gebhart/patrepeval huggingface dataset:
Pseudophase change effects in turbulent channel flow under transcritical temperature conditions (2019)

We have performed direct numerical simulations of compressible turbulent channel flow using R-134a as a working fluid in transcritical temperature ranges ( $\unicode[STIX]{x0394}T=5$ , 10 and 20 K, where $\unicode[STIX]{x0394}T$ is top-to-bottom temperature difference) at supercritical pressure. At these conditions, a pseudophase change occurs at various wall-normal locations within the turbulent channel from $y_{pb}/h=-0.23$ ( $\unicode[STIX]{x0394}T=5$ K) to 0.89 ( $\unicode[STIX]{x0394}T=20$ K), where $h$ is the channel half-height and $y=0$ the centreplane position. Increase in $\unicode[STIX]{x0394}T$ also results in increasing wall-normal gradients in the semi-local friction Reynolds number. Classical, compressible scaling laws of the mean velocity profile are unable to fully collapse real fluid effects in this flow. The proximity to the pseudotransitioning layer inhibits turbulent velocity fluctuations, while locally enhancing the temperature and density fluctuation intensities. Probability distribution analysis reveals that the sheet of fluid undergoing pseudophase change is characterized by a dramatic reduction in the kurtosis of density fluctuations, hence becoming thinner as $\unicode[STIX]{x0394}T$ is increased. Instantaneous visualizations show dense fluid ejections from the pseudoliquid viscous sublayer, some reaching the channel core, causing positive values of density skewness in the respective buffer layer region ( vice versa for the top wall) and an impoverishment of the turbulent flow structure population near pseudotransitioning conditions.
The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer (2020)

Mechanisms driving resistance to cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) in hormone receptor-positive (HR<sup>+</sup>) breast cancer have not been clearly defined. Whole-exome sequencing of 59 tumors with CDK4/6i exposure revealed multiple candidate resistance mechanisms including <i>RB1</i> loss, activating alterations in <i>AKT1, RAS, AURKA, CCNE2, ERBB2</i>, and <i>FGFR2</i>, and loss of estrogen receptor expression. <i>In vitro</i> experiments confirmed that these alterations conferred CDK4/6i resistance. Cancer cells cultured to resistance with CDK4/6i also acquired <i>RB1, KRAS, AURKA</i>, or <i>CCNE2</i> alterations, which conferred sensitivity to AURKA, ERK, or CHEK1 inhibition. Three of these activating alterations-in <i>AKT1, RAS</i>, and <i>AURKA</i>-have not, to our knowledge, been previously demonstrated as mechanisms of resistance to CDK4/6i in breast cancer preclinically or in patient samples. Together, these eight mechanisms were present in 66% of resistant tumors profiled and may define therapeutic opportunities in patients. SIGNIFICANCE: We identified eight distinct mechanisms of resistance to CDK4/6i present in 66% of resistant tumors profiled. Most of these have a therapeutic strategy to overcome or prevent resistance in these tumors. Taken together, these findings have critical implications related to the potential utility of precision-based approaches to overcome resistance in many patients with HR<sup>+</sup> metastatic breast cancer.<i>This article is highlighted in the In This Issue feature, p. 1079</i>.
Identification of a Novel Drug Lead That Inhibits HCV Infection and Cell-to-Cell Transmission by Targeting the HCV E2 Glycoprotein (2014)

Hepatitis C Virus (HCV) infects 200 million individuals worldwide. Although several FDA approved drugs targeting the HCV serine protease and polymerase have shown promising results, there is a need for better drugs that are effective in treating a broader range of HCV genotypes and subtypes without being used in combination with interferon and/or ribavirin. Recently, two crystal structures of the core of the HCV E2 protein (E2c) have been determined, providing structural information that can now be used to target the E2 protein and develop drugs that disrupt the early stages of HCV infection by blocking E2's interaction with different host factors. Using the E2c structure as a template, we have created a structural model of the E2 protein core (residues 421-645) that contains the three amino acid segments that are not present in either structure. Computational docking of a diverse library of 1,715 small molecules to this model led to the identification of a set of 34 ligands predicted to bind near conserved amino acid residues involved in the HCV E2: CD81 interaction. Surface plasmon resonance detection was used to screen the ligand set for binding to recombinant E2 protein, and the best binders were subsequently tested to identify compounds that inhibit the infection of Huh-7 cells by HCV. One compound, 281816, blocked E2 binding to CD81 and inhibited HCV infection in a genotype-independent manner with IC50's ranging from 2.2 µM to 4.6 µM. 281816 blocked the early and late steps of cell-free HCV entry and also abrogated the cell-to-cell transmission of HCV. Collectively the results obtained with this new structural model of E2c suggest the development of small molecule inhibitors such as 281816 that target E2 and disrupt its interaction with CD81 may provide a new paradigm for HCV treatment.
Correlation between the proliferative response to granulocyte colony‐stimulating factor and the positivity of transferrin receptor in acute myeloblastic leukemia cells (1991)

The use of granulocyte colony-stimulating factor (G-CSF) after chemotherapy for acute myeloblastic leukemia (AML) has been reported. However, there is a drawback in that G-CSF may stimulate the proliferation of AML progenitors. To determine the parameter(s) indicative of responsiveness of AML blasts to G-CSF, various surface phenotypes of blasts were examined in relation to the blast colony formation stimulated by G-CSF in 39 AML patients. A correlation was found only with transferrin receptor positivity among the various phenotypes studied. The population mean of percentages of transferrin receptor-positive blasts in the group responding to G-CSF in vitro was significantly higher than that of blasts in the group not responding to G-CSF. A further correlation was found between transferrin receptor positivity and the number of G-CSF receptors on the blasts; that is, blasts expressing more G-CSF receptors have greater transferrin receptor positivity. In our previous study, we observed that blasts with a large number of G-CSF receptors produce more colonies in response to G-CSF. These results indicated that blasts expressing more transferrin receptors have a larger number of G-CSF receptors and may show more active proliferation in response to G-CSF. Therefore, the proliferative response of blasts to G-CSF can be predicted by examining transferrin receptor positivity. The clinical use of G-CSF in AML patients may be recommended when the patient's blasts have a low level of transferrin receptor expression. The measurement of transferrin receptors on blasts, instead of the rather complicated G-CSF receptor determination, would be a useful indicator for the safer application of G-CSF in AML patients.
Passive acoustic localization enhanced with tomography and acoustic thermometry in the ocean (1997)

Abstract Passive localization has application for assessing the spatial distributions of calling animals. Improved localization is demonstrated in the atmosphere when the sound speed and wind fields are simultaneously estimated from sounds recorded on eight microphones spread over a 30 m by 20 m region. Localization errors in the horizontal and vertical dimensions are 15 cm and 40 cm respectively, at two standard deviations. The accuracy degrades by a factor of three if the sound speed and wind fields are not estimated. Two other subjects are discussed. First, a Surface Suspended Acoustic Receiver (SSAR) is under development for studying climatic temperature changes in the ocean. The SSAR's theoretical range limit for detecting many marine mammal calls is about 100 km. Second, techniques are suggested for minimizing the possible impact of low‐frequency sounds from acoustic thermometry transmissions on the marine ecosystem. The simplest technique involves placing sound sources on autonomous moorings in nutrient depleted regions.
Tracer Studies in the Rat Demonstrate Misdirected Filtration and Peritubular Filtrate Spreading in Nephrons with Segmental Glomerulosclerosis (2001)

In two genetic models of "classic" focal segmental glomerulosclerosis (FSGS), the Milan normotensive and the Fawn-hooded hypertensive rats, tracer studies were performed to test the hypothesis that misdirected glomerular filtration and peritubular filtrate spreading are relevant mechanisms that contribute to nephron degeneration in this disease. Two exogenous tracers, lissamine green and horse spleen ferritin, were administered by intravenous injection and subsequently traced histologically in serial kidney sections. In contrast to control rats, both tracers in kidneys of Milan normotensive and Fawn-hooded hypertensive rats with established FSGS were found to accumulate extracellularly at the following sites: (1) within tuft adhesions to Bowman's capsule and associated paraglomerular spaces, (2) at the glomerulotubular junction contained within extensions of the paraglomerular spaces onto the tubule, and (3) within subepithelial peritubular spaces eventually encircling the entire proximal convolution of an affected nephron. This distribution strongly suggests the existence of misdirected filtration into tuft adhesions to Bowman's capsule and subsequent spreading of the filtrate around the entire circumference of a glomerulus and, alongside the glomerulotubular junction, onto the outer aspect of the corresponding tubule. This leads to an interstitial response that consists of the formation of a barrier of sheet-like fibroblast processes around the affected nephron, which confines the filtrate spreading and, subsequently, the destructive process to the affected nephron. No evidence was found that either misdirected filtration and peritubular filtrate spreading themselves or the associated tubulo-interstitial process led to the transfer of the injury from an affected nephron to an unaffected nephron. It is concluded that in the context of FSGS development, misdirected filtration and peritubular filtrate spreading are important damaging mechanisms that underlie the extension of glomerular injury to the corresponding tubulointerstitium, thus leading finally to degeneration of both the glomerulus and the tubule of a severely injured nephron.
Diversity-multiplexing tradeoff in multiple-relay network-part II: Multiple-antenna networks (2008)

This paper studies the setup of a multiple-relay network in which K half-duplex multiple-antenna relays assist in the transmission between a/several multiple-antenna source(s) and a multiple-antenna destination. Each two nodes are assumed to be either connected through a quasi-static Rayleigh fading channel, or disconnected. This paper is comprised of two parts. In this part of the paper, we study multiple-antenna multiple-relay network. We prove that the Random Sequential (RS) scheme proposed in achieves the maximum diversity gain in a general multiple-antenna multiple-relay network. Moreover, we show that utilizing independent random unitary matrix multiplication at the relay nodes enables the RS scheme to achieve better diversity-multiplexing tradeoff (DMT) results comparing with the traditional amplify-and-forward relaying. Indeed, using the RS scheme, we derive a new achievable DMT for the MIMO parallel relay network. Interestingly, it turns out that the DMT of the RS scheme is optimum for the MIMO half-duplex parallel 2-relay (K = 2) setup. Finally, we show that utilizing random unitary matrix multiplication also improves the DMT of the Non-Orthogonal amplify-and-forward relaying scheme of in the MIMO single relay channel.
Dot blots of solubilized extracellular matrix allow quantification of human antibodies bound to epitopes present in decellularized porcine pulmonary heart valves (2020)

The dot blot assay described herein could be a valuable tool to measure preformed antibody levels in human sera against unknown epitopes on decellularized tissue prior to implantation. Ultimately, this prescreening may allow a matching of the porcine xenograft with the respective human recipients in demand and thus may become an important tool for graft long-term survival similar to current allotransplantation settings.
Role of Molecular Weight on the Mechanical Device Properties of Organic Polymer Solar Cells (2014)

For semiconducting polymers, such as regioregular poly(3-hexylthiophene-2,5-diyl) (rr-P3HT), the molecular weight has been correlated to charge carrier field-effect mobilities, surface morphology, and gelation rates in solution and therefore has important implications for long-term reliability, manufacturing, and future applications of electronic organic thin films. In this work, we show that the molecular weight rr-P3HT in organic solar cells can also significantly change the internal cohesion of the photoactive layer using micromechanical testing techniques. Cohesive values ranged from ∼0.5 to ∼17 J m–2, following the general trend of greater cohesion with increasing molecular weight. Using nanodynamic mechanical analysis, we attribute the increase in cohesion to increased plasticity which helps dissipate the applied energy. Finally, we correlate photovoltaic efficiency with cohesion to assess the device physics pertinent to optimizing device reliability. This research elucidates the fundamental parameters which affect both the mechanical stability and efficiency of polymer solar cells.
Insights into the susceptibility of Pseudomonas putida to industrially relevant aromatic hydrocarbons that it can synthesize from sugars (2023)

Pseudomonas putida DOT-T1E is a highly solvent tolerant strain for which many genetic tools have been developed. The strain represents a promising candidate host for the synthesis of aromatic compounds-opening a path towards a green alternative to petrol-derived chemicals. We have engineered this strain to produce phenylalanine, which can then be used as a raw material for the synthesis of styrene via trans-cinnamic acid. To understand the response of this strain to the bioproducts of interest, we have analyzed the in-depth physiological and genetic response of the strain to these compounds. We found that in response to the exposure to the toxic compounds that the strain can produce, the cell launches a multifactorial response to enhance membrane impermeabilization. This process occurs via the activation of a cis to trans isomerase that converts cis unsaturated fatty acids to their corresponding trans isomers. In addition, the bacterial cells initiate a stress response program that involves the synthesis of a number of chaperones and ROS removing enzymes, such as peroxidases and superoxide dismutases. The strain also responds by enhancing the metabolism of glucose through the specific induction of the glucose phosphorylative pathway, Entner-Doudoroff enzymes, Krebs cycle enzymes and Nuo. In step with these changes, the cells induce two efflux pumps to extrude the toxic chemicals. Through analyzing a wide collection of efflux pump mutants, we found that the most relevant pump is TtgGHI, which is controlled by the TtgV regulator.
Simultaneous Analysis of Heparan Sulfate, Chondroitin/Dermatan Sulfates, and Hyaluronan Disaccharides by Glycoblotting-Assisted Sample Preparation Followed by Single-Step Zwitter-Ionic-Hydrophilic Interaction Chromatography (2011)

Glycosaminoglycans (GAGs) play important roles in cell adhesion and growth, maintenance of extracellular matrix (ECM) integrity, and signal transduction. To fully understand the biological functions of GAGs, there is a growing need for sensitive, rapid, and quantitative analysis of GAGs. The present work describes a novel analytical technique that enables high throughput cellular/tissue glycosaminoglycomics for all three families of uronic acid-containing GAGs, hyaluronan (HA), chondroitin sulfate (CS)/dermatan sulfate (DS), and heparan sulfate (HS). A one-pot purification and labeling procedure for GAG Δ-disaccharides was established by chemo-selective ligation of disaccharides onto high density hydrazide beads (glycoblotting) and subsequent labeling by fluorescence. The 17 most common disaccharides (eight comprising HS, eight CS/DS, and one comprising HA) could be separated with a single chromatography for the first time by employing a zwitter-ionic type of hydrophilic-interaction chromatography column. These novel analytical techniques were able to precisely characterize the glycosaminoglycome in various cell types including embryonal carcinoma cells and ocular epithelial tissues (cornea, conjunctiva, and limbus).
Psychological Functioning in Children with Cyanotic Heart Defects (1990)

The relationship between congenital heart disease (CHD) and psychological functioning was studied in 63 children with transposition of the great arteries (TGA) and 77 children with tetralogy of Fallot (TF). These youngsters were compared with a group of 36 children originally diagnosed with CHD, but who spontaneously recovered (SR) without medical intervention. All children were under one year of age when diagnosed and were given psychological testing between 5.5 and 6.3 years. Children with TGA and TF had poorer overall psychological functioning and significantly greater central nervous system (CNS) impairment than the SR children. However when the effects of IQ and CNS impairment were controlled, there were no differences between groups. The diagnosis of a severe cyanotic heart defect does not appear to make a child more likely to have emotional disorder in the absence of other factors.
OpenQASM 3: A Broader and Deeper Quantum Assembly Language (2022)

Quantum assembly languages are machine-independent languages that traditionally describe quantum computation in the circuit model. Open quantum assembly language (OpenQASM 2) was proposed as an imperative programming language for quantum circuits based on earlier QASM dialects. In principle, any quantum computation could be described using OpenQASM 2, but there is a need to describe a broader set of circuits beyond the language of qubits and gates. By examining interactive use cases, we recognize two different timescales of quantum-classical interactions: real-time classical computations that must be performed within the coherence times of the qubits, and near-time computations with less stringent timing. Since the near-time domain is adequately described by existing programming frameworks, we choose in OpenQASM 3 to focus on the real-time domain, which must be more tightly coupled to the execution of quantum operations. We add support for arbitrary control flow as well as calling external classical functions. In addition, we recognize the need to describe circuits at multiple levels of specificity, and therefore we extend the language to include timing, pulse control, and gate modifiers. These new language features create a multi-level intermediate representation for circuit development and optimization, as well as control sequence implementation for calibration, characterization, and error mitigation.
Sociologie de l'action publique (2018)

Ces dernières années, les domaines d’intervention de l’État ont proliféré. De multiples acteurs économiques et sociaux, territoriaux et transnationaux, ont été également mobilisés et interfèrent avec l’État. Ce manuel permet de comprendre ces dynamiques et leurs transformations. Il reprend les principaux concepts et modèles d’analyse et présente une synthèse à partir de deux questions fondamentales :- Qu’est-ce qu’une politique publique ?Un commandement émanant d’une autorité centrale afin de résoudre un problème au nom du bien commun ; ou bien un vaste espace de négociation entre une multitude d’acteurs privés et publics ?- Comment changent les politiques publiques ?Par des mobilisations sociales appelant à une régulation publique ; ou bien en fonction des contextes institutionnels qui formatent ces demandes, selon leurs logiques internes ?
A Fluorescence‐Based Assay for p38α Recruitment Site Binders: Identification of Rooperol as a Novel p38α Kinase Inhibitor (2012)

A new p38α inhibitor: Using a D-recruitment site (DRS) probe for p38α which exploits covalent interaction with Cys119 and alkyne-azide "click" chemistry to identify small molecules that recognize the p38α DRS, the anti-inflammatory natural product rooperol was identified as a novel p38α inhibitor.
ChemInform Abstract: Palladium‐Catalyzed Reductive Homocoupling Reaction of 3‐ Silylpropargyl Carbonates. New Entry into Allene‐Yne Compounds. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Design, synthesis and biological evaluation of new eugenol derivatives containing 1,3,4-oxadiazole as novel inhibitors of thymidylate synthase (2023)

We report the preparation and cytotoxicity of two new eugenol derivatives that contain 1,3,4-oxadiazole, as novel inhibitors of thymidylate synthase; these derivatives are shown to be promising chemotherapeutic agents.
A human histologic analysis of osseotite and machined surfaces using implants with 2 opposing surfaces. (1999)

A human histologic study was conducted to compare the percentage of bone-to-implant contact (BIC) at 6 months for Osseotite and machined, commercially pure titanium implant surfaces. To eliminate potential influences caused by differences in bone density at different intraoral locations, 2 mm x 5 mm, threaded, 2-surfaced titanium implants were manufactured; 1 side received the Osseotite surface modification and the opposite side maintained a machined surface. In each of 11 patients, 1 test implant was placed in the posterior maxilla (Types III and IV bone) during conventional dental implant surgery. Following 6 months of unloaded healing, the conventional implants were uncovered, and the test implants and surrounding hard tissue were removed. Histologic analysis indicated that at 6 months of unloaded healing, the mean BIC value for the Osseotite surfaces (72.96% +/- 25.13%) was statistically significantly higher (P < 0.05) than the mean BIC value for the machined surfaces (33.98% +/- 31.04%). When the BIC values for the machined and Osseotite surface pairs were ranked from high to low based on the machined BIC value range of 93% to 0%, the upper 50th percentile (20 surface pairs) mean BIC value was 86.1% +/- 16.7% for the Osseotite surfaces and 60.1% +/- 18.3% for the machined surfaces. The lower 50th percentile (19 surface pairs) mean BIC value was 59.1% +/- 25.3% for the Osseotite surfaces and 6.5% +/- 10.8% for the machined surfaces. Differences between mean BIC values for the 2 surfaces in both the upper and lower 50th percentiles were statistically significant (P < 0.05). The results of this study indicate that in the poorer quality bone typically found in the posterior maxilla, a statistically significantly higher percentage of bone contacts Osseotite surfaces when compared to opposing machined surfaces on the same implant.