bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal Evolution of the Concentration of Gangliosides GM3 and GD3 in Human Milk
Authors: Giuffrida Francesca , Elmelegy Isabelle Masserey , Thakkar Sagar K. , Marmet Cynthia , Destaillats Frédéric 
Published: September 2014

AbstractIt has been reported that dietary gangliosides may have an important role in preventing infections and in brain development during early infancy. However, data related to the evolution of their concentration over the different stages of lactation are scarce. Liquid chromatography coupled with electrospray ionization high resolution mass spectrometer (LC/ESI‐HR‐MS) has been optimized to quantify the two major ganglioside classes, i.e., aNeu5Ac(2‐8)aNeu5Ac(2‐3)bDGalp(1‐4)bDGlcp(1‐1)Cer (GD3) and aNeu5Ac(2‐3)bDGalp(1‐4)bDGlcp(1‐1)Cer (GM3) in human milk. Gangliosides were extracted using chloroform and methanol, further purified by solid‐phase extraction and separated by reversed‐phase liquid chromatography. Repeatability, intermediate reproducibility, and recovery values were assessed to validate the method. In human milk, GD3 and GM3 could be quantified at the level of 0.1 and 0.2 μg/mL, respectively, with relative standard deviation of repeatability [CV(r)] and intermediate reproducibility [CV(iR)] values ranging from 1.9 to 15.0 % and 1.9 to 22.5 %, respectively. The described method was used to quantify GD3 and GM3 in human milk samples collected from 450 volunteers between 0 and 11 days and at 30, 60 and 120 days postpartum, providing for the first time the concentration of these minor lipids in a large cohort. The content of total gangliosides ranged from 8.1 and 10.7 μg/mL and the mean intake of gangliosides in infants 30, 60 and 120 days postpartum could be estimated at about 5.5, 7.0 and 8.6 mg of total gangliosides per day, respectively, when infants were exclusively breastfed.
Peter Zumthor's ‘Topography of Terror’
Authors: Leoni Claudio 
Published: September 2014

This paper discusses Peter Zumthor's project for the Topography of Terror foundation in Berlin, an institution that aims to research, and communicate, the atrocity of Nazi crimes and to work against the forgetting of history. The site where Topography of Terror is based, in the centre of the city, once housed the major institutions from which the Third Reich wrought terror over Europe and from where genocide was organised /1/. It is thus a unique site where the victims are absent and the perpetrators cannot be commemorated: the primary challenge in dealing with the site.In the late autumn of 2004, Zumthor's project came to an unfortunate end. After eleven years of planning, arguing and constructing, the authorities of Berlin decided to abandon the partially constructed Topography of Terror building and to commission an alternative, while newspapers speculated about spiralling costs, technical problems and the disagreements of those involved. Eventually, in December of the same year, the early stages of Zumthor's construction were demolished. Nevertheless, the project's unique approach to history and remembrance should be discussed further. Unlike most memorials, Zumthor's project did not seek to represent a historical event mimetically or allegorically, but rather tried to embody the limits of representation by confronting the visitor with a non-representational approach to history.
Identification and characterization of novel serum microRNA candidates from deep sequencing in cervical cancer patients
Authors: Juan Li , Tong Hong-li , Zhang Pengjun , Guo Guanghong , Wang Zi , Wen Xinyu , Dong Zhennan , Tian Ya-ping 
Published: September 2014

AbstractSmall non-coding microRNAs (miRNAs) are involved in cancer development and progression and serum profiles of cervical cancer patients may be useful for identifying novel miRNAs. We performed deep sequencing on serum pools of cervical cancer patients and healthy controls with 3 replicates and constructed a small RNA library. We used MIREAP to predict novel miRNAs and identified 2 putative novel miRNAs between serum pools of cervical cancer patients and healthy controls after filtering out pseudo-pre-miRNAs using Triplet-SVM analysis. The 2 putative novel miRNAs were validated by real time PCR and were significantly decreased in cervical cancer patients compared with healthy controls. One novel miRNA had an area under curve (AUC) of 0.921 (95% CI: 0.883, 0.959) with a sensitivity of 85.7% and a specificity of 88.2% when discriminating between cervical cancer patients and healthy controls. Our results suggest that characterizing serum profiles of cervical cancers by Solexa sequencing may be a good method for identifying novel miRNAs and that the validated novel miRNAs described here may be cervical cancer-associated biomarkers.
Connexin hemichannels contribute to spontaneous electrical activity in the human fetal cortex
Authors: Moore Anna R. , Zhou Wen-Liang , Sirois Carissa L. , Belinsky Glenn S. , Zecevic Nada , Antic Srdjan D. 
Published: September 2014

Significance
Young neurons require occasional bursts of action-potential firing to maintain intracellular processes, to drive gene expression, to indicate their presence in a new location, and to attract and keep synaptic contacts. While in the adult cortex electrical activity is driven by synaptic inputs, during early cortical development these synaptic inputs are largely absent. In the absence of synaptic connections and sensory experience, human neurons use an energetically favorable membrane mechanism for generating and maintaining electrical activity: connexin hemichannels. The spontaneous flickering of connexin hemichannels produces depolarizing events (often crowned with bursts of action potentials) to help establish early electrical communication in young subplate neurons. This type of activity dominates the human cortical wall 5 months before birth.
Phospholipase D2 specifically regulates TREK potassium channels via direct interaction and local production of phosphatidic acid
Authors: Comoglio Yannick , Levitz Joshua , Kienzler Michael A. , Lesage Florian , Isacoff Ehud Y. , Sandoz Guillaume 
Published: September 2014

Significance
Our work provides evidence for a mechanism for the formation of membrane microdomains in which the local concentration of a phospholipid can change independently of the bulk membrane to confer selectivity on membrane protein regulation. We found that, despite the fact that all TWIK-related K channel (TREK) family members are sensitive to phosphatidic acid (PA), only TREK1 and TREK2 are potentiated by phospholipase D2 (PLD2) (which produces PA), but not by PLD1. This surprising specificity is due to the direct binding of PLD2 to TREK. This binding allows a local PA production that tonically activates the channel. Furthermore, we found the local signaling via PA to have a secondary focusing effect for primary alcohols, which inhibit the channel by altering the PA microdomain.
Kinesin processivity is gated by phosphate release
Authors: Milic Bojan , Andreasson Johan O. L. , Hancock William O. , Block Steven M. 
Published: September 2014

Significance
Kinesin-1 is a motor protein central to intracellular transport. Prevailing models of the kinesin mechanochemical cycle—which invoke docking of the neck linker domain upon ATP binding—fail to explain the remarkable processivity of kinesin, which represents a competition between dissociation from the microtubule and continuation of the stepping cycle. We show that kinesin dissociation, which characterizes the end of a processive run, is gated by phosphate release following ATP hydrolysis. The structural change driving kinesin motility, likely neck linker docking, is therefore completed only upon hydrolysis. Our results offer insights into gating mechanisms and necessitate revisions to existing models of the kinesin cycle.
Activation of iNKT cells by a distinct constituent of the endogenous glucosylceramide fraction
Authors: Brennan Patrick J. , Tatituri Raju V. V. , Heiss Christian , Watts Gerald F. M. , Hsu Fong-Fu , Veerapen Natacha , Cox Liam R. , Azadi Parastoo , Besra Gurdyal S. , Brenner Michael B. 
Published: September 2014

Significance
Invariant natural killer T (iNKT) cells are a specialized subset of T cells that recognizes lipids, rather than peptides, as antigens. Recognition of both endogenous and exogenous lipids by iNKT cells contributes to immune responses during infection, cancer, autoimmune disease, and allergic disease. The endogenous lipids recognized by iNKT cells in most contexts, however, remain unclear. In this report, we characterize the lipid antigen activity found in mammalian milk and tissues. Our data suggest that activity is related to a minor component of the glucosylceramide fraction. Whether contributed from endogenous sources or from the diet, this rare, yet potent lipid activity may play an important role in driving immune responses.
Marijuana and Alcohol Use and Attempted Smoking Cessation in Adolescent Boys and Girls
Authors: Camenga Deepa R. , Kong Grace , Bagot Kara , Hoff Rani A. , Potenza Marc N. , Krishnan-Sarin Suchitra 
Published: August 2014

Background This study sought to determine the relationship between the frequency of current marijuana and alcohol use and cigarette quit attempts in male and female adolescent smokers. Methods Data from a cross-sectional survey of health behaviors in high-school-aged adolescents were analyzed. Current cigarette smokers ( n = 804) who reported use of at least 1 cigarette in the past month were divided into those with and without a history of at least 1 quit attempt (a self-reported episode of trying to “stop smoking”). Logistic regression models were fit to describe the association between the frequency of marijuana/alcohol use and a history of cigarette quit attempts. Results Among the total sample, higher-frequency marijuana use (more than 6 times in the past 30 days) and frequent binge drinking (more than 5 days of binge drinking in the past 30 days) decreased the odds of having a past cigarette quit attempt (higher-frequency marijuana: adjusted odds ratio [AOR] = 0.56, 95% confidence interval [CI] = 0.36–0.86; frequent binge drinking: AOR = 0.49, 95% CI = 0.29–0.83). A significant gender interaction was observed for the relationship between higher-frequency marijuana use and a history of cigarette quit attempts ( P = .03), with decreased odds in boys (AOR = 0.41, 95% CI = 0.22–0.77) but not in girls (AOR = 0.71, 95% CI = 0.37–1.33). Conclusions Adolescent smokers who report higher-frequency marijuana use or frequent binge drinking have a decreased likelihood of a history of a cigarette quit attempt. The gender-related association between higher-frequency marijuana use and a history of quit attempts suggests that boys with greater substance use may need particularly intensive support to initiate quit attempts.
Improving Compliance with Timely Intraoperative Redosing of Antimicrobials in Surgical Prophylaxis
Authors: Riggi Gina , Castillo Mayela , Fernandez Margaret , Wawrzyniak Andrew , Vigoda Michael , Eber Scott , Lubarsky David , Abbo Lilian M. 
Published: September 2014

Background.Appropriate use of antimicrobials for surgical prophylaxis is an important patient safety issue. Antimicrobial levels should be present during the duration of the surgical procedure until incision site closure. For prolonged surgical procedures in which the tissue concentration of the prophylactic antimicrobial may decrease to below the necessary minimum inhibitory concentration, intraoperative redosing of antimicrobials may be crucial Objective.To evaluate compliance of appropriate intraoperative antimicrobial surgical prophylaxis using real-time intraoperative antimicrobial dosing reminders at a large teaching hospital.Methods.A retrospective review of electronic records (March 2009–October 2012) was performed. Patients were included if they were at least 18 years of age and underwent a procedure requiring antimicrobial surgical prophylaxis. Compliance was determined by comparing 3 time intervals: baseline (March 2009–March 2010); intervention period 1 (IP-1; April 1, 2010–April 30, 2012), and intervention period 2 (IP-2; May 1, 2012–October 31, 2012). Interventions included a hospital-wide standardized protocol comprising an automated intraoperative paging system to notify when antimicrobials should be redosed.Results.A total of 7,461 of 75,230 surgical procedures required intraoperative redosing of antimicrobials and were analyzed. Patient mean age (± standard deviation) was 45 ± 19 years, and 62.6% were female. The most common procedures that required prophylaxis were solid organ transplantation, neurosurgical procedures, and orthopedic procedures. Baseline compliance (n = 2,183) was 15.8%; compliance significantly improved to 65.3% during IP-1 (n = 4,486; P < .001). The compliance rate improved to 76.7% during IP-2 (P > .001 compared with no reminder).Conclusions.Compliance with redosing of intraoperative antimicrobials was improved with the combined approach of guidelines, education to healthcare providers, and real-time automated paging system.
poRe: an R package for the visualization and analysis of nanopore sequencing data
Authors: Watson Mick , Thomson Marian , Risse Judith , Talbot Richard , Santoyo-Lopez Javier , Gharbi Karim , Blaxter Mark 
Published: August 2014

Abstract
Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.
Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.
Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/
Contact: mick.watson@roslin.ed.ac.uk
Supplementary information : Supplementary data are available at Bioinformatics online.
Review and refinement of an existing qualitative risk assessment method for application within an ecosystem-based management framework
Authors: Fletcher Warrick (Rick) J. 
Published: August 2014

Abstract
The adoption of risk-based methodologies is considered essential for the successful implementation of an ecosystem approach to fisheries and broader aquatic management. To assist with these initiatives, one of the qualitative risk assessment methods adapted for fisheries management over a decade ago has been reviewed. This method was updated to ensure compliance with the revised international standards for risk management (ISO 31000) and to enable consideration of ecological, economic, social, and governance risks. The review also addressed the difficulties that have been encountered in stakeholder understanding of the underlying concepts and to increase the discipline in its application. The updates include simplifying the number of consequence and likelihood levels, adopting graphical techniques to represent different consequence levels, and discussing how changes in uncertainty can affect risk scores. Adopting an explicit “weight of evidence” approach has also assisted with determining which consequence scenarios are considered plausible and, where relevant, their specific likelihoods. The revised methods therefore incorporate the conceptual elements from a number of qualitative and quantitative approaches increasing their reliability and enabling a more seamless transition along this spectrum as more lines of evidence are collected. It is expected that with continued application of these methods, further refinements will be identified.
Total Serum Bilirubin Predicts Fat‐Soluble Vitamin Deficiency Better Than Serum Bile Acids in Infants With Biliary Atresia
Authors: Venkat Veena L. , Shneider Benjamin L. , Magee John C. , Turmelle Yumirle , Arnon Ronen , Bezerra Jorge A. , Hertel Paula M. , Karpen Saul J. , Kerkar Nanda , Loomes Kathleen M. , Molleston Jean , Murray Karen F. , Ng Vicky L. , Raghunathan Trivellore , Rosenthal Philip , Schwartz Kathleen , Sherker Averell H. , Sokol Ronald J. , Teckman Jeffrey , Wang Kasper , Whitington Peter F. , Heubi James E. ,   Childhood Liver Disease Research and Education Network (ChiLDReN)
Published: September 2014

ABSTRACTObjective:Fat‐soluble vitamin (FSV) deficiency is a well‐recognized consequence of cholestatic liver disease and reduced intestinal intraluminal bile acid. We hypothesized that serum bile acid (SBA) would predict biochemical FSV deficiency better than serum total bilirubin (TB) level in infants with biliary atresia.Methods:Infants enrolled in the Trial of Corticosteroid Therapy in Infants with Biliary Atresia after hepatoportoenterostomy were the subjects of this investigation. Infants received standardized FSV supplementation and monitoring of TB, SBA, and vitamin levels at 1, 3, and 6 months. A logistic regression model was used with the binary indicator variable insufficient/sufficient as the outcome variable. Linear and nonparametric correlations were made between specific vitamin measurement levels and either TB or SBA.Results:The degree of correlation for any particular vitamin at a specific time point was higher with TB than with SBA (higher for TB in 31 circumstances vs 3 circumstances for SBA). Receiver operating characteristic curve shows that TB performed better than SBA (area under the curve 0.998 vs 0.821). Including both TB and SBA did not perform better than TB alone (area under the curve 0.998).Conclusions:We found that TB was a better predictor of FSV deficiency than SBA in infants with biliary atresia. The role of SBA as a surrogate marker of FSV deficiency in other cholestatic liver diseases, such as progressive familial intrahepatic cholestasis, α‐1‐antitrypsin deficiency, and Alagille syndrome in which the pathophysiology is dominated by intrahepatic cholestasis, warrants further study.
Extrahepatic Portal Vein Obstruction in Egyptian Children
Authors: El‐Karaksy Hanaa M. , El‐Koofy Nehal , Mohsen Nabil , Helmy Heba , Nabil Nevian , El‐Shabrawi Mortada 
Published: September 2014

ABSTRACTBackground and Aim:Extrahepatic portal vein obstruction (EHPVO) is an important cause of portal hypertension in children. The aim of this study was to describe the clinical presentation, possible risk factors, upper gastrointestinal endoscopic findings, and treatment modalities of children with EHPVO.Methods:After ethical approval of our study protocol by our institution review board, we analyzed available data from medical records of patients with EHPVO presenting to the Pediatric Hepatology Unit, Cairo University Pediatric Hospital, Egypt, for a period of 15 years from January 1996 to December 2010.Results:The study included 169 patients. Their ages at presentation ranged from 1 month to 12 years (median 2.5 years, interquartile range 5); 101 were boys. Hematemesis was a presenting symptom in 58%, splenomegaly was present in 87%, esophageal varices were present in 94%, and fundal varices were present in 23%. Possible risk factors, in the form of umbilical catheterization, umbilical sepsis, and exchange transfusion, were elicited in 18%. Propranolol was associated with reduction in bleeding episodes (P < 0.001), but was associated with increased chest symptoms (P < 0.01). Both injection sclerotherapy and band ligation were effective in the management of bleeding varices and for primary and secondary prophylaxis; however, injection sclerotherapy was associated with the development of secondary gastric varices (P = 0.03).Conclusions:This large study of children with EHPVO demonstrates the efficacy of propranolol in the reduction of gastrointestinal bleeding in children with EHPVO. Both injection sclerotherapy and band ligation were effective in the management of esophageal varices, although the former was associated with the development of secondary gastric varices. Randomized clinical trials to choose the best modalities for the management of portal hypertension in children are still lacking.
Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genusSceloporus) in the southern Mexican highlands
Authors: Grummer Jared A. , Calderón-Espinosa Martha L. , Oca Adrián Nieto-Montes de , Smith Eric N. , Méndez-de la Cruz Fausto R. , Leaché Adam D. 
Published: September 2014

AbstractInterspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the ancestral population overlap. In this study, we performed population genetic analyses, species delimitation, simulations, and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of theSceloporus spinosusgroup. The two species in this group,S. spinosusandS. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations ofS. spinosusandS. horridusowing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestralS. spinosusandS. horriduspopulations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.