bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enabling large‐scale next‐generation sequence assembly with Blacklight
Authors: Brian Couger M. , Pipes Lenore , Squina Fabio , Prade Rolf , Siepel Adam , Palermo Robert , Katze Michael G. , Mason Christopher E. , Blood Philip D. 
Published: March 2014

SUMMARYA variety of extremely challenging biological sequence analyses were conducted on the XSEDE large shared memory resource Blacklight, using current bioinformatics tools and encompassing a wide range of scientific applications. These include genomic sequence assembly, very large metagenomic sequence assembly, transcriptome assembly, and sequencing error correction. The data sets used in these analyses included uncategorized fungal species, reference microbial data, very large soil and human gut microbiome sequence data, and primate transcriptomes, composed of both short‐read and long‐read sequence data. A new parallel command execution program was developed on the Blacklight resource to handle some of these analyses. These results, initially reported previously at XSEDE13 and expanded here, represent significant advances for their respective scientific communities. The breadth and depth of the results achieved demonstrate the ease of use, versatility, and unique capabilities of the Blacklight XSEDE resource for scientific analysis of genomic and transcriptomic sequence data, and the power of these resources, together with XSEDE support, in meeting the most challenging scientific problems. Copyright © 2014 John Wiley & Sons, Ltd.
Hematite Photoanodes Modified with an FeIII Water Oxidation Catalyst
Authors: Dalle Carbonare Nicola , Cristino Vito , Berardi Serena , Carli Stefano , Argazzi Roberto , Caramori Stefano , Meda Laura , Tacca Alessandra , Bignozzi Carlo Alberto 
Published: March 2014

AbstractHematite photoelectrodes prepared via a hydrothermal route are functionalized with a water oxidation catalyst consisting of amorphous FeIII oxide, obtained by successive ionic layer adsorption and reaction. The performances of the catalyst‐modified photoanodes are considerably higher than those of the parent electrodes, resulting in a nearly doubled photoanodic current in all the basic aqueous electrolytes explored in this study. The combination of electrochemical impedance spectroscopy and laser flash photolysis indicates that the presence of the catalyst results in enhanced hole trapping in surface reactive states exposed to the electrolyte, allowing for a more successful competition between charge transfer and recombination.
Modifiable clinical and lifestyle factors are associated with elevated alanine aminotransferase levels in newly diagnosed type 2 diabetes patients: results from the nationwide DD2 study
Authors: Mor Anil , Svensson Elisabeth , Rungby Jørgen , Ulrichsen Sinna Pilgaard , Berencsi Klara , Nielsen Jens Steen , Stidsen Jacob Volmer , Friborg Søren , Brandslund Ivan , Christiansen Jens Sandahl , Beck‐Nielsen Henning , Sørensen Henrik Toft , Thomsen Reimar Wernich 
Published: March 2014

AbstractBackgroundCurrent literature lacks data on markers of non‐alcoholic fatty liver disease (NAFLD) in newly diagnosed type 2 diabetes mellitus (T2DM) patients. We therefore, conducted a cross‐sectional study to examine modifiable clinical and lifestyle factors associated with elevated alanine aminotransferase (ALT) levels as a marker of NAFLD in new T2DM patients.MethodsAlanine aminotransferase levels were measured in 1026 incident T2DM patients enrolled in the nationwide Danish Centre for Strategic Research in Type 2 Diabetes (DD2) cohort. We examined prevalence of elevated ALT (>38 IU/L for women and >50 IU/L for men) and calculated prevalence ratios associated with clinical and lifestyle factors using Poisson regression. We examined the association with other biomarkers by linear regression.ResultsThe median value of ALT was 24 IU/L (interquartile range: 18–32 IU/L) in women and 30 IU/L (interquartile range: 22–41 IU/L) in men. Elevated ALT was found in 16% of incident T2DM patients. The risk of elevated ALT was increased in patients who were <40 years old at diabetes debut [adjusted prevalence ratio (aPR): 1.96, 95% confidence interval (CI): 1.15–3.33], in those with alcohol overuse (>14/>21 drinks per week for women/men) (aPR: 1.60, 95% CI: 1.03‐2.50), and in those with no regular physical activity (aPR: 1.42, 95% CI: 1.04–1.93). Obesity and metabolic syndrome per se showed no association with elevated ALT when adjusted for other markers, whereas we found positive associations of ALT with increased C‐peptide (β = 0.14, 95% CI: 0.06–0.21) and fasting blood glucose (β = 0.07, 95% CI: 0.03–0.11).ConclusionsAmong newly diagnosed T2DM patients, several modifiable clinical and lifestyle factors are independent markers of elevated ALT levels. Copyright © 2014 John Wiley & Sons, Ltd.
Degraded auditory processing in a rat model of autism limits the speech representation in non‐primary auditory cortex
Authors: Engineer C.T. , Centanni T.M. , Im K.W. , Borland M.S. , Moreno N.A. , Carraway R.S. , Wilson L.G. , Kilgard M.P. 
Published: March 2014

ABSTRACTAlthough individuals with autism are known to have significant communication problems, the cellular mechanisms responsible for impaired communication are poorly understood. Valproic acid (VPA) is an anticonvulsant that is a known risk factor for autism in prenatally exposed children. Prenatal VPA exposure in rats causes numerous neural and behavioral abnormalities that mimic autism. We predicted that VPA exposure may lead to auditory processing impairments which may contribute to the deficits in communication observed in individuals with autism. In this study, we document auditory cortex responses in rats prenatally exposed to VPA. We recorded local field potentials and multiunit responses to speech sounds in primary auditory cortex, anterior auditory field, ventral auditory field. and posterior auditory field in VPA exposed and control rats. Prenatal VPA exposure severely degrades the precise spatiotemporal patterns evoked by speech sounds in secondary, but not primary auditory cortex. This result parallels findings in humans and suggests that secondary auditory fields may be more sensitive to environmental disturbances and may provide insight into possible mechanisms related to auditory deficits in individuals with autism. © 2014 Wiley Periodicals, Inc. Develop Neurobiol 74: 972–986, 2014
Do females invest more into eggs when males sing more attractively? Postmating sexual selection strategies in a monogamous reed passerine
Authors: Krištofík Ján , Darolová Alžbeta , Majtan Juraj , Okuliarová Monika , Zeman Michal , Hoi Herbert 
Published: March 2014

AbstractMaternal investment can play an important role for offspring fitness, especially in birds, as females have to provide their eggs with all the necessary nutrients for the development of the embryo. It is known that this type of maternal investment can be influenced by the quality of the male partner. In this study, we first verify that male song is important in the mate choice of female Eurasian reed warblers, as males mate faster when their singing is more complex. Furthermore, female egg investment varies in relation to male song characteristics. Interestingly, clutch size, egg weight, or size, which can be considered as an high‐cost investment, is not influenced by male song characteristics, whereas comparably low‐cost investment types like investment into diverse egg components are adjusted to male song characteristics. In line with this, our results suggest that female allocation rules depend on investment type as well as song characteristics. For example, egg white lysozyme is positively correlated with male song complexity. In contrast, a negative correlation exists between‐song speed and syllable repetitiveness and egg yolk weight as well as egg yolk testosterone concentration. Thus, our results suggest that female egg investment is related to male song performance in several aspects, but female investment patterns regarding various egg compounds are not simply correlated.
The genetics of phenotypic plasticity. XIII. Interactions with developmental instability
Authors: Scheiner Samuel M. 
Published: March 2014

AbstractIn a heterogeneous environment, natural selection on a trait can lead to a variety of outcomes, including phenotypic plasticity and bet‐hedging through developmental instability. These outcomes depend on the magnitude and pattern of that heterogeneity and the spatial and temporal distribution of individuals. However, we do not know if and how those two outcomes might interact with each other. I examined the joint evolution of plasticity and instability through the use of an individual‐based simulation in which each could be genetically independent or pleiotropically linked. When plasticity and instability were determined by different loci, the only effect on the evolution of plasticity was the elimination of plasticity as a bet‐hedging strategy. In contrast, the effects on the evolution of instability were more substantial. If conditions were such that the population was likely to evolve to the optimal reaction norm, then instability was disfavored. Instability was favored only when the lack of a reliable environmental cue disfavored plasticity. When plasticity and instability were determined by the same loci, instability acted as a strong limitation on the evolution of plasticity. Under some conditions, selection for instability resulted in maladaptive plasticity. Therefore, before testing any models of plasticity or instability evolution, or interpreting empirical patterns, it is important to know the ecological, life history, developmental, and genetic contexts of trait phenotypic plasticity and developmental instability.
Phenylboronic Acid‐Gold Nanoparticles for Potentiometric Detection of Saccharides
Authors: Shishkanova Tatiana V. , Žvátora Pavel , Král Vladimír 
Published: March 2014

AbstractWe propose a concept for the analytical application of gold nanoparticles modified by mercaptophenylboronic acid as a receptor of saccharides in a potentiometric sensor based on a conducting polymer.
Electrochemical Behavior of Graphene‐Based Sensors on the Redox Mechanism of Aspirin
Authors: Patil Shreekant M. , Sataraddi Sanjeevaraddi R. , Bagoji Atmanand M. , Pathan Riyazkhan M. , Nandibewoor Sharanappa T. 
Published: March 2014

AbstractThe electrochemical behavior of aspirin at a graphene modified glassy carbon electrode has been investigated using cyclic and differential pulse voltammetric techniques. The dependence of the current on pH, concentration and scan rate was investigated to optimize the experimental conditions for determination of aspirin. A plausible oxidation mechanism was proposed. Under the optimum conditions, the oxidation peak current was linearly proportional to the concentration of aspirin in the range from 1.00×10−6 to 2.00×10−4 M with a detection limit of 20.2 nM. The proposed method was successfully applied to aspirin determination in pharmaceutical and real samples.
Electric Transmission: Addressing the National Transmission Challenge Through HVDC
Authors: Bray Sarah , Szalkowski Erin 
Published: March 2014

AbstractThe United States possesses some of the best renewable energy resources in the world, but it also faces a serious challenge: there is a lack of transmission capacity to deliver that energy to market. Clean Line Energy Partners LLC is an independent developer of long‐haul transmission lines that will deliver thousands of megawatts of renewable power from the windiest areas of the United States to communities and cities that have a strong demand for clean, reliable energy but that lack access to clean energy resources.
Natural Gas & Electricity Pricing: Understanding the Recent Volley in Natural Gas Prices
Authors: Bodell Tanya 
Published: March 2014

AbstractLike the action in a volleyball game, this past winter saw spikes, but these spikes were natural gas prices at Henry Hub, to levels not seen since 2010. Basis differentials in a number of markets also experienced unprecedented levels, especially in New England, where the month‐ahead forward for January was over $20 per million Btu's and daily trades on the basis differential rose to nearly four times higher. Winter price spikes are common, but are they indicative of new equilibrium prices so much higher than the past two years?
A coupled stochastic/deterministic model to estimate the evolution of the risk of water contamination by pesticides across Canada
Authors: Gagnon Patrick , Sheedy Claudia , Farenhorst Annemieke , McQueen DA Ross , Cessna Allan J , Newlands Nathaniel K 
Published: March 2014

Abstract
Periodic assessments of the risk of water contamination by pesticides help decision makers improve the sustainability of agricultural management practices. In Canada, when evaluating the risk of water contamination by pesticides, 2 main constraints arise. First, because the area of interest is large, a pesticide transport model with low computational running time is mandatory. Second, some relevant input data for simulations are not known, and most are known only at coarse scale. This study aims to develop a robust methodology to estimate the evolution of the risk of water contamination by pesticides across Canada. To circumvent the 2 aforementioned issues, we constructed a stochastic model and coupled it to the 1-dimensional pesticide fate model Pesticide Root Zone Model (PRZM). To account for input data uncertainty, the stochastic model uses a Monte Carlo approach to generate several pesticide application scenarios and to randomly select PRZM parameter values. One hundred different scenarios were simulated for each of over 2000 regions (Soil Landscapes of Canada [SLC] polygons) for the years 1981 and 2006. Overall, the results indicated that in those regions in which the risk increased from 1981 to 2006, the increase in risk was mainly attributable to the increased area treated by pesticides or an increase in the number of days with runoff. More specifically, this work identifies the areas at higher risk, where further analyses with finer-scale input data should be performed. The model is specific for Canadian data, but the framework could be adapted for other large countries. Integr Environ Assess Manag 2014;10:429–436. © 2014 SETAC
Key Points
A stochastic model is developed and coupled to a pesticide fate model in order to estimate the evolution of the risk of water contamination by pesticides for over 2000 region across Canada for the years 1981 and 2006. Mapping and statistical analyses of the results help to identify the most-at-risk areas were further attention would be needed. Risk level is generally higher for regions where the proportion of the land treated by pesticides and where the number of days with surface runoff are high. The stochastic model developed is specific for Canadian data, but the framework could be adapted for other large countries.
POLICY, SCIENCE AND SOCIETY INTERACTION
Authors: Tollefson L. , El Atfy H. , Facon T. , Kerc A. 
Published: March 2014

ABSTRACTIrrigated agriculture is undergoing rapid change and is facing issues related to climate change, population growth, consumption patterns, competition for resources and cost of development. The challenge is whether water availability for irrigation along with rainfed production will be sufficient to meet growing food demand and improve global food security. Traditionally governments have been responsible for developments in the irrigation sector through planning, design and construction of projects. Trends toward decentralization, fiscal crisis and growth of the private sector have led government to divest some of its role to user organizations and the private sector. This has been known as the participatory approach to irrigation management and has been adopted widely by many countries with a range of institutional arrangements. Many irrigation and drainage schemes worldwide perform below their capacity. To modernize and improve this capacity will require innovation and technical advancement, but in addition issues of policy, governance, management and institution must be addressed. Copyright © 2014 John Wiley & Sons, Ltd.
Diagnosis of liver cancer from blood sera using FTIR microspectroscopy: a preliminary study
Authors: Thumanu Kanjana , Sangrajrang Suleeporn , Khuhaprema Thiravud , Kalalak Anant , Tanthanuch Waraporn , Pongpiachan Siwatt , Heraud Philip 
Published: March 2014

AbstractFTIR microspectroscopy was applied for studying macromolecular changes in human serum samples from patients with healthy livers, and those diagnosed with liver cirrhosis or hepatocellular carcinoma (HCC). Our study demonstrated that the serum samples from HCC and cirrhotic patients could readily be discriminated from those from healthy controls based on macromolecular differences related to their lipid and protein structure. Spectral changes appeared to indicate that the secondary structure of protein from HCC sample groups contained a more distinctive β ‐sheet structure and a lower lipid content compared to samples from the healthy and cirrhosis group. This was correlated with measurements of large decreases in albumin levels in serum from diseased patients. We argue that this technique shows potential as a simple, rapid, inexpensive, and non‐subjective methodology for the screening patients suspected of liver disease. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Secular Trends in Hip Fractures Worldwide: Opposing Trends East Versus West
Authors: Ballane Ghada , Cauley Jane A , Luckey Marjorie M , Fuleihan Ghada El-Hajj 
Published: March 2014

ABSTRACT

Despite wide variations in hip rates fractures worldwide, reasons for such differences are not clear. Furthermore, secular trends in the age-specific hip fracture rates are changing the world map of this devastating disease, with the highest rise projected to occur in developing countries. The aim of our investigation is to systematically characterize secular trends in hip fractures worldwide, examine new data for various ethnic groups in the United States, evidence for divergent temporal patterns, and investigate potential contributing factors for the observed change in their epidemiology. All studies retrieved through a complex Medline Ovid search between 1966 and 2013 were examined. For each selected study, we calculated the percent annual change in age-standardized hip fracture rates de-novo. Although occurring at different time points, trend breaks in hip fracture incidence occurred in most Western countries and Oceania. After a steep rise in age-adjusted rates in these regions, a decrease became evident sometimes between the mid-seventies and nineties, depending on the country. Conversely, the data is scarce in Asia and South America, with evidence for a continuous rise in hip fracture rates, with the exception of Hong-Kong and Taiwan that seem to follow Western trends. The etiologies of these secular patterns in both the developed and the developing countries have not been fully elucidated, but the impact of urbanization is at least one plausible explanation. Data presented here show close parallels between rising rates of urbanization and hip fractures across disparate geographic locations and cultures. Once the proportion of the urban population stabilized, hip fracture rates also stabilize or begin to decrease perhaps due to the influence of other factors such as birth cohort effects, changes in bone mineral density and BMI, osteoporosis medication use and/or lifestyle interventions such as smoking cessation, improvement in nutritional status and fall prevention. © 2014 American Society for Bone and Mineral Research.
Mice Expressing Mutant Trpv4 Recapitulate the Human TRPV4 Disorders
Authors: Weinstein Michael M , Tompson Stuart W , Chen Yuqing , Lee Brendan , Cohn Daniel H 
Published: March 2014

ABSTRACT

Activating mutations in transient receptor potential vanilloid family member 4 (Trpv4) are known to cause a spectrum of skeletal dysplasias ranging from autosomal dominant brachyolmia to lethal metatropic dysplasia. To develop an animal model of these disorders, we created transgenic mice expressing either wild-type or mutant TRPV4. Mice transgenic for wild-type Trpv4 showed no morphological changes at embryonic day 16.5 but did have a delay in bone mineralization. Overexpression of a mutant TRPV4 caused a lethal skeletal dysplasia that phenocopied many abnormalities associated with metatropic dysplasia in humans, including dumbbell-shaped long bones, a small ribcage, abnormalities in the autopod, and abnormal ossification in the vertebrae. The difference in phenotype between embryos transgenic for wild-type or mutant Trpv4 demonstrates that an increased amount of wild-type protein can be tolerated and that an activating mutation of this protein is required to produce a skeletal dysplasia phenotype. © 2014 American Society for Bone and Mineral Research
Antagonizing the αvβ3 Integrin Inhibits Angiogenesis and Impairs Woven but Not Lamellar Bone Formation Induced by Mechanical Loading
Authors: Tomlinson Ryan E , Schmieder Anne H , Quirk James D , Lanza Gregory M , Silva Matthew J 
Published: March 2014

ABSTRACT

Angiogenesis and osteogenesis are critically linked, although the role of angiogenesis is not well understood in osteogenic mechanical loading. In this study, either damaging or non-damaging cyclic axial compression was used to generate woven bone formation (WBF) or lamellar bone formation (LBF), respectively, at the mid-diaphysis of the adult rat forelimb. αvβ3 integrin–targeted nanoparticles or vehicle was injected intravenously after mechanical loading. β3 integrin subunit expression on vasculature was maximal 7 days after damaging mechanical loading, but was still robustly expressed 14 days after loading. Accordingly, targeted nanoparticle delivery in WBF-loaded limbs was increased compared with non-loaded limbs. Vascularity was dramatically increased after WBF loading (+700% on day 14) and modestly increased after LBF loading (+50% on day 14). This increase in vascularity was inhibited by nanoparticle treatment in both WBF- and LBF-loaded limbs at days 7 and 14 after loading. Decreased vascularity led to diminished woven, but not lamellar, bone formation. Decreased woven bone formation resulted in impaired structural properties of the skeletal repair, particularly in post-yield behavior. These results demonstrate that αvβ3 integrin–mediated angiogenesis is critical for recovering fracture resistance after bone injury but is not required for bone modeling after modest mechanical strain. © 2014 American Society for Bone and Mineral Research.
Morphology of the eyeball from the humpback whale (Megaptera novaeangliae)
Authors: Rodrigues Fernanda M. , Silva Fernanda M.O. , Trompieri‐Silveira Ana Carolina , Vergara‐Parente Jociery E. , Miglino Maria Angélica , Guimarães Juliana P. 
Published: March 2014

ABSTRACTAquatic mammals underwent morphological and physiological adaptations due to the transition from terrestrial to aquatic environment. One of the morphological changes regards their vision since cetaceans' eyes are able to withstand mechanical, chemical, osmotic, and optical water conditions. Due to insufficient information about these animals, especially regarding their sense organs, this study aimed to describe the morphology of the Humpback whale (Megaptera novaeangliae) eyeball. Three newborn females, stranded dead on the coast of Sergipe and Bahia, Brazil, were used. Samples were fixed in a 10% formalin solution, dissected, photographed, collected, and evaluated through light and electron microscopy techniques. The Humpback whale sclera was thick and had an irregular surface with mechanoreceptors in its lamina propria. Lens was dense, transparent, and ellipsoidal, consisting of three layers, and the vascularized choroid contains melanocytes, mechanoreceptors, and a fibrous tapetum lucidum. The Humpback whale eyeball is similar to other cetaceans and suggests an adaptation to diving and migration, contributing to the perception of differences in temperature, pressure, and lighting. Microsc. Res. Tech. 77:348–355, 2014. © 2014 Wiley Periodicals, Inc.