bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments
Authors: Freire Caio C. M. , Iamarino Atila , Soumaré Peinda O. Ly , Faye Ousmane , Sall Amadou A. , Zanotto Paolo M. A. 
Published: June 2015

AbstractRift Valley Fever virus (RVFV) is a member of Bunyaviridae family that causes a febrile disease affecting mainly ruminants and occasionally humans in Africa, with symptoms that range from mid to severe. RVFV has a tri-segmented ssRNA genome that permits reassortment and could generate more virulent strains. In this study, we reveal the importance of reassortment for RVFV evolution using viral gene genealogy inference and phylodynamics. We uncovered seven events of reassortment that originated RVFV lineages with discordant origins among segments. Moreover, we also found that despite similar selection regimens, the three segments have distinct evolutionary dynamics; the longer segment L evolves at a significant lower rate. Episodes of discordance between population size estimates per segment also coincided with reassortment dating. Our results show that RVFV segments are decoupled enough to have distinct demographic histories and to evolve under different molecular rates.
Ionizing air affects influenza virus infectivity and prevents airborne-transmission
Authors: Hagbom Marie , Nordgren Johan , Nybom Rolf , Hedlund Kjell-Olof , Wigzell Hans , Svensson Lennart 
Published: June 2015

AbstractBy the use of a modified ionizer device we describe effective prevention of airborne transmitted influenza A (strain Panama 99) virus infection between animals and inactivation of virus (>97%). Active ionizer prevented 100% (4/4) of guinea pigs from infection. Moreover, the device effectively captured airborne transmitted calicivirus, rotavirus and influenza virus, with recovery rates up to 21% after 40 min in a 19 m3 room. The ionizer generates negative ions, rendering airborne particles/aerosol droplets negatively charged and electrostatically attracts them to a positively charged collector plate. Trapped viruses are then identified by reverse transcription quantitative real-time PCR. The device enables unique possibilities for rapid and simple removal of virus from air and offers possibilities to simultaneously identify and prevent airborne transmission of viruses.
Metabolomics reveals impaired maturation of HDL particles in adolescents with hyperinsulinaemic androgen excess
Authors: Samino Sara , Vinaixa Maria , Díaz Marta , Beltran Antoni , Rodríguez Miguel A. , Mallol Roger , Heras Mercedes , Cabre Anna , Garcia Lorena , Canela Nuria , de Zegher Francis , Correig Xavier , Ibáñez Lourdes , Yanes Oscar 
Published: June 2015

AbstractHyperinsulinaemic androgen excess (HIAE) in prepubertal and pubertal girls usually precedes a broader pathological phenotype in adulthood that is associated with anovulatory infertility, metabolic syndrome and type 2 diabetes. The metabolic derangements that determine these long-term health risks remain to be clarified. Here we use NMR and MS-based metabolomics to show that serum levels of methionine sulfoxide in HIAE girls are an indicator of the degree of oxidation of methionine-148 residue in apolipoprotein-A1. Oxidation of apo-A1 in methionine-148, in turn, leads to an impaired maturation of high-density lipoproteins (HDL) that is reflected in a decline of large HDL particles. Notably, such metabolic alterations occur in the absence of impaired glucose tolerance, hyperglycemia and hypertriglyceridemia and were partially restored after 18 months of treatment with a low-dose combination of pioglitazone, metformin and flutamide.
ZnO nanowires array grown on Ga-doped ZnO single crystal for dye-sensitized solar cells
Authors: Hu Qichang , Li Yafeng , Huang Feng , Zhang Zhaojun , Ding Kai , Wei Mingdeng , Lin Zhang 
Published: June 2015

AbstractHigh quality ZnO nanowires arrays were homoepitaxial grown on Ga-doped ZnO single crystal (GZOSC), which have the advantages of high conductivity, high carrier mobility and high thermal stability. When it was employed as a photoanode in the DSSCs, the cell exhibited a 1.44% power-conversion efficiency under the illumination of one sun (AM 1.5G). The performance is superior to our ZnO nanowires/FTO based DSSCs under the same condition. This enhanced performance is mainly attributed to the perfect interface between the ZnO nanowires and the GZOSC substrate that contributes to lower carrier scattering and recombination rates compared with that grown on traditional FTO substrate.
Latent progenitor cells as potential regulators for tympanic membrane regeneration
Authors: Kim Seung Won , Kim Jangho , Seonwoo Hoon , Jang Kyung-Jin , Kim Yeon Ju , Lim Hye Jin , Lim Ki-Taek , Tian Chunjie , Chung Jong Hoon , Choung Yun-Hoon 
Published: June 2015

AbstractTympanic membrane (TM) perforation, in particular chronic otitis media, is one of the most common clinical problems in the world and can present with sensorineural healing loss. Here, we explored an approach for TM regeneration where the latent progenitor or stem cells within TM epithelial layers may play an important regulatory role. We showed that potential TM stem cells present highly positive staining for epithelial stem cell markers in all areas of normal TM tissue. Additionally, they are present at high levels in perforated TMs, especially in proximity to the holes, regardless of acute or chronic status, suggesting that TM stem cells may be a potential factor for TM regeneration. Our study suggests that latent TM stem cells could be potential regulators of regeneration, which provides a new insight into this clinically important process and a potential target for new therapies for chronic otitis media and other eardrum injuries.
A predictive machine learning approach for microstructure optimization and materials design
Authors: Liu Ruoqian , Kumar Abhishek , Chen Zhengzhang , Agrawal Ankit , Sundararaghavan Veera , Choudhary Alok 
Published: June 2015

AbstractThis paper addresses an important materials engineering question: How can one identify the complete space (or as much of it as possible) of microstructures that are theoretically predicted to yield the desired combination of properties demanded by a selected application? We present a problem involving design of magnetoelastic Fe-Ga alloy microstructure for enhanced elastic, plastic and magnetostrictive properties. While theoretical models for computing properties given the microstructure are known for this alloy, inversion of these relationships to obtain microstructures that lead to desired properties is challenging, primarily due to the high dimensionality of microstructure space, multi-objective design requirement and non-uniqueness of solutions. These challenges render traditional search-based optimization methods incompetent in terms of both searching efficiency and result optimality. In this paper, a route to address these challenges using a machine learning methodology is proposed. A systematic framework consisting of random data generation, feature selection and classification algorithms is developed. Experiments with five design problems that involve identification of microstructures that satisfy both linear and nonlinear property constraints show that our framework outperforms traditional optimization methods with the average running time reduced by as much as 80% and with optimality that would not be achieved otherwise.
Constructal thermodynamics combined with infrared experiments to evaluate temperature differences in cells
Authors: Lucia Umberto , Grazzini Giuseppe , Montrucchio Bartolomeo , Grisolia Giulia , Borchiellini Romano , Gervino Gianpiero , Castagnoli Carlotta , Ponzetto Antonio , Silvagno Francesca 
Published: June 2015

AbstractThe aim of this work was to evaluate differences in energy flows between normal and immortalized cells when these distinct biological systems are exposed to environmental stimulation. These differences were considered using a constructal thermodynamic approach and were subsequently verified experimentally. The application of constructal law to cell analysis led to the conclusion that temperature differences between cells with distinct behaviour can be amplified by interaction between cells and external fields. Experimental validation of the principle was carried out on two cellular models exposed to electromagnetic fields. By infrared thermography we were able to assess small changes in heat dissipation measured as a variation in cell internal energy. The experimental data thus obtained are in agreement with the theoretical calculation, because they show a different thermal dispersion pattern when normal and immortalized cells are exposed to electromagnetic fields. By using two methods that support and validate each other, we have demonstrated that the cell/environment interaction can be exploited to enhance cell behavior differences, in particular heat dissipation. We propose infrared thermography as a technique effective in discriminating distinct patterns of thermal dispersion and therefore able to distinguish a normal phenotype from a transformed one.
Translational utility of rodent hippocampal auditory gating in schizophrenia research: a review and evaluation
Authors: Smucny J , Stevens K E , Olincy A , Tregellas J R 
Published: June 2015

AbstractImpaired gating of the auditory evoked P50 potential is one of the most pharmacologically well-characterized features of schizophrenia. This deficit is most commonly modeled in rodents by implanted electrode recordings from the hippocampus of the rodent analog of the P50, the P20–N40. The validity and effectiveness of this tool, however, has not been systematically reviewed. Here, we summarize findings from studies that have examined the effects of pharmacologic modulation on gating of the rodent hippocampal P20–N40 and the human P50. We show that drug effects on the P20–N40 are highly predictive of human effects across similar dose ranges. Furthermore, mental status (for example, anesthetized vs alert) does not appear to diminish the predictive capacity of these recordings. We then discuss hypothesized neuropharmacologic mechanisms that may underlie gating effects for each drug studied. Overall, this review supports continued use of hippocampal P20–N40 gating as a translational tool for schizophrenia research.
Near‐zero dead zone phase frequency detector with wide input frequency difference
Authors: Strzelecki J. , Ren S. 
Published: June 2015

An all‐digital phase frequency detector design capable of accepting an infinite range of input frequency differences and [0 2π] radians input phase difference is presented. The proposed phase frequency detector design minimises the dead zone, supresses unwanted output glitches, achieves a high maximum operating frequency, can drive high‐capacitive loads and avoids differential outputs. The proposed phase frequency detector takes advantage of a fast reset operation from modified tristate inverters acting as a D flip‐flop. Simulation results indicate that the design can detect input phase differences as small as 750 fs apart for all process corners at input operating frequencies of 38 kHz–2.5 GHz in 1.2 V, 90 nm CMOS technology.
Enhanced memory consolidation in mice lacking the circadian modulators Sharp1 and -2 caused by elevated Igf2 signaling in the cortex
Authors: Shahmoradi Ali , Radyushkin Konstantin , Rossner Moritz J. 
Published: June 2015

Significance
SHARP1 and SHARP2 transcription factors are modulators of the sleep/wake homeostasis. Sleep is thought to be important for efficient memory consolidation by gradual stabilization of hippocampus-dependent memory traces in stable cortical modules. Here, SHARP1 and SHARP2 single and double null mutant mice were investigated in cognitive processing. SHARP1 and SHARP2 double null mutants show enhanced cortex-dependent remote fear memory formation, although hippocampus-dependent recent fear memory formation is not changed. Molecular analyses revealed that insulin-related growth factor 2 (IGF2)/MAPK signaling is elevated in the cortex of double mutants and that IGF2 overexpression in the anterior cingulate cortex is sufficient to enhance fear memory consolidation. Our analyses provide evidence that the control of sleep and memory consolidation may share common molecular mechanisms.
Effect of salt on the H-bond symmetrization in ice
Authors: Bove Livia Eleonora , Gaal Richard , Raza Zamaan , Ludl Adriaan-Alexander , Klotz Stefan , Saitta Antonino Marco , Goncharov Alexander F. , Gillet Philippe 
Published: June 2015

Significance
Ice-VII and ice-X phases are the most stable forms of ice at high temperature and extreme pressures, typical of the interiors of satellites and planets. The phase transition between them is a prototypical case of quantum-driven phenomenon, as it can be described as a quantum delocalization of protons in the middle of O–O distances. In this study, we investigate the effect of ions on such quantum effects. We show that the presence of ions significantly modifies the fundamental H-bond properties of water ices. This finding could challenge our present description of the physics of ice bodies, essentially based on the assumption of the properties of pure ice under high pressure.
Pathways to dewetting in hydrophobic confinement
Authors: Remsing Richard C. , Xi Erte , Vembanur Srivathsan , Sharma Sumit , Debenedetti Pablo G. , Garde Shekhar , Patel Amish J. 
Published: June 2015

Significance
Dewetting in hydrophobic confinement plays an important role in diverse phenomena, ranging from protein folding and assembly, to the heterogeneous nucleation of vapor bubbles and superhydrophobicity. Using molecular simulations, we find that dewetting proceeds through the formation of isolated cavities adjacent to one of the confining surfaces. These isolated cavities are stabilized by enhanced water density fluctuations, and their growth is uphill in free energy. Upon growing to a certain size, the isolated cavities transition abruptly into supercritical vapor tubes that span the confined region, and grow spontaneously. Consequently, this nonclassical pathway results in lower free energy barriers than anticipated by macroscopic theory, with important implications for the kinetics of dewetting and hence for water-mediated self-assembly.
Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar
Authors: Baxa Michael C. , Yu Wookyung , Adhikari Aashish N. , Ge Liang , Xia Zhen , Zhou Ruhong , Freed Karl F. , Sosnick Tobin R. 
Published: June 2015

Significance
An outstanding issue in protein science is identifying the relationship between sequence and folding, e.g., do sequences having similar structures have similar folding pathways? The homologs Proteins G & L have been cited as a primary example where sequence variations dramatically affect folding dynamics. However, our new results indicate that the homologs have similar folding behavior. At the highest point on the reaction surface, the pathways converge to similar ensembles. These findings are distinct from descriptions based on the widely used mutational ϕ analysis, partly due to nonnative behavior. Our study emphasizes that significant challenges remain both in characterizing and predicting transition state ensembles even for relatively simple proteins whose folding behavior is believed to be well understood.
Statistical learning and selective inference
Authors: Taylor Jonathan , Tibshirani Robert J. 
Published: June 2015

Significance
Most statistical analyses involve some kind of ‟selection”—searching through the data for the strongest associations. Measuring the strength of the resulting associations is a challenging task, because one must account for the effects of the selection. There are some new tools in selective inference for this task, and we illustrate their use in forward stepwise regression, the lasso, and principal components analysis.
Genetic and epigenetic architecture of sex-biased expression in the jewel wasps
Nasonia vitripennis
and
giraulti
Authors: Wang Xu , Werren John H. , Clark Andrew G. 
Published: June 2015

Significance
This paper provides a comprehensive analysis of sex differential gene expression in haplodiploid jewel wasps. Between two closely related species, 75% of genes display differential expression, despite males having half the genetic complement of females, with no sex chromosomes. These differences are not directly mediated by sex-specific methylation because almost no sex differences in methylation were observed. Genes with sex-specific expression show low frequency of methylation. However, the majority of female-biased genes are methylated (in both sexes), whereas male-biased ones are mostly nonmethylated in either sex. We conclude that female-biased genes are more likely to be recruited from conserved methylated genes over evolutionary time, whereas most male-biased genes are from genes after recent duplication events that are not methylated.
Family poultry and food and nutrition security.
Authors: Bruyn J. de , Wong J. , Bagnol B. , Pengelly B. , Alders R. 
Published: June 2015

Abstract
Family poultry production, which encompasses both extensive and small-scale intensive management systems, is practiced by many households in low-income food-deficit countries. Despite low production levels and potentially high losses due to disease, predation and theft, scavenging systems offer the advantage of requiring minimal land, labour and capital inputs. Human undernutrition remains a major public health challenge globally, contributing to over 3 million preventable maternal and child deaths each year. Animal source foods, including poultry (meat and organs) and eggs, can provide high-quality protein and micronutrients in bioavailable forms which, even in small quantities, substantially increase the nutrient adequacy of traditional diets based on staple crops. Women are recognized as key players in family poultry production systems and successful engagement with this sector should incorporate gender-sensitive approaches. It has been shown that agricultural interventions which target women are more likely to lead to positive nutritional outcomes. A multi-disciplinary research approach, multi-sectoral involvement within government institutions and the implementation of policies which target smallholder farmers is needed in order to maximize the potential impact of improvements to family poultry systems on food and nutritional security.
Bandage: interactive visualization of de novo genome assemblies
Authors: Wick Ryan R. , Schultz Mark B. , Zobel Justin , Holt Kathryn E. 
Published: June 2015

Abstract
Summary: Although de novo assembly graphs contain assembled contigs (nodes), the connections between those contigs (edges) are difficult for users to access. Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone.
Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage.
Contact: rrwick@gmail.com
Supplementary information : Supplementary data are available at Bioinformatics online.
French Visions of Empire: Contesting British Power in India after the Seven Years War
Authors: Margerison Kenneth 
Published: June 2015

Abstract
Britain’s decisive victory in the Seven Years War destroyed much of the French empire in North America and seriously weakened the French position in India, resulting in the demise of the authority of the Compagnie des Indes in 1769. Despite the devastating results of defeat, the French royal government began laying plans to challenge Britain’s global power. The French position in India, however, was quite weak. Pondichéry, the principal French establishment, had been destroyed during the war, and France had only a small armed force on the subcontinent after 1763. However, the colonial officials in India assured the ministry that many important Indian princes chafed under the tyrannical authority of the British East India Company and would eagerly join—and, some argued, even pay for—a French invasion force in order to weaken or destroy that power. The prospect of a colonial uprising in North America added to the French hopes of success. The governor, Jean Law de Lauriston, insisted that France increase its military force and rebuild the fortifications at Pondichéry to demonstrate French power to the Indian rulers. The ministry, however, did not bolster its military presence in India, preferring to believe that the princes would bear the brunt of the expenses and fighting in India while France devoted its resources to the North American conflict. In the end this vision of a restored French presence in India failed to materialise because the Indian rulers saw little evidence that France would undertake a meaningful attack against British authority in India.
The Association of Demodex with Chalazia: A Histopathologic Study of the Eyelid
Authors: Schear Matthew J. , Milman Tatyana , Steiner Tehilla , Shih Carolyn , Udell Ira J. , Steiner Anne 
Published: June 2015

Purpose:
To investigate the association of Demodex with chalazia and to describe the associated histopathologic changes in the eyelid tissue.

Methods:
In a retrospective histopathologic case–control study, 78 ectropion/entropion repair eyelid wedge resections were examined. Serial sections were obtained on formalin-fixed, paraffin-embedded tissues, stained with hematoxylin-eosin and studied by light microscopy. Thirty-eight patient specimens had evidence of chalazia and 40 did not. The main outcome measures included quantification of total eyelid hair follicles, meibomian glands, Demodex folliculorum and Demodex brevis; determining the presence of lipogranulomatous and non-lipogranulomatous inflammation, hair follicle and meibomian gland duct dilatation and hyperkeratinization, and meibomian gland acinar dilation, keratinization, and atrophy.

Results:
There was a significantly greater mean number of D. folliculorum in biopsies with chalazia, when compared with biopsies without chalazia (5.55 vs. 2.68, p = 0.044). The presence of D. folliculorum was strongly associated with hair follicle duct dilatation and hyperkeratinization and with perifollicular nongranulomatous inflammation (p = 0.00). Hair follicle duct dilatation, hyperkeratinization, and perifollicular inflammation were also independently associated with chalazia (p = 0.040 and 0.031, respectively). D. brevis was observed only in meibomian glands with chalazia (mean = 0.342), but this finding did not reach statistical significance; p= 0.068.

Conclusion:
While the authors cannot establish causality between Demodex and chalazia, these findings suggest that D. folliculorum indirectly may be involved in the pathogenesis of chalazia via its effect on the anterior eyelid margin.