gebhart/patrepeval huggingface dataset:
THE KINETICS OF THE ENZYMATIC HYDROLYSIS OF HYALURONIC ACID (1948)

The wide-spread natural occurrence of the enzyme hyaluronidase has been recognized for a number of years.The recent demonstration of the possible rale of testicular hyaluronidase in fertilization (l-3), the inhibition of hyaluronidase by salicylates (4, 5), and the presence of a hyaluronidase inhibitor in human blood have focused attention on this enzyme (6, 7).Relatively little attention has been paid to the kinetics of the reaction catalyzed by hyaluronidase.It is the purpose of this communication to present evidence that, within the usual assay range, this reaction is first order with respect to hyaluronic acid, with changing rate due to changing substrate concentration.A variety of different methods have been devised for the assay of hyaluronidase.These have been discussed in the accompanying paper (8).The viscosity method was first studied in detail by Madinaveitia and Quibbel (9).These workers found that the time required for half reduction in viscosity (half life time) is independent of substrate concentration and inversely proportional to enzyme concentration.This has since been confirmed by McClean (10) and Haas (6).The viscosity reduction method depends on the rate of decrease in the viscosity of a solution of hyaluronic acid.It has been cu&omary to determine the hyaluronidase activity in terms of the reciprocal (or some function thereof) of the half life time.Recently Swyer and Emmens (11) have reinvestigated the relationship of activity and substrate concentration and have found that at lower concentrations of substrate the activity varies with substrat,e concentration.These workers have also raised objections to the expression of activity as a reciprocal of the half life t,ime and suggested an alternate procedure which depends on the relationship of the log of concentration of enzyme and the viscosity at a specific time.When the fall in viscosity is plotted against time, a characteristic curve is obtained.It has been assumed by some that this represents a. first order react,ion.Thus JVcrthessen et crl.( 12) have used this assumption in determining the hyaluronidase content of human semen.'\Vhen one plots log C a,gainst t, a st,ra.ightline is not obt.aincd;thus doubt is cast on the validity of the application of the equation for a first order reaction.
A novel method for the analysis of multiple sequence variants by hybridisation to oligonucleotides (1993)

International audience
The quest for a new vaccine against tuberculosis (2009)

Tuberculosis (TB) is still one of the deadliest human diseases, killing 1,6 million people each year, mostly in developing countries. The vaccine currently used, Bacille Calmette and Guerin (BCG), is effective in preventing the most severe disseminated forms of disease in children and newborns, but its efficacy against active TB in adults has been challenged by several clinical studies. It is a common opinion that only the development of a new and more effective vaccine against TB would significantly ease the pandemic. In the last few years, the search for a new vaccine has gained a new momentum. New live and attenuated strains of M. tuberculosis, improved recombinant BCG strains and subunit vaccines have been tested in preclinical animal models, and some of them showed promising results. Unfortunately, the lack of immunological correlates of protection makes very difficult to anticipate or foresee the efficacy of any of these new vaccines and only phase III clinical trials, that are expected to start in 2009 and last few years, will tell us the real value of these new prophylactic tools. This review highlights the different strategies that are being implemented for the development of an improved vaccine against TB, the rationale behind them and the potential and feasible vaccination schedules that could be implemented.
Diversity of the Fine Specificity Displayed by HLA-A*0201-Restricted CTL Specific for the Immunodominant Melan-A/MART-1 Antigenic Peptide (1998)

HLA-A*0201 melanoma patients often develop a CTL response to an immunodominant peptide derived from the melanocyte lineage-specific protein Melan-A/MART-1. We have shown previously that the antigenic peptide most often involved is the decapeptide Melan-A(26-35) (EAAGIGILTV). We also observed some clonal diversity in the fine specificity of Melan-A-specific CTL. To substantiate this observation, we have now tested a series of Melan-A(26-35) variant peptides containing single alanine substitutions for binding to HLA-A*0201 and recognition by polyclonal and monoclonal Melan-A-specific CTL. Substitution of several residues with alanine reduced peptide binding activity by > 10-fold. In contrast, substitution of E26 with alanine (AAAGIGILTV) resulted in a 5-fold higher binding activity as well as in stronger stability of the corresponding HLA-A*0201/peptide complexes. Interestingly, the peptide variant AAAGIGILTV was recognized more efficiently than the natural decapeptide by short term cultured, tumor-infiltrated lymph node cell cultures and a number of Melan-A-specific CTL clones derived from different individuals. Moreover, this analysis revealed that the fine specificity of the CTL response to the Melan-A immunodominant epitope is quite diverse at the clonal level. At least three distinct patterns of fine specificity were identified. This diversity appears to reflect the diversity of the TCR repertoire available for this Ag, since similar results were obtained with a panel of Melan-A-specific CTL clones derived from a single melanoma patient. These findings have important implications for the formulation of Melan-A peptide-based vaccines as well as for the monitoring of Melan-A-specific CTL responses in melanoma patients.
Automatic classification of protein structure by using Gauss integrals (2002)

We introduce a method of looking at, analyzing, and comparing protein structures. The topology of a protein is captured by 30 numbers inspired by Vassiliev knot invariants. To illustrate the simplicity and power of this topological approach, we construct a measure (scaled Gauss metric, SGM) of similarity of protein shapes. Under this metric, protein chains naturally separate into fold clusters. We use SGM to construct an automatic classification procedure for the CATH2.4 database. The method is very fast because it requires neither alignment of the chains nor any chain-chain comparison. It also has only one adjustable parameter. We assign 95.51% of the chains into the proper C (class), A (architecture), T (topology), and H (homologous superfamily) fold, find all new folds, and detect no false geometric positives. Using the SGM, we display a "map" of the space of folds projected onto two dimensions, show the relative locations of the major structural classes, and "zoom into" the space of proteins to show architecture, topology, and fold clusters. The existence of a simple measure of a protein fold computed from the chain path will have a major impact on automatic fold classification.
Atomic Layer Deposition on Bulk Quantities of Surfactant‐Modified Single‐Walled Carbon Nanotubes (2008)

Atomic layer deposition (ALD) on single‐walled carbon nanotubes (SWNTs) can be achieved through physical surface modification using liquid‐phase pretreatment dispersion techniques. Al 2 O 3 ALD on nonfunctionalized SWNTs produced isolated nodule growth. Ethanol and sodium dodecylsulfate (SDS) pretreatment methods were utilized to disperse and functionalize batches of nanotube powders. Ethanol‐based dispersion techniques provided hydroxylated surfaces that promoted continuous Al 2 O 3 films on SWNT surfaces. The SDS method provided a dense nucleation site pattern that allowed for conformal Al 2 O 3 film growth. Al 2 O 3 ALD processes yielded growth rates of 0.13 nm/cycle, independent of the functionalization technique, at 450 K. X‐ray photoelectron spectroscopy was used to quantify the composition of the films, which were amorphous as deposited. A surfactant‐assisted ALD mechanism is proposed, which retains a physisorbed micelle structure as a template for the dense precursor nucleation site pattern. Liquid‐phase pretreatment was found to be an efficient mechanism to overcome attractive forces associated with nanoscale particle systems, and significantly reduced the size of nanotube bundles. The successful ALD on an individual suspended nanotube in other work was extended to the bulk coating of SWNT powders. This work demonstrates significant progress toward the goal of producing commercially viable SWNT‐based nanocomposite devices that incorporate bulk quantities of ALD‐functionalized nanotubes.
A BioMEMS Review: MEMS Technology for Physiologically Integrated Devices (2004)

MEMS devices are manufactured using similar microfabrication techniques as those used to create integrated circuits. They often, however, have moving components that allow physical or analytical functions to be performed by the device. Although MEMS can be aseptically fabricated and hermetically sealed, biocompatibility of the component materials is a key issue for MEMS used in vivo. Interest in MEMS for biological applications (BioMEMS) is growing rapidly, with opportunities in areas such as biosensors, pacemakers, immunoisolation capsules, and drug delivery. The key to many of these applications lies in the leveraging of features unique to MEMS (for example, analyte sensitivity, electrical responsiveness, temporal control, and feature sizes similar to cells and organelles) for maximum impact. In this paper, we focus on how the biological integration of MEMS and other implantable devices can be improved through the application of microfabrication technology and concepts. Innovative approaches for improved physical and chemical integration of systems with the body are reviewed. An untapped potential for MEMS may lie in the area of nervous and endocrine system actuation, whereby the ability of MEMS to deliver potent drugs or hormones, combined with their precise temporal control, may provide new treatments for disorders of these systems.
Geometrically driven wrinkling observed in free plastic sheets and leaves (2007)

We have measured the multiscale wrinkling that occurs along the edge of torn plastic sheets. The plastic deformations produced by tearing define a new metric on the sheet, which then relaxes elastically. The resultant patterns of wrinkles correspond to a superposition of waves of different wavelengths. Measurements of the variation of the pattern as a function of the distance from the edge reveal a set of transitions, each of which adds a new mode to the cascade. The wavelengths lambda in the cascade depend on both a geometrical length scale Lgeo given by the metric near the sheet's edge, and the sheet thickness t: lambda proportional t0.3Lgeo0.7. This scaling implies vanishingly short wavelengths in the limit t-->0 . A possible geometrical origin of this behavior is discussed. Finally, we show that our measurement and analysis techniques are applicable to the study of some wavy patterns of leaves. These measurements reveal that the intrinsic geometry of a wavy leaf resembles that of the torn plastic sheets. This supports the possibility that some leaves form waves through a spontaneous wrinkling, rather than through an explicit three-dimensional construction.
Supramolecular polymers with tunable topologies via hierarchical coordination-driven self-assembly and hydrogen bonding interfaces (2013)

A powerful strategy to obtain complex supramolecular materials is the bottom-up construction of noncovalently bound materials by hierarchical self-assembly. This assembly process involves stepwise, uniform increases to the architectural complexity of a substrate, starting from discrete precursors and growing in dimensionality through controlled reactivity to a final product. Herein, two orthogonal processes are exploited: coordination-driven self-assembly and hydrogen bonding. The former relies on the predictable formation of metal-ligand bonds wherein the directionalities of the rigid precursors used determines the structural outcome. The latter uses 2-ureido-4-pyrimidinone interfaces that are structurally robust by virtue of the quadruple hydrogen bonding that can occur between subunits. By combining these two processes into a single system, it is possible to generate hierarchical materials that preserve the attractive tunability associated with discrete supramolecular coordination complexes. For instance, the synthesis of a one-dimensional chain comprising linked metalla-rhomboids is readily adapted to a 2D cross-linked hexagonal network by simply selecting a different metal acceptor precursor as an assembly component. The specific interactions between subunits, in this case platinum(II)-pyridyl bonds and the quadruple H-bonding of ureidopyrimidinone, are unchanged, establishing a unique strategy to obtain supramolecular polymers with marked topological differences with minimal synthetic redesign. In addition, the structural rigidity imposed by the inclusion of the platinum metallacycles serves to minimize the formation of cyclic oligomers, increasing the efficacy of formation and improving the properties of the resultant materials. Furthermore, this study taps the potential of organoplatinum(II) metallacycles in materials science.
Causes and Outcomes of the Acute Chest Syndrome in Sickle Cell Disease (2000)

Among patients with sickle cell disease, the acute chest syndrome is commonly precipitated by fat embolism and infection, especially community-acquired pneumonia. Among older patients and those with neurologic symptoms, the syndrome often progresses to respiratory failure. Treatment with transfusions and bronchodilators improves oxygenation, and with aggressive treatment, most patients who have respiratory failure recover.
Functional implication of the interaction between EGF receptor and C-SRC (2003)

EGF receptor (EGFR) and c-Src are the prototypes that individually represent the receptor and nonreceptor tyrosine kinases respectively. Accumulated evidence reveals the association between EGF-activated EGFR and c-Src that leads to activation of both kinases. Importantly, their mutual interaction is required for many EGFR-mediated cellular functions including proliferation, migration, survival and EGFR endocytosis. Interestingly, activation of c-Src and its association with transactivated EGFR is also observed in cells stimulated with non-EGF agonists. This review will not only discuss the structure, function and regulation of these two tyrosine kinases, but also will summarize our current knowledge of the molecular mechanisms depicting the cellular events that require their participation.
Strong designated verifier signature scheme: new definition and construction. (2010)

Abstract: Recently, several strong designated verifier signature schemes have been proposed in the literature. In this paper, we first point out that such so-called strong designated verifier signature scheme is just message authentication code HMAC. Without the key property, unforgeability, for signatures, these schemes cannot enable signers to have complete controls over their signatures as demanded by Chaum and Van Antwerpen originally. No signer would use such Designated Verifier Signature schemes if he does not trust the designated verifier entirely. Then we introduce a new notion for the strong designated verifier signature scheme and its security requirements. We further propose the first strong designated verifier signature scheme based on Schnorr signature scheme, and provide a formal security proof under the DL assumption and the CDH assumption in the random oracle model. Finally, we discuss general methods to construct the strong designated verifier signature scheme.
The Synthesis of Some Pyrimidinyl and Thiazolyl Ureas and Thioureas and Some Related Compounds (1988)

Some pyrimidin-2- and pyrimidin-4-amines were treated with isocyanates and isothiocyanates to give the corresponding disubstituted ureas or thioureas . A pyrimidin-2-amine is more reactive than a pyrimidin-4- amine in these reactions. 2-Aminothiazoles and thiazolinones also react to give the disubstituted ureas or thioureas . The use of ethoxycarbonyl or benzoyl isothiocyanate or isocyanate gives products which are readily hydrolysed to the pyrimidinyl or thiazolyureas or thioureas but with concomitant hydrolysis and decarboxylation of an ethoxycarbonyl substituent . The use of chlorosulfonyl or trimethylsilyl isocyanate gives the urea derivative without isolation of the intermediate disubstituted urea. Some related compounds were also synthesized.
Advances in reliability and operation space of high-voltage GaN power devices on Si substrates (2014)

GaN-on-Si power devices have advantages in both performance and the potential for low cost and high volume production. Advances have been made in extended reliability tests exhibiting an intrinsic life time >10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> hours for qualified 600-V GaN HEMT products. Experimental kV-class devices have shown CW operation at 800V with >99% efficiency at 100 kHz and a 2:1boost ratio. Both are exciting developments reaffirming the validity of the new power semiconductor technology.
Novel Anti-Campylobacter Compounds Identified Using High Throughput Screening of a Pre-selected Enriched Small Molecules Library (2016)

Campylobacter is a leading cause of foodborne bacterial gastroenteritis worldwide and infections can be fatal. The emergence of antibiotic-resistant Campylobacter spp. necessitates the development of new antimicrobials. We identified novel anti-Campylobacter small molecule inhibitors using a high throughput growth inhibition assay. To expedite screening, we made use of a "bioactive" library of 4182 compounds that we have previously shown to be active against diverse microbes. Screening for growth inhibition of Campylobacter jejuni, identified 781 compounds that were either bactericidal or bacteriostatic at a concentration of 200 μM. Seventy nine of the bactericidal compounds were prioritized for secondary screening based on their physico-chemical properties. Based on the minimum inhibitory concentration against a diverse range of C. jejuni and a lack of effect on gut microbes, we selected 12 compounds. No resistance was observed to any of these 12 lead compounds when C. jejuni was cultured with lethal or sub-lethal concentrations suggesting that C. jejuni is less likely to develop resistance to these compounds. Top 12 compounds also possessed low cytotoxicity to human intestinal epithelial cells (Caco-2 cells) and no hemolytic activity against sheep red blood cells. Next, these 12 compounds were evaluated for ability to clear C. jejuni in vitro. A total of 10 compounds had an anti-C. jejuni effect in Caco-2 cells with some effective even at 25 μM concentrations. These novel 12 compounds belong to five established antimicrobial chemical classes; piperazines, aryl amines, piperidines, sulfonamide, and pyridazinone. Exploitation of analogs of these chemical classes may provide Campylobacter specific drugs that can be applied in both human and animal medicine.
Molecular interactions of the Src homology 2 domain protein Shb with phosphotyrosine residues, tyrosine kinase receptors and Src homology 3 domain proteins. (1995)

The molecular interactions of the Src homology 2 (SH2) domain and the N-terminal proline-rich sequence motifs (pro-1 to pro-5) of the SH2 protein Shb with other components were presently characterised. Using a degenerate phosphopeptide library the preferred binding site for the Shb SH2 domain was determined to pTyr-Thr/Val/Ile-X-Leu at positions +1 to +3 relative the phosphotyrosine residue. Experiments with competing peptides and platelet-derived growth factor (PDGF) beta-receptor mutants with Y to F substitutions in autophosphorylation sites revealed multiple binding sites for the Shb SH2 domain in the receptor. The Shb SH2 domain also binds to in vitro phosphorylated fibroblast growth factor receptor-1 (FGFR-1) mainly through position Y776. The receptor experiments suggest that other residues besides the +1 to +3 positions may also be of significance for Shb binding. The pro-4/pro-5 motif of Shb binds in vitro particularly well to the Src, p85 alpha PI3-kinase and Eps8 SH3 domains expressed as GST fusion proteins. However, the GST-SH3 domain fusion proteins tested bind in vitro to peptides corresponding to the pro-1 to pro-5 motifs of Shb with low affinity and selectivity, suggesting that sequences outside the core proline motif may also be important for Shb-SH3 domain interactions. In vivo association between Shb-SH3 domain proteins v-Src and Eps8 was detected by coimmunoprecipitation. PDGF treatment did not affect the association between Eps8 and Shb. The data suggest that Shb is an adaptor protein linking SH3 domain proteins to tyrosine kinases or other tyrosine phosphorylated proteins.
PrefJoin: An efficient preference-aware join operator (2011)

Preference queries are essential to a wide spectrum of applications including multi-criteria decision-making tools and personalized databases. Unfortunately, most of the evaluation techniques for preference queries assume that the set of preferred attributes are stored in only one relation, waiving on a wide set of queries that include preference computations over multiple relations. This paper presents PrefJoin, an efficient preference-aware join query operator, designed specifically to deal with preference queries over multiple relations. PrefJoin consists of four main phases: Local Pruning, Data Preparation, Joining, and Refining that filter out, from each input relation, those tuples that are guaranteed not to be in the final preference set, associate meta data with each non-filtered tuple that will be used to optimize the execution of the next phases, produce a subset of join result that are relevant for the given preference function, and refine these tuples respectively. An interesting characteristic of PrefJoin is that it tightly integrates preference computation with join hence we can early prune those tuples that are guaranteed not to be an answer, and hence it saves significant unnecessary computations cost. PrefJoin supports a variety of preference function including skyline, multi-objective and k-dominance preference queries. We show the correctness of PrefJoin. Experimental evaluation based on a real system implementation inside PostgreSQL shows that PrefJoin consistently achieves from one to three orders of magnitude performance gain over its competitors in various scenarios.
A Cross-Cultural Study of Waiting as a Satisfaction Driver in Selected Service Encounters (2001)

Abstract Waiting is a source of frustration for most time-pressed consumers who often complain about waiting for services. While many different aspects of waiting have been studied, the reported research looks at waiting and its saliency in customer satisfaction across three cultures in three different service-consuming situations. The results indicate that waiting is a satisfaction driver. However, the dimension of waiting that is salient tends to vary across cultures and situations.
Speaker independent audio-visual continuous speech recognition (2003)

The increase in the number of multimedia applications that require robust speech recognition systems determined a large interest in the study of audio-visual speech recognition (AVSR) systems. The use of visual features in AVSR is justified by both the audio and visual modality of the speech generation and the need for features that are invariant to acoustic noise perturbation. The speaker independent audio-visual continuous speech recognition system presented relies on a robust set of visual features obtained from the accurate detection and tracking of the mouth region. Further, the visual and acoustic observation sequences are integrated using a coupled hidden Markov (CHMM) model. The statistical properties of the CHMM can model the audio and visual state asynchrony while preserving their natural correlation over time. The experimental results show that the current system tested on the XM2VTS database reduces by over 55% the error rate of the audio only speech recognition system at SNR of 0 dB.