gebhart/patrepeval huggingface dataset:
Volatile compounds in pyroligneous liquids from karamatsu and chishima-sasa. (1987)

Volatile components in pyroligneous liquids obtained from Karamatsu and Chishima-sasa. were extracted, fractionated into neutral/basic and acidic fractions, and identified by gas chromatography-mass spectrometry. In the neutral/basic fraction, 118 components were identified. Cyclic and acyclic ketones, pyridine derivatives, pyrazine derivatives and furan derivatives were important odorous components. Sixty-nine compounds were identified in the acidic fraction. The main groups were carboxylic acids and phenol compounds. The concentrations of alkyl phenols were almost the same between Karamatsu and Chishima-sasa, but there were large differences in the contents of 2-methoxyphenol derivatives and 2, 6-dimethoxyphenol derivatives between them.
Limited Digestion of Guinea Pig Myelin Basic Protein and Its Carboxy‐Terminal Fragment (Residues 89–169) with Staphylococcus aureus V8 Protease (1982)

Staphylococcus aureus V8 protease has been reported to have a strict specificity for cleavage of the Glu-X bond in ammonium bicarbonate (pH 7.9). With myelin basic protein and one of its major peptic fragments (residues 89-169) as substrates, selective cleavage of Asp(32)-Thr(33), Asp(37)-Ser(38), and Glu(118-Gly(119) bonds was observed, as well as the unusual cleavage of the Gly(127)-Gly(128) bond. The Asp-Glu and Glu-Asn bonds in the sequence of Gln-Asp-Glu-Asn-Pro(81-84) were resistant to V8 protease attack. The following peptides were identified as products of limited cleavage of basic protein by V8 protease: (1-32), (1-37), (33-169), (38-169), (33-118), (38-118), (33-127), (38-127), (119-169), and (128-169). Cleavage of the peptic peptide (89-169) yielded fragments (89-118), (89-127), (119-169), and (128-169). All peptides were identified by amino acid analysis, as well as NH2- and COOH-terminal analyses. Time course studies with basic protein showed that V8 protease initially attacked the bonds between Asp(32) and Thr(33) and Asp(37) and Ser(38). With peptide (89-169) the initial cleavage was between Glu(118) and Gly(119). Peptides (89-118) and (89-127) were encephalitogenic in the Lewis rat. The activity of these peptides in the rat confirms the presence of a minor encephalitogenic site in guinea pig basic protein. Peptide (89-127) was encephalitogenic in the guinea pig, as expected, because it contains the intact encephalitogenic site. V8 protease digestion of basic protein yields some interesting new fragments, not previously available for biologic studies.
A Unique Metastasis Gene Signature Enables Prediction of Tumor Relapse in Early-Stage Hepatocellular Carcinoma Patients (2010)

Metastasis-related recurrence often occurs in hepatocellular carcinoma (HCC) patients who receive curative therapies. At present, it is challenging to identify patients with high risk of recurrence, which would warrant additional therapies. In this study, we sought to analyze a recently developed metastasis-related gene signature for its utility in predicting HCC survival, using 2 independent cohorts consisting of a total of 386 patients who received radical resection. Cohort 1 contained 247 predominantly HBV-positive cases analyzed with an Affymetrix platform, whereas cohort 2 contained 139 cases with mixed etiology analyzed with the NCI Oligo Set microarray platform. We employed a survival risk prediction algorithm with training, test, and independent cross-validation strategies and found that the gene signature is predictive of overall and disease-free survival. Importantly, risk was significantly predicted independently of clinical characteristics and microarray platform. In addition, survival prediction was successful in patients with early disease, such as small (<5 cm in diameter) and solitary tumors, and the signature predicted particularly well for early recurrence risk (<2 years), especially when combined with serum alpha fetoprotein or tumor staging. In conclusion, we have shown in 2 independent cohorts with mixed etiologies and ethnicity that the metastasis gene signature is a useful tool to predict HCC outcome, suggesting the general utility of this classifier. We recommend the use of this classifier as a molecular diagnostic test to assess the risk that an HCC patient will develop tumor relapse within 2 years after surgical resection, particularly for those with early-stage tumors and solitary presentation.
Is There a Role for Inflammation in Contact Lens Discomfort? (2016)

There have been only a few studies that have investigated a role for inflammation in contact lens-induced discomfort, and the strongest associations have been found with lipid degradation processes.
Effect of template conversion from the B to the Z conformation on RNA polymerase activity (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of template conversion from the B to the Z conformation on RNA polymerase activityJames J. Butzow, Yong A. Shin, and Gunther L. EichhornCite this: Biochemistry 1984, 23, 21, 4837–4843Publication Date (Print):October 9, 1984Publication History Published online1 May 2002Published inissue 9 October 1984https://pubs.acs.org/doi/10.1021/bi00316a004https://doi.org/10.1021/bi00316a004research-articleACS PublicationsRequest reuse permissionsArticle Views23Altmetric-Citations26LEARN 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
Capillary electrophoresis–mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery (2005)

Proteome analysis is now emerging as key technology for deciphering biological processes and the discovery of biomarkers for diseases from tissues and body fluids. The complexity and wide dynamic range of protein expression poses a formidable challenge to both peptide separation technologies and mass spectrometry (MS). Here we review the efforts that have been undertaken to date, focussing on capillary electrophoresis coupled to mass spectrometry (CE-MS). We discuss CE-MS from an application point of view evaluating its merits and vices in regard to biomarker discovery and clinical applications. As examples, we present the use of CE-MS for the determination of protein patterns in urine, serum, and other body fluids. Finally, the benefits and limitations of CE-MS for the analysis of proteins in clinical samples are discussed against the background of alternative technologies.
In Vitro Activities of DA-7157 and DA-7218 against <i>Mycobacterium tuberculosis</i> and <i>Nocardia brasiliensis</i> (2006)

The in vitro activities of DA-7157, a novel oxazolidinone, against clinical isolates of Nocardia brasiliensis and Mycobacterium tuberculosis were determined. Equal MIC(50)s and MIC(90)s (0.25 and 0.5 microg/ml, respectively) were found for susceptible and multidrug-resistant isolates of M. tuberculosis. The N. brasiliensis isolates showed an MIC(90) of 1 microg/ml and an MIC(50) of 1 microg/ml. The DA-7157 prodrug, DA-7218, exhibited similar MICs for M. tuberculosis but fivefold-higher MICs for N. brasiliensis.
Polydepsipeptides I. Synthesis and Characterization of Copolymers of α‐Amino and α‐Hydroxy Acids (1972)

Abstract Copolymers of the type magnified image were synthesized and characterized. The syntheses of these copolymers were achieved by copolymerization of an α‐amino acid N‐carboxy anhydride and an α‐hydroxy acid anhydrosulfite in the presence of a catalyst. The copolymers were characterized by spectroscopic methods including infrared, circular dichroism and nuclear magnetic resonance. Specific cleavage of the ester bonds by hydroxylamine in the cold confirmed the A‐B block structure where the A represents the poly(amino acid) segment and the B indicates the polyester segment. Measurements by nmr and viscosity indicate that the blocks consist of short chain lengths.
The Insulin-like Growth Factor Binding Protein Superfamily: New Perspectives (1999)

The insulin-like growth factor (IGF) binding proteins (IGFBPs) were initially identified as carrier proteins for IGF-I and IGF-II in a variety of biologic fluids. Their presumed function was to protect IGF peptides from degradation and clearance, increase the half-life of the IGFs, and deliver them to appropriate tissue receptors. The concept of IGFBPs as simple carrier proteins has been complicated, however, by a number of observations: 1) the six IGFBPs vary in their tissue expression and their regulation by other hormones and growth factors; 2) the IGFBPs are subjected to proteolytic degradation, thereby altering their affinities for the IGFs; 3) IGFBP-3 and IGFBP-5, in addition to binding IGFs, also can associate with an acid-labile subunit, thereby increasing further the half-life of the IGFs; 4) in addition to modifying the access of IGF peptides to IGF and insulin receptors, several of the IGFBPs may be capable of increasing IGF action; 5) some of the IGFBPs may be capable of IGF-independent regulation of cell growth; 6) some of the IGFBPs are associated with cell membranes or possibly with membrane receptors; and 7) some of the IGFBPs have nuclear recognition sites and may be found within the nucleus. Additionally, a number of cDNAs identified recently have been found to encode proteins that bind IGFs, but with substantially lower affinities than is the case with IGFBPs. The N-terminal regions of the predicted proteins are structurally homologous to the classic IGFBPs, with conservation of the cysteine-rich region. These observations suggest that these low-affinity binders are members of an IGFBP superfamily, capable of regulating cell growth by both IGF-dependent and IGF-independent mechanisms.insulin-like growth factor, insulin-like growth factor binding proteins.
Identification and characterization of the genes encoding the type 3 and type 1 fimbrial adhesins of Klebsiella pneumoniae (1989)

Strains of Klebsiella pneumoniae are known to express two morphologically and functionally distinct filaments, the type 3 and the type 1 fimbriae. The gene (mrkD) encoding the adhesion of K. pneumoniae type 3 fimbriae was identified by transcomplementation analysis with the pap fimbrial gene cluster of Escherichia coli. The nucleotide sequence of the mrkD gene was determined. In addition, the determinant coding for the K. pneumoniae type 1 fimbrial adhesion was identified, and its nucleotide sequence was deduced. The predicted amino acid sequences of the K. pneumoniae adhesion proteins are compared, and similarities with the major fimbrial structural proteins (MrkA and FimA) are discussed.
Microbial ecosystem and methanogenesis in ruminants (2010)

Ruminant production is under increased public scrutiny in terms of the importance of cattle and other ruminants as major producers of the greenhouse gas methane. Methanogenesis is performed by methanogenic archaea, a specialised group of microbes present in several anaerobic environments including the rumen. In the rumen, methanogens utilise predominantly H2 and CO2 as substrates to produce methane, filling an important functional niche in the ecosystem. However, in addition to methanogens, other microbes also have an influence on methane production either because they are involved in hydrogen (H2) metabolism or because they affect the numbers of methanogens or other members of the microbiota. This study explores the relationship between some of these microbes and methanogenesis and highlights some functional groups that could play a role in decreasing methane emissions. Dihydrogen ('H2' from this point on) is the key element that drives methane production in the rumen. Among H2 producers, protozoa have a prominent position, which is strengthened by their close physical association with methanogens, which favours H2 transfer from one to the other. A strong positive interaction was found between protozoal numbers and methane emissions, and because this group is possibly not essential for rumen function, protozoa might be a target for methane mitigation. An important function that is associated with production of H2 is the degradation of fibrous plant material. However, not all members of the rumen fibrolytic community produce H2. Increasing the proportion of non-H2 producing fibrolytic microorganisms might decrease methane production without affecting forage degradability. Alternative pathways that use electron acceptors other than CO2 to oxidise H2 also exist in the rumen. Bacteria with this type of metabolism normally occupy a distinct ecological niche and are not dominant members of the microbiota; however, their numbers can increase if the right potential electron acceptor is present in the diet. Nitrate is an alternative electron sinks that can promote the growth of particular bacteria able to compete with methanogens. Because of the toxicity of the intermediate product, nitrite, the use of nitrate has not been fully explored, but in adapted animals, nitrite does not accumulate and nitrate supplementation may be an alternative under some dietary conditions that deserves to be further studied. In conclusion, methanogens in the rumen co-exist with other microbes, which have contrasting activities. A better understanding of these populations and the pathways that compete with methanogenesis may provide novel targets for emissions abatement in ruminant production.
Development and Testing of Cool-Season Grass Species, Varieties and Hybrids for Biomass Feedstock Production in Western North America (2017)

Breeding of native cool-season grasses has the potential to improve forage production and expand the range of bioenergy feedstocks throughout western North America. Basin wildrye (Leymus cinereus) and creeping wildrye (Leymus triticoides) rank among the tallest and most rhizomatous grasses of this region, respectively. The objectives of this study were to develop interspecific creeping wildrye (CWR) × basin wildrye (BWR) hybrids and evaluate their biomass yield relative to tetraploid ‘Trailhead’, octoploid ‘Magnar’ and interploidy-hybrid ‘Continental’ BWR cultivars in comparison with other perennial grasses across diverse single-harvest dryland range sites and a two-harvest irrigated production system. Two half-sib hybrid populations were produced by harvesting seed from the tetraploid self-incompatible Acc:641.T CWR genet, which was clonally propagated by rhizomes into isolated hybridization blocks with two tetraploid BWR pollen parents: Acc:636 and ‘Trailhead’. Full-sib hybrid seed was also produced from a controlled cross of tetraploid ‘Rio’ CWR and ‘Trailhead’ BWR plants. In space-planted range plots, the ‘Rio’ CWR × ‘Trailhead’ BWR and Acc:641.T CWR × Acc:636 BWR hybrids displayed high-parent heterosis with 75% and 36% yield advantages, respectively, but the Acc:641.T CWR × ‘Trailhead’ BWR hybrid yielded significantly less than its BWR high-parent in this evaluation. Half-sib CWR × BWR hybrids of Acc:636 and ‘Trailhead’ both yielded as good as or better than available BWR cultivars, with yields similar to switchgrass (Panicum virgatum), in the irrigated sward plots. These results elucidate opportunity to harness genetic variation among native grass species for the development of forage and bioenergy feedstocks in western North America.
Mannheim Intima-Media Thickness Consensus (2004)

Intima-media thickness (IMT) is increasingly used in clinical trials as a surrogate end point for determining the success of interventions that lower risk factors for atherosclerosis. The necessity for unified criteria to distinguish early atherosclerotic plaque formation from thickening of IMT and to standardize IMT measurements is addressed in this consensus statement. Plaque is defined as a focal structure that encroaches into the arterial lumen of at least 0.5 mm or 50% of the surrounding IMT value or demonstrates a thickness of > or =1.5 mm as measured from the media-adventitia interface to the intima-lumen interface. Standard use of IMT measurements is recommended in all epidemiological and interventional trials dealing with vascular diseases to improve characterization of the population investigated. The consensus concludes that there is no need to 'treat IMT values' nor to monitor IMT values in individual patients apart from few exceptions. Although IMT has been suggested to represent an important risk marker, it does not fulfill the characteristics of an accepted risk factor. Standardized methods recommended in this consensus statement will foster homogenous data collection and analysis. This will help to improve the power of studies incorporating IMT measurements and to facilitate the merging of large databases for meta-analyses.
Integrated catheter for 3-d intracardiac echo cardiography and ultrasound ablation (2004)

A catheter device with integrated ultrasound imaging array and ultrasound ablation transducer is introduced. This device has been designed for use in interventional cardiac procedures in which the cardiac anatomy is first imaged using real-time three-dimensional (3-D) ultrasound, then ablated to treat arrhythmias. The imaging array includes 112 elements operating at 5.4 MHz arranged in a 2-D matrix. Individual elements have a bandwidth of 21% and an insertion loss of 80 dB. The array has an azimuth resolution of 12 degrees and an elevation resolution of 8.7 degrees. The ablation transducer is a concentric piezoelectric transducer PZT-4 ring (outside diameter (O.D.), 4.5 mm, inside diameter (I.D.), 3.1 mm) operating at 10 MHz that surrounds the imaging array. It can produce a spatial-peak, temporal-average intensity up to 16 W/cm2. The entire device fits into a 9 Fr lumen with a 14 Fr tip to accommodate the ablation ring. With this device we have imaged, in realtime 3-D, a variety of targets including wire phantoms, fixed sheep hearts, and fresh bovine tissue. The ablation ring has been used to heat tissue-mimicking rubber 14 degrees C, as well as create lesions in fresh bovine tissue.
Regio- and Chemoselective Multiple Functionalization of Chloropyrazine Derivatives. Application to the Synthesis of Coelenterazine (2009)

Successive regio- and chemoselective metalations of chloropyrazines using TMPMgCl x LiCl and TMPZnCl x LiCl furnish, after trapping with electrophiles, highly functionalized pyrazines in high yields. Application to a synthesis of coelenterazine, a bioluminescent natural product in jellyfish Aequorea victoria, in nine steps (9% overall yield) is reported.
Factors affecting the ultraviolet laser desorption of proteins (1989)

The production of high-mass quasimolecular ions from proteins by matrix-assisted ultraviolet laser desorption is described. A simple time-of-flight system using a Q-switched frequency-quadrupled Nd-YAG laser to desorb protein molecules is shown to have a mass range of up to 116,000 u by the observation of intact, singly charged quasimolecular ions from 700 fmol of beta-galactosidase subunit (mol.wt = 116,336 Da). Both positive- and negative-ion spectra of proteins are shown. Four new matrix materials, with properties as good as or better than nicotinic acid, are described. A mass resolution of approximately 500 (full width at half maximum definition) is demonstrated for proteins with mol.wt less than 20,000 Da. Product species, formed by fast photochemical reactions in the matrix, are observed to form adduct ions with protein molecules. These adduct ions are a significant cause of the observed broadness of protein quasimolecular ion peaks. The practical physical considerations in detection of large-mass quasimolecular ions from laser desorption, such as detector overloading, are discussed.
An Oral Formulation of Angiotensin-(1-7) Produces Cardioprotective Effects in Infarcted and Isoproterenol-Treated Rats (2011)

In this study we evaluated the cardiac effects of a pharmaceutical formulation developed by including angiotensin (Ang)-(1-7) in hydroxypropyl β-cyclodextrin (HPβCD), in normal, infarcted, and isoproterenol-treated rats. Myocardial infarction was produced by left coronary artery occlusion. Isoproterenol (2 mg/kg, IP) was administered daily for 7 days. Oral administration of HPβCD/Ang-(1-7) started immediately before infarction or associated with the first dose of isoproterenol. After 7 days of treatment, the rats were euthanized, and the Langendorff technique was used to analyze cardiac function. In addition, heart function was chronically (15, 30, 50 days) analyzed by echocardiography. Cardiac sections were stained with hematoxylin/eosin and Masson trichrome to evaluate cardiac hypertrophy and damage, respectively. Pharmacokinetic studies showed that oral HPβCD/Ang-(1-7) administration significantly increased Ang-(1-7) on plasma whereas with the free peptide it was without effect. Oral administration of HPβCD/Ang-(1-7) (30 μg/kg) significantly reduced the deleterious effects induced by myocardial infarction on systolic and diastolic tension, ±dT/dt, perfusion pressure, and heart rate. Strikingly, a 50% reduction of the infarcted area was observed in HPβCD/Ang-(1-7)-treated rats. Furthermore, HPβCD/Ang-(1-7) attenuated the heart function impairment and cardiac remodeling induced by isoproterenol. In infarcted rats chronically treated with HPβCD/Ang-(1-7), the reduction of ejection fraction and fractional shorting and the increase in systolic and diastolic left ventricular volumes observed in infarcted rats were attenuated. Altogether, these findings further confirm the cardioprotective effects of Ang-(1-7). More importantly, our data indicate that the HPβCD/Ang-(1-7) is a feasible formulation for oral administration of Ang-(1-7), which can be used as a cardioprotective drug.