gebhart/patrepeval huggingface dataset:
Identification of Amplified Restriction Fragment Length Polymorphism Markers Linked to Genes Controlling Boar Sperm Viability Following Cryopreservation1 (2002)

This study investigated two hypotheses: 1) that consistent between-boar variation in frozen semen quality exists and is genetically determined, and 2) molecular markers linked to genes controlling semen freezability can be identified using amplified restriction fragment length polymorphism (AFLP) technology. Five ejaculates were collected from each of 129 boars. Semen was diluted into a commercial freezing buffer (700 mOsm/kg, 3% glycerol) and five straws (0.5 ml) per ejaculate were cryopreserved (to -5 degrees C at 6 degrees C/min, then -5 degrees C to -80 degrees C at 40 degrees C/min). Semen was assessed for percentage of motile cells, motility characteristics (computer-aided semen analysis; CASA), plasma membrane integrity (SYBR-14 positive), and acrosome integrity (positive for fluorescein-labeled peanut agglutinin; PNA). Consistent between-boar variability was detected for postthaw sperm motility (P < 0.01), membrane integrity (P < 0.01), acrosome integrity (P < 0.01), and all CASA characteristics (P < 0.05). There was no significant difference between ejaculates (P > 0.05) or straws (P > 0.05) for any viability assessment. Multivariate pattern analysis of the viability data set highlighted three groups of boars producing spermatozoa with poor, average, and good postthaw recovery (42, 63, and 24 boars, respectively). DNA from Large White boars (n = 22) previously classified as good and poor freezers was screened for AFLP markers. Twenty-eight polymerase chain reaction primer combinations generated 2182 restriction fragment bands, of which 421 were polymorphic. Sixteen candidate genetic markers (P < 0.005) were identified by comparing the AFLP profile with semen freezability using logistic regression analysis. These findings support the hypothesis that there is a genetic basis for variation in postthaw semen quality between individuals, and that AFLP technology may be able to identify molecular markers linked to genes influencing this variation.
Intestinal absorption of several .BETA.-lactam antibiotics, V. Effect of amino .BETA.-lactam analogues and dipeptides on the absorption of amino .BETA.-lactam antibiotics. (1984)

The absorption mechanism of amino beta-lactam antibiotics was investigated by using the whole small intestine of a rat. Mutual inhibition among amino beta-lactam analogues and the effects of dipeptides were studied. The influences of glycylglycine on the absorption of cephradine at the four different parts of intestine were also studied. Similarly to the case of cephalexin and cephradine, the absorption of amoxicillin was significantly inhibited by cyclacillin, cephradine, and cephalexin, but the absorption of ampicillin was not reduced by all tested antibiotics. In the experiments using dipeptides (6.0 mM), the absorption of cyclacillin was reduced significantly by glycylglycine, not by L-carnosine. And cephalexin absorption was influenced by L-carnosine (6.0, 10 mM), not by glycylglycine (6 mM). On the contrary, the absorption of cephradine was not reduced at all by these dipeptides. And from the experiment using the four different parts of intestine, it was shown that the transport interaction of glycylglycine with cephradine was observed in only one segment (the upper part of jejunum). These result suggest that the carrier-mediated transport system correlated to dipeptides participates only to a small degree in the common absorption mechanisms of these amino beta-lactam antibiotics.
Structure Activity Studies of the Melanocortin-4 Receptor by in Vitro Mutagenesis:  Identification of Agouti-Related Protein (AGRP), Melanocortin Agonist and Synthetic Peptide Antagonist Interaction Determinants (2001)

In vitro mutagenesis of the mouse melanocortin-4 receptor (mMC4R) has been performed, based upon homology molecular modeling and previous melanocortin receptor mutagenesis studies that identified putative ligand-receptor interactions. Twenty-three mMC4 receptor mutants were generated and pharmacologically characterized using several melanocortin-based ligands [alpha-MSH, NDP-MSH, MTII, DNal (1')(7)-MTII, Nal(2')(7)-MTII, SHU9119, and SHU9005]. Selected mutant receptors possessing significant differences in the melanocortin-based peptide agonist and/or antagonist pharmacology were further evaluated using the endogenous antagonist agouti-related protein fragment hAGRP(83-132) and hAGRP(109-118) molecules. These studies of the mouse MC4R provide further experimental data suggesting that the conserved melanocortin receptor residues Glu92 (TM2), Asp114 (TM3), and Asp118 (TM3) (mouse MC4R numbering) are important for melanocortin-based peptide molecular recognition. Additionally, the Glu92 and Asp118 mMC4R residues are important for molecular recognition and binding of AGRP(83-132). We have identified the Phe176 (TM4), Tyr179 (TM4), Phe254 (TM6), and Phe259 (TM6) receptor residues as putatively interacting with the melanocortin-based ligand Phe(7) by differences between alpha-MSH and NDP-MSH agonist potencies. The Glu92, Asp118, and Phe253 mMC4R receptor residues appear to be critical for hAGRP(83-132) molecular recognition and binding while Phe176 appears to be important for functional antagonism of AGRP(83-132) and AGRP(109-118) but not molecular recognition. The Phe253 mMC4R residue appears to be important for AGRP(83-132) molecular recognition and general mMC4 receptor stimulation. The Phe254 and Phe259 mMC4R amino acids may participate in the differentiation of agonist versus antagonist activity of the melanocortin-based peptide antagonists SHU9119 and SHU9005, but not AGRP(83-132) or AGRP(109-118). The Met192 side chain when mutated to a Phe results in a constitutively active mMC4R that does not effect agonist ligand binding or potency. Melanocortin-based peptides modified at the 7 position of MTII with DPhe, DNal(1'), Nal(2'), and DNal(2') have been pharmacologically characterized at these mutant mouse MC4Rs. These data suggest a revised hypothesis for the mechanism of SHU9119 antagonism at the MC4R which may be attributed to the presence of a "bulky" naphthyl moiety at the 7 position (original hypothesis), and additionally that both the stereochemistry and naphthyl ring position (2' versus 1') are important for positioning of the ligand Arg(8) residue with the corresponding mMC4R amino acids.
Tornado-type closed magnetic trap for an electron cyclotron resonance ion source (2000)

We propose to use a Tornado-type closed magnetic trap for creation of a source of multicharged ions with plasma heating by microwave radiation. Plasma loss in closed traps is determined by diffusion across the magnetic field, which increases substantially plasma confinement time as compared to the classical mirror trap. The Tornado trap also possesses merits such as: an opportunity to produce high magnetic fields up to 3 T, which makes possible heating and confinement of plasma with a high density of electrons; an opportunity to use supplementary coils for ion extraction; plasma stability to magnetohydrodynamic perturbations because the magnetic field structure corresponds to the “min B” configuration; and relatively low costs. All estimates and calculations were carried out for the existing Tornado-322 pulse installation (maximal magnetic field 2.8 T) with plasma heating at 53 GHz frequency. The numerical simulation has shown that, by the end of the magnetic field pulse, ion distribution over charge states may reach a maximum at Ar+16 for the plasma density of 1013 cm−3. The current density of ions Ar+16 can be varied from 10 mA/cm2 to approximately 1 A/cm2.
Immunodominant Major Outer Membrane Proteins of Ehrlichia chaffeensis Are Encoded by a Polymorphic Multigene Family (1998)

Several immunodominant major proteins ranging from 23 to 30 kDa were identified in the outer membrane fractions of Ehrlichia chaffeensis and Ehrlichia canis. The N-terminal amino acid sequence of a 28-kDa protein of E. chaffeensis (one of the major proteins) was determined. The gene (p28), almost full length, encoding the 28-kDa protein was cloned by PCR with primers designed based on the N-terminal sequence of the E. chaffeensis 28-kDa protein and the consensus sequence between the C termini of the Cowdria ruminantium MAP-1 and Anaplasma marginale MSP-4 proteins. The p28 gene was overexpressed, and antibody to the recombinant protein was raised in a rabbit. The antibody and serum from a patient infected with E. chaffeensis reacted with the recombinant protein, three proteins (29, 28, and 25 kDa) of E. chaffeensis, and a 30-kDa protein of E. canis. Immunoelectron microscopy with the rabbit antibody revealed that the antigenic epitope of the 28-kDa protein was exposed on the surface of E. chaffeensis. Southern blot analysis with a 32P-labeled p28 gene probe revealed multiple copies of genes homologous to p28 in the E. chaffeensis genome. Six copies of the p28 gene were cloned and sequenced from the genomic DNA by using the same probe. The open reading frames of these gene copies were tandemly arranged with intergenic spaces. They were nonidentical genes and contained a semivariable region and three hypervariable regions in the predicted protein molecules. One of the gene copies encoded a protein with an internal amino acid sequence identical to the chemically determined N-terminal amino acid sequence of a 23-kDa protein of E. chaffeensis. Immunization with the recombinant P28 protein protected mice from infection with E. chaffeensis. These findings suggest that the 30-kDa-range proteins of E. chaffeensis represent a family of antigenically related homologous proteins encoded by a single gene family.
Proinflammatory Effects of IL-10 During Human Endotoxemia (2000)

IL-10 is considered a potent antiinflammatory cytokine that strongly inhibits the production of proinflammatory cytokines. Recent studies have suggested that IL-10 also has immunostimulatory properties on CD4+, CD8+ T cells, and/or NK cells, resulting in increased IFN-gamma production. To determine the effect of IL-10 on IFN-gamma production and related inflammatory responses in humans, 16 healthy subjects received a bolus i.v. injection of LPS (4 ng/kg) in combination with either placebo or recombinant human IL-10 (25 microg/kg), administered just before or 1 h after LPS. IL-10 treatment, particularly when administered after LPS, enhanced LPS-induced IFN-gamma release, as well as the release of the IFN-gamma-dependent chemokines IFN-gamma-inducible protein-10 and monokine induced by IFN-gamma, while inhibiting or not influencing the production of IFN-gamma-inducing cytokines. In addition, IL-10 treatment enhanced activation of CTLs and NK cells after LPS injection, as reflected by increased levels of soluble granzymes. These data indicate that high-dose IL-10 treatment in patients with inflammatory disorders can be associated with undesired proinflammatory effects.
Characterisation of the Klebsiella pneumoniae nitrogen‐fixation regulatory proteins NIFA and NIFL in vitro (1990)

Transcriptional activation by the Klebsiella pneumoniae nitrogen-fixation-specific positive control protein, NIFA, (nifA gene product) has been demonstrated in vitro in S30 extracts from cells which overproduce this protein. The activity of NIFA was dramatically reduced in vitro in the presence of the negative regulatory protein NIFL (nifL gene product) but was not inhibited by the presence of a mutant NIFL protein, NIFL2404. Transcriptional activation from the nifH promoter by NIFA was dependent on the alternative sigma factor, sigma 54, and also required the presence of an upstream activator sequence. NIFA activity was temperature-sensitive in vitro (as it is in vivo) which is due, at least in part, to the intrinsic lability of the protein itself. The majority of overproduced NIFA and NIFL was insoluble after low-speed centrifugation and was inactive in vitro. A low level of less aggregated NIFA protein present in cell extracts was responsible for in vitro activity and this fraction was partially purified.
Immune Responses to Adeno-Associated Virus Vectors (2005)

One of the biggest challenges in optimizing viral vectors for gene therapy relates to the immune response of the host. Adeno-associated virus (AAV) vectors are associated with low immunogenicity and toxicity, resulting in vector persistence and long-term transgene expression. The inability of AAV vectors to efficiently transduce or activate antigen presenting cells (APCs) may account for their decreased immunogenicity. AAV mediated gene therapy however, leads to the development of antibodies against the vector capsid. Anti-AAV antibodies have neutralizing effects that decrease the efficiency of in vivo gene therapy and can prevent vector re-administration. Furthermore, recent studies have shown that AAV vectors can elicit both cellular and humoral immune responses against the transgene product. Both cell-mediated response and humoral response to the delivered gene depend on a number of variables; including the nature of the transgene, the promoter used, the route and site of administration, vector dose and host factors. The response of the host to the vector, in terms of antigen-specific immunity, will play a substantial role in clinical outcome. It is therefore important to understand both, why AAV vectors are able to escape immunity and the circumstances and mechanisms that lead to the induction of immune responses. This review will summarize innate and adaptive immune responses to AAV vectors, discuss possible mechanisms and outline strategies, such as capsid modifications, use of alternative serotypes, or immunosuppression, which have been used to circumvent them.
Molecular Description of the LCST Behavior of an Elastin-Like Polypeptide (2014)

Elastin-like polypeptides (ELPs) with the repeat sequence of VPGVG are widely used as a model system for investigation of lower critical solution temperature (LCST) transition behavior. In this paper, the effect of temperature on the structure, dynamics and association of (VPGVG)18 in aqueous solution is investigated using atomistic molecular dynamics simulations. Our simulations show that as the temperature increases the ELP backbones undergo gradual conformational changes, which are attributed to the formation of more ordered secondary structures such as β-strands. In addition, increasing temperature changes the hydrophobicity of the ELP by exposure of hydrophobic valine-side chains to the solvent and hiding of proline residues. Based on our simulations, we conclude that the transition behavior of (VPGVG)18 can be attributed to a combination of thermal disruption of the water network that surrounds the polypeptide, reduction of solvent accessible surface area of the polypeptide, and increase in its hydrophobicity. Simulations of the association of two (VPGVG)18 molecules demonstrated that the observed gradual changes in the structural properties of the single polypeptide chain are enough to cause the aggregation of polypeptides above the LCST. These results lead us to propose that the LCST phase behavior of poly(VPGVG) is a collective phenomenon that originates from the correlated gradual changes in single polypeptide structure and the abrupt change in properties of hydration water around the peptide and is a result of a competition between peptide-peptide and peptide-water interactions. This is a computational study of an important intrinsically disordered peptide system that provides an atomic-level description of structural features and interactions that are relevant in the LCST phase behavior.
ICP34.5 influences herpes simplex virus type 1 maturation and egress from infected cells in vitro (1994)

We have previously demonstrated that efficient replication of mutant herpes simplex virus which fails to synthesize the polypeptide ICP34.5 is cell type and cell state dependent. ICP34.5 negative viruses do not grow in stationary state mouse embryo fibroblast 3T6 cells whereas the growth kinetics in BHK cells are indistinguishable from those of wild-type. We now demonstrate that this defect is not due to an inability of mutant virus to adsorb to 3T6 cells but rather to an inability to spread from the initially infected cells. Electron microscopic studies with wild-type HSV in both BHK and 3T6 cells revealed virus particles equally distributed between nucleus and cytoplasm, and additionally in the extracellular matrix. In BHK cells infected with the ICP34.5 negative mutant 1716, virus is likewise distributed between nucleus and cytoplasm but in 50% of the infected cells there is marked delamination and swelling of the nuclear membrane. In addition there is evidence of a significant number of particles trapped between the nuclear lamellae. When 1716 is used to infect 3T6 cells, over 90% of the virus particles are confined to the nuclei and the number of infected cells remains constant between 24 and 48 h with no increase in the proportion of extracellular virus. Failure to express ICP34.5 appears therefore to result in a defect in virus maturation and egress from the nuclei of infected cells. Egress of HSV from the nuclei to the extracellular space is thought to occur via two pathways. We postulate that lack of expression of ICP34.5 results in one of these pathways being blocked. In BHK cells this leads to overloading of the alternative pathway with a buildup of particles in the nuclear lamellae and associated endoplasmic reticulum. In stationary state 3T6 cells, it appears that there is no functional alternative pathway. We conclude that ICP34.5 exerts an effect on HSV maturation by controlling the passage of virus through infected cells.
Non-Precious-Metal Catalytic Systems Involving Iron or Cobalt Carboxylates and Alkyl Isocyanides for Hydrosilylation of Alkenes with Hydrosiloxanes (2016)

A mixture of an iron or a cobalt carboxylate and an isocyanide ligand catalyzed the hydrosilylation of alkenes with hydrosiloxanes with high efficiency (TON >10(3)) and high selectivity. The Fe catalyst showed excellent activity for hydrosilylation of styrene derivatives, whereas the Co catalyst was widely effective in reaction of alkenes. Both of them catalyzed the reaction with allylic ethers. Chemical modification and cross-linking of silicones were achieved by choosing the right catalyst and reaction conditions.
PAR-aware multi-user precoder for the large-scale MIMO-OFDM downlink (2012)

We consider an orthogonal frequency-division multiplexing (OFDM)-based downlink transmission scheme for large-scale multi-user (MU) multiple-input multiple-output (MIMO) wireless systems. In order to transmit signals with low peak-to-average (power) ratio (PAR), we propose to exploit the massive degrees-of-freedom available in large-scale MU-MIMO-OFDM systems. Specifically, we jointly perform MU precoding, OFDM modulation, and PAR reduction by solving a convex optimization problem at the base station. Numerical results demonstrate tremendous PAR-reduction capabilities of the proposed method, which eventually enables us to use low-cost RF components for the large-scale MU-MIMO-OFDM downlink.
Automatically Constructing a Normalisation Dictionary for Microblogs (2012)

Microblog normalisation methods often utilise complex models and struggle to differentiate between correctly-spelled unknown words and lexical variants of known words. In this paper, we propose a method for constructing a dictionary of lexical variants of known words that facilitates lexical normalisation via simple string substitution (e.g. tomorrow for tmrw). We use context information to generate possible variant and normalisation pairs and then rank these by string similarity. Highlyranked pairs are selected to populate the dictionary. We show that a dictionary-based approach achieves state-of-the-art performance
Therapeutic temperature management: Why, who, when, where, and how (2009)

From the Surgical Intensive Care Unit, Washington Hospital Center, Washington, DC. The author has not disclosed any potential conflicts of interest. For information regarding this article, E-mail: Daniel.[email protected]
Reduction of aqueous free chlorine with granular activated carbon - pH and temperature effects (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReduction of aqueous free chlorine with granular activated carbon - pH and temperature effectsMakram T. Suidan, Vernon L. Snoeyink, and Roger A. SchmitzCite this: Environ. Sci. Technol. 1977, 11, 8, 785–789Publication Date (Print):August 1, 1977Publication History Published online1 May 2002Published inissue 1 August 1977https://pubs.acs.org/doi/10.1021/es60131a013https://doi.org/10.1021/es60131a013research-articleACS PublicationsRequest reuse permissionsArticle Views761Altmetric-Citations41LEARN 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-Alertsclose Get e-Alerts
Quantitative Struktur‐Wirkungs‐Beziehung bei Polyhydroxyxanthonen, 2. Mitt.1): Synthese mehrfach oxigenierter 2‐Hydroxyxanthone (1990)

Abstract Es wird die Synthese der 2‐Hydroxyxanthone 8 über die entsprechenden Polymethoxyxanthone 7 beschrieben, die in Ring C mehrfach hydroxyliert sind. Die Darstellung verläuft entweder über die 2‐Phenoxybenzosäuren 5 oder die polymethoxylierten 2‐Hydroxybenzophenone 6 .
Archaeology and GIS--The Linux Way (1999)

A description of an archaeology project making use of the freely available geographic information system GRASS
THE AMINO ACID COMPOSITION OF HYPERTENSIN II AND ITS BIOCHEMICAL RELATIONSHIP TO HYPERTENSIN I (1956)

Preparations of hypertensin II, obtained from the treatment of hypertensin I by the action of the hypertensin converting enzyme of plasma and purified by countercurrent distribution, were quantitatively analyzed for their amino acid content. Chromatography on ion exchange columns showed the presence of equimolar amounts of aspartic acid, proline, valine, isoleucine, tyrosine, phenylalanine, histidine, and arginine. Hypertensin I was found to contain one mole of leucine and one mole of histidine in addition to the amino acids of hypertensin II. These two amino acids were isolated from the conversion products of hypertensin I and identified as the peptide histidylleucine. Carboxypeptidase digestion of hypertensin I showed the carboxyl terminal sequence of amino acids to be residue-phenylalanyl-histidylleucine. Similar studies of hypertensin II demonstrated residue-phenylalanine. It was concluded that the conversion of hypertensin I by the plasma hypertensin converting enzyme involved hydrolysis of the phenylalanyl-histidine bond to form hypertensin II and histidylleucine. The further removal by carboxypeptidase of phenylalanine from hypertensin II destroyed all of the vasoconstrictor activity.