gebhart/patrepeval huggingface dataset:
High‐Altitude Pulmonary Hypertension in Cattle (Brisket Disease): Candidate Genes and Gene Expression Profiling of Peripheral Blood Mononuclear Cells (2011)

High-altitude pulmonary hypertension (HAPH) is a consequence of chronic alveolar hypoxia, leading to hypoxic vasoconstriction and remodeling of the pulmonary circulation. Brisket disease in cattle is a naturally occurring animal model of hypoxic pulmonary hypertension. Genetically susceptible cattle develop severe pulmonary hypertension and right heart failure at altitudes >7,000 ft. No information currently exists regarding the identity of the pathways and gene(s) responsible for HAPH or influencing severity. We hypothesized that initial insights into the pathogenesis of the disease could be discovered by a strategy of (1) sequencing of functional candidates revealed by single nucleotide polymorphism (SNP) analysis and (2) gene expression profiling of affected cattle compared with altitude-matched normal controls, with gene set enrichment analysis (GSEA) and Ingenuity pathway analysis (IPA). We isolated blood from a single herd of Black Angus cattle of both genders, aged 12-18 months, by jugular vein puncture. Mean pulmonary arterial pressures were 85.6±13 mmHg STD in the 10 affected and 35.3±1.2 mmHg STD in the 10 resistant cattle, P<0.001. From peripheral blood mononuclear cells, DNA was hybridized to an Affymetrix 10K Gene Chip SNP, and RNA was used to probe an Affymetrix Bovine genome array. SNP loci were remapped using the Btau 4.0 bovine genome assembly. mRNA data was analyzed by the Partek software package to identify sets of genes with an expression that was statistically different between the two groups. GSEA and IPA were conducted on the refined expression data to identify key cellular pathways and to generate networks and conduct functional analyses of the pathways and networks. Ten SNPs were identified by allelelic association and four candidate genes were sequenced in the cohort. Neither endothelial nitric oxide synthetase, NADH dehydrogenase, TG-interacting factor-2 nor BMPR2 were different among affected and resistant cattle. A 60-gene mRNA signature was identified that differentiated affected from unaffected cattle. Forty-six genes were overexpressed in the affected and 14 genes were downregulated in the affected cattle by at least 20%. GSEA and Ingenuity analysis identified respiratory diseases, inflammatory diseases and pathways as the top diseases and disorders (P<5.14×10(-14)), cell development and cell signaling as the top cellular functions (P<1.20×10(-08)), and IL6, TREM, PPAR, NFkB cell signaling (P<8.69×10(-09)) as the top canonical pathways associated with this gene signature. This study provides insights into differences in RNA expression in HAPH at a molecular level, and eliminates four functional gene candidates. Further studies are needed to validate and refine these preliminary findings and to determine the role of transcribed genes in the development of HAPH.
How to get between the sheets: a review of recent works on the electrochemical exfoliation of graphene materials from bulk graphite (2015)

Since the beginning of the 'graphene era' post-2004, there has been significant interest in developing a high purity, high yield, and scalable fabrication route toward graphene materials for both primary research purposes and industrial production. One suitable approach to graphene production lies in the realm of electrochemical exfoliation, in which a potential difference is applied between a graphite anode/cathode in the presence of an electrolyte-containing medium. Herein we review various works on the electrochemical fabrication of graphene materials specifically through the use of electrochemical intercalation and exfoliation of a graphite source electrode, focusing on the quality and purity of products formed. We categorise the most significant works in terms of anodic and cathodic control, highlighting the merits of the respective approaches, as well as indicating the challenges associated with both procedures.
Site-directed Mutagenesis of a Conserved Region (1991)

The active site of the enzyme S-enolpyruvylshikimate-3-phosphate synthase (EPSPS) has been probed using site-directed mutagenesis and inhibitor binding techniques. Replacement of a specific glycyl with an alanyl or a prolyl with a seryl residue in a highly conserved region confers glyphosate tolerance to several bacterial and plant EPSPS enzymes, suggesting a high degree of structural conservation between these enzymes. The glycine to alanine substitution corresponding to Escherichia coli EPSPS G96A increases the K,(,,,,(glyphosate) of petunia EPSPS 5000-fold while increasing the Km(app)(phosphoenolpyruvate) about 40-fold. Substitution of this glycine with serine, however, abolishes EPSPS activity but results in the elicitation of a novel EPSP hydrolase activity whereby EPSP is converted to shikimate 3-phosphate and pyruvate. This highly conserved region is critical for the interaction of the phosphate moiety of phosphoenolpyruvate with EPSPS. Site-directed mutagenesis of enzymes is a powerful technique for investigating active site structure-function relationships (1). While the technique has been used to verify the roles of active site residues, there are no reports of its use in examining the relatedness of active sites of enzymes from different sources. In this paper, we have used site-directed mutagenesis to establish that the active sites of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS)’ enzymes from bacteria and plants are similar. The x-ray crystal structure of Escherichia coli EPSPS has recently been elucidated at 3-A resolution (2). At the present time, however, the structure of the EPSPS complex with the inhibitor glyphosate is not available. In the absence of detailed structural information on the EPSPS binding site for glyphosate, we have used sitedirected mutagenesis to probe the interaction between the enzyme and glyphosate as well as PEP. The enzyme EPSPS (EC 2.5.1.19) catalyzes the formation
Structure of a beta-galactosidase gene of Bacillus stearothermophilus (1986)

The nucleotide sequence of the bgaB gene, which encodes the thermostable beta-galactosidase I of Bacillus stearothermophilus, and its flanking region was determined. A 2,016-base-pair open reading frame observed was concluded to be for beta-galactosidase I (Mr 78,051) from observations that the amino acid composition of the enzyme and the sequence of 14 amino acids from the amino-terminus of the enzyme coincided with those deduced from this open frame. A 107-base-pair HaeIII-AluI fragment just upstream of the estimated Shine-Dalgarno sequence of the bgaB gene had promoter activity toward cat-86 (chloramphenicol acetyltransferase gene) and produced the enzyme at a level equivalent to 7% of the total cellular protein of B. subtilis. From the base sequence of this DNA region and the transcriptional start site determined by S1 nuclease mapping, the -35 and -10 sequences are estimated to be TTGACA and TAATTT, respectively, which are similar to the consensus sequence of B. subtilis sigma 43 RNA polymerase.
Targeting of HIF-α to the von Hippel-Lindau Ubiquitylation Complex by O <sub>2</sub> -Regulated Prolyl Hydroxylation (2001)

Hypoxia-inducible factor (HIF) is a transcriptional complex that plays a central role in the regulation of gene expression by oxygen. In oxygenated and iron replete cells, HIF-alpha subunits are rapidly destroyed by a mechanism that involves ubiquitylation by the von Hippel-Lindau tumor suppressor (pVHL) E3 ligase complex. This process is suppressed by hypoxia and iron chelation, allowing transcriptional activation. Here we show that the interaction between human pVHL and a specific domain of the HIF-1alpha subunit is regulated through hydroxylation of a proline residue (HIF-1alpha P564) by an enzyme we have termed HIF-alpha prolyl-hydroxylase (HIF-PH). An absolute requirement for dioxygen as a cosubstrate and iron as cofactor suggests that HIF-PH functions directly as a cellular oxygen sensor.
Real-Time Scheduling and Control of Single-Arm Cluster Tools with Residency Time Constraint and Activity Time Variation by Using Resource-Oriented Petri Nets (2013)

In semiconductor manufacturing, when a wafer is processed, it requires unloading from its process module in a given time interval, otherwise it is scraped. This requirement is called wafer residency time constraints. Thus, it is crucial to schedule a cluster tool such that the wafer sojourn time in a process module is within a given time window to satisfy the wafer residency time constraints. Besides wafer residency time constraints, in a cluster tool, the activity time is subject to variation. The activity time variation can make a feasible schedule obtained under the assumption of deterministic activity times become infeasible. To solve this problem, it is important to reveal the wafer sojourn time fluctuations with bounded activity time variation. Such an issue is addressed in this chapter for single-arm cluster tools. A single-arm cluster tool is modeled by a resource-oriented Petri net to describe the wafer fabrication processes. Based on it, a real-time control policy is proposed such that it offsets the effect of the activity time variation as much as possible. Then, the wafer sojourn time delay in a process module is analyzed and analytical expressions are derived to calculate the upper bound. With the help of the real-time control policy and wafer sojourn time delay analysis results, schedulability conditions and scheduling algorithms for an off-line schedule are presented in this chapter. The schedulability conditions can be analytically checked. If schedulable, an off-line schedule can be analytically found. The off-line schedule together with the real-time control policy forms the real-time schedule for the system. It is optimal in terms of cycle time minimization. Examples are given to show the application of the proposed approach.
Perivascular Sensory Nerve Ca <sup>2+</sup> Receptor and Ca <sup>2+</sup> -Induced Relaxation of Isolated Arteries (1997)

The present study tested two hypotheses: (1) that a receptor for extracellular Ca2+ (Ca2+ receptor [CaR]) is located in the perivascular sensory nerve system and (2) that activation of this receptor by physiological concentrations of extracellular Ca2+ results in the release of vasodilator substance that mediates Ca2+-induced relaxation. Reverse transcription-polymerase chain reaction using primers derived from rat kidney CaR cDNA sequence showed that mRNA encoding a CaR is present in dorsal root ganglia but not the mesenteric resistance artery. Western blot analysis using monoclonal anti-CaR showed that a 140-kD protein that comigrates with the parathyroid CaR is present in both the dorsal root ganglia and intact mesenteric resistance artery. Immunocytochemical analysis of whole mount preparations of mesenteric resistance arteries showed that the anti-CaR-stained perivascular nerves restricted to the adventitial layer. Biophysical analysis of mesenteric resistance arteries showed that cumulatively raising Ca2+ from 1 to 1.25 mol/L and above relaxes precontracted arteries with an ED50 value of 2.47+/-0.17 mmol/L (n=12). The relaxation is endothelium independent and is unaffected by blockade of nitric oxide synthase but is completely antagonized by acute and subacute phenolic destruction of perivascular nerves. A bioassay showed further that superfusion of Ca2+ across the adventitial surface of resistance arteries releases a diffusible vasodilator substance. Pharmacological analysis indicates that the relaxing substance is not a common sensory nerve peptide transmitter but is a phospholipase A2/cytochrome P450-derived hyperpolarizing factor that we have classified as nerve-derived hyperpolarizing factor. These data demonstrate that a CaR is expressed in the perivascular nerve network, show that raising Ca2+ from 1 to 1.25 mol/L and above causes nerve-dependent relaxation of resistance arteries, and suggest that activation of the CaR induces the release of a diffusible hyperpolarizing vasodilator. We propose that this system could serve as a molecular link between whole-animal Ca2+ balance and arterial tone.
Ultra-dense SNP genetic map construction and identification of SiDt gene controlling the determinate growth habit in Sesamum indicum L. (2016)

Sesame (Sesamum indicum L.) is an important oilseed crop and has an indeterminate growth habit. Here we resequenced the genomes of the parents and 120 progeny of an F2 population derived from crossing Yuzhi 11 (indeterminate, Dt) and Yuzhi DS899 (determinate, dt1), and constructed an ultra-dense SNP map for sesame comprised of 3,041 bins including 30,193 SNPs in 13 linkage groups (LGs) with an average marker density of 0.10 cM. Results indicated that the same recessive gene controls the determinacy trait in dt1 and a second determinate line, dt2 (08TP092). The QDt1 locus for the determinacy trait was located in the 18.0 cM-19.2 cM interval of LG8. The target SNP, SiDt27-1, and the determinacy gene, DS899s00170.023 (named here as SiDt), were identified in Scaffold 00170 of the Yuzhi 11 reference genome, based on genetic mapping and genomic association analysis. Unlike the G397A SNP change in the dt1 genotype, the SiDt allele in dt2 line was lost from the genome. This example of map-based gene cloning in sesame provides proof-of-concept of the utility of ultra-dense SNP maps for accurate genome research in sesame.
An electrically tunable polarization and polarization-independent liquid-crystal microlens array for imaging applications (2017)

In this study, a polarization-independent microlens array composed of two layered nematic liquid crystal (LC) materials with orthogonal alignment and separated by a double-sided indium-tin oxide silica with a thickness of ∼500 μm, is proposed. The functioned stacking of two polarization LC microstructures lead to an electrically tuning polarization and also polarization-independent light control architecture. Experimental investigations reveal key characters such as a high beam utilization efficiency of more than 90% and a compound point spread function tuned electrically. Dual-mode imaging including the polarization mode and the polarization-independent mode can be realized based on the novel configuration with both independent voltage signals applied over two functioned LC layers. The normalized focusing intensity demonstrates a special property of no polarization dependence on beams processed. An image criteria for evaluating the quality of polarization-insensitive images based on the difference image between the horizontal and vertical polarization images, is introduced. Considering the advantages of electrically tunable composed focal length and then switching the polarization and polarization-independent mode, it can be expected that the developed devices can not only be used to measure and further tune the polarization state of beams propagating in LC layers but also acquire high quality target images.
M3R: Increased performance for in-memory Hadoop jobs (2012)

Main Memory Map Reduce (M3R) is a new implementation of the Hadoop Map Reduce (HMR) API targeted at online analytics on high mean-time-to-failure clusters. It does not support resilience, and supports only those workloads which can fit into cluster memory. In return, it can run HMR jobs unchanged -- including jobs produced by compilers for higher-level languages such as Pig, Jaql, and SystemML and interactive front-ends like IBM BigSheets -- while providing significantly better performance than the Hadoop engine on several workloads (e.g. 45x on some input sizes for sparse matrix vector multiply). M3R also supports extensions to the HMR API which can enable Map Reduce jobs to run faster on the M3R engine, while not affecting their performance under the Hadoop engine.
RF MEMS asymmetric capacitive switch with high‐isolation at selected low‐microwave frequency (2007)

Abstract An asymmetric RF microelectromechanical systems (MEMS) capacitive switch with a novel architecture employing mode switching from a coplanar waveguide (CPW) mode to a coupled slotline (CSL) mode is reported for selected frequency within the 2–10 GHz low microwave frequency range. An additional metal‐insulator‐metal (MIM) capacitor is introduced on one end of the switch membrane as a tuning capacitor. The signal line of CSL is used as a tuning inductor. These two tuning elements together can improve the isolation of a regular capacitive RF MEMS switch by about 20 dB at the induced additional low resonant frequency ranging from 2 to 10 GHz. The measurements of the fabricated asymmetric switch demonstrated excellent isolation improvements. © 2007 Wiley Periodicals, Inc. Microwave Opt Technol Lett 49: 702–706, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.22235
High-Speed In Vivo Endoscopic Optical Coherence Tomography (1999)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text J. A. Izatt, A. M. Rollins, R. Ung-arunyawee, A. Chak, R. C. Wong, K. Kobayashi, and M. V. Sivak, "High-Speed In Vivo Endoscopic Optical Coherence Tomography," in Biomedical Optics, OSA Technical Digest (Optica Publishing Group, 1999), paper AWB1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Thin, flexible waveplate of fluorinated polyimide (1993)

A thin optical half-waveplate at 1.55μm, only 14.5μm thick, which is 6.3 times as thin as a zeroth order quartz waveplate, is prepared using fluorinated polyimide. This material has good flexibility, thickness controllability, and high thermal stability. The retardation of the waveplate was retained after annealing at 350°C for 1 h.
Electron tunneling sensors (1992)

Many physical sensors operate by coupling the signal of interest to deflection of a sensor component, and utilizing a displacement transducer to produce an electrical signal. The development of miniature high-performance sensors have been limited by the availability of small, sensitive transducers. A novel accelerometer has been designed that utilizes an electron tunneling transducer to detect the relative motion of a suspended proof mass. The sensitivity of the tunneling transducer allows miniaturization of the device with resolution near 10−8 g/√Hz from 10 Hz to 1 kHz. Thermal noise in the positions of sensor components is important for high-resolution miniature accelerometers, and is the dominant factor in selection of design parameters. Thermal noise for this dual element system will be discussed and compared with other noise sources. A simple closed-loop electronic feedback system that is used with these sensors will also be described. Preliminary test results will be described. This system offers improved resolution, compact geometry, low mass, and low cost relative to present miniature accelerometers or acoustic sensors. A wide range of possible applications exist including underwater acoustics. [Work supported by NAWC, and SDIO/IST.]
Expression of Porcine Fusion Protein IRF7/3(5D) Efficiently Controls Foot-and-Mouth Disease Virus Replication (2014)

FMD remains one of the most devastating diseases that affect livestock worldwide. Effective vaccine formulations are available but are serotype specific and require approximately 7 days before they are able to elicit protective immunity. We have shown that vector-delivered IFN is an option to protect animals against many FMDV serotypes as soon as 24 h and for about 4 days postadministration. Here we demonstrate that delivery of a constitutively active transcription factor that induces the production of endogenous IFNs and potentially other antiviral genes is a viable strategy to protect against FMD.
Self-Adaptive Matrix Completion for Heart Rate Estimation from Face Videos under Realistic Conditions (2016)

Recent studies in computer vision have shown that, while practically invisible to a human observer, skin color changes due to blood flow can be captured on face videos and, surprisingly, be used to estimate the heart rate (HR). While considerable progress has been made in the last few years, still many issues remain open. In particular, state of-the-art approaches are not robust enough to operate in natural conditions (e.g. in case of spontaneous movements, facial expressions, or illumination changes). Opposite to previous approaches that estimate the HR by processing all the skin pixels inside a fixed region of interest, we introduce a strategy to dynamically select face regions useful for robust HR estimation. Our approach, inspired by recent advances on matrix completion theory, allows us to predict the HR while simultaneously discover the best regions of the face to be used for estimation. Thorough experimental evaluation conducted on public benchmarks suggests that the proposed approach significantly outperforms state-of the-art HR estimation methods in naturalistic conditions.
Catalytic Synthesis of Magnesium Hydride under Mild Conditions (1980)

Magnesium hydride, of potential use for reversible storage of hydrogen , has now been synthesized by a method proceeding under mild conditions and which can be performed on a large scale. Especially active catalysts are obtained by reaction of anthracenemagnesium with halides of chromium, titanium, or iron in THF. These solutions are catalytically active at 20°C and under normal pressure.
The discovery, fermentation, isolation, and structure of antibiotic A33853 and its tetraacetyl derivative. (1984)

The structure of antibiotic A33853, isolated from the culture broth of Streptomyces sp., NRRL 12068, is reported. The structure was deduced from an X-ray crystallographic study of its tetraacetyl derivative. Tetraacetyl A33853 is unique because it contains an anhydride moiety, an unexpected product from the reaction of A33853 with acetic anhydride and pyridine.
Use of a Pharmacophore Model for the Design of EGF-R Tyrosine Kinase Inhibitors:  4-(Phenylamino)pyrazolo[3,4-<i>d</i>]pyrimidines (1997)

In the course of the random screening of a pool of CIBA chemicals, the two pyrazolopyrimidines 1 and 2 have been identified as fairly potent inhibitors of the EGF-R tyrosine kinase. Using a pharmacophore model for ATP-competitive inhibitors interacting with the active site of the EGF-R protein tyrosine kinase (PTK), the class of the pyrazolo[3,4-d]pyrimidines was then optimized in an interactive process leading to a series of 4-(phenylamino)-1H-pyrazolo[3,4-d]-pyrimidines as highly potent inhibitors of the EGF-R tyrosine kinase. The most potent compounds 13, 14, 15, 17, 19, 22, 26, 28, and 30 of this series inhibited the EGF-R PTK with IC50 values below 10 nM. High selectivity toward a panel of nonreceptor tyrosine kinases (c-Src, v-Abl and serine/threonine kinases (PKC alpha, CDK1) was observed. In cells, EGF-stimulated cellular tyrosine phosphorylation was inhibited by compounds 13, 15, 19, 22, and 23 at IC50 values below 50 nM, whereas PDGF-induced tyrosine phosphorylation was not affected by concentrations up to 10 microM, thus indicating high selectivity for the inhibition of the ligand-activated EGF-R signal transduction pathway. Compounds 15 and 19 inhibited proliferation of the EGF-dependent MK cell line with IC50 values below 0.5 microM. In addition, two compounds, 9 and 11, showing satisfactory oral bioavailability in mice after oral administration, exhibited good in vivo efficacy at doses of 12.5 and 50 mg/kg in a nude mouse tumor model using xenografts of the EGF-R overexpressing A431 cell line. From SAR studies, a binding mode for 4-(phenylamino)-1H-pyrazolo[3,4-d]pyrimidines, especially for compound 15, at the ATP-binding site of the EGF-R tyrosine kinase is proposed. 4-(Phenylamino)-1H-pyrazolo[3,4-d]pyrimidines represent a new class of highly potent tyrosine kinase inhibitors which preferentially inhibit the EGF-mediated signal transduction pathway and have the potential for further evaluation as anticancer agents.