gebhart/patrepeval huggingface dataset:
Gene-environment interaction testing in family-based association studies with phenotypically ascertained samples: a causal inference approach (2011)

We propose a method for testing gene-environment (G × E) interactions on a complex trait in family-based studies in which a phenotypic ascertainment criterion has been imposed. This novel approach employs G-estimation, a semiparametric estimation technique from the causal inference literature, to avoid modeling of the association between the environmental exposure and the phenotype, to gain robustness against unmeasured confounding due to population substructure, and to acknowledge the ascertainment conditions. The proposed test allows for incomplete parental genotypes. It is compared by simulation studies to an analogous conditional likelihood-based approach and to the QBAT-I test, which also invokes the G-estimation principle but ignores ascertainment. We apply our approach to a study of chronic obstructive pulmonary disorder.
Relative Efficiency of Haplotype Frequency Estimation in Sibships and Nuclear Families Compared to Unrelated Individuals (2007)

The problem of estimating haplotype frequencies from unphased single nucleotide polymorphism (SNP) genotype data in sibships with and without parents is considered. We focus on the Fisher information of the haplotype frequencies of the parents in order to correctly deal with the dependence of haplotypes within sibships. We compare these Fisher information matrices with those obtained for unrelated individuals and study the relative efficiency of sibships with and without parents compared to unrelated individuals in estimating haplotype frequencies. Crudely summarizing, the second sib contributes half the information of the first, except for rare haplotypes, when the second sib counts almost as one. We argue that the relative efficiencies can also be used to correct for dependence in the calculation of standard errors after initially ignoring the dependence in the estimation phase.
Some observations on seed quality and mitochondrial performance. (2003)

This chapter discusses the results of studies on mitochondrial functions during the germination of legume seeds, using pea (cv. Baccara) as the initial material. Mitochondrial integrity and oxidative properties were observed to improve during imbibition of pea seeds, with energy transduction relying mainly on cytosol NADH and succinate oxidation.
M-ary symbol error outage over Nakagami-m fading channels in shadowing environments (2009)

This letter addresses the problem of finding a tractable expression for the symbol error outage (SEO) in flat Nakagami-m fading and shadowing channels. We deal with M-ary phase shift keying (M-PSK) and quadrature amplitude modulation (M-QAM) which extends our previous results on BPSK signaling. We propose a new tight approximation of the symbol error probability (SEP) holding for M-PSK and M-QAM signals which is accurate over all signal to noise ratios (SNRs) of interest. We derive a new generic expression for the inverse SEP which facilitates the derivation of a tight approximation of the SEO in a lognormal shadowing environment.
Thwarting Dyskinesia by Targeting mTORC1 (2009)

In a mouse model of Parkinson's disease, new evidence shows that l-DOPA, which is used to treat the symptoms of the disease but also causes dyskinesia, results in a persistent activation of the protein kinase mTOR (mammalian target of rapamycin) in a subset of striatal medium spiny neurons. Moreover, blockade of a specific type of mTOR signaling (mTORC1) prevents the development of dyskinesia, but not the antiakinetic benefits produced by l-DOPA. Thus, mTORC1 may be a viable therapeutic target for dyskinesia caused by l-DOPA treatment in patients with Parkinson's disease.
<title>Dynamic focusing approach to mixed-level simulation</title> (1997)

The dynamic focusing approach (DFA) has been under development for several years. Its intent is to address several of the issues of mixed level simulations, particularly the aggregational issues. Though the approach requires that the system be able to be modeled within certain constraints, many systems of interest fit well within them. This approach combines a hierarchical representation of knowledge with a stochastic propagation mechanism; this provides capability to gracefully move from coarse granularity to fine granularity under user guidance. Prototype tools have been developed for engineering analysis, combat simulation and TQM process implementation. This paper gives an overview of the approach and its current status.
Effect of Re and Ru Addition on the Solidification and Solute Redistribution Behaviors of Ni-Base Superalloys (2011)

The influence of rhenium (Re) and ruthenium (Ru) addition on the solidification and solute redistribution behaviors in advanced experimental Ni-base superalloys has been investigated. A series of model alloys with different levels of Re and Ru were designed based on the composition of Ni-6Al-8Ta and were prepared by vacuum arc melting of pure metallic elements. In order to identify the influence of Re and Ru addition on the thermo-physical properties, differential scanning calorimetry analyses were carried out. The results showed that Re addition marginally increases the liquidus temperature of the alloy. However, the γ' solvus was significantly increased at a rate of 8.2°C/wt.% by the addition of Re. Ru addition, on the other hand, displayed a much weaker effect on the thermo-physical properties or even no effect at all. The microsegregation behavior of solute elements was also quantitatively estimated by an electron probe microanalysis on a sample quenched during directional solidification of primary γ with the planar solid/liquid interface. It was found that increasing the Re content gradually increases the microsegregation tendency of Re into the dendritic core and γ' forming elements, such as Al and Ta, into the interdendritic area. The strongest effect of Ru addition was found to be Re segregation. Increasing the Ru content up to 6 wt.% significantly alleviated the microsegregation of Re, which resulted in a decrease of Re accumulation in the dendritic core. The influence of Ru on the microstructural stability toward the topologically close-packed phase formation was discussed based on Scheil type calculations with experimentally determined microsegregation results.
The crystal structure of <i>Pyrococcus furiosus</i> ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures (1998)

The Pyrococcus furiosus (PF) ornithine carbamoyltransferase (OTCase; EC 2.1.3.3) is an extremely heat-stable enzyme that maintains about 50% of its activity after heat treatment for 60 min at 100 degrees C. To understand the molecular basis of thermostability of this enzyme, we have determined its three-dimensional structure at a resolution of 2.7 A and compared it with the previously reported structures of OTCases isolated from mesophilic bacteria. Most OTCases investigated up to now are homotrimeric and devoid of allosteric properties. A striking exception is the catabolic OTCase from Pseudomonas aeruginosa, which is allosterically regulated and built up of four trimers disposed in a tetrahedral manner, an architecture that actually underlies the allostery of the enzyme. We now report that the thermostable PF OTCase (420 kDa) presents the same 23-point group symmetry. The enzyme displays Michaelis-Menten kinetics. A detailed comparison of the two enzymes suggests that, in OTCases, not only allostery but also thermophily was achieved through oligomerization of a trimer as a common catalytic motif. Thermal stabilization of the PF OTCase dodecamer is mainly the result of hydrophobic interfaces between trimers, at positions where allosteric binding sites have been identified in the allosteric enzyme. The present crystallographic analysis of PF OTCase provides a structural illustration that oligomerization can play a major role in extreme thermal stabilization.
CTH10-1: Optimization of Coding Gain for Full-Response CPM Space-Time Codes (2006)

Conditions are derived under which M-ary full-response CPM space-time codes will attain full spatial diversity and optimal coding gain. General code construction rules are desirable due to the nonlinearity and inherent memory of CPM signals which make manual design or computer search difficult. Optimization of the coding gain for CPM space-time codes is shown to depend on the CPM frequency/phase shaping pulse, modulation index, and codewords. The modulation indices and phase shaping functions that optimize the coding gain are specified. Finally, optimization of ST-CPM codewords is discussed.
Reduced Cardioprotective Action of Adiponectin in High-Fat Diet–Induced Type II Diabetic Mice and Its Underlying Mechanisms (2010)

Diabetes exacerbates ischemic heart disease morbidity and mortality via incompletely understood mechanisms. Although adiponectin (APN) reduces myocardial ischemia/reperfusion (MI/R) injury in nondiabetic animals, whether APN's cardioprotective actions are altered in diabetes, a pathologic condition with endogenously reduced APN, has never been investigated. High-fat diet (HD)-induced diabetic mice and normal diet (ND) controls were subjected to MI via coronary artery ligation, and given vehicle or APN globular domain (gAPN, 2 μg/g) 10 min before reperfusion. Compared to ND mice (where gAPN exerted pronounced cardioprotection), HD mice manifested greater MI/R injury, and a tripled gAPN dose was requisite to achieve cardioprotective extent seen in ND mice (i.e., infarct size, apoptosis, and cardiac function). APN reduces MI/R injury via AMP-activated protein kinase (AMPK)-dependent metabolic regulation and AMPK-independent antioxidative/antinitrative pathways. Compared to ND, HD mice manifested significantly blunted gAPN-induced AMPK activation, basally and after MI/R (p<0.05). Although both low- and high-dose gAPN equally attenuated MI/R-induced oxidative stress (i.e., NADPH oxidase expression and superoxide production) and nitrative stress (i.e., inducible nitric oxide synthase expression, nitric oxide production, and peroxynitrite formation) in ND mice, only high-dose gAPN efficaciously did so in HD mice. We demonstrate for the first time that HD-induced diabetes diminished both AMPK-dependent and AMPK-independent APN cardioprotection, suggesting an unreported diabetic heart APN resistance.
A New Cembranolide from the Soft Coral <i>Sinularia capillosa</i> (2000)

A new cembranolide, capillolide (1), and three known cembranolides were isolated from the soft coral Sinularia capillosa collected from the South China Sea. Their structures and the relative stereochemistry of 1 were deduced on the basis of spectroscopic methods.
CB1 and TRPV1 receptors mediate protective effects on electrophysiological properties during colonic inflammation (2005)

Aims: CB1 and TRPV1 receptors modulate enteric neurotransmission and colonic inflammation in the GI-tract. Colitis was shown to be more fulminant in CB1-/- and TRPV1-/- mice. Aim: The aim of the present study was to investigate electrophysiological changes on resting membrane potential (RMP) and enteric neurotransmission in inflamed distal colon of mice and additionally in receptor deficient mice which are more susceptible to colitis. Methods: Colitis was induced with DNBS. Electrophysiological properties were evaluated at 8 and 24 hours after DNBS treatment. Intracellular recording techniques were used to record RMP and colonic smooth muscular membrane potentials following electrical field stimulation of enteric nerves. A histological score was evaluated in CB1+/+ and CB1-/- mice. Results: RMP of uninflamed wild-type mice displayed a stable RMP of 51.6±0.9 mV which was not significantly changed at any stage of inflammation in any genetic background. However, inflammation caused spontaneous rhythmic action potential generation in the treated CB1-/- mice and in treated TRPV1-/- mice but not in treated wild-type animals. Focal electrical stimulation of the myenteric plexus induced inhibitory junction potentials (IJP) in the smooth muscle cells. 24 hours after initiation of inflammation, the duration of the IJP was significantly prolonged in all treated mice. Additionally, IJP duration in CB1-/- mice was significantly prolonged as compared to CB1±mice. Amplitude of IJP remained unchanged at any stage of inflammation. Inflammation score increased in treated mice, but did not show a significant difference between CB1+/+ and CB1-/- mice at early colitis stages. Conclusions: We revealed that inflammation of the mouse colon causes changes in electrophysiological properties and these changes correlate with duration and severity of colitis. In mutants where colitis was shown to be more fulminant in the long-term, the electrophysiological differences display a different pattern. Since histological scores were not found to be different at the early time points investigated, our findings argue for a protective effect of these receptors primarily on electrophysiological properties at an early stages after insult, but not on inflammatory responses.
Reformable intramolecular cross‐linking of the N‐terminal domain of heparin cofactor II (2004)

The crystal structure of a heparin cofactor II (HCII)-thrombin Michaelis complex has revealed extensive contacts encompassing the N-terminal domain of HCII and exosite I of the proteinase. In contrast, the location of the N-terminal extension in the uncomplexed inhibitor was unclear. Using a disulfide cross-linking strategy, we demonstrate that at least three different sites (positions 52, 54 and 68) within the N terminus may be tethered in a reformable manner to position 195 in the loop region between helix D and strand s2A of the HCII molecule, suggesting that the N-terminal domain may interact with the inhibitor scaffold in a permissive manner. Cross-linking of the N terminus to the HCII body does not strongly affect the inhibition of alpha-chymotrypsin, indicating that the reactive site loop sequences of the engineered inhibitor variants, required for interaction with one of the HCII target enzymes, are normally accessible. In contrast, intramolecular tethering of the N-terminal extension results in a drastic decrease of alpha-thrombin inhibitory activity, both in the presence and in the absence of glycosaminoglycans. Treatment with dithiothreitol and iodoacetamide restores activity towards alpha-thrombin, suggesting that release of the N terminus of HCII is an important component of the multistep interaction between the inhibitor and alpha-thrombin.
Effects of T3R alpha 1 and T3R alpha 2 gene deletion on T and B lymphocyte development (2000)

International audience
Strontium exerts dual effects on calcium phosphate cement: Accelerating the degradation and enhancing the osteoconductivity both <i>in vitro</i> and <i>in vivo</i> (2014)

Calcium phosphate cements (CPCs) have long been used as osteoconductive bone substitutes in the treatment of bone defects. However, the degradation rate of CPC is typically too slow to match the new bone growth rate. It is known that strontium increases the solubility of hydroxyapatite as well as exerts both anabolic and anticatabolic effects on bone. Therefore, we hypothesized that the incorporation of strontium would accelerate the degradation rate and enhance the osteoconductivity of CPC. In this study, Three groups, CPC (0% Sr-CPC), 5% Sr-CPC, and 10% Sr-CPC, were prepared, with the total molar ratio for Sr/(Sr+Ca) in the cement powder phase being 0, 5, and 10%, respectively. In the immersion test, less residual weight was observed in both 5% Sr-CPC and 10% Sr-CPC groups than CPC group. In addition, a higher osteoblastic cell proliferation rate and alkaline phosphatase activity were obtained in the strontium groups. In a rat femur bone defect model comparing CPC with 10% Sr-CPC, at 2 weeks postoperation, early endochondral ossification was found in the 10% Sr-CPC group, whereas only fibrous tissue was observed in control group; at 4-16 weeks postoperation, progressive osteoconduction toward the cement was observed in both groups. At 32 weeks, a higher peri-cement bone area and reduced cement area were noted in the 10% Sr-CPC group. In conclusion, in the 10% Sr-CPC group, strontium exerts dual effects on CPC: accelerating degradation rate and enhancing osteoconductivity, as shown here both in vitro and in vivo.
Progressive texture video coding (2002)

We present a novel video coding approach which provides the functionality of fine granular bitstream scalability. The proposed progressive texture video coding (PTVC) scheme consists of two parts: the current ITU-T H.26L test model for coding macroblock mode and motion information only; a new technique for progressively coding all intra and inter texture information thus providing an embedded bitstream. It can still be decoded with moderate quality degradation in case of partial loss of the bitstream. It is therefore well suited for multicast or broadcast scenarios where time varying or different fixed bitrates are provided to the clients, as no transcoding or multiple coding process is required.
Choosing the data flow paradigm for EUV mask process corrections (2012)

When compared to conventional chrome absorber masks, electron beam patterning of EUV masks requires additional corrections to account for electron backscattering from the mirror and tantalum (Ta) based absorber layers. Current ebeam systems cannot correct for these additional backscattering effects with in-tool proximity effect correction (PEC) algorithms. Hence new methods of correction are needed, which require an implementation of the correction into the mask writer data prior to exposure. Where these corrections should be performed in the data flow between mask user and mask supplier, and who should calibrate and maintain the corrections is not clear. We present various approaches for model calibration as well as discuss the possible options for inserting mask process correction (MPC) into the mask process landscape. We report on an attempt to calibrate a correction for EUV masks using actual CD data, and an e-beam backscattering model. The resulting Point Spread Functions (PSF) were used to simulate and predict the measured CD data. We also explored the robustness of these models by varying the writing tool and mask blank characteristics. We conclude by recommending an appropriate flow for calibration and use of mask process correction and ownership of the model calibration, maintenance and the data correction processes.
Structural tuning and self-association of (arylimido)vanadium(V) compounds (2009)

Structural tuning and self-association of (arylimido)vanadium(V) compounds are demonstrated to be controlled through π-conjugation by the para -substituents of the aryl moieties.
ChemInform Abstract: Vinyl Carbanions. Part 36. Synthesis of 3‐Deoxy‐D‐manno‐2‐octulosonic Acid (KDO) and Derivatives. (1989)

Abstract The title compound KDO (VIII), an integral constituent of the lipopolysaccharide of Gram‐negative bacteria, as well as the KDO derivatives (IX), a valuable starting material for the KDO α‐glycoside synthesis, and other KDO derivatives are prepared starting from the pyruvate acetal (I).
Left ventricle remodelling is associated with sleep‐disordered breathing in non‐ischaemic cardiopathy with systolic dysfunction (2010)

Sleep-disordered breathing (SDB) is associated with left ventricle (LV) remodelling in patients with normal LV function. Sleep-disordered breathing is common in chronic heart failure (CHF) with systolic LV dysfunction, and may contribute to LV remodelling and CHF progression. Our aim was to determine the consequence of SDB on LV geometry in patients with CHF. We hypothesised that SDB severity was correlated with the degree of LV hypertrophy (LVH). One-hundred and sixty patients with CHF with a non-ischaemic systolic LV dysfunction were assessed by overnight polygraphy and echocardiography. Patients were classified in four groups according to their apnoea-hypopnoea index (AHI): <5 (no-SDB); 5-14 (mild); 15-29 (moderate); ≥30 (severe). Left ventricular mass index (LVM Ind) was calculated using the usual echocardiographic M-Mode parameters. Their mean age, New York Heart Association and left ventricular ejection fraction were, respectively: 56 ± 13 years, 2.4 ± 0.8 and 30 ± 10%, and 77% were men. Body mass index, interventricular septal and posterior LV wall thicknesses, and LVM Ind were significantly increased in severe SDB versus no-SDB. LVM Ind was correlated to the AHI (R = 0.27, P = 0.0006) and, using logistic regression, AHI was the unique independent factor of LVH in this population. In non-ischaemic CHF, SDB severity is associated with LV remodelling.
Definition and acquisition of CM and DM EMI noise for general-purpose adjustable speed motor drives (2004)

Separating conducted EMI noise into different modes, common mode (CM) and differential mode (DM), is important to the appropriate application of emission reduction techniques. While the CM/DM separation is well defined and understood for the single-phase or DC system, the same cannot be said for three-phase converter systems, common for general-purpose adjustable speed drives (ASD). Based on the study of CM and DM propagation characteristics of a three-phase diode-front converter, this paper identify different noise modes for different front-diode conducting patterns. The impact on EMI filter components by these noise modes is summarized. Finally, a time-domain based method is proposed to separate and acquire CM and DM noise components for the diode-front three-phase systems. Simulation and experimental verifications are presented.
A European CDC? (2005)

I nfectious diseases have made an unfortunate comeback. After the Second World War, the development of new vaccines and discoveries of efficient antibiotics meant to many that lethal infectious disorders were enemies of the past. But, not surprisingly, nature has hit back. We now face an increasing
C.W. and flash photoelectrolysis of water using ferroelectric photoanodes (1980)

Abstract Most of the photoeffects in ferroelectrics (e.g., optical storage, photorefractive devices) are basically determined by a photovoltaic effect which ensures a charge transfer process.1,2