gebhart/patrepeval huggingface dataset:
Seroepidemiology of Klebsiella bacteremic isolates and implications for vaccine development (1986)

The frequencies of capsular serotypes among 703 Klebsiella strains isolated from the blood of hospitalized patients were determined. More than 90% of the isolates were typeable, with 69 of the 77 known serotypes being identified. Serotypes 2, 21, and 55, representing 8.9, 7.8, and 4.8% of all the isolates, respectively, were observed at a frequency significantly higher (P less than 0.05) than that for other capsular serotypes. Approximately 43% of the serotypes appeared at a frequency of less than 0.5%. Differences were found when the seroepidemiology of North American and European isolates was compared. The current findings indicate that a capsular polysaccharide-based vaccine against Klebsiella organisms is feasible and should be multivalent, eliciting antibodies directed against the 25 serotypes which make up approximately 70% of all the bacteremic isolates.
Limited proteolysis of Cl‐inhibitor by chymotrypsin‐like proteinases (1989)

Limited proteolysis of C1-inhibitor was observed with human skin chymase, human cathepsin G, and bovine chymotrypsin. In each case, the inhibitor was degraded to one major product migrating slightly faster than the native inhibitor in an SDS-polyacrylamide gel. The inhibitory activity of C1-inhibitor against human plasma kallikrein was not altered by the modification with chymase. Edman degradation of the proteolyzed inhibitor revealed two sequences in a 1:1 ratio: NPNATSSSQ, the N-terminus of native C1-inhibitor, and VEPILEVSSL. This second sequence showed that the Phe33-Val34 bond was hydrolyzed. Our results provide another example of the susceptibility of the N-terminal region of C1-inhibitor to proteolytic cleavage.
Contraction of the Tropolonic Ring of Colchicine by Hydrogen Peroxide Oxidation (1984)

By hydrogen peroxide oxidation of colchicine the tropolonic ring underwent contraction to a benzene ring.Two compounds were obtained and identified (EIMS, 'H NMR) as N-acetylco1chinol methyl ether and 10-carbomethoxy-N-acetylcolchinol.Antimitotic activity is also reported.The tropolonic ring of colchicine (1) has been shown to suffer oxidative attack with chromic acid,lr2 or with aqueous sodium peroxide without ring contraction, the products obtained being 2 and 1 respectively.Oxidative attack of colchiceine (4) by hydrogen peroxide in alkaline medium has been reported to cause contraction of the tropolonic ring, the resulting compound being N-acetylcolchinol ( 5 ) .4Colchicine easily dissolved in 30% hydrogen peroxide and the homogeneous solution, when heated under magnetic stirring on an oil bath at 75-80 OC for 32 h, in a dim light, is transformed in a thick yellow oil which separated from the aqueous phase.Stirring at this point became difficult; at the same time, TLC revealed only traces of colchicine.The glassy oil was extracted with chloroform and passed through a short column of silica gel, with chloroform containing 2.5% methanol and 0.5% ammonia as the eluent, to remove impurities from the main fraction, which solidified after this passage.It gave only one spot on TLC on Si02 F254, CHC13-MeOH-NH40H 90:9:1, Rf 0.63 (corresponding Rf values were: 1, 0.48; 2, 0.55: 3, 0.58).When the same product was developed with CHC13-Me2CO-NH(Et)2 5:4:1, it gave two
Nodulation ofLupinus albusby Strains ofOchrobactrum lupinisp. nov (2005)

ABSTRACT The nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the α- Proteobacteria . However, in the last 3 years four nonrhizobial species, belonging to α and β subclasses of the Proteobacteria , have been described as legume-nodulating bacteria. In the present study, two fast-growing strains, LUP21 and LUP23, were isolated from nodules of Lupinus honoratus. The phylogenetic analysis based on the 16S and 23S rRNA gene sequences showed that the isolates belong to the genus Ochrobactrum . The strains were able to reinfect Lupinus plants. A plasmid profile analysis showed the presence of three plasmids. The nodD and nifH genes were located on these plasmids, and their sequences were obtained. These sequences showed a close resemblance to the nodD and nifH genes of rhizobial species, suggesting that the nodD and nifH genes carried by strain LUP21 T were acquired by horizontal gene transfer. A polyphasic study including phenotypic, chemotaxonomic, and molecular features of the strains isolated in this study showed that they belong to a new species of the genus Ochrobactrum for which we propose the name Ochrobactrum lupini sp. nov. Strain LUP21 T (LMG 20667 T ) is the type strain.
Physical State of HPV16 and Chromosomal Mapping of the Integrated Form in Cervical Carcinomas (2001)

Using a procedure based on restriction enzyme cleavage, self-ligation, and inverse polymerase chain reaction (rliPCR), the authors investigated 18 cervical intraepithelial neoplasia III (CIN III) cases and 37 invasive squamous carcinomas for integration of human papillomavirus type 16 (HPV16). All eighteen CIN III cases (severe dysplasia or high-grade squamous intraepithelial lesion) were found to harbor episomal HPV, but one of the samples contained mixed episomal and integrated forms. Seventeen of 37 invasive cervical carcinoma samples were identified previously as containing the completely integrated HPV16 genome by using PCR covering the entire E1/E2 gene, and this was confirmed by rliPCR in 16 cases. One case, however, showed a low level of episomal deoxyribonucleic acid in addition to the predominant integrated form. Of the remaining 20 carcinoma samples showing episomal forms in the previous analysis, 14 were found to contain integrated forms using rliPCR, and four contained multimeric episomal forms. Thus, in total, 31 of 37 of the carcinomas (84%) showed the integrated HPV16 genome. The rliPCR product from five carcinoma cases was cloned into a plasmid vector and used as a template for "primer walking" deoxyribonucleic acid sequencing to deduce human sequences flanking the integrated HPV genome. Based on this information, bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) clones were obtained and used as probes in fluorescent in situ hybridization experiments on human metaphase chromosomes. The results of the fluorescent in situ hybridization experiments showed evidence for HPV16 integration in chromosome regions 1q25, 3q28, 6p25, 11p13, and 18q22. Sixteen carcinoma samples, containing episomal HPV16, were sequenced in the long control region. Evidence for changes in E2 binding or silencer YY1 sequences was found in only two samples.
Prospective acquisition correction for head motion with image-based tracking for real-time fMRI (2000)

In functional magnetic resonance imaging (fMRI) head motion can corrupt the signal changes induced by brain activation. This paper describes a novel technique called Prospective Acquisition CorrEction (PACE) for reducing motion-induced effects on magnetization history. Full three-dimensional rigid body estimation of head movement is obtained by image-based motion detection to a high level of accuracy. Adjustment of slice position and orientation, as well as regridding of residual volume to volume motion, is performed in real-time during data acquisition. Phantom experiments demonstrate a high level of consistency (translation < 40 microm; rotation < 0.05 degrees ) for detected motion parameters. In vivo experiments were carried out and they showed a significant decrease of variance between successively acquired datasets compared to retrospective correction algorithms.
Adaptive History-Based Memory Schedulers (2005)

As memory performance becomes increasingly important to overall system performance, the need to carefully schedule memory operations also increases. This paper presents a new approach to memory scheduling that considers the history of recently scheduled operations. This history-based approach provides two conceptual advantages: (1) it allows the scheduler to better reason about the delays associated with its scheduling decisions, and (2) it allows the scheduler to select operations so that they match the program's mixture of Reads and Writes, thereby avoiding certain bottlenecks within the memory controller. We evaluate our solution using a cycle-accurate simulator for the recently announced IBM Power5. When compared with an in-order scheduler, our solution achieves IPC improvements of 10.9% on the NAS benchmarks and 63% on the data-intensive Stream benchmarks. Using microbenchmarks, we illustrate the growing importance of memory scheduling in the context of CMP's, hardware controlled prefetching, and faster CPU speeds.
Tryptophan biosynthesis in Saccharomyces cerevisiae: control of the flux through the pathway (1978)

Enzyme derepression and feedback inhibition of the first enzyme are the regulatory mechanisms demonstrated for the tryptophan pathway in Saccharomyces cerevisiae. The relative contributions of the two mechanisms to the control of the flux through the pathway in vivo were analyzed by (i) measuring feedback inhibition of anthranilate synthase in vivo, (ii) determining the effect of regulatory mutations on the level of the tryptophan pool and the flux through the pathway, and (iii) varying the gene dose of individual enzymes of the pathway at the tetraploid level. We conclude that the flux through the pathway is adjusted to the rate of protein synthesis by means of feedback inhibition of the first enzyme by the end product, tryptophan. The synthesis of the tryptophan enzymes could not be repressed below a basal level by tryptophan supplementation of the media. The enzymes are present in excess. Increasing or lowering the concentration of individual enzymes had no noticeable influencing on the overall flux to tryptophan. The uninhibited capacity of the pathway could be observed both upon relieving feedback inhibition by tryptophan limitation and in feedback-insensitive mutants. It exceeded the rate of consumption of the amino acid on minimal medium by a factor of three. Tryptophan limitation caused derepression of four of the five tryptophan enzymes and, as a consequence, led to a further increase in the capacity of the pathway. However, because of the large reserve capacity of the "repressed" pathway, tryptophan limitation could not be imposed on wild-type cells without resorting to the use of analogs. Our results, therefore, suggest that derepression does not serve as an instrument for the specific regulation of the flux through the tryptophan pathway.
Purification and Properties of Clostridiopeptidase B (Clostripain) (1968)

Abstract The proteolytic enzyme, clostridiopeptidase B (clostripain), from Clostridium histolyticum culture filtrates has been purified to apparent homogeneity as judged by ultracentrifugation, electrophoresis in polyacrylamide gels, immunodiffusion, and immunoelectrophoresis. The enzyme has an apparent molecular weight of 50,000 from sedimentation equilibrium studies. Optical rotatory dispersion studies suggest a low α-helical content. Clostridiopeptidase B exhibits proteolytic as well as amidase-esterase properties. The specificity is confined primarily to arginine residues, although hydrolysis proceeds to a minor degree in most lysine-containing substrates.
Genetic studies reveal that myristoylCoA:protein N‐myristoyltransferase is an essential enzyme in Candida albicans (1995)

MyristoylCoA:protein N-myristoyltransferase (Nmt) catalyses the co-translational, covalent attachment of myristate (C14:0) to the amino-terminal glycine residue of a number of eukaryotic proteins involved in cellular growth and signal transduction. The NMT1 gene is essential for vegetative growth of Saccharomyces cerevisiae. Studies were carried out to determine if Nmt is also essential for vegetative growth of the pathogenic fungus Candida albicans. A strain of C. albicans was constructed in which one copy of NMT was partially deleted and disrupted. A Gly-447-->Asp mutation was introduced into the second NMT allele. This mutation produced marked reductions in catalytic efficiency at 24 and 37 degrees C, as judged by in vitro kinetic studies of the wild-type and mutant enzymes which had been expressed in, and purified from, Escherichia coli. The growth characteristics of isogenic NMT/NMT, NMT/delta nmt, and nmt delta/nmtG447D C. albicans strains were assessed under a variety of conditions. Only the nmt delta/nmtG447D strain required myristate for growth. This was true at both 24 and 37 degrees C. Palmitate could not substitute for myristate. Incubation of nmt delta/nmtG447D cells at 37 degrees C in the absence of myristate resulted in cell death as observed by the inability to form colonies on media supplemented with 500 microM myristate. Studies in an immunosuppressed-mouse model of C. albicans infection revealed that the NMT/delta nmt strain produced 100% lethality within 7 d after intravenous administration while the isogenic nmt delta/nmtG447G strain produced no deaths even after 21 d. These observations establish that Nmt is essential for vegetative growth of C. albicans and suggest that inhibitors of this acyltransferase may be therapeutically useful fungicidal agents.
Late Failures of Devices Used for Endovascular Treatment of Abdominal Aortic Aneurysm: What Have We Learned and What is the Task for the Future? (2001)

Since their introduction in 1991, endografts for the exclusion of abdominal aortic aneurysms have evolved by "learning from failures." As significant device failure modes are reported, manufacturers modify device design to improve effectiveness and durability based on analysis of clinical results. This article summarizes what has been learned from a variety of device failures with a view toward understanding the implications for future activity in the continuing development of endovascular technology. Secondary interventions have been used to improve late outcomes of many devices. Long-term durability remains an issue because the limited data on follow-up beyond 3 or 4 years show gradually accumulating device failures in ways that were not anticipated. The future of successful endografting requires more and longer-term follow-up data, better understanding of the interaction between aortoiliac morphology and device design, improved imaging techniques, development of physiologic methods for endograft assessment, investigation of adjunctive measures to control the abdominal aortic aneurysm (AAA) sac environment, and expansion of the dialogue between clinicians and industry.
Toward a stem cell gene therapy for breast cancer (2009)

Current approaches for treatment of late-stage breast cancer rarely result in a long-term cure. In part this is due to tumor stroma that prevents access of systemically or intratumorally applied therapeutics. We propose a stem cell gene therapy approach for controlled tumor stroma degradation that uses the pathophysiologic process of recruitment of inflammatory cells into the tumor. This approach involves genetic modification of hematopoietic stem cells (HSCs) and their subsequent transplantation into tumor-bearing mice. We show that inducible, intratumoral expression of relaxin (Rlx) either by transplanting tumor cells that contained the Rlx gene or by transplantation of mouse HSCs transduced with an Rlx-expressing lentivirus vector delays tumor growth in a mouse model of breast cancer. The antitumor effect of Rlx was mediated through degradation of tumor stroma, which provided increased access of infiltrating antitumor immune cells to their target tumor cells. Furthermore, we have shown in a human/mouse chimeric model that genetically modified HSCs expressing a transgene can access the tumor site. Our findings are relevant for cancer gene therapy and immunotherapy.
Human Arsenic Methyltransferase (AS3MT) Pharmacogenetics (2006)

Arsenic contaminates ground water worldwide. Methylation is an important reaction in the biotransformation of arsenic. We set out to study the pharmacogenetics of human arsenic methyltransferase (AS3MT, previously CYT19). After cloning the human AS3MT cDNA, we annotated the human gene and resequenced its 5'-flanking region, exons, and splice junctions using 60 DNA samples from African-American (AA) and 60 samples from Caucasian-American (CA) subjects. We observed 26 single nucleotide polymorphisms (SNPs), including 3 non-synonymous cSNPs, as well as a variable number of tandem repeats in exon 1 within an area encoding the cDNA 5'-untranslated region. The nonsynonymous cSNPs included T860C (M287T) with frequencies of 10.8 and 10% in AA and CA subjects, respectively, as well as C517T (A173W) in one AA and C917T (T306I) in one CA sample. Haplotype analysis showed that Ile(306) was linked to Thr(287), so this double variant allozyme was also studied functionally. After expression in COS-1 cells and correction for transfection efficiency, the Trp(173) allozyme displayed 31%, Thr(287) 350%, Ile(306) 4.8%, and Thr(287)/Ile(306) 6.2% of the activity of the wild type (WT) allozyme, with 20, 190, 4.4, and 7.9% of the level of WT immunoreactive protein, respectively. Apparent K(m) values for S-adenosyl-l-methionine were 4.6, 3.1, and 11 mum for WT, Trp(173), and Thr(287) allozymes, with K(m) values for sodium arsenite with the same allozymes of 11.8, 8.9, and 4.5mum. The Ile(306) and Thr(287)/Ile(306) allozymes expressed too little activity for inclusion in the substrate kinetic studies. Expression of reporter gene constructs for the 5'-flanking region and the variable number of tandem repeats in the 5'-untranslated region demonstrated cell line-dependent variation in reporter gene expression, with shorter repeats associated with increased transcription in HepG2 cells. These results raise the possibility that inherited variation in AS3MT may contribute to variation in arsenic metabolism and, perhaps, arsenic-dependent carcinogenesis in humans.
Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue (2012)

We report a method for Selective Depletion of abundant RNA (SDRNA) species from Human total RNA isolated from formalin-fixed, paraffin-embedded (FFPE) tissue, here demonstrating removal of ribosomal and mitochondrial transcripts from clinical FFPE tissue RNA archived up to 20 years. Importantly, SDRNA removes 98% of targeted RNAs while preserving relative abundance profiles of non-targeted RNAs, enabling routine whole transcriptome analysis of clinically valuable archival tissue specimens by Next-Generation Sequencing.
Ammonia Capture in Porous Organic Polymers Densely Functionalized with Brønsted Acid Groups (2014)

The elimination of specific environmental and industrial contaminants, which are hazardous at only part per million to part per billion concentrations, poses a significant technological challenge. Adsorptive materials designed for such processes must be engendered with an exceptionally high enthalpy of adsorption for the analyte of interest. Rather than relying on a single strong interaction, the use of multiple chemical interactions is an emerging strategy for achieving this requisite physical parameter. Herein, we describe an efficient, catalytic synthesis of diamondoid porous organic polymers densely functionalized with carboxylic acids. Physical parameters such as pore size distribution, application of these materials to low-pressure ammonia adsorption, and comparison with analogous materials featuring functional groups of varying acidity are presented. In particular, BPP-5, which features a multiply interpenetrated structure dominated by <6 Å pores, is shown to exhibit an uptake of 17.7 mmol/g at 1 bar, the highest capacity yet demonstrated for a readily recyclable material. A complementary framework, BPP-7, features slightly larger pore sizes, and the resulting improvement in uptake kinetics allows for efficient adsorption at low pressure (3.15 mmol/g at 480 ppm). Overall, the data strongly suggest that the spatial arrangement of acidic sites allows for cooperative behavior, which leads to enhanced NH3 adsorption.
Determination of traces of phosphate by thin layer x-ray fluorescence (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of traces of phosphate by thin layer x-ray fluorescenceGhyslain. Dube, Gaston. Boulay, and Frank M. KimmerleCite this: Anal. Chem. 1976, 48, 13, 1950–1953Publication Date (Print):November 1, 1976Publication History Published online1 May 2002Published inissue 1 November 1976https://pubs.acs.org/doi/10.1021/ac50007a036https://doi.org/10.1021/ac50007a036research-articleACS PublicationsRequest reuse permissionsArticle Views75Altmetric-Citations5LEARN 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
CB2 receptors as new therapeutic targets for liver diseases (2007)

Cannabinoid type-1 (CB1) and type-2 (CB2) receptors belong to the family of G protein-coupled receptors and mediate biological effects of phyto-derived and endogenous cannabinoids. Whereas functions of CB1 receptor have been extensively studied, the CB2 receptor has emerged over the last few years as a critical player in regulation of inflammation, pain, atherosclerosis and osteoporosis. Therefore, although still at a preclinical stage, the development of selective CB2 molecules has gained of interest as new targets in drug discovery. Recent data have unravelled a key role of CB2 receptors during chronic and acute liver injury, including fibrogenesis associated to chronic liver diseases, ischaemia-reperfusion-induced liver injury, and hepatic encephalopathy associated to acute liver failure. This review summarizes the latest advances on the recently identified role of CB2 receptors in the pathophysiology of liver diseases.
The effect of cytochrome P450 metabolism on drug response, interactions, and adverse effects. (2007)

Cytochrome P450 enzymes are essential for the metabolism of many medications. Although this class has more than 50 enzymes, six of them metabolize 90 percent of drugs, with the two most significant enzymes being CYP3A4 and CYP2D6. Genetic variability (polymorphism) in these enzymes may influence a patient's response to commonly prescribed drug classes, including beta blockers and antidepressants. Cytochrome P450 enzymes can be inhibited or induced by drugs, resulting in clinically significant drug-drug interactions that can cause unanticipated adverse reactions or therapeutic failures. Interactions with warfarin, antidepressants, antiepileptic drugs, and statins often involve the cytochrome P450 enzymes. Knowledge of the most important drugs metabolized by cytochrome P450 enzymes, as well as the most potent inhibiting and inducing drugs, can help minimize the possibility of adverse drug reactions and interactions. Although genotype tests can determine if a patient has a specific enzyme polymorphism, it has not been determined if routine use of these tests will improve outcomes.