bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allostery and conformational free energy changes in human tryptophanyl‐tRNA synthetase from essential dynamics and structure networks
Authors: Bhattacharyya Moitrayee , Ghosh Amit , Hansia Priti , Vishveshwara Saraswathi 
Published: August 2009

AbstractThe interdependence of the concept of allostery and enzymatic catalysis, and they being guided by conformational mobility is gaining increased prominence. However, to gain a molecular level understanding of allostery and hence of enzymatic catalysis, it is of utter importance that the networks of amino acids participating in allostery be deciphered. Our lab has been exploring the methods of network analysis combined with molecular dynamics simulations to understand allostery at molecular level. Earlier we had outlined methods to obtain communication paths and then to map the rigid/flexible regions of proteins through network parameters like the shortest correlated paths, cliques, and communities. In this article, we advance the methodology to estimate the conformational populations in terms of cliques/communities formed by interactions including the side‐chains and then to compute the ligand‐induced population shift. Finally, we obtain the free‐energy landscape of the protein in equilibrium, characterizing the free‐energy minima accessed by the protein complexes. We have chosen human tryptophanyl‐tRNA synthetase (hTrpRS), a protein responsible for charging tryptophan to its cognate tRNA during protein biosynthesis for this investigation. This is a multidomain protein exhibiting excellent allosteric communication. Our approach has provided valuable structural as well as functional insights into the protein. The methodology adopted here is highly generalized to illuminate the linkage between protein structure networks and conformational mobility involved in the allosteric mechanism in any protein with known structure. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Design of multispecific protein sequences using probabilistic graphical modeling
Authors: Fromer Menachem , Yanover Chen , Linial Michal 
Published: August 2009

AbstractIn nature, proteins partake in numerous protein– protein interactions that mediate their functions. Moreover, proteins have been shown to be physically stable in multiple structures, induced by cellular conditions, small ligands, or covalent modifications. Understanding how protein sequences achieve this structural promiscuity at the atomic level is a fundamental step in the drug design pipeline and a critical question in protein physics. One way to investigate this subject is to computationally predict protein sequences that are compatible with multiple states, i.e., multiple target structures or binding to distinct partners. The goal of engineering such proteins has been termed multispecific protein design. We develop a novel computational framework to efficiently and accurately perform multispecific protein design. This framework utilizes recent advances in probabilistic graphical modeling to predict sequences with low energies in multiple target states. Furthermore, it is also geared to specifically yield positional amino acid probability profiles compatible with these target states. Such profiles can be used as input to randomly bias high‐throughput experimental sequence screening techniques, such as phage display, thus providing an alternative avenue for elucidating the multispecificity of natural proteins and the synthesis of novel proteins with specific functionalities. We prove the utility of such multispecific design techniques in better recovering amino acid sequence diversities similar to those resulting from millions of years of evolution. We then compare the approaches of prediction of low energy ensembles and of amino acid profiles and demonstrate their complementarity in providing more robust predictions for protein design. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Regional covariation and its application for predicting protein contact patches
Authors: Xu YongBai , Tillier Elisabeth R. M. 
Published: August 2009

AbstractCorrelated mutation analysis (CMA) is an effective approach for predicting functional and structural residue interactions from multiple sequence alignments (MSAs) of proteins. As nearby residues may also play a role in a given functional interaction, we were interested in seeing whether covarying sites were clustered, and whether this could be used to enhance the predictive power of CMA. A large‐scale search for coevolving regions within protein domains revealed that if two sites in a MSA covary, then neighboring sites in the alignment also typically covary, resulting in clusters of covarying residues. The program PatchD(http://www.uhnres.utoronto.ca/labs/tillier/) was developed to measure the covariation between disconnected sequence clusters to reveal patch covariation. Patches that exhibit strong covariation identify multiple residues that are generally nearby in the protein structure, suggesting that the detection of covarying patches can be used in conjunction with traditional CMA approaches to reveal functional interaction partners. Proteins 2010. © 2009 Wiley‐Liss, Inc.
An oven explosion: Lessons learned on PSM applications
Authors: Cazabon Michael D. , Erickson Kirby 
Published: August 2009

AbstractAn explosion occurred at one of our customer's locations in late 1998 involving unburned and partially burned natural gas while the unit was in high fire mode. Investigation of the incident led to many contributing causes, most of which can be categorized broadly as lack of process safety information, failure of a fuel combustion control system, contractor control and lack of management of change.Combustion systems are found throughout all industries and homes. Code‐based safeguards are thoroughly and adequately described in NFPA. But is the spirit and intent of the code always applied and interpreted safely? Instrumentation application and installation are similarly well described in manufacturer's literature and the ISA standards. But are these systems installed and arranged properly? Is it important to manage change in something as mundane as fuel fired equipment? Is explosion venting on industrial ovens a sound way to limit damage? Is it even possible in all instances? Are there alternatives?This article highlights the investigation activities, answers these questions, presents conclusions and suggests remedies while showing the applicability of PSM concepts to industries other than the CPI.This article will describe, in general terms: the process, critical changes in design, key components involved, applicable codes, discoveries during the investigation and solutions deployed during the rebuild to address these issues. © 2009 American Institute of Chemical Engineers Process Saf Prog 2010
Variations in fish assemblages in a tributary of the upper Paraná River, Brazil: A comparison between pre and post‐closure phases of dams
Authors: Gubiani Éder André , Gomes Luiz Carlos , Agostinho Angelo Antonio , Baumgartner Gilmar 
Published: August 2009

AbstractThis paper purposed to evaluate alterations in fish assemblage (structure and species richness) and variations in the abundance of the most abundant species captured in the Piquiri River, due to the closure of Porto Primavera (in 1998; located upstream the Piquiri River mouth) and the Itaipu (in 1982; located downstream) dams in the upper Paraná River. The effects of selected environmental variables were also determined. Fishes were sampled during four distinct periods. Six samplings were conducted in each period, at two different sites (Campina and Apertado). For sampling, gill and trammel nets were used. Species abundances were indexed by catch per unit of effort. Spatial and temporal changes in environmental variables were summarized by a principal components analysis (PCA). To summarize structure of the assemblage, a nonmetric multidimensional scaling (NMS) was used. To test the significance of between‐group differences at each periods and sites we used a multiresponse permutation procedure (MRPP). To test the association between fish assemblage and the environmental variables matrices, we used procrustean superimposition approach. A total of 2693 individuals were caught, belonging to 69 species, 4 orders and 19 families. Species richness differed spatially; the Campina site had greater mean richness (13) per sampling than the Apertado site (10). The structure of the fish assemblages showed significant temporal and spatial variations, which were more evident in the last period at the Apertado site (after the closure of Porto Primavera Dam). Spatial and temporal changes in structure of fish assemblages were not associated to environmental variables. Temporal changes in abundance, both in number and in weight, of the most abundant species were verified in both sites. The lack of migratory species was highlighted, which sharply decreased in the last studied period, when they were replaced by sedentary species. These findings appear to be related to regional factors, such as the decrease of floods registered in the upper Paraná basin, exacerbated by the control prompted by dams. Copyright © 2009 John Wiley & Sons, Ltd.
Estimating spawning habitat availability in flooded areas of the river Waal, the Netherlands
Authors: van de Wolfshaar K. E. , Ruizeveld de Winter A. C. , Straatsma M. W. , van den Brink N. G. M. , de Leeuw J. J. 
Published: August 2009

AbstractFish spawning habitat availability in the river Waal is significantly influenced by seasonal and annual variations in discharge. In this paper we develop habitat suitability models, based on a literature survey of spawning preferences of the commonly occurring species roach (Rutilus rutilus), bream (Abramis brama), pikeperch (Sander lucioperca) and bleak (Alburnus alburnus). Within the resulting models water depth, flow velocity, water temperature and vegetation type were the most significant environmental parameters. Spatial data for the parameters were derived from a 2‐D hydrodynamic model and detailed monitoring database. The area of suitable habitat available for spawning was calculated using the HABITAT software, based on species‐specific suitability models and the environmental characteristics of two study sites on the river Waal over a 3 year period (1997–1999). The predicted available spawning area was compared with field data on the recruitment of young fish of each species for the same years and locations. There was a positive relationship between predicted available habitat and observed young of the year (YOY) densities for bream, roach and pikeperch. A negative relationship was recorded between predicted available area and observed YOY densities for bleak. The results indicate that optimal hydrological and hydraulic conditions differ even for species that are widely considered eurytopic. Moreover, annual differences in habitat availability indicate a strong influence of hydrological variability on population dynamics. Copyright © 2009 John Wiley & Sons, Ltd.
Endometrial blood flow is impaired in women with polycystic ovarian syndrome who are clinically hyperandrogenic
Authors: Lam P. , Johnson I. , Raine‐Fenning N. 
Published: August 2009

AbstractObjectivesTo quantify endometrial and subendometrial blood flow in Caucasian women with polycystic ovarian syndrome (PCOS) and to determine whether these values differ according to the phenotypic expression of PCOS.MethodsTransvaginal pelvic ultrasound was performed on the 3rd–5th day of the menstrual cycle in 36 women with PCOS and 36 controls to examine the endometrial and subendometrial vascularity. The subendometrial and endometrial blood flow indices (vascularizaton index (VI), flow index (FI) and vascularization flow index (VFI)) were measured using three‐dimensional power Doppler angiography. Uterine artery blood flow was assessed through analysis of two‐dimensional (2D) pulsed‐wave Doppler waveforms. Analysis was performed to compare PCOS with non‐PCOS women, and subgroup analysis was performed of the PCOS women categorized according to their phenotypic manifestation.ResultsThere were no significant differences in endometrial volume, subendometrial vascularity and uterine artery blood flow between women with PCOS and controls after controlling for body mass index (BMI). On subgroup analysis, compared with anovulatory but clinically normoandrogenic women with polycystic ovaries (PCO) and with controls, women with PCO who were both clinically hyperandrogenic and anovulatory had significantly lower endometrial (VI: 0.57% vs. 1.11% and 0.86%, respectively, both P = 0.01; VFI: 0.14 vs. 0.42 and 0.28, respectively, both P = 0.02) and subendometrial (VI: 1.59% vs. 3.17% and 2.47%, P = 0.01 and 0.02, respectively; VFI: 0.50 vs. 1.67 and 0.96, P = 0.01 and 0.02, respectively) blood flow. Moreover, clinically hyperandrogenic but ovulatory women with PCO also had significantly lower endometrial blood flow (VI: 0.52% vs. 1.11%, P = 0.04) than did anovulatory but clinically normoandrogenic women with PCO. There were no differences in any of the 2D pulsed‐wave Doppler measures of blood flow between the subgroups.ConclusionsSubendometrial and endometrial blood flow is significantly impaired in women with PCOS who have clinical signs of hyperandrogenism. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Fabrication of Carbon Nanotube/SiO2and Carbon Nanotube/SiO2/Ag Nanoparticles Hybrids by Using Plasma Treatment
Authors: Li Haiqing , Ha Chang-Sik , Kim Il 
Published: August 2009

Abstract
Based on plasma-treated single wall carbon nanotubes (SWCNTs), SWCNT/SiO2and thiol groups-functionalized SWCNT/SiO2hybrids have been fabricated through a sol–gel process. By means of thiol groups, Ag nanoparticles have been in situ synthesized and bonded onto the SiO2shell of SWCNT/SiO2in the absence of external reducing agent, resulting in the stable carbon nanotube/SiO2/Ag nanoparticles hybrids. This strategy provides a facile, low–cost, and green methodology for the creation of carbon nanotube/inorganic oxides-metal nanoparticles hybrids.
Physical and psychosocial functioning following motor vehicle trauma: Relationships with chronic pain, posttraumatic stress, and medication use
Authors: Clapp Joshua D. , Masci Jarod , Bennett Shira A. , Beck J. Gayle 
Published: August 2009

ABSTRACTChronic pain and PTSD are known to hold substantial comorbidity following traumatic injury. Although pharmacological agents have been examined in the treatment of pain and PTSD individually, little is known regarding the relationship of medication use with functioning in patients with comorbid conditions. This research examined the relationships of pain, PTSD, and medication use across physical and psychosocial functioning in patients with chronic pain following motor vehicle injury (N=234). Separate analyses were conducted for opioids, SSRIs, and sedative/anxiolytics, respectively. Several relevant effects were noted: (1) Pain evidenced strong associations with reduced functioning across both physical and psychosocial domains, (2) Opioid use held interactive relationships with PTSD across both functioning domains. Specifically, opioids were associated with greater physical impairment in patients without comorbid PTSD. Opioids also were related to greater psychosocial impairment in patients without PTSD while PTSD was associated with greater impairment in patients not using opioids, (3) Opioid use evidenced a marginal interaction with pain on psychosocial functioning. Opioids were associated with greater psychosocial impairment among patients with high‐pain, and high‐pain was associated with greater impairment among opioid users, (4) SSRIs held a marginal interaction with PTSD such that PTSD was related to poorer psychosocial functioning only among individuals not using an SSRI, and (5) Anxiolytic use evidenced a marginal interaction with PTSD on physical functioning although no between‐group differences were noted. These data suggest that PTSD symptomology may be an important consideration in determining treatment modality for patients experiencing pain subsequent to traumatic injury.
Effect of capsinoids on energy metabolism in human subjects
Authors: Galgani Jose E. , Ryan Donna H. , Ravussin Eric 
Published: August 2009

Capsinoids are non-pungent compounds with molecular structures similar to capsaicin, which has accepted thermogenic properties. To assess the acute effect of a plant-derived preparation of capsinoids on energy metabolism, we determined RMR and non-protein respiratory quotient (NPRQ) after ingestion of different doses of the capsinoids. Thirteen healthy subjects received four doses of the capsinoids (1, 3, 6 and 12 mg) and placebo using a crossover, randomised, double-blind trial. After a 10 h overnight fast as inpatients, RMR was measured by indirect calorimetry for 45 min before and 120 min after ingesting capsinoids or placebo. Blood pressure and axillary temperature were measured before ( − 55 and − 5 min) and after (60 and 120 min) dosing. Before dosing, mean RMR was 6247 (se92) kJ/d and NPRQ was 0·86 (se0·01). At 120 min after dosing, metabolic rate and NPRQ remained similar across the four capsinoids and placebo doses. Capsinoids also had no influence on blood pressure or axillary temperature. Capsinoids provided in four doses did not affect metabolic rate and fuel partitioning in human subjects when measured 2 h after exposure. Longer exposure and higher capsinoids doses may be required to cause meaningful acute effects on energy metabolism.
Prevalence and risk factors for obesity in Balearic Islands adolescents
Authors: Bibiloni Maria del Mar , Martinez Elisa , Llull Rosa , Juarez Maria Daniela , Pons Antoni , Tur Josep A. 
Published: August 2009

The aim of this work was to assess the prevalence and risk factors of obesity in the Balearic Islands' adolescents. A cross-sectional nutritional survey was carried out in the Balearic Islands (2007–2008). A random sample (n1231) of the adolescent population (12–17 year old) was interviewed. Anthropometric measurements, two non-consecutive 24 h recalls and a general questionnaire incorporating questions related to sociodemographic and lifestyle variables including the physical activity questionnaire were used. The prevalence of overweight was 19·9 % (boys) and 15·5 % (girls), and obesity 12·7 % (boys) and 8·5 % (girls). The main risk factors associated with a higher prevalence of obesity were low parental education level (boys OR: 3·47; 95 % CI: 1·58, 7·62; girls OR: 3·29; 95 % CI: 1·38, 7·89), to skip meals (boys OR: 4·99; 95 % CI: 2·1, 11·54; girls OR: 2·20; 95 % CI: 0·99, 4·89), age (12–13-year-old boys; OR: 2·75; 95 % CI: 1·14, 6·64), attention to mass media (television (TV)+radio; boys OR: 1·50; 95 % CI: 0·81, 2·84; girls OR: 2·06; 95 % CI: 0·91, 4·68), short sleep (boys OR: 3·42; 95 % CI: 0·88, 13·26), low parental socioeconomic status (girls OR: 3·24, 95% CI: 1·04, 10·05 ) and smoking (girls OR: 2·51; 95 % CI: 0·88, 7·13). A programme of action including school healthy education and promotion programmes targeted at parents and adolescents are needed. These programmes may be mainly focused to increase educational level, to make the adolescents to be aware of to skip meals and to smoke are not appropriate methods to reduce the risk of obesity, but the usefulness is to do not eat while watching TV, to sleep 8–10 h/d and to be physically active.
Chinese tea consumption is associated with longer telomere length in elderly Chinese men
Authors: Chan Ruth , Woo Jean , Suen Eddie , Leung Jason , Tang Nelson 
Published: August 2009

Environmental and lifestyle factors that affect oxidative stress and inflammation may influence telomere length (TL). There are limited data to relate the effect of dietary components on TL. The present study examined the association between food groups and TL in a sample of elderly Chinese. In a sample of 2006 Chinese (976 men and 1030 women) aged 65 years and over, TL was measured by quantitative real-time PCR and daily intake of food groups was assessed by a validated FFQ. Linear regression and analysis of covariance were used to examine the association between food group intake and TL, with adjustment for demographic and lifestyle factors. In men, only Chinese tea consumption was significantly associated with TL after adjustment for demographics and lifestyle factors (P = 0·002). Mean difference in TL for those in the highest quartile of Chinese tea consumption (>3 cups/d or >750 ml/d) as compared with those in the lowest quartile of Chinese tea consumption ( ≤ 0·28 cups/d or ≤ 70 ml/d) was 0·46 kb, corresponding to approximately a difference of 5 years of life. In women, intake of fats and oils was borderline and negatively associated with TL after adjustment for demographic and lifestyle factors (P = 0·037). In conclusion, Chinese tea consumption was positively associated with TL in elderly Chinese men.
The cereal rust miteAbacarus hystrix(Acari: Eriophyoidea) is a complex of species: evidence from mitochondrial and nuclear DNA sequences
Authors: Skoracka A. , Dabert M. 
Published: August 2009

AbstractThe cereal rust miteAbacarus hystrix(Nalepa), a significant pest of grasses, has been regarded as one of a few exceptions among eriophyoid mites with reference to the pattern of host plant utilization. At least 60 grass species have been recorded as its hosts. Thus, the mite has long been considered as a host generalist in which host specialization would not be likely to evolve. However, recent studies have revealed that host-associated specialization is possible inA. hystrix. Here, we aimed to discriminate between the three populations ofA. hystrixassociated with the different hosts (namely quackgrass, ryegrass and smooth brome) on the basis of mitochondrial (COI) and nuclear (D2 region of 28S rDNA) DNA sequences. The phylogenetic trees obtained with the maximum likelihood analysis of both COI and D2 region data sets showed that host-adapted strains ofA. hystrixform distinct clades. Furthermore, on the COI nucleotide tree, the quackgrass- and brome-associated strains were internally divided each into two well-supported monophyletic clusters. The nucleotide D2 region data set tree showed that brome-associated strain is polyphyletic in origin. There is clear co-variation of DNA results with earlier morphological and ecological traits, as well as the results of crossing experiments. We showed that reproductively incompatible strains ofA. hystrixexhibit more than 20% sequence divergence in the COI gene and 0.2% sequence divergence in the D2 28S rDNA. Our results did not confirm the placement of three host-associated strains ofA. hystrixwithin one, ostensibly generalist, species.