bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrasted phylogeographic patterns on mitochondrial DNA of shallow and deep brittle stars across the Atlantic-Mediterranean area
Authors: Taboada Sergi , Pérez-Portela Rocío 
Published: September 2016

AbstractPrevious studies on Ophiothrix in European waters demonstrated the existence of two distinct species, Ophiothrix fragilis and Ophiothrix sp. II. Using phylogenetic and species delimitation techniques based on two mitochondrial genes (cytochrome c oxidase I and 16S rRNA) we prove the existence of a new congeneric species (Ophiothrix sp. III), occurring in the deep Atlantic coast of the Iberian Peninsula and the Alboran Sea. We compared phylogeographic patterns of these three Ophiothrix species to test whether closely related species are differentially affected by past demographic events and current oceanographic barriers. We used 432 sequences (137 of O. fragilis, 215 of Ophiothrix sp. II, and 80 of Ophiothrix sp. III) of the 16S rRNA from 23 Atlantic-Mediterranean locations for the analyses. We observed different geographic and bathymetric distributions, and contrasted phylogeography among species. Ophiothrix fragilis appeared genetically isolated between the Atlantic and Mediterranean basins, attributed to past vicariance during Pleistocene glaciations and a secondary contact associated to demographic expansion. This contrasts with the panmixia observed in Ophiothrix sp. II across the Atlantic-Mediterranean area. Results were not conclusive for Ophiothrix sp. III due to the lack of a more complete sampling within the Mediterranean Sea.
Effect of Surface Defect States on Valence Band and Charge Separation and Transfer Efficiency
Authors: Xu Juan , Teng Yiran , Teng Fei 
Published: September 2016

AbstractBoth energy band and charge separation and transfer are the crucial affecting factor for a photochemical reaction. Herein, the BiOCl nanosheets without and with surface bismuth vacancy (BOC, V-BOC) are prepared by a simple hydrothermal method. It is found that the new surface defect states caused by bismuth vacancy have greatly up-shifted the valence band and efficiently enhanced the separation and transfer rates of photogenerated electron and hole. It is amazing that the photocatalytic activity of V-BOC is 13.6 times higher than that of BOC for the degradation methyl orange (MO). We can develop an efficient photocatalyst by the introduction of defects.
Integrated proteomics and metabolomics analysis of rat testis: Mechanism of arsenic-induced male reproductive toxicity
Authors: Huang Qingyu , Luo Lianzhong , Alamdar Ambreen , Zhang Jie , Liu Liangpo , Tian Meiping , Eqani Syed Ali Musstjab Akber Shah , Shen Heqing 
Published: September 2016

AbstractArsenic is a widespread metalloid in environment, whose exposure has been associated with a broad spectrum of toxic effects. However, a global view of arsenic-induced male reproductive toxicity is still lack, and the underlying mechanisms remain largely unclear. Our results revealed that arsenic exposure decreased testosterone level and reduced sperm quality in rats. By conducting an integrated proteomics and metabolomics analysis, the present study aims to investigate the global influence of arsenic exposure on the proteome and metabolome in rat testis. The abundance of 70 proteins (36 up-regulated and 34 down-regulated) and 13 metabolites (8 increased and 5 decreased) were found to be significantly altered by arsenic treatment. Among these, 19 proteins and 2 metabolites were specifically related to male reproductive system development and function, including spermatogenesis, sperm function and fertilization, fertility, internal genitalia development, and mating behavior. It is further proposed that arsenic mainly impaired spermatogenesis and fertilization via aberrant modulation of these male reproduction-related proteins and metabolites, which may be mediated by the ERK/AKT/NF-κB-dependent signaling pathway. Overall, these findings will aid our understanding of the mechanisms responsible for arsenic-induced male reproductive toxicity, and from such studies useful biomarkers indicative of arsenic exposure could be discovered.
A path-based measurement for human miRNA functional similarities using miRNA-disease associations
Authors: Ding Pingjian , Luo Jiawei , Xiao Qiu , Chen Xiangtao 
Published: September 2016

AbstractCompared with the sequence and expression similarity, miRNA functional similarity is so important for biology researches and many applications such as miRNA clustering, miRNA function prediction, miRNA synergism identification and disease miRNA prioritization. However, the existing methods always utilized the predicted miRNA target which has high false positive and false negative to calculate the miRNA functional similarity. Meanwhile, it is difficult to achieve high reliability of miRNA functional similarity with miRNA-disease associations. Therefore, it is increasingly needed to improve the measurement of miRNA functional similarity. In this study, we develop a novel path-based calculation method of miRNA functional similarity based on miRNA-disease associations, called MFSP. Compared with other methods, our method obtains higher average functional similarity of intra-family and intra-cluster selected groups. Meanwhile, the lower average functional similarity of inter-family and inter-cluster miRNA pair is obtained. In addition, the smaller p-value is achieved, while applying Wilcoxon rank-sum test and Kruskal-Wallis test to different miRNA groups. The relationship between miRNA functional similarity and other information sources is exhibited. Furthermore, the constructed miRNA functional network based on MFSP is a scale-free and small-world network. Moreover, the higher AUC for miRNA-disease prediction indicates the ability of MFSP uncovering miRNA functional similarity.
Localization-delocalization wavepacket transition in Pythagorean aperiodic potentials
Authors: Huang Changming , Ye Fangwei , Chen Xianfeng , Kartashov Yaroslav V. , Konotop Vladimir V. , Torner Lluis 
Published: September 2016

AbstractWe introduce a composite optical lattice created by two mutually rotated square patterns and allowing observation of continuous transformation between incommensurate and completely periodic structures upon variation of the rotation angle θ. Such lattices acquire periodicity only for rotation angles cos θ = a/c, sin θ = b/c, set by Pythagorean triples of natural numbers (a, b, c). While linear eigenmodes supported by lattices associated with Pythagorean triples are always extended, composite patterns generated for intermediate rotation angles allow observation of the localization-delocalization transition of eigenmodes upon modification of the relative strength of two sublattices forming the composite pattern. Sharp delocalization of supported modes for certain θ values can be used for visualization of Pythagorean triples. The effects predicted here are general and also take place in composite structures generated by two rotated hexagonal lattices.
Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls
Authors: Knecht Carolin , Fretter Christoph , Rosenstiel Philip , Krawczak Michael , Hütt Marc-Thorsten 
Published: September 2016

AbstractInformation on biological networks can greatly facilitate the function-orientated interpretation of high-throughput molecular data. Genome-wide metabolic network models of human cells, in particular, can be employed to contextualize gene expression profiles of patients with the goal of both, a better understanding of individual etiologies and an educated reclassification of (clinically defined) phenotypes. We analyzed publicly available expression profiles of intestinal tissues from treatment-naive pediatric inflammatory bowel disease (IBD) patients and age-matched control individuals, using a reaction-centric metabolic network derived from the Recon2 model. By way of defining a measure of ‘coherence’, we quantified how well individual patterns of expression changes matched the metabolic network. We observed a bimodal distribution of metabolic network coherence in both patients and controls, albeit at notably different mixture probabilities. Multidimensional scaling analysis revealed a bisectional pattern as well that overlapped widely with the metabolic network-based results. Expression differences driving the observed bimodality were related to cellular transport of thiamine and bile acid metabolism, thereby highlighting the crosstalk between metabolism and other vital pathways. We demonstrated how classical data mining and network analysis can jointly identify biologically meaningful patterns in gene expression data.
Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley
Authors: Saade Stephanie , Maurer Andreas , Shahid Mohammed , Oakey Helena , Schmöckel Sandra M. , Negrão Sónia , Pillen Klaus , Tester Mark 
Published: September 2016

AbstractProducing sufficient food for nine billion people by 2050 will be constrained by soil salinity, especially in irrigated systems. To improve crop yield, greater understanding of the genetic control of traits contributing to salinity tolerance in the field is needed. Here, we exploit natural variation in exotic germplasm by taking a genome-wide association approach to a new nested association mapping population of barley called HEB-25. The large population (1,336 genotypes) allowed cross-validation of loci, which, along with two years of phenotypic data collected from plants irrigated with fresh and saline water, improved statistical power. We dissect the genetic architecture of flowering time under high salinity and we present genes putatively affecting this trait and salinity tolerance. In addition, we identify a locus on chromosome 2H where, under saline conditions, lines homozygous for the wild allele yielded 30% more than did lines homozygous for the Barke allele. Introgressing this wild allele into elite cultivars could markedly improve yield under saline conditions.
Pleiotropic roles of the matricellular protein Sparc in tendon maturation and ageing
Authors: Gehwolf Renate , Wagner Andrea , Lehner Christine , Bradshaw Amy D. , Scharler Cornelia , Niestrawska Justyna A. , Holzapfel Gerhard A. , Bauer Hans-Christian , Tempfer Herbert , Traweger Andreas 
Published: September 2016

AbstractAcute and chronic tendinopathies remain clinically challenging and tendons are predisposed to degeneration or injury with age. Despite the high prevalence of tendon disease in the elderly, our current understanding of the mechanisms underlying the age-dependent deterioration of tendon function remains very limited. Here, we show that Secreted protein acidic and rich in cysteine (Sparc) expression significantly decreases in healthy-aged mouse Achilles tendons. Loss of Sparc results in tendon collagen fibrillogenesis defects and Sparc−/− tendons are less able to withstand force in comparison with their respective wild type counterparts. On the cellular level, Sparc-null and healthy-aged tendon-derived cells exhibited a more contracted phenotype and an altered actin cytoskeleton. Additionally, an elevated expression of the adipogenic marker genes PPARγ and Cebpα with a concomitant increase in lipid deposits in aged and Sparc−/− tendons was observed. In summary, we propose that Sparc levels in tendons are critical for proper collagen fibril maturation and its age-related decrease, together with a change in ECM properties favors lipid accretion in tendons.
Peptidomimetics Based On Dehydroepiandrosterone Scaffold: Synthesis, Antiproliferation Activity, Structure-Activity Relationship, and Mechanisms
Authors: Wang Xiaohui , Su Haihuan , Wang Wenda , Chen Changshui , Cao Xiufang 
Published: September 2016

AbstractA series of novel peptidomimetics bearing dehydroepiandrosterone moiety were designed, synthesized, and evaluated for their inhibition activities against cell proliferation. According to the preliminary studies on inhibitory activities, some of the newly prepared compounds indicated significantly inhibition activities against human hepatoma cancer (HepG2), human lung cancer (A549), human melanoma (A875) cell lines compared with the control 5-fluorouracil. Especially, compounds Ii (IC50 < 14 μM) and Ik (IC50 < 13 μM) exhibited obvious inhibition activities against all tested cell lines. The highly potential compound Ik induced apoptosis in HepG2 cells were analyzed by flow cytometry, and the apoptotic effects of compound Ik were further evaluated using Annexin V-FITC/propidium iodide dual staining assay, which revealed these highly potential compounds induced cell death in HepG2 cells at least partly by apoptosis.
Keratin 8 limits TLR-triggered inflammatory responses through inhibiting TRAF6 polyubiquitination
Authors: Dong Xiao-Ming , Liu En-Dong , Meng Yun-Xiao , Liu Chao , Bi Ya-Lan , Wu Huan-Wen , Jin Yan-Chao , Yao Jing-Hui , Tang Liu-Jun , Wang Jian , Li Min , Zhang Chao , Yu Miao , Zhan Yi-Qun , Chen Hui , Ge Chang-Hui , Yang Xiao-Ming , Li Chang-Yan 
Published: September 2016

AbstractToll-like receptors (TLRs) have critical roles in innate immunity and inflammation and the detailed mechanisms by which TLR signaling is fine tuned remain unclear. Keratin 8 (CK8) belongs to the type II keratin family and is the major compontent of the intermediate filaments of simple or single-layered epithelia. Here we report that down-regulation of CK8 in mice enhanced TLR-mediated responses, rendering mice more susceptible to lipopolysaccharide (LPS)-induced endotoxin shock and Escherichia coli–caused septic peritonitis with reduced survival, elevated levels of inflammation cytokines and more severe tissue damage. We found that CK8 suppressed TLR-induced nuclear factor (NF)-κB activation and interacted with the adaptor tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) to prevent its polyubiquitination. Our findings demonstrate a novel role of CK8 in negative regulation of TLR/NF-κB signaling and highlight a previously unidentified nonclassical function for CK8 in limiting inflammatory responses.
A facile strategy for rapid preparation of graphene spongy balls
Authors: Wan Shu , Bi Hengchang , Xie Xiao , Su Shi , Du Kai , Jia Haiyang , Xu Tao , He Longbing , Yin Kuibo , Sun Litao 
Published: September 2016

AbstractPorous three dimensional (3D) graphene macrostructures have demonstrated the potential in versatile applications in recent years, including energy storage, sensors, and environment protection, etc. However, great research attention has been focused on the optimization of the structure and properties of graphene-based materials. Comparatively, there are less reports on how to shape 3D graphene macrostructures rapidly and effortlessly, which is critical for mass production in industry. Here, we introduce a facile and efficient method, low temperature frying to form graphene-based spongy balls in liquid nitrogen with a yield of ~400 balls min−1. Moreover, the fabrication process can be easily accelerated by using multi pipettes working at the same time. The graphene spongy balls show energy storage with a specific capacitance of 124 F g−1 and oil adsorbing with a capacity of 105.4 times its own weight. This strategy can be a feasible approach to overcome the low efficiency in production and speed up the development of porous 3D graphene-based macrostructures in industrial applications.
Differences in cooperative behavior among Damaraland mole rats are consequences of an age-related polyethism
Authors: Zöttl Markus , Vullioud Philippe , Mendonça Rute , Torrents Ticó Miquel , Gaynor David , Mitchell Adam , Clutton-Brock Tim 
Published: September 2016

Significance
Nonreproductive group members of naked and Damaraland mole rats are thought to be organized in permanent, distinct castes that differ in behavior and physiology, suggesting that their social organization resembles that of obligatorily eusocial insects. This study tests predictions about the distribution of cooperative behavior based on the suggestion that individual differences represent a caste system. Our data provide no evidence that helpers show fixed, divergent developmental pathways or specialize in particular tasks. Instead, variation in their behavior appears to represent an age-related polyethism. The results suggest that the behavioral organization of social mole-rat groups is similar to that of other singular cooperatively breeding vertebrates, and that similarities to obligatorily eusocial insects have been overestimated.
Selected dehydrogenases in Yarrowia lipolytica JMY 861: their role in the synthesis of flavor compounds
Authors: Aziz Marya , St-Louis Richard , Husson Florence , Kermasha Selim 
Published: September 2016

Abstract
The presence of selected dehydrogenases, including alcohol dehydrogenase (ADH-YL) and aldehyde dehydrogenase (ALDH-YL), in Yarrowia lipolytica JMY 861, and their potential role in flavor synthesis were investigated. The experimental findings showed that using reduced form of nicotinamide adenine dinucleotide (NADH) as cofactor, the ADH-YL activity in vitro was 6-fold higher than that with reduced form of nicotinamide adenine dinucleotide phosphate (NADPH); however, under the experimental conditions used in this study, an ALDH-YL activity was not detected. The in situ hexanal reduction reaction was found to be instantaneous; however, when the yeast cells suspension was diluted 150 times, the initial relative hexanal concentration was increased by 84.1%. The chromatographic analyses indicated the conversion, in situ, of linoleic acid hydroperoxides (HPODs) into volatile C6-compounds after 60 min of HPODs addition to the yeast cells suspension.
Comparison of Phytoplankton Communities in Catfish Split-Pond Aquaculture Systems with Conventional Ponds
Authors: Schrader Kevin K , Tucker Craig S , Brown Travis W , Torrans Eugene L , Whitis Gregory N 
Published: September 2016

Abstract
There has been a growing interest and use of variations of partitioned aquaculture systems (PAS) in recent years by the southeastern U.S. catfish farming industry. Split-pond systems, one type of PAS, are designed to better manage fish waste byproducts (e.g., ammonia) and dissolved oxygen levels than the conventional earthen ponds that have been used by farmers for many decades. Recent studies have focused on design, water flow rates, and other management areas of catfish split-ponds, but so far there has not been a focused examination of phytoplankton community composition and biomass in these split-ponds. In the current study, pond water samples were collected from split-ponds at a research facility in western Mississippi and at a commercial fish farm in western Alabama approximately every 3 weeks during the fish grow-out period (May to November). Water samples were analyzed for chlorophyll a concentration (phytoplankton biomass) of several major phytoplankton divisions and for types of phytoplankton and their abundance. Overall, chlorophyll a concentrations in the split-ponds were maintained within the typical range (0–800 µg/L) found in non-PAS (conventional) catfish ponds. The phytoplankton communities in split-ponds were dominated by cyanobacteria or blue-green algae (Cyanophyta) and by the same common species of cyanobacteria (e.g., Planktothrix agardhii, P. perornata, Microcystis aeruginosa, Raphidiopsis brookii) reported in previous studies for conventional catfish ponds. In addition, many types of phytoplankton in the other major divisions—Chlorophyta (green algae), Bacillariophyta (diatoms), Chrysophyta (golden brown algae), Cryptophyta (cryptomonads), Euglenophyta (euglenophytes), and Pyrrhophyta (dinoflagellates)—present in the split-ponds were the same as those reported previously in conventional catfish ponds. Therefore, issues related to management practices for pond water quality (e.g., dissolved oxygen) and undesirable cyanobacteria are expected to be similar to those used for conventional ponds.
Optimization of a mirror-based neutron source using differential evolution algorithm
Authors: Yurov D.V. , Prikhodko V.V. 
Published: September 2016

Abstract
This study is dedicated to the assessment of capabilities of gas-dynamic trap (GDT) and gas-dynamic multiple-mirror trap (GDMT) as potential neutron sources for subcritical hybrids. In mathematical terms the problem of the study has been formulated as determining the global maximum of fusion gain (Q
pl), the latter represented as a function of trap parameters. A differential evolution method has been applied to perform the search. Considered in all calculations has been a configuration of the neutron source with 20 m long distance between the mirrors and 100 MW heating power. It is important to mention that the numerical study has also taken into account a number of constraints on plasma characteristics so as to provide physical credibility of searched-for trap configurations. According to the results obtained the traps considered have demonstrated fusion gain up to 0.2, depending on the constraints applied. This enables them to be used either as neutron sources within subcritical reactors for minor actinides incineration or as material-testing facilities.
Cooperative DNA binding by a splice variant of the transcription factor ETS1 that lacks autoinhibition
Authors: Samorodnitsky Daniel , Szyjka Courtney , Koudelka Gerald B. 
Published: September 2016

AbstractETS1 is the archetypal member of the metazoan ETS transcription factor family. All the members of this family bind to the conserved GGA(A/T) core ETS binding sequence (EBS). Several ETS family members exhibit autoinhibition, wherein one domain of ETS blocks its own DNA-binding activity until certain conditions are met. Relief of autoinhibition in these proteins is coupled to homo- or hetero-dimer formation. Relief of autoinhibition in full-length ETS1 is catalyzed by non-specific interaction with DNA, which facilitates the formation of protein dimers.The ETS1 splice variant, ETS1-p42, lacks an exon that encodes a crucial part of the autoinhibitory module. Thus,ETS1-p42 does not autoinhibit. We showed that the absence of autoinhibition allows ETS1Δ335, an N-terminal deletion that recapitulates the DNA-binding of ETS1-p42, to form homodimers in the absence of DNA. However, ETS1-p42 is thought to bind its DNA sites only as monomers. Here, we explore this paradox and show that ETS1Δ335 binds cooperatively to DNA containing two EBSs. We also show that residues in ETS1’s DNA recognition helix mediate this DNA-binding cooperativity. Furthermore we also find that a single EBS can bind two ETS1Δ335 subunits. Finally, we show that DNA acts catalytically to separate unbound ETS1Δ335 dimers into monomers. Together,these results suggest a model of ETS1-p42 DNA-binding, where ETS1-p42 can bind to a single EBS with 2:1 stoichiometry.
The impacts of drift and selection on genomic evolution in holometabolous insects
Authors: Tong K. Jun , Duchêne Sebastián , Lo Nathan , Ho Simon Y. W. 
Published: September 2016

AbstractGenomes evolve through a medley of mutation, drift, and selection, all of which act heterogeneously across genes and lineages. The pacemaker models of genomic evolution describe the resulting patterns of evolutionary rate variation: genes that are governed by the same pacemaker exhibit the same pattern of rate heterogeneity across lineages. However, the relative importance of drift and selection in determining the structure of these pacemakers is unknown. Here, we propose a novel phylogenetic approach to explain the formation of pacemakers. We apply this method to a genomic dataset from holometabolous insects, an ancient and diverse group of organisms. We show that when drift is the dominant evolutionary process, each pacemaker tends to govern a large number of fast-evolving genes. In contrast, strong negative selection leads to many distinct pacemakers, each of which governs a few slow-evolving genes. Our results provide new insights into the interplay between drift and selection in driving genomic evolution.