gebhart/patrepeval huggingface dataset:
Structural Basis of the CD8αβ/MHC Class I Interaction: Focused Recognition Orients CD8β to a T Cell Proximal Position (2009)

In the immune system, B cells, dendritic cells, NK cells, and T lymphocytes all respond to signals received via ligand binding to receptors and coreceptors. Although the specificity of T cell recognition is determined by the interaction of T cell receptors with MHC/peptide complexes, the development of T cells in the thymus and their sensitivity to Ag are also dependent on coreceptor molecules CD8 (for MHC class I (MHCI)) and CD4 (for MHCII). The CD8alphabeta heterodimer is a potent coreceptor for T cell activation, but efforts to understand its function fully have been hampered by ignorance of the structural details of its interactions with MHCI. In this study we describe the structure of CD8alphabeta in complex with the murine MHCI molecule H-2D(d) at 2.6 A resolution. The focus of the CD8alphabeta interaction is the acidic loop (residues 222-228) of the alpha3 domain of H-2D(d). The beta subunit occupies a T cell membrane proximal position, defining the relative positions of the CD8alpha and CD8beta subunits. Unlike the CD8alphaalpha homodimer, CD8alphabeta does not contact the MHCI alpha(2)- or beta(2)-microglobulin domains. Movements of the CD8alpha CDR2 and CD8beta CDR1 and CDR2 loops as well as the flexibility of the H-2D(d) CD loop facilitate the monovalent interaction. The structure resolves inconclusive data on the topology of the CD8alphabeta/MHCI interaction, indicates that CD8beta is crucial in orienting the CD8alphabeta heterodimer, provides a framework for understanding the mechanistic role of CD8alphabeta in lymphoid cell signaling, and offers a tangible context for design of structurally altered coreceptors for tumor and viral immunotherapy.
Analysis of tissue-specific methylation patterns of mouse mammary tumor virus DNA by two-dimensional Southern blotting (1985)

We used a two-dimensional Southern blotting procedure to analyze the tissue-specific methylation patterns of the five endogenous mouse mammary tumor viruses in the GR/A mouse strain. Our findings suggest that in certain tissues (brain, kidney, and liver) all proviruses are extensively methylated. In other tissues (spleen, placenta, and testes) all proviruses are hypomethylated to some degree. In these tissues individual proviruses display both quantitative and qualitative differences in methylation. We interpret the general patterns of tissue-specific hypomethylation in terms of a "hitch-hiker" model: mouse mammary tumor virus proviral methylation patterns reflect the tissue-specific activity of neighboring sequences. The observation that certain sites on particular proviruses are differentially methylated in a tissue-specific fashion may reflect tissue-specific differences in the makeup or conformation, or both, of proviral-containing chromatin.
Protection from Experimental Asthma by an Endogenous Bronchodilator (2005)

Mechanisms that protect against asthma remain poorly understood. S-nitrosoglutathione (GSNO), an endogenous bronchodilator, is depleted from asthmatic airways, suggesting a protective role. We report that, following allergen challenge, wild-type mice exhibiting airway hyperresponsivity have increased airway levels of the enzyme GSNO reductase (GSNOR) and are depleted of lung S-nitrosothiols (SNOs). In contrast, mice with genetic deletion of GSNOR exhibit increases in lung SNOs and are protected from airway hyperresponsivity. Our results indicate that endogenous SNOs, governed by GSNOR, are critical regulators of airway responsivity and may provide new therapeutic approaches to asthma.
Energy (FUEL) Conservation through Underwater Removal and Control of Fouling on Hulls of Navy Ships (1975)

Operating costs and performance efficiency of Navy ships have become matters of increasing concern because of the fourfold increase in cost and the unpredictable availability of foreign and domestic supplies of petroleum fuel. Methods whereby the Navy can conserve fuel are urgently needed. A systematic program for underwater removal and control of fouling is one method which has considerable potential merit for attaining the objective of conserving fuel and improving ship performance. This report reviews the characteristics of fouling and describes underwater hull inspection and cleaning methods. It delineates the interactions among fuel consumption, fouling, and the compatibility of underwater cleaning methods with the antifouling paint coating on the hull. It also presents an integrated concept of hull cleaning and fouling control. A program plan is described which, when completed, is presented to result in the conservation of fuel and improved ship performance through the development and Fleet-wide implementation of cost-effective underwater hull-cleaning methodology to remove and control fouling on Navy ships. Conservative estimates place this fuel saving at 15% of the total quantity consumed by the Fleet. With respect to effective control of fouling, this should assure attainment of the current Navy objective of making ships available for 5 years between successive drydockings. With respect to effective control of fouling, this should assure attainment of effective control of fouling, this should assure attainment of the current Navy objective of making ships available for 5 years between successive drydockings.
Synthesis of Carbasugars from Aldonolactones: Ritter-Type Epoxide Opening in the Synthesis of Polyhydroxylated Aminocyclopentanes (1999)

Using the cis-fused cyclopentane-1,4-lactone, (1R,5S,7R,8R)-7,8-dihydroxy-2-oxabicyclo[3.3.0]oct-3-one (1), as starting material, 5-deoxycarba-β-l-xylo-hexofuranose (6) together with α- (12) and β-1-amino-1,5-dideoxycarba-l-xylo-hexofuranose (16) have been prepared using a number of stereoselective transformations. The key step was the regioselective opening of the epoxide (1R,5S,7R,8R)-7,8-epoxy-2-oxabicyclo-[3.3.0]oct-3-one (4) with different nucleophiles.
A Recursive Algorithm for the Three-Dimensional Imaging of Brain Electric Activity: Shrinking LORETA-FOCUSS (2004)

Estimation of intracranial electric activity from the scalp electroencephalogram (EEG) requires a solution to the EEG inverse problem, which is known as an ill-conditioned problem. In order to yield a unique solution, weighted minimum norm least square (MNLS) inverse methods are generally used. This paper proposes a recursive algorithm, termed Shrinking LORETA-FOCUSS, which combines and expands upon the central features of two well-known weighted MNLS methods: LORETA and FOCUSS. This recursive algorithm makes iterative adjustments to the solution space as well as the weighting matrix, thereby dramatically reducing the computation load, and increasing local source resolution. Simulations are conducted on a 3-shell spherical head model registered to the Talairach human brain atlas. A comparative study of four different inverse methods, standard Weighted Minimum Norm, L1-norm, LORETA-FOCUSS and Shrinking LORETA-FOCUSS are presented. The results demonstrate that Shrinking LORETA-FOCUSS is able to reconstruct a three-dimensional source distribution with smaller localization and energy errors compared to the other methods.
A Statistical Model for Signature Verification (2005)

A Bayesian model for off-line signature verification involving the representation of a signature through its curvature is developed. The prior model makes use of a spatial point process for specifying the knots in an approximation restricted to a buffer region close to a template curvature, along with an independent time-warping mechanism. In this way, prior shape information about the signature can be built into the analysis. The observation model is based on additive white noise superimposed on the underlying curvature. The approach is implemented using Markov chain Monte Carlo and applied to a collection of documented instances of William Shakespeare's signature.
Heat shock protein 90 in neurodegenerative diseases (2010)

Hsp90 is a molecular chaperone with important roles in regulating pathogenic transformation. In addition to its well-characterized functions in malignancy, recent evidence from several laboratories suggests a role for Hsp90 in maintaining the functional stability of neuronal proteins of aberrant capacity, whether mutated or over-activated, allowing and sustaining the accumulation of toxic aggregates. In addition, Hsp90 regulates the activity of the transcription factor heat shock factor-1 (HSF-1), the master regulator of the heat shock response, mechanism that cells use for protection when exposed to conditions of stress. These biological functions therefore propose Hsp90 inhibition as a dual therapeutic modality in neurodegenerative diseases. First, by suppressing aberrant neuronal activity, Hsp90 inhibitors may ameliorate protein aggregation and its associated toxicity. Second, by activation of HSF-1 and the subsequent induction of heat shock proteins, such as Hsp70, Hsp90 inhibitors may redirect neuronal aggregate formation, and protect against protein toxicity. This mini-review will summarize our current knowledge on Hsp90 in neurodegeneration and will focus on the potential beneficial application of Hsp90 inhibitors in neurodegenerative diseases.
Two type III effector genes of Xanthomonas oryzae pv. oryzae control the induction of the host genes OsTFIIA γ 1 and OsTFX1 during bacterial blight of rice (2007)

Xanthomonas oryzae pv. oryzae strain PXO99(A) induces the expression of the host gene Os8N3, which results in increased host susceptibility to bacterial blight of rice. Here, we show that PXO99(A) affects the expression of two additional genes in a type III secretion system-dependent manner, one encoding a bZIP transcription factor (OsTFX1) and the other the small subunit of the transcription factor IIA located on chromosome 1 (OsTFIIAgamma1). Induction of OsTFX1 and OsTFIIAgamma1 depended on the type III effector genes pthXo6 and pthXo7, respectively, both encoding two previously undescribed members of the transcription activator-like (TAL) effector family. pthXo7 is strain-specific and may reflect adaptation to the resistance mediated by xa5, an allele of OsTFIIAgamma5 encoding a second form of the TFIIA small subunit on chromosome 5 of rice. The loss of pthXo6 resulted in reduced pathogen virulence, and ectopic expression of OsTFX1 abrogated the requirement for pthXo6 for full virulence. X. oryzae pv. oryzae therefore modulates the expression of multiple host genes using multiple TAL effectors from a single strain, and evidence supports the hypothesis that expression of the associated host genes contributes to host susceptibility to disease.
Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acidTomas Lindahl and Annika AnderssonCite this: Biochemistry 1972, 11, 19, 3618–3623Publication Date (Print):September 12, 1972Publication History Published online1 May 2002Published inissue 12 September 1972https://pubs.acs.org/doi/10.1021/bi00769a019https://doi.org/10.1021/bi00769a019research-articleACS PublicationsRequest reuse permissionsArticle Views1263Altmetric-Citations432LEARN 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
Controlling the Aggregation of Conjugates of Streptavidin with Smart Block Copolymers Prepared via the RAFT Copolymerization Technique (2006)

Block copolymers containing stimuli-responsive segments provide important new opportunities for controlling the activity and aggregation properties of protein-polymer conjugates. We have prepared a RAFT block copolymer of a biotin-terminated poly(N-isopropylacrylamide) (PNIPAAm)-b-poly(acrylic acid) (PAA). The number-average molecular weight (M(n)) of the (PNIPAAm)-b-(PAA) copolymer was determined to be 17.4 kDa (M(w)/M(n) = 1.09). The PNIPAAm block had an M(n) of 9.5 kDa and the poly(acrylic acid) (PAA) block had an M(n) of 7.9 kDa. We conjugated this block copolymer to streptavidin (SA) via the terminal biotin on the PNIPAAm block. We found that the usual aggregation and phase separation of PNIPAAm-SA conjugates that follow the thermally induced collapse and dehydration of PNIPAAm (the lower critical solution temperature (LCST) of PNIPAAm is 32 degrees C in water) is prevented through the shielding action of the PAA block. In addition, we show that the cloud point and aggregation properties (as measured by loss in light transmission) of the [(PNIPAAm)-b-(PAA)]-SA conjugate also depended on pH. At pH 7.0 and at temperatures above the LCST, the block copolymer alone was found to form particles of ca. 60 nm in diameter, while the bioconjugate exhibited very little aggregation. At pH 5.5 and 20 degrees C, the copolymer alone was found to form large aggregates (ca. 218 nm), presumably driven by hydrogen bonding between the -COOH groups of PAA with other -COOH groups and also with the -CONH- groups of PNIPAAm. In comparison, the conjugate formed much smaller particles (ca. 27 nm) at these conditions. At pH 4.0, however, large particles were formed from the conjugate both above and below the LCST (ca. 700 and 540 nm, respectively). These results demonstrate that the aggregation properties of the block copolymer-SA conjugate are very different from those of the free block copolymer, and that the outer-oriented hydrophilic block of PAA shields the intermolecular aggregation of the block copolymer-SA bioconjugate at pH values where the -COOH groups of PAA are significantly ionized.
Branch strategy taxonomy and performance models (1991)

For software designers, classifies and describes six basic branching strategies, present analytic models to evaluate each strategy under various work-load and pipeline parameters, and outlines a modeling methodology for evaluating new branching strategies. No index. Annotation copyright Book News, I
Engineering the Temporal Response of Photoconductive Photodetectors via Selective Introduction of Surface Trap States (2008)

Photoconductive photodetectors fabricated using simple solution-processing have recently been shown to exhibit high gains (>1000) and outstanding sensitivities ( D* > 10(13) Jones). One ostensible disadvantage of exploiting photoconductive gain is that the temporal response is limited by the release of carriers from trap states. Here we show that it is possible to introduce specific chemical species onto the surfaces of colloidal quantum dots to produce only a single, desired trap state having a carefully selected lifetime. In this way we demonstrate a device that exhibits an attractive photoconductive gain (>10) combined with a response time ( approximately 25 ms) useful in imaging. We achieve this by preserving a single surface species, lead sulfite, while eliminating lead sulfate and lead carboxylate. In doing so we preserve the outstanding sensitivity of these devices, achieving a specific detectivity of 10(12) Jones in the visible, while generating a temporal response suited to imaging applications.
Analysis of Regulatory Elements Involved in the Induction of Two Tobacco Genes by Salicylate Treatment and Virus Infection (1990)

Miranda D. Van de Rhee, Jan A. L. Van Kan, , John F. Bol, Analysis of Regulatory Elements Involved in the Induction of Two Tobacco Genes by Salicylate Treatment and Virus Infection, The Plant Cell, Vol. 2, No. 4 (Apr., 1990), pp. 357-366
Biodistribution and efficacy of [131I]A33scFv::CDy, a recombinant antibody-enzyme protein for colon cancer (2008)

In antibody-directed enzyme-prodrug therapy (ADEPT), an antibody-bound enzyme localizes to tumor tissue, where it selectively converts a subsequently administered non-toxic prodrug into a cytotoxic drug. A33scFv::CDy is a bifunctional fusion construct comprising a single chain antibody against the gpA33 antigen and the prodrug-converting enzyme cytosine deaminase. gpA33 is highly and homogeneously expressed in >95% of all colorectal cancers. Here we describe the biodistribution and tumor-targeting capacity of 131I labeled A33scFv::CDy. 131I labeling of A33scFv::CDy was performed by the chloramine-T method, and the properties of the resulting [131I]A33scFv::CDy conjugate were determined in vivo and in vitro, including biodistribution studies in nude mice bearing human LIM1215 colon carcinoma xenografts. The [131I]A33scFv::CDy conjugate bound specifically to colorectal cancer cells in vitro with KD = 15.8 nM as determined by a saturation assay. in vivo, the tumor uptake of [131I]A33scFv::CDy peaked at 87% injected dose/g 47 h post injection. Normal tissue uptake was low, and activity in blood was lower than in tumor at all time-points studied (6-92 h). The tumor-to-blood ratio increased over time with a maximum of 8.1 at 67 h post injection. [131I]A33scFv::CDy thus shows a biodistribution that makes it attractive for both radioimmunotherapy (RIT) and ADEPT. Preliminary therapeutic experiments showed a significant reduction of tumor size in mice treated with the A33scFv::CDy-5-fluorocytosine/5-fluorouracil ADEPT system. This work demonstrates the feasibility of ADEPT and RIT based on the A33scFv::CDy recombinant construct.
Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability (2009)

We found that a selective gut microbiota change controls and increases endogenous GLP-2 production, and consequently improves gut barrier functions by a GLP-2-dependent mechanism, contributing to the improvement of gut barrier functions during obesity and diabetes.
A recommendation system for spots in location-based online social networks (2011)

Centralized Online Social Network services (OSN) are collecting immense amounts of data, containing a wealth of information about preferences of their users. Its exploitation for the benefit of the users, even though quite promising, has not seriously been tackled, yet. For this purpose, we propose a personalized recommender for places in location-based OSNs, based on the check-ins of the entire user base. Following a brief analysis, we first propose an interpretation of the data available to OSN providers and an recommendation scheme based on regularized matrix factorization. To evaluate our approach we acquire a large sample of a real data set by crawling Gowalla, one of the most popular location-based OSNs. An exhaustive experimental evaluation then confirms the feasability of using Collaborative Filtering techniques to make personalized recommendation of potentially interesting spots.
Chemical and mechanical degradation of UHMWPE: Report of the development of an in vitro test (1994)

Abstract Ultra high molecular weight polyethylene (UHMWPE), used in total joint replacement implants, undergoes oxidative degradation due to gamma radiation sterilization and to exposure to oxidizing agents in the body environment. UHMWPE components also experience large stresses both on and near the articulating surface. It is hypothesized that there is a causal relationship between chemical degradation and mechanical loading of UHMWPE joint components. This report describes the development of an in vitro test to examine the combined effects of chemical environment and cyclic loading history on the chemical, physical, and mechanical properties of UHMWPE. The test apparatus consists of modular load trains, in which strings of UHMWPE test specimens can be subjected to cyclic tensile and compression load ranges, while being exposed to either control or degrading environments. Following cyclic loading for specified time intervals, the specimens can be statically loaded to determine the effect of cyclic loading and environment on the monotonic tensile and compressive stress–strain behavior of UHMWPE. To determine the appropriate control and degrading environments, gamma radiation sterilized UHMWPE specimens were maintained (unloaded) for up to 6 months in aqueous environments of distilled water and three concentrations of hydrogen peroxide (0.01, 0.1, and 1.0%) in distilled water at 37°C. Specimens were evaluated with depth from the surface for changes in density. Infrared spectroscopy (IR) analysis was conducted on selected surface sections. No significant changes in density or surface IR spectra occurred for specimens in distilled water as compared with the UHMWPE in the initial radiation sterilized condition. Specimens exposed to hydrogen peroxide solutions demonstrated changes in density and IR spectra consistent with oxidative degradation and comparable to the changes previously observed on retrieved UHMWPE components. Based on these results, distilled water was selected for the control environment. A 0.5% hydrogen peroxide solution was selected for the test environment, to produce moderate changes at a rate compatible with the maximum 12‐month time period of the experiment. © 1994 John Wiley &amp; Sons, Inc.
Carbohydrates in solution: studies with stable isotopes (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbohydrates in solution: studies with stable isotopesRobert Barker and Anthony S. SerianniCite this: Acc. Chem. Res. 1986, 19, 10, 307–313Publication Date (Print):October 1, 1986Publication History Published online1 May 2002Published inissue 1 October 1986https://pubs.acs.org/doi/10.1021/ar00130a003https://doi.org/10.1021/ar00130a003research-articleACS PublicationsRequest reuse permissionsArticle Views218Altmetric-Citations19LEARN 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