gebhart/patrepeval huggingface dataset:
Synthesis of ethynyl(phenyl)iodonium tetrafluoroborate. A new reagent for ethynylation of 1,3-dicarbonyl compounds (1990)

Hydrogen fluoride-induced protiodetrimethylsilylation of trimethylsilylethynyl(phenyl)iodonium tetrafluoroborate (5), prepared from bis(trimethylsilyl)ethyne (4), affords ethynyl(phenyl)iodonium tetrafluoroborate (1), a reagent for α-ethynylation of β-dicarbonyl compounds under mild conditions.
Quantization procedures for the excitation in CELP coders (2005)

Past research on CELP (Code-Excited Linear Predictive) coders has mainly concentrated on the feasibility of the CELP concept and on the reduction of the computational complexity. In this paper we address the problem of finding and encoding the excitation parameters with a limited bit rate, such that high quality speech coding in the 4.8 - 7.2 kb/s range becomes feasible. First, we examine the effect of the various excitation parameters such as code book size, code book population, order of the long-term predictor and update rate on the quality of the reconstructed speech. Second, we investigate procedures for designing and incorporating quantizers for the parameters involved. Finally, using both scalar and vector quantization techniques for the LPC coefficients, we simulated 4.8 kb/s and 7.2 kb/s coders. We also report on the use of postfiltering to further improve the performance of the CELP coder.
Recombinant Full-length Tissue Factor Pathway Inhibitor (TFPI) Prevents Thrombus Formation and Rethrombosis after Lysis in a Rabbit Model of Jugular Vein Thrombosis (1996)

In the jugular vein of rabbits thrombus formation was induced by vessel wall damage using a balloon catheter and following reduction of blood flow by 80-90% for 60 min (partial stasis). The blood flow in the vein was measured continuously and the incidence of primary thrombus formation, the time until lysis with recombinant tissue-type plasminogen activator (rt-PA) as well as the incidence of rethrombosis after lysis were determined. At the end of the experiment the wet weight of the thrombus formed inside the vessel was measured. For the determination of haemostaseological parameters blood was drawn from the cannulated femoral artery. Recombinant full-length tissue factor pathway inhibitor (TFPI) was studied with regard to its effect both on primary thrombus formation and on rethrombosis after lysis. In control animals damage of the vessel wall combined with partial stasis led to the formation of occlusive venous thrombi. In vitro bolus injection of TFPI (5, 10, 20 micrograms/kg) at the time of thrombus induction prevented the formation of venous thrombi during the 1 h period of partial stasis. In the subsequent observation period a dose-dependent inhibition of later occurring partial or complete thrombotic occlusion was found. At the dose of 20 micrograms/kg i.v. in all animals TFPI prevented a complete thrombotic occlusion of the vein up to 3 h after stasis. To study the effectiveness of TFPI on rethrombosis after lysis TFPI was injected i.v. after lysis of the thrombus with rt-PA (600 micrograms/kg i.v. bolus + 600 micrograms/kg i.v. infusion over 60 min). In saline treated control rabbits a reocclusion of the vessel was seen in 8 of 10 animals. TFPI (10, 20, 40 micrograms/kg i.v.) injected at the end of rt-PA administration caused a dose-dependent inhibition of thrombotic reocclusion after lysis. At 40 micrograms/kg i.v. the formation of occlusive thrombi was prevented up to 3 h after lysis. TFPI at the doses used caused modest anticoagulant effects in global clotting assays; activated partial thromboplastin time (APTT), prothrombin time (PT) and thrombin time (TT) were only slightly prolonged. A clear and dose-dependent prolongation of clotting times was only seen in the Heptest assay. The results show that the physiologic coagulation inhibitor TFPI acts as a strong antithrombotic agent in an experimental model of venous thrombus formation and thrombotic reocclusion after lysis in rabbits.
The Asp 9 Asn Mutation in the Lipoprotein Lipase Gene Is Associated With Increased Progression of Coronary Atherosclerosis (1996)

This study shows that heterozygosity for a mutation in the LPL gene, which causes only subtle changes in fasting plasma lipids, may promote the progression of coronary atherosclerosis and diminish clinical event-free survival.
Characteristics ofNeo Red Cells, their Function and Safety:In VivoStudies (1994)

A new type of artificial oxygen carriers, the Neo Red Cells (NRCs) have been developed and investigated for oxygen transporting efficiency and safety in experimental animals. Stroma free hemoglobin from outdated human red blood cells together with inositol hexaphosphate as an allosteric effector under sterile, pyrogen free condition were encapsulated in liposomes and then were coated with polyethylene glycol bond to hydrogenated soy phosphatidylethanolamine as a surface modifier to prevent aggregation of NRCs in plasma. The efficiency of the NRCs in tissue oxygenation was studied in rabbits which were made severely anemic by drawing 85% of their blood and immediately replacing it with NRC solution. The animals, all recovered to pre-anemic conditions within 6-8 hr and lived normally until being sacrificed, 6 months after the exchange transfusion. The circulation half-life and tissue distribution of NRCs were studied using radiolabeled NRCs. Within the circulation, the half-life of NRCs was 21 hr and extravascularly, they were distributed mainly in and metabolized by the reticuloendothelial system within 7 days. Our observations suggest that the NRCs prepared and investigated in this study are efficient oxygen carriers without causing serious adverse reactions and can be prepared free from pathogenic micro-organisms by special filtration technique before encapsulation of Hb. Currently, experiments are ongoing to control auto-oxidation of oxyHb to metHb which is higher in NRCs than in native red cells at physiological conditions.
Application of High-Speed Countercurrent Chromatography for the Isolation of Sulforaphane from Broccoli Seed Meal (2008)

In order to produce large amounts of pure sulforaphane for research purposes, a novel method using high-speed countercurrent chromatography (HSCCC) was developed. Without any initial cleanup steps, sulforaphane was successfully purified from the ethyl acetate extract of the broccoli seed meal by HSCCC. The separation was performed with two-phase solvent systems: n-hexane/ethyl acetate/methanol/water (1:5:1:5, v/v/v/v). From 850 mg of the ethyl acetate extract, 186 mg of sulforaphane was isolated with the solvent system. The purified compound was over 97% purity as determined by HPLC analysis, and the chemical structure was confirmed by MS and (1)H and (13)C NMR.
Disulfide Bond Configuration of Human Cytomegalovirus Glycoprotein B (2002)

Glycoprotein B (gB) is the most highly conserved of the envelope glycoproteins of human herpesviruses. The gB protein of human cytomegalovirus (CMV) serves multiple roles in the life cycle of the virus. To investigate structural properties of gB that give rise to its function, we sought to determine the disulfide bond arrangement of gB. To this end, a recombinant form of gB (gB-S) comprising the entire ectodomain of the glycoprotein (amino acids 1 to 750) was constructed and expressed in insect cells. Proteolytic fragmentation and mass spectrometry were performed using purified gB-S, and the five disulfide bonds that link 10 of the 11 highly conserved cysteine residues of gB were mapped. These bonds are C94-C550, C111-C506, C246-C250, C344-C391, and C573-C610. This configuration closely parallels the disulfide bond configuration of herpes simplex type 2 (HSV-2) gB (N. Norais, D. Tang, S. Kaur, S. H. Chamberlain, F. R. Masiarz, R. L. Burke, and F. Markus, J. Virol. 70:7379-7387, 1996). However, despite the high degree of conservation of cysteine residues between CMV gB and HSV-2 gB, the disulfide bond arrangements of the two homologs are not identical. We detected a disulfide bond between the conserved cysteine residue 246 and the nonconserved cysteine residue 250 of CMV gB. We hypothesize that this disulfide bond stabilizes a tight loop in the amino-terminal fragment of CMV gB that does not exist in HSV-2 gB. We predicted that the cysteine residue not found in a disulfide bond of CMV gB, cysteine residue 185, would play a role in dimerization, but a cysteine substitution mutant in cysteine residue 185 showed no apparent defect in the ability to form dimers. These results indicate that gB oligomerization involves additional interactions other than a single disulfide bond. This work represents the second reported disulfide bond structure for a herpesvirus gB homolog, and the discovery that the two structures are not identical underscores the importance of empirically determining structures even for highly conserved proteins.
Pharmacokinetic optimization of four soluble epoxide hydrolase inhibitors for use in a murine model of inflammation (2009)

t-AUCB is a potent sEHI with improved pharmacokinetic properties. This compound will be a useful tool for pharmacological research and a promising starting point for drug development.
Less is better: when low-value options are valued more highly than high-value options (1998)

This research demonstrates a less-is-better effect in three contexts: (1) a person giving a $45 scarf as a gift was perceived to be more generous than one giving a $55 coat; (2) an overfilled ice cream serving with 7 oz of ice cream was valued more than an underfilled serving with 8 oz of ice cream; (3) a dinnerware set with 24 intact pieces was judged more favourably than one with 31 intact pieces (including the same 24) plus a few broken ones. This less-is-better effect occurred only when the options were evaluated separately, and reversed itself when the options were juxtaposed. These results are explained in terms of the evaluability hypothesis, which states that separate evaluations of objects are often influenced by attributes which are easy to evaluate rather than by those which are important. © 1998 John Wiley & Sons, Ltd.
A placebo double-blind pilot study of dextromethorphan for problematic behaviors in children with autism (2006)

We used a mixed group/single-case, double-blind, placebo-controlled, ABAB design to examine the safety and efficacy of the glutamate antagonist dextromethorphan for the treatment of problematic behaviors and core symptoms in eight children diagnosed with autism. All participants had increased levels of irritability at baseline as measured by the Aberrant Behavior Checklist, and demonstrated a wide variety of problematic behaviors. Group analyses revealed that dextromethorphan was equivalent to placebo in the treatment of problem behaviors and core symptoms. Analyses at the single-subject level demonstrated that three of the eight participants who had a behavioral profile consistent with attention-deficit hyperactivity disorder responded positively to dextromethorphan. Future research that employs a larger, more homogeneous sample is necessary to replicate the findings from this study.
Nasal administration of CTB-insulin induces active tolerance against autoimmune diabetes in non-obese diabetic (NOD) mice (2002)

Nasal administration of beta cell-derived auto-antigens has been reported to suppress the development of autoimmune diabetes. We investigated the tolerogenic effects of insulin conjugated to the B subunit of cholera toxin (CTB). Nasal administration of 1 micro g of CTB-insulin significantly delayed the incidence of diabetes in comparison to CTB treated mice. However, administration of 4 or 8 micro g of the conjugate had no protective effect. Protection induced by CTB-insulin was transferred to naive recipients by splenic CD4+ T cells. This result favours an active cellular mechanism of regulation, which was lost using higher (4-8 micro g) or lower (0.1-0.5 micro g) amounts of the conjugate. When co-administered with diabetogenic T cells, splenic T cells from CTB-insulin-treated mice reduced the lymphocytic infiltration of the islets. Reverse transcription-polymerase chain reaction analysis of recipients' pancreatic glands revealed an increase of TGF-beta and IL-10 transcripts after donor mice tolerization, while levels of IFN-gamma and IL-4 RNAs were unchanged. We observed a significant increase of T cell proliferation after unspecific stimulation in the spleen and pancreatic lymph nodes 24 h after CTB-insulin administration in -comparison to control treatment. Higher amounts of IL-4 and IFN-gamma were noticed in pancreatic lymph nodes of tolerized mice upon in vitro stimulation. Antigen-specific unresponsiveness after immunization and upon subsequent in vitro exposure to homologous antigen was obtained in nasally treated animals. Our results underlined the importance of nasal mucosa as an inducing site of tolerance and provided evidence for similar mechanisms of action to what has been described for the oral route, which favoured a CTB-insulin specific effect.
Microfibril-associated Glycoprotein-2 Specifically Interacts with a Range of Bovine and Human Cell Types via αVβ3 Integrin (1999)

Microfibril-associated glycoprotein (MAGP)-1 and MAGP-2 are small structurally related glycoproteins that are specifically associated with fibrillin-containing microfibrils. MAGP-2, unlike MAGP-1, contains an RGD motif with potential for integrin binding. To determine if the RGD sequence is active, a series of cell binding assays was performed. MAGP-2 was shown to promote the attachment and spreading of bovine nuchal ligament fibroblasts when coated onto plastic wells in molar quantities similar to those of fibronectin. In contrast, approximately 10-fold more MAGP-1 was required to support comparable levels of cell adhesion. The fibroblast binding to MAGP-2 was completely inhibited if the peptide GRGDSP or the MAGP-2-specific peptide GVSGQRGDDVTTVTSET was added to the reaction medium at a 10 microM final concentration. The control peptide GRGESP had no effect on the interaction. These findings indicate that the cell interaction with MAGP-2 is an RGD-mediated event. A monoclonal antibody to human alphaVbeta3 integrin (LM609) almost completely blocked cell attachment to MAGP-2 when added to the medium at 0.5 microgram/ml, whereas two monoclonal antibodies specific for the human beta1 integrin subunit, 4B4 (blocking) and QE2.E5 (activating), had no effect even at 10 microgram/ml. Fetal bovine aortic smooth muscle cells, ear cartilage chondrocytes, and arterial endothelial cells and human skin fibroblasts and osteoblasts were also observed to adhere strongly to MAGP-2. In addition, each cell type was able to spread on MAGP-2 substrate, with the exception of the endothelial cells, which remained spherical after 2 h of incubation. The binding of each cell type was blocked when the anti-alphaVbeta3 integrin antibody was included in the assay, indicating that alphaVbeta3 integrin is the major receptor for MAGP-2 on several cell types. Thus, MAGP-2 may mediate interactions between fibrillin-containing microfibrils and cell surfaces during the development of a variety of tissues.
Biological and clinical effects of intravenous tumor necrosis factor-alpha administered three times weekly. (1991)

Tumor necrosis factor (TNF) is a cytokine with pleiotropic biological and antitumor effects in vitro and in mouse models. The immunological effects of the molecule as a single agent, however, have not been well studied clinically. We conducted a Phase I trial of TNF in 53 patients with advanced malignancies in order to determine the biological and clinical effects of TNF when administered as a 30-min i.v. infusion three times/week. Dose levels of TNF ranged from 5 to 275 micrograms/m2; doses of TNF were escalated between patient groups. The most common clinical toxicities of TNF consisted of rigors, anorexia, headache, and fatigue. Dose-limiting toxicity consisted of hypotension, fatigue, and nausea. Four patients treated at the maximally tolerated dose of 225 micrograms/m2 received dexamethasone to determine whether the toxicities of TNF could be ameliorated. No significant differences in hypotension or subjective symptomatology were observed in those patients receiving dexamethasone and those who did not or between injections in which dexamethasone was administered and when it was not. One patient with colorectal carcinoma treated with 50 micrograms/m2 had a partial response lasting about 9 months. Biological responses were evaluated in 8 patients treated at the maximally tolerated dose before therapy and 24 h afterward. TNF significantly (P less than 0.05 for all) enhanced serum beta 2-microglobulin, serum neopterin, and serum interleukin-2 receptor (Tac antigen) levels. Indoleamine 2,3-dioxygenase activity was also increased 24 h following the administration of TNF, although this increase was only of borderline statistical significance (P = 0.07). TNF did not enhance granulocyte bactericidal activity. The expression of cell surface proteins on monocytes, including HLA-DR, HLA-DQ, beta 2-microglobulin, and the Fc receptor, and serum interleukin-1 activity also were not significantly increased by the administration of TNF. Thus, in humans TNF caused biological response modulation with evidence of HLA Class I (beta 2-microglobulin) increase and T-cell (Tac antigen) and monocyte (neopterin) activation.
Human recombinant migration inhibitory factor activates human macrophages to kill Leishmania donovani (1993)

A recombinant form of the first lymphokine to be discovered, migration inhibitory factor (rMIF) was obtained from COS-1 cells transfected with a cDNA library from a human T cell hybridoma (6). rMIF has an amino acid sequence unrelated to that of any known protein. To learn more about the biology of MIF, we tested its ability to effect the survival of Leishmania donovani in macrophages. We found that rMIF activates blood monocyte-derived macrophages in vitro to suppress the growth of and kill these intracellular parasites. The anti-leishmanial effect (ranging from 50 to 77% reduction of parasites) is maximal when macrophages have been incubated with rMIF 48 to 72 h before infection and is similar to that seen with macrophages activated by IFN-gamma. Of interest, whereas the activation of human macrophages by IFN-gamma is inhibited by IL-4 and not enhanced by LPS, the activation by rMIF is enhanced by LPS but is not inhibited by IL-4. The data presented here demonstrate that rMIF is a potent activator of macrophages and is likely to be critical in cell-mediated immune host defenses.
Biclustering algorithms for biological data analysis: a survey (2004)

A large number of clustering approaches have been proposed for the analysis of gene expression data obtained from microarray experiments. However, the results from the application of standard clustering methods to genes are limited. This limitation is imposed by the existence of a number of experimental conditions where the activity of genes is uncorrelated. A similar limitation exists when clustering of conditions is performed. For this reason, a number of algorithms that perform simultaneous clustering on the row and column dimensions of the data matrix has been proposed. The goal is to find submatrices, that is, subgroups of genes and subgroups of conditions, where the genes exhibit highly correlated activities for every condition. In this paper, we refer to this class of algorithms as biclustering. Biclustering is also referred in the literature as coclustering and direct clustering, among others names, and has also been used in fields such as information retrieval and data mining. In this comprehensive survey, we analyze a large number of existing approaches to biclustering, and classify them in accordance with the type of biclusters they can find, the patterns of biclusters that are discovered, the methods used to perform the search, the approaches used to evaluate the solution, and the target applications.
Data mining and analysis techniques in wind power system applications: abridged (2006)

This panel paper summarizes wind power development in recent years challenges of wind power integration. During the panel session, data mining and analysis techniques are proposed to help solve these challenges
Phenotypic Tolerance: Antibiotic Enrichment of Noninherited Resistance in Bacterial Populations (2005)

When growing bacteria are exposed to bactericidal concentrations of antibiotics, the sensitivity of the bacteria to the antibiotic commonly decreases with time, and substantial fractions of the bacteria survive. Using Escherichia coli CAB1 and antibiotics of five different classes (ampicillin, ciprofloxacin, rifampin, streptomycin, and tetracycline), we examine the details of this phenomenon and, with the aid of mathematical models, develop and explore the properties and predictions of three hypotheses that can account for this phenomenon: (i) antibiotic decay, (ii) inherited resistance, and (iii) phenotypic tolerance. Our experiments cause us to reject the first two hypotheses and provide evidence that this phenomenon can be accounted for by the antibiotic-mediated enrichment of subpopulations physiologically tolerant to but genetically susceptible to these antibiotics, phenotypic tolerance. We demonstrate that tolerant subpopulations generated by exposure to one concentration of an antibiotic are also tolerant to higher concentrations of the same antibiotic and can be tolerant to antibiotics of the other four types. Using a mathematical model, we explore the effects of phenotypic tolerance to the microbiological outcome of antibiotic treatment and demonstrate, a priori, that it can have a profound effect on the rate of clearance of the bacteria and under some conditions can prevent clearance that would be achieved in the absence of tolerance.
A decade of pig genome sequencing: a window on pig domestication and evolution (2016)

Insight into how genomes change and adapt due to selection addresses key questions in evolutionary biology and in domestication of animals and plants by humans. In that regard, the pig and its close relatives found in Africa and Eurasia represent an excellent group of species that enables studies of the effect of both natural and human-mediated selection on the genome. The recent completion of the draft genome sequence of a domestic pig and the development of next-generation sequencing technology during the past decade have created unprecedented possibilities to address these questions in great detail. In this paper, I review recent whole-genome sequencing studies in the pig and closely-related species that provide insight into the demography, admixture and selection of these species and, in particular, how domestication and subsequent selection of Sus scrofa have shaped the genomes of these animals.
Alternating Copolymerizations of Polar and Nonpolar Cyclic Olefins by Ring-Opening Metathesis Polymerization (2001)

The results from copolymerizations of polar 2,3-difunctionalized 7-oxanorbornene derivatives with a series of nonpolar cyclic olefinscyclooctene, cyclooctadiene, cyclopentene, and norborneneusing catalysts RuCl2(CHPh)(PCy3)2 (1) and its mono-1,3-dimesitylimidazolidine-2-ylidene derivative (2) are reported. The resulting polymer microstructures have been analyzed by 1H, 13C, and 1H−1H COSY NMR spectroscopies. Highly alternating structures were observed for the copolymerizations of endo-N-ethyl-7-oxanorbornene-2,3-dicarboxylimide (endo-3), exo,exo-7-oxanorbornene-2,3-dimethylester (exo-4), or exo-7-oxanorbornene-2,3-dicarboxylic anhydride (exo-5) with cyclooctene using catalyst 1. The rates of homopolymerizations of endo-3, exo-5, and cyclooctene were determined. Comparison with the rate of the copolymerization of endo-3 with cyclooctene reveals a rate faster than the homopolymerization of endo-3 but slower than the homopolymerization of cyclooctene. The rate of the copolymerization of exo-5 with cyclooctene was observed to be greater than the rate of homopolymerization of either monomer. The use of catalyst 2 resulted in lower levels of alternation with a tendency toward random polymerization.