bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential role of viruses in white plague coral disease
Authors: Soffer Nitzan , Brandt Marilyn E , Correa Adrienne M S , Smith Tyler B , Thurber Rebecca Vega 
Published: August 2013

Abstract
White plague (WP)-like diseases of tropical corals are implicated in reef decline worldwide, although their etiological cause is generally unknown. Studies thus far have focused on bacterial or eukaryotic pathogens as the source of these diseases; no studies have examined the role of viruses. Using a combination of transmission electron microscopy (TEM) and 454 pyrosequencing, we compared 24 viral metagenomes generated from Montastraea annularis corals showing signs of WP-like disease and/or bleaching, control conspecific corals, and adjacent seawater. TEM was used for visual inspection of diseased coral tissue. No bacteria were visually identified within diseased coral tissues, but viral particles and sequence similarities to eukaryotic circular Rep-encoding single-stranded DNA viruses and their associated satellites (SCSDVs) were abundant in WP diseased tissues. In contrast, sequence similarities to SCSDVs were not found in any healthy coral tissues, suggesting SCSDVs might have a role in WP disease. Furthermore, Herpesviridae gene signatures dominated healthy tissues, corroborating reports that herpes-like viruses infect all corals. Nucleocytoplasmic large DNA virus (NCLDV) sequences, similar to those recently identified in cultures of Symbiodinium (the algal symbionts of corals), were most common in bleached corals. This finding further implicates that these NCLDV viruses may have a role in bleaching, as suggested in previous studies. This study determined that a specific group of viruses is associated with diseased Caribbean corals and highlights the potential for viral disease in regional coral reef decline.
Two-stage microbial community experimental design
Authors: Tickle Timothy L , Segata Nicola , Waldron Levi , Weingart Uri , Huttenhower Curtis 
Published: August 2013

Abstract
Microbial community samples can be efficiently surveyed in high throughput by sequencing markers such as the 16S ribosomal RNA gene. Often, a collection of samples is then selected for subsequent metagenomic, metabolomic or other follow-up. Two-stage study design has long been used in ecology but has not yet been studied in-depth for high-throughput microbial community investigations. To avoid ad hoc sample selection, we developed and validated several purposive sample selection methods for two-stage studies (that is, biological criteria) targeting differing types of microbial communities. These methods select follow-up samples from large community surveys, with criteria including samples typical of the initially surveyed population, targeting specific microbial clades or rare species, maximizing diversity, representing extreme or deviant communities, or identifying communities distinct or discriminating among environment or host phenotypes. The accuracies of each sampling technique and their influences on the characteristics of the resulting selected microbial community were evaluated using both simulated and experimental data. Specifically, all criteria were able to identify samples whose properties were accurately retained in 318 paired 16S amplicon and whole-community metagenomic (follow-up) samples from the Human Microbiome Project. Some selection criteria resulted in follow-up samples that were strongly non-representative of the original survey population; diversity maximization particularly undersampled community configurations. Only selection of intentionally representative samples minimized differences in the selected sample set from the original microbial survey. An implementation is provided as the microPITA (Microbiomes: Picking Interesting Taxa for Analysis) software for two-stage study design of microbial communities.
Compact dual‐band bandpass filter using single meander multimode DGS resonator
Authors: Jin X. , Zhang Z.‐H. , Wang L. , Guan B.‐R. 
Published: August 2013

A novel dual‐band bandpass filter (BPF) with a dual‐plane structure is proposed. The dual‐plane structure consists of a pair of microstrip feed lines with capacitive source–load coupling on the top layer and a meander multimode defected ground structure resonator (MMDGSR) on the bottom layer. Using the intrinsic characteristics of the MMDGSR, two passbands and four transmission zeros can be generated simultaneously. An experimental dual‐band BPF operating at 2.45/5.8 GHz (WLAN application) has been designed and fabricated. This performance is verified by good agreement between the simulated and measured results.
All‐optical frequency chirp magnification based on four‐wave‐mixing for optical comb generation
Authors: Du Jiangbing , Yan Fangfang 
Published: August 2013

An efficient optical comb generation method based on degenerated four‐wave‐mixing process in highly nonlinear fibre is demonstrated. The all‐optical processing of the frequency chirp is wavelength tunable and thus enables the capability of tunable chirp magnification. The magnification of the frequency chirp with a factor tunable from two to five has been demonstrated. An optical comb with 22 sub‐carriers has been obtained which refers to a bandwidth of 210 GHz, about five times the bandwidth of 40 GHz for the original signal.
Miniaturised slot antenna for biomedical applications
Authors: Xu Li‐Jie , Guo Yong‐Xin , Wu Wen 
Published: August 2013

An implantable slot antenna with a miniaturised size of 139.7 mm3 (10 × 11 × 1.27 mm) for biomedical applications is proposed. Operating at the Medical Implant Communications Service (MICS) band, miniaturisation of the antenna is realised by etching a meandered slot on the top metal with one end open. A microstrip line is utilised as excitation with a shorting connected to the radiator. In addition, two U‐shaped stubs are adopted to match the feeding impedance to 50 Ω. The antenna is simulated in a one‐layer skin model as well as in the arm of a human model and measured in skin‐mimicking tissue. Good agreements can be obtained and the measurement results show that a broad bandwidth of 28.3% (from 354 to 469 MHz) for |S11| less than − 10 dB can be achieved.
isomiRID: a framework to identify microRNA isoforms
Authors: de Oliveira Luiz Felipe Valter , Christoff Ana Paula , Margis Rogerio 
Published: August 2013

Abstract
Summary: MicroRNAs (miRNAs) have been extensively studied owing to their important regulatory roles in genic expression. An increasingly number of reports are performing extensive data mining in small RNA sequencing libraries to detect miRNAs isoforms and also 5′ and 3′ post-transcriptional nucleotide additions, as well as edited miRNAs sequences. A ready to use pipeline, isomiRID, was developed to standardize and automatize the search for miRNAs isoforms in high-throughput small RNA sequencing libraries.
Availability: isomiRID is a command line Python script available at http://www.ufrgs.br/RNAi/isomiRID/.
Contact: rogerio.margis@ufrgs.br
Supplementary information: Supplementary Date are available at Bioinformatics online.
omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data
Authors: Müller Sören , Rycak Lukas , Winter Peter , Kahl Günter , Koch Ina , Rotter Björn 
Published: August 2013

Abstract
Summary: Small RNA deep sequencing is widely used to characterize non-coding RNAs (ncRNAs) differentially expressed between two conditions, e.g. healthy and diseased individuals and to reveal insights into molecular mechanisms underlying condition-specific phenotypic traits. The ncRNAome is composed of a multitude of RNAs, such as transfer RNA, small nucleolar RNA and microRNA (miRNA), to name few. Here we present omiRas, a Web server for the annotation, comparison and visualization of interaction networks of ncRNAs derived from next-generation sequencing experiments of two different conditions. The Web tool allows the user to submit raw sequencing data and results are presented as: (i) static annotation results including length distribution, mapping statistics, alignments and quantification tables for each library as well as lists of differentially expressed ncRNAs between conditions and (ii) an interactive network visualization of user-selected miRNAs and their target genes based on the combination of several miRNA–mRNA interaction databases.
Availability and Implementation: The omiRas Web server is implemented in Python, PostgreSQL, R and can be accessed at: http://tools.genxpro.net/omiras/.
Contact: rotter@genxpro.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Radio properties of the magnetar near Sagittarius A* from observations with the Australia Telescope Compact Array
Authors: Shannon R. M. , Johnston S. 
Published: August 2013

Abstract
We have carried out observations of the newly discovered magnetar in the direction of Sagittarius A* using the Australia Telescope Compact Array (ATCA) in four frequency bands from 4.5 to 20 GHz. Radio pulsations are clearly detected at all frequencies. We measure the pulsar's dispersion measure to be 1650 ± 50 cm−3 pc, the highest of any of the known pulsars. Once Faraday rotation has been taken into account, the pulse profile is more than 80 per cent linearly polarized at all frequencies and has a small degree (5 per cent) of circular polarization. The rotation measure of −67000 ± 500 rad m−2 is the largest (in magnitude) ever measured for a pulsar but still a factor of 8 smaller than Sgr A* itself. The combination of the dispersion and rotation measures implies an integrated magnetic field strength of −50 μG along the line of sight. The flux density appears to have increased by about a factor of 2 between observations made 30 d apart. This object therefore joins the small class of radio emitting magnetars.
Managerial Miscalibration*
Authors: Ben-David Itzhak , Graham John R. , Harvey Campbell R. 
Published: August 2013

Abstract
Using a unique 10-year panel that includes more than 13,300 expected stock market return probability distributions, we find that executives are severely miscalibrated, producing distributions that are too narrow: realized market returns are within the executives’ 80% confidence intervals only 36% of the time. We show that executives reduce the lower bound of the forecast confidence interval during times of high market uncertainty; however, ex post miscalibration is worst during periods of high uncertainty. We also find that executives who are miscalibrated about the stock market show similar miscalibration regarding their own firms’ prospects. Finally, firms with miscalibrated executives seem to follow more aggressive corporate policies: investing more and using more debt financing.
Cell-Specific Transcriptional Profiling Reveals Candidate Mechanisms Regulating Development and Function of Uterine Epithelia in Mice
Authors: Filant Justyna , Spencer Thomas E. 
Published: August 2013

AbstractAll mammalian uteri have luminal (LE) and glandular epithelia (GE) in their endometrium. The LE mediates uterine receptivity and blastocyst attachment for implantation, and the GE synthesize and secrete or transport bioactive substances involved in blastocyst implantation, uterine receptivity, and stromal cell decidualization. However, the mechanisms governing uterine epithelial development after birth and their function in the adult are not fully understood. Here, comprehensive microarray analysis was conducted on LE and GE isolated by laser capture microdissection from uteri on Postnatal Day 10 (PD 10) and day of pseudopregnancy (DOPP) 2.5 and 3.5. This data was integrated with analysis of uteri from gland-containing control and aglandular progesterone-induced uterine gland knockout mice from PD 10 and DOPP 3.5. Many genes were expressed in both epithelia, but there was greater expression of genes in the LE than in the GE. In the neonate, GE-expressed genes were enriched for morphogenesis, development, migration, and retinoic acid signaling. In the adult, LE-expressed genes were enriched for metabolic processes and steroid biosynthesis, whereas retinoid signaling, tight junction, extracellular matrix, and regulation of kinase activity were enriched in the GE. The transcriptome differences in the epithelia support the idea that each cell type has a distinct and complementary function in the uterus. The candidate genes and regulatory networks identified here provide a framework to discover new mechanisms regulating development of epithelia in the postnatal uterus and their functions in early pregnancy.
Difference in Abscisic Acid Perception Mechanisms between Closure Induction and Opening Inhibition of Stomata
Authors: Yin Ye , Adachi Yuji , Ye Wenxiu , Hayashi Maki , Nakamura Yoshimasa , Kinoshita Toshinori , Mori Izumi C. , Murata Yoshiyuki 
Published: August 2013

AbstractAbscisic acid (ABA) induces stomatal closure and inhibits light-induced stomatal opening. The mechanisms in these two processes are not necessarily the same. It has been postulated that the ABA receptors involved in opening inhibition are different from those involved in closure induction. Here, we provide evidence that four recently identified ABA receptors (PYRABACTIN RESISTANCE1 [PYR1], PYRABACTIN RESISTANCE-LIKE1 [PYL1], PYL2, and PYL4) are not sufficient for opening inhibition in Arabidopsis (Arabidopsis thaliana). ABA-induced stomatal closure was impaired in the pyr1/pyl1/pyl2/pyl4 quadruple ABA receptor mutant. ABA inhibition of the opening of the mutant’s stomata remained intact. ABA did not induce either the production of reactive oxygen species and nitric oxide or the alkalization of the cytosol in the quadruple mutant, in accordance with the closure phenotype. Whole cell patch-clamp analysis of inward-rectifying K+ current in guard cells showed a partial inhibition by ABA, indicating that the ABA sensitivity of the mutant was not fully impaired. ABA substantially inhibited blue light-induced phosphorylation of H+-ATPase in guard cells in both the mutant and the wild type. On the other hand, in a knockout mutant of the SNF1-related protein kinase, srk2e, stomatal opening and closure, reactive oxygen species and nitric oxide production, cytosolic alkalization, inward-rectifying K+ current inactivation, and H+-ATPase phosphorylation were not sensitive to ABA.
Liver X receptor activation increases hepatic fatty acid desaturation by the induction of SCD1 expression through an LXRα‐SREBP1c‐dependent mechanism (肝X受体活化可通过LXRα‐SREBP1c依赖的机制诱导SCD1表达来增加肝脏脂肪酸不饱和度)
Authors: Zhang Xiaoyan , Liu Jia , Su Wen , Wu Jing , Wang Chunjiong , Kong Xiaomu , Gustafsson Jan‐Åke , Ding Jie , Ma Xiaosong , Guan Youfei 
Published: August 2013

AbstractBackgroundLiver X receptors (LXRs) including LXRα and LXRβ are members of the nuclear hormone receptor superfamily of ligand activated transcription factors, which serve as lipid sensors to regulate expression of genes controlling many aspects of cholesterol and fatty acid metabolism. The liver is the central organ in controlling lipid metabolism. In the present study, we aimed at elucidating the role of LXR activation in hepatic fatty acid homeostasis.MethodsWe treated C57BL/6 mice with a synthetic non‐selective LXR agonist TO901317. Fatty acid profile of lipid esters in the livers was analyzed by gas‐liquid chromatography. Real‐time polymerase chain reaction (PCR) and western blot were used to determine the expression of SREBP1c and SCD1 in TO901317‐treated livers and HepG2 cells.ResultsOral administration of TO901317 resulted in increased fatty acid desaturation in the liver, with concomitant increase in hepatic stearoyl CoA desaturase‐1 (SCD1) expression. TO901317‐induced SCD1 expression was observed in LXRβ‐/‐ mice, but not in LXRα‐/‐ mice. Furthermore, TO901317 significantly increased expression of sterol regulatory element‐binding protein 1c (SREBP1c), the deficiency of which almost completely abolished the induction of SCD1 by TO901317. This drug induced both SREBP1c and SCD1 expression in HepG2 cells. Overexpression of SREBP1c resulted in a significant increase in SCD1 promoter activity and expression.ConclusionsTaken together, the present studies demonstrate that pan‐LXR activation increases hepatic fatty acid desaturation via the induction of SCD1 expression in an LXRα‐dependent and SREBP1c‐mediated manner.
Exposure (mAs) optimisation of a multi‐detector CT protocol for hepatic lesion detection: Are thinner slices better?
Authors: Dobeli Karen Leigh , Lewis Sarah Jane , Meikle Steven Richard , Thiele David Lewis , Brennan Patrick Christopher 
Published: August 2013

AbstractIntroductionThe purpose of this work was to determine the exposure‐optimised slice thickness for hepatic lesion detection with CT.MethodsA phantom containing spheres (diameter 9.5, 4.8 and 2.4 mm) with CT density 10 HU below the background (50 HU) was scanned at 125, 100, 75 and 50 mAs. Data were reconstructed at 5‐, 3‐ and 1‐mm slice thicknesses. Noise, contrast‐to‐noise ratio (CNR), area under the curve (AUC) as calculated using receiver operating characteristic analysis and sensitivity representing lesion detection were calculated and compared.ResultsCompared with the 125 mAs/5 mm slice thickness setting, significant reductions in AUC were found for 75 mAs (P < 0.01) and 50 mAs (P < 0.05) at 1‐ and 3‐mm thicknesses, respectively; sensitivity for the 9.5‐mm sphere was significantly reduced for 75 (P < 0.05) and 50 mAs (P < 0.01) at 1‐mm thickness; sensitivity for the 4.8‐mm sphere was significantly lower for 100, 75 and 50 mAs at all three slice thicknesses (P < 0.05). The 2.4‐mm sphere was rarely detected. At each slice thickness, noise at 100, 75 and 50 mAs exposures was approximately 10, 30 and 50% higher, respectively, than that at 125 mAs exposure. CNRs decreased in an irregular manner with reductions in exposure and slice thickness.ConclusionThis study demonstrated no advantage to using slices below 5 mm thickness, and consequently thinner slices are not necessarily better.
Evaluating multimodal literacies in student blogs
Authors: O'Byrne Barbara , Murrell Stacey 
Published: August 2013

AbstractThis research presents ways in which high school students used the multimodal and interactive affordances of blogs to create, organize, communicate and participate on an educational blog. Their actions demonstrated how plural modes of literacy are infiltrating digital environments and reshaping literacy and learning. Multimodal blogging practices of participants broaden the discourse about educational blogs to include an understanding of blogs as media‐rich platforms in which learners operate with plural modes of literacy to construct meaning, communicate and participate.
Convection‐Enhanced Drug Delivery to the Brain: Therapeutic Potential and Neuropathological Considerations
Authors: Barua Neil U. , Gill Steven S. , Love Seth 
Published: August 2013

AbstractConvection‐enhanced delivery (CED) describes a direct method of drug delivery to the brain through intraparenchymal microcatheters. By establishing a pressure gradient at the tip of the infusion catheter in order to exploit bulk flow through the interstitial spaces of the brain, CED offers a number of advantages over conventional drug delivery methods—bypass of the blood–brain barrier, targeted distribution through large brain volumes and minimization of systemic side effects. Despite showing early promise, CED is yet to fulfill its potential as a mainstream strategy for the treatment of neurological disease. Substantial research effort has been dedicated to optimize the technology for CED and identify the parameters, which govern successful drug distribution. It seems likely that successful clinical translation of CED will depend on suitable catheter technology being used in combination with drugs with optimal physicochemical characteristics, and on neuropathological analysis in appropriate preclinical models. In this review, we consider the factors most likely to influence the success or failure of CED, and review its application to the treatment of high‐grade glioma, Parkinson's disease (PD) and Alzheimer's disease (AD).
Histamine pharmacology: four years on
Authors: Chazot Paul L 
Published: August 2013

The histamine field has moved on rapidly in the last four years, with expansion in roles and clinical development, particularly in the newest two of four histamine receptors. This themed volume is a testament to this expansion with 16 original and review articles spanning a wide spectrum of histamine‐related topics, with therapeutic translational relevance to addiction, dementias, anxiety disorders, cancers, vestibular disorders, migraine and autoimmune disorders.Linked ArticlesThis article is part of a themed issue on Histamine Pharmacology Update. To view the other articles in this issue visit http://dx.doi.org/
10.1111/bph.2013.170.issue‐1
A “Choreography of Becoming”: Fathering, Embodied Care, and New Materialisms
Authors: Doucet Andrea 
Published: August 2013

Cet article souligne l'absence du corps dans les études sur la division sexuelle des responsabilités parentales et soutient qu'on doit y intégrer le concept clé de l'embodiment masculin dans les soins proférés aux enfants. Issue d'une recherche qualitative qui se penche depuis vingt ans sur les mères pourvoyeuses économiques et les pères pourvoyeurs des soins, je cite les penseurs fondateurs de ce concept (Dorothy E. Smith, Merleau‐Ponty, Bourdieu, Goffman) et aboutis à une réflexion informée par de nouvelles approches matérialistes, en postulant l'indivisibilité ontologique du lien corps/social et l'interrelation entre donneurs et receveurs de soins. L'article se veut une invitation au débat, une réponse tentative à l'exhortation d'Anne Fausto‐Sterling () de “reformuler nos vieilles questions pour pouvoir arriver à une façon systématique d'aborder l'entrelacement corps‐culture” (pp. 1516–1517).This article points to the recurring invisibility of the body in studies of parental care giving and argues that one critical missing link within our understandings of gender differences in care work is that of male embodiment in care giving. Rooted in a two‐decade‐long qualitative and ethnographic research program on breadwinning mothers and care‐giving fathers, I begin with several key thinkers on embodiment (Dorothy E. Smith, Merleau‐Ponty, Bourdieu, Goffman) and I end the article with thinking‐in‐progress, informed by new materialist lenses, and argue for the ontological inseparability of body‐social linkages and care‐giving relations between carers and the cared‐for. This article is an invitation to debate and a quiet taking up of Anne Fausto‐Sterling's (2005) plea that “(w)e need to ask old questions in new ways so that we can think systematically about the interweaving of bodies and culture” (pp. 1516–1517).