gebhart/patrepeval huggingface dataset:
The In Vitro Interaction ofStreptococcus pyogeneswith Human Pharyngeal Cells Induces a Phage-Encoded Extracellular DNase (2002)

The role lysogenic bacteriophage play in the pathogenesis of the host bacterium is poorly understood. In a previous study, we found that streptococcal coculture with human pharyngeal cells resulted in the induction of lysogenic bacteriophage as well as the phage-associated streptococcal pyrogenic exotoxin C (SpeC). In this study, we have determined that in addition to SpeC induction, a number of other streptococcal proteins are also released by the bacteria during coculture with pharyngeal cells. Among these, we identified and characterized a novel 27-kDa secreted protein. Sequence analysis of this novel protein demonstrated it to be encoded by the same lysogenic bacteriophage which harbors speC. Protein sequence analysis revealed varied homologies with several streptococcal DNases. Further biochemical characterization of the recombinantly expressed protein verified it to be a divalent cation-dependent streptococcal phage-encoded DNase (Spd1). Although functionally distinct, SpeC and Spd1 are associated by a number of parameters, including genetic proximity and transcriptional regulation. Finally, we speculate on the induction of phage-encoded DNase (Spd1) enhancing the fitness of both bacteria and phage.
ChemInform Abstract: Skeletal Rearrangements on Clusters: Reaction of ((tBuP)Fe3(CO)10) with Diphenylacetylene. (1987)

Abstract The very similar energies of PC, PFe, and CFe bonds in clusters are supported by the formation of the compounds (II) and (III) from the title cluster (I) and diphenylacetylene on irradiation.
Radical Additions of Aryl Iodides to Arenes Are Facilitated by Oxidative Rearomatization with Dioxygen (2006)

Inter- and intramolecular additions of aryl radicals derived from aryl iodides to arenes are promoted by tris(trimethylsilyl)silane and occur under exceptionally mild conditions (15-30 min at 25 degrees C) in nondegassed benzene. A chain mechanism involving reaction of the intermediate cyclohexadienyl radical with oxygen to directly generate the aromatized product and the hydroperoxy radical is proposed.
Analysis of microearthquake data at Cold Lake and its applications to reservoir monitoring (2007)

Over four months of continuously recorded micro‐earthquake data acquired at Cold Lake, Canada was analyzed using advanced algorithms for micro‐earthquake location and subsurface imaging. Robust determination of the spatial, temporal and magnitude distribution of seismicity is the first step towards understanding the relationship between the stress perturbations caused by the Cyclic Steam Stimulation (CSS) process and seismicity. The acquisition geometry was constrained because the receivers were only located in a single vertical borehole. Despite this constraint, we were successful in improving event locations, which highlight several tight clusters of events. The clusters migrate to shallower depths with successive steam cycles. This shows that repeated steaming causes the deformation to spread to shallower depths, thus increasing the risk for fluid incursion in the overburden shales. Though some of the largest events occur in or below the Clearwater reservoir, we observe very few events in the reservoir itself. The size and distribution of seismicity agree to the first order with predictions from simple geomechanical modeling, but are also probably controlled by lithologic variations.
A 10 kV 4H-SiC Bipolar Turn Off Thyristor (BTO) with Positive Temperature Coefficient of V<sub>F</sub>, Current Saturation Capability and Fast Switching Speed (2010)

A novel power device configuration, the Bipolar Turn Off thyristor (BTO), was proposed and demonstrated in SiC. The BTO operates in anode switch configuration consisting of a 9 kV SiC p-type Gate Turn Off thyristor (GTO) and a 1600 V SiC n-type Bipolar Junction Transistor (BJT). Compared with SiC GTOs, several new features have been accomplished in the BTO: (1) A positive temperature coefficient of forward voltage drop, (2) Anode current saturation capability, and (3) A simple gate driver and fast switching speed.
Bicarbonate secretion and chloride absorption by rabbit cortical collecting ducts. Role of chloride/bicarbonate exchange. (1985)

Cortical collecting ducts (CCD) from rabbits treated with deoxycorticosterone (DOC) actively secrete bicarbonate at high rates. To investigate the mechanism of bicarbonate secretion, we measured bicarbonate and chloride transport in CCD from rabbits treated with DOC for 9-24 d. Removal of chloride (replaced with gluconate) from both perfusate and bath inhibited bicarbonate secretion without changing transepithelial voltage. Removal of chloride only from the bath increased bicarbonate secretion, while removal of chloride only from the perfusate inhibited secretion. In contrast to the effect of removing chloride, removal of sodium from both the perfusate and bath (replacement with N-methyl-D-glucamine) did not change the rate of bicarbonate secretion. The rate of bicarbonate secretion equaled the rate of chloride absorption in tubules bathed with 0.1 mM ouabain to inhibit any cation-dependent chloride transport. Under these conditions, chloride absorption occurred against an electrochemical gradient. Removal of bicarbonate from both the perfusate and bath inhibited chloride absorption. Removal of bicarbonate only from the bath inhibited chloride absorption, while removal of bicarbonate from the lumen stimulated chloride absorption. We conclude that CCD from DOC-treated rabbits actively secrete bicarbonate and actively absorb chloride by an electroneutral mechanism involving 1:1 chloride/bicarbonate exchange. The process is independent of sodium.
Temporal selective dereverberation of noisy speech using one microphone (2008)

Reverberant speech can be described as sounding distant with noticeable coloration and echo. These detrimental perceptual effects are caused by early and late reflections, respectively, and reduces the fidelity and intelligibility of speech. It is well-known that the echo density of the reflections increases with time. Therefore, the temporal structure of early and late reflections differs. In this paper, we combine two different dereverberation techniques that were recently developed to suppress early and late reverberation separately. First, late reverberation is suppressed using a spectral processing technique that is based on a statistical reverberation model. Secondly, early reverberation and residual late reverberation are suppressed using a linear prediction (LP) residual processing technique. In addition, an objective measure based on the kurtosis of the LP residual is proposed to measure the coloration caused by early reflections. Experimental results demonstrate the beneficial use of the new single microphone system that reduces echo and coloration with little speech distortion.
Synthesis and characterization of positively charged, alumina‐coated silica/polystyrene hybrid nanoparticles via pickering miniemulsion polymerization (2011)

Abstract Positively charged, raspberry‐like hybrid nanoparticles, consisting of a polystyrene core and an alumina‐coated silica shell were successfully prepared in a surfactant free system via the radical copolymerization of styrene (St) and different comonomers (acrylic acid, methacrylic acid, and acrylamide) by using a cationic silica sol as the sole emulsifier in Pickering miniemulsion polymerization. The influence of different parameters like pH of the dispersion, comonomer content, and the amount and size of silica nanoparticles on the colloidal stability of the systems, prepared with different comonomers, was examined. The particles' morphology was observed via high‐resolution scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The removal of free silica particles via centrifugation was proved by TEM and SEM, and the content of free and adsorbed silica was quantified via thermogravimetric analysis (TGA). © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Learning to Dress 3D People in Generative Clothing (2019)

Three-dimensional human body models are widely used in the analysis of human pose and motion. Existing models, however, are learned from minimally-clothed 3D scans and thus do not generalize to the complexity of dressed people in common images and videos. Additionally, current models lack the expressive power needed to represent the complex non-linear geometry of pose-dependent clothing shapes. To address this, we learn a generative 3D mesh model of clothed people from 3D scans with varying pose and clothing. Specifically, we train a conditional Mesh-VAE-GAN to learn the clothing deformation from the SMPL body model, making clothing an additional term in SMPL. Our model is conditioned on both pose and clothing type, giving the ability to draw samples of clothing to dress different body shapes in a variety of styles and poses. To preserve wrinkle detail, our Mesh-VAE-GAN extends patchwise discriminators to 3D meshes. Our model, named CAPE, represents global shape and fine local structure, effectively extending the SMPL body model to clothing. To our knowledge, this is the first generative model that directly dresses 3D human body meshes and generalizes to different poses. The model, code and data are available for research purposes at https://cape.is.tue.mpg.de.
A Class of Cellular Architectures to Support Physical Design Automation (1984)

Special-purpose hardware has been proposed as a solution to several increasingly complex problems in design automation. This paper examines a class of cellular architectures called raster pipeline subarrays--RPS architectures--applicable to problems in physical DA that are (1) representable on a cellular grid, and (2) characterized by local functional dependencies among grid cells. Machines with this architecture first evolved in conventional cellular applications that exhibit similarities to grid-based DA problems. To analyze the properties of the RPS organization in context, machines designed for cellular applications are reviewed, and it is shown that many DA machines proposed/constructed for grid-based problems fit naturally into a taxonomy of cellular machines. The implementation of DA algorithms on RPS hardware is partitioned into local issues that involve the processing of individual cell neighborhoods, and global issues that involve strategies for handling complete grids in a pipeline environment. Design rule checking and routing algorithms are examined in an RPS environment with respect to these issues. Experimental measurements for such algorithms running on an existing RPS machine exhibit significant speedups. From these studies are derived the necessary performance characteristics of RPS hardware optimized specifically for grid-based DA. Finally, the practical merits of such an architecture are evaluated.
Pratique ambulatoire des procédures endovasculaires pour traitement des artériopathies oblitérantes des membres inférieurs. (2011)

Objectifs: Evaluer la faisabilité et l'évolution de la pratique ambulatoire des procédures endovasculaires pour traitement des artériopathies des membres inférieurs . Matériels et méthodes: 89 patients ont bénéficié d'une procédure endovasculaire ambulatoire (séjour hospitalier de moins de 24 heures) pour traitement d'une artériopathie desmembres inférieurs entre janvier 2005 et décembre 2005. Sont étudiés, le stade de l'artériopathie, la complexité des lésions, le type de procédure, lesco-morbidités, les complications, la reconversion en hospitalisation. Résultats: La majorité des patients présentait une artériopathie de stade de II (95%). Les lésions des artères fémorales superficielles représentaient 45% des procédures etcelles des axes iliaques 41%. La majorité des lésions étaient des sténoses (83%) de TASC a ou B. Cependant, l'évolution au court du temps montre que deslésions de plus en plus complexes étaient traitées en ambulatoire. La taille de l'introducteur était de 6 F dans 82% des cas. Le succès technique était de 98% et letaux des complications de 4,2%. Le taux de reconversion en hospitalisation était de 5,2%. Conclusion: Les procédures endovasculaires pour artériopathies des membres inférieurs de stade II peuvent être faites en ambulatoire y compris pour des lésions complexesavec un taux de complication et un taux de reconversion faibles.
Targeted DNA Methylation Analysis by High Throughput Sequencing in Porcine Peri-attachment Embryos (2013)

The purpose of this experiment was to implement and evaluate the effectiveness of a next-generation sequencing-based method for DNA methylation analysis in porcine embryonic samples. Fourteen discrete genomic regions were amplified by PCR using bisulfite-converted genomic DNA derived from day 14 in vivo-derived (IVV) and parthenogenetic (PA) porcine embryos as template DNA. Resulting PCR products were subjected to high-throughput sequencing using the Illumina Genome Analyzer IIx platform. The average depth of sequencing coverage was 14,611 for IVV and 17,068 for PA. Quantitative analysis of the methylation profiles of both input samples for each genomic locus showed distinct differences in methylation profiles between IVV and PA samples for six of the target loci, and subtle differences in four loci. It was concluded that high throughput sequencing technologies can be effectively applied to provide a powerful, cost-effective approach to targeted DNA methylation analysis of embryonic and other reproductive tissues.
Glycome and Transcriptome Regulation of Vasculogenesis (2009)

The present study for the first time implicates interplay between the glycome and the transcriptome during vasculogenesis, revealing the possibility of harnessing specific cellular glyco-microenvironments for therapeutic vascularization.
Machine learning-assisted fluoroscopy of bladder function in awake mice (2022)

Abstract Understanding the lower urinary tract (LUT) and development of highly needed novel therapies to treat LUT disorders depends on accurate techniques to monitor LUT (dys)function in preclinical models. We recently developed videocystometry in rodents, which combines intravesical pressure measurements with X-ray-based fluoroscopy of the LUT, allowing the in vivo analysis of the process of urine storage and voiding with unprecedented detail. Videocystometry relies on the precise contrast-based determination of the bladder volume at high temporal resolution, which can readily be achieved in anesthetized or otherwise motion-restricted mice but not in awake and freely moving animals. To overcome this limitation, we developed a machine-learning method, in which we trained a neural network to automatically detect the bladder in fluoroscopic images, allowing the automatic analysis of bladder filling and voiding cycles based on large sets of time-lapse fluoroscopic images (&gt;3 hours at 30 images/second) from behaving mice and in a non-invasive manner. With this approach, we found that urethane, an injectable anesthetic that is commonly used in preclinical urological research, has a profound, dose-dependent effect on urethral relaxation and voiding duration and that implantation of a suprapubic catheter, as is standardly performed for cystometric analyses, leads to a ∼4-fold reduction in bladder capacity. Our findings provide a paradigm for the non-invasive, in vivo monitoring of a hollow organ in behaving animals and pinpoint important limitations of the current gold standard techniques to study the LUT in mice.
A Stiff Injectable Biodegradable Elastomer (2012)

Injectable materials often have shortcomings in mechanical and drug-eluting properties that are attributable to their high water contents. A water-free, liquid four-armed PEG modified with dopamine end groups is described which changed from liquid to elastic solid by reaction with a small volume of Fe<sup>3+</sup> solution. The elastic modulus and degradation times increased with increasing Fe<sup>3+</sup> concentrations. Both the free base and the water-soluble form of lidocaine could be dissolved in the PEG<sub>4</sub>-dopamine and released in a sustained manner from the cross-linked matrix. PEG<sub>4</sub>-dopamine was retained in the subcutaneous space in vivo for up to 3 weeks with minimal inflammation. This material's tailorable mechanical properties, biocompatibility, ability to incorporate hydrophilic and hydrophobic drugs and release them slowly are desirable traits for drug delivery and other biomedical applications.
Exploring experiences and impact of the COVID-19 pandemic on young racially minoritised people in the United Kingdom: A qualitative study (2022)

Within high-income-countries, the COVID-19 pandemic has disproportionately impacted people from racially minoritised backgrounds. There has been significant research interrogating the disparate impact of the virus, and recently, interest in the long-term implications of the global crisis on young people's mental health and wellbeing. However, less work explores the experiences of young people from racialised backgrounds as they navigate the pandemic, and the specific consequences this has for their mental health. Forty young people (age 16-25) from Black, mixed and other minority backgrounds and living in London, participated in consecutive focus group discussions over a two-month period, to explore the impact of the pandemic on their lives and emotional wellbeing. Thematic analysis identified seven thematic categories describing the impact of the pandemic, indicating: deepening of existing socioeconomic and emotional challenges; efforts to navigate racism and difference within the response; and survival strategies drawing on communal and individual resources. Young people also articulated visions for a future public health response which addressed gaps in current strategies. Findings point to the need to contextualize public health responses to the pandemic in line with the lived experiences of racialised young people. We specifically note the importance of long-term culturally and socio-politically relevant support interventions. Implications for policy and practice are discussed.
The causal relationship between gastro-esophageal reflux disease and idiopathic pulmonary fibrosis: A bidirectional two-sample Mendelian randomization study (2022)

Abstract Background Gastro-esophageal reflux disease (GERD) is associated with idiopathic pulmonary fibrosis (IPF) in observational studies. It is not known if this association arises because GERD causes IPF, or IPF causes GERD, or because of confounding by factors, such as smoking, associated with both GERD and IPF. We used bidirectional Mendelian randomisation (MR), where genetic variants are used as instrumental variables to address issues of confounding and reverse causation, to examine how, if at all, GERD and IPF are causally related. Methods and results A bidirectional two-sample MR was performed to estimate the causal effect of GERD on IPF risk, and of IPF on GERD risk, using genetic data from the largest GERD (78,707 cases and 288,734 controls) and IPF (4,125 cases and 20,464 controls) genome-wide association meta-analyses currently available. GERD increased the risk of IPF, with an odds ratio (OR) of 1.6 (95% Confidence Interval, CI: 1.04-2.49; p=0.032). There was no evidence of a causal effect of IPF on the risk of GERD, with an OR of 0.99 (95%CI: 0.97-1.02; p=0.615). Conclusion We found that GERD increases the risk of IPF, but found no evidence that IPF increases the risk of GERD. GERD should be considered in future studies of IPF risk, and interest in it as a potential therapeutic target should be renewed. The mechanisms underlying the effect of GERD on IPF should also be investigated.
A Novel Bone Marrow Stimulation Technique Augmented by Administration of Ultrapurified Alginate Gel Enhances Osteochondral Repair in a Rabbit Model (2015)

Cartilage injuries are a common health problem resulting in the loss of daily activities. Bone marrow stimulation technique, one of the surgical techniques for the cartilage injuries, is characterized by technical simplicity and less invasiveness. However, it has been shown to result in fibrous or fibrocartilaginous repair with inferior long-term results. This study focused on using ultrapurified alginate gel (UPAL gel) as an adjuvant scaffold in combination with a bone marrow stimulation technique. The objective of this study was to assess the efficacy of a bone marrow stimulation technique augmented by UPAL gel in a rabbit osteochondral defect model. To achieve this goal, three experimental groups were prepared as follows: defects without intervention, defects treated with a bone marrow stimulation technique, and defects treated with a bone marrow stimulation technique augmented by UPAL gel. The macroscopic and histological findings of the defects augmented by UPAL gel improved significantly more than those of the others at 16 weeks postoperatively. The combination technique elicited hyaline-like cartilage repair, unlike bone marrow stimulation technique alone. This combination procedure has the potential of improving clinical outcomes after use of a bone marrow stimulation technique for articular cartilage injuries.
P‐18: Improvement of Reliability in Coplanar a‐IGZO TFTs by Multilayer SiO 2 Gate Insulator (2018)

We investigated the PBTS instability of top‐gate self‐aligned coplanar a‐IGZO TFTs with multilayer SiO 2 GI. It is confirmed that the PBTS instability due to the deep charge trapping in GI bulk can be improved by increasing activation energy through the interfacial formation with hydrogen‐low SiO 2 deposition, and it is demonstrated experimentally that the PBTS instability due to the excess oxygen in the active region can be improved by hydrogen diffusion process through sequential hydrogen‐rich SiO 2 deposition after ACT/GI interface formation.
Photonic and Thermofluidic Analysis of Colloidal Plasmonic Nanorings and Nanotori for Pulsed-Laser Photothermal Applications (2013)

We propose the use of plasmonic nanorings and nanotori for enhanced colloidal photothermal energy conversion in the visible (vis) to near-infrared (NIR) spectrum. We use full-wave field analysis to demonstrate for the first time that the plasmon resonant absorption of these structures remains high over a broad range of orientations relative to the polarization of the incident field. The finding of strong orientation-independent plasmon absorption is a key result as it indicates that the structures can provide enhanced photothermal heating for colloidal applications. We use computational fluid dynamic analysis to investigate pulsed-laser plasmon-enhanced heating of the nanostructures in a fluid. We quantify the laser intensity and pulse duration needed to superheat the nanostructures to initiate bubble nucleation, and we simulate the dynamics of generated nanobubbles. The modeling provides insight into the plasmonic and thermofluidic behavior of colloidal nanostructures, thereby enabling rational design of novel plasmon-enhanced photothermal processes.
An Anisotropic Constitutive Equation for the Stress Tensor of Blood Based on Mixture Theory (2008)

Based on ideas proposed by Massoudi and Rajagopal (M‐R), we develop a model for blood using the theory of interacting continua, that is, the mixture theory. We first provide a brief review of mixture theory, and then discuss certain issues in constitutive modeling of a two‐component mixture. In the present formulation, we ignore the biochemistry of blood and assume that blood is composed of red blood cells (RBCs) suspended in plasma, where the plasma behaves as a linearly viscous fluid and the RBCs are modeled as an anisotropic nonlinear density‐gradient‐type fluid. We obtain a constitutive relation for blood, based on the simplified constitutive relations derived for plasma and RBCs. A simple shear flow is discussed, and an exact solution is obtained for a very special case; for more general cases, it is necessary to solve the nonlinear coupled equations numerically.