gebhart/patrepeval huggingface dataset:
Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity (2007)

Lactobacillus casei strains are lactic acid bacteria (LAB) that colonize diverse ecological niches, and have broad commercial applications. To probe their evolution and phylogeny, 40 L. casei strains were characterized; the strains included isolates from plant materials (n=9), human gastrointestinal tracts (n=7), human blood (n=1), cheeses from different geographical locations (n=22), and one strain of unknown origin. API biochemical testing identified niche-specific carbohydrate fermentation profiles. A multilocus sequence typing (MLST) scheme was developed for L. casei. Partial sequencing of six housekeeping genes (ftsZ, metRS, mutL, nrdD, pgm and polA) revealed between 11 (nrdD) and 20 (mutL) allelic types, as well as 36 sequence types. Phylogenetic analysis of MLST data by Reticulate and split decomposition analysis indicated frequent intra-species recombination. Purifying selection was detected, and is likely to have contributed to the evolution of certain L. casei genes. Pulsed-field gel electrophoresis (PFGE) using SfiI was able to discriminate all the isolates, even those not differentiated by MLST. Phylogenetic trees reconstructed based on the MLST data using minimum evolution algorithm, and the SfiI-PFGE restriction patterns using the unweighted-pair group method with arithmetic mean (UPGMA), revealed consensus clusters of strains specific to cheese and silage. Topological discrepancies between the MLST and PFGE trees were also observed, suggesting that intragenic point mutations have accumulated at a slower rate than indels and genome rearrangements in L. casei. The L. casei population analysed in this study demonstrated both a high level of phenotypic and genotypic diversity, as well as specificity to different ecological niches.
Evaluation of a Virtual Reality Simulation System for Porcelain Fused to Metal Crown Preparation at Tokyo Medical and Dental University (2013)

The use of virtual reality simulation (VRS) is a new teaching modality in dentistry, and there is scope for further research evaluating its use under different educational programs. The purpose of this study was to evaluate how VRS with or without instructor feedback influenced students' learning and skills related to porcelain fused to metal (PFM) crown preparation. In this study, forty-three dental students in their fifth year of study at Tokyo Medical and Dental University, Tokyo, Japan, were randomly divided into three groups: the first group used VRS (DentSim) with the instructor's feedback (DSF) (n=15), the second group used VRS without the instructor's feedback (DS) (n=15), and the third group neither used features of VRS (NDS) (n=13) nor received the instructor's feedback. All the students performed PFM crown preparation under the same setup once a week for four weeks. Total scores, preparation time, and twelve evaluation items were compared among the three groups and four experiments. The total scores of students in the DSF and DS groups were significantly higher than those in the NDS group. The presence of the instructor did not result in significant difference when VRS was used for training, while it shortened the preparation time at early stages. The results of this study suggested that the use of the VRS system improved student training for PFM crown preparation.
Tunable couplers fabricated in K <sup>+</sup> /Na <sup>+</sup> ion exchanged glass (1990)

The characteristics of optical directional couplers fabricated in K+/Na+ ion exchanged glass are shown to be dependent on the refractive index of the overlayer material. This effect was experimentally observed using index matching oils, and electrical switching using liquid crystal overlayers was demonstrated.
A Fast and Reliable Policy Improvement Algorithm (2016)

We introduce a simple, efficient method that improves stochastic policies for Markov decision processes. The computational complexity is the same as that of the value estimation problem. We prove that when the value estimation error is small, this method gives an improvement in performance that increases with certain variance properties of the initial policy and transition dynamics. Performance in numerical experiments compares favorably with previous policy improvement algorithms.
Preliminary Results with the Design and Implementation of an Academic Management Information System (1984)

This paper provides an overview of aspects of an academic management information system (AMIS) at Creighton University's Academic Health Center. This report summarizes briefly some of the features of the system, our experiences in implementing it, some of the reactions from our academic community to a “foreign” body (and our attempts to reduce the rejection mechanism), as well as successes to date. Lastly we describe steps underway to expand the system into a full-fledged example of the system as envisioned in the Matheson and Cooper report on “Academic Information in the Academic Health Sciences Center.”
Anticoagulants in heart disease: current status and perspectives (2007)

Udgivelsesdato: 2007-Apr
Analysis by gas chromatography of fatty acids found in whole cultural extracts of <i>Neisseria</i> species (1971)

Sixty-five strains of Neisseria were tested. They included 12 species and several serogroups of N. meningitidis. A variety of acids, including keto acids, were detected by gas chromatography. Many of the acids detected have not been previously reported. Strains of N. meningitidis and N. catarrhalis were found to comprise a heterogeneous group. Cultures of N. flavescens, N. sicca, N. subflava, N. perflava, and N. cinerea produced acid patterns like N. meningitidis serogroup B. N. flava and N. mucosa were also like this group except that phenylpyruvic acid was detected in cultures of the former organisms. Strains of N. gonorrhoeae differed from strains of N. meningitidis in that acetic acid was produced, propionic acid was not used, and only a moderate amount of α-ketoisocaproic acid was detected. Strains of N. lactamicus, N. haemolysans, N. ovis, and N. catarrhalis also produced characteristic patterns that distinguished them from other species tested. The data indicate that criteria in addition to those now routinely used should be established to identify some members of the genus properly.
Inhibition of the multiplication of<i>Mycobacterium leprae</i>in nude mice by intermittent administration of a new rifamycin derivative, 3'-hydroxy-5'-(4-isobutyl-1-piperazinyl)benzoxazinorifamycin (KRM-1648) combined with sparfloxacin (1995)

Inhibition of the multiplication of Mycobacterium leprae in the footpads of nude mice by the oral administration of sparfloxacin, a new quinolone, and 3'-hydroxy-5'-(4-isobutyl-1-piperazinyl)benzoxazinorifamycin (KRM-1648), selected from a series of newly synthesized benzoxazinorifamycins, was studied. When the 2 drugs were administered alternately at intervals of 3 or 4 days, (i.e., each drug was administered once weekly), or simultaneously once weekly, between 3 and 5 months after inoculation of nude mice with M. leprae, 10 mg sparfloxacin and 0.6 mg KRM-1648 per kg bodyweight were sufficient to prevent multiplication of the organisms. Only partial inhibition of multiplication was achieved by alternate administration of 5 mg sparfloxacin and 0.3 mg KRM-1648 per kg, as was the case for 20 mg sparfloxacin per kg or 1 mg KRM-1648, each drug administered alone once weekly. The addition to these 2 drugs of dapsone, administered in the diet in a concentration of 0.001 g per 100 g, enhanced their effect. The potential usefulness of multidrug regimens including these compounds is considered.
Vaccination with dendritic cells loaded with allogeneic brain tumor cells for recurrent malignant brain tumors induces a CD4+IL17+ response (2014)

This first-in-human study shows that the GBM6-AD/DC vaccine was well tolerated and was associated with an immune response in a subset of patients. No MTD was achieved in this trial. This small-scale pilot provides information for larger scale investigations into the use of this allogeneic vaccine source.
TRANSFER PLASMAS DESTROY PCB FLUIDS (1988)

High voltage, ac transfer arcs were used as a reaction zone to destroy polychlorinated biphenyls dissolved in transformer fluid. The extremely high temperature of the arc is of sufficient magnitude that it destroys both the PCB's and the oil in which the PCB's are dissolved. Although fast pyrolysis is the major destructive mechanism, several other features of the process are unique. For example, the transfer arc discharge is submerged. The arc is created beneath the surface of the transformer oil at a water interface. Furthermore, the water phase is part of the electrical circuit; but it also participates in the reaction chemistry of the plasma arc. Water vapor created by the discharge reacts with the carbon and acetylene formed by pyrolysis to produce hydrogen and carbon monoxide. This retards carbon buildup within the system. The presence of the water phase also provides a convenient adsorption medium for acid gases (HC1) which are formed by pyrolysis of the PCB's, These gases are infinitely more soluble in the water phase than they are in the transformer oil through which they would have to pass to escape the submerged reaction zone. As a result, this new technology provides a convenient small-scale destruction for oils contaminated with PCB
Relative photoelectron signal intensities obtained with a magnesium x-ray source (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRelative photoelectron signal intensities obtained with a magnesium x-ray sourceHerve. Berthou and Christian K. JorgensenCite this: Anal. Chem. 1975, 47, 3, 482–488Publication Date (Print):March 1, 1975Publication History Published online1 May 2002Published inissue 1 March 1975https://pubs.acs.org/doi/10.1021/ac60353a023https://doi.org/10.1021/ac60353a023research-articleACS PublicationsRequest reuse permissionsArticle Views92Altmetric-Citations96LEARN 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
Decomposition of pyridine-2- and -4-diazotates (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDecomposition of pyridine-2- and -4-diazotatesClifford A. Bunton, Michael J. Minch, and Barry B. WolfeCite this: J. Am. Chem. Soc. 1974, 96, 10, 3267–3275Publication Date (Print):May 1, 1974Publication History Published online1 May 2002Published inissue 1 May 1974https://pubs.acs.org/doi/10.1021/ja00817a040https://doi.org/10.1021/ja00817a040research-articleACS PublicationsRequest reuse permissionsArticle Views325Altmetric-Citations9LEARN 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
The Molecular Mechanism of Peptide-mediated Erythromycin Resistance (2006)

The macrolide antibiotic erythromycin binds at the entrance of the nascent peptide exit tunnel of the large ribosomal subunit and blocks synthesis of peptides longer than between six and eight amino acids. Expression of a short open reading frame in 23 S rRNA encoding five amino acids confers resistance to erythromycin by a mechanism that depends strongly on both the sequence and the length of the peptide. In this work we have used a cell-free system for protein synthesis with components of high purity to clarify the molecular basis of the mechanism. We have found that the nascent resistance peptide interacts with erythromycin and destabilizes its interaction with 23 S rRNA. It is, however, in the termination step when the pentapeptide is removed from the peptidyl-tRNA by a class 1 release factor that erythromycin is ejected from the ribosome with high probability. Synthesis of a hexa- or heptapeptide with the same five N-terminal amino acids neither leads to ejection of erythromycin nor to drug resistance. We propose a structural model for the resistance mechanism, which is supported by docking studies. The rate constants obtained from our biochemical experiments are also used to predict the degree of erythromycin resistance conferred by varying levels of resistance peptide expression in living Escherichia coli cells subjected to varying concentrations of erythromycin. These model predictions are compared with experimental observations from growing bacterial cultures, and excellent agreement is found between theoretical prediction and experimental observation.
Strain-Related Bone Remodeling in Distraction Osteogenesis of the Mandible (1999)

Distraction osteogenesis has become a mainstay in craniofacial surgery. However, there are several unresolved problems concerning the biology of bone regeneration. We investigated the biomechanical effects of mandibular lengthening in 32 rabbits on a cellular and histologic level. The mandible was subjected to a corticotomy, held in a neutral position for 4 days, and then lengthened at various strain rates and frequencies for 10 days. Radiographic, histologic, and electron microscopic examinations showed a strain-related bone regeneration. Application of physiologic strain rates (2000 microstrains or 0.2 percent) led to a bridging of the artificial fracture exhibiting woven ossification, whereas at 20,000 microstrains trabecular bone formation was demonstrated. In contrast, hyperphysiologic strain magnitudes (200,000 microstrains and 300,000 microstrains) showed a fibrous tissue formation. Multiple strain applications (10 cycles/day versus 1 cycle/day) increased the width of the distraction gap without changing the stage of bone regeneration. The gradual distraction of bone in physiologic magnitudes at higher frequencies seems to be desirable for a bony differentiation and may help to improve clinical applications.
Recombinant von Willebrand factor Arg578–>Gln. A type IIB von Willebrand disease mutation affects binding to glycoprotein Ib but not to collagen or heparin. (1992)

von Willebrand factor (vWF) is a multimeric plasma glycoprotein that mediates platelet adhesion to the subendothelium via binding to platelet glycoprotein Ib (GPIb) and to components of the vessel wall. Recently, missense mutations that cause type IIB von Willebrand disease (vWD) were described, clustered within a disulfide loop in the A1 domain of vWF that has binding sites for GPIb, collagen, and heparin. In type IIB vWD, plasma vWF exhibits increased affinity for platelet GPIb, but decreased binding to collagen and heparin. The effect was studied of a type IIB vWD mutation, Arg578-->Gln, on the interaction of vWF with GPIb, collagen, and heparin. Recombinant wild type rvWF and mutant rvWF(R578Q) were expressed in COS-7 cells. Ristocetin-induced binding of rvWF(R578Q) to GPIb was markedly increased compared with rvWF, confirming that the Arg578-->Gln mutation causes the characteristic gain-of-function abnormality of type IIB vWD; botrocetin-induced binding was only slightly increased. Binding to collagen type III and heparin-agarose was compared for rvWF(R578Q) and plasma vWF from patients with four different type IIB mutations: Arg543-->Trp, Arg545-->Cys, Val553-->Met, Arg578-->Gln. For all of the plasma samples, binding to collagen and to heparin was reduced compared with normal plasma. In contrast, binding of rvWF(R578Q) to collagen and heparin was normal compared with wild type rvWF. Therefore, the Arg578-->Gln mutation increases the affinity of vWF for GPIb but does not directly impair vWF interaction with collagen or heparin. Arg578 may therefore be necessary to prevent normal vWF from interacting with GPIb. In type IIB vWD, the defective binding of plasma vWF to collagen and heparin may be secondary to post-synthetic modifications that occur in vivo, such as the loss of high molecular weight vWF multimers.
Hexsyn Trileaflet Valve: Application to Temporary Blood Pumps (1982)

A trileaflet valve, compression molded of Hexsyn rubber, was evaluated as a component in temporary blood pumps. A pair of valves was integrated into an LVAD which was tested in vitro and in vivo. The valve's hemodynamic performance was satisfactory and the blood compatibility was excellent in a three-week, in vivo experiment conducted to demonstrate performance in a short-term application. Hexsyn, which has excellent properties and produces high quality, complex components with ease of fabrication, offers a potential for low-cost blood pump valves.
Via design optimisation for high speed device packaging (2002)

This paper presents the design and electrical characterization of a circular via hole applied to single and multi chip modules. A typical strip line-to-strip line configuration incorporating the via hole is designed, modelled and simulated using the Maxwell Strata mixed potential integration equation (MPIE)-based field solver. This configuration is modelled on a practical user-defined transmission line structure consisting of conductors of finite conductivity. We investigated the effects of three critical parameters, via hole diameter, ground plane opening and via height, on the frequency response. It is found that the via hole diameter should be minimized while the other two parameters should be maximized for better performance. This paper thus provides useful optimization criteria for circular vias, given the practical limitations of manufacturing technologies.
Cytolytic activity of antigen-specific T cells with helper phenotype. (1986)

We have investigated an unusual cytolytic activity displayed in vitro by cloned T cells which have the cell surface phenotype of helper T cells. When the cloned T cells are cultured with the appropriate antigen and antigen-presenting cells (APC), the T cells become activated in that they produce lymphokines and proliferate in an antigen-specific and major histocompatibility complex-restricted manner. At the same time, these T cells cause lysis of the APC. In addition, innocent non-histocompatible bystander cells present in the cultures can also be killed. The cytolytic activity may be involved in a mechanism of immune regulation.
Study of ketone body kinetics in children by a combined perfusion of 13C and 2H3 tracers (1987)

Ketone body kinetics were quantified in six children (3-5 yr old), who were fasted for 13-22 h, by a combined perfusion of [3-13C]acetoacetate ([13C]AcAc) and D-(-)-beta-[4,4,4-2H3]hydroxybutyrate (beta-[2H3]OHB) and gas chromatography-mass spectrometry analysis. Results were analyzed according to the "single-pool" (combined enrichments) or the "two-accessible pools" models. After 20-22 h of fasting, ketone body turnover rate was 30-50 mumol.kg-1.min-1, a rate achieved after several days of fasting in adults. At low ketosis, acetoacetate was the ketone body preferentially synthesized de novo and utilized irreversibly. When ketosis increased, acetoacetate irreversible disposal was not enhanced, since it was largely converted into beta-OHB, whereas beta-OHB irreversible disposal was very much increased. The single-pool and two-pool models gave similar ketone body turnover rates when [13C]AcAc was the tracer, whereas the use of beta-[2H3]OHB gave some more divergent results, especially at low ketosis. These studies demonstrate that ketogenesis is very active in short-term fasted children and that the use of a combined infusion of [13C]AcAc and beta-[2H3]OHB is a convenient way to give insight into individual ketone body kinetics.
Polarization-sensitive optical coherence tomography based on polarization-maintaining fibers and frequency multiplexing (2008)

We report a novel polarization-maintaining fiber based optical coherence tomography for single detector imaging of tissue reflectivity and birefringence. A single depth scan yields quantitative birefringence information along the A-line accurately. Since the orthogonal polarization channels are frequency multiplexed, the polarization information is extracted by using digital band-pass filters. Here, we introduce the optical system and present the reflectivity and birefringence images of biological tissues with an axial resolution of 7.9 microm and SNR of 30 dB.
Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis (2011)

Phosphoryl-transfer reactions are central to biology. These reactions also have some of the slowest nonenzymatic rates and thus require enormous rate accelerations from biological catalysts. Despite the central importance of phosphoryl transfer and the fascinating catalytic challenges it presents, substantial confusion persists about the properties of these reactions. This confusion exists despite decades of research on the chemical mechanisms underlying these reactions. Here we review phosphoryl-transfer reactions with the goal of providing the reader with the conceptual and experimental background to understand this body of work, to evaluate new results and proposals, and to apply this understanding to enzymes. We describe likely resolutions to some controversies, while emphasizing the limits of our current approaches and understanding. We apply this understanding to enzyme-catalyzed phosphoryl transfer and provide illustrative examples of how this mechanistic background can guide and deepen our understanding of enzymes and their mechanisms of action. Finally, we present important future challenges for this field.
Water-quality data for pharmaceuticals, hormones, and other organic wastewater contaminants in U.S. streams, 1999-2000 (2002)

Water-quality data collected during 1999 and 2000 as part of the first nationwide reconnaissance of the occurrence of pharmaceuticals, hormones, and other organic wastewater contaminants (OWCs) are presented in this report. A network of 139 streams in 30 states were sampled and analyzed for 95 different OWCs using five new research methods developed by the U.S. Geological Survey. Site selection was biased toward streams more susceptible to OWC contamination because of proximity to urban areas or livestock production. At least one OWC was detected in 80% of the streams sampled, with 82 of the 95 analyzed OWCs determined in this study detected in at least one sample.