bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synergistic use of NMR and MD simulations to study the structural heterogeneity of proteins
Authors: Esteban‐Martín Santiago , Bryn Fenwick Robert , Salvatella Xavier 
Published: April 2012

AbstractNuclear magnetic resonance spectroscopy (NMR) and molecular dynamics (MD) simulations are powerful techniques for the structural characterization of macromolecules. NMR is unique in its ability to provide experimental information at atomic level on the structure as well as on the amplitude and rate of structural fluctuations. MD provides physically sound models and potential mechanisms that connect conformations in time. Nevertheless, none of these techniques allow yet obtaining experimentally validated movies of protein motions at atomic resolution. Instead, it is their complementarity and synergy which offer a unique opportunity toward this end. Here, we overview recent examples that illustrate how much these two techniques benefit from each other, both passively and actively, for the characterization of the structural heterogeneity in proteins. © 2012 John Wiley & Sons, Ltd.This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Hansch analysis 50 years on
Authors: Martin Yvonne Connolly 
Published: April 2012

AbstractThe invention of quantitative structure–activity relationships (QSAR) launched the use of computers to understand the multiple factors that contribute to the relationship between the chemical and biological properties of molecules. The original Hansch–Fujita QSAR continues to be performed to this day, fifty years since its inception. In addition, it has inspired vigorous research that has inspired many related methods: for example, methods that use descriptors such as substructures or three‐dimensional features or methods that are based on mathematical models such as partial least squares or recursive partitioning. The influence of QSAR is felt in the recognition of the value of predictions from such models by regulatory agencies and by the widespread use of octanol–water log P in agricultural, environmental, and medicinal chemistry.This article is categorized under:

Computer and Information Science > Chemoinformatics
Evolution and development in cave animals: from fish to crustaceans
Authors: Protas Meredith , Jeffery William R. 
Published: April 2012

AbstractCave animals are excellent models to study the general principles of evolution as well as the mechanisms of adaptation to a novel environment: the perpetual darkness of caves. In this article, two of the major model systems used to study the evolution and development (evo–devo) of cave animals are described: the teleost fish Astyanax mexicanus and the isopod crustacean Asellus aquaticus. The ways in which these animals match the major attributes expected of an evo–devo cave animal model system are described. For both species, we enumerate the regressive and constructive troglomorphic traits that have evolved during their adaptation to cave life, the developmental and genetic basis of these traits, the possible evolutionary forces responsible for them, and potential new areas in which these model systems could be used for further exploration of the evolution of cave animals. Furthermore, we compare the two model cave animals to investigate the mechanisms of troglomorphic evolution. Finally, we propose a few other cave animal systems that would be suitable for development as additional models to obtain a more comprehensive understanding of the developmental and genetic mechanisms involved in troglomorphic evolution. WIREs Dev Biol 2012. doi: 10.1002/wdev.61This article is categorized under:

Comparative Development and Evolution > Evolutionary Novelties
Sensitivity of berry productivity to climatic variation in the Cabinet–Yaak grizzly bear recovery zone, Northwest United States, 1989–2010
Authors: Holden Zachary A. , Kasworm Wayne F. , Servheen Christopher , Hahn Beth , Dobrowski Solomon 
Published: April 2012

AbstractBerry‐producing shrubs are culturally, economically, and ecologically important for both people and animals in the Pacific Northwest of the United States. We examined huckleberry (Vaccinium membranaceum) and serviceberry (Amelanchier alnifolia) productivity across the Cabinet–Yaak grizzly bear recovery zone in Northern Idaho and Western Montana. An index of annual berry productivity was measured at field plots from 1989 to 2010. Temperature, precipitation, and snow indices were derived from nearby Snowpack Telemetry (SNOTEL) stations. Huckleberry production was highest during cool springs with high July diurnal temperature ranges. April–June growing‐degree days and July temperature range explain 70% of the inter‐annual variability in huckleberry productivity. Serviceberry production was correlated with maximum snow‐water equivalent and April–June growing‐degree days, which explained 86% of the variance in annual serviceberry production. These models show potential to forecast annual berry production and to anticipate potential bear–human interactions. Further development of models is essential to better predict the potential changes in important wildlife resources in the context of climate change. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.
Market-based measures for greenhouse gas emissions from ships: a review
Authors: Psaraftis Harilaos N. 
Published: April 2012

Abstract
The purpose of this paper is to review several distinct proposals for market-based measures (MBMs) that are under consideration by the International Maritime Organization (IMO) for greenhouse gases (GHGs). Thus far, some ten distinct MBM proposals have been submitted to the IMO. The paper discusses the general concept of an MBM, the mechanisms used by MBMs, and attempts to discuss the pros and cons of the submitted proposals, according to some specific criteria.
Swept-wing boundary-layer receptivity
Authors: Tempelmann David , Hanifi Ardeshir , Henningson Dan S. 
Published: April 2012

AbstractAdjoint solutions of the linearized incompressible Navier–Stokes equations are presented for a cross-flow-dominated swept-wing boundary layer. For the first time these have been computed in the region upstream of the swept leading edge and may therefore be used to predict receptivity to any disturbances of the incoming free stream as well as to surface roughness. In this paper we present worst-case scenarios, i.e. those external disturbances yielding maximum receptivity amplitudes of a steady cross-flow disturbance. In the free stream, such an ‘optimal’ disturbance takes the form of a streak which, while being convected downstream, penetrates the boundary layer and smoothly turns into a growing cross-flow mode. The ‘worst-case’ surface roughness has a wavy shape and is distributed in the chordwise direction. It is shown that, under such optimal conditions, the boundary layer is more receptive to surface roughness than to incoming free stream disturbances.
Hydraulic control of continuously stratified flow over an obstacle
Authors: Winters Kraig B. , Armi Laurence 
Published: April 2012

AbstractMotivated by the laboratory experiments of Browand & Winant (Geophys. Fluid Dyn., vol. 4, 1972, pp. 29–53), a series of two-dimensional numerical simulations of flow past a cylinder of diameter $d$ are run for different values of the approach Froude number ${\mathit{Fr}}_{o} = U/ Nd$ between $0. 02$ and $0. 2$ at $\mathit{Re}= O(100)$. The observed flow is characterized by blocking and upstream influence in front of the cylinder and by relatively thin, fast jets over the top and bottom of the cylinder. This continuously stratified flow can be understood in terms of an inviscid non-diffusive integral inertia–buoyancy balance reminiscent of reduced-gravity single-layer hydraulics, but one where the reduced gravity is coupled to the thickness of the jets. The proposed theoretical framework describes the flow upstream of the obstacle and at its crest. The most important elements of the theory are the inclusion of upstream influence in the form of blocked flow within an energetically constrained depth range and the recognition that the flow well above and well below the active, accelerated layers is dynamically uncoupled. These constraints determine, through continuity, the transport in the accelerated layers. Combining these results with the observation that the flow is asymmetric around the cylinder, i.e. hydraulically controlled, allows us to determine the active layer thicknesses, the effective reduced gravity and thus all of the integral flow properties of the fast layers in good agreement with the numerically computed flows.
Cognitive behavioural therapy for occupational trauma: a systematic literature review exploring the effects of occupational trauma and the existing CBT support pathways and interventions for staff working within mental healthcare including allied professions
Authors: Graham Judith 
Published: April 2012

AbstractThis study performed a systematic literature review to examine existing and recommended CBT support for staff working within mental healthcare, who experienced occupational traumatization. The following questions were posed: (1) What are the effects of differing levels of occupational trauma on the individual and/or organization? (2) Are there any current CBT-specific models, or treatment pathways, aimed at supporting those experiencing the effects of occupational trauma? Conclusions showed the effects of occupational trauma are significant, varied and predominantly negative to both employees, and the organizations where they work. There were no CBT-specific models or pathways sourced to address occupational trauma; however, interventions were highlighted which may form parts of a larger pathway. Reviewed evidence suggests that development of a stepped CBT pathway for occupational trauma will be beneficial.
Campanian‐Maastrichtian intermediate‐ to deep‐water changes in the high latitudes: Benthic foraminiferal evidence
Authors: Koch Mirjam C. , Friedrich Oliver 
Published: April 2012

During the latest Cretaceous cooling phase, a positive shift in benthic foraminiferal δ18O values lasting about 1.5 Myr (71.5–70 Ma) can be observed at a global scale (Campanian‐Maastrichtian Boundary Event, CMBE). This δ18O excursion is interpreted as being influenced by a change in intermediate‐ to deep‐water circulation or by temporal build‐up of Antarctic ice sheets. Here we test whether benthic foraminiferal assemblages from a southern high‐latitudinal site near Antarctica (ODP Site 690) are influenced by the CMBE. If the δ18O transition reflects a change in intermediate‐ to deep‐water circulation from low‐latitude to high‐latitude water masses, then this change would result in cooler temperatures, higher oxygen concentration, and possibly lower organic‐matter flux at the seafloor, resulting in a major benthic foraminiferal assemblage change. If, however, the δ18O transition was mainly triggered by ice formation, no considerable compositional difference in benthic foraminiferal assemblages would be expected. Our data show a separation of the studied succession into two parts with distinctly different benthic foraminiferal assemblages. Species dominating the older part (73.0–70.5 Ma) tolerate less bottom water oxygenation and are typical components of low‐latitude assemblages. In contrast, the younger part (70.0–68.0 Ma) is characterized by species that indicate well‐oxygenated bottom waters and species common in high‐latitude assemblages. We interpret the observed change in benthic foraminiferal assemblages toward a well‐oxygenated environment to reflect the onset of a shift from low‐latitude toward high‐latitude dominated intermediate‐ to deep‐water sources. This implies that a change in oceanic circulation was at least a major component of the CMBE.
The efficacy and safety of lixivaptan in outpatients with heart failure and volume overload: results of a multicentre, randomized, double‐blind, placebo‐controlled, parallel‐group study
Authors: Ghali Jalal K. , Orlandi Cesare , Abraham William T. ,   for the CK‐LX2401 Study Investigators
Published: April 2012

AimsVolume overload is the dominant feature of decompensated heart failure (HF) and it often results in adverse clinical outcomes. Vasopressin receptor antagonists such as lixivaptan may provide effective volume unloading. This study assessed weight loss after 1 day and 8 weeks of treatment with lixivaptan in outpatients with HF and volume overload.Methods and resultsThis phase II, 8‐week, multicentre, double‐blind, parallel‐group study randomized participants (2:1) to receive lixivaptan 100 mg or placebo once daily (in addition to standard HF therapy). Body weight and cardiovascular assessments were made at baseline, Day 1 (not cardiovascular), Weeks 1, 2, 4, and 8, and 7 days post‐treatment. The Trail‐making Test, part B (TMT‐B) and the Medical Outcomes Survey 6‐item cognitive function scale (MOS‐6) were assessed at baseline and Week 4. The study randomized 170 participants (lixivaptan, n = 111; placebo, n = 59). Most (97.1%) were receiving pharmacological therapy for HF at baseline. Demographic characteristics were generally similar between the two groups. Body weight decreased significantly from baseline to Day 1 with lixivaptan vs. placebo (least‐square mean change ± standard error: − 0.38 ± 0.08 kg vs. +0.13 ± 0.11 kg; P < 0.001) and at Weeks 1, 2, and 4 (P < 0.01). Cardiovascular changes were generally similar in both groups, though orthopnoea and dyspnoea improved in the lixivaptan group vs. placebo. The TMT‐B and MOS‐6 showed no significant differences between groups. Lixivaptan was well tolerated—thirst and polyuria occurred more frequently vs. placebo.ConclusionsIn outpatients with HF and volume overload, lixivaptan 100 mg once daily, when added to standard therapy, reduced body weight, improved dyspnoea and orthopnoea, and was well tolerated.Trial registration: NCT01055912
SALSEA North America: a pelagic ecosystem survey targeting Atlantic salmon in the Northwest Atlantic
Authors: Sheehan Timothy F. , Reddin David G. , Chaput Gérald , Renkawitz Mark D. 
Published: April 2012

AbstractSheehan, T. F., Reddin, D. G., Chaput, G., and Renkawitz, M. D. 2012. SALSEA North America: a pelagic ecosystem survey targeting Atlantic salmon in the Northwest Atlantic. – ICES Journal of Marine Science, 69: 1580–1588. Pelagic ecosystem surveys were conducted in the Labrador Sea during 2008 and 2009 as part of SALSEA North America. In total, 107 Atlantic salmon (Salmo salar) were captured using a pelagic surface trawl and multipanel surface gillnets. Surface trawling provided a broad spatial sampling of the fish and macroinvertebrate communities in the upper 10 m of the water column, but caught few salmon (23). Gillnetting was more effective at capturing post-smolt (60) and adult (24) salmon. Multiple smolt cohorts were captured, indicating that post-smolts and returning adults from different rivers in North America have similar autumnal habitat requirements. Post-smolts were caught at night and in water temperatures exceeding 10°C, both novel results. Post-smolts and adults consumed similar and diverse prey species, although Themisto compressa was the most important prey item. Intestinal macroparasite loads were substantial and could be a significant source of mortality. Concurrent planktonic assemblage and oceanographic conditions were also quantified. A full exploration of these data, historical datasets, and parallel data collected during SALSEA Greenland and SALSEA-Merge will further understanding of the ecology of marine-phase Atlantic salmon and inform investigations into stock-specific differences in marine productivity.
A two‐step approach to map quantitative trait loci for meat quality in connected porcine F2 crosses considering main and epistatic effects
Authors: Stratz P. , Baes C. , Rückert C. , Preuss S. , Bennewitz J. 
Published: April 2012

SummaryThe aim of this study was to map QTL for meat quality traits in three connected porcine F2 crosses comprising around 1000 individuals. The three crosses were derived from the founder breeds Chinese Meishan, European Wild Boar and Pietrain. The animals were genotyped genomewide for approximately 250 genetic markers, mostly microsatellites. They were phenotyped for seven meat quality traits (pH at 45 min and 24 h after slaughter, conductivity at 45 min and 24 h after slaughter, meat colour, drip loss and rigour). QTL mapping was conducted using a two‐step procedure. In the first step, the QTL were mapped using a multi‐QTL multi‐allele model that was tailored to analyse multiple connected F2 crosses. It considered additive, dominance and imprinting effects. The major gene RYR1:g.1843C>T affecting the meat quality on SSC6 was included as a cofactor in the model. The mapped QTL were tested for pairwise epistatic effects in the second step. All possible epistatic effects between additive, dominant and imprinting effects were considered, leading to nine orthogonal forms of epistasis. Numerous QTL were found. The most interesting chromosome was SSC6. Not all genetic variance of meat quality was explained by RYR1:g.1843C>T. A small confidence interval was obtained, which facilitated the identification of candidate genes underlying the QTL. Epistasis was significant for the pairwise QTL on SSC12 and SSC14 for pH24 and for the QTL on SSC2 and SSC5 for rigour. Some evidence for additional pairwise epistatic effects was found, although not significant. Imprinting was involved in epistasis.
Circulating ficolin-2 and ficolin-3 in normal pregnancy and pre-eclampsia
Authors: Halmos A , Rigó J , Szijártó J , Füst G , Prohászka Z , Molvarec A 
Published: April 2012

Summary
Ficolins are soluble molecules of the innate immune system that recognize carbohydrate molecules on microbial pathogens, apoptotic and necrotic cells. They act through two distinct routes: initiating the lectin pathway of complement activation and mediating a primitive opsonophagocytosis. In this study, we measured plasma levels of ficolin-2 and ficolin-3 in 60 pre-eclamptic patients, 60 healthy pregnant women and 59 healthy non-pregnant women by enzyme-linked immunosorbent assay (ELISA). Circulating levels of complement activation products (C4d, C3a, SC5b9), angiogenic factors (soluble fms-like tyrosine kinase-1, placental growth factor) and markers of endothelial activation (von Willebrand factor antigen), endothelial injury (fibronectin) and trophoblast debris (cell-free fetal DNA) were also determined. Plasma levels of ficolin-2 were significantly lower in healthy pregnant than in healthy non-pregnant women, while ficolin-3 levels did not differ significantly between the two groups. Furthermore, pre-eclamptic patients had significantly lower ficolin-2 and ficolin-3 concentrations than healthy non-pregnant and pregnant women. In the pre-eclamptic group, plasma ficolin-2 levels showed a significant positive correlation with serum placental growth factor (PlGF) concentrations and significant inverse correlations with serum levels of soluble fms-like tyrosine kinase-1 (sFlt-1), blood urea nitrogen and creatinine, serum lactate dehydrogenase activities, as well as with plasma VWF:antigen, fibronectin and cell-free fetal DNA concentrations. In conclusion, circulating levels of ficolin-2 are decreased in the third trimester of normal pregnancy. There is a further decrease in plasma ficolin-2 concentrations in pre-eclampsia, which might contribute to the development of the maternal syndrome of the disease through impaired removal of the trophoblast-derived material released into the maternal circulation by the hypoxic and oxidatively stressed pre-eclamptic placenta.
Effects of testosterone therapy on sleep and breathing in obese men with severe obstructive sleep apnoea: a randomized placebo‐controlled trial
Authors: Hoyos Camilla M. , Killick Roo , Yee Brendon J. , Grunstein Ronald R. , Liu Peter Y. 
Published: April 2012

SummaryStudy objectivesHigh doses of short‐term testosterone have been shown to acutely worsen sleep‐disordered breathing in men with obstructive sleep apnoea (OSA). The effects of lower, near‐conventional doses of testosterone in obese men with OSA may differ over the longer term but have not been systematically studied. We assessed sleep and breathing effects of near‐conventional testosterone treatment as an adjunct to weight loss in obese men with severe OSA.DesignAn 18‐week randomized, double‐blind, placebo‐controlled, parallel group trial in 67 men.InterventionsAll subjects were placed on a hypocaloric diet and then received intramuscular injections of 1000 mg testosterone undecanoate or placebo at 0, 6 and 12 weeks.Measurements and ResultsSleep and breathing were measured by nocturnal polysomnography at 0, 7 and 18 weeks. Testosterone, compared to placebo, worsened the oxygen desaturation index (ODI) by 10·3 events/h (95%CI, 0·8–19·8 events/h; P = 0·03) and nocturnal hypoxaemia (sleep time with oxygen saturation <90%, SpO2T90%) by 6·1% (95%CI, 1·5–10·6; P = 0·01) at 7 weeks. Testosterone therapy did not alter ODI (4·5, −5·4 to 14·4 events/h; P = 0·36) or SpO2T90% at 18 weeks (2·9, −1·9–7·7%; P = 0·23) compared to placebo. The testosterone treatment effects on ODI and SpO2T90% were not influenced by baseline testosterone concentrations (testosterone by treatment interactions, all P > 0·35). Blood testosterone concentrations did not correlate with ODI or SpO2T90% (all P > 0·19).ConclusionsTestosterone therapy in obese men with severe OSA mildly worsens sleep‐disordered breathing in a time‐limited manner, irrespective of initial testosterone concentrations. This time‐dependency was not related to testosterone concentrations.Trial Registrationwww.anzctr.org.au Identifier: ACTRN1260‐6000404527.
Lower incidence and severity of tomato virus in elevated CO2 is accompanied by modulated plant induced defence in tomato
Authors: Huang L. , Ren Q. , Sun Y. , Ye L. , Cao H. , Ge F. 
Published: April 2012

AbstractElevation in atmospheric CO2 concentration broadly affects plant phenology and physiology, and these effects may alter the performance of plant viruses. The effects of elevated CO2 on the susceptibility of tomato plants to Tomato yellow leaf curl virus (TYLCV) were examined for two successive years in open top chambers (OTC) in the field. We experimentally tested the hypothesis that elevated CO2 would reduce the incidence and severity of TYLCV on tomato by altering plant defence strategies. Our results showed that elevated CO2 decreased TYLCV disease incidence (by 14.6% in 2009 and 11.8% in 2010) and decreased disease severity (by 20.0% in 2009 and 10.4% in 2010). Elevated CO2 also decreased the level of TYLCV coat protein in tomato leaves. Regardless of virus infection, elevated CO2 increased plant height and aboveground biomass. Additionally, elevated CO2 increased the leaf C:N ratio of tomato, but decreased soluble protein content in leaves. Notably, elevated CO2 increased the salicylic acid (SA) level in uninfected and infected plants. In contrast, elevated CO2 reduced jasmonic acid (JA) in uninfected plants while it increased JA and abscisic acid (ABA) in virus‐infected plants. Furthermore, combined exogenous SA and JA application enhanced resistance to TYLCV more than application of either SA or JA alone. Our results suggest that the modulated antagonistic relationship between SA and JA under elevated CO2 makes a great contribution to increased tomato resistance to TYLCV, and the predicted increases in tomato productivity may be enhanced by reduced plant virus susceptibility under projected rising CO2 conditions.