gebhart/patrepeval huggingface dataset:
Characterization of epidermal growth factor receptor gene expression in malignant and normal human cell lines. (1984)

To investigate the possibility that the epidermal growth factor (EGF) receptor functions as an oncogene product, we have determined the levels of EGF receptor protein and RNA in a variety of malignant and normal human cells, using a specific polyclonal antibody to the EGF receptor and a cDNA clone (plasmid pE7) that encodes the EGF receptor, respectively. Besides A431 epidermoid carcinoma cells, which are known to make large amounts of EGF receptor, cell lines from two ovarian cancers, two cervical cancers, and one kidney cancer were found to contain substantial amounts of receptor protein (11-22% of A431). Normal human fibroblasts (Detroit 551), a human lymphocyte line (IM-9), and a leukemic lymphocyte line (CEM) contained low or undetectable levels of EGF receptor. RNA blot analysis showed that among the human cell lines examined the levels of a 10- and a 5.6-kilobase species of pE7-specific RNA generally correlated with the amount of the EGF receptor protein. Genomic DNA blot analysis revealed that except for A431 none of these cell lines expressing high levels of EGF receptor protein possessed amplified receptor gene sequences. A431 cells are known to secrete a truncated form of the EGF receptor. An abundant 2.9-kilobase RNA is found only in A431 cells; it could encode the truncated form of the EGF receptor.
Simultaneous liquid viscosity and density determination with piezoelectric unimorph cantilevers (2001)

We have examined both experimentally and theoretically a piezoelectric unimorph cantilever as a liquid viscosity-and-density sensor. The fabricated piezoelectric unimorph consisted of a PbO⋅ZrO2⋅TiO2 (PZT) layer on a thin stainless-steel plate. In addition to a driving electrode, a sensing electrode was placed on top of the PZT layer, permitting the direct measurement of the resonance frequency. The cantilever was tested using water–glycerol solutions of different compositions. In all three of the tested modes, the resonance frequency decreased while the width of the resonance peak increased with increasing glycerol content. To account for the liquid effect, we consider the cantilever as a sphere of radius R oscillating in a liquid. By including the high and low frequency terms in the induced mass and the damping coefficient of the liquid, we show that for a given liquid density and viscosity the oscillating-sphere model predicts a resonance frequency and peak width that closely agree with experiment. Furthermore, the viscosity and the density of a liquid have been determined simultaneously using the experimentally measured resonance frequency and peak width as inputs to the oscillating-sphere model. The calculated liquid viscosity and density closely agreed with the known values, indicating that our cantilever-based sensor is effective in determining viscosity and density, simultaneously. We also show that scaling analysis predicts an increase in the width of the resonance peak with decreasing cantilever size, an observation in agreement with the large peak widths observed for microcantilevers.
Rapid Screening of Complex DNA Samples by Single-Molecule Amplification and Sequencing (2011)

Microbial cloning makes Sanger sequencing of complex DNA samples possible but is labor intensive. We present a simple, rapid and robust method that enables laboratories without special equipment to perform single-molecule amplicon sequencing, although in a low-throughput manner, from sub-picogram quantities of DNA. The method can also be used for quick quality control of next-generation sequencing libraries, as was demonstrated for a metagenomic sample.
Gremlin negatively modulates BMP-4 induction of embryonic mouse lung branching morphogenesis (2001)

Bone morphogenetic protein-4 (BMP-4) is a key morphogen for embryonic lung development that is expressed at high levels in the peripheral epithelium, but the mechanisms that modulate BMP-4 function in early mouse lung branching morphogenesis are unclear. Here, we studied the BMP-4 antagonist Gremlin, which is a member of the DAN family of BMP antagonists that can bind and block BMP-2/4 activity. The expression level of gremlin in embryonic mouse lungs is highest in the early embryonic pseudoglandular stage [embryonic days (E) 11.5-14.5] and is reduced during fetal lung maturation (E18.5 to postnatal day 1). In situ hybridization indicates that gremlin is diffusely expressed in peripheral lung mesenchyme and epithelium, but relatively high epithelial expression occurs in branching buds at E11.5 and in large airways after E16.5. In E11.5 lung organ culture, we found that exogenous BMP-4 dramatically enhanced peripheral lung epithelial branching morphogenesis, whereas reduction of endogenous gremlin expression with antisense oligonucleotides achieved the same gain-of-function phenotype as exogenous BMP-4, including increased epithelial cell proliferation and surfactant protein C expression. On the other hand, adenoviral overexpression of gremlin blocked the stimulatory effects of exogenous BMP-4. Therefore, our data support the hypothesis that Gremlin is a physiologically negative regulator of BMP-4 in lung branching morphogenesis.
The Oct-2 transcription factor represses tyrosine hydroxylase expression via a heptamer TAATGARAT-like motif in the gene promoter (1994)

The tyrosine hydroxylase (TH) gene promoter contains adjacent octamer and heptamer motifs which act as target sites for octamer binding transcription factors. Mutation of the heptamer motif but not the octamer motif enhances TH promoter activity in neuronal cells expressing Oct-2 but not in non-expressing fibroblasts. Similarly addition of the heptamer motif to a minimal TH promoter represses gene expression in neuronal cells but not in fibroblasts. These effects can be reproduced by the artificial expression of neuronal isoforms of Oct-2 in fibroblasts which results in the repression of transfected TH promoters containing an intact heptamer motif but not those in which this motif has been mutated or deleted. The TH promoter thus represents the first example of a cellular promoter which is repressed by Oct-2. The significance of this effect is discussed in terms of the cell type specificity of the TH promoter and its induction by different physiological stimuli.
Active steering of a tractor–semi-trailer (2011)

This paper develops a path-following steering control strategy for an articulated heavy goods vehicle. The controller steers the axles of the semi-trailer so that its rear end follows the path of the fifth wheel coupling: for all paths and all speeds. This substantially improves low-speed manoeuvrability, off-tracking, and tyre scrubbing (wear). It also increases high-speed stability, reduces ‘rearward amplification’, and reduces the propensity to roll over in high-speed transient manoeuvres. The design of a novel experimental heavy goods vehicle with three independent hydraulically actuated steering axles is presented. The path-following controller is tested on the experimental vehicle, at low and high speeds. The field test results are compared with vehicle simulations and found to agree well. The benefits of this steering control approach are quantified. In a low-speed ‘roundabout’ manoeuvre, low-speed off-tracking was reduced by 73 per cent, from 4.25 m for a conventional vehicle to 1.15 m for the experimental vehicle; swept-path width was reduced by 2 m (28 per cent); peak scrubbing tyre forces were reduced by 83 per cent; and entry tail-swing was eliminated. In an 80 km/h lane-change manoeuvre, peak path error for the experimental vehicle was 33 per cent less than for the conventional vehicle, and rearward amplification of the trailer was 35 per cent less. Increasing the bandwidth of the steering actuators improved the high-speed dynamic performance of the vehicle, but at the expense of increased oil flow.
Coordination of Transcription Factor Phosphorylation and Histone Methylation by the P-TEFb Kinase during Human Immunodeficiency Virus Type 1 Transcription (2004)

The human immunodeficiency virus type 1 (HIV-1) Tat protein recruits positive transcription elongation factor b (P-TEFb) to the transactivation response (TAR) RNA structure to facilitate formation of processive transcription elongation complexes (TECs). Here we examine the role of the Tat/TAR-specified cyclin-dependent kinase 9 (CDK9) kinase activity in regulation of HIV-1 transcription elongation and histone methylation. In HIV-1 TECs, P-TEFb phosphorylates the RNA polymerase II (RNAP II) carboxyl-terminal domain (CTD) and the transcription elongation factors SPT5 and Tat-SF1 in a Tat/TAR-dependent manner. Using in vivo chromatin immunoprecipitation analysis, we demonstrate the following distinct properties of the HIV-1 transcription complexes. First, the RNAP II CTD is phosphorylated at Ser 2 and Ser 5 near the promoter and at downstream coding regions. Second, the stable association of SPT5 with the TECs is dependent upon P-TEFb kinase activity. Third, P-TEFb kinase activity is critical for the induction of methylation of histone H3 at lysine 4 and lysine 36 on HIV-1 genes. Flavopiridol, a potent P-TEFb kinase inhibitor, inhibits CTD phosphorylation, stable SPT5 binding, and histone methylation, suggesting that its potent antiviral activity is due to its ability to inhibit several critical and unique steps in HIV-1 transcription elongation.
A Human Aware Mobile Robot Motion Planner (2007)

Robot navigation in the presence of humans raises new issues for motion planning and control when the humans must be taken explicitly into account. We claim that a human aware motion planner (HAMP) must not only provide safe robot paths, but also synthesize good, socially acceptable and legible paths. This paper focuses on a motion planner that takes explicitly into account its human partners by reasoning about their accessibility, their vision field and their preferences in terms of relative human-robot placement and motions in realistic environments. This planner is part of a human-aware motion and manipulation planning and control system that we aim to develop in order to achieve motion and manipulation tasks in the presence or in synergy with humans.
Molecular Tectonics. Three-Dimensional Organic Networks with Zeolitic Properties (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Tectonics. Three-Dimensional Organic Networks with Zeolitic PropertiesXin Wang, Michel Simard, and James D. WuestCite this: J. Am. Chem. Soc. 1994, 116, 26, 12119–12120Publication Date (Print):December 1, 1994Publication History Published online1 May 2002Published inissue 1 December 1994https://pubs.acs.org/doi/10.1021/ja00105a089https://doi.org/10.1021/ja00105a089research-articleACS PublicationsRequest reuse permissionsArticle Views1093Altmetric-Citations224LEARN 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 (3)»Supporting Information Supporting Information Get e-Alerts
The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae (1998)

The currently available yeast mitochondrial DNA (mtDNA) sequence is incomplete, contains many errors and is derived from several polymorphic strains. Here, we report that the mtDNA sequence of the strain used for nuclear genome sequencing assembles into a circular map of 85,779 bp which includes 10 kb of new sequence. We give a list of seven small hypothetical open reading frames (ORFs). Hot spots of point mutations are found in exons near the insertion sites of optional mobile group I intron-related sequences. Our data suggest that shuffling of mobile elements plays an important role in the remodelling of the yeast mitochondrial genome.
Analgesic Efficacy of Preoperative Parecoxib Sodium in an Orthopedic Pain Model (2004)

The efficacy and safety of preoperative intravenous administration of parecoxib sodium, a novel parenteral prodrug of a cyclooxygenase-2 selective inhibitor, in treating postoperative pain resulting from bunionectomy were evaluated in 50 patients who were part of a larger cohort of orthopedic and podiatric patients. Following bunionectomy, the median time to rescue medication (survival analysis) was 4 hours 18 min (95% confidence interval, 3 hours 4 min to 4 hours 37 min) in the placebo group, 7 hours 5 min (95% confidence interval, 3 hours 20 min to >24 hours) in the 20-mg parecoxib sodium group, and 10 hours 43 min (95% confidence interval, 4 hours 42 min to 14 hours 7 min) in the 40-mg parecoxib sodium group (significant for 40-mg parecoxib sodium versus placebo). Four or more hours after surgery, the mean pain-intensity (categorical) score was significantly lower in both parecoxib sodium groups than in the placebo group. Preoperative administration of parecoxib sodium was well tolerated and significantly reduced postoperative pain in patients who had undergone bunionectomy.
mTOR, metabolism, and the regulation of T‐cell differentiation and function (2012)

Upon antigen recognition, naive T cells undergo rapid expansion and activation. The energy requirements for this expansion are formidable, and T-cell activation is accompanied by dramatic changes in cellular metabolism. Furthermore, the outcome of antigen engagement is guided by multiple cues derived from the immune microenvironment. Mammalian target of rapamycin (mTOR) is emerging as a central integrator of these signals playing a critical role in driving T-cell differentiation and function. Indeed, multiple metabolic programs are controlled by mTOR signaling. In this review, we discuss the role of mTOR in regulating metabolism and how these pathways intersect with the ability of mTOR to integrate cues that guide the outcome of T-cell receptor engagement.
Role of Protein Dynamics in Reaction Rate Enhancement by Enzymes (2005)

An integrated view of protein structure, dynamics, and function is emerging, where proteins are considered as dynamically active assemblies and internal motions are closely linked to function such as enzyme catalysis. Further, the motion of solvent bound to external regions of protein impacts internal motions and, therefore, protein function. Recently, we discovered a network of protein vibrations in enzyme cyclophilin A, coupled to its catalytic activity of peptidyl-prolyl cis-trans isomerization. Detailed studies suggest that this network, extending from surface regions to active site, is a conserved part of enzyme structure and has a role in promoting catalysis. In this report, theoretical investigations of concerted conformational fluctuations occurring on microsecond and longer time scales within the discovered network are presented. Using a new technique, kinetic energy was added to protein vibrational modes corresponding to conformational fluctuations in the network. The results reveal that protein dynamics promotes catalysis by altering transition state barrier crossing behavior of reaction trajectories. An increase in transmission coefficient and number of productive trajectories with increasing amounts of kinetic energy in vibrational modes is observed. Variations in active site enzyme-substrate interactions near transition state are found to be correlated with barrier recrossings. Simulations also showed that energy transferred from first solvation shell to surface residues impacts catalysis through network fluctuations. The detailed characterization of network presented here indicates that protein dynamics plays a role in rate enhancement by enzymes. Therefore, coupled networks in enzymes have wide implications in understanding allostericity and cooperative effects, as well as protein engineering and drug design.
Purification and Characterization of the Coniferyl Aldehyde Dehydrogenase from Pseudomonas sp. Strain HR199 and Molecular Characterization of the Gene (1998)

The coniferyl aldehyde dehydrogenase (CALDH) of Pseudomonas sp. strain HR199 (DSM7063), which catalyzes the NAD+-dependent oxidation of coniferyl aldehyde to ferulic acid and which is induced during growth with eugenol as the carbon source, was purified and characterized. The native protein exhibited an apparent molecular mass of 86,000 +/- 5,000 Da, and the subunit mass was 49.5 +/- 2.5 kDa, indicating an alpha2 structure of the native enzyme. The optimal oxidation of coniferyl aldehyde to ferulic acid was obtained at a pH of 8.8 and a temperature of 26 degreesC. The Km values for coniferyl aldehyde and NAD+ were about 7 to 12 microM and 334 microM, respectively. The enzyme also accepted other aromatic aldehydes as substrates, whereas aliphatic aldehydes were not accepted. The NH2-terminal amino acid sequence of CALDH was determined in order to clone the encoding gene (calB). The corresponding nucleotide sequence was localized on a 9.4-kbp EcoRI fragment (E94), which was subcloned from a Pseudomonas sp. strain HR199 genomic library in the cosmid pVK100. The partial sequencing of this fragment revealed an open reading frame of 1,446 bp encoding a protein with a relative molecular weight of 51,822. The deduced amino acid sequence, which is reported for the first time for a structural gene of a CALDH, exhibited up to 38.5% amino acid identity (60% similarity) to NAD+-dependent aldehyde dehydrogenases from different sources.
Measuring Capacity Bandwidth of Targeted Path Segments (2008)

Accurate measurement of network bandwidth is important for network management applications as well as flexible Internet applications and protocols which actively manage and dynamically adapt to changing utilization of network resources. Extensive work has focused on two approaches to measuring bandwidth: measuring it hop-by-hop, and measuring it end-to-end along a path. Unfortunately, best-practice techniques for the former are inefficient and techniques for the latter are only able to observe bottlenecks visible at end-to-end scope. In this paper, we develop end-to-end probing methods which can measure bottleneck capacity bandwidth along <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">arbitrary,</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">targeted</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">subpaths</i> of a path in the network, including subpaths <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">shared</i> by a set of flows. We evaluate our technique through ns simulations, then provide a comparative Internet performance evaluation against hop-by-hop and end-to-end techniques. We also describe a number of applications which we foresee as standing to benefit from solutions to this problem, ranging from network troubleshooting and capacity provisioning to optimizing the layout of application-level overlay networks, to optimized replica placement.
Two coupled enzymes perform in parallel the ‘AND’ and ‘InhibAND’ logic gate operations (2006)

The coupled activation of two enzymes: glucose dehydrogenase (GDH) and horseradish peroxidase (HRP), is used to construct the parallel-operating AND and InhibAND logic gates. The added substrates for the respective enzymes, glucose and H(2)O(2), act as the gate inputs, while the biocatalytically generated NADH and gluconic acid provide the output signals that follow the operations of the gates. The two gates are generated in the same vial, thus allowing the logic operations to take place in parallel, and the simultaneous readout of the functions of the gates.
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance (2010)

The spontaneously hypertensive rat (SHR) is the most widely studied animal model of hypertension. Scores of SHR quantitative loci (QTLs) have been mapped for hypertension and other phenotypes. We have sequenced the SHR/OlaIpcv genome at 10.7-fold coverage by paired-end sequencing on the Illumina platform. We identified 3.6 million high-quality single nucleotide polymorphisms (SNPs) between the SHR/OlaIpcv and Brown Norway (BN) reference genome, with a high rate of validation (sensitivity 96.3%-98.0% and specificity 99%-100%). We also identified 343,243 short indels between the SHR/OlaIpcv and reference genomes. These SNPs and indels resulted in 161 gain or loss of stop codons and 629 frameshifts compared with the BN reference sequence. We also identified 13,438 larger deletions that result in complete or partial absence of 107 genes in the SHR/OlaIpcv genome compared with the BN reference and 588 copy number variants (CNVs) that overlap with the gene regions of 688 genes. Genomic regions containing genes whose expression had been previously mapped as cis-regulated expression quantitative trait loci (eQTLs) were significantly enriched with SNPs, short indels, and larger deletions, suggesting that some of these variants have functional effects on gene expression. Genes that were affected by major alterations in their coding sequence were highly enriched for genes related to ion transport, transport, and plasma membrane localization, providing insights into the likely molecular and cellular basis of hypertension and other phenotypes specific to the SHR strain. This near complete catalog of genomic differences between two extensively studied rat strains provides the starting point for complete elucidation, at the molecular level, of the physiological and pathophysiological phenotypic differences between individuals from these strains.