gebhart/patrepeval huggingface dataset:
Antibody Specific B-Cell Epitope Predictions: Leveraging Information From Antibody-Antigen Protein Complexes (2019)

B-cells can neutralize pathogenic molecules by targeting them with extreme specificity using receptors secreted or expressed on their surface (antibodies). This is achieved via molecular interactions between the paratope (i.e., the antibody residues involved in the binding) and the interacting region (epitope) of its target molecule (antigen). Discerning the rules that define this specificity would have profound implications for our understanding of humoral immunogenicity and its applications. The aim of this work is to produce improved, antibody-specific epitope predictions by exploiting features derived from the antigens and their cognate antibodies structures, and combining them using statistical and machine learning algorithms. We have identified several geometric and physicochemical features that are correlated in interacting paratopes and epitopes, used them to develop a Monte Carlo algorithm to generate putative epitopes-paratope pairs, and train a machine-learning model to score them. We show that, by including the structural and physicochemical properties of the paratope, we improve the prediction of the target of a given B-cell receptor. Moreover, we demonstrate a gain in predictive power both in terms of identifying the cognate antigen target for a given antibody and the antibody target for a given antigen, exceeding the results of other available tools.
Using Deception to Enhance Security: A Taxonomy, Model, and Novel Uses (2015)

As the convergence between our physical and digital worlds continue at a rapid pace, securing our digital information is vital to our prosperity. Most current typical computer systems are unwittingly helpful to attackers through their predictable responses. In everyday security, deception plays a prominent role in our lives and digital security is no different. The use of deception has been a cornerstone technique in many successful computer breaches. Phishing, social engineering, and drive-by-downloads are some prime examples. The work in this dissertation is structured to enhance the security of computer systems by using means of deception and deceit. Deception-based security mechanisms focus on altering adversaries' perception of computer systems in a way that can confuse them and waste their time and resources. These techniques exploit adversaries' biases and present them with a plausible alternative to the truth bringing a number of unique advantages to computer security. In addition, deception has been widely used in many areas of computing for decades and security is no different. However, deception has only been used haphazardly in computer security. In this dissertation we present a framework where deception can be planned and integrated into computer defenses. We posit how the well-known Kerckhoffs's principle has been misinterpreted to drive the security community away from deception-based mechanisms. We present two schemes that employ deception to protect users' passwords during transmission and at rest when they are stored on a computer server. Moreover, we designed and built a centralized deceptive server that can be hooked to internet-facing servers giving them the ability to return deceptive responses. These three schemes are designed, implemented, and analyzed for their security and performance. The use of deception in security, and in computing in general, shows some fruitful results. This dissertation discusses some of the unique advantages of such mechanisms and presents a framework to show how they can be integrated into computer defenses. Also, it provides three practical schemes that employ deception in their design to address some existing security challenges. We postulate that the use of deception can effectively enhance the effectiveness of current security defenses and present novel ways to address many security challenges.
Bringing probability judgments into policy debates via forecasting tournaments (2017)

Political debates often suffer from vague-verbiage predictions that make it difficult to assess accuracy and improve policy. A tournament sponsored by the U.S. intelligence community revealed ways in which forecasters can better use probability estimates to make predictions-even for seemingly "unique" events-and showed that tournaments are a useful tool for generating knowledge. Drawing on the literature about the effects of accountability, the authors suggest that tournaments may hold even greater potential as tools for depolarizing political debates and resolving policy disputes.
Impact of Image-Derived Instrumentation on Total Knee Arthroplasty Revision Rates (2019)

Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Applying the Delta method in metric analytics: A practical guide with novel ideas (2018)

During the last decade, the information technology industry has adopted a data-driven culture, relying on online metrics to measure and monitor business performance. Under the setting of big data, the majority of such metrics approximately follow normal distributions, opening up potential opportunities to model them directly without extra model assumptions and solve big data problems via closed-form formulas using distributed algorithms at a fraction of the cost of simulation-based procedures like bootstrap. However, certain attributes of the metrics, such as their corresponding data generating processes and aggregation levels, pose numerous challenges for constructing trustworthy estimation and inference procedures. Motivated by four real-life examples in metric development and analytics for large-scale A/B testing, we provide a practical guide to applying the Delta method, one of the most important tools from the classic statistics literature, to address the aforementioned challenges. We emphasize the central role of the Delta method in metric analytics by highlighting both its classic and novel applications.
A Pilot Study of the Predictive Value of Plasma Tumor Necrosis Factor α. and Interleukin 1β for <i>Streptococcus pneumoniae</i> Bacteremia in Febrile Children (1997)

Like the WBC count, TNF and IL1 are good negative but poor positive predictors of Streptococcus pneumoniae bacteremia in nontoxic-appearing, febrile children. At present, the addition of plasma TNF or IL1 levels would add little to emergency physicians' ability to predict Streptococcus pneumoniae bacteremia. However, as the quantification of these cytokines becomes more rapid, available, and standardized, and more knowledge of TNF and IL1 levels during various illnesses is gained, their utility in the clinical setting for ruling out bacteremia should be further assessed.
JAPAN FRP INDUSTRY (1997)

The article surveys the development in FRP application,market,production and moulding prcess along the lines of three stages of Japan FRP industry.
Nondegenerate multiwave mixing in polydiacetylene: phase conjugation with frequency conversion (1991)

We present an analysis of optical phase conjugation with frequency doubling in terms of nondegenerate six-wave mixing fifth-order nonlinear susceptibility. We show how the Bragg phase-matching condition is achieved at small angles. The process under picosecond-pulse conditions in a polydiacetylene solution pumped at two-photon resonance and probed at one-photon resonance is experimentally demonstrated. Results are discussed in terms of a one-dimensional quantum three-level system. The proximity of one- and two-photon resonance in conjugated polymers makes these polymers efficient nonlinear-optical materials for this original application. The experiment permits artifact-free measurement of the two-photon state recovery time of the red form of polydiacetylene.
In Situ Optical Analysis of the Gas Phase during the Deposition of Silicon Carbide from Methyltrichlorosilane (1996)

Coherent anti‐Stokes Raman spectroscopy (CARS) was used for analysis of the gas phase during chemical vapor deposition (CVD) of silicon carbide (SiC) from a methyltrichlorosilane (MTS; )‐hydrogen precursor mixture. CARS experiments were carried out in a low‐pressure hot‐wall reactor under the selected conditions: temperature T = 1000 to 1300 K, total pressure Ptot = 2 to 5 kPa, , to MTS flow rate ratio α = 3 to 20, and total gas flow rate Q = 50 to 400 sccm. A systematic search for the radical and stable species present in the hot zone of the reactor was first conducted. Then partial pressures of MTS and were measured at the hot‐zone outlet as a function of temperature, initial partial pressures of MTS and , and residence time. Partial pressure of HCl was also measured vs. initial pressure of MTS. A reaction mechanism was tentatively drawn up to describe the decomposition of MTS in the gas phase. Then the experimental results were compared to those of a computer model which calculated concentrations of the gaseous species at the output of the hot zone by numerical integration of reaction rates.
Deadlock freedom using edge locks (1982)

We define a series of locking protocols for database systems that all have three main features: freedom from deadlock, multiple granularity, and support for general collections of locking primitives. A rooted directed acyclic graph is used to represent multiple granularities, as in System R. Deadlock freedom is guaranteed by extending the System R protocol to require locks on edges of the graph in addition to the locks required on nodes.
High-Resolution Structure of the Extracellular Aspartic Proteinase from<i>Candida tropicalis</i>Yeast (1997)

The crystal structure of the secreted aspartic proteinase from Candida tropicalis yeast (SAPT) has been determined to 1.8 A resolution. The classic aspartic proteinase bilobal structure and domain topology is conserved in SAPT, with the substrate binding cleft situated between the two domains. Structural comparisons made with pepsin indicate that insertions and deletions in the primary sequence modify the SAPT structure to create a more spacious substrate binding cleft with altered specificity. An unexpected tetrapeptide has been found to occupy binding sites S1'-S3', and this suggests the order of release of peptide products in the catalytic mechanism of these enzymes. Structural features are considered with regard to previous substrate specificity data.
Muestrario de lujo: SpotBank, el primer banco de spots que se crea en España, comienzo a funcionar de la mano de Pedro Solana (1993)

Por un modico precio- no mas de 5 millones de pesetas-, es posible lucirse con la mas espectacular de las producciones o con una idea original de la mas creativa de las boutiques norteamericanas, o britanicas, o australianas, o de cualquier rincon del mundo. Bien es verdad que seran piezas de segunda mano, cedidas por el anunciante despues de haberlas utilizado pare el producto para el que fueron creadas, pero no dejaran de ser piezas de manifiesto valor. Esta, la reutilizacion de spots, es la labor de SpotBank, la compania espanola que dirige Pedro Solana y que acaba de comenzar sus operaciones. SpotBank, especie de filial de la norteamericana AdExchange, posee un catalogo internacional de anuncios que ella misma se presta a adaptar a las necesidades de sus clientes.
Evaluation of the Flexibility, Efficacy, and Safety of a Foldable Capsular Vitreous Body in the Treatment of Severe Retinal Detachment (2010)

The FCVB was shown to be flexible, effective, and safe as a vitreous substitute over a 3-month implantation time. (ClinicalTrials.gov number, NCT00910702.).
Platelet interaction with poly(ethylene oxide) networks (1990)

Abstract Interpenetrating polymer networks (IPNs) of poly(ethylene oxide) (PEO) and a polyether substituted polysiloxane were synthesized containing variations of PEO content (35 and 65% dry network weight) and PEO systematically varied from low to high molecular weight (2,000, 8,000, and 20,000). Biocompatibility was assessed by measureing 111 In platelet deposition in a baboon femoral ex vivo shunt. Mass transfer analysis revealed that platelet transport to PEO/polysiloxane surfaces was kinetically limited and correlated with both PEO content and molecular weight. Differences in material performance were noted particularly after the initial 30 min blood contact period. In mid and high PEO molecular weight networks (8,000 and 20,000), reduced platelet deposition was noted with increased PEO content. In materials of high PEO content (65%), mid and high PEO molecular weight samples had significantly lower levels of platelet adsorption than PDMS (60 min; p < 0.05) or networks of low PEO molecular weight, coded 2K‐65 (30 and 60 min; p < 0.05). The lowest level of platelet deposition was noted on 20K‐65 networks, less than one platelet per 1,000 μm 2 .
The Enemy Within (1999)

Abstract There is an emergent consensus that the disposition of Black young men is an important determinant of their labor market troubles. The problem, we are told, is not labor market discrimination but the fatalistic attitudes (the “enemy within”) held by many Black youth. This article uses data from the National Longitudinal Survey of Youth (NLSY) to examine race differences in fatalism and joblessness. I find that the greater fatalism of Blacks is explained by their more disadvantaged background and subsequent problems in schools and the labor market, not by their distinctive cultural orientations. I also find a modest effect of measures of fatalism on subsequent joblessness and a more pronounced effect for more disadvantaged White and Black young men.
Continuous-wave operation of terahertz quantum-cascade lasers above liquid-nitrogen temperature (2004)

We report cw operation of a quantum-cascade laser at 3.2 THz (λ≈94 μm) up to a heat-sink temperature of 93 K. Resonant longitudinal-optical phonon scattering is used to depopulate the lower radiative state and a low-loss metal–metal waveguide is used to provide high modal confinement. Optical powers of ∼1.8 mW at 10 K and ∼400 μW at 78 K are observed from a single facet of a 40-μm-wide and 1.35-mm-long laser device. A threshold current density of 432 A/cm2 at 10 K and 552 A/cm2 at 78 K was obtained in cw mode. The same device lased up to 129 K in pulsed mode with a threshold current density of 419 A/cm2 at 5 K.
Faithfulness and Reduplicative Identity (1995)

This paper proposes a revised view of faithfulness in Optimality Theory (Prince & Smolensky 1993), relating it to reduplicative identity (McCarthy & Prince 1993). Faithfulness and identity are unified in a theory of Correspondence relations between structures. The theory is investigated by way of a study of over- and underapplication effects in reduplicated structures.
Incentive-based coordinated charging control of plug-in electric vehicles at the distribution-transformer level (2012)

Distribution utilities are becoming increasingly aware that their networks may struggle to accommodate large numbers of plug-in electric vehicles (PEVs). In particular, uncoordinated overnight charging is expected to be problematic, as the corresponding aggregated power demand exceeds the capacity of most distribution substation transformers. In this paper, a dynamical model of PEVs served by a single temperature-constrained substation transformer is presented and a centralized scheduling scheme is formulated to coordinate charging of a heterogeneous PEV fleet. We employ the dual-ascent method to derive an iterative, incentive-based and non-centralized implementation of the PEV charging algorithm, which is optimal upon convergence. Then, the distributed open-loop problem is embedded in a predictive control scheme to introduce robustness against disturbances. Simulations of an overnight charging scenario illustrate the effectiveness of the so-obtained incentive-based coordinated PEV control scheme in terms of performance and enforcing the transformer's thermal constraint.
Purification and properties of bovine spleen heme oxygenase. Amino acid composition and sites of action of inhibitors of heme oxidation. (1982)

Microsomal heme oxygenase has been purified from bovine spleen to homogeneity using DEAE-cellulose chromatography, initial hydroxyapatite chromatography, gel filtration, and repeat hydroxyapatite chromatography. The purified enzyme showed a single protein band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a molecular weight of congruent to 31,000. It had a Km for heme of 0.93 microM, a specific activity of 6770 units/mg of protein, and a turnover number of 3.5 mol/mol of enzyme/min. Amino acid analysis of the purified enzyme revealed an abundance of glutamine and glutamic acid residues, a log tryptophan content (2 tryptophan residues/mol of enzyme), and four free sulfhydryl groups, only two of which were accessible to sulfhydryl (--SH) inactivating reagents without unfolding of the protein. Consistent with these findings, the purified enzyme had a relatively low extinction coefficient at 280 nm (E11%cm = 8.12) and was relatively resistant to inactivation by --SH inactivating reagents. NADPH-cytochrome c reductase from bovine liver was purified to homogeneity and biliverdin reductase from bovine spleen was partially purified. The heme oxygenase system was reconstituted from preparations of all three purified enzymes and, utilizing this reconstituted system, the specific sites of the inhibitory actions of --SH inactivating reagents, inorganic metals, and metalloporphyrins on the heme degrading sequence of reactions were examined. Sn-, Co-, Zn-, and Mn-protoporphyrin strongly inhibited heme degradation in a competitive manner. The Ki values for Sn-, Co-, and Zn-protoporphyrin were determined to be 0;033, 0.082, and 0.13 microM, respectively. Mg-, Ni-, and Cu-protoporphyrin had little effect on heme degradation by the reconstituted system. Metals such as Pt2+ and Hg2+ strongly inhibited the activity of the reconstituted heme oxygenase system, but the principal site of action of these metals was at the level of NADPH-cytochrome c reductase or biliverdin reductase. Similarly --SH inactivating reagents, such as p-chloromercuribenzoate, 5,5'-dithiobis-(2-nitrobenzoate), or N-ethylmaleimide inhibited the reaction catalyzed by the reconstituted heme oxygenase system principally by inhibiting the activity of NADPH-cytochrome c reductase.
Effect of Extracellular Metabolites from<i>Gliocladium virens</i>on Germination of Sporangia and Mycelial Growth of<i>Pythium ultimum</i> (1990)

Culture supernatants from G.v. grown in 5% bran extract or in minimal medium supplemented with autoclaved hyphae of P.u. inhibited sporangial germination and mycelial growth of P.u. They contained gliotoxin and laminarinase, amylase, carboxymethylcellulase, chitinase and protease activities. They remained inhibitory after the above enzyme activities were inactivated by heating or removed by size-fractionation. Grown in the supplemented minimal medium, which did not contain these enzyme activities, they strongly inhibited sporangial germination and mycelial growth (...)
Evidence that Arg‐295, Glu‐378, and Glu‐380 are active‐site residues of the ADP‐ribosyltransferase activity of iota toxin (1996)

The active site of the enzymatic component (Ia) of the Clostridium perfringens iota toxin has been studied by site‐directed mutagenesis. Sequence alignment showed that Ia and C3 enzymes display a segment in their C‐terminal part which is homologous to that forming the active domain of pertussis toxin, cholera toxin, and Escherichia coli thermolabile toxins. This structure consists of a β‐strand and an α‐helix which forms the NAD‐binding cavity and which is flanked by two catalytic spatially conserved residues involved in catalysis [Domenighini et al. (1994) Mol. Microbiol. 14, 41–50]. Substitutions (Arg‐295‐Lys, Glu‐378‐Ala, Glu‐380‐Asp, and Glu‐380‐Ala) induced a drastic decrease in ADP‐ribosylation and cytotoxic activities, while substitution of the adjacent Arg (Arg‐296‐Lys) only partially affected the enzymatic activity and cytotoxicity. These results indicate that Arg‐295, Glu‐378 and Glu‐380 of Ia are involved in the ADP‐ribosylation activity which is essential for the morphological changes of cells treated with iota toxin.
Tissue- and development-specific expression in transgenic mice of a type I procollagen (COL1A1) minigene construct with 2.3 kb of the promoter region and 2 kb of the 3'-flanking region. Specificity is independent of the putative regulatory sequences in the first intron (1993)

Previous reports have provided inconsistent data as to the cis-regulatory elements that are essential for correct expression of the gene for the pro alpha 1 (I) chain of type I procollagen (COL1A1) in the many tissues in which the protein is synthesized. Here, two internally deleted minigene versions of the human COL1A1 gene were used to prepare transgenic mice. The constructs made it possible to test regulatory sequences in the normal context of the gene. Also, in contrast to the reporter genes used in previous experiments, the constructs made it possible to assay quantitatively expression of the exogenous genes relative to expression of the endogenous COL1A1 gene, both as mRNA and as protein. The average level of expression of the minigenes varied among three transgenic lines, but the ratio of expression of the minigenes to expression of the endogenous gene was the same in all transgenic mice of a given line. Within the same line, the ratio of expression was essentially the same in nine or more tissues in which expression of the endogenous gene varied widely. Also, the ratio of expression within a given line was the same in 15-day-old embryos and in mice ranging in age from 4 days to 4 months. In addition, the ratio remained constant during repair of a surgical wound. The results demonstrated, therefore, that the minigene constructs with about 2.3 kb of the promoter region and about 2 kb of the 3'-flanking region contained all of the sequences necessary for correct expression of the genes in a tissue-specific and development-specific manner.(ABSTRACT TRUNCATED AT 250 WORDS)
Spin valves and spin-torque oscillators with perpendicualr magnetic anisotropy (2012)

Researches in spintronics, especially those remarkably classified in the current induced spin-transfer torque (STT) framework, circumvent challenges with different materials and geometries. Perpend ...
Sigles et abrévations utilisés (2004)

AAMRACF Association des aînés des mouvements ruraux d’Action catholique du Finistère ACA Assemblée des cardinaux et archevêques ACCF Association catholique des ches de familles ACJF Association catholique de la jeunesse française ACO Action catholique ouvrière ALP Action libérale populaire APEL Association des parents d’élèves de l’enseignement libre CALS Comité d’action pour la liberté scolaire CDJA Cercle départemental des jeunes agriculteurs CDMO Conseil diocésain de la Mission ouvrière CE...
Induction of the death-promoting genebax-? sensitizes cultured breast-cancer cells to drug-induced apoptosis (1996)

Resistance to apoptosis plays an important role in malignancies that are refractory to chemotherapy treatment. Recently we have shown that the expression of bax-alpha, a death-promoting member of the bcl-2 family, is down-regulated in breast cancer and have provided evidence that low bax expression might contribute to the pathogenesis of breast cancer. In this study we were able to demonstrate the role of this gene in chemotherapy-induced apoptosis. We transfected bax-alpha into the breast-cancer cell lines R30C and MCF-7 under the control of an inducible tetracycline-dependent expression system. Induction of bax-alpha expression did not affect viability by itself but strongly increased chemosensitivity to epirubicin. We were able to demonstrate that this sensitization is due to apoptosis. These data might explain the recently published observation that reduced expression of bax is associated with poor response rates to chemotherapy in breast cancer.