gebhart/patrepeval huggingface dataset:
Peptide:MHC Tetramer-based Enrichment of Epitope-specific T cells (2012)

A basic necessity for researchers studying adaptive immunity with in vivo experimental models is an ability to identify T cells based on their T cell antigen receptor (TCR) specificity. Many indirect methods are available in which a bulk population of T cells is stimulated in vitro with a specific antigen and epitope-specific T cells are identified through the measurement of a functional response such as proliferation, cytokine production, or expression of activation markers(1). However, these methods only identify epitope-specific T cells exhibiting one of many possible functions, and they are not sensitive enough to detect epitope-specific T cells at naive precursor frequencies. A popular alternative is the TCR transgenic adoptive transfer model, in which monoclonal T cells from a TCR transgenic mouse are seeded into histocompatible hosts to create a large precursor population of epitope-specific T cells that can be easily tracked with the use of a congenic marker antibody(2,3). While powerful, this method suffers from experimental artifacts associated with the unphysiological frequency of T cells with specificity for a single epitope(4,5). Moreover, this system cannot be used to investigate the functional heterogeneity of epitope-specific T cell clones within a polyclonal population. The ideal way to study adaptive immunity should involve the direct detection of epitope-specific T cells from the endogenous T cell repertoire using a method that distinguishes TCR specificity solely by its binding to cognate peptide:MHC (pMHC) complexes. The use of pMHC tetramers and flow cytometry accomplishes this(6), but is limited to the detection of high frequency populations of epitope-specific T cells only found following antigen-induced clonal expansion. In this protocol, we describe a method that coordinates the use of pMHC tetramers and magnetic cell enrichment technology to enable detection of extremely low frequency epitope-specific T cells from mouse lymphoid tissues(3,7). With this technique, one can comprehensively track entire epitope-specific populations of endogenous T cells in mice at all stages of the immune response.
Measures of gene expression for affymetrix high density oligonucleotide arrays (2003)

High density oligonucleotide expression array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression.In Affymetrix GeneChip array technology, each gene is typically represented by a set of 11-20 pairs of oligonucleotides, separately referred to as probes, arrayed on a silicon chip.After chip measurements are preprocessed, a fluorescence intensity value for each probe is obtained.A necessary step for defining a measure of expression (ME) is to summarize the probe intensities for a given gene.In this paper, we review the ideas that motivate a summary statistic, referred to as the robust multi-array average (RMA) 9 that improves the default Affymetrix approach and provides substantial benefits to users of the GeneChip technology.
Brain MR Imaging at Ultra-low Radiofrequency Power (2011)

The 3D techniques adopted here led to a decrease in the absorbed RF power by two orders of magnitude at 1.5 T, and still the image quality was preserved within clinically acceptable imaging times.
Nonpolluting automobiles (1994)

The advantages/disadvantages of energy storage devices, which can provide nonpolluting automobile systems are discussed. Four types of storage devices are identified: electrochemical (batteries); hydrogen; electromechanical (flywheels); and molten salt heat storage. A high-speed flywheel with a small permanent magnet motor/generator has more advantages than any of the other systems and might become a real competitor to the internal combustion engine. A flywheel/motor/generator system for automobiles now becomes practical, because of the technological advances in materials, bearings and solid state control circuits. The motor of choice is the squirrel cage induction motor, specially designed for automobile applications. The preferred controller for the induction motor is a forced commutated cycloconverter, which transforms a variable voltage/variable frequency source into a controlled variable-voltage/variable-frequency supply. A modulation strategy of the cycloconverter elements is selected to maintain a unity input displacement factor (power factor) under all conditions of loads voltages and frequencies. The system is similar to that of the existing automobile, if only one motor is used: master controller-controller-motor-gears (fixed)-differential-wheels. In the case of two motors, the mechanical differential is replaced by an electric one: master controller-controller-motor-gears (fixed)-wheel. A four-wheel drive vehicle is obtained when four motors with their own controllers are used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Frame Splitting Scheme for Error-Robust Audio Streaming over Packet-Switching Networks (2008)

This letter presents a novel frame splitting scheme for an error-robust audio streaming over packet-switching networks. In our approach to perceptual audio coding, an audio frame is split into several subframes based on the network configuration such that each packet can be decoded independently at the receiver. Through a subjective comparison category rating (CCR) test, it is discovered that our approach enhances the quality of the decoded audio signal under the lossy packet-switching networks environment.
Heparanase Is Essential for the Development of Diabetic Nephropathy in Mice (2011)

Diabetic nephropathy (DN) is the major life-threatening complication of diabetes. Abnormal permselectivity of glomerular basement membrane (GBM) plays an important role in DN pathogenesis. Heparanase is the predominant enzyme that degrades heparan sulfate (HS), the main polysaccharide of the GBM. Loss of GBM HS in diabetic kidney was associated with increased glomerular expression of heparanase; however, the causal involvement of heparanase in the pathogenesis of DN has not been demonstrated. We report for the first time the essential involvement of heparanase in DN. With the use of Hpse-KO mice, we found that deletion of the heparanase gene protects diabetic mice from DN. Furthermore, by investigating the molecular mechanism underlying induction of the enzyme in DN, we found that transcription factor early growth response 1 (Egr1) is responsible for activation of heparanase promoter under diabetic conditions. The specific heparanase inhibitor SST0001 markedly decreased the extent of albuminuria and renal damage in mouse models of DN. Our results collectively underscore the crucial role of heparanase in the pathogenesis of DN and its potential as a highly relevant target for therapeutic interventions in patients with DN.
Asymptotics for kernel estimate of sliced inverse regression (1996)

To explore nonlinear structures hidden in high-dimensional data and to estimate the effective dimension reduction directions in multivariate nonparametric regression, Li and Duan proposed the sliced inverse regression (SIR) method which is simple to use. In this paper, the asymptotic properties of the kernel estimate of sliced inverse regression are investigated. It turns out that regardless of the kernel function, the asymptotic distribution remains the same for a wide range of smoothing parameters.
PubMed-supported clinical term weighting approach for improving inter-patient similarity measure in diagnosis prediction (2015)

Our findings suggest that the optimized similarity measure with specific term weighting to EHRs can improve significantly the accuracy for predicting the inter-patient co-occurrence of diagnosis when compared with equal and generic term weighting approaches.
FEEDBACK STABILIZATION OF A CLASS OF NONLINEAR PLANTS (1988)

We generalize the right-coprimeness definition by requiring only that the corresponding plant's pseudo-state can be reconstructed by a two-input one-output stable observer. We obtain right-coprime factorizations for a class of nonlinear plants, where a two-input one-output pseudo-state observer is constructed. A feedback stabilization scheme is given using this observer.
Hanukkah in Alaska by Barbara Brown (review) (2013)

Reviewed by: Hanukkah in Alaska by Barbara Brown Deborah Stevenson Brown, Barbara Hanukkah in Alaska; illus. by Stacey Schuett. Holt, 2013 [32p] ISBN 978-0-8050-9748-1 $16.99 Reviewed from galleys R 5-8 yrs Winter in Alaska is a different experience, marked by limited daylight and fearlessly marauding moose, who enjoy the convenience of human-plowed streets and driveways. Even the promise of Hanukkah isn't enough to cheer up the narrator, a young girl who's worried that the moose hanging around her family's backyard will wreck her beloved blue swing. She still manages to thrill to a splendid display of the aurora borealis ("Our very own Hanukkah Festival of Lights"), though, and the holiday celebrations give her an excellent idea for a moose-diverting treat: latkes. The text (adapted from a previously published short story) is an inviting [End Page 140] combination of matter-of-factness and vivid local detail ("When my friends and I are playing outside and a moose comes along, we have to hug a tree. A moose can't step on you or knock you over if you're hugging a tree") that makes it sound like a real-life incident, and the gentle intermixing of holiday and unusual setting avoids didactic overfocusing on either. Schuett's softly rounded and rosy-faced figures are particularly suited to the story, and the acrylic and gouache illustrations give the snow-mounded scenery a cozy domesticity with occasional comic touches (the scene of a pack of kids calmly and obediently clutching trees as the moose inspects them is quite adorable). For residents in the lower 48, this will be an enchanting new take on winter and winter holidays, a sound addition to a Hanukkah-themed storytime, and an invitation to discuss local wildlife encounters. An author's note briefly describes the aurora borealis and the holiday of Hanukkah. Copyright © 2013 The Board of Trustees of the University of Illinois
A new method to find an optimal warping function in image stitching (2009)

In image stitching applications, it is very important to find a suitable warping function for the visual quality of a composite (stitching result). In this paper, we present a new mathematical criterion to select an optimal warping function among a set of possible candidates (e.g., parametric family). The proposed criterion can be considered as a direct view condition for image stitching , i.e., it is desirable that each part of the composite image looks like its corresponding input image. More specifically, we do not use an explicit modeling of a compositing surface, but, we focus on the differential properties of a warping function. That is we design a cost function so that the Jacobian matrix of a warping function is close to a shape preserving matrix such as rotation and reflection matrices. The proposed cost function can be effectively minimized by using Levenberg-Marquardt algorithm. The experimental results show that the proposed method results in visually pleasing stitched results because the original shape of each image is preserved in the composite.
Nine <i>N</i>-aryl-2-chloronicotinamides: supramolecular structures in one, two and three dimensions (2006)

Structures are reported here for eight further substituted N-aryl-2-chloronicotinamides, 2-ClC(5)H(3)NCONHC(6)H(4)X-4'. When X = H, compound (I) (C(12)H(9)ClN(2)O), the molecules are linked into sheets by N-H...N, C-H...pi(pyridyl) and C-H...pi(arene) hydrogen bonds. For X = CH(3), compound (II) (C(13)H(11)ClN(2)O, triclinic P1 with Z' = 2), the molecules are linked into sheets by N-H...O, C-H...O and C-H...pi(arene) hydrogen bonds. Compound (III), where X = F, crystallizes as a monohydrate (C(12)H(8)ClFN(2)O.H(2)O) and sheets are formed by N-H...O, O-H...O and O-H...N hydrogen bonds and aromatic pi...pi stacking interactions. Crystals of compound (IV), where X = Cl (C(12)H(8)Cl(2)N(2)O, monoclinic P2(1) with Z' = 4) exhibit inversion twinning: the molecules are linked by N-H...O hydrogen bonds into four independent chains, linked in pairs by C-H...pi(arene) hydrogen bonds. When X = Br, compound (V) (C(12)H(8)BrClN(2)O), the molecules are linked into sheets by N-H...O and C-H...N hydrogen bonds, while in compound (VI), where X = I (C(12)H(8)ClIN(2)O), the molecules are linked into a three-dimensional framework by N-H...O and C-H...pi(arene) hydrogen bonds and an iodo...N(pyridyl) interaction. For X = CH(3)O, compound (VII) (C(13)H(11)ClN(2)O(2)), the molecules are linked into chains by a single N-H...O hydrogen bond. Compound (VIII) (C(13)H(8)ClN(3)O, triclinic P1 with Z' = 2), where X = CN, forms a complex three-dimensional framework by N-H...N, C-H...N and C-H...O hydrogen bonds and two independent aromatic pi...pi stacking interactions.
Murine Model of Wound Healing (2013)

Wound healing and repair are the most complex biological processes that occur in human life. After injury, multiple biological pathways become activated. Impaired wound healing, which occurs in diabetic patients for example, can lead to severe unfavorable outcomes such as amputation. There is, therefore, an increasing impetus to develop novel agents that promote wound repair. The testing of these has been limited to large animal models such as swine, which are often impractical. Mice represent the ideal preclinical model, as they are economical and amenable to genetic manipulation, which allows for mechanistic investigation. However, wound healing in a mouse is fundamentally different to that of humans as it primarily occurs via contraction. Our murine model overcomes this by incorporating a splint around the wound. By splinting the wound, the repair process is then dependent on epithelialization, cellular proliferation and angiogenesis, which closely mirror the biological processes of human wound healing. Whilst requiring consistency and care, this murine model does not involve complicated surgical techniques and allows for the robust testing of promising agents that may, for example, promote angiogenesis or inhibit inflammation. Furthermore, each mouse acts as its own control as two wounds are prepared, enabling the application of both the test compound and the vehicle control on the same animal. In conclusion, we demonstrate a practical, easy-to-learn, and robust model of wound healing, which is comparable to that of humans.
Investigations into the Silica/Silane Reaction System (1997)

Abstract Silica in combination with organosilanes ( e.g. [bis(3-triethoxysilylpropyl)tetrasulfane] = TESPT) has recently become more important in tire applications. Their use in tire treads leads to an improvement in rolling resistance and wet traction. The requirements for the attainment of these properties are, that the triethoxysilyl groups of TESPT react with the silanol groups on the silica surface during compounding, and the polymer active groups react with the polymer during cure. The reaction of precipitated silica with this silane was investigated. The influence of various parameters on the reaction type and the reaction kinetics was considered. The results of the investigation obtained using 29 Si-CP/MAS solid state NMR spectroscopy agree well with a horizontal reaction model in which a single siloxane bond is first formed with the silica surface (primary reaction). It is followed by condensation reactions between silanol groups of silane molecules which are already bound to the silica surface (secondary reaction). The kinetic studies data show a clear difference between the fast primary reaction and the slow secondary reaction. Both reactions become more rapid in acidic and alkaline pH ranges. The primary reaction accelerates up to a particular H 2 O content after which the rate remains constant. The secondary reaction keeps on accelerating with rising H 2 O content. Modification with different silane concentrations showed a higher rate constant at low concentrations.
The phytocannabinoid, Δ<sup>9</sup>‐tetrahydrocannabivarin, can act through 5‐<scp>HT</scp><sub>1</sub><scp><sub>A</sub></scp> receptors to produce antipsychotic effects (2014)

Our findings suggest that THCV can enhance 5-HT₁A receptor activation, and that some of its apparent antipsychotic effects may depend on this enhancement. We conclude that THCV has therapeutic potential for ameliorating some of the negative, cognitive and positive symptoms of schizophrenia.
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR-α (PPARα) REGULATES ISCHEMIC LIVER INJURY (2003)

Laboratory of Trauma, Sepsis & Inflammation Research, Department of Surgery, University of Cincinnati, Cincinnati, OH 45267.
A Monolithic FE Formulation for the Analysis of Membranes in Fluids (2009)

We propose here an efficient approach for treating the interaction between membranes and fluids. Slight compressibility of the fluid is assumed. Classical total Lagrangian formulation including wrinkling is adopted for the membrane representation, whereas fluid is treated in an updated Lagrangian manner, developed in the current work. Assumption of slight compressibility of the fluid enables one to define the monolithic fluid-membrane system in a natural way. The displacements are the primary variables of both the fluid and the membrane domains. The formulation adopts the Particle Finite Element Method (PFEM) philosophy for free-surface identification and mesh regeneration. Three examples illustrate the functionality of the formulation in application to FSI problems involving motion of membranes in water.
Thermal Analysis (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal AnalysisC. B. MurphyCite this: Anal. Chem. 1964, 36, 5, 347–354Publication Date (Print):April 1, 1964Publication History Published online1 May 2002Published inissue 1 April 1964https://pubs.acs.org/doi/10.1021/ac60211a029https://doi.org/10.1021/ac60211a029research-articleACS PublicationsRequest reuse permissionsArticle Views166Altmetric-Citations21LEARN 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
POPMUSIC for the world location-routing problem (2013)

POPMUSIC—partial optimization metaheuristic under special intensification conditions—is a template for tackling large problem instances. This template has been shown to be very efficient for various combinatorial problems like p-median, sum of squares clustering, vehicle routing and map labelling. In terms of algorithmic complexity, one of the most complex part of POPMUSIC template is to find an initial solution. This article presents a method for generating an appropriate initial solution to the location-routing problem by producing in O (n3/2) an approximate solution to the capacitated p-median problem. The method is tested on LRP instances with millions of entities.
The Bacillus thuringiensis delta-endotoxin. Evidence for a two domain structure of the minimal toxic fragment. (1990)

The conformational characteristics of the minimal toxic fragment of the delta-endotoxin from Bacillus thuringiensis berliner 1715 were examined by fluorescence and circular dichroism spectroscopy. This insecticidal protein, specifically toxic to lepidopteran species, was found to consist of two structural domains. Experimental evidence for this conclusion was provided by biphasic guanidine hydrochloride unfolding curves at different pH values and electrophoretic patterns of protease digests. Two stable fragments of comparable molecular weight were obtained using four different broad specificity proteolytic enzymes. A secondary structure model was constructed using seven B. thuringiensis toxin sequences. These toxins were selected on the basis of their limited sequence homology and represent all known insecticidal specificities. Despite this divergence, a consensus secondary structure pattern was obtained, confirming the structural homology among the toxins. The N-terminal halves of all toxins are predicted to be relatively rich in alpha-helix structure and the C-terminal parts to contain alternating beta-strand and coil structures. The latter seems characteristic for a beta-sheet conformation. Comparing this model to the unfolding data obtained by circular dichroism, whose far UV signal gives a measure of the alpha-helix content, allowed us to delineate the structural domains into the primary structure.
Molecular electronics by the numbers (2002)

Molecules are an attractive option to develop nanoscale electronic devices. Experimental measurements of current-voltage characteristics of individual molecules have been possible for several years and have revealed rich structure and diverse behavior. This paper reviews recent theoretical work by the authors in which current-voltage characteristics of individual molecules are computed using a fully quantum-mechanical parameter-free method. The results provide detailed understanding of transport in molecules in the context of data and go further by obtaining information about the role of molecule-electrode contacts and predicting the behavior of three-terminal molecular devices and the factors that control their performance.
Synthesis of cyclic peptide analogues of the 310 helical Pro138-Gly144 segment of human aquaporin-4 by olefin metathesis (2009)

Four cyclic pentapeptides and two cyclic heptapeptides modelled on the 3(10) helical Pro138-Gly144 segment of the water channel aquaporin-4 (AQP4) postulated to mediate adhesive interactions between AQP4 tetramers were synthesised by olefin metathesis. Three related acyclic pentapeptides Boc-Ser(All)-Xaa1-Val-Ser(All)-Gly-OMe (Xaa1 = Val, Aib; Boc = tert-butoxycarbonyl; All = allyl) and Boc-Ser(Bn)-Val-Val-Gly-Gly-OMe (Bn = benzyl) and two acyclic heptapeptides Boc-Pro-Pro-Ser(All)-Val-Val-Ser(All)-Gly-OMe and Boc-Pro-Pro-Ser(Bn)-Val-Val-Gly-Gly-OMe were also prepared. NMR, CD and IR data provided evidence that the peptides can access a 3(10) helical structure in apolar solvents and pointed to a significant stabilising effect of the olefinic bridge on helicity in an aqueous environment. Thus we could demonstrate the viability of using ring closing olefin metathesis to stabilise short protein segments in the helical conformation that they adopt in their native protein environment. Our approach provides access to a set of peptides with potential binding affinity for AQP4.