gebhart/patrepeval huggingface dataset:
The Gut Microbiome Associates with Immune Checkpoint Inhibition Outcomes in Patients with Advanced Non–Small Cell Lung Cancer (2020)

The gut microbiome (GM) plays an important role in shaping systemic immune responses and influences immune checkpoint inhibitor (ICI) efficacy. Antibiotics worsen clinical outcomes in patients receiving ICI. However, whether GM profiling and baseline antibiotic can be a biomarker of ICI efficacy in advanced non-small cell lung cancer (NSCLC) remains unknown. We prospectively collected baseline (pre-ICI) fecal samples and clinical data of 70 Japanese patients suffering from advanced NSCLC and treated them with anti-PD-1/PD-L1 antibodies as a first-line or treatment-refractory therapy. We performed 16S rRNA V3-V4 sequencing of gene amplicons of fecal samples, and bacteria diversity and differential abundance analysis was performed. The clinical endpoints were objective response rate (ORR), progression-free survival (PFS), overall survival (OS), and immune-related adverse events (irAE). ORR was 34%, and median PFS and OS were 5.2 and 16.2 months, respectively. Patients who received pre-ICI antibiotic had lower alpha diversity at baseline and underrepresentation of <i>Ruminococcaceae</i> UCG 13 and <i>Agathobacter</i> When analyzing antibiotic-free patients, alpha diversity correlated with OS. In addition, <i>Ruminococcaceae</i> UCG 13 and <i>Agathobacter</i> were enriched in patients with favorable ORR and PFS >6 months. <i>Ruminococcaceae</i> UCG 13 was enriched in patients with OS >12 months. GM differences were observed between patients who experienced low- versus high-grade irAE. We demonstrated the negative influence of antibiotic on the GM composition and identified the bacteria repertoire in patients experiencing favorable responses to ICI.<i>See articles by Tomita et al., p. 1236, and Peng et al., p. 1251</i>.
poly(4,4′‐oxybibenzoate): Polymerization, morphology, transitions, and crystal structures (1993)

Abstract 4‐Acetoxy 4′‐carboxy biphenyl has been polymerized from solution, the bulk melt, and in constrained thin films, all below the melting point of the monomer as measured by differential scanning calorimetry (DSC). An isothermal sublimation–recrystallization–melting (and chemical change)–polymerization–crystallization process is proposed. From solution and in the thin films, single crystals consisting of ca. 100 Å thick lamellae are observed, with evidence for monomer addition–reaction on the end (top and bottom) surfaces. The bulk samples are fibrous, the “fibers” consisting of whisker‐like single crystals. The polymer is highly heat and radiation (electron beam) resistant, with numerous successive electron diffraction (ED) patterns from the same crystal or sheared sample permitting comparison of the changes in ED patterns with transitions seen by DSC at ca. 350, 530, and 590°C. Phase I ( a = 7.8, b = 5.5, c = 10.8 Å), a possible phase II ( a = 15.6, b = 3.6 Å c = unknown), and a phase III ( a = 9.0, b = 5.2 = √3 a , c = 10.8 Å). Phases I and II are seen in samples polymerized at temperatures at and below 310°C; phase III is observed in samples polymerized at and above 350°C and in sheared samples. © 1993 John Wiley &amp; Sons, Inc.
TSXProf: Profiling Hardware Transactions (2015)

The availability of commercial hardware transactionalmemory (TM) systems has not yet been met with a rise in the numberof large-scale programs that use memory transactions explicitly. Asignificant impediment to the use of TM is the lack of tool support, specifically profilers that can identify and explain performance anomalies. In this paper, we introduce an end-to-end system that enables lowoverheadperformance profiling of large-scale transactional programs. We present algorithms and an implementation for Intel's Haswellprocessors. With our system, it is possible to record a transactionalprogram's execution with minimal overhead, and then replay it withina custom profiling tool to identify causes of contention and aborts, down to the granularity of individual memory accesses. Evaluationshows that our algorithms have low overhead, and our tools enableprogrammers to effectively explain performance anomalies.
Encapsulating 111In in Nanocontainers for Scintigraphic Imaging: Synthesis, Characterization, and In Vivo Biodistribution (2010)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionEncapsulating 111In in Nanocontainers for Scintigraphic Imaging: Synthesis, Characterization, and In Vivo BiodistributionManuel M. Tsotsalas, Klaus Kopka, Gianluigi Luppi, Stefan Wagner, Marilyn P. Law, Michael Schäfers, and Luisa De Cola*Cite this: ACS Nano 2010, 4, 4, 2486Publication Date (Web):March 25, 2010Publication History Published online25 March 2010Published inissue 27 April 2010https://pubs.acs.org/doi/10.1021/nn100074khttps://doi.org/10.1021/nn100074kcorrectionACS PublicationsCopyright © 2010 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views501Altmetric-Citations2LEARN 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 PDF (114 KB) Get e-AlertscloseSUBJECTS:Biodistribution,Biological imaging,Encapsulation,Molecular imaging,Molecules Get e-Alerts
Speed-curvature relation for a discrete model of myocardium (2002)

The authors derive the curvature relation (the dependence of the wave speed on wavefront curvature) for a discrete model of an excitable medium allowing inhomogeneities in the limiting case of a medium with no recovery process. The model incorporates an element weighting distribution w that is varied locally to match the required values of the local plane wave speed, critical curvature, and effective diffusion constant. The authors successfully linked their discrete model to myocardium using valves obtained from the Luo-Rudy model.
Characteristics of Atomic-Layer-Deposited Al[sub 2]O[sub 3] High-k Dielectric Films Grown on Ge Substrates (2008)

This paper describes the structural and electrical properties of thin films grown through atomic layer deposition onto Ge substrates over a wide deposition temperature range . From grazing-incidence X-ray reflectivity and X-ray photoelectron spectroscopy, we found that increasing the deposition temperature improved the film density and its dielectric stoichiometry; nevertheless, dielectric intermixing between main and interfacial appeared at temperatures above , along with degradation of the interface. Accordingly, a relatively large gate leakage current and a high density of interfacial states were observed as a result of deterioration of the entire structure at higher deposition temperatures. In addition, although subsequent high-temperature processing at in a ambient could relieve the oxygen-excessive behavior further, i.e., to provide a more stoichiometric film, the accompanying volatilization close to the dielectric interface caused greater damage to the electrical performance. Only forming gas annealing (, 1:10) at low temperature improved the capacitance–voltage characteristics of the structure, in terms of providing a lower value of (ca. ), a lower value of , and a reduced hysteresis width.
Invited Industry Session at ISSCC 2023 [Conference Reports] (2023)

Provides society information that may include news, reviews or technical notes that should be of interest to practitioners and researchers.
ChemInform Abstract: 2,2‐Dicyanovinyl as a Nonaromatic Aryl Bioisostere: Synthesis, Binding Experiments, and SAR Studies of Highly Selective Dopamine D4 Receptor Ligands. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: The Chemistry of Cyanotrimethylsilane (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Molecular Mechanisms of Tenofovir Resistance Conferred by Human Immunodeficiency Virus Type 1 Reverse Transcriptase Containing a Diserine Insertion after Residue 69 and Multiple Thymidine Analog-Associated Mutations (2004)

Two amino acids inserted between residues 69 and 70 of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) are rare mutations that may develop in viruses containing multiple thymidine analog (zidovudine [AZT], stavudine)-associated mutations and that confer high-level resistance to all currently approved chain-terminating nucleoside and nucleotide RT inhibitors (NRTIs). The two known mechanisms of resistance to NRTIs are decreased incorporation and increased excision. The mechanism used by RT insertion mutants has not been described for tenofovir (TFV), a recently approved agent in this class. A patient-derived HIV-1 strain (strain FS-SSS) that contained an insertion mutation in a background of additional resistance mutations M41L, L74V, L210W, and T215Y was obtained. A second virus (strain FS) was derived from FS-SSS. In strain FS the insertion and T69S were reverted but the other resistance mutations were retained. The FS virus showed strong resistance to AZT but low-level changes in susceptibilities to other NRTIs and TFV. The FS-SSS virus showed reduced susceptibilities to all NRTIs including TFV. Steady-state kinetics demonstrated that the relative binding or incorporation of TFV was slightly decreased for FS-SSS RT compared to those for wild-type RT. However, significant ATP-mediated excision of TFV was detected for both mutant RT enzymes and followed the order FS-SSS RT > FS RT > wild-type RT. The presence of physiological concentrations of the +1 nucleotide inhibited TFV excision by the wild-type RT and slightly inhibited excision by the FS RT, whereas the level of excision by the FS-SSS RT remained high. Computer modeling suggests that the increased mobility of the beta3-beta4 loop may contribute to the high-level and broad NRTI resistance caused by the T69 insertion mutation.
Methods to Detect MHC-Specific IgE in Mice and Men (2020)

Humoral immunity is a major barrier limiting long-term outcome after organ transplantation. Especially, the production of antibodies directed against donor HLA/MHC antigens (i.e. donor-specific antibodies (DSA)) leading to antibody-mediated rejection (ABMR) is considered to be a major factor negatively affecting allograft survival. DSAs of the IgG isotype are routinely measured in transplant patients. However, not all patients diagnosed with IgG-DSA develop ABMR events. Therefore, research in better understanding the mechanisms of ABMR is of great importance. We recently demonstrated the production of MHC-specific IgE upon allograft rejection in mice and in transplant patients. IgE is classically connected with allergy and is known to be important for the humoral defense against helminths and worms. However, its role in autoimmune diseases and cancer has been reported recently as well. The concentration of IgE in blood is extremely low compared to other antibody isotypes. Therefore, detection of MHC-specific IgE from serum requires methods of high sensitivity. Since MHC-specific IgG-typically present at much higher serum levels-develops as well, high specificity is also required of IgE detection methods. In the murine model we developed an enzyme linked immunosorbent assay (ELISA) using MHC monomers for measurement of MHC-specific IgE, allowing us to distinguish between specificities of antibodies against different class I and class II antigens. For measurement of functional activity of MHC-specific IgE <i>in vitro</i>, a release assay using a rat basophil cell line (RBL-2H3) was established. For functional analysis of MHC-specific IgE <i>in vivo</i>, a cutaneous hypersensitivity reaction assay was adapted for this purpose using MHC monomers. Humanized RBL-2H3 cells transfected with cDNA coding for the human-high affinity IgE receptor were used for functionality measurement of donor-specific IgE in sensitized transplant patients. For detection of HLA-specific IgE, a bead assay was adapted, using beads expressing single HLA antigens. The aim of this publication is to demonstrate currently established methods for the detection and characterization of MHC-specific IgE in the murine and human setting.
Clinical characteristics of children evaluated for suspected pulmonary embolism with D-dimer testing (2017)

The rate of PE diagnosis in children with D-dimer was 6.4%, similar to that seen in adults; most children with PE are over 13 years and had clinical predictors known to increase probability of PE in symptomatic adults. Future studies should use these criteria to develop a clinical decision rule for PE in children.
Astrovirus Diagnostics (2017)

Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.
Colitis in sheep due to a Campylobacter‐like bacterium (1984)

Epidemic diarrhoea was observed in approximately 2,000 of 6,700 sheep on 9 farms. The disease, called weaner colitis, caused mortality of 1%, while morbidity varied from 20 to 75%. Colon contents from affected sheep were inoculated into 17 sheep, 13 of which developed diarrhoea 5 to 7 days after inoculation. Naturally and experimentally infected sheep had mild, erosive typhlitis and colitis. Microscopic examination of washed scrapings of colonic mucosa from all affected sheep revealed masses of curved bacteria that were not seen in controls. Electron microscopic examination showed similar bacteria adherent to colonic epithelium of an experimentally infected sheep. Curved, motile bacteria were isolated from 2 naturally occurring cases. One isolate was inoculated into 9 sheep, 2 of which developed diarrhoea. The other isolate was given to 4 sheep without observable effect. The curved bacteria grew only on media containing blood, in an atmosphere of approximately 10% air, 10% CO2 and 80% H2. They were Gram-negative, with a polar flagellum at one or both ends, they did not ferment glucose or give a positive catalase reaction. It is suggested that these bacteria are a new Campylobacter species and that they play a major role in the aetiology of weaner colitis.
The Effect of Cyclic Loading Simulating Oscillatory Joint Mobilization on the Posterior Capsule of the Glenohumeral Joint: A Cadaveric Study (2011)

While oscillatory joint mobilization to a force of 5 N resulted in temporary elongation of the posterior capsule, mobilization to loads of 20 and 40 N resulted in sustained elongation of the capsule for up to 1 hour. Our findings also suggest that mobilization up to loads that represent the beginning of the linear region of the load displacement curve could be performed without serious damage to the posterior capsule.
Structural Basis for the Specific Recognition of the Major Antigenic Peptide from the Japanese Cedar Pollen Allergen Cry j 1 by HLA-DP5 (2014)

The major allergen, Cry j 1, was isolated from Japanese cedar Cryptomeria japonica (Cry j) pollen and was shown to react with immunoglobulin E antibodies in the sera from pollinosis patients. We previously reported that the frequency of HLA-DP5 was significantly higher in pollinosis patients and the immunodominant peptides from Cry j 1 bound to HLA-DP5 to activate Th2 cells. In the present study, we determined the crystal structure of the HLA-DP5 heterodimer in complex with a Cry j 1-derived nine-residue peptide, at 2.4Å resolution. The peptide-binding groove recognizes the minimal peptide with 10 hydrogen bonds, including those between the negatively charged P1 pocket and the Lys side chain at the first position in the peptide sequence. We confirmed that HLA-DP5 exhibits the same Cry j 1-binding mode in solution, through pull-down experiments using structure-based mutations of Cry j 1. We also identified the characteristic residues of HLA-DP5 that are responsible for the distinct properties of the groove, by comparing the structure of HLA-DP5 and the previously reported structures of HLA-DP2 in complexes with pDRA of the self-antigen. The comparison revealed that the HLA-DP5·pCry j 1 complex forms several hydrogen bond/salt bridge networks between the receptor and the antigen that were not observed in the HLA-DP2·pDRA complex. Evolutionary considerations have led us to conclude that HLA-DP5 and HLA-DP2 represent two major groups of the HLA-DP family, in which the properties of the P1 and P4 pockets have evolved and acquired the present ranges of epitope peptide-binding specificities.
Analysis of experimental errors in bioprocesses. 1. Production of lactobionic acid and sorbitol using the GFOR (glucose-fructose oxidoreductase) enzyme from permeabilized cells of Zymomonas mobilis (2011)

The proper determination of experimental errors in bioprocesses can be very important because experimental errors can exert a major impact on the analysis of experimental results. Despite this, the effect of experimental errors on the analysis of bioprocess data has been largely overlooked in the literature. For this reason, we performed detailed statistical analyses of experimental errors obtained during the production of lactobionic acid and sorbitol in a system utilizing as catalyst the GFOR (glucose-fructose oxidoreductase) enzyme from permeabilized cells of the bacteria Zymomonas mobilis. The magnitude of the experimental errors thus obtained were then correlated with the process operation conditions and with the composition of the culture media used for bacterial growth. It is shown that experimental errors can depend very significantly on the operation conditions and affect the interpretation of available experimental data. More specifically, in this study, experimental errors depended on the nutritional supplements added to the cultivation medium, the inoculation process, and the reaction time, which may be of fundamental importance for actual process development. The results obtained also indicate, for the first time, that GFOR activity can be affected by the composition of the medium in which cells are cultivated.
VIDEOIMAGE SENSING FOR A SMART CONTROLLER AT DIAMOND INTERCHANGES (1995)

This paper presents a videoimage-based vehicle-detection/classification methodology that is of importance to intelligent vehicle-highway system (IVHS) deployment. This technology constitutes the front-end sensing mechanism of a smart diamond interchange controller currently being developed at the Texas A&M IVHS Research Center. It is anticipated that videoimage sensing will augment, perhaps replace, inductive loops in traffic-control systems. Inductive loops require installation in the pavement, which is disruptive to traffic and requires on-going maintenance. Use of videoimaging in place of inductive loops as a front-end sensor offers the potential to overcome these difficulties. The methodology herein employs intensity variations of scan lines taken along lanes. Such an approach allows an image to be processed in less than one second on a PC-486 platform.
Effect of Hydrogen Dilution on the Metastability of Hydrogenated Amorphous Silicon Oxide Solar Cells (2011)

We investigated the effect of H2 dilution on the stability of hydrogenated amorphous silicon oxide (a-Si1-xOx:H) films and solar cells. a-Si1-xOx:H films were prepared by very high frequency plasma-enhanced chemical vapor deposition (VHF-PECVD) using a gas mixture of silane (SiH4), hydrogen (H2), and carbon dioxide (CO2). The degradation results after light soaking for 310 h under AM1.5, 125 mW/cm2 at 48 °C clearly showed that the film and device stabilities were improved substantially with increasing H2 dilution. Our best stable result with a high open-circuit voltage (Voc) of 1.03 V for a-Si1-xOx:H single-junction solar cells showed a degradation of 16.6%. This result indicates that the stability against the light soaking of the a-Si1-xOx:H material is not inferior to that of a conventional hydrogenated amorphous silicon (a-Si:H) material. The temperature dependences of current–voltage (I–V) characteristics observed before and after light soaking showed that a-Si1-xOx:H solar cells had a similar temperature dependence to conventional a-Si:H solar cells.
Sulfobetaine zwitterionic inhibitors of squalene synthase (1996)

Zwitterions such as farnesyl sulfobetaine 8 are a new type of inhibitor of squalene synthase that, while maintaining overall neutrality, mimic both the carbocationic and anionic moieties of presumed reaction intermediates. The most effective zwitterionic sulfobetaines discovered to date are aromatic derivatives 17 (IC50 = 2 μM) and 20 (IC50 = 5 μM).
Development and Application of an Assay to Evaluate the Anti-Parasitic Effect of Humoral Responses against Trypanosoma cruzi (2023)

Mounting a balanced and robust humoral immune response is of utmost importance for reducing the infectivity of <i>Trypanosoma cruzi</i>. While the role of such a response in controlling the infection is well known, there is a lack of tools that can be used to quickly evaluate it. We developed a serum parasite inhibition assay (to evaluate changes in the parasite infection after exposing infective <i>T. cruzi</i> trypomastigotes to serum samples from infected patients). It is based on Vero cells as the hosts and the Tulahuen β-galactosidase parasite strain, genetically engineered to be quantifiable by spectrophotometry. In parallel, we developed an in-house ELISA to correlate the anti-<i>T. cruzi</i> antibody titres of the clinical samples with their observed anti-parasitic effect in the serum parasite inhibition assay. Serum samples from chronically <i>T. cruzi</i>-infected patients significantly inhibited parasite invasion in a titre-dependant manner, regardless of the patient's clinical status, compared to samples from the non-infected controls. In addition, there was a clear correlation between the reactivity of the samples to the whole-parasite lysates by ELISA and the inhibitory effect. The results of this work confirm the previously described anti-parasitic effect of the serum of individuals exposed to <i>T. cruzi</i> and present a framework for its large-scale evaluation in further studies. The serum parasite inhibition assay represents a reproducible way to evaluate the intensity and anti-parasitic effect of humoral responses against <i>T. cruzi</i>, which could be applied to the evaluation of candidate antigens/epitopes in the design of Chagas disease vaccine candidates.