bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inventing the Future of Surgery
Authors: Marescaux Jacques , Diana Michele 
Published: November 2014

AbstractSurgical innovation relies on patient safety and quality of life, which require a drastic iatrogenic impact reduction. A parallel development toward less invasive approaches has occurred in the field of surgery, interventional radiology, and endoscopy. Minimally invasive techniques provide unquestionable benefits to patients in terms of postoperative outcome. However, those techniques are not intuitive, and extensive training is required to overcome the inherent challenges and to be proficient and consequently to achieve a steep learning curve. Technologies have been developed by computer science and robotics departments, which might improve minimally invasive techniques. A new concept of cyber therapies is emerging through the development of computer and robotic sciences aiming at human–machine integration. Additionally, the convergence of surgery, endoscopy, and interventional radiology toward a hybrid therapeutic modality, namely image‐guided minimally invasive procedures, holds promises insofar as they could well maximize benefits in terms of efficacy and iatrogenic impact. In the present manuscript, the mainstays of these new paradigm developments are briefly outlined in light of our experience and vision of the future.
Reversible infantile mitochondrial diseases
Authors: Boczonadi Veronika , Bansagi Boglarka , Horvath Rita 
Published: November 2014

AbstractMitochondrial diseases are usually severe and progressive conditions; however, there are rare forms that show remarkable spontaneous recoveries. Two homoplasmic mitochondrial tRNA mutations (m.14674T>C/G in mt‐tRNAGlu) have been reported to cause severe infantile mitochondrial myopathy in the first months of life. If these patients survive the first year of life by extensive life‐sustaining measures they usually recover and develop normally. Another mitochondrial disease due to deficiency of the 5‐methylaminomethyl‐2‐thiouridylate methyltransferase (TRMU) causes severe liver failure in infancy, but similar to the reversible mitochondrial myopathy, within the first year of life these infants may also recover completely. Partial recovery has been noted in some other rare forms of mitochondrial disease due to deficiency of mitochondrial tRNA synthetases and mitochondrial tRNA modifying enzymes. Here we summarize the clinical presentation of these unique reversible mitochondrial diseases and discuss potential molecular mechanisms behind the reversibility. Understanding these mechanisms may provide the key to treatments of potential broader relevance in mitochondrial disease, where for the majority of the patients no effective treatment is currently available.
Education and Parental Involvement in Decision‐Making About Newborn Screening: Understanding Goals to Clarify Content
Authors: Potter Beth K. , Etchegary Holly , Nicholls Stuart G. , Wilson Brenda J. , Craigie Samantha M. , Araia Makda H. 
Published: November 2014

AbstractA challenge in designing effective education for parents about newborn screening (NBS) has been uncertainty about appropriate content. Arguing that the goals of education may be usefully tied to parental decision‐making, we sought to: (1) explore how different ways of implementing NBS differ in their approaches to parental engagement in decision‐making; (2) map the potential goals of education onto these “implementation models”; and (3) consider the content that may be needed to support these goals. The resulting conceptual framework supports the availability of comprehensive information about NBS for parents, irrespective of the model of implementation. This is largely because we argue that meeting parental expectations and preferences for communication is an important goal regardless of whether or notparents are actively involved in making a decision. Our analysis supports a flexible approach, in which some educational messages are emphasized as important for all parents to understand while others are made available depending on parents’ preferences. We have begun to define the content of NBS education for parents needed to support specific goals. Further research and discussion is important to determine the most appropriate strategies for delivering the tailored approach to education that emerged from our analysis.
Disclosing Genetic Information to Family Members About Inherited Cardiac Arrhythmias: An Obligation or a Choice?
Authors: Vavolizza Rick D. , Kalia Isha , Aaron Kathleen Erskine , Silverstein Louise B. , Barlevy Dorit , Wasserman David , Walsh Christine , Marion Robert W. , Dolan Siobhan M. 
Published: November 2014

AbstractInherited cardiac arrhythmias such as long QT syndrome and Brugada syndrome, present clinical as well as ethical, legal, and social challenges. Many individuals who carry a deleterious mutation are largely asymptomatic and therefore may not be diagnosed until after the occurrence of a personal or family member's cardiac event. The familial nature of inherited genetic information raises numerous ethical, legal, and social issues regarding the sharing of genetic information, particularly when an individual found to carry a deleterious mutation refuses to disclose his or her results to at‐risk family members who could benefit from life‐saving treatments. This qualitative study sought to understand the experiences with genetic testing for individuals (n = 50) with a personal or family history of cardiac events or sudden death. Unstructured in‐person focus groups or interviews were conducted for each participant in the study. The recordings of these interviews were transcribed verbatim and subsequently analyzed and coded. Participants’ comments regarding sharing of genetic information centered around four main themes: (1) motivation to disclose; (2) extent of disclosure; (3) effect of disclosure on family dynamics; and (4) reasons for not sharing genetic information. The majority of individuals believed that affected individuals are obligated to disclose genetic information to family members. In the era of personalized medicine, the disclosure of genetic information provides individuals the opportunities to learn about the genetics, disease characteristics, and treatment options in order to reduce morbidity and mortality in themselves and their family members. Further research is necessary to identify and explore the barriers to sharing genetic information with at‐risk family members.
A Three‐Step Assay for Ceramide Synthase Activity Using a Fluorescent Substrate and HPLC
Authors: Couttas Timothy A. , Lim Xin Y. , Don Anthony S. 
Published: November 2014

AbstractCeramides are a family of signalling lipids with diverse physiological functions that include pro‐differentiative and pro‐apoptotic signalling. Ceramides and their derivatives are major constituents of myelin, maintaining neuronal conductivity. Ceramides are synthesized by ceramide synthases, of which there are six isoforms in mammals (CERS1–6). These enzymes catalyse the transfer of a variable length fatty acid to a sphingoid base, typically sphingosine or dihydrosphingosine. We previously reported a fluorescent thin‐layer chromatography assay for ceramide synthase activity. In this paper we describe an improved fluorescent assay, using HPLC to achieve clear resolution of closely related ceramide species and to facilitate easy quantification of both product and substrate. Our HPLC assay protocol eliminates the need for a chloroform extraction step. Instead a simple three‐step procedure is used: (1) reactions are run; (2) reactions are terminated with addition of methanol and centrifuged; (3) products are quantified with HPLC. HPLC resolution enables assays in which multiple fatty acid substrates are used in the same reaction. Using this approach, we show that CERS2 demonstrates a preference for the monounsaturated C24:1 fatty acid substrate compared to the saturated C24:0 substrate, potentially explaining why myelin is enriched in ceramides containing the monounsaturated form of very long chain fatty acids.
2D Resistivity Imaging for Delineation of Waterlogged Coal Workings in Unapproachable Underground Coal Mines to Check Inundation Hazard
Authors: Singh K. K. K. 
Published: November 2014

Abstract:
2D Resistivity Imaging survey is a relatively a new technique used for detecting old, abandoned & unapproachable waterlogged areas in underground mines in recent years. Hingir Rampur Colliery of Mahanadi Coalfields Limited (MCL) was facing problem due to presence of unapproachable underground waterlogged coal workings. Mine management was extracting coal in Seam I of Hingir Rampur seam (HR Seam) at the depth of 100 m. As they had planned to progress the workings of Seam I towards waterlogged goaves of 9 & 11 pits, they proposed to explore the status of waterlogged workings between Seam I of Hingir Rampur colliery and waterlogged goaves of 9 & 11 pits so that they could leave at least 60 m coal barrier from the waterlogged area to check inundation hazard.
For this purpose, Resistivity Imaging (RI) survey were conducted along the six profiles A, B, C, D, E and F in Hingir Rampur colliery in the proposed area for exploration of the waterlogged workings between Seam I and waterlogged goaves of 9 & 11 pits. Pole-pole array of RI survey was used in this study. Considering the indirect approach of geophysical methods, two boreholes (CMRI-31&CMRI-32) were being drilled along the profiles D and F to confirm the RI data, which were nearer to the coal extraction site. After correlating and corroborating of borehole data with RI data, it was confirmed that strata were hard, compact and dry at 60 m from the surface and continued up to 146 m depth. Hence, it was concluded that mining can be done safely at the depths varying from 100 m to 146 m.
Occurrence of Helicobacter pylori in saliva from preschool‐age children
Authors: Ueda Jun , Yamaguchi Akira , Shibasaki Kohichi 
Published: November 2014

AbstractIntroduction: It is known that initial infection with Helicobacter pylori can occur in children aged 5 years or less, but there have been no studies investigating the period of initial infection. Here, 418 children attending preschool, and their parents, were tested for H. pylori DNA by real‐time PCR using saliva samples in order to infer the period of initial infection of H. pylori.Methods: Subjects took samples of their saliva by chewing on a sterile absorbent cotton roll for 2 minutes, and samples were stored at −80°C until they were examined. DNA was extracted from 100 μl of saliva and was tested for H. pylori DNA using the TaqMan method.Result: The H. pylori DNA detection rate among children was: 4.1% among 3‐year‐olds, 4.9% among 4‐year‐olds, 10.0% among 5‐year‐olds, and 13.3% among 6‐year‐olds. The detection rate thus increased with age, showing a sharp increase from age 4 to 5 years. The rate of H. pylori detection among mothers of H. pylori‐positive children was 56.2%, which was significantly greater than the rate among mothers of H. pylori‐negative children (17.2%).Conclusion: These results suggest that initial infection occurs even in children aged under 3 years, and the rise in detection rate between age 4 and 5 years suggests that there is a high risk of H. pylori infection during this period. Furthermore, the finding that the positivity rate was significantly higher among mothers of H. pylori‐positive children than mothers of H. pylori‐negative children indicates that mother‐child infection is the most important route.
A cryptic species ofAphis gossypii(Hemiptera: Aphididae) complex revealed by genetic divergence and different host plant association
Authors: Lee Y. , Lee W. , Lee S. , Kim H. 
Published: November 2014

AbstractThree cryptic species,Aphis gossypii,Aphis glycines, andAphis rhamnicolasp. nov., are recognized as sharing buckthorn plant,Rhamnusspp. as primary hosts. These aphid species have morphological similarities; however, there are significant genetic differences between the three cryptic species. Based on the high level of genetic divergence and the different secondary host association, we described a new species,Aphis rhamnicolasp. nov., for apterous and alate vivipara, fundatrix, ovipara, and gynopara, including diagnostic key for the host sharing species in the genusAphis.
A framework for evaluating the effectiveness of conservation attention at the species level
Authors: Washington Harriet , Baillie Jonathan , Waterman Carly , Milner-Gulland E.J. 
Published: November 2014

AbstractIt is essential to understand whether conservation interventions are having the desired effect, particularly in light of increasing pressures on biodiversity and because of requirements by donors that project success be demonstrated. Whilst most evaluations look at effectiveness at a project or organizational level, local efforts need to be connected to an understanding of the effectiveness of conservation directed at a species as a whole, particularly as most metrics of conservation success are at the level of species. We present a framework for measuring the effectiveness of conservation attention at a species level over time, based on scoring eight factors essential for species conservation (engaging stakeholders, management programme, education and awareness, funding and resource mobilization, addressing threats, communication, capacity building and status knowledge), across input, output and outcome stages, in relation to the proportion of the species’ range where each factor attains its highest score. The framework was tested using expert elicitation for 35 mammal and amphibian species on the Zoological Society of London's list of Evolutionarily Distinct and Globally Endangered species. Broad patterns in the index produced by the framework could suggest potential mechanisms underlying change in species status. Assigning an uncertainty score to information demonstrates not only where gaps in knowledge exist, but discrepancies in knowledge between experts. This framework could be a useful tool to link local and global scales of impact on species conservation, and could provide a simple and visually appealing way of tracking conservation over time.
Volumetric modulated arc therapy versus 3D conformal radiotherapy for selected childhood neoplasms
Authors: Chojnacka Marzanna , Zygmuntowicz-Piętka Anna , Semaniak Anna , Pędziwiatr Katarzyna , Dąbrowski Ryszard , Skowrońska-Gardas Anna 
Published: November 2014

AbstractAimThe comparative study of the plan quality between volumetric modulated arc therapy (VMAT) and 3D conformal therapy (3DCRT) for the treatment of selected representative childhood neoplasms was performed.Materials and methodsDuring the year 2013, 44 children with neoplasms were irradiated using VMAT. The 3DCRT plans were created retrospectively and compared with the VMAT plans for four tumour locations. The conformity parameters, dose volume histograms for target volume and organs at risk, number of monitor units and time used to deliver the single fraction were evaluated and compared for each plan. Additionally, for patients with brain tumour the comparison of different arcs configuration was made.ResultsVMAT modality presented the superiority over older conformal methods with regard to the improvement in the dose conformity and normal tissue sparing. The noncoplanar arcs arrangement was beneficial in the decrease of high-dose volume and the protection of the organs at risk located oppositely to the target volume.FindingsVMAT could be preferred technique for treating childhood neoplasms, especially when the complex-shaped target volume is localised close to the critical structures. The noncoplanar arcs arrangement could be the method of choice in the reirradiated patients and in these with laterally located brain tumours.
Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3
Authors: Shan Chun-Min , Shangguan Xiao-Xia , Zhao Bo , Zhang Xiu-Fang , Chao Lu-men , Yang Chang-Qing , Wang Ling-Jian , Zhu Hua-Yu , Zeng Yan-Da , Guo Wang-Zhen , Zhou Bao-Liang , Hu Guan-Jing , Guan Xue-Ying , Chen Z. Jeffrey , Wendel Jonathan F. , Zhang Tian-Zhen , Chen Xiao-Ya 
Published: November 2014

AbstractCotton fibres are unusually long, single-celled epidermal seed trichomes and a model for plant cell growth, but little is known about the regulation of fibre cell elongation. Here we report that a homeodomain-leucine zipper (HD-ZIP) transcription factor, GhHOX3, controls cotton fibre elongation.GhHOX3genes are localized to the 12th homoeologous chromosome set of allotetraploid cotton cultivars, associated with quantitative trait loci (QTLs) for fibre length. Silencing ofGhHOX3greatly reduces (>80%) fibre length, whereas its overexpression leads to longer fibre. Combined transcriptomic and biochemical analyses identify target genes of GhHOX3 that also contain the L1-boxcis-element, including two cell wall loosening protein genesGhRDL1andGhEXPA1. GhHOX3 interacts with GhHD1, another homeodomain protein, resulting in enhanced transcriptional activity, and with cotton DELLA, GhSLR1, repressor of the growth hormone gibberellin (GA). GhSLR1 interferes with the GhHOX3–GhHD1 interaction and represses target gene transcription. Our results uncover a novel mechanism whereby a homeodomain protein transduces GA signal to promote fibre cell elongation.
Comparison of the transcriptional landscapes between human and mouse tissues
Authors: Lin Shin , Lin Yiing , Nery Joseph R. , Urich Mark A. , Breschi Alessandra , Davis Carrie A. , Dobin Alexander , Zaleski Christopher , Beer Michael A. , Chapman William C. , Gingeras Thomas R. , Ecker Joseph R. , Snyder Michael P. 
Published: November 2014

Significance
To date, various studies have found similarities between humans and mice on a molecular level, and indeed, the murine model serves as an important experimental system for biomedical science. In this study of a broad number of tissues between humans and mice, high-throughput sequencing assays on the transcriptome and epigenome reveal that, in general, differences dominate similarities between the two species. These findings provide the basis for understanding the differences in phenotypes and responses to conditions in humans and mice.
SAMNetWeb: identifying condition-specific networks linking signaling and transcription
Authors: Gosline Sara J. C. , Oh Coyin , Fraenkel Ernest 
Published: November 2014

Abstract
Motivation : High-throughput datasets such as genetic screens, mRNA expression assays and global phospho-proteomic experiments are often difficult to interpret due to inherent noise in each experimental system. Computational tools have improved interpretation of these datasets by enabling the identification of biological processes and pathways that are most likely to explain the measured results. These tools are primarily designed to analyse data from a single experiment (e.g. drug treatment versus control), creating a need for computational algorithms that can handle heterogeneous datasets across multiple experimental conditions at once.
Summary: We introduce SAMNetWeb, a web-based tool that enables functional enrichment analysis and visualization of high-throughput datasets. SAMNetWeb can analyse two distinct data types (e.g. mRNA expression and global proteomics) simultaneously across multiple experimental systems to identify pathways activated in these experiments and then visualize the pathways in a single interaction network. Through the use of a multi-commodity flow based algorithm that requires each experiment ‘share’ underlying protein interactions, SAMNetWeb can identify distinct and common pathways across experiments.
Availability and implementation: SAMNetWeb is freely available at http://fraenkel.mit.edu/samnetweb.
Contact: fraenkel-admin@mit.edu
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data
Authors: Kyoda Koji , Tohsato Yukako , Ho Kenneth H. L. , Onami Shuichi 
Published: November 2014

Abstract
Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats.
Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis.
Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/.
Contact: sonami@riken.jp
Supplementary Information: Supplementary data are available at Bioinformatics online.
Looking in the rear-view mirror: bias and retrospective patterns in
integrated, age-structured stock assessment models
Authors: Hurtado-Ferro Felipe , Szuwalski Cody S. , Valero Juan L. , Anderson Sean C. , Cunningham Curry J. , Johnson Kelli F. , Licandeo Roberto , McGilliard Carey R. , Monnahan Cole C. , Muradian Melissa L. , Ono Kotaro , Vert-Pre Katyana A. , Whitten Athol R. , Punt André E. 
Published: November 2014

Abstract
Retrospective patterns are systematic changes in estimates of population size, or other assessment model-derived quantities, that occur as additional years of data are added to, or removed from, a stock assessment. These patterns are an insidious problem, and can lead to severe errors when providing management advice. Here, we use a simulation framework to show that temporal changes in selectivity, natural mortality, and growth can induce retrospective patterns in integrated, age-structured models. We explore the potential effects on retrospective patterns of catch history patterns, as well as model misspecification due to not accounting for time-varying biological parameters and selectivity. We show that non-zero values for Mohn’s ρ (a common measure for retrospective patterns) can be generated even where there is no model misspecification, but the magnitude of Mohn’s ρ tends to be lower when the model is not misspecified. The magnitude and sign of Mohn’s ρ differed among life histories, with different life histories reacting differently from each type of temporal change. The value of Mohn’s ρ is not related to either the sign or magnitude of bias in the estimate of terminal year biomass. We propose a rule of thumb for values of Mohn’s ρ which can be used to determine whether a stock assessment shows a retrospective pattern.