gebhart/patrepeval huggingface dataset:
Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage (2020)

The handling and treatment of biological samples is critical when characterizing the composition of the intestinal microbiota between different ecological niches or diseases. Specifically, exposure of fecal samples to room temperature or long term storage in deep freezing conditions may alter the composition of the microbiota. Thus, we stored fecal samples at room temperature and monitored the stability of the microbiota over twenty four hours. We also investigated the stability of the microbiota in fecal samples during a six month storage period at −80°C. As the stability of the fecal microbiota may be affected by intestinal disease, we analyzed two healthy controls and two patients with irritable bowel syndrome (IBS). We used high-throughput pyrosequencing of the 16S rRNA gene to characterize the microbiota in fecal samples stored at room temperature or −80°C at six and seven time points, respectively. The composition of microbial communities in IBS patients and healthy controls were determined and compared using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline. The composition of the microbiota in fecal samples stored for different lengths of time at room temperature or −80°C clustered strongly based on the host each sample originated from. Our data demonstrates that fecal samples exposed to room or deep freezing temperatures for up to twenty four hours and six months, respectively, exhibit a microbial composition and diversity that shares more identity with its host of origin than any other sample.
Optimization of Specimen-Handling Procedures for Accurate Quantitation of Levels of Human Immunodeficiency Virus RNA in Plasma by Reverse Transcriptase PCR (1998)

Human immunodeficiency virus type 1 (HIV-1) RNA levels in plasma are currently widely used clinically for prognostication and in monitoring antiretroviral therapy. Accurate and reproducible results are critical for patient management. To determine the effects of specimen collection and handling procedures on quantitative measurement of HIV-1 RNA, we compared anticoagulants and sample processing times. Whole blood was collected from 20 HIV-1-infected patients in EDTA, acid citrate dextrose (ACD), and heparin tubes, aliquoted, and stored at room temperature. Plasma was separated from whole-blood aliquots prepared at < or =1, 3, 6, 24, and 48 h postcollection and then stored at -70 degrees C until use. HIV-1 RNA levels were determined by the AMPLICOR HIV-1 MONITOR assay. Heparinized plasma samples, which were pretreated with heparinase prior to analysis, had the lowest baseline HIV-1 RNA levels. In the first 6 h, HIV-1 RNA levels decreased by 10, 20, and 31% in EDTA, ACD, and heparin tubes, respectively. From 6 to 48 h postcollection, HIV-1 RNA levels decreased in all anticoagulants, albeit at a slower, more consistent rate. Our results indicate that EDTA should be the anticoagulant of choice for plasma HIV-1 RNA measurement by reverse transcriptase PCR, but ACD tubes are acceptable if the plasma is separated within 6 h of blood collection. Caution must be applied in the interpretation of absolute HIV-1 RNA copy number values obtained with suboptimal specimen collection and processing procedures.
Progress in superconducting qubits from the perspective of coherence and readout (2013)

Superconducting qubits are Josephson junction-based circuits that exhibit macroscopic quantum behavior and can be manipulated as artificial atoms. Benefiting from the well-developed technology of microfabrication and microwave engineering, superconducting qubits have great advantages in design flexibility, controllability, and scalability. Over the past decade, there has been rapid progress in the field, which greatly improved our understanding of qubit decoherence and circuit optimization. The single-qubit coherence time has been steadily raised to the order of 10 to 100 μs, allowing for the demonstration of high-fidelity gate operations and measurement-based feedback control. Here we review recent progress in the coherence and readout of superconducting qubits.
Recent Advances in the Chemoenzymatic Synthesis of Carbohydrates and Carbohydrate Mimetics (1996)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRecent Advances in the Chemoenzymatic Synthesis of Carbohydrates and Carbohydrate MimeticsHarrie J. M. Gijsen, Lei Qiao, Wolfgang Fitz, and Chi-Huey WongView Author Information Department of Chemistry, The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, California 92037 Cite this: Chem. Rev. 1996, 96, 1, 443–474Publication Date (Web):February 1, 1996Publication History Received30 May 1995Revised31 August 1995Published online1 February 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/cr950031qhttps://doi.org/10.1021/cr950031qresearch-articleACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views3218Altmetric-Citations356LEARN 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 SUBJECTS:Aldehydes,Aldol reactions,Carbohydrates,Oligosaccharides,Peptides and proteins Get e-Alerts
Full field phase imaging using a harmonically matched diffraction grating pair based homodyne quadrature interferometer (2007)

In this letter, the authors present a novel quadrature interferometry method based on the use of a harmonically matched shallow grating pair. Unlike a simple beam splitter or single shallow grating, the grating pair can confer a nontrivial interference phase shift (other than 0° or 180°) between the output ports of the interferometer. Using the grating pair as the beam splitter/combiner, the authors implement a homodyne quadrature full field phase interferometer and demonstrate the system’s capability to acquire phase and amplitude images.
Flashproxy (2008)

It is now common for Web sites to use active Web content, such as Flash, Silverlight, or Java applets, to support rich, interactive applications. For many mobile devices, however, supporting active content is problematic. First, the physical resource requirements of the browser plug-ins that execute active content may exceed the capabilities of the device. Second, plug-ins are simply not available for many devices. Finally, active code and the plug-ins that execute it often contain security flaws, potentially exposing a user's device or private data to harm.
Isozeaxanthine: Chiralität und enantioselektive Synthese von (4R,4′R)‐Isozeaxanthin ((−)‐(4R, 4′R)‐β, β‐Carotin‐4,4′‐diol) (1982)

Isozeaxanthin: Chirality and Enantioselective Synthesis of (4 R ,4′ R )‐Isozeaxanthin ((−)‐(4 R ,4′ R )‐β, β‐Carotin‐4,4′‐diol) The absolute configuration of optically active isozeaxanthin was established by synthesis using (−)‐( R )‐4‐hydroxy‐β‐ionon ( 2 ) [18] as starting material.
An in vitro study of proximal femoral allograft strains in revision hip arthroplasty (1994)

Bone allografts are used frequently to replace bone stock subsequent to total hip arthroplasty. Revision of the failed hip replacement results in a complex structure of allograft bone, host bone and a metal femoral component. To evaluate the mechanics of the allograft-implant-host bone structure at the time of surgery, a strain gauge study was undertaken with six fresh/frozen human femora. Under defined loading conditions, cortical strain distributions were measured for five different cases: (1) normal bone, (2) bone with a femoral implant, (3) bone with the femoral component and an osteotomy at the mid-stem level of the implant (i.e. to stimulate the proximal allograft-host junction around the femoral stem), (4) bone with an osteotomy and an implant cemented into the 'allograft' (i.e. the proximal end of the femur), and (5) bone with an osteotomy and the implant cemented into both the proximal 'allograft' and the distal host bone. The results showed that, prior to making the osteotomy, proximal femoral strains were decreased with the insertion of a femoral stem. These strains were further decreased when an osteotomy had been made. This strain distribution did not change when the stem was cemented into the proximal 'allograft' bone, or cemented into the proximal 'allograft' and distal host bone. The decreases in strain for these test cases implied that the discontinuity between the bony segments caused an extended reduction in the tensile or compressive stresses transmitted through the cortices.(ABSTRACT TRUNCATED AT 250 WORDS)
A Bifunctional Air Electrode Catalyzed by Lead Ruthenate for Li-Air Batteries (2015)

The performance of a catalyst enforced commercially available gas diffusion layer (GDL) electrode was evaluated at different discharge rates and depths in non-aqueous Li-O 2 batteries. The lead ruthenate (PbRuO) powder with a pyrochlore structure was employed as the catalyst. The lead ruthenate pyrochlore was prepared using a direct soft template method and characterized by X-ray diffraction (XRD), nitrogen physisorption techniques and transmission electron microscopy (TEM). The charge/discharge capabilities of the PbRuO/Ketjenblack (KB) composite were studied in tetraethyleneglycol dimethyl ether (TEGDME) containing 1M lithium triflate. The results show that PbRuO/KB can enhance the cell performance at high charge/discharge rates. Moreover, at a current density of 0.1mA/cm 2 it significantly increases the cell cyclability. With a cut-off capacity of 1000 mAh/g (PbRuO/KB only) the cell reached 100 cycles. As such, lead ruthenate has the potential to be used as an efficient bifunctional electrocatalyst for non-aqueous Li-O 2 batteries.
Enzyme Fingerprints of Activity, and Stereo- and Enantioselectivity from Fluorogenic and Chromogenic Substrate Arrays (2002)

A series of stereochemically and structurally diverse fluorogenic and chromogenic substrates for hydrolytic enzymes has been synthesized and used to characterize enzyme activity profiles of esterases, lipases, proteases, peptidases, phosphatases, and epoxide hydrolases. The substrates used are particularly resilient to nonspecific reactions due to their mechanism of activation. The activities recorded with the individual substrates are therefore remarkably reproducible, and enable us to use the overall pattern of activity as a specific fingerprint for the enzyme sample. Fingerprints of activity, and enantio- and stereoselectivity are displayed as arrays of color-scale squares that are easily analyzed visually. Such fingerprints might be useful for quality control, enzyme discovery, and possibly for addressing the issue of functional convergence in enzymes.
A 12.5 GSample/s optical digital-to-analog converter with 3.8 effective bits (2004)

Optical techniques have the potential to overcome speed limitations: for digital-to-analog conversion. In this paper, we present a novel scheme for an optical digital-to-analog converter based on the coherent summation of optical phase-modulated signals. A first demonstration using commercial discrete components yielded in a 12.5 Gsample digital-to-analog converter with a nominal resolution of 6 bits and an effective number of bits (ENOB) of 3.8.
Conformation-sensitive gel electrophoresis for rapid detection of single-base differences in double-stranded PCR products and DNA fragments: evidence for solvent-induced bends in DNA heteroduplexes. (1993)

Several techniques have recently been developed to detect single-base mismatches in DNA heteroduplexes that contain one strand of wild-type and one strand of mutated DNA. Here we tested the hypothesis that an appropriate system of mildly denaturing solvents can amplify the tendency of single-base mismatches to produce conformational changes, such as bends in the double helix, and thereby increase the differential migration of DNA heteroduplexes and homoduplexes during gel electrophoresis. The best separations of heteroduplexes and homoduplexes were obtained with a standard 6% polyacrylamide gel polymerized in 10% ethylene glycol/15% formamide/Tris-taurine buffer. As predicted by the hypothesis of solvent-induced bends, when the concentration of either ethylene glycol or formamide was increased, the differential migration decreased. Also, single-base mismatches within 50 bp of one end of a heteroduplex did not produce differential migration. Sixty of 68 single-base mismatches in a series of PCR products were detected in some 59 different sequence contexts. The eight mismatches not detected were either within 50 bp of the nearest end of the PCR product or in isolated high-melting-temperature domains. Therefore, it was possible to predict in advance the end regions and sequence contexts in which mismatches may be difficult to detect. The procedure can be applied to any PCR products of 200-800 bp and requires no special equipment or preparation of samples.
[Canal laminoplasty with titanium miniplate re-implantation of vertebral lamina]. (2006)

The result demonstrates that canal laminoplasty with the titanium miniplate re-implantation of the vertebral lamina in lumbar spine can restore the normal anatomy, keep stability of the spine, and avoid adhesion and scar in the canal.
Zika Virus (I). Isolations and serological specificity (1952)

Journal Article Zika Virus (I). Isolations and serological specificity Get access G. W. A. Dick, G. W. A. Dick The National Institute for Medical Research, London, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar S. F. Kitchen, S. F. Kitchen Formerly staff member of the Division of Medicine and Public Health, The Rockefeller Foundation, New York, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar A. J. Haddow A. J. Haddow aFormerly staff member of International Health Division, The Rockefeller Foundation, New York, USAbFrom the Virus Research Institute, Entebbe, Uganda Search for other works by this author on: Oxford Academic PubMed Google Scholar Transactions of The Royal Society of Tropical Medicine and Hygiene, Volume 46, Issue 5, September 1952, Pages 509–520, https://doi.org/10.1016/0035-9203(52)90042-4 Published: 01 September 1952
The Hospital Anxiety And Depression Scale. (2003)

There is a need to assess the contribution of mood disorder, especially anxiety and depression, in order to understand the experience of suffering in the setting of medical practice. Most physicians are aware of this aspect of the illness of their patients but many feel incompetent to provide the patient with reliable information. The Hospital Anxiety And Depression Scale, or HADS, was designed to provide a simple yet reliable tool for use in medical practice. The term 'hospital' in its title suggests that it is only valid in such a setting but many studies conducted throughout the world have confirmed that it is valid when used in community settings and primary care medical practice. It should be emphasised that self-assessment scales are only valid for screening purposes; definitive diagnosis must rest on the process of clinical examination.
Architectural verification of processors using symbolic instruction graphs (2002)

High performance processor designs use techniques such as pipelining, multiple execution units, register renaming, bypass paths, and branch prediction to meet their goals. These techniques make them susceptible to design errors that are triggered only when executing complex sequences of instructions. We introduce a language called SIGL for specifying symbolic instruction graphs (SIGs) that can be used as templates for such test cases. SIGL allows specification of constraints in a high level template from which many test cases can be generated, all targeting some specific characteristic of a processor design. SIGL has been used successfully to check the conformance of various industrial processor designs to their architectural specifications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
MENTAL DEFICIENCY, 2nd ed (1967)

psycho-analysis will be of great interest to those con- cerned with the nature and theory of the treatment: but it is not easy reading.
Neutrophil Activation by Monomeric Interleukin-8 (1994)

Interleukin-8 (IL-8), a pro-inflammatory protein, has been shown by nuclear magnetic resonance (NMR) and x-ray techniques to exist as a homodimer. An IL-8 analog was chemically synthesized, with the amide nitrogen of leucine-25 methylated to selectivity block formation of hydrogen bonds between monomers and thereby prevent dimerization. This analog was shown to be a monomer, as assessed by analytical ultracentrifugation and NMR. Nevertheless, it was equivalent to IL-8 in assays of neutrophil activation, which indicates that the monomer is a functional form of IL-8.
Antibody Targeting of Stem Cells to Infarcted Myocardium (2006)

Hematopoietic stem cell (HSC) therapy for myocardial repair is limited by the number of stem cells that migrate to, engraft in, and proliferate at sites of injured myocardium. To alleviate this limitation, we studied whether a strategy using a bispecific antibody (BiAb) could target human stem cells specifically to injured myocardium and preserve myocardial function. Using a xenogeneic rat model whereby ischemic injury was induced by transient ligation of the left anterior descending artery (LAD), we determined the ability of a bispecific antibody to target human CD34+ cells to specific antigens expressed in ischemic injured myocardium. A bispecific antibody comprising an anti-CD45 antibody recognizing the common leukocyte antigen found on HSCs and an antibody recognizing myosin light chain, an organ-specific injury antigen expressed by infarcted myocardium, was prepared by chemical conjugation. CD34+ cells armed and unarmed with this BiAb were injected intravenously in rats 2 days postmyocardial injury. Immunohistochemistry studies showed that the armed CD34+ cells specifically localized to the infarcted region of the heart, colocalized with troponin T-stained cells, and colocalization with vascular structures. Compared to unarmed CD34+ cells, the bispecific antibody improved delivery of the stem cells to injured myocardium, and such targeted delivery was correlated with improved myocardial function 5 weeks after infarction (p < .01). Bispecific antibody targeting offers a unique means to improve the delivery of stem cells to facilitate organ repair and a tool to study stem cell biology.
SEL‐10 interacts with presenilin 1, facilitates its ubiquitination, and alters A‐beta peptide production (2002)

Mutations in the human presenilin genes (PS1 or PS2) have been linked to autosomal dominant, early onset Alzheimer's disease (AD). Presenilins, probably as an essential part of gamma-secretase, modulate gamma-cleavage of the amyloid protein precursor (APP) to the amyloid beta-peptide (Abeta). Mutations in sel-12, a Caenorhabditis elegans presenilin homologue, cause a defect in egg laying that can be suppressed by loss of function mutations in a second gene, SEL-10. SEL-10 protein is a homologue of yeast Cdc4, a member of the SCF (Skp1-Cdc53/CUL1-F-box protein) E2-E3 ubiquitin ligase family. In this study, we show that human SEL-10 interacts with PS1 and enhances PS1 ubiquitination, thus altering cellular levels of unprocessed PS1 and its N- and C-terminal fragments. Co-transfection of sel-10 and APP cDNAs in HEK293 cells leads to an alteration in the metabolism of APP and to an increase in the production of amyloid beta-peptide, the principal component of amyloid plaque in Alzheimer's disease.
A Thousand Frames in Just a Few Words: Lingual Description of Videos through Latent Topics and Sparse Object Stitching (2013)

The problem of describing images through natural language has gained importance in the computer vision community. Solutions to image description have either focused on a top-down approach of generating language through combinations of object detections and language models or bottom-up propagation of keyword tags from training images to test images through probabilistic or nearest neighbor techniques. In contrast, describing videos with natural language is a less studied problem. In this paper, we combine ideas from the bottom-up and top-down approaches to image description and propose a method for video description that captures the most relevant contents of a video in a natural language description. We propose a hybrid system consisting of a low level multimodal latent topic model for initial keyword annotation, a middle level of concept detectors and a high level module to produce final lingual descriptions. We compare the results of our system to human descriptions in both short and long forms on two datasets, and demonstrate that final system output has greater agreement with the human descriptions than any single level.
Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum (2008)

The rapidly evolving field of metabolomics aims at a comprehensive measurement of ideally all endogenous metabolites in a cell or body fluid. It thereby provides a functional readout of the physiological state of the human body. Genetic variants that associate with changes in the homeostasis of key lipids, carbohydrates, or amino acids are not only expected to display much larger effect sizes due to their direct involvement in metabolite conversion modification, but should also provide access to the biochemical context of such variations, in particular when enzyme coding genes are concerned. To test this hypothesis, we conducted what is, to the best of our knowledge, the first GWA study with metabolomics based on the quantitative measurement of 363 metabolites in serum of 284 male participants of the KORA study. We found associations of frequent single nucleotide polymorphisms (SNPs) with considerable differences in the metabolic homeostasis of the human body, explaining up to 12% of the observed variance. Using ratios of certain metabolite concentrations as a proxy for enzymatic activity, up to 28% of the variance can be explained (p-values 10 216 to 10 221 ). We identified four genetic variants in genes coding for enzymes (FADS1, LIPC, SCAD, MCAD) where the corresponding metabolic phenotype (metabotype) clearly matches the biochemical pathways in which these enzymes are active. Our results suggest that common genetic polymorphisms induce major differentiations in the metabolic make-up of the human population. This may lead to a novel approach to personalized health care based on a combination of genotyping and metabolic characterization. These genetically determined metabotypes may subscribe the risk for a certain medical phenotype, the response to a given drug treatment, or the reaction to a nutritional intervention or environmental challenge.