gebhart/patrepeval huggingface dataset:
1176 Effect of OmniGen-AF® supplementation to heat stressed cows during late gestation on blood parameters and immune cells of their calves (2016)

Exposure to heat (HT) stress during the dry period negatively impacts cow immune status. Feeding OmniGen-AF® (OG) has been shown to improve the immune status of the HT cow, but the effect on the calf is unknown. We evaluated the effect of OG supplementation pre-calving (56 g/d, for approximately 105 d) to cows under HT (shade) or cooled (CL; shade, fans, soakers) environmental conditions during the dry period (∼56 d) on the immune and stress response of their calves. The experimental design was a 2 × 2 factorial with four treatments: CL (n = 4), CLOG (n = 6), HT (n = 6), HTOG (n = 7). Data were analyzed with a one- or two-way ANOVA, d as a repeated measure. At birth, heifers were fed maternal colostrum (5.7 L, two meals the first 24h). Blood samples were collected at 0 h, 24 h, d 10, and d 28 to measure cortisol, haptoglobin, (HPT), and serum amyloid-A (SAA). Hematology parameters and immune cell counts were assessed in the circulation of calves at birth and at 24 h (before and after colostrum feeding). Total cortisol concentrations were elevated at birth, but markedly decreased after feeding colostrum and on d 10 (P < 0.01) for all groups. Calves born to OG fed cows tended to have increased circulating cortisol (P = 0.09). Haptoglobin and SAA levels were higher on d 10 for all groups except for the CL calves (P < 0.01). Calves born to OG fed cows, and those born to HT cows, had higher SAA on d 10 (P < 0.03). White blood cell counts were similar at birth, and increased at 24 h after colostrum feeding except in the calves born to CLOG cows. Red blood cell counts (RBC) were elevated at birth and decreased significantly at 24 h for all groups (P < 0.05), except for the CL calves. Calves born to OG fed cows had more RBC (P < 0.02). Neutrophil counts were similar for all groups at birth and increased, after colostrum feeding, only for the HT and CL calves. Calves born to OG fed cows had more lymphocytes at birth compared to those born to cows not fed OG (P < 0.05). Heifers born to HT cows had fewer lymphocytes compared to CL if they weren't fed OG, but if they were born to HTOG cows their lymphocyte count was similar to the CLOG. In summary, in-utero exposure to heat stress during late-gestation negatively affects the immune and stress responses of the calf ex-utero. OmniGen-AF® supplementation to the dam could potentially benefit the offspring.
Ultra-thin multi-element Si pin photodiode arrays for medical imaging applications (2005)

Results of comparative studies of opto-electrical properties of photodiode arrays built on 30-um, 75-um, and 100-um thick single Silicon dies are presented. The size of the square pixels varied from 1.5 mm to 250-um for different arrays with the gaps between adjacent elements as small as 20 um. The internal quantum efficiency was close to 100%, DC and AC cross talks were smaller than 0.01% within the spectral range 400 to 800 nm. The arrays were characterized with very low leakage currents and high shunt resistance - above 1 G&Omega;hm. The features of the array structure are discussed for the first time.
Determination of Crude Protein and Fat in Carcass and Breast Muscle Samples of Poultry by Near Infrared Reflectance Spectroscopy (1986)

Near infrared reflectance spectroscopy (NIR) equipment used consisted of an InfraAlyzer 400+ fitted with 19 discrete filters and an HP-85 microcomputer. Calibrations were developed with chicken broiler carcass samples. Samples were divided into two sets: a calibration (CAL) from which equations were developed and a prediction (PRE) set used to validate the equations. The CAL and PRE sets in the carcass calibration consisted of 45 and 54 samples, respectively. Two equations were developed for the prediction of fat in carcass samples (FAT1 and FAT2). Calibration for breast muscle samples included 30 and 27 samples for CAL and PRE sets, respectively. The accuracy of the calibrations was measured by the coefficient of determination (r2), standard error of the estimate (SEE), coefficient of variation (CV), and the mean difference between NIR and chemical values (d). Repeatabilities of chemical and NIR procedures were determined by the F-ratio of the variance of the differences between replicates. The result of the regression analysis between chemical and NIR values indicated good predictions for crude protein (CP) and fat in carcass samples. The r2 and SEE for CP, FAT1, and FAT2 were .98, .94; .91, 2.48; and .91, 2.51 in CAL set; and .91, 1.03; .68, 2.32; and .69, 2.30 in PRE set samples, respectively. No differences were found between FAT1 and FAT2 equations. The carcass calibration equations were tested with samples from laying hens. Higher SEE were found for CP (1.78), but SEE for fat were similar to broiler carcasses. The calibration for breast samples showed higher SEE for CP and fat when compared with carcass samples.(ABSTRACT TRUNCATED AT 250 WORDS)
Simple algorithms for complex relation extraction with applications to biomedical IE (2005)

A complex relation is any n-ary relation in which some of the arguments may be be unspecified. We present here a simple two-stage method for extracting complex relations between named entities in text. The first stage creates a graph from pairs of entities that are likely to be related, and the second stage scores maximal cliques in that graph as potential complex relation instances. We evaluate the new method against a standard baseline for extracting genomic variation relations from biomedical text.
Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces (1989)

This is the first of four papers that begin to explore the possibility of automated site-directed drug design. A general outline is given of the logical steps involved in approaching the problem. The starting point is the process of knowledge acquisition about the site. An algorithm is described here for the construction of a map of hydrogen-bonding regions at protein surfaces directly from the Brookhaven Protein Data Bank coordinates. Hydrogen-bonding atoms are located, intramolecular bonds are searched for, hydrogen-bonding atoms at the surface are found and hydrogen-bonding regions are computed at the accessible surface. A grid is placed within each region discovered and the probability of hydrogen bonding at each grid point is computed. The output of the program is a map of hydrogen-bonding regions displayed within a user-defined window. This information can be used as part of a knowledge base for the automatic construction of novel ligands to fit specified binding sites.
A Recyclable Ru-Based Metathesis Catalyst (1999)

A Ru carbene (8, Scheme 2) that contains an internal metal−oxygen chelate is an active metathesis catalyst and is readily obtained by the sequential treatment of Cl2Ru(PPh3)3 with (2-isopropoxyphenyl)diazomethane and PCy3. This Ru-carbene complex offers excellent stability to air and moisture and can be recycled in high yield by silica gel column chromatography. The structures of this and related complexes have been unambiguously established by NMR and single-crystal X-ray diffraction studies.
The emerging role of asymmetric dimethylarginine as a novel cardiovascular risk factor (2003)

There is abundant evidence that the endothelium plays a crucial role in the maintenance of vascular tone and structure. One of the major endothelium-derived vasoactive mediators is nitric oxide (NO). Asymmetric dimethylarginine (ADMA) is an endogenous inhibitor of NO synthase. ADMA inhibits vascular NO production at concentrations found in pathophysiological conditions (i.e., 3-15 micromol/l); ADMA also causes local vasoconstriction when it is infused intraarterially. The biochemical and physiological pathways related to ADMA are now well understood: dimethylarginines are the result of the degradation of methylated proteins; the methyl group is derived from S-adenosylmethionine. Both ADMA and its regioisomer, SDMA, are eliminated from the body by renal excretion, whereas only ADMA, but not SDMA, is metabolized via hydrolytic degradation to citrulline and dimethylamine by the enzyme dimethylarginine dimethylaminohydrolase (DDAH). DDAH activity and/or expression may therefore contribute to the pathogenesis of endothelial dysfunction in various diseases. ADMA is increased in the plasma of humans with hypercholesterolemia, atherosclerosis, hypertension, chronic renal failure, and chronic heart failure. Increased ADMA levels are associated with reduced NO synthesis as assessed by impaired endothelium-dependent vasodilation. In several prospective and cross-sectional studies, ADMA evolved as a marker of cardiovascular risk. With our increasing knowledge of the role of ADMA in the pathogenesis of cardiovascular disease, ADMA is becoming a goal for pharmacotherapeutic intervention. Among other treatments, the administration of L-arginine has been shown to improve endothelium-dependent vascular function in subjects with high ADMA levels.
Fyn-Kinase as a Determinant of Ethanol Sensitivity: Relation to NMDA-Receptor Function (1997)

Animals vary in their sensitivity to ethanol, a trait at least partly determined by genetic factors. In order to identify possible responsible genes, mice lacking Fyn, a non-receptor type tyrosine kinase, were investigated. These mice were hypersensitive to the hypnotic effect of ethanol. The administration of ethanol enhanced tyrosine phosphorylation of the N-methyl-D-aspartate receptor (NMDAR) in the hippocampus of control mice but not in Fyn-deficient mice. An acute tolerance to ethanol inhibition of NMDAR-mediated excitatory postsynaptic potentials in hippocampal slices developed in control mice but not in Fyn-deficient mice. These results indicate that Fyn affects behavioral, biochemical, and physiological responses to ethanol.
Photochemotherapy of Dominant, Diffuse, Cutaneous Mastocytosis (1990)

Diffuse, cutaneous mastocytosis is a rare variant of cutaneous mast cell infiltration that can arise in neonates or infants as a generalized bullous eruption. The mode of transmission is suggested as autosomal dominant. We report four infants from two unrelated families with diffuse cutaneous mastocytosis whose cutaneous disease was not controlled by initial therapies. Treatment of the four infants with photochemotherapy dramatically reduced or eliminated symptoms. One course of therapy resulted in improvement, and retreatment has not been required two to six years later.
Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments (2001)

We introduce a general technique for making statistical inference from clustering tools applied to gene expression microarray data. The approach utilizes an analysis of variance model to achieve normalization and estimate differential expression of genes across multiple conditions. Statistical inference is based on the application of a randomization technique, bootstrapping. Bootstrapping has previously been used to obtain confidence intervals for estimates of differential expression for individual genes. Here we apply bootstrapping to assess the stability of results from a cluster analysis. We illustrate the technique with a publicly available data set and draw conclusions about the reliability of clustering results in light of variation in the data. The bootstrapping procedure relies on experimental replication. We discuss the implications of replication and good design in microarray experiments.
ETO, a Target of t(8;21) in Acute Leukemia, Interacts with the N-CoR and mSin3 Corepressors (1998)

t(8;21) is one of the most frequent translocations associated with acute myeloid leukemia. It produces a chimeric protein, acute myeloid leukemia-1 (AML-1)-eight-twenty-one (ETO), that contains the amino-terminal DNA binding domain of the AML-1 transcriptional regulator fused to nearly all of ETO. Here we demonstrate that ETO interacts with the nuclear receptor corepressor N-CoR, the mSin3 corepressors, and histone deacetylases. Endogenous ETO also cosediments on sucrose gradients with mSin3A, N-CoR, and histone deacetylases, suggesting that it is a component of one or more corepressor complexes. Deletion mutagenesis indicates that ETO interacts with mSin3A independently of its association with N-CoR. Single amino acid mutations that impair the ability of ETO to interact with the central portion of N-CoR affect the ability of the t(8;21) fusion protein to repress transcription. Finally, AML-1/ETO associates with histone deacetylase activity and a histone deacetylase inhibitor impairs the ability of the fusion protein to repress transcription. Thus, t(8;21) fuses a component of a corepressor complex to AML-1 to repress transcription.
Phage probes for malignant glial cells. (2003)

Early diagnosis and effective treatment of malignant gliomas, which are heterogeneous brain tumors with variable expression of cell surface markers, are inhibited by the lack of means to characterize and target tumor-selective molecules. To create molecular profiles for RG2 rat glioma cells, we used phage display technology, an approach capable of producing valuable ligands to unknown cell surface targets. The ligands were selected from libraries of peptides displayed as fusion molecules on phage particles. Modifications of the selection conditions resulted in identification of three distinctive families of peptide ligands for malignant glioma cells. The first family with V (D)/(G) L P (E)/(T) H(3) binding motif appeared to target a marker that is common for glioma cells, normal brain cells, and cells of non-brain origin. The second group of peptide-presented phage displayed D (T)/S/(L) T K consensus sequence and contained peptides with pronounced glioma-selective properties. Phage clones expressing peptides with E (L)/V/(S) R G D S motif were found in cell lysates and represented the third family of glioma-specific ligands. All peptides within this family contain the RGD amino acid sequence, which is known to bind to a number of integrins. Phage clones that belong to this family were internalized by RG2 glioma cells about 63-fold more efficiently than by astrocytes. The approach described could be applicable for accurate detection of glioma expression patterns in individual tumors. Such patterns could be beneficial in the design of effective combinations of drugs for anti-glioma treatments.
Cremophor EL causes (pseudo-) non-linear pharmacokinetics of paclitaxel in patients (1999)

The non-linear plasma pharmacokinetics of paclitaxel in patients has been well established, however, the exact underlying mechanism remains to be elucidated. We have previously shown that the non-linear plasma pharmacokinetics of paclitaxel in mice results from Cremophor EL. To investigate whether Cremophor EL also plays a role in the non-linear pharmacokinetics of paclitaxel in patients, we have established its pharmacokinetics in patients receiving paclitaxel by 3-, 24- or 96-h intravenous infusion. The pharmacokinetics of Cremophor EL itself was non-linear as the clearance (Cl) in the 3-h schedules was significantly lower than when using the longer 24- or 96-h infusions (Cl175-3 h = 42.8+/-24.9 ml h(-1) m(-2); CI175-24 h = 79.7+/-24.3; P = 0.035 and Cl135-3 h = 44.1+/-21.8 ml h(-1) m(-1); Cl140-96 h = 211.8+/-32.0; P < 0.001). Consequently, the maximum plasma levels were much higher (0.62%) in the 3-h infusions than when using longer infusion durations. By using an in vitro equilibrium assay and determination in plasma ultrafiltrate we have established that the fraction of unbound paclitaxel in plasma is inversely related with the Cremophor EL level. Despite its relatively low molecular weight, no Cremophor EL was found in the ultrafiltrate fraction. Our results strongly suggest that entrapment of paclitaxel in plasma by Cremophor EL, probably by inclusion in micelles, is the cause of the apparent nonlinear plasma pharmacokinetics of paclitaxel. This mechanism of a (pseudo-)non-linearity contrasts previous postulations about saturable distribution and elimination kinetics and means that we must re-evaluate previous assumptions on pharmacokinetics-pharmacodynamics relationships.
Automated benchmarking of peptide-MHC class I binding predictions (2015)

Supplementary data are available at Bioinformatics online.
Handbook of Synthetic Organic Chemistry Ed. 2 (2016)

Handbook of Synthetic Organic Chemistry, Second Edition updates and expands the author's popular 2007 work, Synthetic Organic Chemist's Companion. This new handbook provides valuable, practical guidance; incorporates corrections, and includes coverage on important topics, such as lyophylization, crystallization, precipitation, HPLC detectors, gases, and microwave reactions. The book maintains the useful organization of the author's earlier work, beginning with a basic overview and walking through every practical step of the process of organic synthesis, from reagents, solvents, and temperature control, to documentation, implementation, purification, and analytical methods for the product. From planning and setting up reactions, to recording them, the book provides insight and valuable guidance into every step of the process. Practical guidance for planning, working up, documenting, analyzing, and improving reactions in synthetic organic chemistry
Structural Insight into Substrate Differentiation of the Sugar-metabolizing Enzyme Galactitol Dehydrogenase from Rhodobacter sphaeroides D (2010)

Galactitol 2-dehydrogenase (GatDH) belongs to the protein superfamily of short-chain dehydrogenases. As an enzyme capable of the stereo- and regioselective modification of carbohydrates, it exhibits a high potential for application in biotechnology as a biocatalyst. We have determined the crystal structure of the binary form of GatDH in complex with its cofactor NAD(H) and of the ternary form in complex with NAD(H) and three different substrates. The active form of GatDH constitutes a homo-tetramer with two magnesium-ion binding sites each formed by two opposing C termini. The catalytic tetrad is formed by Asn(116), Ser(144), Tyr(159), and Lys(163). GatDH structurally aligns well with related members of the short-chain dehydrogenase family. The substrate binding pocket can be divided into two parts of different size and polarity. In the smaller part, the side chains of amino acids Ser(144), Ser(146), and Asn(151) are important determinants for the binding specificity and the orientation of (pro-) chiral compounds. The larger part of the pocket is elongated and flanked by polar and non-polar residues, enabling a rather broad substrate spectrum. The presented structures provide valuable information for a rational design of this enzyme to improve its stability against pH, temperature, or solvent concentration and to optimize product yield in bioreactors.
Structural and Electron-Transfer Characteristics of O-, S-, and Se-Tethered Porphyrin Monolayers on Si(100) [J. Am. Chem. Soc. 2004, 126, 15603−15612]. (2005)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionStructural and Electron-Transfer Characteristics of O-, S-, and Se-Tethered Porphyrin Monolayers on Si(100) [J. Am. Chem. Soc. 2004, 126, 15603−15612].Amir A. Yasseri, Dennis Syomin, Robert S. Loewe, Jonathan S. Lindsey, Francisco Zaera, and David F. BocianCite this: J. Am. Chem. Soc. 2005, 127, 25, 9308Publication Date (Web):June 2, 2005Publication History Published online2 June 2005Published inissue 1 June 2005https://pubs.acs.org/doi/10.1021/ja053081dhttps://doi.org/10.1021/ja053081dcorrectionACS PublicationsCopyright © 2005 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views461Altmetric-Citations8LEARN 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 PDF (10 KB) Get e-Alertsclose Get e-Alerts
A correction to the state-machine-decoder for Stacked Multicell converters (2014)

Natural capacitor voltage balancing for Flying Capacitor and Stacked Multicell converters require uniform distribution of switching transitions among cells. The state-machine-decoder has been known as the optimal technique to achieve this goal. In this paper, however, it is shown that the conventional state-machine-decoder may not generate the optimal balancing scheme for Stacked Multicell converters. The reason behind the suboptimal distribution is investigated and a correction to the state-machine-decoder is proposed to achieve the optimal distribution. Simulation results are included to support the proposed correction.
Determination of molecular dipole orientation in doped fluorescent organic thin films by photoluminescence measurements (2010)

The orientation of the transition dipole moments of fluorescent organic molecules doped into a matrix material is determined by photoluminescence measurements of the angular dependent emission spectra and by comparison with simulations. The analysis of two small molecular materials doped into a 4,4′-bis(N-carbazole)-biphenyl matrix is demonstrated, yielding a horizontal orientation of 91% for 4,4′-bis[4-(diphenylamino)styryl]biphenyl and a completely random orientation in case of tris-(8-hydroxyquinoline)aluminum (Alq3). This expeditious technique does not require detailed information about the optical properties of the dopant, making this method particularly suitable for characterizing newly developed materials for organic light-emitting diodes with enhanced light-outcoupling efficiency.