gebhart/patrepeval huggingface dataset:
Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial (2010)

Amino acid substitution models are essential to most methods to infer phylogenies from protein data. These models represent the ways in which proteins evolve and substitutions accumulate along the course of time. It is widely accepted that the substitution processes vary depending on the structural configuration of the protein residues. However, this information is very rarely used in phylogenetic studies, though the 3-dimensional structure of dozens of thousands of proteins has been elucidated. Here, we reinvestigate the question in order to fill this gap. We use an improved estimation methodology and a very large database comprising 1471 nonredundant globular protein alignments with structural annotations to estimate new amino acid substitution models accounting for the secondary structure and solvent accessibility of the residues. These models incorporate a confidence coefficient that is estimated from the data and reflects the reliability and usefulness of structural annotations in the analyzed sequences. Our results with 300 independent test alignments show an impressive likelihood gain compared with standard models such as JTT or WAG. Moreover, the use of these models induces significant topological changes in the inferred trees, which should be of primary interest to phylogeneticists. Our data, models, and software are available for download from http://atgc.lirmm.fr/phyml-structure/.
An information-theoretic approach to traffic matrix estimation (2003)

Traffic matrices are required inputs for many IP network management tasks: for instance, capacity planning, traffic engineering and network reliability analysis. However, it is difficult to measure these matrices directly, and so there has been recent interest in inferring traffic matrices from link measurements and other more easily measured data. Typically, this inference problem is ill-posed, as it involves significantly more unknowns than data. Experience in many scientific and engineering fields has shown that it is essential to approach such ill-posed problems via "regularization". This paper presents a new approach to traffic matrix estimation using a regularization based on "entropy penalization". Our solution chooses the traffic matrix consistent with the measured data that is information-theoretically closest to a model in which source/destination pairs are stochastically independent. We use fast algorithms based on modern convex optimization theory to solve for our traffic matrices. We evaluate the algorithm with real backbone traffic and routing data, and demonstrate that it is fast, accurate, robust, and flexible.
Database compression on graphics processors (2010)

Query co-processing on graphics processors (GPUs) has become an effective means to improve the performance of main memory databases. However, this co-processing requires the data transfer between the main memory and the GPU memory via a low-bandwidth PCI-E bus. The overhead of such data transfer becomes an important factor, even a bottleneck, for query co-processing performance on the GPU. In this paper, we propose to use compression to alleviate this performance problem. Specifically, we implement nine lightweight compression schemes on the GPU and further study the combinations of these schemes for a better compression ratio. We design a compression planner to find the optimal combination. Our experiments demonstrate that the GPU-based compression and decompression achieved a processing speed up to 45 and 56 GB/s respectively. Using partial decompression, we were able to significantly improve GPU-based query co-processing performance. As a side product, we have integrated our GPU-based compression into MonetDB, an open source column-oriented DBMS, and demonstrated the feasibility of offloading compression and decompression to the GPU.
Infection and persistence of erythrovirus B19 in benign and cancerous thyroid tissues (2013)

Human erythrovirus B19 (EVB19) is a small, pathogenic DNA virus that has been associated with a wide range of illnesses. The primary site of replication is in bone marrow-derived erythroid progenitor cells, but EVB19 DNA has been detected in a wide range of organs. Recently, studies have linked EVB19 to thyroid cancers and other thyroid diseases. Previous studies from multiple laboratories have detected EVB19 capsid proteins in Graves' disease, Hashimoto's thyroiditis, and thyroid cancer tissues. Data on viral gene expression and mechanism of infection in the thyroid are lacking. To investigate EVB19 infection and persistence in the thyroid, previously archived adult and pediatric tissue sections were examined for EVB19 DNA, RNA, and capsid proteins, as well as EVB19 receptor P-antigen and co-receptor α5β1 integrin. EVB19 DNA and protein were detected in a majority of tissues examined (87% and 68%, respectively). Detection was similar in adult and pediatric samples. Quantification of viral genomes revealed no significant difference in the amount of viral DNA in benign, cancerous, or metastatic thyroid tissues. EVB19 capsid RNA was detected in 67% of the tissues examined, confirming at least low-level viral gene expression. Immunohistochemical staining for P-antigen and α5β1 detected the receptor and co-receptor most frequently on normal thyroid epithelial cells. EVB19 capsid staining could be detected in tumors lacking viral receptors. These results suggest that normal thyroid epithelial cells are the initial target for EVB19 infection in the thyroid and allow for continued persistence in both normal and cancerous thyroid tissues.
Identification and Design of Antimicrobial Peptides for Therapeutic Applications (2012)

Indiscriminate use of antibiotics has led to a rapid increase of antibiotic resistance among microbes which has increased the need to develop novel antimicrobial agents to fight various infectious diseases. Peptide antibiotics signify a novel class of therapeutic agents and have been isolated from a wide variety of multi-cellular organisms. Peptide antibiotics have shown broad-spectrum antimicrobial activity and they not only kill different bacteria, but also kill various fungi, parasites, protozoans and cancerous cells. Peptides bear several properties that make them particularly attractive such as their small size, rapid activity and a low chance for development of resistance. Because of these distinct properties, the focus for research on antimicrobial peptides has increased tremendously in the recent years. Despite their potential, only selected cationic antimicrobial peptides have been able to enter in clinical trials. Therefore, there is a pressing need to develop new approaches to identify novel antimicrobial peptide therapeutics replacing conventional antibiotics. Recent findings strongly suggest that one can design a new generation of antimicrobials peptides with a wide range of systemic and topical applications against bacterial infections. In this review, we focus on the identification and design of novel antimicrobial peptides for therapeutic applications based on different approaches and strategies. This review also highlights some recent advances in the study of the molecular basis of anti-microbial activity in these peptides, their current pharmacological and clinical development and future directions and applications.
Release rate controls biological activity of nerve growth factor released from fibrin matrices containing affinity‐based delivery systems (2007)

Previously, combinatorial techniques were used to identify peptide sequences exhibiting high, medium, and low affinity for heparin. Bidomain peptides were synthesized containing a transglutaminase sequence for one domain and one of the heparin-affinity sequences for the other domain. A delivery system was made consisting of bi-domain peptides, heparin, and nerve growth factor (NGF), which binds to heparin with moderate affinity. The goal of this research was to determine whether peptide affinity for heparin and the molar ratio of peptide to heparin affected the release rate of NGF from the delivery system and the biological activity of NGF released. This study also explored whether peptide affinity modulated biological activity independent of release rate. Mathematically modeling the delivery system confirmed that release could be controlled by both peptide affinity and molar ratio of peptide to heparin. Experimentally, the rate of NGF release from the delivery system was found to be affected by peptide affinity and molar ratio. The delivery system presented biologically active NGF as assayed by embryonic chick dorsal root ganglia (DRGs) neurite extension, where extension was similar to or increased for DRGs grown in fibrin matrices containing the delivery system compared to DRGs grown with NGF in the culture media. Furthermore, by modulating the molar ratio of peptide to heparin in the delivery system, similar release rates of NGF were obtained for different affinity peptides and these conditions promoted similar levels of neurite extension, demonstrating that release rate appears to be the main mechanism controlling the biological activity of released NGF.
Helicobacter pylori antimicrobial resistance in the United Kingdom: the effect of age, sex and socio‐economic status (2001)

Metronidazole resistance in H. pylori is highly prevalent and more common in women and the young, but does not appear to be related to socio-economic status.
Nanocrystalline Orthoferrite GdFeO3 from a Novel Heterobimetallic Precursor. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Upregulation of Store Operated Ca<sup>2+</sup> Channel Orai1, Stimulation of Ca<sup>2+</sup> Entry and Triggering of Cell Membrane Scrambling in Platelets by Mineralocorticoid DOCA (2013)

DOCA (10 µg/ml) treatment of murine platelets was followed by a significant increase of Orai1 protein abundance, [Ca(2+)]i, percentage of phosphatidylserine exposing platelets and platelet swelling. The effect on [Ca(2+)]i, phosphatidylserine abundance and cell volume were completely abrogated by addition of the specific SGK inhibitor EMD638683 (50 µM) CONCLUSIONS: The mineralocorticoid DOCA upregulates Orai1 protein abundance in the cell membrane, thus increasing [Ca(2+)]i and triggering phosphatidylserine abundance, effects paralleled by platelet swelling.
Fatigue life prediction after laser forming (2003)

The current models cannot predict the fatigue life after laser forming accurately because of differences in assumptions. This work presents a model to predict fatigue life of sheet metal after laser forming. Results from microstructure integrated finite element modeling of laser forming are incorporated in the fatigue life model. Low carbon steel is used in this work to validate the model. It is shown that the proposed model can predict the fatigue life of sheet metal after laser forming with good accuracy. The predictions from the model are consistent with experimental results. Effects of laser forming conditions on fatigue life of sheet metal are under investigation.
Regulation of the p53 protein by the MDM2 oncoprotein--thirty-eighth G.H.A. Clowes Memorial Award Lecture. (1999)

It was, indeed, a wonderful honor to receive the G. H. A. Clowes Memorial Award and present the Clowes Lecture at the Meeting for the American Association for Cancer Research. I have been fortunate to carry out research in the area of cancer biology at a remarkable time and to have had many truly
The alpha/beta fold family of proteins database and the cholinesterase gene server ESTHER. (1997)

ESTHER (for esterases, alpha/betahydrolase enzyme and relatives) is a database of sequences phylogenetically related to cholinesterases. These sequences define a homogeneous group of enzymes (carboxylesterases, lipases and hormone-sensitive lipases) sharing a similar structure of a central beta-sheet surrounded by alpha-helices. Among these proteins a wide range of functions can be found (hydrolases, adhesion molecules, hormone precursors). The purpose of ESTHER is to help comparison of structures and functions of members of the family. Since the last release, new features have been added to the server. A BLAST comparison tool allows sequence homology searches within the database sequences. New sections are available: kinetics and inhibitors of cholinesterases, fasciculin-acetylcholinesterase interaction and a gene structure review. The mutation analysis compilation has been improved with three-dimensional images. A mailing list has been created.
System for Automated Interactive Lighting (SAIL) (2009)

Successful lighting in video games is more than a physically accurate illumination model. Aesthetics and function are of equal or greater importance. Lighting designers may deviate from physical accuracy to help a player identify an important object or to more powerfully evoke a desired emotion. Under the assumption that fulfilling the pipeline needs of interactive lighting design requires more than solving the computer rendering equation, we set out to develop a System for Automated Interactive Lighting (SAIL). The goal for SAIL was to develop an adaptive system that maintains lighting design goals (aesthetic and functional) in the context of unpredictable, interactive experiences. This paper presents SAIL and the results of a qualitative evaluation of SAIL's contributions. We describe the algorithms of SAIL, where it succeeds, and where it fails. We conclude with a plan for future work.
Etude de la chimie interfaciale des heterostructures a base de cu(in,ga)se2. Application a la conversion photovoltaique de l'energie solaire (2000)

Ce memoire presente les resultats d'une etude concernant la chimie interfaciale des heterostructures a base de cu(in, ga)se 2 (cigs), materiau utilise en tant qu'absorbeur de lumiere dans les cellules solaires en couches minces. Un des points cle de l'obtention de cellules solaires performantes repose sur la construction de l'interface par des methodes chimiques en solution a partir du depot d'une fine couche de cds. Dans ce travail, nous avons essaye de mieux comprendre les mecanismes de formation de l'hetero-jonction n-p puis nous avons propose une nouvelle facon d'elaborer la jonction a partir de traitements chimiques ou electrochimiques du cu(in, ga)se 2. Nous avons tout d'abord etudie par xps la surface du cigs non traitee et identifie les composes presents. Nous avons egalement discute en detail des modifications chimiques de surface induites par differents traitements, que ce soit d'oxydation ou de decapage. L'oxydation electrochimique du cu(in,ga)se 2 dans differents milieux sera presentee et ces resultats discutes a partir des analyses de surface et des previsions thermodynamiques. Nous etudierons ensuite les modifications chimiques et electrochimiques de surface du cigs en milieu ammoniaque, en presence ou non de differents ions. Nous presenterons alors les mecanismes de reaction permettant d'expliquer la formation des composes de surface, et discuterons de mecanismes envisageables tels que des reactions d'echange ionique ou d'electro-insertion. Enfin, nous etudierons les proprietes electroniques, par des mesures de sonde kelvin, et photovoltaiques des surfaces modifiees. Nous montrerons que ces proprietes dependent fortement des traitements utilises, et notamment de la chimie de surface. Des dispositifs photovoltaiques de structure zno / cu(in,ga)se 2 modifie / mo / verre ont ete elabores avec des rendements de pres de 13%, valeur proche de celle obtenue en presence de cds. Enfin, nous etudierons en detail la construction de la barriere au sein des cellules en fonction des traitements du cigs. Nous discuterons notamment de la passivation des etats d'interface et du role de la couche fenetre de zno dans l'elaboration de la jonction.
Core-Size Dispersity Dominates the Self-Assembly of Polymer-Grafted Nanoparticles in Solution (2019)

In polymer-grafted nanoparticles (PGN), covalent tethering of apolar polymer chains to a polar inorganic nanoparticle core induces the formation of self-assembled aggregates. Since the nature of these aggregates determines bulk mechanical and transport properties, it is of importance to understand the factors that determine the underlying assembly processes. In the literature, the solution assembly of PGNs has been understood in analogy to small-molecule amphiphiles. However, in any experimental realization, PGNs are invariably characterized by additional structural complexity, such as the distributions in the inorganic core size and in the grafted chains (both in their length and grafting density). These strongly influence the assembly of amphiphilic PGNs. We have previously demonstrated that dispersity in core size qualitatively affects the structure of PGN aggregates, and Jayaraman et al. demonstrated the effect of grafted chain-length dispersity. The combined effects of dispersity in the size of the core and grafted chains have not been explored previously. Here, we develop a model that builds on the work of Daoud and Cotton to explore a wide parameter space of PGN with dispersity simultaneously in core size and grafted chain length. We demonstrate that dispersity in core size is the dominant factor affecting the self-assembled solution structure of PGN aggregates. Our work suggests the importance of focusing on synthetic strategies for control of core-size dispersity to control aggregate structure in PGN.
Does Routine Stress-Thallium Cardiac Scanning Reduce Postoperative Cardiac Complications? (1994)

Preoperative stress-thallium testing confirmed a high incidence of significant coronary artery disease in patients undergoing aortic reconstruction, but prophylactic cardiac intervention does not reduce operative or long-term mortality. Thus, the risk and expense of routine stress-thallium testing and subsequent cardiac revascularization cannot be justified.
Exploring the algorithmic design space using high level synthesis (2002)

HYPER is a high level synthesis system, targeted at numerically intensive applications. By shifting the emphasis from the traditional high level synthesis tasks (such as scheduling and assignment) to the domain of transformations, new venues for high level synthesis are opened. One of the most exciting among them, with potentially the largest impact on the quality of the design, is design and selection of the algorithms for a given application. After a brief overview of the HYPER system, the authors concentrate on the exploration of the algorithmic design space. They show how HYPER can improve the performance or cost of real life applications with orders of magnitude by guiding and conducting a proper algorithmic design selection process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Qualitative comparison between different biopolymers for usage in two-photon polymerization towards liver regeneration (2022)

Femtosecond laser-based two-photon polymerization is becoming increasingly popular in biofabrication. One of the key selling points of the technology is the possibility to use a variety of different materials to produce biology-oriented structures, for instance, liver cell regeneration. These include hybrid materials, lithographic resins, and hydrogels to name a few. However, while these materials are investigated separately, there is a severe lack of studies dedicated to directly comparing them in terms of structurability. Therefore, in this work, popular pre-polymers such as SZ2080, SU8, and GelMA are compared side by side in this manner. They are photosensitized using photoinitiators Irgacure 369, Irgacure 2959, and LAP. Structurability is tested using two different popular wavelengths - 800 nm and 515 nm. Acquired differences are subsequently partially explained by two-photon absorption measurement, giving insights into the efficiency of the photopolymerization process. Finally, biocompatibility is compared showing surprisingly small differences between all the tested materials.
Very fast optimal bandwidth selection for univariate kernel density estimation (2006)

Most automatic bandwidth selection procedures for kernel density estimates require estimation of quantities involving the density derivatives. Estimation of modes and inflexion points of densities also require derivative estimates. The computational complexity of evaluating the density derivative at M evaluation points given N sample points from the density is O(MN). In this paper we propose a computationally efficient $\epsilon$-exact approximation algorithm for univariate, Gaussian kernel based, density derivative estimation that reduces the computational complexity from O(MN) to linear order (O(N+M)). The constant depends on the desired arbitrary accuracy, $\epsilon$. We apply the density derivative evaluation procedure to estimate the optimal bandwidth for kernel density estimation, a process that is often intractable for large data sets. For example for N = M = 409,600 points while the direct evaluation of the density derivative takes around 12.76 hours the fast evaluation requires only 65 seconds with an error of around $10^{-12)$. Algorithm details, error bounds, procedure to choose the parameters and numerical experiments are presented. We demonstrate the speedup achieved on the bandwidth selection using the ``solve-the-equation plug-in method'' [18]. We also demonstrate that the proposed procedure can be extremely useful for speeding up exploratory projection pursuit techniques.
High-Risk Human Papillomavirus E5 Oncoprotein Displays Channel-Forming Activity Sensitive to Small-Molecule Inhibitors (2012)

High-risk human papillomavirus type 16 (HPV16) is the primary causative agent of cervical cancer and therefore is responsible for significant morbidity and mortality worldwide. Cellular transformation is mediated directly by the expression of viral oncogenes, the least characterized of which, E5, subverts cellular proliferation and immune recognition processes. Despite a growing catalogue of E5-specific host interactions, little is understood regarding the molecular basis of its function. Here we describe a novel function for HPV16 E5 as an oligomeric channel-forming protein, placing it within the virus-encoded "viroporin" family. The development of a novel recombinant E5 expression system showed that E5 formed oligomeric assemblies of a defined luminal diameter and stoichiometry in membranous environments and that such channels mediated fluorescent dye release from liposomes. Hexameric E5 channel stoichiometry was suggested by native PAGE studies. In lieu of high-resolution structural information, established de novo molecular modeling and design methods permitted the development of the first specific small-molecule E5 inhibitor, capable of both abrogating channel activity in vitro and reducing E5-mediated effects on cell signaling pathways. The identification of channel activity should enhance the future understanding of the physiological function of E5 and could represent an important target for antiviral intervention.