bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond
Authors: Scemama Anthony , Caffarel Michel , Oseret Emmanuel , Jalby William 
Published: January 2013

AbstractVarious strategies to implement efficiently quantum Monte Carlo (QMC) simulations for large chemical systems are presented. These include: (i) the introduction of an efficient algorithm to calculate the computationally expensive Slater matrices. This novel scheme is based on the use of the highly localized character of atomic Gaussian basis functions (not the molecular orbitals as usually done), (ii) the possibility of keeping the memory footprint minimal, (iii) the important enhancement of single‐core performance when efficient optimization tools are used, and (iv) the definition of a universal, dynamic, fault‐tolerant, and load‐balanced framework adapted to all kinds of computational platforms (massively parallel machines, clusters, or distributed grids). These strategies have been implemented in the QMC=Chem code developed at Toulouse and illustrated with numerical applications on small peptides of increasing sizes (158, 434, 1056, and 1731 electrons). Using 10–80 k computing cores of the Curie machine (GENCI‐TGCC‐CEA, France), QMC=Chem has been shown to be capable of running at the petascale level, thus demonstrating that for this machine a large part of the peak performance can be achieved. Implementation of large‐scale QMC simulations for future exascale platforms with a comparable level of efficiency is expected to be feasible. © 2013 Wiley Periodicals, Inc.
After the electronic field: Structure, bonding, and the first hyperpolarizability of HArF
Authors: Wu Heng‐Qing , Zhong Rong‐Lin , Kan Yu‐He , Sun Shi‐Ling , Zhang Min , Xu Hong‐Liang , Su Zhong‐Min 
Published: January 2013

AbstractIn this work, we add different strength of external electric field (Eext) along molecule axis (Z‐axis) to investigate the electric field induced effect on HArF structure. The H‐Ar bond is the shortest atEext= −189 × 10−4and the Ar‐F bond show shortest value atEext= 185 × 10−4au. Furthermore, the wiberg bond index analyses show that with the variation of HArF structure, the covalent bond H‐Ar shows downtrend (ranging from0.79 to 0.69) and ionic bond Ar‐F shows uptrend (ranging from 0.04 to 0.17). Interestingly, the natural bond orbital analyses show that the charges of F atom range from −0.961 to −0.771 and the charges of H atoms range from 0.402 to 0.246. Due to weakened charge transfer, the first hyperpolarizability (βtot) can be modulated from 4078 to 1087 au. On the other hand, make our results more useful to experimentalists, the frequency‐dependent first hyperpolarizabilities were investigated by the coupled perturbed Hartree‐Fork method. We hope that this work may offer a new idea for application of noble‐gas hydrides. © 2013 Wiley Periodicals, Inc.
Hydroxylation of 4‐Amino‐5‐hydroxynaphthalene‐2,7‐disulfonic Acid Monosodium Salt Catalysed by Horseradish Peroxidase and Hydrogen Peroxide: Computation of Kinetic Parameters Including Its Application to Crude Plant Extracts
Authors: Krishna Honnur , Nagaraja Padmarajaiah , Shivakumar Anantharaman , Avinash Krishnegowda , Lingaiah Vasanthkumar 
Published: January 2013

AbstractThe new spectrophotometric assay method for the quantification of peroxidase activity uses 4‐amino‐5‐hydroxynaphthalene‐2,7‐disulfonicacid monosodium salt (AHNDSA) as chromogenic co‐substrate. The method is based on hydroxylation of AHNDSA in presence of H2O2/peroxidase forming quinone, having λmax = 460 nm in the acetate buffer (pH = 4.0) at 30 °C.The linearity of H2O2 by kinetic method was 10–332 µM and for peroxidase by kinetic and fixed time methods were 1.18–18.92 and 1.18–9.46 nM, respectively. Catalytic efficiency and catalytic power for peroxidase assay were 7.965 × 104 M−1min−1 and 3.76 × 10−4 min−1, respectively. From the plot of d(1/Ao) vs d(1/Vo) and d(1/Ho) vs d(1/Vo), the apparent Michaelis‐Menten constants for H2O2 and AHNDSA were K = 68 and K = 275 µM, respectively. The method was tested with some plant extracts and also compared with guaiacol/peroxidase system. Except Boerhavia diffusa, all other tested plant samples showed highest peroxidase activity. The proposed method is a rapid and convenient method to determine peroxidase activity by spectrophotometer. This method for the first time reports peroxidase activity in Lantana camara and Oplismenus compositus plants. Kinetic results showed that AHNDSA/peroxidase system can be better hydrogen donor for peroxidase assay than guaiacol system.
Degradation of X‐ray contrast media diatrizoate in different water matrices by gamma irradiation
Authors: Velo Gala Inmaculada , López Peñalver Jesús J. , Sánchez Polo Manuel , Rivera Utrilla José 
Published: January 2013

AbstractBackgroundThis study analyzes the effectiveness of gamma irradiation in removing diatrizoate contrast from different water matrices: ultrapure water, surface water, groundwater and wastewater. The use of gamma irradiation for degradation is influenced by coexisting substances in natural waters and wastewaters. The influence of the presence of anions on the degradation of diatrizoate by gamma irradiation was investigated.ResultsStudy results indicate that: (1) diatrizoate radiolysis fits pseudo‐first‐order kinetics; removal of  91.9% of the diatrizoate was achieved at a dose of 1000 Gy; (2) diatrizoate degradation depends on the type of water matrix, with the radiolysis being affected by the presence of anions, as follows: (i) high concentrations of Cl− increase the efficacy of the process; and (ii) low concentrations of markedly decrease the degradation rate, because nitrite ions act as scavengers of , hydroxyl radical and hydrogen radical; (3) TOC values showed that diatrizoate does not mineralize at a dose of 1000 Gy.ConclusionsRadiolysis degrades diatrizoate by more than 90%; results obtained indicate that it is not mineralized, with TOC values remaining constant in all waters studied. © 2013 Society of Chemical Industry
Effect of thermal processing of cow and buffalo milk on the allergenic response to caseins and whey proteins in mice
Authors: Shandilya Umesh Kumar , Kapila Rajeev , Haq Raies M , Kapila Suman , Kansal VK 
Published: January 2013

AbstractBackgroundHeat treatment is the most common method for reducing pathogen load, but it remains controversial in reducing the incidence of hyperimmune reactions. The aim of this study was to compare the allergenicity of caseins (CSN) and whey proteins (WP) of thermally processed cow and buffalo milk in a mouse model. Swiss albino mice were sensitised by intraperitoneal injections (administered in three doses at weekly intervals) of CSN or WP from cow or buffalo milk for the evaluation of humoral response and splenocyte stimulation index.ResultsAfter 3 weeks of intraperitoneal stimulation of mice with milk proteins, the sterilised milk protein group displayed significantly lowered (P ≤ 0.05) serum IgG and IgE levels, while considerably increased cow milk protein‐specific responses (IgE) were shown by proteins of pasteurised milk compared with those of raw milk. The stimulation index of splenocytes induced by CSN or WP of boiled and sterilised milk was also lower (P ≤ 0.05) than that of raw milk of both cow and buffalo.ConclusionThe experiment showed that boiling and sterilisation of cow and buffalo milk clearly affect the allergenicity by decreasing the humoral and cell‐mediated responses in mice. All results indicated that CSN and WP of sterilised milk are less allergenic than those of raw milk in mice. © 2013 Society of Chemical Industry
Two‐fraction anaerobic fermentation of grass waste
Authors: Maroušek Josef 
Published: January 2013

AbstractBackgroundWaste from public green areas represents large quantities of grassy phytomass. The grass is usually utilised by composting, combustion or anaerobic fermentation. However, the classical composts are time‐demanding, the quality of accelerated composts is low, combustion is under increasing criticism and conventional anaerobic fermentation requires high investment.ResultsA new method of two‐fraction anaerobic fermentation of grass waste consisting from a hot maceration, up‐flow anaerobic sludge blanket reactor, steam explosion, horizontally stirred batch anaerobic fermentors and a charcoal kiln, all run on waste heat from a co‐generation unit was investigated on a commercial scale.ConclusionThe results shows that due to faster energy utilisation the two‐fraction technology requires smaller fermentors and hence the technology is approximately one‐third less costly than conventional systems, with 4 years shorter payback time. Additionally, huge amounts of charcoal are produced. However, the process control and optimisation is more demanding. © 2013 Society of Chemical Industry
Enzyme‐Degradable Self‐Assembled Hydrogels From Polyalanine‐Modified Poly(ethylene glycol) Star Polymers
Authors: Thornton Paul D. , Billah Shah M. Reduwan , Cameron Neil R. 
Published: January 2013

AbstractThe generation of a range of star‐shaped block copolymers composed of a biocompatible poly(ethylene glycol) (PEG) core tethered to a polyalanine (PAla) shell that possesses the capability to (reversibly) self‐assemble in water is described. The hydrogels formed offer a hydrophilic environment ideal for biological processes involving proteins and are able to withhold albumin for prolonged periods before its triggered release following the targeted material degradation by the proteolytic enzyme elastase. Consequently, the materials formed offer significant promise for the delivery of proteins, and possibly inhibitors, in response to a proteolytic enzyme overexpressed in chronic wounds.
Metallkatalysierte dehydrierende Kreuzkupplung
Authors: Tamke Sergej , Paradies Jan 
Published: January 2013

AbstractDie Kreuzkupplung zweier C‐H‐Gruppen ist der effizienteste Weg, um zwei organische Fragmente durch eine C‐C‐Bindung zu verbinden. Retrosynthetisch ist dieser Schnitt widersprüchlich, er bietet jedoch neue Möglichkeiten.
Umweltchemie und die Ängste um die Gesundheit
Authors: Pauls Alfred 
Published: January 2013

AbstractMethodisch fragwürdige epidemiologische Studien am Menschen scheinen Beweise für die Vorhersagekraft toxikologischer Befunde zu liefern. Dabei ist die Dosierung der Chemikalien in den Studien höher als die Exposition der Verbraucher. Nur hochwertige, unabhängige epidemiologische Untersuchungen können belastbare Daten liefern.
The natural radial element method
Authors: Belinha J. , Dinis L.M.J.S. , Natal Jorge R.M. 
Published: January 2013

SUMMARYIn this work an innovative numerical approach is proposed, which combines the simplicity of low‐order finite elements connectivity with the geometric flexibility of meshless methods. The natural neighbour concept is applied to enforce the nodal connectivity. Resorting to the Delaunay triangulation a background integration mesh is constructed, completely dependent on the nodal mesh. The nodal connectivity is imposed through nodal sets with reduce size, reducing significantly the test function construction cost. The interpolations functions, constructed using Euclidian norms, are easily obtained. To prove the good behaviour of the proposed interpolation function several data‐fitting examples and first‐order partial differential equations are solved. The proposed numerical method is also extended to the elastostatic analysis, where classic solid mechanics benchmark examples are solved. Copyright © 2013 John Wiley & Sons, Ltd.
Increased protein intake and meal frequency reduces abdominal fat during energy balance and energy deficit
Authors: Arciero Paul J. , Ormsbee Michael J. , Gentile Christopher L. , Nindl Bradley C. , Brestoff Jonathan R. , Ruby Maxwell 
Published: January 2013

ObjectiveUnrefined, complex carbohydrates and lean protein diets are used to combat obesity, although it's unknown whether more frequent meals may improve this response. The effects of consuming traditional (∼15%) versus higher (∼35%) protein intakes as three or six meals/day on abdominal fat, postprandial thermogenesis (TEM), and cardiometabolic biomarkers in overweight individuals during 28 days of energy balance (BAL) and deficit (NEG), respectively were compared.Design and MethodsOverweight individuals (n = 30) were randomized into three groups: two high‐protein groups (35% of energy) consumed as three (HP3) or six (HP6) meals/day and one group consumed three meals/day of a traditional intake (TD3). Following a 5‐day baseline control (CON), subjects consumed their respective diets throughout a 56‐day intervention consisting of two, 28 day phases: a BAL followed by a NEG phase (75% of energy needs). Total body fat (BF) and abdominal BF (ABF), body weight (BW), TEM, and fasting biomarkers were assessed at the end of CON, BAL, and NEG phases.ResultsBW remained stable throughout CON and BAL in all groups, whereas BF (P < 0.001) and ABF (P < 0.01) decreased in HP groups and lean body mass (LBM) and leptin increased in HP6. Following NEG, BW decreased in all groups. BF, ABF, and leptin decreased in HP groups; LBM remained higher (P < 0.05), and TEM was highest in HP6 (P < 0.05).ConclusionsConsuming increased protein (∼35%) more frequently (6×) throughout the day decreases BF and ABF, increases LBM and TEM, and favorably affects adipokines more than current recommendations for macronutrients consumed over three meals/day in overweight individuals during both BAL and NEG.
Healthcare provider accuracy at estimating women's BMI and intent to provide counseling based on appearance alone
Authors: Evans‐Hoeker Emily A. , Calhoun Kathryn C. , Mersereau Jennifer E. 
Published: January 2013

ObjectiveTo assess healthcare providers' ability to estimate women's body mass index (BMI) based on physical appearance and determine the prevalence of, and barriers to, weight‐related counseling.MethodsA web‐based survey was distributed to healthcare providers (“participants”) at a university‐based hospital and contained photographs of anonymous women (“photographed women (PW)”) as well as questions regarding participant demographics. Participants were asked to estimate BMI category based on physical appearance, state whether they would provide weight‐loss counseling for each PW and identify barriers to counseling.ResultsOne hundred forty‐two participants completed the survey. BMI estimations were poor among all participants, with an overall accuracy of only 41% and a large proportion of underestimations. Standardization of PW clothing did not improve accuracy; 41% for own clothing versus 40% for scrubs, P = 0.2. BMI assessments were more accurate for Caucasian versus African American PW (45% versus 36%, P < 0.001) and PW with normal weight (84%) and obesity III (38%) compared to PW with mid‐range BMI (P < 0.001). Although the frequency of weight loss counseling was positively associated with PW BMI, participants only intended to counsel 69% of overweight and obese PW. The most commonly cited reason for lack of counseling was time constraints (54%).ConclusionsHealthcare providers are inaccurate at appearance‐based BMI categorization and thus, BMI should be routinely calculated in order to improve identification of those in need of counseling. When appropriately identified, time constraints may prevent practitioners from providing appropriate weight‐loss counseling—further complicating the already difficult task of fighting obesity.
Effects of household composition and income security on body weight in working‐age men
Authors: Barnes Michael G. , Smith Trenton G. , Yoder Jonathan K. 
Published: January 2013

ObjectiveMany recent studies have provided evidence suggesting that increases in body weight may spread via social networks. The mechanism(s) by which this might occur have become the subject of much speculation, but to date little direct evidence has been available. Building on evidence from economics, anthropology, and behavioral biology, within‐household peers might influence body weight via implicit provision of income security was hypothesized.Design and MethodsUsing a sample of 2,541 working‐age men from the National Longitudinal Survey of Youth (1979), the effect of cohabitation on weight gain over a 6‐year period was estimated. The potential confound caused by the joint determination of economic insecurity and cohabitation status with instrumental variables that exploit variation in local and state‐level macroeconomic conditions and the presence of children in the home was addressed.ResultsThe marginal effect of cohabitation with adults on body weight is negative. Moreover, the magnitude of the effect is more than six times greater when the cohabitant is engaged in paid employment.ConclusionsIncome insecurity may play an important role in peer‐to‐peer transmission of weight gain.
Combining integrated genomics and functional genomics to dissect the biology of a cancer‐associated, aberrant transcription factor, the ASPSCR1–TFE3 fusion oncoprotein
Authors: Kobos Rachel , Nagai Makoto , Tsuda Masumi , Merl Man Yee , Saito Tsuyoshi , Laé Marick , Mo Qianxing , Olshen Adam , Lianoglou Steven , Leslie Christina , Ostrovnaya Irina , Antczak Christophe , Djaballah Hakim , Ladanyi Marc 
Published: January 2013

AbstractOncogenic rearrangements of the TFE3 transcription factor gene are found in two distinct human cancers. These include ASPSCR1–TFE3 in all cases of alveolar soft part sarcoma (ASPS) and ASPSCR1–TFE3, PRCC‐TFE3, SFPQ‐TFE3 and others in a subset of paediatric and adult RCCs. Here we examined the functional properties of the ASPSCR1–TFE3 fusion oncoprotein, defined its target promoters on a genome‐wide basis and performed a high‐throughput RNA interference screen to identify which of its transcriptional targets contribute to cancer cell proliferation. We first confirmed that ASPSCR1–TFE3 has a predominantly nuclear localization and functions as a stronger transactivator than native TFE3. Genome‐wide location analysis performed on the FU‐UR‐1 cell line, which expresses endogenous ASPSCR1–TFE3, identified 2193 genes bound by ASPSCR1–TFE3. Integration of these data with expression profiles of ASPS tumour samples and inducible cell lines expressing ASPSCR1–TFE3 defined a subset of 332 genes as putative up‐regulated direct targets of ASPSCR1–TFE3, including MET (a previously known target gene) and 64 genes as down‐regulated targets of ASPSCR1–TFE3. As validation of this approach to identify genuine ASPSCR1–TFE3 target genes, two up‐regulated genes bound by ASPSCR1–TFE3, CYP17A1 and UPP1, were shown by multiple lines of evidence to be direct, endogenous targets of transactivation by ASPSCR1–TFE3. As the results indicated that ASPSCR1–TFE3 functions predominantly as a strong transcriptional activator, we hypothesized that a subset of its up‐regulated direct targets mediate its oncogenic properties. We therefore chose 130 of these up‐regulated direct target genes to study in high‐throughput RNAi screens, using FU‐UR‐1 cells. In addition to MET, we provide evidence that 11 other ASPSCR1–TFE3 target genes contribute to the growth of ASPSCR1–TFE3‐positive cells. Our data suggest new therapeutic possibilities for cancers driven by TFE3 fusions. More generally, this work establishes a combined integrated genomics/functional genomics strategy to dissect the biology of oncogenic, chimeric transcription factors. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Left‐sided cryptorchidism in mice with Wilms' tumour 1 gene deletion in gubernaculum testis
Authors: Kaftanovskaya Elena M , Neukirchner Giselle , Huff Vicki , Agoulnik Alexander I 
Published: January 2013

AbstractA significant number of patients with germline mutations in the Wilms' tumour 1 ( WT1) gene, a transcriptional factor essential for early renal and gonadal development, display cryptorchidism or non‐scrotal testis position. We show here that WT1 is expressed during development in the mouse gubernacular ligament connecting the testis to the abdominal wall. Conditional inactivation of Wt1 in the gubernaculum (GU‐WT1KO animals) resulted in abnormal differentiation of the gubernacula during development and, in about 40% of adult males, unilateral, always left‐sided, cryptorchidism. At birth the right testis was positioned above the processus vaginalis and eventually moved into the developing scrotal pouch. In affected mutants the left testis was displaced from the normal position and the left processus vaginalis failed to form. The analysis of testicular descent at different stages of postnatal development suggests that unilateral cryptorchidism might be caused by asymmetry in the positions of the abdominal organs providing a higher degree of mobility for the left testis. Spermatogenesis in GU‐WT1KO animals was blocked in cryptorchid testes located in a high pararenal position, but was maintained in testes located in a low abdominal position. Conditional inactivation of both Wt1 and androgen receptor (Ar) genes in the gubernaculum led to a bilateral asymmetrical cryptorchidism in all mutant males, with the left testis again located higher than the right one. The malformations induced by WT1 and AR deficiency in the gubernaculum and processus vaginalis, in combination with mechanical constraints on testis descent, determine the final position of the testes. In summary, our data indicate that WT1 is directly involved in gubernaculum differentiation. Taken together, the results of the study underline the complex nature of testicular descent, with an involvement in this process of several genetic factors and developmental events. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
An improved circuit model for polymer solar cells
Authors: Gaur Ankita , Kumar Pankaj 
Published: January 2013

ABSTRACTAuthenticity of conventional circuit model, to interpret the characteristics of polymer solar cells (PSCs) is examined. Conventional circuit model is found to be quite limited, and various assumptions used there are not valid for PSCs. By understanding the nature of photovoltaic characteristics, through detailed investigations, we developed an improved circuit model, which explains correctly the behavior of PSCs under different environmental conditions. Investigations are carried out on the solar cells, made of the blend of regioregular poly(3‐hexylethiophene) (P3HT) and phenyl [6,6] C61 butyric acid methyl ester (PCBM). The model is developed by treating both the dark and illuminated characteristics separately, even the characteristics were dealt with separately in reverse and forward biases. The formulated equivalent circuit model helps us in explaining many other important features, observed in the characteristics of PSCs. Copyright © 2013 John Wiley & Sons, Ltd.