gebhart/patrepeval huggingface dataset:
On the streamwise evolution of turbulent boundary layers in arbitrary pressure gradients (2002)

A new approach to the classic closure problem for turbulent boundary layers is presented. This involves, first, using the well-known mean-flow scaling laws such as the log law of the wall and the law of the wake of Coles (1956) together with the mean continuity and the mean momentum differential and integral equations. The important parameters governing the flow in the general non-equilibrium case are identified and are used for establishing a framework for closure. Initially closure is achieved here empirically and the potential for achieving closure in the future using the wall-wake attached eddy model of Perry & Marusic (1995) is outlined. Comparisons are made with experiments covering adverse-pressure-gradient flows in relaxing and developing states and flows approaching equilibrium sink flow. Mean velocity profiles, total shear stress and Reynolds stress profiles can be computed for different streamwise stations, given an initial upstream mean velocity profile and the streamwise variation of free-stream velocity. The attached eddy model of Perry & Marusic (1995) can then be utilized, with some refinement, to compute the remaining unknown quantities such as Reynolds normal stresses and associated spectra and cross-power spectra in the fully turbulent part of the flow.
Chaperone Control of the Activity and Specificity of the Histone H3 Acetyltransferase Rtt109 (2008)

Acetylation of Saccharomyces cerevisiae histone H3 on K56 by the histone acetyltransferase (HAT) Rtt109 is important for repairing replication-associated lesions. Rtt109 purifies from yeast in complex with the histone chaperone Vps75, which stabilizes the HAT in vivo. A whole-genome screen to identify genes whose deletions have synthetic genetic interactions with rtt109Delta suggests Rtt109 has functions in addition to DNA repair. We show that in addition to its known H3-K56 acetylation activity, Rtt109 is also an H3-K9 HAT, and we show that Rtt109 and Gcn5 are the only H3-K9 HATs in vivo. Rtt109's H3-K9 acetylation activity in vitro is enhanced strongly by Vps75. Another histone chaperone, Asf1, and Vps75 are both required for acetylation of lysine 9 on H3 (H3-K9ac) in vivo by Rtt109, whereas H3-K56ac in vivo requires only Asf1. Asf1 also physically interacts with the nuclear Hat1/Hat2/Hif1 complex that acetylates H4-K5 and H4-K12. We suggest Asf1 is capable of assembling into chromatin H3-H4 dimers diacetylated on both H4-K5/12 and H3-K9/56.
Building a Smooth Medical Service for Operating Room Using RFID Technologies (2014)

Due to the information technology advancement, the feasibility for the establishment of mobile medical environments has been strengthened. Using RFID to facilitate the tracing of patients’ mobile position in hospital has attracted more attentions from researchers due to the demand on advanced features. Traditionally, the management of surgical treatment is generally manually operated and there is no consistent operating procedure for patients transferring among wards, surgery waiting rooms, operating rooms, and recovery rooms, resulting in panicky and urgent transferring work among departments and, thus, leading to delays and errors. In this paper, we propose a new framework using radio frequency identification (RFID) technology for a mobilized surgical process monitoring system. Through the active tag, an application management system used before, during, and after the surgical processes has been proposed. The concept of signal level matrix, SLM, was proposed to accurately identify patients and dynamically track patients’ location. By updating patient’s information real-time, the preprocessing time needed for various tasks and incomplete transfers among departments can be reduced, the medical resources can be effectively used, unnecessary medical disputes can be reduced, and more comprehensive health care environment can be provided. The feasibility and effectiveness of our proposed system are demonstrated with a number of experimental results.
DNA Methylation Markers for Prostate Cancer with a Stem Cell Twist (2010)

This perspective on Ibragimova et al. (beginning on page 1084 in this issue of the journal) highlights the potential role of DNA methylation-based markers in the early detection of prostate cancer (PCa), with a focus on the global reactivation of expression of genes epigenetically silenced in PCa cell lines. Novel findings of these investigators identified four genes methylated specifically in PCa, including the stem cell marker TACSTD2, which seems to discriminate PCa (methylated TACSTD2) from prostatic intraepithelial neoplasia (unmethylated). These genes add significantly to the list of epigenetic markers showing promise for clinical early detection of PCa in the near future.
Alkylating properties of synthetic trioxanes related to artemisinin (2000)

The synthesis and reactivity toward a haem model of trioxane derivatives bearing a 1,2-dioxacyclohexane cycle instead of a 1,2-dioxacycloheptane as in artemisinin, and lacking the lactone ring, are reported. The fact that a trioxane able to generate a C-centred radical (without alkylating ability toward a haem model) was devoid of toxicity against Plasmodium also suggests that the efficiency of antimalarial trioxanes is not due to an oxidant stress.
Investigation of the plasmonic effect in air-processed PbS/CdS core–shell quantum dot based solar cells (2016)

Plasmon enhanced performance of bulk heterojunction solar cells involving Au nanostars, PbS/CdS core–shell QDs and TiO<sub>2</sub> nanorod arrays is demonstrated.
Sparse and stable Markowitz portfolios (2009)

We consider the problem of portfolio selection within the classical Markowitz mean-variance framework, reformulated as a constrained least-squares regression problem. We propose to add to the objective function a penalty proportional to the sum of the absolute values of the portfolio weights. This penalty regularizes (stabilizes) the optimization problem, encourages sparse portfolios (i.e., portfolios with only few active positions), and allows accounting for transaction costs. Our approach recovers as special cases the no-short-positions portfolios, but does allow for short positions in limited number. We implement this methodology on two benchmark data sets constructed by Fama and French. Using only a modest amount of training data, we construct portfolios whose out-of-sample performance, as measured by Sharpe ratio, is consistently and significantly better than that of the naïve evenly weighted portfolio.
Time-dependent angular analysis of the decay $ B_s^0\to {J \left/ {{\psi \phi }} \right.} $ and extraction of ΔΓ s and the CP-violating weak phase ϕ s by ATLAS (2012)

A bstract A measurement of $ B_s^0\to {J \left/ {{\psi \phi }} \right.} $ decay parameters, including the CP -violating weak phase ϕ s and the decay width difference ΔΓ s is reported, using 4 . 9 fb −1 of integrated luminosity collected in 2011 by the ATLAS detector from LHC pp collisions at a centre-of-mass energy $ \sqrt{s}=7 $ TeV. The mean decay width Γ s and the transversity amplitudes | A 0 (0)| 2 and | A ∥ (0)| 2 are also measured. The values reported for these parameters are: $ \begin{array}{*{20}{c}} {{\phi_s}=0.22 \pm 0.41\ \left( {\mathrm{s}\mathrm{tat}.} \right) \pm 0.10\ \left( {\mathrm{s}\mathrm{yst}.} \right)\ \mathrm{rad}} \\ {\varDelta {\varGamma_s}=0.053 \pm 0.021\ \left( {\mathrm{s}\mathrm{tat}.} \right) \pm 0.010\ \left( {\mathrm{s}\mathrm{yst}.} \right)\ \mathrm{p}{{\mathrm{s}}^{-1 }}} \\ {{\varGamma_s}=0.677 \pm 0.007\ \left( {\mathrm{s}\mathrm{tat}.} \right) \pm 0.004\ \left( {\mathrm{s}\mathrm{yst}.} \right)\ \mathrm{p}{{\mathrm{s}}^{-1 }}} \\ {|{A_0}(0){|^2} = 0.528 \pm 0.006\ \left( {\mathrm{s}\mathrm{tat}.} \right) \pm 0.009\ \left( {\mathrm{s}\mathrm{yst}.} \right)} \\ {|{A_{\parallel }}(0){|^2} = 0.220 \pm 0.008\ \left( {\mathrm{s}\mathrm{tat}.} \right) \pm 0.007\ \left( {\mathrm{s}\mathrm{yst}.} \right)} \\ \end{array} $ where the values quoted for ϕ s and ΔΓ s correspond to the solution compatible with the external measurements to which the strong phase δ ⊥ is constrained and where ΔΓ s is constrained to be positive. The fraction of S -wave KK or f 0 contamination through the decays $ B_s^0\to {J \left/ {{\psi {K^{+}}{K^{-}}\left( {{f_0}} \right)}} \right.} $ is measured as well and is found to be consistent with zero. Results for ϕ s and ΔΓ s are also presented as 68%, 90% and 95% likelihood contours, which show agreement with Standard Model expectations.
Pentafluorophenyl and phenyl substituted azidoborates (2002)

The azidoborates [(C 6 F 5 ) 4 n B(N 3 ) n ]  (n = 13) (13) were synthesized by reacting the corresponding borane with [R]N 3 (R = Me 4 N, Ph 4 P). To study the influence of the electron withdrawing C 6 F 5 -substituent on the boron atom, [Me 4 N][(C 6 H 5 ) 3 BN 3 ] (4) was also prepared. All compounds were fully characterized by IR, Raman, and multinuclear NMR spectroscopy in addition to characterization by single crystal diffraction analyses.Key words: azidoborate, pentafluorophenyl, multinuclear NMR spectroscopy, X-ray crystallography.
Liquid‐phase microextraction of basic drugs – Selection of extraction mode based on computer calculated solubility data (2005)

The extractability of 58 different basic drugs by 3-phase liquid-phase microextraction (LPME) was studied. Extraction recoveries were correlated to solubility data and log D data calculated with a commercial computer program. The basic drugs were extracted from 1.5 mL water samples (pH 13) through approximately 15 microL of dodecyl acetate immobilized within the pores of a porous polypropylene hollow fibre (organic phase), and into 15 microL of 10 mM HCl (acceptor solution) present inside the lumen of the hollow fibre. Compounds with a calculated solubility below 1 mg/mL at pH 2 were poorly recovered and remained principally in the organic phase. For these drugs, 2-phase LPME may be used as an alternative technique, where the aqueous acceptor phase is replaced by an organic solvent. In the solubility range 1-5 mg/mL, most drugs were effectively extracted (recovery >30%), whereas drugs belonging to the solubility range 5-150 mg/mL were all extracted with recoveries above 30% by 3-phase LPME. The hydrophilic nature of most drugs with solubilities above 150 mg/mL prevented them from entering the organic phase, and only those with log D >1.8 were effectively recovered by 3-phase LPME. For drugs with log D < 1.8 (and solubility >150 mg/mL), carrier-mediated LPME was found to be the preferred technique, where an ion-pair reagent (octanoic acid) was added to the sample. In the case of carrier-mediated LPME, the volume of sample was decreased to 100 microL to facilitate rapid extractions. Based on the present work, the extractability of new compounds may easily be predicted to speed up method development. Extractions were also accomplished from plasma samples, where interactions between proteins and the drugs may reduce the extraction recovery. However, dilution of the plasma samples with water and adjustment of pH into the alkaline region effectively suppressed drug-protein interactions for most of the drugs studied.
Molecular orientational ordering in the smectic C* and H* phases of chiral tbaca (1980)

Abstract In this paper a detailed analysis of 14N NQR experimental data of the chiral liquid crystal TBACA is presented. The effects of the possible orientational ordering of the short molecular axes and of the fluctuations in the direction of the long molecular axis are taken into account. It is shown that in the smectic H* phase polar orientational ordering of the -CH=N-groups exists with the values of ⟨cos ϕ⟩ between∼0.1 and∼0.01. In the smectic C* phase this ordering is even smaller. Anisotropic fluctuations in the direction of the long molecular axes definitely take place in the smectic C* phase.
Role of Arg-401 of cytosolic serine hydroxymethyltransferase in subunit assembly and interaction with the substrate carboxy group (1997)

In an attempt to identify the arginine residue involved in binding of the carboxylate group of serine to mammalian serine hydroxymethyltransferase, a highly conserved Arg-401 was mutated to Ala by site-directed mutagenesis. The mutant enzyme had a characteristic visible absorbance at 425 nm indicative of the presence of bound pyridoxal 5'-phosphate as an internal aldimine with a lysine residue. However, it had only 0.003% of the catalytic activity of the wild-type enzyme. It was also unable to perform reactions with glycine, beta-phenylserine or d-alanine, suggesting that the binding of these substrates to the mutant enzyme was affected. This was also evident from the interaction of amino-oxyacetic acid, which was very slow (8.4x10(-4) s-1 at 50 microM) for the R401A mutant enzyme compared with the wild-type enzyme (44.6 s-1 at 50 microM). In contrast, methoxyamine (which lacks the carboxy group) reacted with the mutant enzyme (1.72 s-1 at 250 microM) more rapidly than the wild-type enzyme (0.2 s-1 at 250 microM). Further, both wild-type and the mutant enzymes were capable of forming unique quinonoid intermediates absorbing at 440 and 464 nm on interaction with thiosemicarbazide, which also does not have a carboxy group. These results implicate Arg-401 in the binding of the substrate carboxy group. In addition, gel-filtration profiles of the apoenzyme and the reconstituted holoenzyme of R401A and the wild-type enzyme showed that the mutant enzyme remained in a tetrameric form even when the cofactor had been removed. However, the wild-type enzyme underwent partial dissociation to a dimer, suggesting that the oligomeric structure was rendered more stable by the mutation of Arg-401. The increased stability of the mutant enzyme was also reflected in the higher apparent melting temperature (Tm) (61 degrees C) than that of the wild-type enzyme (56 degrees C). The addition of serine or serinamide did not change the apparent Tm of R401A mutant enzyme. These results suggest that the mutant enzyme might be in a permanently 'open' form and the increased apparent Tm could be due to enhanced subunit interactions.
Titin mutation segregates with hereditary myopathy with early respiratory failure (2012)

In 2001, we described an autosomal dominant myopathy characterized by neuromuscular ventilatory failure in ambulant patients. Here we describe the underlying genetic basis for the disorder, and we define the neuromuscular, respiratory and radiological phenotype in a study of 31 mutation carriers followed for up to 31 years. A combination of genome-wide linkage and whole exome sequencing revealed the likely causal genetic variant in the titin (TTN) gene (g.274375T>C; p.Cys30071Arg) within a shared haplotype of 2.93 Mbp on chromosome 2. This segregated with the phenotype in 21 individuals from the original family, nine subjects in a second family with the same highly selective pattern of muscle involvement on magnetic resonance imaging and a third familial case with a similar phenotype. Comparing the mutation carriers revealed novel features not apparent in our original report. The clinical presentation included predominant distal, proximal or respiratory muscle weakness. The age of onset was highly variable, from early adulthood, and including a mild phenotype in advanced age. Muscle weakness was earlier onset and more severe in the lower extremities in nearly all patients. Seven patients also had axial muscle weakness. Respiratory function studies demonstrated a gradual deterioration over time, reflecting the progressive nature of this condition. Cardiomyopathy was not present in any of our patients despite up to 31 years of follow-up. Magnetic resonance muscle imaging was performed in 21 affected patients and revealed characteristic abnormalities with semitendinosus involvement in 20 of 21 patients studied, including 3 patients who were presymptomatic. Diagnostic muscle histopathology most frequently revealed eosinophilic inclusions (inclusion bodies) and rimmed vacuoles, but was non-specific in a minority of patients. These findings have important clinical implications. This disease should be considered in patients with adult-onset proximal or distal myopathy and early respiratory failure, even in the presence of non-specific muscle pathology. Muscle magnetic resonance imaging findings are characteristic and should be considered as an initial investigation, and if positive should prompt screening for mutations in TTN. With 363 exons, screening TTN presented a major challenge until recently. However, whole exome sequencing provides a reliable cost-effective approach, providing the gene of interest is adequately captured.
Effects of losartan on cerebral and ocular circulation in healthy subjects (1997)

The present data suggest that Ang II is not a major determinant of cerebral and ocular blood flow in vivo. The observed changes in cerebral and ocular haemodynamic parameters after losartan administration reflect effects on systemic blood pressure.
Regulation of Cellular Osmolarity and Volume in <i>Tetrahymena</i> (1970)

ABSTRACT Tetrahymena pyrifor mis are hyperosmotic to external media of osmolarities from 2 to 171 m-osmole/1. The intracellular osmolarity, determined by freezing-point depression, is 111 m-osmole/kg cells in dilute media, and increases linearly with increasing external osmolarities. Over 80% of the intracellular osmolarity can be attributed to the concentration of sodium, potassium, chloride and the free amino acids. In response to an increase in the external osmolarity, Tetrahymena regulates its intracellular osmolarity by increasing the concentrations of free amino acids. The regulation of cellular volume under conditions of osmotic stress is achieved by an increase in the amount of osmotically active solutes and the regulation of the rate of elimination of fluid by the contractile vacuole.
On “Liberation” (2009)

When the editor asked me along with other ex-editors to offer some thoughts on the occasion of The China Quarterly 's 50th anniversary, I was at a loss. At the celebration which David Shambaugh held for the 35th anniversary in 1995, I wrote fairly extensively about the founding and early development of the journal (No.143, pp. 692–96) and did not have much to add. So I made the suggestion that I should reprise a special feature of the first China Quarterly . For that founding issue, I solicited a number of senior Sinologues to give their appraisal of the PRC on the occasion of its tenth anniversary. Could I, now senior, be given a similar opportunity to look back at the founding of the PRC on the occasion of its 60th anniversary? This article is the consequence of the editor's kind agreement.
High-Mobility Group Box 1: A Novel Target for Treatment of <i>Pseudomonas aeruginosa</i> Keratitis (2015)

High-mobility group box 1 (HMGB1), a prototypic alarmin, mediates the systemic inflammatory response syndrome. Treatment with vasoactive intestinal peptide, an anti-inflammatory neuropeptide, downregulates proinflammatory cytokines and promotes healing in a susceptible (cornea perforates) model of Pseudomonas aeruginosa keratitis, and also significantly downregulates HMGB1 expression. Therefore, we examined targeting HMGB1 for the treatment of P. aeruginosa keratitis to avoid delivery and other issues associated with vasoactive intestinal peptide. For this, HMGB1 was silenced using small interfering RNA, whereas controls were treated with a nonspecific scrambled sequence small interfering RNA. Less disease was seen postinfection in siHMGB1 compared with control mice and was documented by clinical score and photographs with a slit lamp. Real-time RT-PCR and ELISA confirmed HMGB1 knockdown. RT-PCR analysis also revealed reduced mRNA levels of IL-1β, MIP-2, TNF-α, TLR4, and receptor for advanced glycation end products, whereas mRNA levels of anti-inflammatory TLRs single Ig IL-1-related receptor and ST2 were increased significantly. HMGB1 knockdown also decreased IL-1β and MIP-2 proteins, reducing polymorphonuclear cell number in the infected cornea. mRNA and protein levels of CXCL12 and CXCR4, as well as mononuclear cells, were reduced significantly after HMGB1 knockdown. Ab neutralization of HMGB1, infection with a clinical isolate, and recombinant HMGB1 treatment of resistant mice supported the silencing studies. These data provide evidence that silencing HMGB1 promotes better resolution of P. aeruginosa keratitis by decreasing levels of proinflammatory mediators (decreasing polymorphonuclear cell infiltration), increasing anti-inflammatory TLRs, reducing CXCL12 (preventing HMGB1/CXCL12 heterodimer formation), and signaling through CXCR4, reducing monocyte/macrophage infiltration.
Role of Intraspecies Recombination in the Spread of Pathogenicity Islands within the Escherichia coli Species (2009)

Horizontal gene transfer is a key step in the evolution of bacterial pathogens. Besides phages and plasmids, pathogenicity islands (PAIs) are subjected to horizontal transfer. The transfer mechanisms of PAIs within a certain bacterial species or between different species are still not well understood. This study is focused on the High-Pathogenicity Island (HPI), which is a PAI widely spread among extraintestinal pathogenic Escherichia coli and serves as a model for horizontal transfer of PAIs in general. We applied a phylogenetic approach using multilocus sequence typing on HPI-positive and -negative natural E. coli isolates representative of the species diversity to infer the mechanism of horizontal HPI transfer within the E. coli species. In each strain, the partial nucleotide sequences of 6 HPI-encoded genes and 6 housekeeping genes of the genomic backbone, as well as DNA fragments immediately upstream and downstream of the HPI were compared. This revealed that the HPI is not solely vertically transmitted, but that recombination of large DNA fragments beyond the HPI plays a major role in the spread of the HPI within E. coli species. In support of the results of the phylogenetic analyses, we experimentally demonstrated that HPI can be transferred between different E. coli strains by F-plasmid mediated mobilization. Sequencing of the chromosomal DNA regions immediately upstream and downstream of the HPI in the recipient strain indicated that the HPI was transferred and integrated together with HPI-flanking DNA regions of the donor strain. The results of this study demonstrate for the first time that conjugative transfer and homologous DNA recombination play a major role in horizontal transfer of a pathogenicity island within the species E. coli.