gebhart/patrepeval huggingface dataset:
Crystallographic Structures of Human α-Thrombin Complexed to Peptide Boronic Acids Lacking a Positive Charge at P1. Evidence of Novel Interactions (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTCrystallographic Structures of Human α-Thrombin Complexed to Peptide Boronic Acids Lacking a Positive Charge at P1. Evidence of Novel InteractionsEmmanuel Skordalakes, Richard Tyrell, Said Elgendy, Christopher A. Goodwin, Donovan Green, Guy Dodson, Michael F. Scully, Jean-Marie H. Freyssinet, Vijay V. Kakkar, and John J. DeadmanView Author Information Thrombosis Research Institute Emmanuel Kaye Building, London SW3 6LR, U.K. Protein Structure Laboratory National Institute of Medical Research the Ridgeway, Mill Hill, London NW7 1AA, U.K. Faculté de Médecine Institut d'Hématologie et d'Immunologie 4 rue Kirschleger, F-67085 Strasbourg, France Cite this: J. Am. Chem. Soc. 1997, 119, 41, 9935–9936Publication Date (Web):October 15, 1997Publication History Received28 April 1997Published online15 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/ja9713338https://doi.org/10.1021/ja9713338rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views132Altmetric-Citations13LEARN 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 SUBJECTS:Inhibitors,Molecular mechanics,Monomers,Oxygen,Peptides and proteins Get e-Alerts
Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications (1998)

Amplified fragment length polymorphism (AFLP) is a novel molecular fingerprinting technique that can be applied to DNAs of any source or complexity. Total genomic DNA is digested using two restriction enzymes. Double-stranded nucleotide adapters are ligated to the DNA fragments to serve as primer binding sites for PCR amplification. Primers complementary to the adapter and restriction site sequence, with additional nucleotides at the 3′-end, are used as selective agents to amplify a subset of ligated fragments. Polymorphisms are identified by the presence or absence of DNA fragments following analysis on polyacrylamide gels. This technique has been extensively used with plant DNA for the development of high-resolution genetic maps and for the positional cloning of genes of interest. However, its application is rapidly expanding in bacteria and higher eukaryotes for determining genetic relationships and for epidemiological typing. This review describes the AFLP procedure, and recent, novel applications in the molecular fingerprinting of DNA from both eukaryotic and prokaryotic organisms.
Molecular Diversity and Functional Evolution of Scorpion Potassium Channel Toxins (2010)

Scorpion toxins affecting K(+) channels (KTxs) represent important pharmacological tools and potential drug candidates. Here, we report molecular characterization of seven new KTxs in the scorpion Mesobuthus eupeus by cDNA cloning combined with biochemical approaches. Comparative modeling supports that all these KTxs share a conserved cysteine-stabilized α-helix/β-sheet structural motif despite the differences in protein sequence and size. We investigated functional diversification of two orthologous α-KTxs (MeuTXKα1 from M. eupeus and BmP01 from Mesobuthus martensii) by comparing their K(+) channel-blocking activities. Pharmacologically, MeuTXKα1 selectively blocked Kv1.3 channel with nanomolar affinity (IC(50), 2.36 ± 0.9 nM), whereas only 35% of Kv1.1 currents were inhibited at 3 μM concentration, showing more than 1271-fold selectivity for Kv1.3 over Kv1.1. This peptide displayed a weak effect on Drosophila Shaker channel and no activity on Kv1.2, Kv1.4, Kv1.5, Kv1.6, and human ether-a-go-go-related gene (hERG) K(+) channels. Although BmB01 and MeuTXKα1 have a similar channel spectrum, their affinity and selectivity for these channels largely varies. In comparison with MeuTXKα1, BmP01 only exhibits a submicromolar affinity (IC(50), 133.72 ± 10.98 nM) for Kv1.3, showing 57-fold less activity than MeuTXKα1. Moreover, it lacks the ability to distinguish between Kv1.1 and Kv1.3. We also found that MeuTXKα1 inhibited the proliferation of activated T cells induced by phorbol myristate acetate and ionomycin at micromolar concentrations. Our results demonstrate that accelerated evolution drives affinity variations of orthologous α-KTxs on Kv channels and indicate that MeuTXKα1 is a promising candidate to develop an immune modulation agent for human autoimmune diseases.
The cellular niche of <i>Listeria monocytogenes</i> infection changes rapidly in the spleen (2009)

The spleen is an important organ for the host response to systemic bacterial infections. Many cell types and cell surface receptors have been shown to play role in the capture and control of bacteria, yet these are often studied individually and a coherent picture has yet to emerge of how various phagocytes collaborate to control bacterial infection. We analyzed the cellular distribution of Listeria monocytogenes (LM) in situ during the early phase of infection. Using an immunohistochemistry approach, five distinct phagocyte populations contained LM after i.v. challenge and accounted for roughly all bacterial signal in tissue sections. Our analysis showed that LM was initially captured by a wide range of phagocytes in the marginal zone, where the growth of LM appeared to be controlled. The cellular distribution of LM within phagocyte populations changed rapidly during the first few hours, decreasing in marginal zone macrophages and transiently increasing in CD11c(+) DC. After 4-6 h LM was transported to the periarteriolar lymphoid sheath where the infective foci developed and LM grew exponentially.
The case for independent updates (2003)

The authors present the case for allowing independent updates on replicated databases. In autonomous, heterogeneous, or large scale systems, using two-phase commit for updates may be infeasible. Instead, the authors propose that a site may perform updates independently. Sites that are available can receive these updates immediately. But sites that are unavailable, or otherwise do not participate in the update transaction receive these updates later through propagation, rather than preventing the execution of the update transaction until sufficient sites can participate. Two or more sites come to agreement using a reconciliation procedure that uses reception vectors to determine how much of the history log should be transferred from one site to another. They also consider what events can initiate a reconciliation procedure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Berberine – a novel approach to cholesterol lowering (2005)

Although low-density lipoprotein (LDL)-cholesterol lowering with the statins reduces the mortality and morbidity associated with coronary artery disease, considerable mortality and morbidity remains. Berberine upregulates the LDL receptor (LDLR) by a mechanism distinct from that of the statins, which involves stabilising the LDLR mRNA. In hamsters fed a high-fat and high-cholesterol diet for 2 weeks, the oral administration of berberine 100 mg/kg for 10 days reduced total serum cholesterol from approximately 4.8 to 2.7 mmol/l, and LDL-cholesterol from approximately 2.5 to 1.4 mmol/l. In subjects with hypercholesterolaemia, berberine hydrochloride (0.5 g b.i.d. for 3 months) reduced LDL-cholesterol (from 3.2 to 2.4 mmol/l) without any effect on high-density lipoprotein-cholesterol. Berberine also caused a reduction in triglyceride levels from 2.3 to 1.5 mmol/l. As berberine and statins both upregulate LDLR, their lipid-lowering profiles are similar. Thus, this mechanism is unlikely to make berberine an attractive alternative to statins for lipid lowering in most circumstances. However, the other effects of berberine (antihypertensive, inotropic and class III antiarrhythmic properties) may make it a useful agent in the treatment of cardiovascular disease.
A framework for studying synaptic plasticity with neural spike train data (2014)

Learning and memory in the brain are implemented by complex, time-varying changes in neural circuitry. The computational rules according to which synaptic weights change over time are the subject of much research, and are not precisely understood. Until recently, limitations in experimental methods have made it challenging to test hypotheses about synaptic plasticity on a large scale. However, as such data become available and these barriers are lifted, it becomes necessary to develop analysis techniques to validate plasticity models. Here, we present a highly extensible framework for modeling arbitrary synaptic plasticity rules on spike train data in populations of interconnected neurons. We treat synaptic weights as a (potentially nonlinear) dynamical system embedded in a fully-Bayesian generalized linear model (GLM). In addition, we provide an algorithm for inferring synaptic weight trajectories alongside the parameters of the GLM and of the learning rules. Using this method, we perform model comparison of two proposed variants of the well-known spike-timing-dependent plasticity (STDP) rule, where nonlinear effects play a substantial role. On synthetic data generated from the biophysical simulator NEURON, we show that we can recover the weight trajectories, the pattern of connectivity, and the underlying learning rules.
A unique photoemission method to measure semiconductor heterojunction band offsets (2013)

We report a unique way to measure the energy band offset of a heterojunction by exploiting the light absorption profile in the heterojunction under visible-ultraviolet internal photoemission. This method was used to determine the band alignment of W/Al2O3/n+InAs/p+Al0.45Ga0.55Sb heterojunctions that are of interest for tunnel field-effect transistors. The barrier heights from the InAs and Al0.45Ga0.55Sb valence band maxima to the Al2O3 conduction band minimum are found to be 3.24 eV± 0.05 eV and 2.79 eV± 0.05 eV, respectively, yielding a 0.4 eV± 0.1 eV offset at the InAs/AlGaSb interface. This approach can readily be applied to characterize a wide range of other semiconductor heterojunctions.
Two‐Day Regimen of Acyclovir for Treatment of Recurrent Genital Herpes Simplex Virus Type 2 Infection (2002)

The standard course of antiviral therapy for recurrent genital herpes requires administration of multiple doses of medication for 5 days. To assess the efficacy of a shorter course of antiviral therapy, patients with recurrent genital herpes simplex virus type 2 (HSV-2) infection were enrolled in a randomized, double-blind, placebo-controlled study of acyclovir (800 mg given by mouth 3 times per day [t.i.d.]) for 2 days. Of 131 people enrolled in the study, 84 (51 women and 33 men) were observed for >/=1 recurrence and 65 were observed for 2 recurrences, for which the patient was administered the same study drug (acyclovir or placebo). Acyclovir therapy (800 mg given by mouth t.i.d. for 2 days) significantly reduced the duration of lesions (median for acyclovir versus placebo, 4 days versus 6 days; P=.001), episode (4 days versus 6 days; P<.001), and viral shedding (25 hours versus 58.5 hours; P=.04), and it increased the proportion of aborted episodes (P=.029). A 2-day course of acyclovir is a convenient alternative for treatment of recurrent genital herpes.
Single Polymer Chain Elongation by Atomic Force Microscopy (1999)

The elastic deformation of single polystyrene-b-poly-2-vinylpyridine chains from spun cast films was investigated by atomic force microscopy. A nonlinear elastic response is shown to be present hundreds of nanometers above the bulk surface. The length of the elastic response monotonically increases with molecular weight of the polymer. These nonlinear elastic responses are fit to wormlike chain and freely joined chain models giving persistence and Kuhn lengths of approximately 3 and 4 Å, respectively. The entropic models reveal that the polymer chains are stretched to 80−90% of their contour length before the attachment to the tip is ruptured.
A Generic Temporal Integration Approach for Enhancing Feature-based Road-detection Systems (2008)

Visual feature-based approaches for detecting the drivable area on unmarked streets and roads were introduced in recent years. Although the accumulated results are promising, the detected street segments often contain holes and show a detection performance that strongly varies in time depending on environmental conditions. This paper presents a real-time capable approach for improving the road detection results for this type of state-of-the-art systems by adding a generic postprocessing step. Our proposed architecture removes the drawbacks of said systems using a temporal integration approach based on the bird's eye view. In order to test the proposed approach, one typical visual feature-based road detection system was implemented. Still, the used road detection system can be exchanged with any other state-of-the-art system. Evaluation results computed on inner-city data show that this approach is an important enhancement for all visual feature-based road-detection systems. One of the used streams and corresponding ground truth data is accessible on the internet for benchmark testing. The proposed approach is a crucial step toward robust road detection in complex scenarios that allows building high-level applications, as, e.g., active collision avoidance or trajectory planning, based on vision as the major cue.
Augmented reality for enhanced visual inspection through knowledge-based deep learning (2020)

A two-stage knowledge-based deep learning algorithm is presented for enabling automated damage detection in real-time using the augmented reality smart glasses. The first stage of the algorithm entails the identification of damage prone zones within the region of interest. This requires domain knowledge about the damage as well as the structure being inspected. In the second stage, automated damage detection is performed independently within each of the identified zones starting with the one that is the most damage prone. For real-time visual inspection enhancement using the augmented reality smart glasses, this two-stage approach not only ensures computational feasibility and efficiency but also significantly improves the probability of detection when dealing with structures with complex geometric features. A pilot study is conducted using hands-free Epson BT-300 smart glasses during which two distinct tasks are performed: First, using a single deep learning model deployed on the augmented reality smart glasses, automatic detection and classification of corrosion/fatigue, which is the most common cause of failure in high-strength materials, is performed. Then, in order to highlight the efficacy of the proposed two-stage approach, the more challenging task of defect detection in a multi-joint bolted region is addressed. The pilot study is conducted without any artificial control of external conditions like acquisition angles, lighting, and so on. While automating the visual inspection process is not a new concept for large-scale structures, in most cases, assessment of the collected data is performed offline. The algorithms/techniques used therein cannot be implemented directly on computationally limited devices such as the hands-free augmented reality glasses which could then be used by inspectors in the field for real-time assistance. The proposed approach serves to overcome this bottleneck.
The Role of the Nasopharyngeal Airway for Obstructive Sleep Apnea in Syndromic Craniosynostosis (2008)

Syndromic craniosynostosis is known to be associated with obstructive sleep apnea (OSA), which can often present in infancy. Although multifactorial, a predominant contributing factor is midface hypoplasia. Nasal continuous positive airway pressure has proven to be an effective treatment modality but may be poorly tolerated in certain cases. This study looks at the effectiveness of bypassing midface obstruction with a nasopharyngeal airway (NPA). Twenty-seven children with syndromic craniosynostosis with confirmed moderate to severe OSA were initially treated with an NPA. The mean age of NPA insertion was 12.3 months (range, 0.5-48 mo). Seventeen had severe OSA, and 10 had moderate OSA preinsertion. Post-NPA insertion, 26 of 27 children (96%) demonstrated an improvement in sleep severity scores, resulting in 3 with moderate OSA and 24 with mild OSA. There was a significant improvement in mean oxygen saturation, mean number of saturation dips greater than 4% per hour, percentage time spent less than 90% SpO2, and number of pulse rate rises per hour. There were no significant differences in mean pulse rate. The NPA was well tolerated by this patient group, with 24 of 26 children retaining it for at least 6 weeks. We believe that an NPA is therefore an effective first-line treatment modality in the management of OSA in children with syndromic craniosynostosis. It is well tolerated by the patient and may obviate the need for continuous positive airway pressure or tracheostomy.
Integration of CMOS-MEMS resonators for radiofrequency applications in the VHF and UHF bands (2007)

Aquesta tesi doctoral te com a objectiu fonamental la integracio monolitica de microressonadors en una tecnologia comercial, AMS 0.35um, tot utilitzant les capes disponibles del proces tecnologic. Les estructures son alliberades en un proces post-CMOS consistint en un atac humit basat en una solucio HF, sense la necessitat de utilitzar cap mascara ni cap proces fotolitografia. Per tal de dissenyar i modelitzar aquests ressonadors, un model electromecanic basat en la deflexio real dels ressonadors sera descrit permetent al dissenyador predir el maxim de corrent a la ressonancia. A mes a mes, un conjunt d'equacions de disseny sera presentat per tots els dispositius fabricats. Al llarg d'aquesta tesi diferents aproximacions tecnologiques tot utilitzant les capes disponibles de la tecnologia estandard per fabricar microressonadors seran introduits i discutits. Des del punt de vista del disseny, reduir la distancia del gap entre el ressonador i el electrode esdeve un dels parametres mes rellevants que potenciaran la resposta electrica del dispositiu. Aleshores, les aproximacions tecnologiques estaran encaminades a reduir la distancia del gap tan com sigui possible. Per a les aproximacions tecnologiques mes prometedores, limitacions basades en el col·lapse vertical en el proces de alliberament seran considerats per tal de evitar el disseny s'estructures amb limitacio en el seu funcionament. Una aproximacio tecnologica basada en les capes del modul estandard per a la fabricacio de capacitats integrades, ha resultat en una de les aproximacions mes prometedores per a la fabricacio integrada de ressonadors MEMS en el rangs de frequencies VHF i UHF, aconseguint gaps laterals de 40nm. Dispositius exhibint frequencies en el rang VHF, amb factors de qualitat fins a 3000 a 290MHz, seran presentats, obtenint una figura de merit de Qxf=9.1011 Hz. A mes a mes, resultats preliminars en la caracteritzacio d'un anell ressonant en mode acustic a 1GHz sera descrit.
A comparison of tension-type headache in migraineurs and in non-migraineurs: a population-based study (1996)

The prevalence, sex-ratio and clinical characteristics of tension-type headache were analyzed in 4000 people from the general population. The one-year-period prevalence of tension-type headache was not significantly different in people with migraine without aura (83%), in people with migraine with aura (75%) and in people who had never had migraine (76%). The male/female ratio varied from 1:1.19 to 1:1.23 and was not significantly different in the three subgroups. Tension-type headache was significantly more frequent within the last year and lasted longer in migraineurs than in people who had never had migraine. The pain characteristics and accompanying symptoms were very similar in the three subgroups. Tension-type headache was often precipitated by stress, mental tension and tiredness. Only migraineurs had episodes of tension-type headache precipitated by alcohol, over-matured cheese, chocolate and physical activity. We conclude that tension-type headache and migraine are separate disorders and not part of a continuum of headache disorders. However, migraine may aggravate and precipitate tension-type headache possibly due to convergence of various noxious peripheral input into the trigeminal nucleus.
Play, Argumentation and Social Constructivism (1998)

This paper explores the notion that some social interactions are more conducive to the construction of knowledge than others. Using transcripts of the interactions of four‐and‐a‐half year old children in a play context, the use of the discourse of argumentation is highlighted as having the potential to promote learning. Implications for early childhood education are derived from these examples and from a theoretical discussion of argumentation.
A Stability-based Validation Procedure for Differentially Private Machine Learning (2013)

Differential privacy is a cryptographically motivated definition of privacy which has gained considerable attention in the algorithms, machine-learning and data-mining communities. While there has been an explosion of work on differentially private machine learning algorithms, a major barrier to achieving end-to-end dif-ferential privacy in practical machine learning applications is the lack of an ef-fective procedure for differentially private parameter tuning, or, determining the parameter value, such as a bin size in a histogram, or a regularization parameter, that is suitable for a particular application. In this paper, we introduce a generic validation procedure for differentially private machine learning algorithms that apply when a certain stability condition holds on the training algorithm and the validation performance metric. The training data size and the privacy budget used for training in our procedure is independent of the number of parameter values searched over. We apply our generic procedure to two fundamental tasks in statistics and machine-learning – training a regularized linear classifier and building a histogram density estimator that result in end-to-end differentially private solutions for these problems. 1