bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synergetic Action of Domain II and IV Underlies Persistent Current Generation in Nav1.3 as revealed by a tarantula toxin
Authors: Tang Cheng , Zhou Xi , Zhang Yunxiao , xiao Zhaohua , Hu Zhaotun , Zhang Changxin , Huang Ying , Chen Bo , Liu Zhonghua , Liang Songping 
Published: March 2015

AbstractThe persistent current (INaP) through voltage-gated sodium channels enhances neuronal excitability by causing prolonged depolarization of membranes. Nav1.3 intrinsically generates a small INaP, although the mechanism underlying its generation remains unclear. In this study, the involvement of the four domains of Nav1.3 in INaP generation was investigated using the tarantula toxin α-hexatoxin-MrVII (RTX-VII). RTX-VII activated Nav1.3 and induced a large INaP. A pre-activated state binding model was proposed to explain the kinetics of toxin-channel interaction. Of the four domains of Nav1.3, both domain II and IV might play important roles in the toxin-induced INaP. Domain IV constructed the binding site for RTX-VII, while domain II might not participate in interacting with RTX-VII but could determine the efficacy of RTX-VII. Our results based on the use of RTX-VII as a probe suggest that domain II and IV cooperatively contribute to the generation of INaP in Nav1.3.
How the vortex lattice of a superconductor becomes disordered: a study by scanning tunneling spectroscopy
Authors: Zehetmayer M. 
Published: March 2015

AbstractOrder-disorder transitions take place in many physical systems, but observing them in detail in real materials is difficult. In two- or quasi-two-dimensional systems, the transition has been studied by computer simulations and experimentally in electron sheets, dusty plasmas, colloidal and other systems. Here I show the different stages of defect formation in the vortex lattice of a superconductor while it undergoes an order-disorder transition by presenting real-space images of the lattice from scanning tunneling spectroscopy. When the system evolves from the ordered to the disordered state, the predominant kind of defect changes from dislocation pairs to single dislocations and finally to defect clusters forming grain boundaries. Correlation functions indicate a hexatic-like state preceding the disordered state. The transition in the microscopic vortex distribution is mirrored by the well-known spectacular second peak effect observed in the macroscopic current density of the superconductor.
Overexpression of DHX32 contributes to the growth and metastasis of colorectal cancer
Authors: Lin Huayue , Liu Wenjuan , Fang Zanxi , Liang Xianming , Li Juan , Bai Yongying , Lin Lingqing , You Hanyu , Pei Yihua , Wang Fen , Zhang Zhong-Ying 
Published: March 2015

AbstractOur previous work demonstrates that DHX32 is upregulated in colorectal cancer (CRC) compared to its adjacent normal tissues. However, how overexpressed DHX32 contributes to CRC remains largely unknown. In this study, we reported that DHX32 was overexpressed in human colon cancer cells. Overexpressed DHX32 promoted SW480 cancer cells proliferation, migration and invasion, as well as decreased the susceptibility to chemotherapy agent 5-Fluorouracil. Furthermore, PCR array analyses revealed that depleting DHX32 in SW480 colon cancer cells suppressed expression of WISP1, MMP7 and VEGFA in the Wnt pathway and anti-apoptotic gene BCL2 and CA9, however, elevated expression of pro-apoptotic gene ACSL5. The findings suggested that overexpressed DHX32 played an important role in CRC progression and metastasis and that DHX32 has the potential to serve as a biomarker and a novel therapeutic target for CRC.
Possible superconductivity in Sr2IrO4 probed by quasiparticle interference
Authors: Gao Yi , Zhou Tao , Huang Huaixiang , Wang Qiang-Hua 
Published: March 2015

AbstractBased on the possible superconducting (SC) pairing symmetries recently proposed, the quasiparticle interference (QPI) patterns in electron- and hole-doped Sr2IrO4 are theoretically investigated. In the electron-doped case, the QPI spectra can be explained based on a model similar to the octet model of the cuprates while in the hole-doped case, both the Fermi surface topology and the sign of the SC order parameter resemble those of the iron pnictides and there exists a QPI vector resulting from the interpocket scattering between the electron and hole pockets. In both cases, the evolution of the QPI vectors with energy and their behaviors in the nonmagnetic and magnetic impurity scattering cases can well be explained based on the evolution of the constant-energy contours and the sign structure of the SC order parameter. The QPI spectra presented in this paper can be compared with future scanning tunneling microscopy experiments to test whether there are SC phases in electron- and hole-doped Sr2IrO4 and what the pairing symmetry is.
Effects of Magnetic Nanoparticles and External Magnetostatic Field on the Bulk Heterojunction Polymer Solar Cells
Authors: Wang Kai , Yi Chao , Liu Chang , Hu Xiaowen , Chuang Steven , Gong Xiong 
Published: March 2015

AbstractThe price of energy to separate tightly bound electron-hole pair (or charge-transfer state) and extract freely movable charges from low-mobility materials represents fundamental losses for many low-cost photovoltaic devices. In bulk heterojunction (BHJ) polymer solar cells (PSCs), approximately 50% of the total efficiency lost among all energy loss pathways is due to the photogenerated charge carrier recombination within PSCs and low charge carrier mobility of disordered organic materials. To address these issues, we introduce magnetic nanoparticles (MNPs) and orientate these MNPS within BHJ composite by an external magnetostatic field. Over 50% enhanced efficiency was observed from BHJ PSCs incorporated with MNPs and an external magnetostatic field alignment when compared to the control BHJ PSCs. The optimization of BHJ thin film morphology, suppression of charge carrier recombination and enhancement in charge carrier collection result in a greatly increased short-circuit current density and fill factor, as a result, enhanced power conversion efficiency.
Breeding scheme and maternal small RNAs affect the efficiency of transgenerational inheritance of a paramutation in mice
Authors: Yuan Shuiqiao , Oliver Daniel , Schuster Andrew , Zheng Huili , Yan Wei 
Published: March 2015

AbstractParamutations result from interactions between two alleles at a single locus, whereby one induces a heritable change in the other. Although common in plants, paramutations are rarely studied in animals. Here, we report a new paramutation mouse model, in which the paramutant allele was induced by an insertional mutation and displayed the “white-tail-tip” (WTT) phenotype. The paramutation phenotype could be transmitted across multiple generations and the breeding scheme (intercrossing vs. outcrossing) drastically affected the transmission efficiency. Paternal (i.e., sperm-borne) RNAs isolated from paramutant mice could induce the paramutation phenotype, which, however, failed to be transmitted to subsequent generations. Maternal miRNAs and piRNAs appeared to have an inhibitory effect on the efficiency of germline transmission of the paramutation. This paramutation mouse model represents an important tool for dissecting the underlying mechanism, which should be applicable to the phenomenon of epigenetic transgenerational inheritance (ETI) in general. Mechanistic insights of ETI will help us understand how organisms establish new heritable epigenetic states during development, or in times of environmental or nutritional stress.
Food for thought: edible gardens in New Zealand primary and secondary schools
Authors: Collins C. , Richards R. , Reeder A. I. , Gray A. R. 
Published: March 2015

Issue addressedSchool gardens are a potentially important health promotion tool, allowing the growth and consumption of fruit and vegetables to be embedded within the students' educational experience. This study aimed to investigate the implementation of edible gardens in New Zealand (NZ) primary and secondary schools.MethodsA questionnaire mailed to principals from a randomly selected sample of 764 NZ schools included questions on whether or not the school had a garden and, if so, what produce was grown; how long the garden had been in place; how harvested crops were distributed; and curriculum integration.ResultsAmong 491 responding schools (64.3% response rate), 52.9% currently had an edible garden – with most gardens started in the previous two years. Vegetables, herbs and tree fruit were commonly grown. Gardens were integrated into curriculum subjects, cooking lessons, recipes and messages promoting increased fruit and vegetable consumption.ConclusionsEdible gardens were common within NZ schools, though often relatively new, and were used for teaching in a variety of curriculum areas.
Novel Epac fluorescent ligand reveals distinct Epac1 vs. Epac2 distribution and function in cardiomyocytes
Authors: Pereira Laëtitia , Rehmann Holger , Lao Dieu Hung , Erickson Jeffrey R. , Bossuyt Julie , Chen Ju , Bers Donald M. 
Published: March 2015

Significance
β-Adrenergic activation in heart has many important effects (physiological and pathological) that had been mainly attributed to cAMP and protein kinase A-dependent signaling. The discovery of exchange protein directly activated by cAMP (Epac1 and Epac2) has uncovered new parallel cAMP signaling pathways in β-adrenergic signaling, but Epac isoform localization and function were not well understood. Here we show, using a novel fluorescent Epac analog, that Epac1 and Epac2 are differentially concentrated at the nucleus vs. at Z lines in cardiomyocytes, and that this corresponds to functional roles in nucleus vs. calcium handling and arrhythmias, respectively. This finding may be essential to develop more targeted therapeutics for cardiomyopathy.
Inversion of Sonic hedgehog action on its canonical pathway by electrical activity
Authors: Belgacem Yesser H. , Borodinsky Laura N. 
Published: March 2015

Significance
Morphogenic proteins drive the formation and patterning of tissues during embryonic development. Once tissues are formed, their cells progressively differentiate to perform the required specialized functions of the maturing tissue. Whether this transition is accompanied by changes in morphogen signaling remains unclear. Here we identify a striking inversion in Sonic hedgehog (Shh) action on its canonical Gli-dependent pathway driven by the emerging electrical activity in differentiating spinal neurons. This mechanism may allow for switching off Shh proliferative action and thus may prevent pediatric brain tumor formation and occurrence of neurodevelopmental defects.
Effective saccharification of kraft pulp by using a cellulase cocktail prepared from genetically engineered Aspergillus oryzae
Authors: Yamada Ryosuke , Yoshie Toshihide , Sakai Shoji , Wakai Satoshi , Asai-Nakashima Nanami , Okazaki Fumiyoshi , Ogino Chiaki , Hisada Hiromoto , Tsutsumi Hiroko , Hata Yoji , Kondo Akihiko 
Published: March 2015

Abstract
Kraft pulp is a promising feedstock for bioproduction. The efficiency of kraft pulp saccharification was improved by using a cellulase cocktail prepared from genetically engineered Aspergillus oryzae. Application of the cellulase cocktail was demonstrated by simultaneous saccharification and fermentation, using kraft pulp and non-cellulolytic yeast. Such application would make possible to do an efficient production of other chemicals from kraft pulp.
A new drought tipping point for conifer mortality
Authors: Kolb Thomas E 
Published: March 2015

Abstract
(Huang et al 2015 Environ. Res. Lett.

10 024011) present a method for predicting mortality of ponderosa pine (Pinus ponderosa) and pinyon pine (Pinus edulis) in the Southwestern US during severe drought based on the relationship between the standardized precipitation–evapotranspiration index (SPEI) and annual tree ring growth. Ring growth was zero when SPEI for September to July was −1.64. The threshold SPEI of −1.64 was successful in distinguishing areas with high tree mortality during recent severe drought from areas with low mortality, and is proposed to be a tipping point of drought severity leading to tree mortality. Below, I discuss this work in more detail.
Analgesic Effect of Perioperative Escitalopram in High Pain Catastrophizing Patients after Total Knee Arthroplasty
Authors: Lunn Troels H. , Frokjaer Vibe G. , Hansen Torben B. , Kristensen Per W. , Lind Thomas , Kehlet Henrik 
Published: March 2015

AbstractAbstract
In 120 patients with high pain catastrophizing scores before total knee arthroplasty, 1 week treatment with the serotonin selective reuptake inhibitor escitalopram did not differ from placebo in pain on ambulation 24 h after surgery.

Background:
Sufficient pain treatment remains a challenge after total knee arthroplasty (TKA), especially in high pain catastrophizing patients. Serotonergic signaling may be involved in pain processing, but the effect of selective serotonin reuptake inhibitors on well-defined postoperative pain has not previously been investigated. The authors hypothesized that perioperative escitalopram would reduce pain after TKA in high pain catastrophizing patients.

Methods:
A total of 120 pain catastrophizing patients (selected using the pain catastrophizing scale as preoperative screening tool) scheduled for TKA were randomized in a double-blind manner to either 10 mg escitalopram or placebo daily from preanesthesia to postoperative day 6 in addition to a standardized analgesic regime. The primary outcome was pain upon ambulation 24 h after surgery. Secondary outcomes were overall pain during well-defined mobilizations and at rest from 2 to 48 h and from days 2 to 6, morphine equivalents, anxiety, depression, and side effects.

Results:
Pain upon ambulation (mean [95% CI]) 24 h after surgery in the escitalopram versus placebo group was 58 (53 to 64) versus 64 (58 to 69), the mean difference being −5 (−13 to 3), P = 0.20. Overall pain upon ambulation and at rest from days 2 to 6 was lower in the escitalopram versus placebo group, as was depression score at day 6 (all P ≤ 0.01 in analyses uncorrected for multiple tests). Side effects were nonsignificant except for reduced tendency to sweat and prolonged sleep in the escitalopram group. No other between-group differences were observed.

Conclusions:
Escitalopram did not reduce pain upon ambulation 24 h after TKA in high pain catastrophizing patients. Future studies on optimal timing, dose, and duration of selective serotonin reuptake inhibitor treatment might be warranted.
Wireless Capsule Endoscopy of the Small Intestine in Children
Authors: Zevit Noam , Shamir Raanan 
Published: March 2015

ABSTRACTWireless capsule endoscopy (CE) for the diagnosis of small‐bowel disease has been in clinical use for more than a decade, and is no longer an emerging technology, but rather one that has reached fruition. This noninvasive technology has been readily embraced by both physicians and patients. Used in the diagnosis of inflammatory bowel disease, for locating sources of obscure gastrointestinal bleeding, and for assessing small‐bowel polyp burden in polyposis syndromes as well as for less common indications, CE has transformed the diagnostic algorithms of small‐bowel investigations. Although already in widespread use, the technology incorporated into the various CE platforms continues to improve and expand. Here, we briefly review the indications, limitations, and advances in video capsule technology, with an emphasis on its use in pediatrics.
Gluten‐Free Diet and Lipid Profile in Children With Celiac Disease
Authors: Forchielli M. Luisa , Fernicola Paola , Diani Lucia , Scrivo Barbara , Salfi Nunzio C. , Pessina Achille C. , Lima Mario , Conti Veronica , Pession Andrea 
Published: March 2015

ABSTRACTObjectives:A gluten‐free diet (GFD) may carry high energy and fat load. We verified lipid profile and dietary indicators cross‐sectionally and prospectively in patients with celiac disease (CD).Methods:In any consecutive child receiving a GFD (group 1) or newly diagnosed as having CD (group 2), total cholesterol (TC), triglycerides (TG), high‐density lipoprotein (HDL) cholesterol, blood pressure (BP), anthropometric data, physical activity, and a 24‐hour food diary were collected during follow‐up visits (yearly in group 1 and during the first year of GFD in group 2).Results:In group 1 (132 girls, 73 boys, 10.7 ± 4.2 years), TC (P = 0.006), TG (P = 0.014), and HDL (P = 0.019) were significantly higher in girls than in boys. Compared with the general pediatric population, group 1 girls had higher TC, TG, HDL, and low‐density lipoprotein; group 1 boys had lower TC, TG, and low‐density lipoprotein and higher HDL. TC was significantly and positively affected by age, sex, and time receiving GFD, whereas HDL was significantly and positively affected by body mass index, diastolic BP, and sex; TG was negatively affected by diastolic BP. Compared with recommendations, group 1 children introduced less calories, iron, and calcium; one‐third more sodium; similar amounts of fiber; and twice as many proteins. In group 2 (20 girls, 10 boys, 8.6 ± 3.55 years), TC did not change over time and TG diminished, whereas HDL, blood glucose, and body mass index increased; saturated fats and caloric intake were below recommendations, whereas proteins were excessively introduced. Fibers were optimal. HDL was inversely correlated to calories and saturated fat (R2 = 80, P = 0.011).Conclusions:Lipid profiles of children with CD differ across sexes and from reference population. GFD, being unexpectedly appropriate in fibers and fat proportion, may be a contributor.
CIDER: a pipeline for detecting waves of coordinated transcriptional regulation in gene expression time-course data
Authors: Mina Marco , Jurman Giuseppe , Furlanello Cesare 
Published: March 2015

AbstractCell adaptability to environmental changes is conferred by complex transcriptional regulatory networks, which respond to external stimuli by modulating the expression dynamics of each gene. Hence, deciphering the network of transcriptional regulation is remarkably important, but proves to be extremely challenging, mainly due to the unfavorable ratio between the number of available observations and the number of parameters to estimate. Most of the existing computational methods for the inference of transcriptional networks consider steady-state gene expression datasets, and produce models of transcriptional regulation best explaining the observed static gene expression.Gene expression time-courses are an emergent typology of gene expression data, paving the way to the characterization of the time-dependent dynamics of transcriptional regulation.In this work we introduce the Complexity Invariant Dynamic Time Warping motif EnRichment (CIDER) analysis, a novel computational pipeline to identify the prominent waves of coordinated gene transcription induced in cells by external stimuli, and determine which TFs are involved in the coordination of gene transcription. The CIDER pipeline combines unsupervised time series clustering and motif enrichment analysis to first detect transcriptional expression patterns, and then identify the TFs over-represented in the promoter regions of gene sets with similar expression dynamics.The ability of CIDER to correctly identify regulatory interactions is assessed on a realistic synthetic dataset of gene expression timecourses, generated by simulating the effects of knock-out perturbations on the E. coli regulatory network.The CIDER source code and the validation datasets are available on request from the corresponding author.
Introgression obscures and reveals historical relationships among the American live oaks
Authors: Eaton Deren A. R. , Hipp Andrew L. , González-Rodríguez Antonio , Cavender-Bares Jeannine 
Published: March 2015

AbstractIntrogressive hybridization challenges the concepts we use to define species and infer phylogenetic relationships. Methods for inferring historical introgression from the genomes of extant species are now widely used, however, few guidelines have been articulated for how best to interpret results. Because these tests are inherently comparative, they are sensitive to the effects of missing data (unsampled species) and non-independence (hierarchical relationships among species). We demonstrate this using genomic RADseq data sampled from all extant species in the American live oaks (Quercus series Virentes), a group notorious for hybridization. By considering all species, and their phylogenetic relationships, we were able to distinguish true hybridizing lineages from those that falsely appear admixed. Six of seven species show evidence of admixture, often with multiple other species, but which is explained by hybrid introgression among few related lineages occurring in close proximity. We identify the Cuban oak as the most admixed lineage and test alternative scenarios for its origin. The live oaks form a continuous ring-like distribution around the Gulf of Mexico, connected in Cuba, across which they could effectively exchange alleles. However, introgression appears highly localized, suggesting that oak species boundaries, and their geographic ranges have remained relatively stable over evolutionary time.
regionReport: Interactive reports for region-based analyses
Authors: Collado-Torres Leonardo , Jaffe Andrew E. , Leek Jeffrey T. 
Published: March 2015

SummaryregionReportis aRpackage for generating detailed interactive reports from regions of the genome. The report includes quality-control checks, an overview of the results, an interactive table of the genomic regions, and reproducibility information.regionReportcan easily be expanded with report templates for other specialized analyses. In particular,regionReporthas an extensive report template for exploringderfinderresults from annotation-agnostic RNA-seq differential expression analyses.AvailabilityregionReportis freely available via Bioconductor atbioconductor.org/packages/release/bioc/html/regionReport.html.
Distributed Bayesian Networks Reconstruction on the Whole Genome Scale
Authors: Frolova Alina , Wilczynski Bartek 
Published: March 2015

AbstractBackgroundBayesian networks are directed acyclic graphical models widely used to represent the probabilistic relationships between random variables. They have been applied in various biological contexts, including gene regulatory networks and protein-protein interactions inference. Generally, learning Bayesian networks from experimental data is NP-hard, leading to widespread use of heuristic search methods giving suboptimal results. However, in cases when the acyclicity of the graph can be externally ensured, it is possible to find the optimal network in polynomial time. While our previously developed tool BNFinder implements polynomial time algorithm, reconstructing networks with the large amount of experimental data still leads to computations on single CPU growing exceedingly.ResultsIn the present paper we propose parallelized algorithm designed for multi-core and distributed systems and its implementation in the improved version of BNFinder - tool for learning optimal Bayesian networks. The new algorithm has been tested on different simulated and experimental datasets showing that it has much better efficiency of parallelization than the previous version. BNFinder gives comparable results in terms of accuracy with respect to current state-of-the-art inference methods, giving significant advantage in cases when external information such as regulators list or prior edge probability can be introduced.ConclusionsWe show that the new method can be used to reconstruct networks in the size range of thousands of genes making it practically applicable to whole genome datasets of prokaryotic systems and large components of eukaryotic genomes. Our benchmarking results on realistic datasets indicate that the tool should be useful to wide audience of researchers interested in discovering dependencies in their large-scale transcriptomic datasets.