential Diagnosis of Acute Pulmonary Embolism (1974)

Angiographic features of nine pulmonary conditions which may simulate acute pulmonary embolism are presented and the differential angiographic features emphasized. A firm angiographic diagnosis of acute pulmonary embolism must be based solely on the demonstration of intraluminal defects or arterial occlusions. Segmental injections are often crucial for a confident differential diagnosis of embolism.
Regulation of innate and adaptive immune responses by the related cytokines IL-12, IL-23, and IL-27 (2006)

The functional characterization and subsequent purification of T cell growth factor/interleukin (IL)-2 in the early 1980s established this secreted protein as a key mediator of immune cell activation and provided the prototype that enabled the discovery of numerous cytokines over the ensuing two decades. While soluble immunoregulatory factors were initially identified functionally as biological activities present in the culture supernatants of activated lymphocytes/monocytes, this methodology shifted radically following the completion of the human genome sequence. Computer-generated structural modeling algorithms have replaced functional assays and biochemical purification as the initial means of discovering new cytokines. To date, a total of 31 interleukins, as well as over a dozen other related hematopoietic factors, have been identified. These cytokines and their receptors may be grouped on the basis of structural homologies as well as by shared ligand and receptor subunits. The challenge now at hand is to define the biological functions of the newly identified cytokines and to elucidate the common and divergent roles of related family members. This point is well illustrated by the IL-12/IL-23/IL-27 family, whose members share ligand and receptor subunits and play somewhat overlapping roles in innate and adaptive immune responses. These three cytokines are not entirely redundant, as they may preferentially activate naïve or memory T cells, induce discrete T cell cytokine profiles, contribute to distinct stages of host immune responses to infectious agents, and differentially promote autoimmunity. Further elucidation of the unique functions of the IL-12 family members may lead to improved immunodiagnostics and therapies.
PISCES: a protein sequence culling server (2003)

PISCES is a public server for culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled from the entire PDB or from lists of PDB entries or chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output.
Regioselective Hydroformylation of Allylic Alcohols (2011)

A highly regioselective hydroformylation of allylic alcohols is reported toward the synthesis of β-hydroxy-acid and aldehyde products. The selectivity is achieved through the use of a ligand that reversibly binds to alcohols in situ, allowing for a directed hydroformylation to occur. The application to trisubstituted olefins was also demonstrated, which yields a single diastereomer product consistent with a stereospecific addition of CO and hydrogen.
Inpatient treatment patterns of human immunodeficiency virus-associated Pneumocystis carinii pneumonia in New York State Medicare patients. (1996)

Hospital charts were reviewed to ascertain the frequency with which patients with human immunodeficiency virus (HIV)-associated Pneumocystis carinii pneumonia (PCP) were being managed in accordance with current guidelines or recommendations in New York State for the calendar year 1993. Comparisons were made between hospitals that are designated by the New York State Department of Health as comprehensive treatment centers--designated acquired immunodeficiency syndrome (AIDS) centers--and all other hospitals. For patients who had been on PCP prophylaxis before admission, 34% had documentation of positive histologic evidence for PCP infection during the studied hospitalization period. Of all patients not on PCP prophylaxis at the time of admission, 94% had at least one of the diagnostic tests for PCP done during the PCP hospitalization. Eighty-one percent of all patients had either pulse oximetry or an arterial blood gas determination. Seventy-seven percent of all patients with a PO2 equal to or less than 70 mm Hg received steroids. All eligible patients received one of nine possible treatment combinations, which included either single drug therapy, multiple drug therapy, or participation in a clinical trial. Sixteen percent of eligible patients had no documentation of receiving PCP medication at discharge. Proportions receiving diagnostic or treatment interventions were usually higher in designated AIDS centers than in non-designated AIDS centers.
Wallflower: principles and practice of background maintenance (1999)

Background maintenance is a frequent element of video surveillance systems. We develop Wallflower, a three-component system for background maintenance: the pixel-level component performs Wiener filtering to make probabilistic predictions of the expected background; the region-level component fills in homogeneous regions of foreground objects; and the frame-level component detects sudden, global changes in the image and swaps in better approximations of the background. We compare our system with 8 other background subtraction algorithms. Wallflower is shown to outperform previous algorithms by handling a greater set of the difficult situations that can occur. Finally, we analyze the experimental results and propose normative principles for background maintenance.
Regulation of the Mycobacterium tuberculosis mce1 Operon (2005)

In the murine model of infection, a Mycobacterium tuberculosis mce1 operon mutant elicits an aberrant granulomatous response, resulting in uncontrolled replication and failure to enter a persistent state. In this study, we demonstrate that the mce1 genes can be transcribed as a 13-gene polycistronic message encompassing Rv0166 to Rv0178. Quantitative reverse transcriptase PCR and immunoblot analyses revealed that the mce1 genes and proteins are expressed during in vitro growth but are significantly down-regulated in intracellular bacilli isolated from murine macrophages. A homologue of the FadR subfamily of GntR transcriptional regulators, Rv0165c (designated Mce1R), lies upstream and is divergently transcribed from the operon. To investigate whether this gene plays a role in regulation of mce1 expression, we created an M. tuberculosis mce1R deletion mutant. There was no difference in expression of mce1 operon genes in Deltamce1R compared to expression in the wild type during logarithmic growth in vitro. However, in bacilli isolated from murine macrophages, expression of mce1 genes was significantly higher in Deltamce1R. In addition, overexpression of mce1R resulted in repression of the mce1 genes. These data demonstrate that Mce1R is a negative regulator that acts intracellularly to repress expression of the mce1 operon. We propose that Mce1R facilitates balanced temporal expression of the mce1 products required for organized granuloma formation, which is both protective to the host and necessary for the persistence of M. tuberculosis.
Overactive bladder: magnetic versus electrical stimulation (2003)

Magnetic stimulation appears to induce inhibitory effects on detrusor overactivity in a similar manner to electrical stimulation, with significant clinical advantages. Although further studies are needed to establish long-term efficacy, magnetic stimulation of the sacral nerve roots may be a promising alternative treatment for overactive bladder.
A novel lead for specific anti-HIV-1 agents: 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA novel lead for specific anti-HIV-1 agents: 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymineTadashi Miyasaka, Hiromichi Tanaka, Masanori Baba, Hiroyuki Hayakawa, Richard T. Walker, Jan Balzarini, and Erik De ClercqCite this: J. Med. Chem. 1989, 32, 12, 2507–2509Publication Date (Print):December 1, 1989Publication History Published online1 May 2002Published inissue 1 December 1989https://pubs.acs.org/doi/10.1021/jm00132a002https://doi.org/10.1021/jm00132a002research-articleACS PublicationsRequest reuse permissionsArticle Views503Altmetric-Citations339LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Cellular Differences in the Molecular Mechanisms of Vaccinia Virus Host Range Restriction (1980)

The biochemistry of vaccinia virus replication in two permissive (BSC-40, L-929), and two non-permissive (CHO, MDBK) cell lines has been compared. While CHO and MDBK cells differentially allowed expression of the various stages in the vaccinia developmental programme, neither cell supported production of any infectious progeny virions.
Mechanistic Insight into Pentatricopeptide Repeat Proteins as Sequence-Specific RNA-Binding Proteins for Organellar RNAs in Plants (2012)

The pentatricopeptide repeat (PPR) protein family is highly expanded in terrestrial plants. Arabidopsis contains 450 PPR genes, which represents 2% of the total protein-coding genes. PPR proteins are eukaryote-specific RNA-binding proteins implicated in multiple aspects of RNA metabolism of organellar genes. Most PPR proteins affect a single or small subset of gene(s), acting in a gene-specific manner. Studies over the last 10 years have revealed the significance of this protein family in coordinated gene expression in different compartments: the nucleus, chloroplast and mitochondrion. Here, we summarize recent studies addressing the mechanistic aspect of PPR proteins.
Detection of blocking artifacts of compressed still images (2002)

A novel frequency domain technique for image blocking artifact detection is presented. The algorithm detects the regions of the image which present visible blocking artifacts. This detection is performed in the frequency domain and uses the estimated relative quantization error calculated when the DCT coefficients are modeled by a Laplacian probability function. Experimental results illustrating the performance of the proposed method are presented and evaluated.
Auto-encoder bottleneck features using deep belief networks (2012)

Neural network (NN) bottleneck (BN) features are typically created by training a NN with a middle bottleneck layer. Recently, an alternative structure was proposed which trains a NN with a constant number of hidden units to predict output targets, and then reduces the dimensionality of these output probabilities through an auto-encoder, to create auto-encoder bottleneck (AE-BN) features. The benefit of placing the BN after the posterior estimation network is that it avoids the loss in frame classification accuracy incurred by networks that place the BN before the softmax. In this work, we investigate the use of pre-training when creating AE-BN features. Our experiments indicate that with the AE-BN architecture, pre-trained and deeper NNs produce better AE-BN features. On a 50-hour English Broadcast News task, the AE-BN features provide over a 1% absolute improvement compared to a state-of-the-art GMM/HMM with a WER of 18.8% and pre-trained NN hybrid system with a WER of 18.4%. In addition, on a larger 430-hour Broadcast News task, AE-BN features provide a 0.5% absolute improvement over a strong GMM/HMM baseline with a WER of 16.0%. Finally, system combination with the GMM/HMM baseline and AE-BN systems provides an additional 0.5% absolute on 430 hours over the AE-BN system alone, yielding a final WER of 15.0%.
Achieving Accurate and Fast Base-calling by a Block Model of the Illumina Sequencing Data (2015)

Base-calling accuracy is crucial for high-throughput DNA sequencing and we considered the de-convolution of the intensity data of Illumina systems. While the phasing and color crosstalk are considered with fixed parameters in existing base-calling softwares, we found that these processes are not constant in different part of the data. We thus model and deal with the data in blocks, and by this approach we improve the base calling accuracy as well as reduce the model complexity. A block method based on a linear statistical model is then developed, which balances the accuracy against the computational speed. The performances under different blocking conditions are also analyzed.
Depletion-mode GaAs MOSFETs with negligible drain current drift and hysteresis (2002)

For the first time, depletion-mode GaAs MOSFETs with undetectable hysteresis and negligible drain current drift I-V characteristics were successfully fabricated using MBE grown Ga/sub 2/O/sub 3/(Gd/sub 2/O/sub 3/) as the gate oxide. The absence of drain current drift and hysteresis is a significant advance towards the manufacture of commercially useful GaAs MOSFETs.
Stimulation of Platelet Activation and Aggregation by a Carboxyl-terminal Peptide from Thrombospondin Binding to the Integrin-associated Protein Receptor (1997)

Thrombospondin, a major secretory product of the alpha-granules of activated platelets, is a large trimeric glycoprotein that plays an important role in platelet aggregation. On resting platelets, thrombospondin binds to a single receptor in a cation-independent manner, but upon platelet activation it binds at least two further, distinct receptors that are both dependent upon divalent cations. Each of these receptors on the platelet surface binds to different regions of the thrombospondin molecule, and such binding may be responsible for the multifunctional role of thrombospondin in aggregation. We show here that a peptide from the carboxyl terminus of thrombospondin, RFYVVMWK, directly and specifically induces the activation and aggregation of washed human platelets from different donors at concentrations of 5-25 microM. At lower concentrations the peptide synergizes with suboptimal concentrations of ADP to induce aggregation. Peptide affinity chromatography and immunoprecipitation with a monoclonal antibody were used to identify the receptor for the carboxyl-terminal peptide as the integrin-associated protein. The integrin-associated protein remained bound to the RFYVVMWK-containing peptide column when washed with a scrambled peptide in the presence of 5 mM EDTA, indicating a divalent cation-independent association. It is suggested that integrin-associated protein is the primary receptor for thrombospondin on the surface of resting platelets and is implicated in potentiating the platelet aggregation response.
Transformation of Brassica napus and Brassica oleracea Using Agrobacterium tumefaciens and the Expression of the bar and neo Genes in the Transgenic Plants (1989)

An efficient and largely genotype-independent transformation method for Brassica napus and Brassica oleracea was established based on neo or bar as selectable marker genes. Hypocotyl explants of Brassica napus and Brassica oleracea cultivars were infected with Agrobacterium strains containing chimeric neo and bar genes. The use of AgNO(3) was a prerequisite for efficient shoot regeneration under selective conditions. Vitrification was avoided by decreasing the water potential of the medium, by decreasing the relative humidity in the tissue culture vessel, and by lowering the cytokinin concentration. In this way, rooted transformed shoots were obtained with a 30% efficiency in 9 to 12 weeks. Southern blottings and genetic analysis of S1-progeny showed that the transformants contained on average between one and three copies of the chimeric genes. A wide range of expression levels of the chimeric genes was observed among independent transformants. Up to 25% of the transformants showed no detectable phosphinotricin acetyltransferase or neomycin phosphotransferase II enzyme activities although Southern blottings demonstrated that these plants were indeed transformed.
Omasal Flow of Soluble Proteins, Peptides, and Free Amino Acids in Dairy Cows Fed Diets Supplemented with Proteins of Varying Ruminal Degradabilities (2007)

Three ruminally and duodenally cannulated cows were assigned to an incomplete 4 4 Latin square with four 14-d periods and were fed diets supplemented with urea, solvent soybean meal, xylosetreated soybean meal (XSBM), or corn gluten meal to study the effects of crude protein source on omasal canal flows of soluble AA. Soluble AA in omasal digesta were fractionated by ultrafiltration into soluble proteins greater than 10 kDa (10K), oligopeptides between 3 and 10 kDa (3-10K), peptides smaller than 3 kDa (small peptides), and free AA (FAA). Omasal flow of total soluble AA ranged from 254 to 377 g/d and accounted for 9.2 to 15.9% of total AA flow. Averaged across diets, flows of AA in 10K, 3-10K, small peptides, and FAA were 29, 217, 50, and 5 g/d, respectively, and accounted for 10.3, 71.0, 17.5, and 1.6% of the total soluble AA flow. Cows with diets supplemented with solvent soybean meal had higher flows of Met, Val, and total AA associated with small peptides than those whose diets were supplemented with XSBM, whereas supplementation with corn gluten meal resulted in higher total small peptide-AA flows than did XSBM. Averaged across diets, 27, 75, and 93% of soluble AA in 10K, 3-10K, and peptides plus FAA flowing out of the rumen were of dietary origin. On average, 10% of
Targeting FGFR4 Inhibits Hepatocellular Carcinoma in Preclinical Mouse Models (2012)

The fibroblast growth factor (FGF)-FGF receptor (FGFR) signaling system plays critical roles in a variety of normal developmental and physiological processes. It is also well documented that dysregulation of FGF-FGFR signaling may have important roles in tumor development and progression. The FGFR4-FGF19 signaling axis has been implicated in the development of hepatocellular carcinomas (HCCs) in mice, and potentially in humans. In this study, we demonstrate that FGFR4 is required for hepatocarcinogenesis; the progeny of FGF19 transgenic mice, which have previously been shown to develop HCCs, bred with FGFR4 knockout mice fail to develop liver tumors. To further test the importance of FGFR4 in HCC, we developed a blocking anti-FGFR4 monoclonal antibody (LD1). LD1 inhibited: 1) FGF1 and FGF19 binding to FGFR4, 2) FGFR4-mediated signaling, colony formation, and proliferation in vitro, and 3) tumor growth in a preclinical model of liver cancer in vivo. Finally, we show that FGFR4 expression is elevated in several types of cancer, including liver cancer, as compared to normal tissues. These findings suggest a modulatory role for FGFR4 in the development and progression of hepatocellular carcinoma and that FGFR4 may be an important and novel therapeutic target in treating this disease.
Clinical Trials in Traumatic Brain Injury: Past Experience and Current Developments (2010)

In this article, we review past and current experience in clinical trials of traumatic brain injuries (TBIs), we discuss limitations and challenges, and we summarize current directions. The focus is on severe and moderate TBIs. A systematic literature search of the years from 1980 to 2009 revealed 27 large phase III trials in TBI; we were aware of a further 6 unpublished trials. Analysis of these 33 trials yielded interesting observations: There was a peak incidence of trial initiations that occurred in the mid-1990s with a sharp decline during the period from 2000 to 2004. Most trials that reported a significant treatment effect were studies on a therapeutic strategy (e.g., decompressive craniectomy, hypothermia), and these were single-center studies. Increasingly, studies have been shifting toward the Far East. The currently existing trial registries permit insight into ongoing or recently conducted trials. Compared with the past decade, the number of studies on neuroprotective agents taken forward into efficacy-oriented studies is low. In contrast, the number of studies on therapeutic strategies appears to be increasing again. The disappointing results in trials on neuroprotective agents in TBI have led to a critical reappraisal of clinical trial methodology. This has resulted in recommendations for preclinical workup and has triggered extensive analysis on approaches to improve the design and analysis of clinical trials in TBI. An interagency initiative toward standardization on selection and coding of data elements across the broad spectrum of TBI is ongoing, and will facilitate comparison of research findings across studies and encourage high-quality meta-analysis of individual patient data in the future.