bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence
Authors: Payne Rebecca , Muenchhoff Maximilian , Mann Jaclyn , Roberts Hannah E. , Matthews Philippa , Adland Emily , Hempenstall Allison , Huang Kuan-Hsiang , Brockman Mark , Brumme Zabrina , Sinclair Marc , Miura Toshiyuki , Frater John , Essex Myron , Shapiro Roger , Walker Bruce D. , Ndung’u Thumbi , McLean Angela R. , Carlson Jonathan M. , Goulder Philip J. R. 
Published: December 2014

Significance
Factors that influence the virulence of HIV are of direct relevance to ongoing efforts to contain, and ultimately eradicate, the HIV epidemic. We here investigate in Botswana and South Africa, countries severely affected by HIV, the impact on HIV virulence of adaptation of HIV to protective HLA alleles such as HLA-B*57. In Botswana, where the epidemic started earlier and reached higher adult seroprevalence than in South Africa, HIV replication capacity is lower. HIV is also better adapted to HLA-B*57, which in Botswana has no protective effect, in contrast to its impact in South Africa. Modelling studies indicate that increasing antiretroviral therapy access may also contribute to accelerated declines in HIV virulence over the coming decades.
Carnivorous leaves from Baltic amber
Authors: Sadowski Eva-Maria , Seyfullah Leyla J. , Sadowski Friederike , Fleischmann Andreas , Behling Hermann , Schmidt Alexander R. 
Published: December 2014

SignificanceAmber, fossil tree resin, preserves organisms in microscopic fidelity, and frequently fossils preserved in amber are otherwise absent in the entire fossil record. Plant remains, however, are rarely entrapped in amber, compared with the vast amount of insects and other animals. Our newly discovered fossils from Eocene Baltic amber are the only documented case of fossilized carnivorous plant traps and represent the first fossil evidence of the carnivorous plant family Roridulaceae, which is today a narrow endemic of South Africa. Hence, our results shed light onto the paleobiogeography of the Roridulaceae, indicating a wide Eocene distribution of the roridulid ancestors and challenging previous notions about a Gondwanan origin of this plant family.
Escherichia coli
dihydrofolate reductase catalyzed proton and hydride transfers: Temporal order and the roles of Asp27 and Tyr100
Authors: Liu C. Tony , Francis Kevin , Layfield Joshua P. , Huang Xinyi , Hammes-Schiffer Sharon , Kohen Amnon , Benkovic Stephen J. 
Published: December 2014

Significance
Dihydrofolate reductase is a classic drug target because it promotes the NADPH-dependent reduction of 7,8-dihydrofolate (DHF) to yield 5,6,7,8-tetrahydrofolate (THF), which is involved in the biosynthesis of purines, thymidylate, and several amino acids. It is also a popular model system for various biochemical/biophysical studies. However, there are many unresolved mechanistic issues regarding the mechanism of catalysis. We combined primary, solvent, and multiple kinetic isotope effects; their temperature dependence; theoretical calculations; and site-specific mutagenesis to elucidate the reaction mechanism, which involves stepwise protonation of DHF by a water molecule prior to the hydride transfer. These two events are facilitated by two active site residues (D27 and Y100) that operate synergistically to ensure catalysis and to enable efficient DHF protonation over a wide pH range.
The second demographic transition: A concise overview of its development
Authors: Lesthaeghe Ron 
Published: December 2014

SignificanceAt the end of the historical declines in both mortality and fertility (the “first demographic transition”), new demographic phenomena developed in the Western World. Therefore, new theoretical frameworks were needed to explain features such as the baby bust, the systematic postponement of marriage and parenthood, subreplacement fertility, the rise of alternative forms of partnerships, and parenthood outside marriage. The “second demographic transition” (SDT) theory is such an attempt. Although it accepts the major tenets of bounded rational economic choice, it also allows for autonomous preference drift by relying on Maslow’s theory of shifting needs. As such, an essentially cultural component is being added.
Repurposing of bisphosphonates for the prevention and therapy of nonsmall cell lung and breast cancer
Authors: Stachnik Agnes , Yuen Tony , Iqbal Jameel , Sgobba Miriam , Gupta Yogesh , Lu Ping , Colaianni Graziana , Ji Yaoting , Zhu Ling-Ling , Kim Se-Min , Li Jianhua , Liu Peng , Izadmehr Sudeh , Sangodkar Jaya , Scherer Thomas , Mujtaba Shiraz , Galsky Matthew , Gomez Jorge , Epstein Solomon , Buettner Christoph , Bian Zhuan , Zallone Alberta , Aggarwal Aneel K. , Haider Shozeb , New Maria I. , Sun Li , Narla Goutham , Zaidi Mone 
Published: December 2014

SignificanceSmall molecules to target oncogenic signaling cascades in cancer have achieved success in molecularly defined patient subsets. The path to approval is often protracted and plagued with failures. Repositioning Food and Drug Administration-approved drugs with known side effects has become a major focus. Bisphosphonates are a commonly prescribed therapy for osteoporosis and skeletal metastases. The drugs have also been associated with reduced tumor burden in some patients, but the mechanism is unknown. Here we provide evidence that bisphosphonates inhibit the human EGFR (HER) receptor tyrosine kinase, including the commonly mutated forms that drive nonsmall cell lung cancer, as well as a resistance mutation. This new mechanism lays the basis for the future use of bisphosphonates for the prevention and therapy of HER family-driven cancers.
Effect of three-dimensional conducting structures on vertical stability in EAST
Authors: Chen S.L. , Villone F. , Barbato L. , Mastrostefano S. , Xiao B.J. , Luo Z.P. 
Published: December 2014

Abstract
The vertical stability of the Experimental Advanced Superconducting Tokamak (EAST) is studied in detail in the present paper. It is found that correct modelling of the detailed three-dimensional (3D) features of the conducting structures surrounding the plasma is essential in order to get reliable estimates of the growth rate of vertical displacement events. The numerical model developed, based on the CarMa0 code, can take 3D effects into account, and provides results very close to experimental values for a wide range of plasma configurations. A deep insight about the current density patterns induced in passive structures is gained.
Suppression of energetic particle driven instabilities with HHFW heating
Authors: Fredrickson E.D. , Taylor G. , Bertelli N. , Darrow D.S. , Gorelenkov N. , Kramer G. , Liu D. , Crocker N.A. , Kubota S. , White R. 
Published: December 2014

Abstract
In plasmas in the National Spherical Torus Experiment (NSTX) (Ono et al 2000 Nucl. Fusion
40 557) heated with neutral beams, the beam ions typically excite energetic particle modes (or fishbones), and toroidal, global or compressional Alfvén eigenmodes. These modes can redistribute the energetic beam ions, altering the beam driven current profile and the plasma heating profile, or they may affect electron thermal transport or cause losses of the beam ions. In this paper we present experimental results where these instabilities, driven by the super-thermal beam ions, are suppressed with the application of high harmonic fast wave heating.
Impact of Te and ne on edge current density profiles in ELM mitigated regimes on ASDEX Upgrade
Authors: Dunne M.G. , Rathgeber S. , Burckhart A. , Fischer R. , Giannone L. , McCarthy P.J. , Schneider P.A. , Wolfrum E. 
Published: December 2014

Abstract
ELM resolved edge current density profiles are reconstructed using the CLISTE equilibrium code. As input, highly spatially and temporally resolved edge electron temperature and density profiles are used in addition to data from the extensive set of external poloidal field measurements available at ASDEX Upgrade, flux loop difference measurements, and current measurements in the scrape-off layer. Both the local and flux surface averaged current density profiles are analysed for several ELM mitigation regimes. The focus throughout is on the impact of altered temperature and density profiles on the current density. In particular, many ELM mitigation regimes rely on operation at high density. Two reference plasmas with type-I ELMs are analysed, one with a deuterium gas puff and one without, in order to provide a reference for the behaviour in type-II ELMy regimes and high density ELM mitigation with external magnetic perturbations at ASDEX Upgrade. For type-II ELMs it is found that while a similar pedestal top pressure is sustained at the higher density, the temperature gradient decreases in the pedestal. This results in lower local and flux surface averaged current densities in these phases, which reduces the drive for the peeling mode. No significant differences between the current density measured in the type-I phase and ELM mitigated phase is seen when external perturbations are applied, though the pedestal top density was increased. Finally, ELMs during the nitrogen seeded phase of a high performance discharge are analysed and compared to ELMs in the reference phase. An increased pedestal pressure gradient, which is the source of confinement improvement in impurity seeded discharges, causes a local current density increase. However, the increased Z
eff in the pedestal acts to reduce the flux surface averaged current density. This dichotomy, which is not observed in other mitigation regimes, could act to stabilize both the ballooning mode and the peeling mode at the same time.
The Yield of Plant Variety Protection
Authors: Thomson Russell 
Published: December 2014

AbstractThe prospects for plant variety protection to deliver improved varieties of self‐pollinating crops is assessed using the experience of the Australian wheat breeding sector as a natural experiment. The analysis is based on detailed new data on the agronomic performance of all wheat varieties released by Australian breeders between 1976 and 2011. The results indicate that plant variety protection, and associated reforms, led to a substantial fall in breeder output. Qualitative evidence indicates that this was caused by a combination of fewer research spillovers, lower release standards, and a possible fall in total investment in breeding.
Should Blood Pressure Targets After Lacunar Stroke Vary by Body Size? The SPS3 Trial
Authors: Field Thalia S. , McClure Leslie A. , White Carole L. , Pergola Pablo E. , Hart Robert G. , Benavente Oscar R. , Hill Michael D. 
Published: December 2014

BACKGROUND
It is unknown whether the physiological impact of a given blood pressure (BP) varies by body size. We explored interactions between higher vs. lower systolic BP (SBP) targets and anthropometric measures (body mass index (BMI), body surface area (BSA), height, weight) and recurrent stroke and death in the Secondary Prevention of Small Subcortical Strokes (SPS3) Trial.

METHODS
Patients with recent magnetic resonance imaging-proven lacunar infarcts were randomized to 2 BP targets (130–149mm Hg vs. &lt;130) in a prospective, open-label, blinded end-point design. Time to outcome was evaluated with Cox proportional hazard models and compared between targets. We examined multiplicative interactions between each anthropometric measure and target and mean difference in achieved BP 1 year after randomization between BP groups by quartile. We also computed rates of recurrent stroke and death by quartiles of anthropometrics.

RESULTS
Three thousand and twenty patients were followed over a mean of 3.7 (SD 2.0) years. Mean age was 63; 63% were male. Mean height was 167 (SD 11) cm, weight 81 (18) kg, BMI 29 (5.9) kg/m2, and BSA 1.9 (0.25) m2. Achieved BP at 1 year was comparable between quartiles for each anthropometric measurement. We found no consistent interactions between BP target and anthropometrics for either outcome, nor were there any significant associations between hazard of stroke or death when assessed by BMI, BSA, height, or weight.

CONCLUSIONS
We found no interactions between BP target groups and quartiles of anthropometrics for rates of stroke and death in SPS3. There is no evidence at this time supporting body size-based modifications to current BP targets for secondary prevention after lacunar stroke.

CLINICAL TRIALS REGISTRATION
Trial Number NCT00059306
Linkage and trade‐off in trophic morphology and behavioural performance of birds
Authors: Corbin Clay E. , Lowenberger Lauren K. , Gray Brandan L. 
Published: December 2014

Summary

Bill closing behaviour involves a complex suite of tissue types, kinematics, morphological states and muscle architectural arrangements that has been under the scrutiny of natural selection for millions of years. Hence, an evolutionary shift to specialize in closing force may come at a cost to closing velocity and vice versa.

Using field measurements on behavioural performance and morphological data from museum specimens, we tested predictions of the force–velocity trade‐off hypothesis in 18 species of North American birds with diverse phylogenetic and ecological backgrounds.

Linear models revealed that size and shape are excellent predictors of both bite force and closing velocity. However, taken one at a time, they each have a somewhat unique set of morphological predictors. In‐lever length, mandibular depth and bill width comprise the best model of prediction for force, while a combination of out‐lever length and total skull length provides the best prediction of closing velocity. Additionally, in our sample, only force is size‐dependent. Hence, the predicted trade‐off is revealed only after correcting bite force for head size.

Various modes of predation and decoupled morphological prediction models for performance suggest that specialization towards one strategy (e.g. increase force) may not necessarily come at a cost to the other.
Food Policy in 2013: Ending Hunger and Undernutrition Sustainably by 2025
Authors: Fan Shenggen 
Published: December 2014

SummaryThe challenge of ensuring future food and nutrition security received widespread attention in 2013. The Millennium Development Goal (MDG) to halve global hunger by 2015 has not yet been met. Although progress has been made, one in eight people still suffer from hunger, and nearly 2 billion are affected by hidden hunger, or micronutrient deficiencies. Hunger and undernutrition can be eliminated sustainably by 2025. The experiences of successful countries in substantially reducing hunger and undernutrition suggest that it is realistic to strive for this goal by accelerating the pace of progress. But to achieve this goal, governments and donors must devote sufficient resources and implement appropriate policies and investments. Discussions of a post‐2015 development agenda, including a set of Sustainable Development Goals, which will advance what began with the MDGs are now well underway. Environmental sustainability is certainly integral to the post‐2015 agenda, but it should be pursued in ways that do not undermine the food and nutrition security and well‐being of poor and hungry people. The agenda must be grounded in a multisectoral, sustainable, people‐focused approach that (1) focuses on clear goals and targets, (2) uses comprehensive data and indicators to monitor and measure the goals and targets accurately, (3) supports partnerships among all stakeholders, and (4) promotes accountability.
Estimating pairwise relatedness between individuals with different levels of ploidy
Authors: Huang Kang , Ritland Kermit , Guo Songtao , Dunn Derek W. , Chen Dan , Ren Yi , Qi Xiaoguang , Zhang Pei , He Gang , Li Baoguo 
Published: December 2014

AbstractEstimates of relatedness coefficients, based on genetic marker data, are often necessary for studies of genetics and ecology. Whilst many estimates based on method‐of‐moment or maximum‐likelihood methods exist for diploid organisms, no such estimators exist for organisms with multiple ploidy levels, which occur in some insect and plant species. Here, we extend five estimators to account for different levels of ploidy: one relatedness coefficient estimator, three coefficients of coancestry estimators and one maximum‐likelihood estimator. We use arrhenotoky (when unfertilized eggs develop into haploid males) as an example in evaluations of estimator performance by Monte Carlo simulation. Also, three virtual sex‐determination systems are simulated to evaluate their performances for higher levels of ploidy. Additionally, we used two real data sets to test the robustness of these estimators under actual conditions. We make available a software package, PolyRelatedness, for other researchers to apply to organisms that have various levels of ploidy.
Universal and blocking primer mismatches limit the use of high‐throughput DNA sequencing for the quantitative metabarcoding of arthropods
Authors: Piñol J. , Mir G. , Gomez‐Polo P. , Agustí N. 
Published: December 2014

AbstractThe quantification of the biological diversity in environmental samples using high‐throughput DNA sequencing is hindered by the PCR bias caused by variable primer–template mismatches of the individual species. In some dietary studies, there is the added problem that samples are enriched with predator DNA, so often a predator‐specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could coblock nontarget species to some degree. Here, we accurately estimate the extent of the PCR biases induced by universal and blocking primers on a mock community prepared with DNA of twelve species of terrestrial arthropods. We also compare universal and blocking primer biases with those induced by variable annealing temperature and number of PCR cycles. The results show that reads of all species were recovered after PCR enrichment at our control conditions (no blocking oligonucleotide, 45 °C annealing temperature and 40 cycles) and high‐throughput sequencing. They also show that the four factors considered biased the final proportions of the species to some degree. Among these factors, the number of primer–template mismatches of each species had a disproportionate effect (up to five orders of magnitude) on the amplification efficiency. In particular, the number of primer–template mismatches explained most of the variation (~3/4) in the amplification efficiency of the species. The effect of blocking oligonucleotide concentration on nontarget species relative abundance was also significant, but less important (below one order of magnitude). Considering the results reported here, the quantitative potential of the technique is limited, and only qualitative results (the species list) are reliable, at least when targeting the barcoding COI region.
Exercise augmentation compared with usual care for post‐traumatic stress disorder: a randomized controlled trial
Authors: Rosenbaum S. , Sherrington C. , Tiedemann A. 
Published: December 2014

ObjectiveTo investigate the impact of a 12‐week exercise programme in addition to usual care for post‐traumatic stress disorder (PTSD).MethodAn assessor‐blinded randomized controlled trial was conducted among 81 participants with a DSM‐IV‐TR diagnosis of primary PTSD. Participants were recruited after admission to an in‐patient programme at a private hospital. Participants were randomized to receive either usual care (n = 42), or exercise in addition to usual care (n = 39). The exercise intervention involved three, 30‐min resistance‐training sessions/week and a pedometer‐based walking programme. Usual care involved psychotherapy, pharmaceutical interventions, and group therapy. Primary outcome was PTSD symptoms assessed via the PTSD checklist–civilian version (PCL‐C). Secondary outcomes included symptoms of depression, anthropometry, physical activity, mobility, strength, and sleep quality.ResultsParticipants had a mean (SD) age of 47.8 years (12.1), 84% male. PTSD symptoms in the intervention group significantly reduced compared with the usual care group (mean difference = −5.4, 95% CI −10.5 to −0.3, P = 0.04, n = 58). There were significant between‐group differences at follow‐up for depressive symptoms, waist circumference, sleep quality, and sedentary time.ConclusionThis study provides the first evidence that an exercise intervention is associated with reduced PTSD and depressive symptoms, reduced waist circumference, and improved sleep quality.
The Benefit Corporation: Corporate Governance and the For‐profit Social Entrepreneur
Authors: Hemphill Thomas A. , Cullari Francine 
Published: December 2014

AbstractThe adoption by 19 states and the District of Columbia of a new variant of the business corporation form—known as the benefit corporation—presents several issues for legislatures, for entrepreneurs electing to organize as benefit corporations, for existing corporations that are converting to the new form, and for the stakeholders (other than shareholders) who are intended to be considered in benefit corporation governance. The article presents the history and structure of the new business form and a discussion of what has become its predecessor—the constituency statute. The model benefit corporation statute provisions are reviewed, which many states have adopted in toto. The authors address the obstacles that should be overcome by legislatures, businesses, and stakeholders before further legislative adoptions occur, as well as considerations for effective implementation by government, corporations, and stakeholders under existing and proposed variations of the statute.
Testing the bi‐dimensional effects of attitudes on behavioural intentions and subsequent behaviour
Authors: Elliott Mark A. , Brewster Sarah E. , Thomson James A. , Malcolm Carly , Rasmussen Susan 
Published: November 2014

Attitudes are typically treated as unidimensional predictors of both behavioural intentions and subsequent behaviour. On the basis of previous research showing that attitudes comprise two independent, positive and negative dimensions, we hypothesized that attitudes would be bi‐dimensional predictors of both behavioural intentions and subsequent behaviour. We focused on health‐risk behaviours. We therefore also hypothesized that the positive dimension of attitude (evaluations of positive behavioural outcomes) would better predict both behavioural intentions and subsequent behaviour than would the negative dimension, consistent with the positivity bias/offset principle. In Study 1 (cross sectional design), N = 109 university students completed questionnaire measures of their intentions to binge‐drink and the positive and negative dimensions of attitude. Consistent with the hypotheses, both attitude dimensions independently predicted behavioural intentions and the positive dimension was a significantly better predictor than was the negative dimension. The same pattern of findings emerged in Study 2 (cross sectional design; N = 186 university students) when we predicted intentions to binge‐drink, smoke and consume a high‐fat diet. Similarly, in Study 3 (prospective design; N = 1,232 speed limit offenders), both the positive and negative dimensions of attitude predicted subsequent (6‐month post‐baseline) speeding behaviour on two different road types and the positive dimension was the better predictor. The implications for understanding the motivation of behaviour and the development of behaviour‐change interventions are discussed.