bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of PBDE‐209 exposure during pregnancy on placental ET‐1 and eNOS expression and the birth weight of offspring
Authors: Du Peili , Li Zhihua , Du Lili , Zhang Huili , Zhou Yanmei , Sun Wen , Xiao Xue , He Yutian , Sun Bin , Yu Yanhong , Chen Dunjin 
Published: May 2015

AbstractDecabrominated diphenyl ether (PBDE‐209) is a persistent organic pollutant. Gestational exposure to PBDE‐209 can accumulate in pregnant women and fetuses via the placenta and umbilical cord, affecting perinatal outcome. In this study, pregnant Sprague–Dawley (SD) rats were randomly divided into five groups and intragastrically administered peanut oil (vehicle) 1, 5 and 10 mg/kg by body weight (b.w.) of PBDE‐209, or nothing (control) from day 0 (G0) to day 21 (G21) gestation, respectively. Placental samples were collected on G21 by cesarean section. The mRNA and protein expressions of ET‐1, eNOS and iNOS in the placenta were examined using qRT‐PCR and Western blot, respectively. Total nitric oxide (NO) in the placenta was measured using a specific ELISA kit. Compared with the control and vehicle groups, the mRNA expression of ET‐1 and iNOS in the placenta was gradually and significantly increased after exposure to increasing concentrations of PBDE‐209 (P < 0.05), while the mRNA level of eNOS in the placenta was gradually and significantly reduced after exposure to increasing concentrations of PBDE‐209 (P < 0.05). The expression trends of ET‐1, eNOS and iNOS proteins were consistent with those of mRNA expression. Interestingly, the production of total NO was significantly increased after exposure to 5 and 10 mg/kg b.w. PBDE‐209 (P < 0.05). Finally, the birth weight of the offspring rats was significantly reduced after maternal exposure to 5 and 10 mg/kg b.w. PBDE‐209 compared with the control and vehicle groups (P < 0.05). These results suggest that PBDE‐209 exposure during pregnancy upregulates ET‐1 and iNOS expression, but decreases eNOS expression in the placenta, as well as reduces the birth weight of offspring.
The effect of economic downturns on maternal mortality among pregnancies with abortive outcomes in 81 countries, 1981–2010
Authors: Ng Ka Ying Bonnie , Maruthappu Mahiben , Farrukh Jawaad , Williams Callum , Atun Rifat , Zeltner Thomas 
Published: May 2015

AbstractObjectiveTo determine the association between economic downturns and abortion‐related maternal mortality in multiple countries over 30 years.MethodsIn a retrospective study, WHO data were obtained for maternal deaths among pregnancies with abortive outcomes between January 1, 1981, and December 31, 2010. Economic data for the same period were obtained from The World Bank. An economic downturn was defined as an annual decline in gross domestic product per head. Multivariate regression—controlling for country‐specific differences in infrastructure, population size, and demographic structure—and 5‐year lag analyses were performed.ResultsData were available for 81 countries. Abortion‐related maternal mortality was significantly increased in years of economic downturns (R= 0.0708; 95% confidence interval [CI] 0.0264–0.1151; P= 0.0018). The association was sustained for 4 years after an economic downturn (year 1: R= 0.0709 [95% CI 0.0231–0.1187], P= 0.0037; year 2: R= 0.0634 [0.0178–0.1089], P= 0.0065; year 3: R= 0.0554 [0.0105–0.1004], P= 0.0157; year 4: R= 0.0593 [0.0148–0.1037], P= 0.009). There was an annual 36% increase in deaths associated with unsafe abortion during economic downturn years.ConclusionEconomic downturns were associated with increased abortion‐related maternal mortality, possibly due to changes in government healthcare spending and service provision. A global economic downturn could impede a reduction in maternal mortality.
The effects of resource improvement on decision‐to‐delivery times for cesarean deliveries in a Ghanaian regional hospital
Authors: Onuoha Onyi , Ramaswamy Rohit , Srofenyoh Emmanuel K. , Kim Sung M. , Owen Medge D. 
Published: May 2015

AbstractObjectiveTo evaluate the effects of having a dedicated obstetric operating room (OR) on the decision‐to‐delivery interval (DDI) in a large referral hospital in Ghana.MethodsAn observational study was undertaken of all patients undergoing cesarean delivery at Ridge Regional Hospital, Accra, before (pre‐OR; August–September 2011) and after (post‐OR; August–September 2012) introduction of an obstetric OR. The primary outcome was the DDI.ResultsIn total, 581 cesareans were performed in the pre‐OR period and 574 in the post‐OR period. Overall, the median DDI decreased from 259 min (interquartile range [IQR] 161–432) in the pre‐OR period to 195 min (IQR 138–319) in the post‐OR period (P < 0.001). DDI was lower in the post‐OR period than in the pre‐OR period for both emergency (175 min [IQR 126–241] vs 220 min [IQR 146–315]; P < 0.001) and elective (1828 min [IQR 1432–2985] vs 4291 min [IQR 2992–5862]; P < 0.001) cesarean deliveries. Only one emergency cesarean—in the post‐OR period—was conducted within the recommended 30‐minute timeframe.ConclusionAn obstetric OR lowered the DDI for cesarean delivery; however, a realistic timeframe for emergency cesareans in low‐income countries remains to be determined.
The benefits of behaving badly on occasion: Successful regulation by planned hedonic deviations
Authors: Coelho do Vale Rita , Pieters Rik , Zeelenberg Marcel 
Published: May 2015

AbstractThis research tests the idea that goal‐pursuit that requires extended inhibition of desires, such as weight loss and financial saving, can benefit from including planned hedonic deviations in the goal‐striving plan. Two controlled experiments (simulated and real dieting) demonstrate that including planned goal deviations during extended goal striving, compared with following a straight and rigid goal striving process, (1) helps regain self‐regulatory resources, (2) helps maintain consumers' motivation to pursue with regulatory tasks, and (3) has a positive impact on affect experienced, which all contribute to facilitate long‐term goal‐adherence. A third study, conducted with current goal‐strivers provides further evidence of the benefits of planned hedonic deviations for goal pursuit across a variety of goals. This reveals that it may be beneficial for long‐term goal‐success to occasionally be bad, as long it is planned.
TIPIN depletion leads to apoptosis in breast cancer cells
Authors: Baldeyron Céline , Brisson Amélie , Tesson Bruno , Némati Fariba , Koundrioukoff Stéphane , Saliba Elie , De Koning Leanne , Martel Elise , Ye Mengliang , Rigaill Guillem , Meseure Didier , Nicolas André , Gentien David , Decaudin Didier , Debatisse Michelle , Depil Stéphane , Cruzalegui Francisco , Pierré Alain , Roman-Roman Sergio , Tucker Gordon C. , Dubois Thierry 
Published: May 2015

Triple‐negative breast cancer (TNBC) is the breast cancer subgroup with the most aggressive clinical behavior. Alternatives to conventional chemotherapy are required to improve the survival of TNBC patients. Gene‐expression analyses for different breast cancer subtypes revealed significant overexpression of the Timeless‐interacting protein (TIPIN), which is involved in the stability of DNA replication forks, in the highly proliferative associated TNBC samples. Immunohistochemistry analysis showed higher expression of TIPIN in the most proliferative and aggressive breast cancer subtypes including TNBC, and no TIPIN expression in healthy breast tissues. The depletion of TIPIN by RNA interference impairs the proliferation of both human breast cancer and non‐tumorigenic cell lines. However, this effect may be specifically associated with apoptosis in breast cancer cells. TIPIN silencing results in higher levels of single‐stranded DNA (ssDNA), indicative of replicative stress (RS), in TNBC compared to non‐tumorigenic cells. Upon TIPIN depletion, the speed of DNA replication fork was significantly decreased in all BC cells. However, TIPIN‐depleted TNBC cells are unable to fire additional replication origins in response to RS and therefore undergo apoptosis. TIPIN knockdown in TNBC cells decreases tumorigenicity in vitro and delays tumor growth in vivo. Our findings suggest that TIPIN is important for the maintenance of DNA replication and represents a potential treatment target for the worst prognosis associated breast cancers, such as TNBC.
Gener: a minimal programming module for chemical controllers based on DNA strand displacement
Authors: Kahramanoğulları Ozan , Cardelli Luca 
Published: May 2015

Abstract
Summary: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research’s DSD tool as well as to LaTeX.
Availability and implementation: Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono.
Contact: ozan@cosbi.eu
INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments
Authors: de Pretis Stefano , Kress Theresia , Morelli Marco J. , Melloni Giorgio E. M. , Riva Laura , Amati Bruno , Pelizzola Mattia 
Published: May 2015

Abstract
Motivation: Cellular mRNA levels originate from the combined action of multiple regulatory processes, which can be recapitulated by the rates of pre-mRNA synthesis, pre-mRNA processing and mRNA degradation. Recent experimental and computational advances set the basis to study these intertwined levels of regulation. Nevertheless, software for the comprehensive quantification of RNA dynamics is still lacking.
Results: INSPEcT is an R package for the integrative analysis of RNA- and 4sU-seq data to study the dynamics of transcriptional regulation. INSPEcT provides gene-level quantification of these rates, and a modeling framework to identify which of these regulatory processes are most likely to explain the observed mRNA and pre-mRNA concentrations. Software performance is tested on a synthetic dataset, instrumental to guide the choice of the modeling parameters and the experimental design.
Availability and implementation: INSPEcT is submitted to Bioconductor and is currently available as Supplementary Additional File S1.
Contact: mattia.pelizzola@iit.it
Supplementary Information: Supplementary data are available at Bioinformatics online.
INPS: predicting the impact of non-synonymous variations on protein stability from sequence
Authors: Fariselli Piero , Martelli Pier Luigi , Savojardo Castrense , Casadio Rita 
Published: May 2015

Abstract
Motivation: A tool for reliably predicting the impact of variations on protein stability is extremely important for both protein engineering and for understanding the effects of Mendelian and somatic mutations in the genome. Next Generation Sequencing studies are constantly increasing the number of protein sequences. Given the huge disproportion between protein sequences and structures, there is a need for tools suited to annotate the effect of mutations starting from protein sequence without relying on the structure. Here, we describe INPS, a novel approach for annotating the effect of non-synonymous mutations on the protein stability from its sequence. INPS is based on SVM regression and it is trained to predict the thermodynamic free energy change upon single-point variations in protein sequences.
Results: We show that INPS performs similarly to the state-of-the-art methods based on protein structure when tested in cross-validation on a non-redundant dataset. INPS performs very well also on a newly generated dataset consisting of a number of variations occurring in the tumor suppressor protein p53. Our results suggest that INPS is a tool suited for computing the effect of non-synonymous polymorphisms on protein stability when the protein structure is not available. We also show that INPS predictions are complementary to those of the state-of-the-art, structure-based method mCSM. When the two methods are combined, the overall prediction on the p53 set scores significantly higher than those of the single methods.
Availability and implementation: The presented method is available as web server at http://inps.biocomp.unibo.it.
Contact: piero.fariselli@unibo.it
Supplementary information: Supplementary Materials are available at Bioinformatics online.
Using combined evidence from replicates to evaluate ChIP-seq peaks
Authors: Jalili Vahid , Matteucci Matteo , Masseroli Marco , Morelli Marco J 
Published: May 2015

Abstract

Motivation
Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) detects genome-wide DNA–protein interactions and chromatin modifications, returning enriched regions (ERs), usually associated with a significance score. Moderately significant interactions can correspond to true, weak interactions, or to false positives; replicates of a ChIP-seq experiment can provide co-localised evidence to decide between the two cases. We designed a general methodological framework to rigorously combine the evidence of ERs in ChIP-seq replicates, with the option to set a significance threshold on the repeated evidence and a minimum number of samples bearing this evidence.

Results
We applied our method to Myc transcription factor ChIP-seq datasets in K562 cells available in the ENCODE project. Using replicates, we could extend up to 3 times the ER number with respect to single-sample analysis with equivalent significance threshold. We validated the ‘rescued’ ERs by checking for the overlap with open chromatin regions and for the enrichment of the motif that Myc binds with strongest affinity; we compared our results with alternative methods (IDR and jMOSAiCS), obtaining more validated peaks than the former and less peaks than latter, but with a better validation.

Availability and implementation
An implementation of the proposed method and its source code under GPLv3 license are freely available at http://www.bioinformatics.deib.polimi.it/MSPC/ and https://github.com/Genometric/MSPC, respectively.

Contact
marco.morelli@iit.it

Supplementary information
Supplementary Material are available at Bioinformatics online.
Report on a characteristic oscillation about 38 mHz (26 s) in northeastern Japan following surface wave of the 2011 Tohoku megathrust earthquake
Authors: Mitsui Yuta , Heki Kosuke 
Published: May 2015

AbstractWe try to detect an unidentified signal from the surface motion at northeastern Japan immediately after the 2011 Tohoku earthquake. A focused frequency range is 10–100 mHz (10–100 s). We find a peaky signal with frequency of about 38 mHz (26 s) based on the horizontal-to-vertical (H/V) spectral ratio using the high-rate GNSS data at 382 GEONET stations. We are not able to identify locality of the signal. The signal appears several minutes after the passing of surface wave fronts. The duration of the signal is about 2 min. Since the origin of the 38 mHz signal is unlikely to be local hydrologic tremors, tectonic tremors, or the tsunami, we speculate that the 38 mHz signal originates from a kind of a characteristic oscillation of Northeastern Japan triggered by the 2011 Tohoku earthquake. A normal-mode simulation implies that high-order radial overtones could create the signal with a spherically-layered velocity structure, however, the detailed mechanism of the signal still remains a mystery.
Examining the functional role of current area closures used for the conservation of an overexploited and highly mobile fishery species
Authors: McAllister Jaime D. , Barnett Adam , Lyle Jeremy M. , Semmens Jayson M. 
Published: May 2015

Abstract
Protecting essential habitats through the implementation of area closures has been recognized as a useful management tool for rebuilding overfished populations and minimizing habitat degradation. School shark (Galeorhinus galeus) have suffered significant stock declines in Australia; however, recent stock assessments suggest the population may have stabilized and the protection of closed nursery areas has been identified as a key management strategy to rebuilding their numbers. Young-of-the-year (YOY) and juvenile G. galeus were acoustically tagged and monitored to determine ontogenetic differences in residency and seasonal use of an important protected nursery area (Shark Refuge Area or SRA) in southeastern Tasmania. Both YOY and juvenile G. galeus showed a distinct seasonal pattern of occurrence in the SRA with most departing the area during winter and only a small proportion of YOY (33%) and no juveniles returning the following spring, suggesting areas outside the SRA may also be important during these early life-history stages. While these behaviors confirm SRAs continue to function as essential habitat during G. galeus early life history, evidence of YOY and juveniles emigrating from these areas within their first 1–2 years and the fact that few YOY return suggest that these areas may only afford protection for a more limited amount of time than previously thought. Determining the importance of neighbouring coastal waters and maintaining the use of traditional fisheries management tools are therefore required to ensure effective conservation of G. galeus during early life history.
The cell surface receptor Slamf6 modulates innate immune responses during Citrobacter rodentium-induced colitis
Authors: van Driel Boaz , Wang Guoxing , Liao Gongxian , Halibozek Peter J. , Keszei Marton , O’Keeffe Michael S. , Bhan Atul K. , Wang Ninghai , Terhorst Cox 
Published: May 2015

Abstract
The homophilic cell surface receptors CD150 (Slamf1) and CD352 (Slamf6) are known to modulate adaptive immune responses. Although the Th17 response was enhanced in Slamf6−/− C57BL/6 mice upon oral infection with Citrobacter rodentium, the pathologic consequences are indistinguishable from an infection of wild-type C57BL/6 mice. Using a reporter-based binding assay, we show that Slamf6 can engage structures on the outer cell membrane of several Gram− bacteria. Therefore, we examined whether Slamf6, like Slamf1, is also involved in innate responses to bacteria and regulates peripheral inflammation by assessing the outcome of C. rodentium infections in Rag−/− mice. Surprisingly, the pathology and immune responses in the lamina propria of C. rodentium-infected Slamf6−/−Rag−/− mice were markedly reduced as compared with those of Rag−/− mice. Infiltration of inflammatory phagocytes into the lamina propria was consistently lower in Slamf6−/−Rag−/− mice than in Rag−/− animals. Concomitant with the reduced systemic translocation of the bacteria was an enhanced production of IL-22, suggesting that Slamf6 suppresses a mucosal protective program. Furthermore, administering a mAb (330) that inhibits bacterial interactions with Slamf6 to Rag−/− mice ameliorated the infection compared with a control antibody. We conclude that Slamf6-mediated interactions of colonic innate immune cells with specific Gram− bacteria reduce mucosal protection and enhance inflammation, contributing to lethal colitis that is caused by C. rodentium infections in Rag−/− mice.
Integration of experiments across diverse environments identifies the genetic determinants of variation inSorghum bicolorseed element composition
Authors: Shakoor Nadia , Ziegler Greg , Dilkes Brian P. , Brenton Zachary , Boyles Richard , Connolly Erin L. , Kresovich Stephen , Baxter Ivan 
Published: May 2015

AbstractSeedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. Identification of genes and alleles that modify element content in the grains of cereals, includingSorghum bicolor, is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high throughput workflow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel (SAP), representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome wide association was demonstrated by implementing rank transformation and a multilocus mixed model (MLMM) to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc (Zn) manganese (Mn), nickel (Ni), calcium (Ca) and cadmium (Cd) in sorghum seed. In addition to strong candidates for these four elements, we provide a list of candidate loci for several other elements. Our approach enabled identification of SNPs in strong LD with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement.One sentence summaryHigh-throughput measurements of element accumulation and genome-wide association analysis across multiple environments identified novel alleles controlling seed element accumulation inSorghum bicolor.This project was partially funded by the iHUB Visiting Scientist Program (http://www.ionomicshub.org), Chromatin, Inc., NSF EAGER (1450341) to I.B. and BPD, NSF IOS 1126950 to IB, NSF IOS-0919739 to EC, and BMGF (OPP 1052924) to B.P.D.
Improving the Power of Structural Variation Detection by Augmenting the Reference
Authors: Schröder Jan , Girirajan Santhosh , Papenfuss Anthony T. , Medvedev Paul 
Published: May 2015

AbstractThe uses of the Genome Reference Consortium’s human reference sequence can be roughly categorized into three related but distinct categories: as a representative species genome, as a coordinate system for identifying variants, and as an alignment reference for variation detection algorithms. However, the use of this reference sequence as simultaneously a representative species genome and as an alignment reference leads to unnecessary artifacts for structural variation detection algorithms and limits their accuracy. We show how decoupling these two references and developing a separate alignment reference can significantly improve the accuracy of structural variation detection, lead to improved genotyping of disease related genes, and decrease the cost of studying polymorphism in a population.