gebhart/patrepeval huggingface dataset:
Effect of liquid and solid test meals on symptoms and gastric myoelectrical activity in patients with gastroparesis and functional dyspepsia (2022)

The similarity in GMA responses and symptoms after ingestion of solid or liquid test meals suggests GP and FD are closely related gastric neuromuscular disorders.
Comparison of electron density properties in frozen and relaxed electronic distributions (2003)

Two kinds of electron densities for several small molecules (H(2), FH, CH(3)CH(3), CH(3)NH(2), CH(3)OH, and CH(3)F) have been generated for a wide range of bond distances. The first one, as the sum of the electron density of the isolated fragments, and the second one by optimizing the electron density at each given geometrical disposition. A number of properties of this two electronic distributions have been compared (position of the bond critical points, electron density, Laplacian, curvatures, and local energies). The differences, associated to the bond formation, are found to be very important for most of the cases.
Use of Current and New Endpoints in the Evaluation of Experimental Hepatitis B Therapeutics (2017)

New hepatitis B virus (HBV) therapies are expected to have breakthrough benefit for patients. HBV functional cure is sustained hepatitis B surface antigen loss and anti-HBs gain, with normalization of serum aminotransferases off therapy. Virologic or complete cure additionally includes loss of HBV covalently closed circular DNA. Currently available endpoints of therapy are inadequate to evaluate the efficacy of many of the new therapeutics. Therefore, either new ways of using the existing virologic endpoints and laboratory values or entirely new biomarkers are needed. In this review, we discuss the currently used endpoints, potential new endpoints, as well as what new markers are needed to assess the ability of HBV therapeutics to achieve functional and virologic cure in various phases of HBV infection. In addition, we discuss how patient selection from differing phases of HBV impacts the choice of HBV drug(s) needed to achieve cure.
Edge and top/bottom losses in non-inductive coated conductor coils with small separation between tapes (2010)

In this paper we consider two different finite-element models for computing ac losses in coils composed of coated conductors: a 2D model based on solving Maxwell's equations by means of edge elements and a 1D model based on solving the integral equations for the current density in the tapes. The models are tested for a configuration of practical interest, a non-inductive solenoidal coil for fault current limiter applications. We focused our attention on the conditions when differences between the two models are expected to emerge, for example when the tapes are closely packed or when the dependence of the critical current density on the local magnetic field is taken into account. We present and discuss several cases, offering possible explanations for the observed differences of ac loss values.
Nephrotoxicity ofN‐(3,5‐dihalophenyl)succinimides in fischer 344 rats (1987)

Previous studies have demonstrated that N-(3,5-dichlorophenyl)succinimide (NDCPS) is the most nephrotoxic compound among the N-(mono- or dichlorophenyl)succinimides. The purpose of this study was to examine the nephrotoxic potential of the different N-(3,5-dihalophenyl)succinimides (NDHPS) to determine the importance of the halogen species for NDHPS-induced nephrotoxicity. Male Fischer 344 rats were administered a single intraperitoneal injection of an NDHPS (0.4, 0.8, or 1.0 mmol/kg) or vehicle (2.5 ml/kg), and renal function was monitored at 24 and 48 h. NDCPS or N-(3,5-diiodophenyl)succinimide administration produced the greatest nephrotoxic response. Nephrotoxicity was characterized by diuresis, increased proteinuria, glucosuria, increased kidney weight and blood urea nitrogen (BUN) concentration, decreased accumulation of p-aminohippurate (PAH) and tetraethylammonium (TEA) by renal cortical slices and proximal tubular necrosis. N-(3,5-Dibromophenyl)succinimide injection produced mild nephrotoxicity, while N-(3,5,-difluorophenyl)succinimide administration did not result in nephrotoxicity. These results indicate that the halogen species can influence the nephrotoxicity produced by the NDHPS. In addition, nephrotoxic potential did not correlate with fungicidal efficacy, which suggests that the nephrotoxic and fungicidal mechanisms of these compounds might be different.
Clinical course and spectrum of intensive care unit patients reactivating herpes simplex-1 virus: A retrospective analysis (2008)

Identification of susceptible populations and definition of clinical features of HSV-1 related respiratory disease can enable diagnosis of HSV-1 infection in ICU patients. Although detection by a PCR technique can rapidly diagnose HSV-1 reactivation, prospective studies are required to clarify HSV disease versus mere shedding, and understand the impact of HSV-1 reactivation in hospitalized patients.
Coordinated Scheduling for the Downlink of Cloud Radio-Access Networks (2014)

This paper addresses the coordinated scheduling problem in cloud-enabled networks. Consider the downlink of a cloud-radio access network (C-RAN), where the cloud is only responsible for the scheduling policy and the synchronization of the transmit frames across the connected base-stations (BS). The transmitted frame of every BS consists of several time/frequency blocks, called power-zones (PZ), maintained at fixed transmit power. The paper considers the problem of scheduling users to PZs and BSs in a coordinated fashion across the network, by maximizing a network-wide utility under the practical constraint that each user cannot be served by more than one base-station, but can be served by one or more power-zone within each base-station frame. The paper solves the problem using a graph theoretical approach by introducing the scheduling graph in which each vertex represents an association of users, PZs and BSs. The problem is formulated as a maximum weight clique, in which the weight of each vertex is the benefit of the association represented by that vertex. The paper further presents heuristic algorithms with low computational complexity. Simulation results show the performance of the proposed algorithms and suggest that the heuristics perform near optimal in low shadowing environments
Arginine Biosynthesis Modulates Pyoverdine Production and Release in Pseudomonas putida as Part of the Mechanism of Adaptation to Oxidative Stress (2019)

Iron is essential for most life forms. Under iron-limiting conditions, many bacteria produce and release siderophores-molecules with high affinity for iron-which are then transported into the cell in their iron-bound form, allowing incorporation of the metal into a wide range of cellular processes. However, free iron can also be a source of reactive oxygen species that cause DNA, protein, and lipid damage. Not surprisingly, iron capture is finely regulated and linked to oxidative-stress responses. Here, we provide evidence indicating that in the plant-beneficial bacterium <i>Pseudomonas putida</i> KT2440, the amino acid l-arginine is a metabolic connector between iron capture and oxidative stress. Mutants defective in arginine biosynthesis show reduced production and release of the siderophore pyoverdine and altered expression of certain pyoverdine-related genes, resulting in higher sensitivity to iron limitation. Although the amino acid is not part of the siderophore side chain, addition of exogenous l-arginine restores pyoverdine release in the mutants, and increased pyoverdine production is observed in the presence of polyamines (agmatine and spermidine), of which arginine is a precursor. Spermidine also has a protective role against hydrogen peroxide in <i>P. putida</i>, whereas defects in arginine and pyoverdine synthesis result in increased production of reactive oxygen species.<b>IMPORTANCE</b> The results of this study show a previously unidentified connection between arginine metabolism, siderophore turnover, and oxidative stress in <i>Pseudomonas putida</i> Although the precise molecular mechanisms involved have yet to be characterized in full detail, our data are consistent with a model in which arginine biosynthesis and the derived pathway leading to polyamine production function as a homeostasis mechanism that helps maintain the balance between iron uptake and oxidative-stress response systems.
THE W. M. KECK OBSERVATORY INFRARED VORTEX CORONAGRAPH AND A FIRST IMAGE OF HIP 79124 B (2017)

ABSTRACT An optical vortex coronagraph has been implemented within the NIRC2 camera on the Keck II telescope and used to carry out on-sky tests and observations. The development of this new L ′-band observational mode is described, and an initial demonstration of the new capability is presented: a resolved image of the low-mass companion to HIP 79124, which had previously been detected by means of interferometry. With HIP 79124 B at a projected separation of 186.5 mas, both the small inner working angle of the vortex coronagraph and the related imaging improvements were crucial in imaging this close companion directly. Due to higher Strehl ratios and more relaxed contrasts in L ′ band versus H band, this new coronagraphic capability will enable high-contrast, small-angle observations of nearby young exoplanets and disks on a par with those of shorter-wavelength extreme adaptive optics coronagraphs.
Syntheses, Structure, and Selected Physical Properties of CsLnMnSe3 (Ln: Sm, Gd, Tb, Dy, Ho, Er, Tm, Yb, Y) and AYbZnQ3 (A: Rb, Cs; Q: S, Se, Te). (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
β-Hydroxyisovalerylshikonin promotes reactive oxygen species production in HCT116 colon cancer cells, leading to caspase-mediated apoptosis (2018)

Although -hydroxyisovalerylshikonin is suggested as a potential therapeutic agent for preventing various cancers, the underlying molecular mechanisms are not completely understood. In the present study, we investigated whether -hydroxyisovalerylshikonin enhances apoptosis by triggering reactive oxygen species production in colon cancer HCT116 cells. -Hydroxyisovalerylshikonin significantly inhibited the viability of HCT116 cells with maximum inhibition at 4 M. Furthermore, treatment with -hydroxyisovalerylshikonin subsequently increased sub-G 1 cells and annexin-V + cell population. Additionally, pretreatment with the caspase-8 inhibitor, z-IETD-fmk, and the caspase-9 inhibitor, z-LETD-fmk, significantly decreased -hydroxyisovalerylshikonin-induced apoptosis, suggesting that hydroxyisovalerylshikonin promotes apoptosis through both the intrinsic and the extrinsic apoptotic pathways by activating caspase-8 and caspase-9. We also found that mitochondria played an important role in -hydroxyisovalerylshikonin-mediated apoptosis via the intrinsic pathway. Accordingly, -hydroxyisovalerylshikonin-induced reactive oxygen species production was evident after treatment with -hydroxyisovalerylshikonin, and pretreatment with reactive oxygen species inhibitors, N-acetyl-l-cysteine and glutathione, significantly decreased -hydroxyisovalerylshikonin-induced reactive oxygen species production, resulting in inhibition of apoptosis, which suggests that ROS generation is required for -hydroxyisovalerylshikonin-mediated apoptosis. Taken together, these results demonstrated that the apoptotic effect of -hydroxyisovalerylshikonin is enhanced in colon cancer HCT116 cells via reactive oxygen species generation and triggering of the caspase pathways, indicating that -hydroxyisovalerylshikonin has potential as a therapeutic in the treatment of colon cancers.
Automating Your Existing Clinical Instruments (1997)

Laboratory automation systems (LAS) provide full automation of the pre-, peri-, and post-analytical specimen processing tasks in clinical laboratories. However, many existing instruments are difficult to interface, both mechanically and electronically, to specimen transportation systems. The AxSYM (Abbott Laboratories, Abbott Park, IL) analyzer is a popular method to perform immunoassay and toxicology measurements. In order for the large installed base of AxSYM instruments to take advantage of the efficiencies of automation, a prototype interface was developed for a popular LAS, the Coutler/IDS Model CLA (Coulter Corporation, Miami, FL). The automated instrument interface was designed for automatic loading and unloading of the AxSYM analyzer. The automated system can accept one or two AxSYM analyzers depending on the throughput and sample distribution needs of the laboratory. At the heart of the AxSYM automation is a CRS (Burlington, Ontario, Canada) robotic arm that is used to remove specimens from the model CLA, place them in an AxSYM sample tray, load the analyzer, and then automatically unload the finished specimens and return them to the Coulter/IDS. The system is projected to load and unload up to 200 specimens per hour from and to the conveyor system. While supporting automated loading, the system allows the AxSYM analyzer(s) to run manually loaded specimens. Minimal interfacing is required to install and operate the automated AxSYM so that the system can be up and running quickly. No physical connections are made to the Coulter/IDS thus simplifying installation and maintenance.
Novel Conantokins from Conus parius Venom Are Specific Antagonists of N-Methyl-D-aspartate Receptors (2007)

We report the discovery and characterization of three conantokin peptides from the venom of Conus parius. Each peptide (conantokin-Pr1, -Pr2, and -Pr3) contains 19 amino acids with three gamma-carboxyglutamate (Gla) residues, a post-translationally modified amino acid characteristic of conantokins. The new peptides contain several amino acid residues that differ from previous conantokin consensus sequences. Notably, the new conantokins lack Gla at the 3rd position from the N terminus, where the Gla residue is replaced by either aspartate or by another post-translationally modified residue, 4-trans-hydroxyproline. Conantokin-Pr3 is the first conantokin peptide to have three different post-translational modifications. Conantokins-Pr1 and -Pr2 adopt alpha-helical conformations in the presence of divalent cations (Mg2+ and Ca2+) but are generally unstructured in the absence of divalent cations. Conantokin-Pr3 adopts an alpha-helical conformation even in the absence of divalent cations. Like other conantokins, the new peptides induced sleep in young mice and hyperactivity in older mice upon intracranial injection. Electrophysiological assays confirmed that conantokins-Pr1, -Pr2, and -Pr3 are N-methyl-d-aspartate (NMDA) receptor antagonists, with highest potency for NR2B-containing NMDA receptors. Conantokin-Pr3 demonstrated approximately 10-fold selectivity for NR2B-containing NMDA receptors. However, conantokin-Pr2 showed minimal differences in potency between NR2B and NR2D. Conantokins-Pr1, -Pr2, and -Pr3 all demonstrated high specificity of block for NMDA receptors, when tested against various ligand-gated ion channels. Conus parius conantokins allow for a better definition of structural and functional features of conantokins as ligands targeting NMDA receptors.
Nonlinear particle behavior during cross-type optical particle separation (2009)

The effects of varying the ratio of the optical force to the viscous drag force, termed S, on cross-type optical particle separation were investigated experimentally to test previous theoretical predictions. The experiments were performed for various flow velocities, powers of the laser beam, and radii of the laser beam waist and the particles. The behaviors of the particles during optical separation were examined by measuring the retention distances and analyzing the particle trajectories. For small values of S, the particles move with constant velocity in the flow direction and the retention distance increases linearly with S. However, the particles accelerate and decelerate within the laser beam and the retention distance increases nonlinearly with S when S increases further.
Clinical Characteristics and Biopsy Specimen Features in African-American and White Men Without Prostate Cancer (1999)

No AccessJournal of UrologyUrological Survey: Abstracts: Benign and Malignant Neoplasms of Prostate1 Jan 1999Clinical Characteristics and Biopsy Specimen Features in African-American and White Men Without Prostate Cancer J.A. Eastham, R.A. May, T. Whatley, A. Crow, D.D. Venable, and O. Sartor J.A. EasthamJ.A. Eastham More articles by this author , R.A. MayR.A. May More articles by this author , T. WhatleyT. Whatley More articles by this author , A. CrowA. Crow More articles by this author , D.D. VenableD.D. Venable More articles by this author , and O. SartorO. Sartor More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(01)62147-5AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Clinical Characteristics and Biopsy Specimen Features in African-American and White Men Without Prostate Cancer." The Journal of Urology, 161(1), pp. 351–352 Departments of Urology and Hematology/Oncology, Louisiana State University Medical Center and Section of Urology, Overton Brooks Veterans Affairs Medical Center, Shreveport, Louisiana© 1999 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 161Issue 1January 1999Page: 351-352 Advertisement Copyright & Permissions© 1999 by American Urological Association, Inc.MetricsAuthor Information J.A. Eastham More articles by this author R.A. May More articles by this author T. Whatley More articles by this author A. Crow More articles by this author D.D. Venable More articles by this author O. Sartor More articles by this author Expand All Advertisement PDF downloadLoading ...
<title>Holographic memory with data file overlapping</title> (1996)

The noise effect on the storage density of a holographic carrier with data file overlapping is considered. The limit storage capacity for ID-hologram recording is calculated and investigated. The methods of increasing storage density by using multilayer carriers are studied.
Potential Impact of Adjusting the Threshold of the Quantitative D‐dimer Based on Pretest Probability of Acute Pulmonary Embolism (2009)

This large multicenter observational sample demonstrates that emergency medicine clinicians currently order a D-dimer in the majority of patients tested for PE, including a large proportion with intermediate PTP and high PTP. Varying the D-dimer's cutoff according to PTP can increase specificity with no measurable decrease in NPV.
Deoxyguanosine-Linked Bifunctional Inhibitor of SAMHD1 dNTPase Activity and Nucleic Acid Binding (2023)

Sterile alpha motif histidine-aspartate domain protein 1 (SAMHD1) is a deoxynucleotide triphosphohydrolase that exists in monomeric, dimeric, and tetrameric forms. It is activated by GTP binding to an A1 allosteric site on each monomer subunit, which induces dimerization, a prerequisite for dNTP-induced tetramerization. SAMHD1 is a validated drug target stemming from its inactivation of many anticancer nucleoside drugs leading to drug resistance. The enzyme also possesses a single-strand nucleic acid binding function that promotes RNA and DNA homeostasis by several mechanisms. To discover small molecule inhibitors of SAMHD1, we screened a custom ∼69 000-compound library for dNTPase inhibitors. Surprisingly, this effort yielded no viable hits and indicated that exceptional barriers for discovery of small molecule inhibitors existed. We then took a rational fragment-based inhibitor design approach using a deoxyguanosine (dG) A1 site targeting fragment. A targeted chemical library was synthesized by coupling a 5'-phosphoryl propylamine dG fragment (dGpC<sub>3</sub>NH<sub>2</sub>) to 376 carboxylic acids (RCOOH). Direct screening of the products (dGpC<sub>3</sub>NHCO-R) yielded nine initial hits, one of which (R = 3-(3'-bromo-[1,1'-biphenyl]), <b>5a</b>) was investigated extensively. Amide <b>5a</b> is a competitive inhibitor against GTP binding to the A1 site and induces inactive dimers that are deficient in tetramerization. Surprisingly, <b>5a</b> also prevented ssDNA and ssRNA binding, demonstrating that the dNTPase and nucleic acid binding functions of SAMHD1 can be disrupted by a single small molecule. A structure of the SAMHD1-<b>5a</b> complex indicates that the biphenyl fragment impedes a conformational change in the C-terminal lobe that is required for tetramerization.
Fragment-Based Discovery of an Apolipoprotein E4 (apoE4) Stabilizer. (2019)

Apolipoprotein E is a 299-residue lipid carrier protein produced in both the liver and the brain. The protein has three major isoforms denoted apoE2, apoE3, and apoE4 which differ at positions 112 and 158 and which occur at different frequencies in the human population. Genome-wide association studies indicate that the possession of two apoE4 alleles is a strong genetic risk factor for late-onset Alzheimer's disease (LOAD). In an attempt to identify a small molecule stabilizer of apoE4 function that may have utility as a therapy for Alzheimer's disease, we carried out an NMR-based fragment screen on the N-terminal domain of apoE4 and identified a benzyl amidine based fragment binder. In addition to NMR, binding was characterized using various other biophysical techniques, and a crystal structure of the bound core was obtained. Core elaboration ultimately yielded a compound that showed activity in an IL-6 and IL-8 cytokine release assay.
The gut microbiota and mucosal homeostasis (2013)

The intimate interplay between the gut microbiota and the host may contribute to health and disease in the host. Experiments using conventionalized and conventionally raised animal models have illustrated the role of the intestinal microbiota in shaping and maintaining the host immune system. However, it is still unclear whether colonization at birth or at adulthood induces different host responses. Here, we perform comparative transcriptome analyses to elucidate the impact of the gut microbiota on the development and maintenance of the immune system in adult conventionalized (after 16 and 30 days of colonization) and conventionally raised mice, which were obtained in two independent laboratories. Transcriptional profiles of jejunum, ileum and colon were compared between germfree, conventionally raised mice and conventionalized mice. Germfree mice from the two different facilities clustered together, establishing the validity of the comparative analysis. Nevertheless, significant spatial differences were detected along the gut; the jejunum and colon exhibited a transient response (conventionalized mice) that eventually returned to a homeostatic level (conventionally raised). In contrast, the ileal response to microbiota was similar in conventionalized and conventionally raised mice. Overall, this comparative analysis supports the hypothesis that co-development of the gut microbiota and its host initiates at early stage of development and indicates that despite the achieved homeostasis, immune development is substantially different in mice conventionalized in adulthood. These findings imply that colonization during development is required to meet the window of opportunity where the gut microbiota can imprint the host's mucosal immune-homeostasis in a way that cannot be achieved at later stages in life.
Density of States Simulations of Proteins, Liquid Crystals, and DNA (2003)

Three variations of the Wang‐Landau density of states (WLDOS) scheme are presented: 1) combining WLDOS with parallel tempering, 2) obtaining the density of states from the configurational temperature, and 3) performing DOS simulations in an expanded ensemble. Results for the folding of small peptides (methods 1 and 2), the behavior of liquid crystals around colloidal particles (method 3), and the hybridization of DNA base pairs (method 3) are presented.