gebhart/patrepeval huggingface dataset:
Population Analysis of Staphylococcus aureus Reveals a Cryptic, Highly Prevalent Superantigen SElW That Contributes to the Pathogenesis of Bacteremia (2020)

Staphylococcal superantigens (SAgs) are a family of secreted toxins that stimulate T cell activation and are associated with an array of diseases in humans and livestock. Most SAgs produced by <i>Staphylococcus aureus</i> are encoded by mobile genetic elements, such as pathogenicity islands, bacteriophages, and plasmids, in a strain-dependent manner. Here, we carried out a population genomic analysis of >800 staphylococcal isolates representing the breadth of <i>S. aureus</i> diversity to investigate the distribution of all 26 identified SAg genes. Up to 14 SAg genes were identified per isolate with the most common gene <i>selw</i> (encoding a putative SAg, SElW) identified in 97% of isolates. Most isolates (62.5%) have a full-length open reading frame of <i>selw</i> with an alternative TTG start codon that may have precluded functional characterization of SElW to date. Here, we demonstrate that <i>S. aureus</i> uses the TTG start codon to translate a potent SAg SElW that induces Vβ-specific T cell proliferation, a defining feature of classical SAgs. SElW is the only SAg predicted to be expressed by isolates of the CC398 lineage, an important human and livestock epidemic clone. Deletion of <i>selw</i> in a representative CC398 clinical isolate, <i>S. aureus</i> NM001, resulted in complete loss of T cell mitogenicity <i>in vitro</i>, and <i>in vivo</i> expression of SElW by <i>S. aureus</i> increased the bacterial load in the liver during bloodstream infection of SAg-sensitive HLA-DR4 transgenic mice. Overall, we report the characterization of a novel, highly prevalent, and potent SAg that contributes to the pathogenesis of <i>S. aureus</i> infection.<b>IMPORTANCE</b><i>Staphylococcus aureus</i> is an important human and animal pathogen associated with an array of diseases, including life-threatening necrotizing pneumonia and infective endocarditis. The success of <i>S. aureus</i> as a pathogen has been linked in part to its ability to manipulate the host immune response through the secretion of toxins and immune evasion molecules. The staphylococcal superantigens (SAgs) have been studied for decades, but their role in <i>S. aureus</i> pathogenesis is not well understood, and an appreciation for how SAgs manipulate the host immune response to promote infection may be crucial for the development of novel intervention strategies. Here, we characterized a widely prevalent, previously cryptic, staphylococcal SAg, SElW, that contributes to the severity of <i>S. aureus</i> infections caused by an important epidemic clone of <i>S. aureus</i> CC398. Our findings add to the understanding of staphylococcal SAg diversity and function and provide new insights into the capacity of <i>S. aureus</i> to cause disease.
Editorial Commentary (2016)

No AccessUrology PracticeBusiness of Urology1 Mar 2017Editorial Commentary J. Stephen Jones J. Stephen JonesJ. Stephen Jones More articles by this author View All Author Informationhttps://doi.org/10.1016/j.urpr.2016.04.010AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Editorial Commentary." Urology Practice, 4(2), p. 110 © 2017 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 4Issue 2March 2017Page: 110 Advertisement Copyright & Permissions© 2017 by American Urological Association Education and Research, Inc.MetricsAuthor Information J. Stephen Jones More articles by this author Expand All Advertisement PDF downloadLoading ...
Photochemical degradation of crude oils on sea surfaces under simulated conditions[1] (1997)

Under wave‐like aeration, three crude oils of low, medium and high viscosity are spread in 0.5 mm films on artificial seawater and irradiated by artificial sunlight. In intervals up to 28 days, the amount of water soluble compounds and the toxicity of the aqueous layer are determined, using small crabs (artemia salina). A variety of compounds are identified by GC/ MS and FT‐IR spectroscopy.—The intrinsic photosensitizing properties of the aforementioned oils is determined and compared with that of additive photosensitizers. The synthesis of a sensitizer especially adapted to hydrocarbons is described.
Simple, Efficient Object Encoding using Intersection Types (1999)

| m iv m iu h v rh ex ¤m ij tx ¤v l Dm in w }l
<title>Direct Phase Measurement In Spherical Wave Fizeau Interferometers</title> (1980)

For generations optical technicians have judged the accuracy of an optical surface by estimating the straightness of the fringes in an interference pattern. The eye, however, is not capable of estimating fringe straightness accurately enough to satisfy present-day demands for twentieth-wave or hundredth-wave accuracy. More rigorous quantitative methods must be used to attain the desired precision. Digital analysis of photographs is a help but the data obtained from photographs are noisy and such a method is greatly influenced by distortion in the imaging system and the problems associated with the necessity of providing many closely spaced fringes for analysis.
Synthesis and self-assembly of aminyl and alkynyl substituted sophorolipids (2020)

Sophorolipids are one of the most important microbial biosurfactants, because of their large-scale production and applications developed so far in the fields of detergency, microbiology, cosmetics or environmental science.
Transposed firing activation of motor units (2014)

Muscles are composed of groups of muscle fibers, called motor units, each innervated by a single motoneuron originating in the spinal cord. During constant or linearly varying voluntary force contractions, motor units are activated in a hierarchical order, with the earlier-recruited motor units having greater firing rates than the later-recruited ones. We found that this normal pattern of firing activation can be altered during oscillatory contractions where the force oscillates at frequencies ≥2 Hz. During these high-frequency oscillations, the activation of the lower-threshold motor units effectively decreases and that of the higher-threshold motor units effectively increases. This transposition of firing activation provides means to activate higher-threshold motor units preferentially. Our results demonstrate that the hierarchical regulation of motor unit activation can be manipulated to activate specific motoneuron populations preferentially. This finding can be exploited to develop new forms of physical therapies and exercise programs that enhance muscle performance or that target the preferential atrophy of high-threshold motor units as a result of aging or motor disorders such as stroke and amyotrophic lateral sclerosis.
Comparative Analyses of Total Phenols, Antioxidant Activity, and Flavonol Glycoside Profile of Cladode Flours from Different Varieties of Opuntia spp. (2011)

The phenolic, flavonoid, and antioxidant contents of methanol extracts of nine samples of Mexican cactus ( Opuntia spp.) cladodes processed into flours were studied. Opuntia undulata contained the highest amount of phenols [905.08 ± 64.51 μg of gallic acid equivalents (GAE)/g]. The oxygen radical absorbance capacity (ORAC) of the cladode flour extracts indicated that Opuntia robusta var. Gavia [738.8 ± 89.9 μmol of Trolox equivalents (TE)/g] contained the highest antioxidant capacity. ORAC values significantly correlated to total phenols but not to flavonoid contents and were comparable to cranberries and blackberries. Glycosidic forms of isorhamnetin and kaempferol were identified via high-performance liquid chromatography-photodiode array (HPLC-PDA) and HPLC-mass spectrometry (MS), with isorhamnetin being the most abundant flavonol in all samples, except for Opuntia lindheimeri . The effectiveness of acid hydrolysis varied among species because of the different flavonol profiles. For some varieties, the triglycosidic forms were partially acid-hydrolyzed, giving an increase in the content of diglycosides. Optimization of hydrolysis for each species is required to estimate the total amount of each flavonol.
Synthesis and Evaluation in Monkey of Two Sensitive11C-Labeled Aryloxyanilide Ligands for Imaging Brain Peripheral Benzodiazepine Receptors In Vivo (2007)

We sought to develop (11)C-labeled ligands for sensitive imaging of brain peripheral benzodiazepine receptors (PBR) in vivo. Two aryloxyanilides with high affinity for PBR were identified and synthesized, namely, N-acetyl- N-(2-methoxycarbonylbenzyl)-2-phenoxyaniline ( 3, PBR01) and N-(2-methoxybenzyl)- N-(4-phenoxypyridin-3-yl)acetamide ( 10, PBR28). 3 was hydrolyzed to 4, which was esterified with [ (11)C]iodomethane to provide [ (11)C] 3. The O-desmethyl analogue of 10 was converted into [ (11)C] 10 with [ (11)C]iodomethane. [ (11)C] 3 and [ (11)C] 10 were each injected into monkey to assess their brain kinetics with positron emission tomography (PET). After administration of either radioligand there was moderately high brain uptake of radioactivity. Receptor blocking and displacement experiments showed that a high proportion of this radioactivity was bound specifically to PBR. In monkey and rat, 3 and 10 were rapidly metabolized by ester hydrolysis and N-debenzylation, respectively, each to a single polar radiometabolite. [ (11)C] 3 and [ (11)C] 10 are effective for imaging PBR in monkey brain. [ (11)C] 10 especially warrants further evaluation in human subjects.
A rational unsharp masking method for TV applications (2003)

In this paper, we present an unsharp masking-based approach for edge enhancing for TV application. The proposed scheme enhances the true details, limits the overshoot near sharp edges and attenuates the temporal artifacts which are visible in an image sequence. Simulations show that the processed sequence presents sharp edges which make it more pleasant to the human eye. Moreover, the amount of noise and nonhomogeneities in the sequence are clearly reduced.
Clinical and Radiographic Outcomes of Revision Total Ankle Arthroplasty Using an Intramedullary Referencing Implant (2018)

Category: Ankle Arthritis Introduction/Purpose: Treatment of the failed total ankle arthroplasty (TAA) is challenging, and historically arthrodesis was advocated as the salvage treatment of choice. Currently, there is limited available literature reporting on options and outcomes of revision arthroplasty despite the persistent relatively high failure rate ranging from 10-23% within the first ten years after primary TAA. Early published outcomes of intramedullary-referencing implants for primary TAA have shown improvement in clinical outcomes and radiographic parameters, sustained correction of coronal deformity, and excellent survivorship with few associated complications. The purpose of this study is to report the clinical and radiographic outcomes of revision TAA using an intramedullary-referencing implant. Methods: We reviewed a consecutive series of 24 cases (14 female and 10 male; median age, 57.9 (28.2-74.6) years; median BMI, 31 (19.4-40.2)) between 2008 to 2015 in which a failed TAA underwent revision using InBone, an intramedullary-referencing, fixed-bearing, two-component total ankle system. Demographic, radiographic, and functional outcome data were collected preoperatively, immediately postoperatively, and at the most recent follow up. The primary outcome was implant survival defined by no reoperation for subsidence/loosening or revision of the implant. Secondary outcomes included radiographic (coronal and sagittal component alignment, osteolysis, and subsidence) and functional (American Orthopaedic Foot &amp; Ankle Society [AOFAS] score and foot function index [FFI]) outcome data. Results: Twenty-four patients underwent revision TAA with intramedullary-referencing with 87.5% implant survival at average follow up of 30.4 months. Revision was performed most commonly for aseptic talar subsidence (45.8%) or implant loosening (tibia, 12.5%; talus, 16.7%). Following revision, three (12.5%) patients required reoperation for talar subsidence or loosening at average 37.7 months. Progression of osteolysis of the tibia, talus, and fibula was observed in 14 (58%), 4 (17%), and 6 (25%) of patients, respectively, although osteolysis was present preoperatively in 17 (70.1%), 9 (37.5%), and 10 (41.7%), respectively. Subsidence of the tibial and talar components was observed in 8 (33%) and 9 (38%) patients, respectively. Clinically, the average AOFAS and FFI score were 72 (57-100) and 27.1 (11.8-82.9), respectively. Conclusion: Early results of intramedullary-referencing revision TAA demonstrated improved patient-reported outcomes and maintenance of radiographic outcomes at an average follow-up of 30 months. Additionally, early results of revision arthroplasty after failed TAA were similar to those after primary arthroplasty. Aseptic talar subsidence or loosening were the main postoperative complications which required reoperation. Revision arthroplasty utilizing an intramedullary-referencing implant is a viable option for the failed TAA.
Urea and Thiourea Derivatives as Low Molecular‐Mass Organogelators (2005)

The properties of a series of organogels consisting of a urea or thiourea derivative with one or two n-alkyl substitutuents at the nitrogen atoms (a low molecular-mass organogelator (LMOG)) and an organic liquid are described. They include N,N'-dimethylurea, the LMOG of lowest molecular mass (M(W) 88) we are aware of. The efficiencies of the LMOGs, based the diversity of liquids gelated, the minimum amount required for gelation of a liquid at room temperature, and the temporal and thermal stabilities of the gels formed, have been investigated as a function of the number, length, and substitution pattern of their n-alkyl chains. The gels are thermally reversible and require generally very low concentrations (<2 wt %) of an LMOG. Some of the LMOGs with shorter chains are more efficient than their longer chained analogues. The structural and thermodynamic properties of the gels have been examined by IR, DSC, and X-ray diffraction techniques. Polarizing optical microscopic analyses of the gels show that the nature of gelator aggregates depends mainly on the alkyl chain length. Changes in the aggregation ability have been examined systematically by perturbing the molecular structure.
Precision grasping of a prosthetic hand based on virtual spring damper hypothesis (2010)

A control strategy for achieving object precision grasping by a prosthetic hand is proposed. The control strategy is based on defining virtual spring-damper between two finger tips and damping force at each finger joint. It is shown that the proposed control strategy provides a satisfactory performance in precision grasping of a prosthetic hand, without the need for additional complexity regarding equations for inverse kinematics, or inverse dynamics, and the information on tactile or force sensing or even object shape.
(E)-5, (Z)-7-DODECADIENAL, A SEX PHEROMONE COMPONENT OF THE WESTERN TENT CATERPILLAR, MALACOSOMA CALIFORNICUM (LEPIDOPTERA: LASIOCAMPIDAE) (1980)

Tent caterpillars of the genus Malacosoma frequently appear in outbreak numbers causing widespread defoliation of trees and shrubs in North America. The western tent caterpillar, M . californicum (Packard), with six subspecies, occurs over most of temperate western North America and although there is a large number of host plants on which it will oviposit and feed (Stehr and Cook 1968), most have little commercial value. We report here the identification of a component of the female sex pheromone of M . californicum .
Discovery of a low order drug-cell response surface for applications in personalized medicine (2014)

The cell is a complex system involving numerous components, which may often interact in a non-linear dynamic manner. Diseases at the cellular level are thus likely to involve multiple cellular constituents and pathways. As some drugs, or drug combinations, may act synergistically on these multiple pathways, they might be more effective than the respective single target agents. Optimizing a drug mixture for a given disease in a particular patient is particularly challenging due to both the difficulty in the selection of the drug mixture components to start out with, and the all-important doses of these drugs to be applied. For n concentrations of m drugs, in principle, n(m) combinations will have to be tested. As this may lead to a costly and time-consuming investigation for each individual patient, we have developed a Feedback System Control (FSC) technique which can rapidly select the optimal drug-dose combination from the often millions of possible combinations. By testing this FSC technique in a number of experimental systems representing different disease states, we found that the response of cells to multiple drugs is well described by a low order, rather smooth, drug-mixture-input/drug-effect-output multidimensional surface. The main consequences of this are that optimal drug combinations can be found in a surprisingly small number of tests, and that translation from in vitro to in vivo is simplified. This points to the possibility of personalized optimal drug mixtures in the near future. This unexpectedly simple input-output relationship may also lead to a simple solution for handling the issue of human diversity in cancer therapeutics.
Mitral Annular Dynamics in Myxomatous Valve Disease (2010)

Real-time 3-dimensional transesophageal echocardiography provides insights into normal, dynamic mitral annulus function with early-systolic area contraction and saddle-shape deepening contributing to mitral competency. MVD annulus is also dynamic but considerably different with loss of early-systolic area contraction and saddle-shape deepening despite similar magnitude of ventricular contraction, suggestive of ventricular-annular decoupling. Subsequent area enlargement may contribute to mitral incompetence. After mitral repair, MVD annulus remains dynamic without systolic saddle-shape accentuation. Thus, real-time 3-dimensional transesophageal echocardiography provides new insights that allow the refining of mitral pathophysiology concepts and repair strategies.
Cyclophanes: From Planar Chirality and Helicity to Cyclochirality (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
The Modern Student Laboratory: Polyaniline-A Conducting Polymer: Electrochemical Synthesis and Electrochromic Properties (1994)

The dramatic nature of the color changes of the PAN films will guarantee an enthusiastic response when used as either a demonstration for high school chemistry students and nonscience audiences or as an undergraduate laboratory experiment. The multifaceted nature of this experiment allows for its incorporation into an organic, analytical, or physical chemistry laboratory syllabus depending on how the emphasis is placed. The electrochemical synthetic approach is complementary to the standard chemical synthesis and finds application far beyond polyaniline. As an analytical electrochemical experiment, Faraday's law can be utilized to relate applied charge to film growth. Conductivity measurements also can be made. Kinetic studies can be done on both the synthesis and electrochromic transitions. As stated above, many factors affect the reaction rates, such as the acid or substrate used. In addition, this experiment can serve as an introduction to either solid-state chemistry or polymer chemistry, as well. The electrochromic response of PAN could complement many chemistry courses. The breadth of application of a PAN experiment is large. The academic level can be tailored to suit a high school chemistry class just as well as a research project for a college senior. The two-battery apparatus is inexpensive, easy to build, and straightforward to use. This article has been specifically left as a general guide and not presented in a rigid format in order to facilitate as wide a degree of application as possible. General references have been included to aid the interested reader in broaching the vast literature on PAN. If you are looking for a way to spice up your chemistry course with a current topic, give the PAN experiment a try.
Atherosclerosis in hemodialysis patients: traditional and nontraditional risk factors. (2006)

The results indicate that hemodialysis patients showed advanced atherosclerosis that is associated with traditional as well as nontraditional risk factors such as apolipoprotein B.
Color moving pictures quality metric (2002)

This paper presents a comprehensive quality metric for color moving pictures which is based on a spatio-temporal vision model and on the opponent-colors theory. The metric is used to assess the quality of MPEG compressed video streams and is compared with a grayscale video quality metric.
Inflammatory pseudo bladder tumour: Clinical case (1997)

– An inflammatory pseudoneoplasm of the bladder is an uncommon benign lesion. The case described involves a 46-year-old man with macrohematuria. Diagnosis from the ultrasound image tended towards urothelioma, while endoscopy showed a lesion with indefinite characteristics. The histological exam finally allowed correct diagnosis, showing the benign nature of the disease.
Synthesis and characterization of a disubstituted piperazine derivative with T-type channel blocking action and analgesic properties (2016)

Altogether, our data identify a novel T-type calcium channel blocker with tight structure activity relationship (SAR) and relevant in vivo efficacy in inflammatory pain conditions.
Analysis of Maximum-Likelihood Sequence Estimation Performance for Quadrature Amplitude Modulation (1981)

This paper considers maximum-likelihood sequence estimation (MLSE) for quadrature amplitude modulation (QAM) signaling at rates approaching several baud/Hz. In this regime, intersymbol interference and possibly cross channel coupling are the dominant transmission impairments. We derive the structure of a detector that optimally accommodates both impairments. A bit error rate performance bound is found, and the concept of an error state transition matrix is introduced to facilitate the analysis. We explore a modulation scheme wherein cross-channel coupling is intentionally introduced, and find that it improves detection efficiency. The use of MLSE may be an important consideration for power and spectrally efficient digital radio systems, either terrestrial or satellite, since rates approaching the Shannon limit may be attainable without channel coding, and frequency selective fading is handled in an optimum manner.
[Measurement of biological activity of hLH. Multicenter study]. (1997)

This report describes the results of a multicentric study of biological methods for luteinizing hormone (hLH). The production of testosterone by animal Leydig cells is used by five laboratories with different methodologies including rat, mouse and pig cells. Dose-response curves of testosterone production, quality criteria and results on a physiological population of men and women, are reported and discussed. It is concluded that the bioactive determination of hLH must be considered as a reference method used in discordances between clinic and immunological methods.