gebhart/patrepeval huggingface dataset:
Identification of Rare High-Avidity, Tumor-Reactive CD8+ T Cells by Monomeric TCR–Ligand Off-Rates Measurements on Living Cells (2015)

The avidity of the T-cell receptor (TCR) for antigenic peptides presented by the peptide-MHC (pMHC) on cells is a key parameter for cell-mediated immunity. Yet a fundamental feature of most tumor antigen-specific CD8(+) T cells is that this avidity is low. In this study, we addressed the need to identify and select tumor-specific CD8(+) T cells of highest avidity, which are of the greatest interest for adoptive cell therapy in patients with cancer. To identify these rare cells, we developed a peptide-MHC multimer technology, which uses reversible Ni(2+)-nitrilotriacetic acid histidine tags (NTAmers). NTAmers are highly stable but upon imidazole addition, they decay rapidly to pMHC monomers, allowing flow-cytometric-based measurements of monomeric TCR-pMHC dissociation rates of living CD8(+) T cells on a wide avidity spectrum. We documented strong correlations between NTAmer kinetic results and those obtained by surface plasmon resonance. Using NTAmers that were deficient for CD8 binding to pMHC, we found that CD8 itself stabilized the TCR-pMHC complex, prolonging the dissociation half-life several fold. Notably, our NTAmer technology accurately predicted the function of large panels of tumor-specific T cells that were isolated prospectively from patients with cancer. Overall, our results demonstrated that NTAmers are effective tools to isolate rare high-avidity cytotoxic T cells from patients for use in adoptive therapies for cancer treatment.
Umbelliferyl-labeled galactosaminide as an aid in identification of Candida albicans (1987)

The initial evaluation of a fluorescence, nonmicroscopic method of rapid identification of Candida albicans is described. A total of 524 yeast isolates were evaluated in parallel by the umbelliferyl-conjugated N-acetyl-beta-D-galactosaminide (UAG) test and the germ tube (GT) test in comparison with the API 20C Yeast Identification System. The UAG test correctly identified 333 of the 334 isolates of C. albicans (99.7%), and the GT test identified 328 (98%). There were three false-positive GT reactions and five false-positive UAG reactions with 69 isolates of C. tropicalis. The sensitivity and specificity were 99 and 97%, respectively, for the UAG test and were both 98% for the GT test. The UAG test requires less than 2 h for test completion compared with 2 to 4 h for the GT test, is similar in cost, has a nonmicroscopic visual endpoint, and eliminates the health hazards of handling pooled human sera.
Suture techniques with high breaking strength and low gliding resistance: Experiments in the dog flexor digitorum profundus tendon (2001)

We studied the breaking strength and gliding resistance between the pulley and flexor tendon for various suture techniques. Canine flexor digitorum profundus tendons were transected and sutured using one of eight repair techniques: modified Kessler (MK); Tsuge (Tsuge); two variations of a double modified Kessler (DK1, DK2); combined modified Kessler-modified Tsuge (MKT); augmented Becker (Becker); Cruciate (Cruciate); and modified double Tsuge (DT). The force to produce a 1.5 mm gap, ultimate failure load, resistance to gap formation, and gliding resistance were measured. The force to produce a 1.5 mm gap and the ultimate breaking force were higher with the DK1, DK2, MKT, Becker, Cruciate, and DT repairs than they were with the MK and Tsuge repair, while the gliding resistance of the Becker was higher than that of the MK, DK1, DK2, MKT. Cruciate, and UT repairs. In addition to confirming that repair strength increases as the number of strands crossing the repair increases, we also found that these stronger repairs need not produce higher gliding resistance than less robust repairs.
Incidentally Discovered Adrenal Masses* (1995)

Independently, endocrinology, radiology, and nuclear medicine can not optimally differentiate the etiology of the incidental adrenal mass. Rather, the insight necessary for this task must be contributed by all three disciplines. Incidentally discovered adrenal masses are being detected at an increasing rate. This trend is expected to continue based on the incidence of adrenal masses in autopsy series and the increasing use of high resolution abdominal imaging techniques. CT and MRI are able to definitely characterize only a minority of these lesions (simple cyst, myelolipoma, obvious local malignant invasion). Biochemical screening for hormone excess is essential regardless of a nonsuggestive complete history and physical examination. An argument may be made for not further pursuing nonhypersecreting lesions with the typical features of a benign adenoma on CT scan and an attenuation value of 0 HU or less. Adrenocortical scintigraphy is recommended in all patients with normal biochemical screening tests, especially those with CT attenuation values greater than 0 HU. In this setting, we believe that the functional and anatomical information provided by NP-59 and [75Se]selenomethylnorcholesterol scintigraphy allows one to noninvasively, accurately, and less expensively (Table 9) categorize adrenal masses as benign nonhypersecretory adenomas (the vast majority) vs. a possibly malignant lesion (the minority). In the presence of normal biochemistry, a concordant NP-59 imaging pattern is diagnostic of a nonhypersecretory benign adrenal adenoma and requires no immediate therapeutic intervention. Conversely, patients with discordant patterns of NP-59 scintigraphy have lesions that carry a significant risk for malignancy, and the pursuit of a tissue diagnosis is indicated, usually by means of FNA. Normal adrenocortical tissue on cytological studies in this setting may represent inadvertent sampling of adjacent normal adrenocortical tissues or the presence of a well differentiated adrenocortical carcinoma. In patients with lesions larger than 2 cm in whom NP-59 scintigraphy is nonlateralizing, the possibility of a periadrenal or pseudoadrenal mass is likely and should prompt review, or perhaps even repeat, of high resolution adrenal imaging (occasionally angiography may be helpful). In lesions shown to be 2 cm or less in size with a nonlateralizing NP-59-scan, there is a possibility of a periadrenal or pseudoadrenal mass; however, once this is excluded it must be recognized that benign and malignant lesions, because of the limitations of scintigraphy, cannot always be clearly distinguished by this method when masses are small.(ABSTRACT TRUNCATED AT 400 WORDS)
A general post-processing approach to leakage current reduction in SRAM-based FPGAs (2004)

A negative effect of ever-shrinking supply and threshold voltages is the larger percentage of total power consumption that comes from leakage current. Several techniques have been developed to help reduce leakage in SRAM-based memory, in which the percent leakage power is especially acute. SRAM-based field programmable gate arrays (FPGAs) pose similar leakage problems, but their structure and function require different solutions. This paper introduces a low complexity post-processing approach to reducing FPGA leakage current by ground-gating off SRAM cells that are unused in a particular device configuration. The approach is general enough to apply to any device configuration, and results reveal that the significant leakage current reduction can be achieved with no delay penalty and acceptable area overhead.
Propranolol reduces viability and induces apoptosis in hemangioblastoma cells from von Hippel-Lindau patients (2015)

Our results suggest that propranolol could reduce the growth of HIF-dependent tumors and may thus be a promising treatment to delay surgery in VHL patients.
Approximating Bayesian belief networks by arc removal (1997)

I propose a general framework for approximating Bayesian belief networks through model simplification by arc removal. Given an upper bound on the absolute error allowed on the prior and posterior probability distributions of the approximated network, a subset of arcs is removed, thereby speeding up probabilistic inference.
An Update of Applicable Automotive Engine Rotary Stratified Charge Developments (1982)

<div class="htmlview paragraph">Curtiss-Wright's rig results to support development of a large Rotary (Wankel-type) direct injected stratified charge multi-fuel Military engine are related to earlier automotive -sized engine data. The comparisons indicate similar thermal efficiency of the larger 350 C.I.D. single rotor rig and the 60 C.I.D. size. However, improved configurations and basic technology advances have been realized during development of the larger module which have not been tested on the smaller engine.</div> <div class="htmlview paragraph">Relevant growth studies for General Aviation engines are summarized and test data indicating directions for significant improvements in specific fuel consumption at lean mixture strengths, via turbocharging, are presented and reflected in automotive model Rotary engine projections. System analysis shows sizeable fuel economy gains of naturally aspirated and turbocharged Rotary stratified charge over existing automotive engines. These improvements would be additive to refining and increased energy yield benefits that accrue to use of a broad-base middle distillate fuel by an engine configuration of demonstrated wide fuel tolerance.</div>
Protein Structure Determination by High-Resolution Solid-State NMR Spectroscopy:  Application to Microcrystalline Ubiquitin (2005)

High-resolution solid-state NMR spectroscopy has become a promising method for the determination of three-dimensional protein structures for systems which are difficult to crystallize or exhibit low solubility. Here we describe the structure determination of microcrystalline ubiquitin using 2D (13)C-(13)C correlation spectroscopy under magic angle spinning conditions. High-resolution (13)C spectra have been acquired from hydrated microcrystals of site-directed (13)C-enriched ubiquitin. Inter-residue carbon-carbon distance constraints defining the global protein structure have been evaluated from 'dipolar-assisted rotational resonance' experiments recorded at various mixing times. Additional constraints on the backbone torsion angles have been derived from chemical shift analysis. Using both distance and dihedral angle constraints, the structure of microcrystalline ubiquitin has been refined to a root-mean-square deviation of about 1 A. The structure determination strategies for solid samples described herein are likely to be generally applicable to many proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy.
A Formal Security Analysis of the Signal Messaging Protocol (2017)

Signal is a new security protocol and accompanying app that provides end-to-end encryption for instant messaging. The core protocol has recently been adopted by WhatsApp, Facebook Messenger, and Google Allo among many others, the first two of these have at least 1 billion active users. Signal includes several uncommon security properties (such as "future secrecy" or "post-compromise security"), enabled by a novel technique called ratcheting in which session keys are updated with every message sent. Despite its importance and novelty, there has been little to no academic analysis of the Signal protocol. We conduct the first security analysis of Signal's key agreement and double ratchet as a multi-stage key exchange protocol. We extract from the implementation a formal description of the abstract protocol, and define a security model which can capture the "ratcheting" key update structure. We then prove the security of Signal's core in our model, demonstrating several standard security properties. We have found no major flaws in the design, and hope that our presentation and results can serve as a starting point for other analyses of this widely adopted protocol.
Working-class cultural spaces: comparing the old and the new (2012)

The expert contributors illustrate how the development of the urban economic environment has led to changes in the urban working class, through an exploration of the workplace experiences of rural migrant workers, and of the plight of the old working class in the state-owned sector. They address questions on the extent to which migrant workers have become a new working class, are absorbed into the old working class, or simply remain as migrant workers. Changes in class relations in villages in the urban periphery – where the urbanization drive and in-migration has lead to a new local politics of class differentiation – are also raised.
Reaction of S-Nitrosoglutathione with the Heme Group of Deoxyhemoglobin (2000)

The mechanism of interaction between S-nitrosoglutathione (GSNO) and hemoglobin is a crucial component of hypotheses concerning the role played by S-nitrosohemoglobin in vivo. We previously demonstrated (Patel, R. P., Hogg, N., Spencer, N. Y., Kalyanaraman, B., Matalon, S., and Darley-Usmar, V. M. (1999) J. Biol. Chem. 274, 15487-15492) that transnitrosation between oxygenated hemoglobin and GSNO is a slow, reversible process, and that the reaction between GSNO and deoxygenated hemoglobin (deoxyHb) did not conform to second order reversible kinetics. In this study we have reinvestigated this reaction and show that GSNO reacts with deoxyHb to form glutathione, nitric oxide, and ferric hemoglobin. Nitric oxide formed from this reaction is immediately autocaptured to form nitrosylated hemoglobin. GSNO reduction by deoxyHb is essentially irreversible. The kinetics of this reaction depended upon the conformation of the protein, with more rapid kinetics occurring in the high oxygen affinity state (i.e. modification of the Cysbeta-93) than in the low oxygen affinity state (i.e. treatment with inositol hexaphosphate). A more rapid reaction occurred when deoxymyoglobin was used, further supporting the observation that the kinetics of reduction are directly proportional to oxygen affinity. This observation provides a mechanism for how deoxygenation of hemoglobin/myoglobin could facilitate nitric oxide release from S-nitrosothiols and represents a potential physiological mechanism of S-nitrosothiol metabolism.
Synthesis, Characterization and Antimicrobial Activity of 5‐(4‐Methyl piperazinyl methylene)‐8‐hydroxy quinoline and its Various Metal Chelates (2006)

5‐Chloromethyl‐8‐quinolinol was condensed with 4‐methyl piperazine in presence of sodium bicarbonate. The resulting 5‐(4‐methyl piper‐azinylmethylene)‐8‐quinolinol (MPQ) was characterized by elemental analysis and spectral studies. The transition metal chelates viz Cu +2 , Ni +2 , Co +2 , Mn +2 , Zn +2 , Cd +2 , and Fe +3 of MPQ were prepared and characterized by metal‐ligand (M:L) ratio, IR and reflectance spectroscopies and magnetic properties. The antifungal activity of MPQ and its metal chelates was screened against various fungi. The results show that all these samples are good antifungal agents.
MOCVD of Ag thin films (2001)

The new mixed ligand complex [(n-Bu 3 P)Ag((CH 3 ) 3 CCOO)] (I) is suggested as precursor for MOCVD of Ag thin films. It was characterized by elemental, TG analysis and by mass-spectrometry. It was shown that gas phase consisted only from monomeric molecules of I. X-ray study of (I) shows that crystal structure is build up from dimeric units with van der Waals interactions between them. Ag films were grown on Si and oxide substrates using I and [(Ag((CH 3 ) 3 CCOO)] (II) precursors by CVD technique in presence of oxygen. The dependence of the films' thickness, orientation and microstructure on the process parameters was defined. The use of the adduct was found to be at least 20 times more effective (regarding the film thickness) in comparison to that of II.
Modifications of Alkaline Microgel Electrophoresis for Sensitive Detection of DNA Damage (1994)

The alkaline microgel electrophoresis technique was modified to achieve a substantial increase in sensitivity for the detection of radiation-induced DNA damage in human lymphocytes. This increased sensitivity was achieved through: (1) the addition of free radical scavengers to the electrophoresis solution to reduce DNA damage generated during alkaline unwinding and electrophoresis; (2) the modification of the electrophoresis unit to achieve a more uniform electric field; (3) the use of YOYO-1, a DNA dye, producing fluorescence 500-fold more intense than ethidium bromide; and (4) the introduction of an image analysis system for the quantitation of DNA migration. In addition to increasing sensitivity, these modifications have increased the speed with which observations can be quantified, and improved reproducibility from experiment to experiment. In human lymphocytes, these modifications have resulted in an increased sensitivity of several fold, allowing the detection of DNA damage in the range of 50 mGy. This increased sensitivity for the detection of DNA damage should extend the utility of this technique.
Polymer-supported transition-metal complexes. 2. Synthesis and Moessbauer investigation of copolymers containing polynuclear iron carbonyl complexes (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer-supported transition-metal complexes. 2. Synthesis and Moessbauer investigation of copolymers containing polynuclear iron carbonyl complexesJ. C. Gressier, G. Levesque, H. Patin, and F. VarretCite this: Macromolecules 1983, 16, 10, 1577–1581Publication Date (Print):October 1, 1983Publication History Published online1 May 2002Published inissue 1 October 1983https://pubs.acs.org/doi/10.1021/ma00244a005https://doi.org/10.1021/ma00244a005research-articleACS PublicationsRequest reuse permissionsArticle Views109Altmetric-Citations11LEARN 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
Functional role of catalytic triad and oxyanion hole-forming residues on enzyme activity of <i>Escherichia coli</i> thioesterase I/protease I/phospholipase L1 (2006)

Escherichia coli TAP (thioesterase I, EC 3.1.2.2) is a multifunctional enzyme with thioesterase, esterase, arylesterase, protease and lysophospholipase activities. Previous crystal structural analyses identified its essential amino acid residues as those that form a catalytic triad (Ser10-Asp154-His157) and those involved in forming an oxyanion hole (Ser10-Gly44-Asn73). To gain an insight into the biochemical roles of each residue, site-directed mutagenesis was employed to mutate these residues to alanine, and enzyme kinetic studies were conducted using esterase, thioesterase and amino-acid-derived substrates. Of the residues, His157 is the most important, as it plays a vital role in the catalytic triad, and may also play a role in stabilizing oxyanion conformation. Ser10 also plays a very important role, although the small residual activity of the S10A variant suggests that a water molecule may act as a poor substitute. The water molecule could possibly be endowed with the nucleophilic-attacking character by His157 hydrogen-bonding. Asp154 is not as essential compared with the other two residues in the triad. It is close to the entrance of the substrate tunnel, therefore it predominantly affects substrate accessibility. Gly44 plays a role in stabilizing the oxyanion intermediate and additionally in acyl-enzyme-intermediate transformation. N73A had the highest residual enzyme activity among all the mutants, which indicates that Asn73 is not as essential as the other mutated residues. The role of Asn73 is proposed to be involved in a loop75-80 switch-move motion, which is essential for the accommodation of substrates with longer acyl-chain lengths.
Simple two-dimensional position sensitive detector with short dead-time for coincidence experiments (1994)

The design and construction of an X-Y position-sensitive detector based on a delay-line anode assembly mounted behind a multichannel plate electron multiplier are described. The dead-time is less than 60 ns for all particle pairs, and can easily be reduced further.
<title>Formation of ultrahard metal oxide nanocluster coatings at room temperature by electrostatic self-assembly</title> (1999)

Different structures of multilayer hard coating thin-films have been fabricated on single crystal silicon and quartz substrates at room temperature by electrostatic self- assembly (ESA) method. This process involves the alternate dipping of oppositely charged polyelectrolytes. The ESA films have shown the formation of highly ordered and homogeneous structures with reduced voids. UV/VIs spectroscopy and ellipsometry were used to observe the ESA deposition process. The hardness and Young's modulus of the films were measured using nanoindentation technique.
Operating a three-phase diode rectifier with a low-input current distortion using a series-connected dual boost converter (1996)

This paper describes a technique for shaping the input current to a three-phase diode rectifier using a two-switch series-connected dual boost converter and a three-phase bidirectional switch circuit. Circuits are described for generating a single voltage DC output, "single DC-rail", or a dual output DC voltage using center-tapped capacitors, "split DC-rail". Both rectifier types can be operated with the boost inductors located either on the DC or the AC side of the rectifier. The resultant rectifier circuit configurations have an excellent immunity to the "shoot-through" fault condition and use active switching elements with low per-unit current ratings and low switching losses. These features increase the reliability factor and lower the cost penalty associated with unity fundamental power factor three-phase rectifiers. Test results are presented for the rectifiers using simulation and experimental results.
WebGestalt: an integrated system for exploring gene sets in various biological contexts (2005)

High-throughput technologies have led to the rapid generation of large-scale datasets about genes and gene products. These technologies have also shifted our research focus from 'single genes' to 'gene sets'. We have developed a web-based integrated data mining system, WebGestalt (http://genereg.ornl.gov/webgestalt/), to help biologists in exploring large sets of genes. WebGestalt is composed of four modules: gene set management, information retrieval, organization/visualization, and statistics. The management module uploads, saves, retrieves and deletes gene sets, as well as performs Boolean operations to generate the unions, intersections or differences between different gene sets. The information retrieval module currently retrieves information for up to 20 attributes for all genes in a gene set. The organization/visualization module organizes and visualizes gene sets in various biological contexts, including Gene Ontology, tissue expression pattern, chromosome distribution, metabolic and signaling pathways, protein domain information and publications. The statistics module recommends and performs statistical tests to suggest biological areas that are important to a gene set and warrant further investigation. In order to demonstrate the use of WebGestalt, we have generated 48 gene sets with genes over-represented in various human tissue types. Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php.