gebhart/patrepeval huggingface dataset:
On the influence of hydrated imidazolium-based ionic liquid on protein structure stability: A molecular dynamics simulation study (2013)

The structure stability of three α-helix bundle (the B domain of protein A) in an imidazolium-based ionic liquid (1-butyl-3-methylimidazolium chloride (BMIM-Cl)) is studied by molecular dynamics simulations. Consistent with previous experiments, the present simulation results show that the native structure of the protein is consistently stabilized in BMIM-Cl solutions with different concentrations. It is observed that BMIM(+) cations have a strong tendency to accumulate on protein surface whereas Cl(-) anions are expelled from protein. BMIM(+) cations cannot only have electrostatic interactions with the carbonyl groups on backbone and the carboxylate groups on negatively charged side chains, but also have hydrophobic interactions with the side chains of non-polar residues. In the meanwhile, the accumulation of large-size BMIM(+) cations on protein surface could remove the surrounding water molecules, reduce the hydrogen bonding from water to protein, and thus stabilize the backbone hydrogen bonds. In summary, the present study could improve our understanding of the molecular mechanism of the impact of water-miscible ionic liquid on protein structure.
Dynamic Surface Roughness for Aerodynamic Flow Control (2004)

This study addresses the issue of controlling flow separation through the use of dynamic surface roughness. The work focuses on two areas: 1) development of simulation tools for detailed analysis of moving flow boundaries and 2) investigation of the effects of dynamic roughness on aerodynamic flow separation. The process of generating a quality grid for a surface that contains complex roughness can be a laborintensive project. The addition of dynamic surface roughness, or roughness that grows (or shrinks) in time, can further complicate this process. The current study proposes a method that not only accounts for the perturbations to the surface, but also allows for the surface to move dynamically, which produces a robust gridding method that is well suited for this application. The method is applied to dynamic surface roughness in the leading-edge region of an airfoil, but could also be used for analysis of internal surface roughness. The dynamic surface roughness examined in this study showed that it can have a major impact on the flow field, with the resulting flow being significantly different that the flow found with similar static surface roughness. The dynamic roughness was able to delay or eliminate the unsteady flow separation for the conditions tested at both constant angle-of-attack and dynamic stall regimes and shows strong potential as an aerodynamic flow control mechanism.
Conformal Copper Coating of True Three-Dimensional Through-Holes Using Supercritical Carbon Dioxide (2012)

Copper thin films were deposited inside true three-dimensional, high aspect ratio, and complex shaped through-holes that were formed in glass substrates. The deposition was carried out in a supercritical carbon dioxide solution from a copper complex via hydrogen reduction. The conformal thin films were successfully deposited on the sidewalls of straight, crank-shaped, and Y-shaped through-holes. The coating length increased with decreasing the deposition temperature. Numerical simulations suggested an importance of the presence of a fluid motion in the through-holes.
Mitigating the risk of African swine fever virus in feed with anti‐viral chemical additives (2020)

African swine fever (ASF) is currently considered the most significant global threat to pork production worldwide. Disease caused by the ASF virus (ASFV) results in high case fatality of pigs. Importantly, ASF is a trade-limiting disease with substantial implications on both global pork and agricultural feed commodities. ASFV is transmissible through natural consumption of contaminated swine feed and is broadly stable across a wide range of commonly imported feed ingredients and conditions. The objective of the current study was to investigate the efficacy of medium-chain fatty acid and formaldehyde-based feed additives in inactivating ASFV. Feed additives were tested in cell culture and in feed ingredients under a transoceanic shipment model. Both chemical additives reduced ASFV infectivity in a dose-dependent manner. This study provides evidence that chemical feed additives may potentially serve as mitigants for reducing the risk of ASFV introduction and transmission through feed.
Ranking diffusion tensor measures of brain aging and Alzheimer’s disease (2018)

Diffusion-weighted MRI (dMRI) offers a range of measures that are sensitive to brain aging and neurodegeneration. Here we analyzed data from 318 participants (mean age: 75.4&plusmn;7.9 years; 143 men/175 women) from the third phase of the Alzheimer’s Disease Neuroimaging Initiative (ADNI3), who were each scanned with one of six different diffusion MRI protocols using scanners from three different manufacturers. We computed 4 standard diffusion tensor imaging (DTI) anisotropy and diffusivity indices, and one advanced anisotropy index based on the tensor distribution function (TDF), in 24 white matter regions of interest. Modeling protocol effects, we ranked the diffusion indices for their strength of correlation with 3 standard clinical measures of cognitive impairment: the ADAS-Cog, MMSE, and sum-of-boxes Clinical Dementia Rating. Across all dMRI indices and cognitive measures, the cingulum-hippocampal region and the uncinate showed some of the strongest associations with cognitive impairment; largest effect sizes were detected with axial diffusivity (Ax<sup>DDT</sup>I). While fractional anisotropy (FA) derived from the DTI model was the weakest in detecting associations with cognitive measures, FA derived from the TDF detected widespread, robust associations. Protocol differences affected dMRI indices; however by modeling protocol effects, we were able to pool dMRI data from multiple acquisition protocols and detect consistent associations with cognitive impairment and age. dMRI indices computed from the upgraded scanning protocols in ADNI3 were sensitive to cognitive impairment in brain aging, offering a benchmark to compare to future multi-shell or multi-compartment diffusion indices.
In-Source Microdroplet Derivatization Using Coaxial Contained-Electrospray Mass Spectrometry for Enhanced Sensitivity in Saccharide Analysis (2021)

Online, droplet-based in-source chemical derivatization is accomplished using a coaxial-flow contained-electrospray ionization (contained-ESI) source to enhance sensitivity for the mass spectrometric analysis of saccharides. Derivatization is completed in microseconds by exploiting the reaction rate acceleration afforded by electrospray microdroplets. Significant improvements in method sensitivity are realized with minimal sample preparation and few resources when compared to traditional benchtop derivatizations. For this work, the formation of easily ionizable phenylboronate ester derivatives of several mono-, di-, and oligosaccharides is achieved. Various reaction parameters including concentration and pH were evaluated, and a Design of Experiments approach was used to optimize ion source parameters. Signal enhancements of greater than two orders of magnitude were observed for many mono- and disaccharides using in-source phenylboronic acid derivatization, resulting in parts-per-trillion (picomolar) limits of detection. In addition, amino sugars such as glucosamine, which do not ionize in negative mode, were detected at low parts-per-billion concentrations, and isobaric sugars such as lactose and sucrose were easily distinguished. The new in-source derivatization approach can be employed to expand the utility of ESI-MS analysis for compounds that historically experience limited sensitivity and detectability, while avoiding resource-intensive, bulk-phase derivatization procedures.
Mycoherbicides and other biocontrol agents for Senecio spp (1993)

Abstract Classical biocontrol of Senecio jacobaea (ragwort) has generally utilised herbivorous insects, although the nisi Puccinia expansa has also been considered. Although this rust is specific and damaging in the glasshouse. It has not been used in the field. Research into the ecophysiology of Senecio vulgaris (groundsel) infected by the rust Puccinia lagenophorae has revealed the extent to which the effects of infection are dependent on environmental factors. The damage caused by rust is enhanced under mild drought conditions, during periods of frost in winter and by competition between groundsel and neighbouring plants, bui is reduced by nutrient deficiency. Rust injury is also greatly increased by secondary infection of pustules by necrotrophic fungi. Such secondary infection can be achieved artificially with a range of opportunistic necrolrophs and can selectively kill groundsel: the effective inoculum dose of both fungi is significantly reduced. Attempts to apply our understanding of rust‐necrotroph injury to ragwort have been partially successful but we have not succeeded in causing significant mortality of this host. This paper discusses these, and other weed—pathogen—environment interactions, and their possible application to biocontrol.
ChemInform Abstract: Intramolecular Cyclizations of Hantzsch 1,4‐Dihydropyridines: Synthesis of Di‐ and Tetrahydroindeno(2,1‐c)pyridines. (1988)

Abstract Reaction of the 4‐(o‐formylphenyl)‐1,4‐dihydropyridines (I) with trimethylsilyl cyanide (II) followed by treatment with tetrabutylammonium fluoride gives the cyclization products (III) ‐ (V).
Multiuser detection of quasisynchronous CDMA signals using linear decorrelators (1996)

A linear decorrelator detector is proposed for a quasisynchronous code-division multiple-access (QS-CDMA) cellular system. It is assumed that each of N users has a Global Positioning System (GPS) generated local clock and attempts to transmit synchronously with the other users in its cell. The base station thus receives N signature waveforms which are approximately synchronized, but with a small timing error due to local oscillator drift, Doppler shifts, and variable distances from the mobiles to the base. The residual timing offset is discretized, and a decorrelator is constructed which attempts to reject the multiuser interference vectors corresponding to the set of possible offsets. A noncoherent version of the decorrelator detector is presented, along with a maximum-likelihood scheme for synchronizing to the desired signal. Bounds and analytical results for the bit-error rate (BER) are obtained for various interferer conditions.
CLASSIFICATION OF CEREAL GRAINS USING MACHINE VISION: I. MORPHOLOGY MODELS (2000)

An algorithm was developed based on morphological features to classify individual kernels of CanadaWestern Red Spring (CWRS) wheat, Canada Western Amber Durum (CWAD) wheat, barley, oats, and rye. Twenty-threemorphological features were used for the discriminant analysis. Grains from 15 growing regions (300 kernels pergrowing region) across Western Canada were used as the training data set and from another five growing regions as thetest data set. The classification accuracies of individual kernels using the 10 most significant features in the morphologymodel were 98.9, 93.7, 96.8, 99.9, and 81.6%, respectively for CWRS wheat, CWAD wheat, barley, oats, and rye whentested on an independent data set (i.e., the test data set where the total number of kernels used was 10 500; for CWRSwheat, 300 kernels each were selected for three grades). When the model was tested on the training data set (total numberof kernels used was 31 500), the classification accuracies of CWRS wheat, CWAD wheat, barley, oats, and rye were 98.9,91.6, 97.9, 100.0, and 91.6%, respectively.
Cloning and Regulation of a Stress-regulated Pennisetum glaucum Vacuolar ATPase c Gene and Characterization of its Promoter that is Expressed in Shoot Hairs and Floral Organs (2005)

We have cloned and characterized the cDNA, genomic clone and upstream promoter region of a vacuolar ATPase (V-ATPase) c subunit (PgVHA-c1) from Pennisetum glaucum. The deduced amino acid sequence shows 98-71% sequence identity with V-ATPase from rice and Arabidopsis, and is a highly hydrophobic protein with four transmembrane regions. PgVHA-c1-GFP fusion protein is expressed in BY2 cells on the endo-membranes surrounding vacuoles; however, PgVHA-c1 could not functionally complement V-ATPase-c deletion mutants of yeast. The sequence analysis of the genomic clone revealed the presence of two introns in the coding region, and the splice junctions followed the typical canonical GU-AG consensus sequence. The transcript analysis showed that the expression of PgVHA-c1 was stimulated more in response to salinity stress and very marginally in response to drought and low temperature stress. Exogenous application of abscisic acid, salicylic acid and calcium stimulated the transcript level in the absence of stress. We have cloned the 5'-flanking regions of PgVHA-c1 and mapped its transcript start site at 78 bp upstream of ATG. Transgenic tobacco with promoter::GUS constructs showed that the region -288/+78 was sufficient for GUS expression. The expression of the reporter gene even with the full-length promoter was limited to shoot hairs and to male and female reproductive organs. The dehydration-responsive element (DRE) and ABA-responsive element (ABRE) in the promoter did not show consensus flanking regions; however, gel mobility shift assays showed that Pennisetum has specific transacting factors that showed binding to the core DRE, ABRE and TCA elements.
Transmembrane Channels Based on Tartaric Acid-Gramicidin A Hybrids (1989)

The gramicidin A transmembrane channel is believed to consist of two head-to-head beta helices. Computer-generated models were used to formulate the structure of new single-chain channel molecules based on the gramicidin motif. The chemical synthesis of two tartaric acid-gramicidin A hybrids and single-channel analyses of their conducting properties are reported. These studies illustrate the rational design and synthesis of long-lived channels with tunable conductance properties and provide support for current molecular models of the natural (dimeric) gramicidin channel.
Chemical and biological study on constituents of Populus tremuloides buds = (2009)

De nos jours, un grand nombre de composés d'origine végétale sont utilisés dans la médecine moderne. Plusieurs d'entre eux ont été développés en s'inspirant des informations de la médecine traditionnelle. Environ 60 % des anticancéreux et 75 % des antimicrobiens de l'arsenal thérapeutique actuel sont des produits naturels ou des dérivés. Seulement 5-15 % des 250 000 plantes ont été étudiées afin d'en évaluer le potentiel pharmacologique. Les plantes de la forêt boréale québécoise ont été très peu étudiées au niveau de leur composition chimique et de leur potentiel pharmacologique. Au cours des dernières années, le laboratoire LASEVE a évalué le potentiel pharmacologique de plusieurs plantes et il en est ressorti que les bourgeons du Populus tremuloides représentaient un sujet d'étude intéressant au niveau chimique et pharmacologique. De plus, cette espèce a été utilisée en médecine traditionnelle pour traiter de nombreuses maladies. L'objectif de ce projet était d'isoler et de caractériser les composés phénoliques majoritaires des bourgeons de Populus tremuloides et d'en évaluer l'activité biologique (anticancéreuse, anti-inflammatoire et antibactérienne). Les travaux effectués sur l'extrait éthanolique des bourgeons de Populus tremuloides ont mené à l'identification de 24 composés phénoliques. Un de ces composés n'a jamais été rapporté auparavant dans la littérature scientifique et deux autres n'ont jamais été signalés dans la famille des Salicacées. De plus, dix de ces composés sont identifiés pour la première fois dans le Populus tremuloides. Trois des composés identifiés ont démontré une cytotoxicité de forte à modérée (5-20 uM) envers certaines des lignées cellulaires testées (WS1, DLD-1, A-549). L'activité anti-inflammatoire de cinq composés phénoliques constitués d'une section glycérol a été évaluée sur des macrophages de souris RAW 264.7 stimulé avec le LPS (lipopolysaccharide). Un seul des composés testés a significativement inhibé, sans cytotoxicité, la production d'oxyde nitrique avec une IC50 de 6.5 ± 0.4 uM. Finalement, aucun des composés phénoliques isolés dans ces travaux n'a démontré une activité importante contre Staphylococcus aureus et Escherichia coli.
A contrario matching of SIFT-like descriptors (2008)

In this paper, the matching of SIFT-like features [5] between images is studied. The goal is to decide which matches between descriptors of two datasets should be selected. This matching procedure is often a preliminary step towards some computer vision applications, such as object detection and image registration for instance. The distances between the query descriptors and the database candidates being computed, the classical approach is to select for each query its nearest neighbor, depending on a global threshold on dissimilarity measure. In this contribution, an a contrario framework for the matching procedure is introduced, based on a threshold on a probability of false detections. This approach yields dissimilarity thresholds automatically adapted to each query descriptor and to the diversity and size of the database. We show on various experiments on a large image database, the ability of such a method to decide whether a query and its candidates should be matched.
Designing Cast Partial Dentures in Relation to Partial Edentulism (2022)

Objective: To determine the pattern of partial edentulism and the cast removable dental prosthesis design in relation to the Classes recorded.&#x0D; Study Design: Cross-sectional study.&#x0D; Place and Duration of Study: Department of Prosthodontics, Armed Forces Institute of Dentistry (AFID), Rawalpindi Pakistan, from Apr to Sep 2021.&#x0D; Methodology: A total of 67 partially dentate male and female patients presenting to the Prosthodontics Department requiring partial cast dentures were included in the study. Visual inspection of the master casts and partial denture frameworks was carried out in the laboratory. Kennedy's Classification, modification areas, type of major connector, direct retainer, rest and use of indirect retention were recorded.&#x0D; Results: The most prevalent Class of partially dentate arch was Kennedy Class-II in maxilla 10 (45.5%) and Class-I and III in mandible 15 (33.3%) each. Major connectors most frequently encountered were anteroposterior palatal strap (59.1%) and lingual bar (57.8%). Circumferential clasp (35.8%) was the most used retainer type in Classes II and III, whereas RPI was mostly found in Classes I and II (32.1%). Occlusal rests were most commonly used (72.4%). Indirect retention was mostly used in Class-I and II denture frameworks (95.9%).&#x0D; Conclusion: The most commonly encountered partial edentulism pattern was Kennedy's Class I and II. Following basic principles of RPD design can help elevate the standards of removable denture treatment.
Comparison of chronic lymphocytic leukemia patients expressing high or low level of ZAP70 mRNA: new prognostic factors differences in microRNA expression and interaction with the microenvironment (2008)

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Supplementary Table S2 from Pharmacologic Screening Identifies Metabolic Vulnerabilities of CD8<sup>+</sup> T Cells (2023)

&lt;p&gt;Supplementary Table S2&lt;/p&gt;
In Vivo Assessment of Antimicrobial Efficacy of Silver-Impregnated Contact Lens Storage Cases (2012)

More than 70% of the storage cases used in daily wear CL care for a month was contaminated irrespective of the types of cases. However, silver-impregnated cases were colonized by reduced levels of Gram-negative bacteria.
Iron Oxyhydroxide Reduction in Simulated Wetland Soils: Effects of Mineralogical Composition of IRIS Paints (2008)

Reducing conditions in soils can be documented by the voltage measured between Pt and reference electrodes (Eh) or by using dyes like α,α‐dipyridyl for identifying reduced species (such as Fe 2+ ). Indicator of Reduction in Soils (IRIS) tubes have been recently introduced as an alternative approach for documenting reducing conditions in soils, where a synthetic Fe oxyhydroxide painted on polyvinyl chloride tubes can be reduced, dissolved, and removed by respiring soil microorganisms. In order for the Fe oxyhydroxide paint to adhere to the tubes, it must be synthesized as a mixture of ferrihydrite and goethite. Based on thermodynamics, ferrihydrite is predicted to be more easily reduced at higher redox potentials than goethite. We hypothesized that IRIS tubes made using paint composed of different proportions of ferrihydrite and goethite would perform differently in wetland soils. This experiment evaluated the performance of IRIS tubes created using nine Fe oxyhydroxide paints with different proportions of ferrihydrite and goethite ranging from 15.2 to 70.9 mol % goethite. Tubes were evaluated following placement in mesocosms in the laboratory using two different wetland soil materials for 13 d. An ANOVA indicated that there were highly significant differences ( P &lt; 0.0001) in full or intermediate removal of paint due to paint type. In general, the extent of paint removal was inversely related to goethite content. The minimum goethite content needed to successfully manufacture IRIS tubes is approximately 40%, and we recommend that IRIS tubes not be used when the goethite content is beyond the range of 40 to 60 mol %.
Hypoxemia regulates effect of lipopolysaccharide on polymorphonuclear leukocyte CD11b/CD18 expression (1994)

Expression of the receptor CD11b/CD18 on the polymorphonuclear leukocyte (PMN) surface is important for several aspects of PMN function during endotoxemia. The mechanisms underlying regulation of CD11b/CD18 expression during hypoxemia and endotoxemia, however, are less clear. We investigated the effects of exposure of whole blood PMNs to lipopolysaccharide (LPS) during hypoxemia. During hypoxemia (10-30% O2 saturation), LPS reduced CD11b/CD18 expression. Both kinetic assays and experiments with microfilament stabilizers (phalloidin, cytochalasin B) demonstrated that this was most likely due to receptor shedding. Incubation of whole blood PMNs with an anti-CD14 monoclonal antibody (MEM18) largely prevented the LPS-induced reduction of CD11b/CD18 expression. Decreased CD11b/CD18 expression reduced PMN functional capability, as the binding of its ligand (erythrocytes opsonized with the 3rd component of complement Cbi) and intracellular H2O2 production were reduced. After exposure to LPS, N-formyl-methionyl-leucyl-phenylalanine could rapidly induce new CD11b/CD18 receptors to the cell surface, and this was not inhibited by actinomycin D or cycloheximide. After reoxygenation (> 90% O2 saturation), CD11b/CD18 expression was restored, and this was abrogated by exposure to cytochalasin B. Lipid A was able to reproduce the effects of LPS during hypoxemia and hypoxemia-reoxygenation but required a 10-fold greater concentration to do so. These results demonstrate that during hypoxemia an important pathophysiological property of LPS is to reduce CD11b/CD18 expression. This results in diminished PMN functional capability, which would contribute to the pathogenicity of LPS during acute infectious states.