gebhart/patrepeval huggingface dataset:
Effects of thymic selection of the T cell repertoire on HLA-class I associated control of HIV infection (2010)

Without therapy, most people infected with human immunodeficiency virus (HIV) ultimately progress to AIDS. Rare individuals ('elite controllers') maintain very low levels of HIV RNA without therapy, thereby making disease progression and transmission unlikely. Certain HLA class I alleles are markedly enriched in elite controllers, with the highest association observed for HLA-B57 (ref. 1). Because HLA molecules present viral peptides that activate CD8(+) T cells, an immune-mediated mechanism is probably responsible for superior control of HIV. Here we describe how the peptide-binding characteristics of HLA-B57 molecules affect thymic development such that, compared to other HLA-restricted T cells, a larger fraction of the naive repertoire of B57-restricted clones recognizes a viral epitope, and these T cells are more cross-reactive to mutants of targeted epitopes. Our calculations predict that such a T-cell repertoire imposes strong immune pressure on immunodominant HIV epitopes and emergent mutants, thereby promoting efficient control of the virus. Supporting these predictions, in a large cohort of HLA-typed individuals, our experiments show that the relative ability of HLA-B alleles to control HIV correlates with their peptide-binding characteristics that affect thymic development. Our results provide a conceptual framework that unifies diverse empirical observations, and have implications for vaccination strategies.
User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries (2003)

Directed evolution of proteins depends on the production of molecular diversity by random mutagenesis. While a number of methods have been developed for introducing this diversity, the best ways to sample it are not always clear. Here we used simple statistics to analyse completeness and diversity in randomized libraries generated by oligonucleotide-directed mutagenesis, error-prone polymerase chain reaction (epPCR) and in vitro recombination of highly homologous sequences. For oligonucleotide-directed mutagenesis, we derive equations to estimate how complete a given library is expected to be and also to predict the size of library required to give a fixed probability of being 100% complete. We describe the statistical bases for computer programs which estimate the number of distinct variants represented in epPCR and shuffled libraries, dubbed PEDEL and DRIVeR, respectively. These programs allow the user to calculate (rather than guess) the diversity represented in a given library and also provide empirical guidelines for maximizing this diversity. PEDEL and DRIVeR are available at www.bio.cam.ac.uk/ approximately blackburn/stats.html.
Recurrent faulting in the vicinity of Reelfoot Lake, northwestern Tennessee (1979)

Research Article| November 01, 1979 Recurrent faulting in the vicinity of Reelfoot Lake, northwestern Tennessee MARK D. ZOBACK MARK D. ZOBACK 1U.S. Geological Survey, Menlo Park, California 94025 Search for other works by this author on: GSW Google Scholar GSA Bulletin (1979) 90 (11): 1019–1024. https://doi.org/10.1130/0016-7606(1979)90<1019:RFITVO>2.0.CO;2 Article history first online: 01 Jun 2017 Cite View This Citation Add to Citation Manager Share Icon Share MailTo Twitter LinkedIn Tools Icon Tools Get Permissions Search Site Citation MARK D. ZOBACK; Recurrent faulting in the vicinity of Reelfoot Lake, northwestern Tennessee. GSA Bulletin 1979;; 90 (11): 1019–1024. doi: https://doi.org/10.1130/0016-7606(1979)90<1019:RFITVO>2.0.CO;2 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyGSA Bulletin Search Advanced Search Abstract Reelfoot Lake in northwestern Tennessee was the site of considerable ground motion at the time of the 1811–1812 New Madrid earthquakes. Thirty-two kilometres of conventional seismic-reflection profiling in the vicinity of the lake has revealed the existence of many faults. Most significant are two high-angle faults with 50 to 60 m of vertical offset at the contact of the Late Cretaceous embayment sediments and Paleozoic bedrock. One fault is associated with the scarp on the western edge of Reelfoot Lake and the other, with a major northeast-trending lineament that passes through the town of Ridgely, Tennessee, and near the southeast edge of Reelfoot Lake. The nature of the observed vertical offsets suggests recurrent motion on faults of Late Cretaceous, or older, age. This content is PDF only. Please click on the PDF icon to access. First Page Preview Close Modal You do not have access to this content, please speak to your institutional administrator if you feel you should have access.
Large area silicon sheet by EFG. Fourth quarterly report, October 1--December 31, 1976 (1976)

During this reporting period, 5 cm wide ribbons, some with no measurable residual stress, have been grown at speeds up to 5 cm/min. The relationship between residual stress and system vertical temperature gradient was further defined. The problems associated with the purity of the ribbons are being investigated. The influence of light on the recombination characteristics of defects in the ribbons has been investigated. Procedures and results are reported.
Biosynthesis of Desosamine:  Molecular Evidence Suggesting β-Glucosylation as a Self-Resistance Mechanism in Methymycin/Neomethymycin Producing Strain, Streptomyces venezuelae (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTBiosynthesis of Desosamine: Molecular Evidence Suggesting β-Glucosylation as a Self-Resistance Mechanism in Methymycin/Neomethymycin Producing Strain, Streptomyces venezuelaeLishan Zhao, David H. Sherman, and Hung-wen LiuView Author Information Department of Chemistry, University of Minnesota Department of Microbiology and Biological Process Technology Institute, University of Minnesota Minneapolis, Minnesota 55455 Cite this: J. Am. Chem. Soc. 1998, 120, 36, 9374–9375Publication Date (Web):August 25, 1998Publication History Received1 May 1998Published online25 August 1998Published inissue 1 September 1998https://pubs.acs.org/doi/10.1021/ja981500jhttps://doi.org/10.1021/ja981500jrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views220Altmetric-Citations23LEARN 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:Antimicrobial agents,Carbohydrates,Cluster chemistry,Lactones,Macrocyclic compounds Get e-Alerts
How to reduce power in 3D IC designs: A case study with OpenSPARC T2 core (2013)

Low power is considered by many as the driving force for 3D ICs, yet there have been few thorough design studies on how to reduce power in 3D ICs. In this paper, we discuss design methodologies to reduce power consumption in 3D IC designs using a commercial-grade CPU core (OpenSPARC T2 core). To demonstrate power benefits in 3D ICs, four design techniques are explored: (1) 3D floorplanning, (2) metal layer usage control for intra-block-level routing, (3) dual-Vth design, and (4) functional unit block (FUB) folding. With aforementioned methods combined, our 2-tier 3D designs provide up to 52.3% reduced footprint, 25.5% shorter wirelength, 30.2% decreased buffer cell count, and 21.2% power reduction over the 2D counterpart under the same performance.
Correction to Stimuli-Triggered Activity of Nanoreactors by Biomimetic Engineering Polymer Membranes (2015)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to Stimuli-Triggered Activity of Nanoreactors by Biomimetic Engineering Polymer MembranesTomaz Einfalt, R. Goers, I. A. Dinu, A. Najer, M. Spulber, O. Onaca-Fischer, and C. G. Palivan*Cite this: Nano Lett. 2016, 16, 1, 823Publication Date (Web):December 8, 2015Publication History Published online8 December 2015Published inissue 13 January 2016https://pubs.acs.org/doi/10.1021/acs.nanolett.5b04911https://doi.org/10.1021/acs.nanolett.5b04911correctionACS PublicationsCopyright © 2015 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 Views987Altmetric-Citations1LEARN 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 (139 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Conception, synthèse et évaluation biologique d'inhibiteurs de la dimérisation de STAT3 à activité anti-tumorale potentielle (2007)

STATS is a latent cytoplasmic transcription factor that regulates as a dimer the main processes of tumorigenesis. STATS is overactivated in numerous tumors and constitutes as such a promising cancer target. Our work has firstly consisted in validating the inhibition of STATS dimerization as an anti-tumoral approach. A powerful phosphopeptidic ligand targeted to the STATS-SH2 domain was found to inhibit STATS dimerization with an activity in the low micromolar range and was capable of inhibiting STATS oncogenic activity in a tumoral STATS-dependent cell line (NIH 3T3/v-Src), once vectorized. Some of it pharmacological effects were also characterized. In the same time, a novel non-phosphorylated peptide inhibitor of STATS oncogenic activity was also identified. Both peptides were next evaluated on a colon cancer cell line and demonstrated significant apoptotic effects. The second approach has consisted in the conception of different kind of inhibitors (phosphopeptidic, peptidomimetic and non-peptidic compounds). Phosphopeptides demonstrated modest activities on STATS dimerization, whereas conception of peptidomimetics incorporating non-hydrolyzable phosphotyrosine analogs led to the identification of the first non-phosphorous peptidomimetic active on STATS dimerization. The first non-peptidic compounds, based on the 1,4-benzodiazepine scaffold, were found inactive on STATS dimerization but displayed antiproliferative effects on HeLa, A2058 and NIH 3T3/v-src tumor cells. Chalcone derivatives were finally prepared. Modifications done on the reference compound led to molecules displaying greatly enhanced affinities, around hundred micromolars on STATS dimerization.
Effects of daily intake of Harudori-kombu: A randomized, double-blind, placebo-controlled, parallel-group study (2019)

Background: Kombu (Laminariaceae) is traditionally consumed in Japan. “Harudori-kombu” is young kombu harvested in spring. Harudori-kombu contains functional components, such as fucoxanthin—a carotenoid—which confer various biological effects.Methods: In this study, we investigated effects of the continuous intake of dried Harudori-kombu (2.0 g/day) for 6 weeks. We conducted a randomized, double-blind, placebo-controlled, parallel-group study including 70 healthy Japanese subjects with body mass index between 22 and 30 kg/m2 and low-density lipoprotein cholesterol levels between 120 and 160 mg/dL. Subjects were randomly assigned to either Harudori-kombu group or placebo group. Subjects ingested 9 capsules per day for 6 weeks. We conducted medical interviews, vital sign examinations, and blood sampling at weeks 0 (baseline), 2, and 6. Moreover, we assessed body composition at weeks 0 and 6.Results: Harudori-kombu intake did not improve the lipid profile but did reduce body fat. In addition, adiponectin levels were significantly improved.Conclusions: Harudori-kombu intake showed beneficial health effects, such as reduction in body fat and improvement of adiponectin levels, and was deemed safe at the dose administered in this study.
Achieving ultrahigh triboelectric charge density for efficient energy harvesting (2017)

With its light weight, low cost and high efficiency even at low operation frequency, the triboelectric nanogenerator is considered a potential solution for self-powered sensor networks and large-scale renewable blue energy. As an energy harvester, its output power density and efficiency are dictated by the triboelectric charge density. Here we report a method for increasing the triboelectric charge density by coupling surface polarization from triboelectrification and hysteretic dielectric polarization from ferroelectric material in vacuum (P ~ 10<sup>-6</sup> torr). Without the constraint of air breakdown, a triboelectric charge density of 1003 µC m<sup>-2</sup>, which is close to the limit of dielectric breakdown, is attained. Our findings establish an optimization methodology for triboelectric nanogenerators and enable their more promising usage in applications ranging from powering electronic devices to harvesting large-scale blue energy.Triboelectric nanogenerators (TENGs) harvest ambient mechanical energy and convert it into electrical energy. Here, the authors couple surface polarization from contact electrification with dielectric polarization from a ferroelectric material in vacuum to dramatically enhance the TENG output power.
A review on current eCall systems for autonomous car accident detection (2017)

The aim of the paper is to give an overview on the existing eCall solutions for autonomous car accident detection. The requirements and expectations for such systems, considering both technological possibilities, legal regulatory criteria and market demands are discussed. Sensors utilized in e-call systems (crash sensing, systems for positional and velocity data, and communication solutions) are overviewed in the paper. Furthermore, the existing solutions for eCall devices are compared based on their level of autonomy, technical implementation and provided services.
Recent Developments using Background Oriented Schlieren with a Plenoptic Camera. (2019)

Abstract not provided.
On the interpretation and identification of dynamic Takagi-Sugeno fuzzy models (2000)

Dynamic Takagi-Sugeno fuzzy models are not always easy to interpret, in particular when they are identified from experimental data. It is shown that there exists a close relationship between dynamic Takagi-Sugeno fuzzy models and dynamic linearization when using affine local model structures, which suggests that a solution to the multiobjective identification problem exists. However, it is also shown that the affine local model structure is a highly sensitive parametrization when applied in transient operating regimes. Due to the multiobjective nature of the identification problem studied here, special considerations must be made during model structure selection, experiment design, and identification in order to meet both objectives. Some guidelines for experiment design are suggested and some robust nonlinear identification algorithms are studied. These include constrained and regularized identification and locally weighted identification. Their usefulness in the present context is illustrated by examples.
The Color-Box alignment vernier: a sensitive lithographic alignment vernier read at low magnification (1990)

A lithographic alignment vernier based on low-magnification imaging of line-space patterns has been developed. Its resolution is limited only by the lithographic process used; a vernier that can be interpolated to 1/16 µm is demonstrated, using step-and-repeat optical lithography. This vernier can be read quickly and easily because it is read at low magnification, where there are no problems with depth of focus, even for multilevel resists. The vernier is tolerant to variations in linewidth, resist thickness, and edge profile. A machine-readable version of this vernier is also described.
Early corrosion monitoring of prestressed concrete piles using acoustic emission (2013)

The depassivation and corrosion of bonded prestressing steel strands in concrete bridge members may lead to major damage or collapse before visual inspections uncover evident signs of damage, and well before the end of the design life. Recognizing corrosion in its early stage is desirable to plan and prioritize remediation strategies. The Acoustic Emission (AE) technique is a rational means to develop structural health monitoring and prognosis systems for the early detection and location of corrosion in concrete. Compelling features are the sensitivity to events related to micro- and macrodamage, non-intrusiveness, and suitability for remote and wireless applications. There is little understanding of the correlation between AE and the morphology and extent of early damage on the steel surface. In this paper, the evidence collected from prestressed concrete (PC) specimens that are exposed to salt water is discussed vis-à-vis AE data from continuous monitoring. The specimens consist of PC strips that are subjected to wet/dry salt water cycles, representing portions of bridge piles that are exposed to tidal action. Evidence collected from the specimens includes: (a) values of half-cell potential and linear polarization resistance to recognize active corrosion in its early stage; and (b) scanning electron microscopy micrographs of steel areas from two specimens that were decommissioned once the electrochemical measurements indicated a high probability of active corrosion. These results are used to evaluate the AE activity resulting from early corrosion.
Activation Mechanism of Nickel(0) N -Heterocyclic Carbene Catalysts Stabilized by Fumarate Ligands (2022)

Nickel(0) catalysts of <i>N</i>-heterocyclic carbenes (NHCs) that are stabilized by electron-deficient alkenes possess desirable properties of air tolerance and ease of handling while also retaining high catalytic activities. Since catalyst stability often comes at the expense of catalytic activity, we have undertaken a detailed study of the activation mechanism of an IMes-nickel(0) catalyst stabilized by di(<i>o</i>-tolyl) fumarate that converts the stable precatalyst form into a catalytically active species. Computational evaluation provided evidence against a simple ligand exchange as the activation mechanism for this catalyst, and a stoichiometric activation process that covalently modifies the stabilizing ligand was identified. A detailed computational picture for the activation process was developed, with predictive insights that elucidate an unexpected catalyst activation pathway that operates when ligand exchange is thermodynamically unfavorable.
Estimating Surface Water Presence and Infiltration in Ephemeral to Intermittent Streams in the Southwestern US (2020)

Streamflow in arid and semi-arid regions is predominantly temporary, an integral part of mountain block hydrology and of significant importance for groundwater recharge and biogeochemical processes. However, temporary streamflow regimes, especially ephemeral flow, remain poorly quantified. We use electrical resistance sensors and USGS stream gauge data in 15 southern Arizona streams spanning a climate gradient (mean annual precipitation from 160 to 750 mm) to quantify temporary streamflow as streamflow presence and water presence, which includes streamflow, ponding and soil moisture. We use stream channel sediment data to estimate saturated hydraulic conductivity and potential annual infiltration. Annual streamflow ranged 0.6–82.4% or 2–301 days; while water presence ranged from 2.6 to 82.4% or 10 to over 301 days, or 4–33 times longer than streamflow. We identified 5 statistically distinct flow regimes based on the annual percent streamflow and water presence: (1) dry-ephemeral, (2) wet-ephemeral, (3) dry-intermittent, (4) wet-intermittent, and (5) seasonally-intermittent. In contrast to our expectations, stream channel density was a better predictor of annual streamflow and water presence than annual rainfall alone. Whereas, the dry-ephemeral and wet-ephemeral flow regimes varied with seasonal precipitation, the dry-intermittent, wet intermittent and seasonally-intermittent flow regimes did not. These results coupled with the potential infiltration estimates indicate that streamflow at the driest sites occurs in response to rainfall and overland flow while groundwater discharge and vadose zone contributions enhance streamflow at the wetter sites. We suggest that on a short temporal scale, and with respect to water presence, wetter sites might be buffered better against shifts in the timing and distribution of precipitation in response to climate change. Flow regime classifications that include both stream flow and water presence, rather than on stream flow alone, may be important for predicting thresholds in ecological functions and refugia in these dryland systems.
Seed quality: basic mechanisms and agricultural implications (1996)

ContentsPreface * Seed Viability * Seed Vigor * Methods of Viability and Vigor Testing: A Critical Appraisal * Production Environment and Seed Quality * Seed Quality and Microorganisms * Storage of Orthodox Seeds * Storage of Recalcitrant Seeds * Mechanisms of Seed Deterioration * Variety Identification: Modern Techniques and Applications * Low Water Potential and Pre-Sowing Germinating Treatments to Improve Seed Quality * Influence of Seed Quality on Crop Establishment, Growth, and Yield * Index