gebhart/patrepeval huggingface dataset:
Alarming rate of transmitted drug resistance mutations and genetic diversity in newly HIV-1-infected patients in Benin (2020)

Abstract Background Seventeen years after the start of the IBAARV (Beninese initiative for access to antiretrovirals), transmitted drug resistance mutations in ARV naïve patients and HIV-1 genetic diversity were investigated in Benin. Methods 353 plasma samples were collected between October and December 2017 in nineteen facilities care in Benin from HIV-1 positive and ARV naive individuals. Pol (protease + partial RT) region was amplified and sequenced in 248 samples. Results Drug resistance mutations were detected in (27/248; 10.9%) according to the WHO SDRM 2009 list, with predominance of mutations directed to NNRTIs drugs (24/248; 10%).Phylogenetic and recombination analyses showed a predominance of CRF02_AG strains (165/248; 66.5%) and a high genetic diversity with five other variants and 39 URFs (15.7%) which contained portions of strains that co-circulate in Benin. Eight recent transmission chains revealed active ongoing transmission of HIV-1 strains among ARV naïve patients. Conclusions Our study showed a high primary drug resistance rate and a complex genetic diversity. Regular monitoring of primary drug resistance is required to adapt HIV-1 treatment strategies and adoption of new WHO recommendations in Benin.
Ultrafast Photoluminescence in Quantum-Confined Silicon Nanocrystals Arises from an Amorphous Surface Layer (2014)

Here, we examine ultrafast photoluminescence produced from plasma-grown, colloidal silicon nanocrystals as a function of both particle size and lattice crystallinity. In particular, we quantify the decay time and spectral profiles of nominally few-picosecond direct-gap emission previously attributed to phononless electron–hole recombination. We find that the high-energy (400–600 nm, 2–3 eV) photoluminescence component consists of two decay processes with distinct time scales. The fastest photoluminescence exhibits an ∼30 ps decay constant largely independent of emission energy and particle size. Importantly, nearly identical temporal components and blue spectral features appear for amorphous particles. We thus associate high-energy, rapid emission with an amorphous component in all measured samples, as supported by Raman analysis and molecular dynamics simulation. Based on these observations, we advise that the observed dynamics proceed too slowly to originate from intraband carrier thermalization and instead suggest a nonradiative origin associated with the amorphous component.
Understanding Enterprise Risk Across an Aquisition Portfolio: A Grounded Theory Approach (2008)

Every acquisition program contains risks. But what impact do these risks have on the entire portfolio of acquisition activities? What does risk at the Enterprise level really mean? For example, risk collectively could portend great danger to the acquisition manager’s overall portfolio which might be otherwise masked by traditional program performance and analysis. Alternatively, these risks also might represent opportunities to achieve greater results when analyzed from a portfolio perspective. Initial review of the literature suggests that most leaders are unable to articulate the risk carried by their portfolio of product development activities or what this means to them. However, the same literature suggests they strongly desire this capability. Beginning with a review of the applicable literature in the areas of risk, product development (acquisition) and product portfolio management, portfolio-level risk applications are found to be sparse and ill-conceived. Initial analysis of interviews with portfolio leaders involving military product development activities in portfolios of large, complex, system development will be presented with a discussion of the implications of enterprise risk for product portfolio management.
Discovery and characterization of an F420-dependent glucose-6-phosphate dehydrogenase (Rh-FGD1) from Rhodococcus jostii RHA1 (2016)

Cofactor F<sub>420</sub>, a 5-deazaflavin involved in obligatory hydride transfer, is widely distributed among archaeal methanogens and actinomycetes. Owing to the low redox potential of the cofactor, F<sub>420</sub>-dependent enzymes play a pivotal role in central catabolic pathways and xenobiotic degradation processes in these organisms. A physiologically essential deazaflavoenzyme is the F<sub>420</sub>-dependent glucose-6-phosphate dehydrogenase (FGD), which catalyzes the reaction F<sub>420</sub> + glucose-6-phosphate → F<sub>420</sub>H<sub>2</sub> + 6-phospho-gluconolactone. Thereby, FGDs generate the reduced F<sub>420</sub> cofactor required for numerous F<sub>420</sub>H<sub>2</sub>-dependent reductases, involved e.g., in the bioreductive activation of the antitubercular prodrugs pretomanid and delamanid. We report here the identification, production, and characterization of three FGDs from Rhodococcus jostii RHA1 (Rh-FGDs), being the first experimental evidence of F<sub>420</sub>-dependent enzymes in this bacterium. The crystal structure of Rh-FGD1 has also been determined at 1.5 Å resolution, showing a high similarity with FGD from Mycobacterium tuberculosis (Mtb) (Mtb-FGD1). The cofactor-binding pocket and active-site catalytic residues are largely conserved in Rh-FGD1 compared with Mtb-FGD1, except for an extremely flexible insertion region capping the active site at the C-terminal end of the TIM-barrel, which also markedly differs from other structurally related proteins. The role of the three positively charged residues (Lys197, Lys258, and Arg282) constituting the binding site of the substrate phosphate moiety was experimentally corroborated by means of mutagenesis study. The biochemical and structural data presented here provide the first step towards tailoring Rh-FGD1 into a more economical biocatalyst, e.g., an F<sub>420</sub>-dependent glucose dehydrogenase that requires a cheaper cosubstrate and can better match the demands for the growing applications of F<sub>420</sub>H<sub>2</sub>-dependent reductases in industry and bioremediation.
Novel System for Real-Time Integration of 3-D Echocardiography and Fluoroscopy for Image-Guided Cardiac Interventions: Preclinical Validation and Clinical Feasibility Evaluation (2014)

Real-time imaging is required to guide minimally invasive catheter-based cardiac interventions. While transesophageal echocardiography allows for high-quality visualization of cardiac anatomy, X-ray fluoroscopy provides excellent visualization of devices. We have developed a novel image fusion system that allows real-time integration of 3-D echocardiography and the X-ray fluoroscopy. The system was validated in the following two stages: 1) preclinical to determine function and validate accuracy; and 2) in the clinical setting to assess clinical workflow feasibility and determine overall system accuracy. In the preclinical phase, the system was assessed using both phantom and porcine experimental studies. Median 2-D projection errors of 4.5 and 3.3 mm were found for the phantom and porcine studies, respectively. The clinical phase focused on extending the use of the system to interventions in patients undergoing either atrial fibrillation catheter ablation (CA) or transcatheter aortic valve implantation (TAVI). Eleven patients were studied with nine in the CA group and two in the TAVI group. Successful real-time view synchronization was achieved in all cases with a calculated median distance error of 2.2 mm in the CA group and 3.4 mm in the TAVI group. A standard clinical workflow was established using the image fusion system. These pilot data confirm the technical feasibility of accurate real-time echo-fluoroscopic image overlay in clinical practice, which may be a useful adjunct for real-time guidance during interventional cardiac procedures.
Experimental and theoretical aspects of hydration isotherms for biomolecules (1977)

A resonating quartz crystal microbalance technique has been used to obtain room temperature water sorption isotherms for cytochrome-c, DNA, lecithin, lysozyme and serum albumin. The results compare favourably with earlier work using more conventional techniques. A completely general formula describing the sorption isotherms is derived. With the assumption of identical and non-interacting primary sorption sites, this general formula gives exact values for the monolayer site capacity and the thermodynamic activities of all the hydration states. However, it is shown that at least one of these assumptions is not valid for the materials studied here, accordingly only limited information can be derived using this theory. This restricted usefulness also applies to other sorption theories described in the literature, most of which are based on purely modelistic or kinetic considerations. The significance of a sorption activity parameter having values greater or less than unity is discussed for the materials examined.
The relationship between wave and geometrical optics models of coded aperture type x-ray phase contrast imaging systems (2010)

X-ray phase contrast imaging is a very promising technique which may lead to significant advancements in medical imaging. One of the impediments to the clinical implementation of the technique is the general requirement to have an x-ray source of high coherence. The radiation physics group at UCL is currently developing an x-ray phase contrast imaging technique which works with laboratory x-ray sources. Validation of the system requires extensive modelling of relatively large samples of tissue. To aid this, we have undertaken a study of when geometrical optics may be employed to model the system in order to avoid the need to perform a computationally expensive wave optics calculation. In this paper, we derive the relationship between the geometrical and wave optics model for our system imaging an infinite cylinder. From this model we are able to draw conclusions regarding the general applicability of the geometrical optics approximation.
Risk factors for coronary heart disease in children and young adults (2004)

This review covers two ongoing studies in Finland: the Cardiovascular Risk in Young Finns study, which started in 1978, and the Special Turku Coronary Risk Factor Intervention Project for Children (STRIP), which started in 1989. In the cross-sectional Cardiovascular Risk in Young Finns study, cardiovascular risk factors were first assessed in 1980 in 3596 children and adolescents covering ages between 3 and 18 y at 3-y intervals. The latest follow-up examination was performed in 2001, when risk factors and early markers of atherosclerosis in carotid and brachial arteries were examined in 2264 subjects from the original cohorts, now covering ages from 24 to 39 y. The results clearly show that an individual's coronary heart disease (CHD) risk factor profile is regulated by early lifestyle-related factors and that exposure to risk factors in childhood induces changes in arteries that contribute to the development of atherosclerosis in adulthood. In the STRIP study, 1062 infants were randomized into an intervention group (n = 540; low-saturated-fat, low-cholesterol diet) or a control group (n = 522) at 7 mo of age. Fat, saturated fat and cholesterol intakes have been lower, while the polyunsaturated to saturated fat ratio has been higher in the intervention children than in the control children throughout the ongoing trial. During the first 7 y of life, serum cholesterol concentration was 0.2-0.3 mmol/l lower in the intervention boys than in the control boys, but the difference was negligible in girls. Neurological development of the intervention children at age 5 y was at least as good as that of the control children. Counselling had no effect on children's growth.
Glastonbury: ynysvitrin (1883)

Glastonbury: ynysvitrin Get access Thomas Kerslake Thomas Kerslake Search for other works by this author on: Oxford Academic Google Scholar Notes and Queries, Volume s6-VIII, Issue 199, 20 October 1883, Pages 314–315, https://doi.org/10.1093/nq/s6-VIII.199.314i Published: 20 October 1883
ChemInform Abstract: ISOLATION AND CHARACTERIZATION OF THE FIRST STABLE DIPHOSPHAALLENE: P,P′‐BIS(2,4,6,‐TRI‐TERT‐BUTYLPHENYL)‐1,3‐DIPHOSPHAALLENE (1984)

Abstract Das Phosphin (I) wird zur Verbindung (II) silyliert, die zum stabilen Phosphinoimethylenphosphin (IIIl führt.
Abstract B62: Zinc supplementation reduces forestomach tumor burden in N-nitrosomethylbenzylamine-treated mice (2010)

Abstract Zinc deficiency is associated with high incidences of esophageal and other human cancers. In addition, zinc status in plasma and white blood cells is a better indicator of tumor burden and stage of the disease in head and neck cancer patients than overall nutritional status. Research in rodents found that zinc insufficiency leads to a highly proliferative hyperplastic condition in the upper gastrointestinal tract. Zn replenishment reduces the incidence of lingual, esophageal, and forestomach tumors in Zn-deficient rats and mice. While previous animal studies focused on the effect of Zn deficiency on cancer prevention and development, in this study we investigated the effect of Zn supplementation on carcinogenesis in Zn-sufficient mice of wild type and three tumor suppressor-deficient mouse strains, Fhit−/−, Fhit−/−Nit1−/−, and Fhit−/−Rassf1a−/−. About fifty mice from each strain received 6-8 doses of N-nitrosomethylbenzylamine (NMBA). Half the mice then received Zn supplemented water while another half received regular water. Sixteen weeks after last NMBA administration, mice were sacrificed and tumors were found only in forestomach. Mice without Zn supplementation had developed more tumors than Zn-supplemented mice: wild type C57BL/6 mice developed an average of 7.0 vs 5.0 tumors for Zn supplemented (p&lt;0.05); Zn-supplemented Fhit−/− mice averaged 5.7 vs 8.0 for control mice (p&lt; 0.01); Zn-supplemented Fhit−/−Nit1−/− mice averaged 5.4 vs 9.2 for control mice (p&lt; 0.01); and Zn-supplemented Fhit−/−Rassf1a−/−mice averaged 5.9 vs 9.1 for control mice (p&lt; 0.01). Zn supplementation reduced tumor burdens by 28% (wild type) to 42% (Fhit−/−Nit1−/−). Histological analysis of forestomach tissues also showed significant decreases in severity of preneoplastic and neoplastic lesions in Zn-supplemented cohorts of each mouse strain. Thus, Zn supplementation significantly reduced tumor burdens in mice with multiple tumor suppressor deficiencies. When Zn supplementation was begun at 7 weeks after the final carcinogen dose, the reduction in tumor burden was the same as observed when supplementation began immediately after carcinogen dosing, suggesting that Zn supplementation may affect tumor progression rather than tumor initiation. Our study suggests that Zn could have an important role in tumor prevention and perhaps treatment of specific human cancers and should be more thoroughly studied in preclinical models. Citation Information: Cancer Prev Res 2010;3(12 Suppl):B62.
Selective hydroxylation of methyl groups by platinum salts in aqueous medium. Direct conversion of ethanol to ethylene glycol (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective hydroxylation of methyl groups by platinum salts in aqueous medium. Direct conversion of ethanol to ethylene glycolJay A. Labinger, Andrew M. Herring, and John E. BercawCite this: J. Am. Chem. Soc. 1990, 112, 14, 5628–5629Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://pubs.acs.org/doi/10.1021/ja00170a031https://doi.org/10.1021/ja00170a031research-articleACS PublicationsRequest reuse permissionsArticle Views752Altmetric-Citations61LEARN 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 Get e-Alerts
HW / SW partitioning approach for reconfigurable system design (2002)

This paper presents a Genetic Algorithm (GA) based approach for Hardware/Software partitioning targeting an architecture composed of a processor and a dynamically reconfigurable datapath (FPGA). From an acyclic task graph and a set of Area-Time implementation trade off points for each task, our GA performs HW/SW partitioning and scheduling such that the global application execution time is minimized. The efficiency of our GA is established through its application to an AC-3 decoder function and its performance is compared with a greedy algorithm.
Abstract 2248: The implication of STAT3 degradation and its mitochondrial functions in cellular senescence (2014)

Abstract Cellular senescence is a stable growth arrest of the cell cycle considered to be a mechanism of tumor suppression. We have recently described a senescence associated protein degradation or SAPD process that targets many proteins required for tumor progression. The Signal transducer and activator of transcription 3 is one of the targets of SAPD and its downregualtion by RNAi is sufficient to trigger senescence. In the last decade several different functions of STAT3 have been described. Beyond its canonical role as a transcription factor, it has been shown that STAT3 is imported into mitochondria and regulate the activity of the respiratory chain. In this study we want to clarify which function of STAT3 is required to prevent senescence. To do that we have made several mutants of STAT3 affecting different domains of the protein and tested their ability to rescue the senescence response to an anti-Stat3 shRNA. We have found that phosphorylation on residue S727 of STAT3 is important to reestablish proliferation in shSTAT3 induced senescence. Further, transcriptional activity of STAT3 is not required to rescue senescence as a mutant unable to enter the nucleus or the transcriptionally death STAT3 K180A are both able to bypass shSTAT3-induced senescence. Moreover, phosphorylation on Y705 seems not to be important as Y705F STAT3 is also able to reestablish proliferation. All in all, it seems that mitochondrial function of STAT3 is required to prevent senescence since STAT3 S727 phosphorylation is linked to the mitochondrial import of STAT3. Citation Format: Sebastian Igelmann, Xavier Deschênes-Simard, Frédéric Lessard, Véronique Bourdeau, Gerardo Ferbeyre. The implication of STAT3 degradation and its mitochondrial functions in cellular senescence. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2248. doi:10.1158/1538-7445.AM2014-2248
Temperature and strain sensitivities of high-birefringence elliptical fibers (1992)

We have analyzed and calculated the temperature and strain sensitivities of a high-birefringence double-clad elliptical fiber. We propose a method to minimize these sensitivities without increasing the fiber size or weight; this is achieved by selecting suitable fiber parameters-core ellipticity, refractive index difference, and thickness of the inner cladding. In addition, we discuss the design of temperature- or strain-insensitive fibers which may be used in polarimetric strain or temperature sensors. This method may also be used to minimize or enhance other external effects.
Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains (2010)

There is a growing realization that some aging-associated phenotypes/diseases have an epigenetic basis. Here, we report the first genome-scale study of epigenomic dynamics during normal human aging. We identify aging-associated differentially methylated regions (aDMRs) in whole blood in a discovery cohort, and then replicate these aDMRs in sorted CD4(+) T-cells and CD14(+) monocytes in an independent cohort, suggesting that aDMRs occur in precursor haematopoietic cells. Further replication of the aDMRs in buccal cells, representing a tissue that originates from a different germ layer compared with blood, demonstrates that the aDMR signature is a multitissue phenomenon. Moreover, we demonstrate that aging-associated DNA hypermethylation occurs predominantly at bivalent chromatin domain promoters. This same category of promoters, associated with key developmental genes, is frequently hypermethylated in cancers and in vitro cell culture, pointing to a novel mechanistic link between aberrant hypermethylation in cancer, aging, and cell culture.
Analysis of Basic Features in Dynamic Network Models (2018)

Time evolving Random Network Models are presented as a mathematical framework for modelling and analyzing the evolution of complex networks. This framework allows the analysis over time of several network characterizing features such as link density, clustering coefficient, degree distribution, as well as entropy-based complexity measures, providing new insight on the evolution of random networks. First, some simple dynamic network models, based only on edge density, are analyzed to serve as a baseline reference for assessing more complex models. Then, a model that depends on network structure with the aim of reflecting some characteristics of real networks is also analyzed. Such model shows a more sophisticated behavior with two different regimes, one of them leading to the generation of high clustering coefficient/link density ratio values when compared with the baseline values, as it happens in many real networks. Simulation examples are discussed to illustrate the behavior of the proposed models.
Automatic text reduction for changing size constraints (2002)

This paper introduces a technique for viewing text objects under changing size constraints in 2D environments. Our approach automatically combines font size reduction and content reduction to preserve legibility of key words. Unlike traditional semantic zooming, our approach creates intermediate representations and transitions automatically. The main benefit is that it provides more meaningful views for different object sizes without additional authoring effort.
Joint DOA and fundamental frequency estimation methods based on 2-D filtering (2010)

It is well-known that ﬁltering methods can be used for processing of signals in both time and space. This comprises, for example, fundamental frequency estimation and direction-of-arrival (DOA) estimation. In this paper, we propose two novel 2-D ﬁltering methods for joint estimation of the fundamental frequency and the DOA of spatio-temporarily sampled periodic signals. The ﬁrst and simplest method is based on the 2-D periodogram, whereas the second method is a generalization of the 2-D Capon method. In the experimental part, both qualitative and quantitative measurements show that the proposed methods are well-suited for solving the joint estimation problem. Furthermore, it is shown that the methods are able to resolve signals separated sufﬁciently in only one dimension. In the case of closely spaced sources, however, the 2-D Capon-based method shows the best performance.
ChemInform Abstract: β‐Carbonyl Radicals as Three‐Carbon Building Blocks for Carbon (1986)

Abstract Carbon Bond Forming Reactions.