gebhart/patrepeval huggingface dataset:
Latest Developments on Streptococcus Suis : An Emerging Zoonotic Pathogen: Part 1 (2014)

First International Workshop on Streptococcus suis, Beijing, China, 12-13 August 2013 The first international workshop on Streptococcus suis, which is an important swine pathogen and emerging zoonotic agent, took place in Beijing, jointly organized by the Faculty of Veterinary Medicine, University of Montreal, Canada and the National Institute for Communicable Disease Control and Prevention, China CDC. The aim of the meeting was to gather together, for the first time, more than 80 researchers working on S. suis, from countries including China, Canada, Japan, The Netherlands, Germany, Thailand, the UK and Vietnam. This article, the first of a two-part report on this First International Workshop, reviews current aspects of the epidemiology and population genomics of S. suis, covers public health concerns and discusses questions about S. suis serotyping and molecular diagnostics.
Polarization Anisotropy of DNA in Nanochannels (2008)

The local alignment of DNA stretched in nanofluidic channels is measured using polarization sensitive detection. With increased degree of stretching the polarization anisotropy increases both in the deGennes and the Odijk regime. The technique is expected to find use in studies of, for example, local conformational changes in polymer physics in confined spaces, studies of protein-DNA interactions and compactation of DNA.
λPMV: A Bacteriophage Vector Allowing Single-Step Retrieval of cDNAs Following Expression in Mammalian Cells (1988)

A general strategy has been developed for expression and rescue of cDNAs in mammalian cells. cDNA libraries are constructed in a new phage vector, lambda PMV, which contains simian virus 40 (SV40) early region promoter sequences for transcription of cDNA inserts, as well as a dominant-acting selectable marker neo. Efficient transfer of the cDNA library to mammalian cells can be achieved by phage particle-mediated transfection. Following selection in the antibiotic G418, cells expressing the phenotype of interest are identified and isolated. Rapid recovery of the transfected cDNA is achieved through cell fusion of the transduced cells with COS cells. Replication at the SV40 origin promotes excision of the integrated cDNA as small circular DNA, which after isolation in this form is used to transform bacteria to ampicillin resistance. To test this strategy, a cDNA encoding the human lymphocyte differentiation antigen CD8 was inserted into lambda PMV. CD8 expression on the surface of mouse L cells and the efficient recovery of full-length CD8 cDNA inserts confirm the feasibility of this system. It is anticipated that the single-step screening of libraries constructed in lambda PMV will allow for the isolation of rare cDNAs and will prove less laborious than methods currently available.
Identification of the First Human Glutaredoxin Pseudogene Localized to Human Chromosome 20qll.2 (2001)

Thiol-disulfide interchange reactions are one of the most important regulatory systems in cells. Two kinds of molecules are responsible for this process: non-protein low molecular weight thiols and thiol-containing proteins of higher molecular weight (Zlieger, 1985). Among the first type, glutathione arises as the most important reductant in cell, while thioredoxin (Trx), glutaredoxin (Grx) and protein disulfide isomer-ase (PDI) are the best known examples of regulatory proteins by thiol-disulfide interchange reactions (Holmgren, 1989). Thioredoxins and glutaredoxins share many common features like being small, heat-stable, globular proteins (around 12 kDa), with a similar tridimensional structure (thioredoxin fold) and both using NADPH as source of reducing equivalents (Holmgren, 1989). However, while the electron from NADPH is transferred to the flavoenzyme thioredoxin reductase that in turn reduces thioredoxin (the so-called thioredoxin system), glutaredoxin is reduced by the sequential transfer of reducing power from NADPH to glutathione reductase and glutathione (the so-called glutaredoxin system) (Holmgren, 1989). Once reduced, Trx and Grx can act as general disulfide oxidoreductases with preference shown by Trx for peptide substrates while Grx shows preference for low-molecular weight dithiol- containing molecules (Holmgren, 1989). Grx was initially discovered as an alternative hydrogen donor for the essential enzyme ribonucleotide reductase in a thioredoxin-deficient mutant of E. coli (Holmgren, 1976; Holmgren, 1979). Since then Grx has also been shown to be an electron donor for enzymes like adenosine 3′-phos- phate-5′-phosphosulfate reductase and methionine sulfoxide reductase, functions that Trx also displays (Holmgren, 1989). In addition, Grx has been implicated in deiodination of thyroxine to triiodothyronine and has shown dehydroascor- bate reductase activity that generates ascorbic acid which protects neutrophils against the deleterious effects of the respiratory burst (Goswami and Rosenberg, 1985; Park and Levine, 1996).
CXCL13 is a plasma biomarker of germinal center activity (2016)

Significantly higher levels of plasma CXCL13 [chemokine (C-X-C motif) ligand 13] were associated with the generation of broadly neutralizing antibodies (bnAbs) against HIV in a large longitudinal cohort of HIV-infected individuals. Germinal centers (GCs) perform the remarkable task of optimizing B-cell Ab responses. GCs are required for almost all B-cell receptor affinity maturation and will be a critical parameter to monitor if HIV bnAbs are to be induced by vaccination. However, lymphoid tissue is rarely available from immunized humans, making the monitoring of GC activity by direct assessment of GC B cells and germinal center CD4(+) T follicular helper (GC Tfh) cells problematic. The CXCL13-CXCR5 [chemokine (C-X-C motif) receptor 5] chemokine axis plays a central role in organizing both B-cell follicles and GCs. Because GC Tfh cells can produce CXCL13, we explored the potential use of CXCL13 as a blood biomarker to indicate GC activity. In a series of studies, we found that plasma CXCL13 levels correlated with GC activity in draining lymph nodes of immunized mice, immunized macaques, and HIV-infected humans. Furthermore, plasma CXCL13 levels in immunized humans correlated with the magnitude of Ab responses and the frequency of ICOS(+) (inducible T-cell costimulator) Tfh-like cells in blood. Together, these findings support the potential use of CXCL13 as a plasma biomarker of GC activity in human vaccine trials and other clinical settings.
ChemInform Abstract: Functional Hybrid Materials with Polymer Nanoparticles as Templates (2010)

Abstract Review: 104 refs.
1210: Reduced Activity of Afferent Neurons Innervating Urinary Bladder in Rats with Dibetic Cystopathy (2005)

You have accessJournal of UrologyDiscussed Poster, Tuesday, May 24, 2005, 1:00 - 5:00 pm1 Apr 20051210: Reduced Activity of Afferent Neurons Innervating Urinary Bladder in Rats with Dibetic Cystopathy Yukio Hayashi, Kazumasa Torimoto, Michael B. Chancellor, William C. de Groat, and Naoki Yoshimura Yukio HayashiYukio Hayashi More articles by this author , Kazumasa TorimotoKazumasa Torimoto More articles by this author , Michael B. ChancellorMichael B. Chancellor More articles by this author , William C. de GroatWilliam C. de Groat More articles by this author , and Naoki YoshimuraNaoki Yoshimura More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)35355-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1210: Reduced Activity of Afferent Neurons Innervating Urinary Bladder in Rats with Dibetic Cystopathy." The Journal of Urology, 173(4S), p. 328 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 173Issue 4SApril 2005Page: 328 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Yukio Hayashi More articles by this author Kazumasa Torimoto More articles by this author Michael B. Chancellor More articles by this author William C. de Groat More articles by this author Naoki Yoshimura More articles by this author Expand All Advertisement PDF DownloadLoading ...
In vitro testing protocols for the cruciate ligaments and ligament reconstructions (1998)

The techniques that have been used to characterize the biomechanical behavior of the knee, cruciate ligaments, and cruciate ligament replacements differ, making comparisons between studies difficult or, at times, impossible. Therefore, it is important to standardize the testing protocols and techniques that describe the biomechanical behavior of the knee and cruciate ligaments. This will allow investigators to express opinions with respect to the interpretation of data, rather than based on differences between testing techniques. Standardized techniques are proposed to locate the origins of the tibial and femoral coordinate systems, and thus, allow comparisons of knee kinematics (e.g., displacements and rotations) between investigations. Standard techniques that can be used to measure the load-displacement behavior of the knee are described, and important considerations that should be appreciated with respect to preparing and testing of the joint are summarized. It is important to evaluate the single cycle load-to-failure characteristics and the cyclic loading response of an anterior cruciate ligament graft, and techniques to evaluate cruciate ligament graft fixation are proposed. The strengths of different models to characterize the biomechanical behavior of the knee are reviewed.
On Using Page Cooccurrences for Computing Clickstream Similarity (2003)

Clickstream analysis provides valuable insight into the behavior of users and can be translated into better business opportunities and increased user satisfaction. A fundamental problem in clickstream analysis is the computation of the distance (or the similarity) between two clickstreams. While, there exists a considerable amount of literature which propose methods of computing path similarities, they rely on the edit distance or the related longest common subsequence to align the two clickstreams. The edit distance provides a least cost sequence of transformations that result in the two clickstreams to be identical. Often, measures of path similarity are defined on these “aligned” clickstreams. However, the replacement cost used in the “alignment” process used by the edit distance is assumed to be fixed and ignores the degree of similarity of the two page views. Proposed in this paper is a method for computing the replacement cost that is based on the assumption that the degree of similarity between two page views is proportional to their relative frequency of cooccurrence. We define a method, which includes the order of the sequence as well as the time spent on each page, for obtaining the replacement cost of two arbitrary web pages. Though less accurate than content based analysis, our experiments with data generated from a simulator as well as data from an actual web site show that our assumption is well founded and that the proposed method provides a fast and accurate method of computing the similarity between two page views.
Enigmatic Reservoir Properties Deciphered Using Petroleum System Modeling and Reservoir Fluid Geodynamics (2023)

Two adjacent reservoirs in offshore oil fields have been evaluated using extensive data acquisition across multiple disciplines; several surprising observations were made. Differing levels of biodegradation were measured in the nearly adjacent reservoirs, yet related standard geochemical markers are contradictory. Unexpectedly, the more biodegraded oil had less asphaltene content, and this reservoir had some heavy end deposition in the core but upstructure, not at the oil-water contact (OWC) as would be expected, especially with biodegradation. Wax appears to be an issue in the nonbiodegraded oil. These many puzzling observations, along with unclear connectivity, gave rise to uncertainties about field development planning. Combined petroleum systems and reservoir fluid geodynamic considerations resolved the observations into a single, self-consistent geo-scenario, the co-evolution of reservoir rock and fluids in geologic time. A spill-fill sequence of trap filling with biodegradation helps explain differences in biodegradation and wax content. A subsequent, recent charge of condensate, stacked in one fault block and mixed in the target oil reservoir in the second fault block, explains conflicting metrics of biodegradation between C7 vs. C16 indices. Asphaltene instability and deposition at the upstructure contact between the condensate and black oil, and the motion of this contact during condensate charge, explain heavy end deposition in core. Moreover, this process accounts for asphaltene dilution and depletion in the corresponding oil. Downhole fluid analysis (DFA) asphaltene gradients and variations in geochemical markers with seismic imaging clarify likely connectivity in these reservoirs. The geo-scenario provides a benchmark of comparison for all types of reservoir data and readily projects into production concerns. The initial apparent puzzles of this oil field have been resolved with a robust understanding of the corresponding reservoirs and development strategies.
In vitro translation of mRNA for arginine esterase, the major secretory protein of dog prostate, and in vitro processing of the translation product (1985)

Poly(A)+ rich RNA was isolated from prostate of adult dogs and translated in the rabbit reticulocyte lysate cell-free protein-synthesizing system. Two-dimensional gel electrophoresis of the translation products showed that a protein with a molecular weight of 31 000 was predominantly synthesized. This protein was immunoprecipitated with antibodies directed against purified arginine esterase from dog seminal plasma. mRNA isolated from the prostate of animals castrated for 1 or 2 weeks was unable to direct the synthesis of arginine esterase. However, the synthesis of the enzyme could be stimulated by androgens in castrated animals, presumably by increasing prostatic concentrations of arginine esterase mRNA. The single chain translation product could be further processed in vitro by the addition of dog pancreas microsomes and purified arginine esterase. This procedure yielded split chains of arginine esterase which had identical electrophoretic mobilities as seminal plasma enzyme by two-dimensional gel electrophoresis. When prostatic tissue slices were incubated with tunicamycin, the unglycosylated arginine esterase obtained had a lower molecular weight than the in vitro translation product, suggesting that a signal peptide had been removed in the living cells. These results indicate that arginine esterase processing may include the following steps: removal of a signal peptide, glycosylation, and splitting of the polypeptide chain by active arginine esterase in the secretory granules or outside the cell.
Plasma DCLK1 is a marker of hepatocellular carcinoma (HCC): Targeting DCLK1 prevents HCC tumor xenograft growth via a microRNA-dependent mechanism (2015)

Tumor stem cell marker Doublecortin-like kinase1 (DCLK1) is upregulated in several solid tumors. The role of DCLK1 in hepatocellular carcinoma (HCC) is unclear. We immunostained tissues from human livers with HCC, cirrhosis controls (CC), and non-cirrhosis controls (NCC) for DCLK1. Western blot and ELISA analyses for DCLK1 were performed with stored plasma samples. We observed increased immunoreactive DCLK1 in epithelia and stroma in HCC and CCs compared with NCCs, and observed a marked increase in plasma DCLK1 from patients with HCC compared with CC and NCC. Analysis of the Cancer Genome Atlas' HCC dataset revealed that DCLK1 is overexpressed in HCC tumors relative to adjacent normal tissues. High DCLK1-expressing cells had more epithelial-mesenchymal transition (EMT). Various tumor suppressor miRNAs were also downregulated in HCC tumors. We evaluated the effects of DCLK1 knockdown on Huh7.5-derived tumor xenograft growth. This was associated with growth arrest and a marked downregulation of cMYC, and EMT transcription factors ZEB1, ZEB2, SNAIL, and SLUG via let-7a and miR-200 miRNA-dependent mechanisms. Furthermore, upregulation of miR-143/145, a corresponding decrease in pluripotency factors OCT4, NANOG, KLF4, and LIN28, and a reduction of let-7a, miR-143/145, and miR-200-specific luciferase activity was observed. These findings suggest that the detection of elevated plasma DCLK1 may provide a cost-effective, less invasive tool for confirmation of clinical signs of cirrhosis, and a potential companion diagnostic marker for patients with cirrhosis and HCC. Our results support evaluating DCLK1 as a biomarker for detection and as a therapeutic target for eradicating HCC.
Electrical battery model for use in dynamic electric vehicle simulations (2008)

Simulation of electric vehicles, hybrid electric vehicles, and plug-in hybrid electric vehicles over driving schedules within a full dynamic hybrid and electric vehicle simulator requires battery models capable of predicting state-of-charge, I-V characteristics, and dynamic behavior of different battery types. A battery model capable of reproducing lithium-ion, nickel-metal hydride, and lead- acid I-V characteristics (with minimal model alterations) is proposed. A battery-testing apparatus was designed to measure the proposed parameters of the battery model for all three battery types and simulate driving schedules with a programmed source and load configuration. A multiple time-constant battery model was used for modeling lithium- ion batteries; verification of time constants in the seconds to minutes and hour ranges has been shown in numerous research articles and a time constant in the millisecond range is verified here with experiments. Lack of significant time constants in the millisecond range is validated through direct testing. A modeled capacity-rate effect within the state-of-charge determination portion of the proposed model is verified experimentally to ensure accurate prediction of battery state of charge after lengthy driving schedules. The battery model was programmed into a Matlab/Simulink environment and used as a power source for plug-in hybrid electric vehicle simulations. Results from simulations of lithium-ion battery packs show that the proposed battery model behaves well with the other subcomponents of the vehicle simulator; accuracy of the model and prediction of battery internal losses depends on the extent of tests performed on the battery used for the simulation. Extraction of model parameters and their dependence on temperature and cycle number is ongoing, as well as validation of the Simulink model with hardware- in-the-loop "driving schedule" cycling of real batteries.
Generalized Ambiguity Decomposition for Understanding Ensemble Diversity (2013)

Diversity or complementarity of experts in ensemble pattern recognition and information processing systems is widely-observed by researchers to be crucial for achieving performance improvement upon fusion. Understanding this link between ensemble diversity and fusion performance is thus an important research question. However, prior works have theoretically characterized ensemble diversity and have linked it with ensemble performance in very restricted settings. We present a generalized ambiguity decomposition (GAD) theorem as a broad framework for answering these questions. The GAD theorem applies to a generic convex ensemble of experts for any arbitrary twice-differentiable loss function. It shows that the ensemble performance approximately decomposes into a difference of the average expert performance and the diversity of the ensemble. It thus provides a theoretical explanation for the empirically-observed benefit of fusing outputs from diverse classifiers and regressors. It also provides a loss function-dependent, ensemble-dependent, and data-dependent definition of diversity. We present extensions of this decomposition to common regression and classification loss functions, and report a simulation-based analysis of the diversity term and the accuracy of the decomposition. We finally present experiments on standard pattern recognition data sets which indicate the accuracy of the decomposition for real-world classification and regression problems.
A Phase II, Prospective, Randomized, Multicenter, Open-Label Study of GX-188E, an HPV DNA Vaccine, in Patients with Cervical Intraepithelial Neoplasia 3 (2019)

GX-188E is an effective therapeutic vaccine against a cohort containing only CIN3 patients.
Forward-viewing EUS-guided esophageal repermeabilization (2022)

Complete esophageal obstruction with associated aphagia is a severe complication of of locoregionally advanced head and neck cancer. Endoscopic combined anterograde-retrograde rendezvous procedure with repermeabilization and dilatation has been increasingly adopted to manage it. However, in cases of a large gap between the proximal and distal esophagus and absence of transillumination, this classical approach is not possible. In this report, we describe a novel, relatively simple and safe method of endoscopic anterograde-retrograde rendezvous esophageal repermeabilization using forward-viewing endoscopic ultrasound (EUS). EUS allows clearly targeting of the lumen and puncture, avoiding potential interposed vessels. Specifically, this type of echoendoscope, designed with a short rigid portion and wide angulation capability that increases maneuverability and controlled visualization and puncture in the direct axis of the scope, has an additional advantage in cases such as ours, in which narrowing of both esophageal ends could hamper performance of a puncture with a regular side-viewing echoendoscope.
Activation of adenosine A2A receptor protects sympathetic neurons against nerve growth factor withdrawal (2004)

Adenosine mediates a range of effects in the central nervous system (CNS), including the promotion of neuronal survival, but its actions on sympathetic neurons are less well characterized. We therefore sought to understand the role of endogenous adenosine in contributing to the survival of neurotrophin-dependent sympathetic neurons. Rat superior cervical ganglion (SCG) cultures were maintained in the continuous presence of nerve growth factor (NGF) and then exposed to adenosine deaminase (ADA), to deplete endogenous adenosine. This resulted in a marked increase in cellular apoptosis, to a level that approximated the effect of NGF withdrawal. Furthermore, the addition of exogenous adenosine to NGF-deprived SCG neurons resulted in enhanced cell survival. Analysis of adenosine receptor (AR) subtypes on these neurons, using real-time RT-PCR and receptor binding analyses, revealed that the A2A receptor was the major subtype present. Accordingly, the A2A receptor agonist CGS21680 significantly reduced both ADA-induced and NGF-withdrawal-induced neuronal apoptosis, whereas the A1 receptor agonist R-PIA had no such effect. The survival-promoting effect of CGS21680 was eliminated when cells were coincubated with a molar excess of an A2A receptor antagonist. Finally, follow-up experiments revealed that CGS21680 prevented the induction of early apoptotic events, such as changes in mitochondrial integrity and caspase activation, and that it also triggered an increase in ERK activation, which was essential for neurotrophin-independent cell survival. Taken together, these findings provide evidence that endogenous adenosine may be important in mediating protection of sympathetic neurons and that it may act via the A2A receptor subtype.