gebhart/patrepeval huggingface dataset:
1641. Treatment of Recurrent Clostridium difficile Infection With SER-109 Reduces Gastrointestinal Carriage of Antimicrobial Resistance Genes (2018)

Abstract Background A healthy gut microbiome is associated with colonization resistance against C. difficile and other pathogens, including bacteria carrying antibiotic resistance genes (AbRG). Designed to facilitate microbiome restoration and reduce the risk of recurrent C. difficile infection (rCDI), SER-109, an investigational microbiome therapeutic, is an ecology of bacterial spores purified from stool from healthy screened donors. We evaluated the impact of engraftment of SER-109 dose species on the abundance of AbRG in rCDI subjects. Methods We generated whole metagenomic shotgun (WMS) data for a subset of study subjects with available stool samples receiving SER-109 (n = 66) or placebo (n = 25) from 2 clinical trials (a dose-ranging Phase 1b study and a fixed-dose Phase 2 trial). WMS data from stool was analyzed to (1) quantify the abundance of AbRG (Comprehensive Antibiotic Resistance Database CARD v.1.1.8) and (2) define subjects with significant engraftment of SER-109 dose species. For each subject and antibiotic drug class, we calculated the change in abundance of AbRG between samples collected at baseline (after antibiotic therapy for an episode of C. difficile infection) and following treatment with SER-109 or placebo. We evaluated the effect of SER-109 engraftment on AbRG abundance, independent of dose. Results In subjects with significant high-confidence engraftment of SER-109 organisms (n = 30) we observed significantly greater reduction in AbRG relative to placebo at week 1 post treatment. These AbRG were associated with multiple classes of antibiotics including, but not limited to, cephalosporins (P = 0.035), and fluoroquinolones (P = 0.035) (Figure 1). Furthermore, the reduction of AbRG was correlated with the increased abundance of SER-109 dose species, and with a reduction in Proteobacteria (e.g., Enterobactericeae) (Figure 2). Conclusion Restoration of the gut microbiome with SER-109 in subjects with a history of rCDI is associated with a reduction in abundance of antibiotic resistance genes. These observations suggest that microbiome therapeutics could play a role in more rapidly decolonizing drug-resistant bacteria. Disclosures C. Ford, Seres Therapeutics, Inc: Employee and Shareholder, Salary. M. Henn, Seres Therapeutics, Inc: Employee and Shareholder, Salary. J. Bryant, Seres Therapeutics, Inc: Employee and Shareholder, Salary. L. Diao, Seres Therapeutics, Inc: Employee and Shareholder, Salary. J. Wortman, Seres Therapeutics, Inc: Employee and Shareholder, Salary. A. Tomlinson, Seres Therapeutics, Inc: Employee and Shareholder, Salary. K. Litcofsky, Seres Therapeutics, Inc: Employee and Shareholder, Salary. P. Bernardo, Seres Therapeutics, Inc: Employee and Shareholder, Salary. B. McGovern, Seres Therapeutics, Inc: Employee and Shareholder, Salary. J. G. Aunins, Seres Therapeutics, Inc: Employee and Shareholder, Salary. D. N. Cook, Seres Therapeutics, Inc: Employee and Shareholder, Salary. M. Trucksis, Seres Therapeutics, Inc: Employee and Shareholder, Salary.
Parallel k-Means++ for Multiple Shared-Memory Architectures (2016)

In recent years k-means++ has become a popular initialization technique for improved k-means clustering. To date, most of the work done to improve its performance has involved parallelizing algorithms that are only approximations of k-means++. In this paper we present a parallelization of the exact k-means++ algorithm, with a proof of its correctness. We develop implementations for three distinct shared-memory architectures: multicore CPU, high performance GPU, and the massively multithreaded Cray XMT platform. We demonstrate the scalability of the algorithm on each platform. In addition we present a visual approach for showing which platform performed k-means++ the fastest for varying data sizes.
A high power ion thruster for deep space missions (2012)

The Nuclear Electric Xenon Ion System ion thruster was developed for potential outer planet robotic missions using nuclear electric propulsion (NEP). This engine was designed to operate at power levels ranging from 13 to 28 kW at specific impulses of 6000-8500 s and for burn times of up to 10 years. State-of-the-art performance and life assessment tools were used to design the thruster, which featured 57-cm-diameter carbon-carbon composite grids operating at voltages of 3.5-6.5 kV. Preliminary validation of the thruster performance was accomplished with a laboratory model thruster, while in parallel, a flight-like development model (DM) thruster was completed and two DM thrusters fabricated. The first thruster completed full performance testing and a 2000-h wear test. The second successfully completed vibration tests at the full protoflight levels defined for this NEP program and then passed performance validation testing. The thruster design, performance, and the experimental validation of the design tools are discussed in this paper.
Supplemental figure legends from Fas Ligand Deficiency Impairs Tumor Immunity by Promoting an Accumulation of Monocytic Myeloid-Derived Suppressor Cells (2023)

&lt;p&gt;Supplemental figure legends&lt;/p&gt;
Total Ion Current Profile (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Abuse liability and therapeutic potential of theMitragyna speciosa(kratom) alkaloids mitragynine and 7‐hydroxymitragynine (2018)

Kratom, derived from the plant Mitragyna speciosa, is receiving increased attention as an alternative to traditional opiates and as a replacement therapy for opiate dependence. Mitragynine (MG) and 7-hydroxymitragynine (7-HMG) are major psychoactive constituents of kratom. While MG and 7-HMG share behavioral and analgesic properties with morphine, their reinforcing effects have not been examined to date. 7-HMG, but not MG, substituted for morphine self-administration in a dose-dependent manner in the rat self-administration paradigm. Following the substitution procedure, re-assessment of morphine self-administration revealed a significant increase following 7-HMG and a significant decrease following MG substitution. In a separate cohort, 7-HMG, but not MG, engendered and maintained intravenous self-administration in a dose-dependent manner. The effects of pretreatment with nalxonaxine (NLXZ), a μ1 opiate receptor antagonist, and naltrindole (NTI), a δ opiate receptor antagonist, on 7-HMG and morphine self-administration were also examined. Both NLXZ and NTI reduced 7-HMG self-administration, whereas only NLXZ decreased morphine intake. The present results are the first to demonstrate that 7-HMG is readily self-administered, and the reinforcing effects of 7-HMG are mediated in part by μ and δ opiate receptors. In addition, prior exposure to 7-HMG increased subsequent morphine intake whereas prior exposure to MG decreased morphine intake. The present findings indicate that MG does not have abuse potential and reduces morphine intake, desired characteristics of candidate pharmacotherapies for opiate addiction and withdrawal, whereas 7-HMG should be considered a kratom constituent with high abuse potential that may also increase the intake of other opiates.
Data from Optimizing Radiolabeled Engineered Anti-p185<sup>HER2</sup> Antibody Fragments for <i>In vivo</i> Imaging (2023)

&lt;div&gt;Abstract&lt;p&gt;We have recently described the &lt;i&gt;in vivo&lt;/i&gt; properties of an iodinated anti-p185&lt;sup&gt;HER2&lt;/sup&gt; engineered antibody fragment [minibody (scFv-C&lt;sub&gt;H&lt;/sub&gt;3)&lt;sub&gt;2&lt;/sub&gt;; 80 kDa], made from the internalizing 10H8 monoclonal antibody. Although the 10H8 minibody showed excellent binding to the target &lt;i&gt;in vitro&lt;/i&gt;, only modest tumor uptake [5.6 ± 1.7% injected dose per gram (ID/g) of tissue] was achieved in nude mice bearing MCF7/HER2 breast cancer tumors. Here, in an attempt to improve targeting, the 10H8 minibody was conjugated to 1,4,7,10-tetraazacyclododecane-&lt;i&gt;N&lt;/i&gt;, &lt;i&gt;N&lt;/i&gt;′, &lt;i&gt;N&lt;/i&gt;′′, &lt;i&gt;N&lt;/i&gt;′′′-tetraacetic acid (DOTA), radiometal labeled, and evaluated &lt;i&gt;in vivo&lt;/i&gt;. The tumor uptake of &lt;sup&gt;111&lt;/sup&gt;In-DOTA 10H8 minibody was 5.7 ± 0.1% ID/g, similar to the radioiodinated 10H8 minibody. However, in addition to the expected liver clearance, the kidneys had unexpectedly high activity (34.0 ± 4.0% ID/g). A minibody derived from a second anti-p185&lt;sup&gt;HER2&lt;/sup&gt; antibody (trastuzumab; hu4D5v8) was also made. Tumor uptakes, evaluated by quantitative microPET using &lt;sup&gt;64&lt;/sup&gt;Cu-DOTA hu4D5v8 minibody, were 4.2 ± 0.5% ID/g. Furthermore, in non-tumor-bearing mice, &lt;sup&gt;111&lt;/sup&gt;In-DOTA hu4D5v8 minibody exhibited similar elevated uptake in the kidneys (28.4 ± 6.5% ID/g). Immunohistochemical staining of kidneys from non-tumor-bearing mice showed strong specific staining of the proximal tubules, and Western blot analysis of kidney lysate confirmed the presence of cross-reactive antigen. To further improve tumor uptake and normal tissue distribution, a larger hu4D5v8 fragment [(scFv-C&lt;sub&gt;H&lt;/sub&gt;2-C&lt;sub&gt;H&lt;/sub&gt;3)&lt;sub&gt;2&lt;/sub&gt;; 105 kDa] was made, engineered to exhibit rapid clearance kinetics. This fragment, when evaluated by microPET, exhibited improved tumor targeting (12.2 ± 2.4% ID/g) and reduced kidney uptake (13.1 ± 1.5% ID/g). Thus, by manipulating the size and format of anti-p185&lt;sup&gt;HER2&lt;/sup&gt; antibody fragments, the kidney activity was reduced and high or low expression of p185&lt;sup&gt;HER2&lt;/sup&gt; in xenografts could be distinguished by microPET imaging.&lt;/p&gt;&lt;/div&gt;
Time-resolved reflectance spectroscopy for buried flaps monitoring (2021)

International audience
SiC die-attachment with minor elements added pure Zn under formic acid reflow (2012)

Pure Zn is one of the best candidates, as it has a high melting, good electrical/thermal conductivity, and excellent thermal shock resistance. To improve the properties of pure Zn, the effect of the addition of 0.1 mass% Cr and Ti was examined the formic acid reflow soldering. The minor elements are expected to form a surface protective oxide layer on Zn and the formic acid reflow soldering can replace the hydrogen reduction treatment. The addition of 0.1 mass% Cr or with 0.1 mass% Ti to pure Zn improves ductility and oxidation resistance. Among the solder alloys, the addition of Cr has the most effective improvement of ductility and oxidation resistance. The Pure Zn and Zn-X solders exhibit the excellent heat-cycle resistance for the DBC die-attach structure between −50 °C and 300 °C.
Environmental Testing Methodology for Real-Time Soil Health Monitoring System (2023)

Soil health monitoring is highly essential for modern agriculture to sustain the quality and yield of technologically advanced agricultural industry over the globe. The working and optimal performance of these systems used for soil health monitoring, is very critical. Failure or false reports due to varied climatic conditions is a big concern. The current paper establishes a testing procedure for climatic or environmental testing of these sensors and systems under extreme conditions that may be faced in agricultural fields. We demonstrate testing and successful working of an indigenously developed soil monitoring system under extreme climatic conditions ranging from $5^{\circ} \mathrm{C}$ to $50^{\circ} \mathrm{C}$ in temperature along with relative humidity variation of 20 % to 95 % relative humidity.
Quantitative Elastography of Liver Fibrosis and Spleen Stiffness in Chronic Hepatitis B Carriers: Comparison of Shear-Wave Elastography and Transient Elastography with Liver Biopsy Correlation (2013)

SW elastography provides more accurate correlation of liver elasticity with liver fibrosis stage compared with transient elastography, especially in identification of stage F2 or greater.
Sparse nonnegative deconvolution for compressive calcium imaging: algorithms and phase transitions (2013)

We propose a compressed sensing (CS) calcium imaging framework for monitoring large neuronal populations, where we image randomized projections of the spatial calcium concentration at each timestep, instead of measuring the concentration at individual locations. We develop scalable nonnegative deconvolution methods for extracting the neuronal spike time series from such observations. We also address the problem of demixing the spatial locations of the neurons using rank-penalized matrix factorization methods. By exploiting the sparsity of neural spiking we demonstrate that the number of measurements needed per timestep is significantly smaller than the total number of neurons, a result that can potentially enable imaging of larger populations at considerably faster rates compared to traditional raster-scanning techniques. Unlike traditional CS setups, our problem involves a block-diagonal sensing matrix and a non-orthogonal sparse basis that spans multiple timesteps. We study the effect of these distinctive features in a noiseless setup using recent results relating conic geometry to CS. We provide tight approximations to the number of measurements needed for perfect deconvolution for certain classes of spiking processes, and show that this number displays a “phase transition, ” similar to phenomena observed in more standard CS settings; however, in this case the required measurement rate depends not just on the mean sparsity level but also on other details of the underlying spiking process. 1
Thermal Conductivity and Thermal Gradient Cyclic Behavior of Refractory Silicate Coatings on Sic/Sic Ceramic Matrix Composites (2008)

Plasma-sprayed mullite and BSAS coatings have been developed to protect SiC/SiC ceramic matrix composites from high temperature environmental attack. in this study, thermal conductivity and thermal barrier functions of these coating systems are evaluated using a laser high-heat-flux test rig. the effects of water vapor on coating thermal conductivity and durability are studied by using alternating fiunace and laser thermal gradient cyclic tests. the influence of laser high-thermal-gradient cycling on coating failure modes is also investigated.
Pepsin, a Biomarker of Gastric Aspiration in Lung Allografts (2007)

We have shown that elevated levels of pepsin, a biomarker of gastric aspiration, are consistently identified in the BAL of lung allografts. The highest levels were seen in patients with > or = grade A2 acute rejection. This provides further evidence supporting the possible role of aspiration in the development of overall allograft injury.
Endocrine Neoplasia (2019)

This chapter reviews the epidemiology, clinical presentation, diagnosis and management of the most common pediatric endocrine neoplastic diseases that physicians deal with in daily clinical practice. Since endocrine neoplasia is often associated with inherited genetic abnormalities, it reviews the most common hereditary syndromes that predispose to these conditions. The chapter emphasizes the need of national and international collaboration for the optimal management of these patients given the lack of data from randomized controlled trials due to the rarity of these tumours. Genetic counselling and genetic testing are recommended for children with medullary thyroid carcinoma, paragangliomas and phaeochromocytomas and adrenocortical cancer. The virilizing syndrome is the most common presentation for adrenocortical cancer. Ovarian neoplasms (benign and malignant) account for ~1 percent of all tumours in children and adolescents. Ovarian enlargement, whether cystic or solid, must be evaluated to exclude malignancy (10-20 percent malignancy rate).
Simplifying Nickel(0) Catalysis: An Air-Stable Nickel Precatalyst for the Internally Selective Benzylation of Terminal Alkenes (2013)

The synthesis and characterization of the air-stable nickel(II) complex trans-(PCy(2)Ph)(2)Ni(o-tolyl)Cl is described in conjunction with an investigation of its use for the Mizoroki-Heck-type, room temperature, internally selective coupling of substituted benzyl chlorides with terminal alkenes. This reaction, which employs a terminal alkene as an alkenylmetal equivalent, provides rapid, convergent access to substituted allylbenzene derivatives in high yield and with regioselectivity greater than 95:5 in nearly all cases. The reaction is operationally simple, can be carried out on the benchtop with no purification or degassing of solvents or reagents, and requires no exclusion of air or water during setup. Synthesis of the precatalyst is accomplished through a straightforward procedure that employs inexpensive, commercially available reagents, requires no purification steps, and proceeds in high yield.
Role of remote sensing, geographic bioinformatics system and bioinformatics in kala-azar epidemiology (2011)

内脏的 leishmaniasis 或 kala-azar 是一个有势力每年引起几千个人的死亡的寄生感染。为 kala-azar 的治疗当前可得到的药用的混合物由于抵抗紧张的出现有严肃的副作用和减少的功效。有免疫力的反应的类型也是在感染利什曼原虫 donovani 的病人被考虑(L。donovani ) 。为这疾病的完全的根除，高级现代研究当前在分子的水平以及在领域水平正在被使用。象遥感，地理信息系统(GIS ) 和生物信息学一样的计算途径是为向量，模式，生态、环境的因素和 genomic 和 proteomic 分析的察觉和分发的关键资源。象 GIS 和生物信息学一样的新奇途径是适当地在决定 visearal leishmaniasis 并且在为阻止疾病从一个区域传播到另外一个设计策略的原因利用的更多。
Uncoupling effect of fatty acids on heart muscle mitochondria and submitochondrial particles (1991)

The effect of ATP/ADP-antiporter inhibitors on palmitate-induced uncoupling was studied in heart muscle mitochondria and inside-out submitochondrial particles. In both systems palmitate is found to decrease the respiration-generated membrane potential. In mitochondria, this effect is specifically abolished by carboxyatractylate (CAtr) a non-penetrating inhibitor of antiporter. In submitochondrial particles, CAtr does not abolish the palmitate-induced potential decrease. At the same time, bongkrekic acid, a penetrating inhibitor of the antiporter, suppresses the palmitate effect on the potential both in mitochondria and particles. Palmitoyl-CoA which is known to inhibit the antiporter in mitochondria as well as in particles decreases the palmitate uncoupling efficiency in both these systems. These data are in agreement with the hypothesis that the ATP/ADP-antiporter is involved in the action of free fatty acids as natural uncouplers of oxidative phosphorylation.
The Argus II epiretinal prosthesis system allows letter and word reading and long-term function in patients with profound vision loss (2013)

Multiple blind subjects fitted with the Argus II system consistently identified letters and words using the device, indicating reproducible spatial resolution. This, in combination with stable, long-term function, represents significant progress in the evolution of artificial sight.
Determination of copper in a copper-nickel alloy: A new experiment for the general chemistry laboratory (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of copper in a copper-nickel alloy: A new experiment for the general chemistry laboratoryKristin Gallagher and Charles R. Cantor Cite this: J. Chem. Educ. 1978, 55, 10, 660Publication Date (Print):October 1, 1978Publication History Received3 August 2009Published online1 October 1978Published inissue 1 October 1978https://doi.org/10.1021/ed055p660RIGHTS & PERMISSIONSArticle Views941Altmetric-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 InReddit PDF (673 KB) Get e-Alerts Get e-Alerts
ChemInform Abstract: Concise Preparation of 2,2‐Difluorohomopropargyl Carbonyl Derivatives. Application to the Synthesis of 4,4‐Difluoroisoquinolinone Congeners. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Combining handcrafted features with latent variables in machine learning for prediction of radiation‐induced lung damage (2019)

The potential for combination of traditional machine learning methods and deep learning VAE techniques has been demonstrated for dealing with limited datasets in modeling radiotherapy toxicities. Specifically, latent variables from a VAE-MLP joint architecture are able to complement handcrafted features for the prediction of RP and improve prediction over either method alone.
Cell-Autonomous Defects in Thymic Epithelial Cells Disrupt Endothelial-Perivascular Cell Interactions in the Mouse Thymus (2013)

The thymus is composed of multiple stromal elements comprising specialized stromal microenvironments responsible for the development of self-tolerant and self-restricted T cells. Here, we investigated the ontogeny and maturation of the thymic vasculature. We show that endothelial cells initially enter the thymus at E13.5, with PDGFR-β(+) mesenchymal cells following at E14.5. Using an allelic series of the thymic epithelial cell (TEC) specific transcription factor Foxn1, we showed that these events are delayed by 1-2 days in Foxn1 (Δ/Δ) mice, and this phenotype was exacerbated with reduced Foxn1 dosage. At subsequent stages there were fewer capillaries, leaky blood vessels, disrupted endothelium - perivascular cell interactions, endothelial cell vacuolization, and an overall failure of vascular organization. The expression of both VEGF-A and PDGF-B, which are both primarily expressed in vasculature-associated mesenchyme or endothelium in the thymus, were reduced at E13.5 and E15.5 in Foxn1 (Δ/Δ) mice compared with controls. These data suggest that Foxn1 is required in TECs both to recruit endothelial cells and for endothelial cells to communicate with thymic mesenchyme, and for the differentiation of vascular-associated mesenchymal cells. These data show that Foxn1 function in TECs is required for normal thymus size and to generate the cellular and molecular environment needed for normal thymic vascularization. These data further demonstrate a novel TEC-mesenchyme-endothelial interaction required for proper fetal thymus organogenesis.