gebhart/patrepeval huggingface dataset:
Anharmonic atomic vibrations in the relaxor ferroelectric Pb(Mg1/3Nb2/3)O3under pressure (2012)

Structural analyses of the relaxor ferroelectric material Pb(Mg${}_{1/3}$Nb${}_{2/3}$)O${}_{3}$ (PMN) with single-crystal x-ray diffraction under pressure in a diamond anvil cell indicate static atomic displacement and chemical disorder. A difference Fourier analysis within the framework of a harmonic oscillator model for the atomic vibrations reveals residual electron density on both the Pb and Nb(Mg) sites. Pb atoms in the $A$ site of the $AB$O${}_{3}$ perovskite structure exhibit a greater displacement than the Nb(Mg) atoms in the $B$ site, despite the fact that Pb is a much heavier atom. The displacement is interpreted in terms of an anharmonic statistical atomic motion. At pressures above 2.5 GPa the displacement disappears, consistent with previous observations. The difference Fourier maps reveal no residual electron densities greater than 1 $e$/\AA{}${}^{3}$ at any atomic position, and these appear to be induced by the violation of local electrical neutrality arising from both Mg${}^{2+}$ and Nb${}^{5+}$ ions located at the octahedral site. Similar electron densities are observed at all experimental pressures and in refinements based on both harmonic and anharmonic models. The anharmonic parameters taken into account are the higher-order tensors of atomic elastic motion. At high pressure, where the relaxor transforms to a paraelectric phase, the residual electron densities disappear.
Coral reef carbonate budgets and ecological drivers in the naturally high temperature and high alkalinity environment of the Red Sea (2017)

Abstract The coral structural framework is crucial for maintaining reef ecosystem function and services. In the central Red Sea, a naturally high alkalinity is beneficial to reef growth, but rising water temperatures impair the calcification capacity of reef-building organisms. However, it is currently unknown how beneficial and detrimental factors affect the balance between calcification and erosion, and thereby the overall growth of the reef framework. To provide insight into present-day carbonate budgets and reef growth dynamics in the central Red Sea, we measured in situ net-accretion and net-erosion rates (G net ) by deployment of limestone blocks and estimated census-based carbonate budgets (G budget ) in four reef sites along a cross-shelf gradient (25 km). We assessed abiotic variables (i.e., temperature, inorganic nutrients, and carbonate system variables) and biotic drivers (i.e., calcifier and bioeroder abundances). On average, total alkalinity A T (2346 - 2431 μmol kg −1 ), aragonite saturation state (4.5 - 5.2 Ω a ), and pCO 2 (283 -315 μatm) were close to estimates of pre-industrial global ocean surface waters. Despite these calcification-favorable carbonate system conditions, G net and G budget encompassed positive (offshore) and negative net-production (midshore-lagoon and exposed nearshore site) estimates. Notably, G budget maxima were lower compared to reef growth from pristine Indian Ocean sites. Yet, a comparison with historical data from the northern Red Sea suggests that overall reef growth in the Red Sea has likely remained similar since 1995. When assessing sites across the shelf gradient, A T correlated well with reef growth rates (ρ = 0.89), while temperature was a weaker, negative correlate (ρ = −0.71). Further, A T explained about 65 % of G budget in a best fitting distance-based linear model. Interestingly, parrotfish abundances added up to 82% of explained variation, further substantiating recent studies highlighting the importance of parrotfish to reef ecosystem function. Our study provides a baseline that will be particularly useful in assessing future trajectories of reef growth capacities in the Red Sea under continuous ocean warming and acidification.
Imaging the total wavefields by reflectivity inversion using amplitude-normalized wavefield decomposition: Field data example (2016)

Based on an example acquired with dual-sensor towed-streamers and time and depth distributed sources, we image the total upand downgoing wavefields using primaries and multiples. The imaging framework is based on computing the subsurface impulse response (i.e., reflectivity). At every depth level, the latter can be obtained by inverting the matrix form of an integral equation defined in terms of the amplitude-normalized upgoing pressure and downgoing vertical velocity wavefields. This procedure gives the reflectivity matrix. The total upgoing wavefield used in the imaging scheme is composed of the scattered energy from primaries and multiples. The primary reflected wavefield is generated by a direct downgoing source wavefield, which is mostly passing the acquisition surface at offsets smaller than the nearest data channel. Hence, the most relevant part of the direct wavefield is not measured in the studied example. From the near-field pressure measurements, we predict the missing direct arrivals needed to image the primary reflected wavefield; and we then synthesize the total downgoing wavefield by adding the downgoing scattered energy. By downward extrapolating the total up- and downgoing wave-fields, the information of the subsurface is extracted from the reflectivity matrix in the spatial and angular domains. Presentation Date: Tuesday, October 18, 2016 Start Time: 4:10:00 PM Location: 171/173 Presentation Type: ORAL
Managing the Effects of Shift Work in Medicine (2009)

Physicians have been practicing in a shift-work environment since the early days of medicine. What has changed is the recognition of how much shift work can degrade the physical and mental performance of physicians, with sleep deprivation in particular impairing not only patient care and safety but also physician health and safety.
SYNTHESIS OF 7-CYANO-7-DEAZAGUANINE, ONE OF THE NUCLEOSIDE Q (QUEUOSINE) PRECURSORS FOR THE POST-TRANSCRIPTIONAL MODIFICATION OF tRNA (1980)

Abstract 7-Cyano-7-deazaguanine, which is one of the precursors of nucleoside Q (queuosine) biosynthesis, was synthesized from 2-methylthio-6-methoxy-7-methyl-7-deazapurine; methoxymethyl protecting group at 9 position could be removed by transformation to acetoxymethyl group followed by hydrolysis with aq. ammonia.
Early cytomegalovirus infections following allogeneic stem cell transplantation: a comparison between non-malignant and malignant haematological disorders (2010)

The haematological indications for allogeneic stem cell transplantation can be broadly divided into non-malignant and malignant disorders. We compared the incidence and risk factors for post-transplant cytomegalovirus (CMV) infections between these two biologically diverse subgroups of haematological conditions. Out of 105 allogeneic transplants, 64 and 41 were for underlying non-malignant and malignant indications respectively. CMV infections were significantly more frequent (P=0.016) in the malignant subgroup. Pre-transplant recipient CMV seropositivity in both subgroups (negative versus positive; non-malignant,P=0.023; malignant, p<0.001), donor seropositivity (P=0.002) and acute graft-versus-host disease (GVHD) (P=0.02) in the non-malignant subgroup and > or =3 courses of previous cytotoxic therapy (P=0.023) in the malignant subgroup were found to be associated with an increased risk of CMV infections. On multivariate analysis, donor seropositivity in the non-malignant patients (negative versus positive,P=0.022; odds ratio: 0.18) and recipient seropositivity in patients with malignancies (negative versus positive; P=0.001, odds ratio: 0.01) were identified to be significant factors for risk of CMV infection.
Large scale elections by coordinating electoral colleges (1997)

In this paper we propose a truly very large scale voting scheme useful in national and international elections. We offer an implementable solution in which the voting authority is distributed among several voting centres. Each centre acts as an electoral college, carrying out a local scale ballot. The global tally is therefore computed by joining all partial tallies. Our proposal consists on a hierarchical arrangement of the voting centres, strongly based on the use of X.500 Directory Service. Our scheme allows to solve many coordination problems: distribution of voters, coordination of the opening and closing times, management of the electoral roll, distribution of public keys, distribution of partial tallies, and computation of the global tally.
Sizing DB2 UDB ® servers for business intelligence workloads (2004)

Computer system sizing involves estimating the amount of hardware resources needed to support a new application that has not been run in a production environment. Sizing assumes that little system environment information or performance measurements are available for the specific workload, thus a sizing expert must use extrapolations from similar workloads, industry benchmarks, rules-of-thumb, and hardware performance guidelines to determine the type and quantity of resources required. In this paper, we describe a structured approach to size the database tier of a business intelligence (BI) application. We also describe a prototype software tool we created based on the approach. We evaluate the tool using real customer data obtained from IBM and compare its results to the recommendations of a sizing expert.
Delivery setup compatible for in vitro impedance measurements and exposures to electromagnetic fields: nanosecond pulse electric fields and radiofrequency signals (2017)

International audience
Novel functional degradable block copolymers for the building of reactive micelles (2012)

Amphiphilic biocompatible copolymers are promising materials for the elaboration of nanosystems for drug delivery applications. This paper aims at reporting on the synthesis of new functional amphiphilic copolymers based on biocompatible and bioeliminable blocks. Poly(ethylene oxide) was selected as the hydrophilic block, whereas an aliphatic polyester, i.e. poly(ε-caprolactone), or a polycarbonate, i.e. poly(trimethylene carbonate), was chosen as the degradable hydrophobic block. In order to allow a post-functionalization of the micelles core, azide groups were introduced on the hydrophobic segment to provide reactivity towards functional alkyne derivatives by the copper azide–alkyne cycloaddition (CuAAC). For this purpose, a functional lactone, i.e. α-chloro-ε-caprolactone, was introduced during the polymerization of the hydrophobic block before being converted into azide on the preformed copolymer. Such reactivity of the block copolymers and their self-assemblies is of prime interest for drugs or fluorescent dyes grafting, or for the crosslinking of the micelle's core. The influence of the azides distribution along the degradable block on the micelles post-functionalization ability has been studied by using alkyne bearing fluorescent dyes as models for drugs. The hydrophilicity of the dye on the micelles post-functionalization efficiency has also been investigated.
In Vivo Measurement of Blood‐Brain Barrier Permeability (2002)

This unit describes various protocols for the in vivo quantitation of drug permeability across the rodent blood-brain barrier. Methods for the measurement of drug influx and efflux are described, and support protocols are provided for determining intravascular capillary volume and cerebral perfusion flow. An in situ perfusion technique is also provided for assessing whether transport of a test compound occurs by carrier-mediated or saturable transport.
High-speed transparent switch via frequency up-conversion (2006)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text A. P. VanDevender and P. G. Kwiat, "High-speed transparent switch via frequency up-conversion," in Frontiers in Optics, OSA Technical Digest (CD) (Optica Publishing Group, 2006), paper FTuP4. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Structural basis of cholesterol binding by a novel clade of dendritic cell modulators from ticks (2017)

Two crystal structures of Japanin, an 18 kDa immune-modulatory lipocalin from the Brown Ear Tick (Rhipicephalus appendiculatus), have been determined at 2.2 and 2.4 Å resolution. In both crystal forms the protein is in complex with cholesterol, which sits in a closed pocket at the centre of the lipocalin barrel. Both crystal forms are dimers, which are also observed in solution. Molecular modelling suggests that previously-described members of a tick protein family bearing high sequence homology to Japanin are also likely to bind cholesterol or cholesterol derivatives.
Tissue Uptake of Human Sex Hormone-Binding Globulin and its Influence on Ligand Kinetics in the Adult Female Rat1 (1992)

The distribution of human sex hormone-binding globulin (hSHBG) and its influence upon the kinetics of its ligands were assessed in the adult female rat, which lacks a comparable protein in serum. Purified hSHBG was administered i.v. to adult female rats as a single bolus. The plasma disappearance rate of immunoreactive hSHBG had one component with a half-life of 15 h. The estradiol (E2) binding activity of serum attributable to hSHBG was elevated 2-fold; during a continuous infusion of E2, hSHBG increased E2 serum levels above those of control infused animals. Treatment with hSHBG did not modify the plasma clearance of endogenous E2, but accelerated the disappearance rate of 5 alpha-dihydrotestosterone (DHT). In animals injected with a tracer dose of radioactive steroids, pretreatment with hSHBG increased uterine and oviductal accumulation of E2- but not DHT-associated radioactivity. This effect was specific to some E2 target tissues since hSHBG did not alter the concentration of E2- or DHT-associated radioactivity in the hypophysis, liver, diaphragm, or brain. Treatment with anti-E2 antibodies, which elevated E2 binding activity in serum, decreased the accumulation of E2-associated radioactivity in uterus and oviduct. Immunofluorescent localization of hSHBG revealed intense labeling of the uterine and oviductal epithelium. We conclude that this foreign hormone-binding globulin introduced in serum at concentrations that have minimal circulating reservoir effect on E2 can reach intracellular domains and affect the concentration of this ligand in target tissues.
Data from Tissue Inhibitor of Metalloproteinases-1 Promotes Liver Metastasis by Induction of Hepatocyte Growth Factor Signaling (2023)

&lt;div&gt;Abstract&lt;p&gt;Balanced expression of proteases and their inhibitors is one prerequisite of tissue homeostasis. Metastatic spread of tumor cells through the organism depends on proteolytic activity and is the death determinant for cancer patients. Paradoxically, increased expression of tissue inhibitor of metalloproteinases-1 (TIMP-1), a natural inhibitor of several endometalloproteinases, including matrix metalloproteinases and a disintegrin and metalloproteinase-10 (ADAM-10), in cancer patients is negatively correlated with their survival, although TIMP-1 itself inhibits invasion of some tumor cells. Here, we show that elevated stromal expression of TIMP-1 promotes liver metastasis in two independent tumor models by inducing the hepatocyte growth factor (HGF) signaling pathway and expression of several metastasis-associated genes, including &lt;i&gt;HGF&lt;/i&gt; and HGF-activating proteases, in the liver. We also found in an &lt;i&gt;in vitro&lt;/i&gt; assay that suppression of ADAM-10 is in principle able to prevent shedding of cMet, which may be one explanation for the increase of cell-associated HGF receptor cMet in livers with elevated TIMP-1. Similar TIMP-1–associated changes in gene expression were detected in livers of patients with metastatic colorectal cancer. The newly identified role of TIMP-1 to create a prometastatic niche may also explain the TIMP-1 paradoxon. [Cancer Res 2007;67(18):8615–23]&lt;/p&gt;&lt;/div&gt;
Serum testosterone as a prognostic factor in patients with advanced prostatic carcinoma. (1994)

In 245 patients with previously untreated advanced carcinoma of the prostate, serum concentrations of testosterone have been measured before androgen deprivation therapy, and patients were divided in quartiles according to their serum concentration. Pretreatment level of serum testosterone was confirmed as having significant prognostic value on progression-free, overall, and cancer-specific survival, and the hazard ratios of lower quartiles compared to the upper quartile for these endpoints were 2.3, 2.1, and 2.0, respectively. However, correlations with symptomatology and other pretreatment parameters suggest that low serum testosterone merely is a consequence of the advanced malignancy rather than a causative factor in the pathogenesis of prostatic cancer.
The Staphylococcus aureus Transcriptome during Cystic Fibrosis Lung Infection (2019)

Laboratory models have been invaluable for the field of microbiology for over 100 years and have provided key insights into core aspects of bacterial physiology such as regulation and metabolism. However, it is important to identify the extent to which these models recapitulate bacterial physiology within a human infection environment. Here, we performed transcriptomics (RNA-seq), focusing on the physiology of the prominent pathogen <i>Staphylococcus aureus</i><i>in situ</i> in human cystic fibrosis (CF) infection. Through principal-component and hierarchal clustering analyses, we found remarkable conservation in <i>S. aureus</i> gene expression in the CF lung despite differences in the patient clinic, clinical status, age, and therapeutic regimen. We used a machine learning approach to identify an <i>S. aureus</i> transcriptomic signature of 32 genes that can reliably distinguish between <i>S. aureus</i> transcriptomes in the CF lung and <i>in vitro</i> The majority of these genes were involved in virulence and metabolism and were used to improve a common CF infection model. Collectively, these results advance our knowledge of <i>S. aureus</i> physiology during human CF lung infection and demonstrate how <i>in vitro</i> models can be improved to better capture bacterial physiology in infection.<b>IMPORTANCE</b> Although bacteria have been studied in infection for over 100 years, the majority of these studies have utilized laboratory and animal models that often have unknown relevance to the human infections they are meant to represent. A primary challenge has been to assess bacterial physiology in the human host. To address this challenge, we performed transcriptomics of <i>S. aureus</i> during human cystic fibrosis (CF) lung infection. Using a machine learning framework, we defined a "human CF lung transcriptome signature" that primarily included genes involved in metabolism and virulence. In addition, we were able to apply our findings to improve an <i>in vitro</i> model of CF infection. Understanding bacterial gene expression within human infection is a critical step toward the development of improved laboratory models and new therapeutics.
Multi-peptide ELISAs overcome cross-reactivity and inadequate sensitivity of conventional Chlamydia pneumoniae serology (2019)

Cross-reactivity of classical chlamydial antigens compromises Chlamydia (C.) pneumoniae serology. By testing with 185 human antisera, we expanded 18 previously discovered C. pneumoniae-specific B-cell epitopes to 48 peptide antigens from 12 C. pneumoniae immunodominant proteins. For specific detection of antibodies against C. pneumoniae, we developed novel ELISAs with strongly reactive individual peptide antigens and mixtures of these peptides. By comparison to a composite reference standard (CRS) for anti-C. pneumoniae antibody status of human sera, the top-performing CpnMixF12 peptide assay showed 91% sensitivity at 95% specificity, significantly higher than 4 commercial anti-C. pneumoniae IgG ELISAs (36-12% sensitivity at 95% specificity). Human C. pneumoniae (Cpn) and C. trachomatis (Ctr) seroreactivity was 54% biased towards co-positivity in commercial Cpn and Ctr ELISAs, but unbiased in Cpn and Ctr peptide antibody assays, suggesting severe cross-reactivity of commercial ELISAs. Using hyperimmune mouse sera against each of 11 Chlamydia spp., we confirm that commercial Cpn and Ctr ELISA antigens are cross-reactive among all Chlamydia spp., but Cpn and Ctr peptide antigens react only with antisera against the cognate chlamydial species. With simultaneously high specificity and sensitivity, and convenient use for non-specialized laboratories, these ELISAs have the potential to improve serodiagnosis of C. pneumoniae infection.
Open Luxatio Erecta: A Case Report and Literature Review (2011)

Luxatio erecta humeri is a rare clinical entity, comprising 0.5% of all glenohumeral dislocations. Even more uncommon, open luxatio erecta has only been described three times dating back to the 1800s. These cases report poor results including death from sepsis, avascular necrosis, and severely limited motion. We now report a fourth case of open luxatio erecta secondary to a work-related injury.
ChemInform Abstract: Chiral Metal‐Organic Frameworks and Their Application in Asymmetric Catalysis and Stereoselective Separation (2011)

Abstract Review: 64 refs.
Synthesis and Antimicrobial Activity of Nitroalkenyl Arenes (2013)

We report here on the synthesis of substituted nitroalkenyl arenes and their evaluation for microbiological activity and for development as anti-infective drugs. Twenty compounds, based on the nitropropenyl benzene structure (1), were synthesized, chemically characterized and investigated for their minimum inhibitory concentration (MIC) to bacteria and fungi and for toxicity to zebrafish eggs and embryos for comparative evaluation of potential mammalian toxicity. The compounds were broadly antimicrobial, with greater activity overall against Gram-positive bacteria and fungi and less against enteric Gram-negative rods. The antimicrobial activity spectrum of the compounds varied greatly. Two compounds, 14 (5-[(E)-2-nitroprop-1-enyl]-1,3-benzodioxole) and 9 ((4-[(E)-2-nitroprop-1-enyl]-1-fluorobenzene), were the most broadly antimicrobial. The chemical groups most closely associated with microbial toxicity were the β-nitropropenyl side chain, fluoro, methylenedioxy and thiazole substitutions on the benzene ring. Thirteen compounds inhibited hatching of zebrafish eggs at concentrations ≤6 µg/mL. Egg toxicity did not correlate with inhibition of microbial growth or with rodent toxicity where data were available. Four compounds were investigated for effect on zebrafish embryonic development. The major effect observed was reduction of heart rate at 24 h with minimal or no morphological abnormalities at the highest doses. It is hypothesised that this series of compounds act as tyrosine mimetics, inhibiting protein tyrosine phosphatases (PTP) and interfering with cell signaling in microorganisms. The data confirms the diversity in function and distribution of bacterial PTPs and the potential for the design of further nitroalkenyl arenes active against specific pathogens. Keywords: Antibacterial, antifungal, nitropropenyl arenes, structure-activity relationships, tyrosine phosphatase, zebrafish.