bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotype calling from next-generation sequencing data using haplotype information of reads
Authors: Zhi Degui , Wu Jihua , Liu Nianjun , Zhang Kui 
Published: January 2012

Abstract
Motivation: Low coverage sequencing provides an economic strategy for whole genome sequencing. When sequencing a set of individuals, genotype calling can be challenging due to low sequencing coverage. Linkage disequilibrium (LD) based refinement of genotyping calling is essential to improve the accuracy. Current LD-based methods use read counts or genotype likelihoods at individual potential polymorphic sites (PPSs). Reads that span multiple PPSs (jumping reads) can provide additional haplotype information overlooked by current methods.
Results: In this article, we introduce a new Hidden Markov Model (HMM)-based method that can take into account jumping reads information across adjacent PPSs and implement it in the HapSeq program. Our method extends the HMM in Thunder and explicitly models jumping reads information as emission probabilities conditional on the states of adjacent PPSs. Our simulation results show that, compared to Thunder, HapSeq reduces the genotyping error rate by 30%, from 0.86% to 0.60%. The results from the 1000 Genomes Project show that HapSeq reduces the genotyping error rate by 12 and 9%, from 2.24% and 2.76% to 1.97% and 2.50% for individuals with European and African ancestry, respectively. We expect our program can improve genotyping qualities of the large number of ongoing and planned whole genome sequencing projects.
Contact: dzhi@ms.soph.uab.edu; kzhang@ms.soph.uab.edu
Availability: The software package HapSeq and its manual can be found and downloaded at www.ssg.uab.edu/hapseq/.
Supplementary information: Supplementary data are available at Bioinformatics online.
vHOG, a multispecies vertebrate ontology of homologous organs groups
Authors: Niknejad Anne , Comte Aurélie , Parmentier Gilles , Roux Julien , Bastian Frederic B. , Robinson-Rechavi Marc 
Published: January 2012

AbstractMotivation: Most anatomical ontologies are species-specific, whereas a framework for comparative studies is needed. We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species.Results: vHOG is a multispecies anatomical ontology for the vertebrate lineage. It is based on the HOGs used in the Bgee database of gene expression evolution. vHOG version 1.4 includes 1184 terms, follows OBO principles and is based on the Common Anatomy Reference Ontology (CARO). vHOG only describes structures with historical homology relations between model vertebrate species. The mapping to species-specific anatomical ontologies is provided as a separate file, so that no homology hypothesis is stated within the ontology itself. Each mapping has been manually reviewed, and we provide support codes and references when available.Availability and implementation: vHOG is available from the Bgee download site (http://bgee.unil.ch/), as well as from the OBO Foundry and the NCBO Bioportal websites.Contact: bgee@isb-sib.ch; frederic.bastian@unil.ch
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data
Authors: Roth Andrew , Ding Jiarui , Morin Ryan , Crisan Anamaria , Ha Gavin , Giuliany Ryan , Bashashati Ali , Hirst Martin , Turashvili Gulisa , Oloumi Arusha , Marra Marco A. , Aparicio Samuel , Shah Sohrab P. 
Published: January 2012

Abstract
Motivation: Identification of somatic single nucleotide variants (SNVs) in tumour genomes is a necessary step in defining the mutational landscapes of cancers. Experimental designs for genome-wide ascertainment of somatic mutations now routinely include next-generation sequencing (NGS) of tumour DNA and matched constitutional DNA from the same individual. This allows investigators to control for germline polymorphisms and distinguish somatic mutations that are unique to the tumour, thus reducing the burden of labour-intensive and expensive downstream experiments needed to verify initial predictions. In order to make full use of such paired datasets, computational tools for simultaneous analysis of tumour–normal paired sequence data are required, but are currently under-developed and under-represented in the bioinformatics literature.
Results: In this contribution, we introduce two novel probabilistic graphical models called JointSNVMix1 and JointSNVMix2 for jointly analysing paired tumour–normal digital allelic count data from NGS experiments. In contrast to independent analysis of the tumour and normal data, our method allows statistical strength to be borrowed across the samples and therefore amplifies the statistical power to identify and distinguish both germline and somatic events in a unified probabilistic framework.
Availability: The JointSNVMix models and four other models discussed in the article are part of the JointSNVMix software package available for download at http://compbio.bccrc.ca
Contact: sshah@bccrc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
A randomized study of haemodynamic effects and left ventricular dyssynchrony in right ventricular apical vs. high posterior septal pacing in cardiac resynchronization therapy
Authors: Kristiansen H.M. , Vollan G. , Hovstad T. , Keilegavlen H. , Faerestrand S. 
Published: January 2012

AimsThe effect on left ventricular (LV) systolic function and LV dyssynchrony by alternative right ventricular (RV) lead position in cardiac resynchronization therapy (CRT) is unclear. In the present study, RV apical (RV‐A) was compared with RV high posterior septal (RV‐HS) lead position in CRT.Methods and resultsIn 85 consecutive CRT patients (mean age 66 ±11 years) the RV lead placement was randomized to RV‐A (n = 43) or RV‐HS (n = 42). The LV lead was targeted to the latest activated LV segment (concordant LV lead), identified by two‐dimensional speckle tracking radial strain (ST‐RS) echocardiography. Concordant LV leads were obtained in 72%, similar in RV‐A and RV‐HS (79% vs. 64%; P = 0.13). Six months after CRT, no difference was found in LV reverse remodelling (reduction of LV end‐systolic volume ≥15%) according to RV‐A and RV‐HS leads [26 (65%) vs. 25 (64%); P = 0.93]. Superior LV reverse remodelling was observed in concordant LV leads compared with discordant LV leads [41 (73%) vs. 10 (43%); P = 0.01]. At 6‐month follow‐up, LV reverse dyssynchrony (reduction of anteroseptal to posterior delay ≥50%) using ST‐RS imaging was similar in RV‐A and RV‐HS [25 (63%) vs. 24 (62%); P = 0.93]. More LV reverse dyssynchrony was found in concordant LV leads vs. discordant LV leads [39 (70%) vs. 10 (43%); P = 0.03]. A concordant LV lead was an independent predictor of LV reverse remodelling (odds ratio, 3.65; P = 0.01) and LV reverse dyssynchrony (odds ratio, 4.22; P = 0.02) 6 months after CRT.ConclusionRV‐A and RV‐HS in CRT demonstrated similar LV reverse remodelling and LV reverse dyssynchrony at 6‐month follow‐up. Concordant LV leads provided superior LV reverse remodelling and LV reverse dyssynchrony.Trial registration: NCT01035489
Bone mass loss in chronic heart failure is associated with secondary hyperparathyroidism and has prognostic significance
Authors: Terrovitis John , Zotos Panagiotis , Kaldara Elissavet , Diakos Nikolaos , Tseliou Eleni , Vakrou Stella , Kapelios Chris , Chalazonitis Athanasios , Nanas Serafeim , Toumanidis Savas , Kontoyannis Dimitrios , Karga Eleni , Nanas John 
Published: January 2012

AimsChronic heart failure (CHF) is associated with increased risk of osteoporosis. We investigated the relationship between severity of CHF and bone loss, underlying pathophysiological mechanisms, and the prognostic significance of bone mass changes in heart failure.Methods and resultsTotal body (TB) and femoral (F) bone mineral density (BMD), and T‐ and Z‐scores in the femur were measured in 60 men with CHF (56 ± 11 years) and 13 age‐matched men free from CHF. The composite study endpoint was death, implantation of a left ventricular assist device (LVAD), or inotrope dependency during a median 2‐year follow‐up. Parathyroid hormone (PTH) and vitamin D were measured in all subjects. TBBMD, FBMD, T‐score, and Z‐score were significantly lower in men with CHF. Their PTH levels were also significantly increased (111 ± 59 vs. 39 ± 14; P < 0.001). Patients in New York Heart Association classes III–IV compared with those in classes I–II demonstrated significantly lower TBBMD, FBMD, T‐score, and Z‐score, and higher PTH (136 ± 69 vs. 86 ± 31; P= 0.001). Increased PTH levels were correlated with reduced TBBMD (P = 0.003), FBMD (P = 0.002), and femur T‐score (P = 0.001), reduced cardiac index (P = 0.01) and VO2 peak (P < 0.0001), and increased wedge pressure (P = 0.001). Low TBBMD [hazard ratio (HR) 0.003, 95% confidence interval (CI) 0.00–0.58; P = 0.03] and Z‐score (HR 0.56, 95% CI 0.35–0.90; P = 0.017) were associated with adverse outcome.ConclusionsSecondary hyperparathyroidism and reduction in bone density occur in CHF patients and are associated with disease severity. Increased bone mass loss in CHF has prognostic significance.
The influence of the freshwater environment and the biological characteristics of Atlantic salmon smolts on their subsequent marine survival
Authors: Russell Ian C. , Aprahamian Miran W. , Barry Jon , Davidson Ian C. , Fiske Peder , Ibbotson Anton T. , Kennedy Richard J. , Maclean Julian C. , Moore Andrew , Otero Jaime , Potter Ted (E. C. E.) , Todd Christopher D. 
Published: January 2012

Abstract
Russell, I. C., Aprahamian, M. W., Barry, J., Davidson, I. C., Fiske, P., Ibbotson, A. T., Kennedy, R. J., Maclean, J. C., Moore, A., Otero, J., Potter, E. C. E., and Todd, C. D. 2012. The influence of the freshwater environment and the biological characteristics of Atlantic salmon smolts on their subsequent marine survival. – ICES Journal of Marine Science, 69: 1563–1573. Atlantic salmon have declined markedly in the past 20–30 years throughout their range. Much of the focus for this decline has been on increased mortality during the marine phase of the life cycle. However, marine mortality does not operate independently of factors acting in freshwater and the biological characteristics of smolts migrating to sea. Over recent decades, juvenile salmon in many rivers have grown faster and migrated to sea at a younger age, so have been typically smaller than earlier. This has shortened the generation time for many individuals and may dampen the impact of increased marine mortality, assuming that expected higher in-river survival prior to smolting is not outweighed by increased mortality of smaller smolts at sea. Over the same period, smolt run-timing across the geographic range has been earlier, at an average rate of almost 3 d per decade. This has given rise to growing concerns about smolts potentially missing the optimum environmental migration “window”, the timing of which may also be changing. Contaminants and other factors operating in freshwater also impact smolt quality with adverse consequences for their physiological readiness for life at sea. Given that managers have very limited ability to influence the broad scale factors limiting salmon survival at sea, it is vital that freshwater habitats are managed to both maximize the smolt output and to minimize the impact of factors acting in freshwater that may compromise salmon once they migrate to sea.
TheArabidopsisTRM1–TON1 Interaction Reveals a Recruitment Network Common to Plant Cortical Microtubule Arrays and Eukaryotic Centrosomes
Authors: Drevensek Stéphanie , Goussot Magali , Duroc Yann , Christodoulidou Anna , Steyaert Sylvie , Schaefer Estelle , Duvernois Evelyne , Grandjean Olivier , Vantard Marylin , Bouchez David , Pastuglia Martine 
Published: January 2012

AbstractLand plant cells assemble microtubule arrays without a conspicuous microtubule organizing center like a centrosome. In Arabidopsis thaliana, the TONNEAU1 (TON1) proteins, which share similarity with FOP, a human centrosomal protein, are essential for microtubule organization at the cortex. We have identified a novel superfamily of 34 proteins conserved in land plants, the TON1 Recruiting Motif (TRM) proteins, which share six short conserved motifs, including a TON1-interacting motif present in all TRMs. An archetypal member of this family, TRM1, is a microtubule-associated protein that localizes to cortical microtubules and binds microtubules in vitro. Not all TRM proteins can bind microtubules, suggesting a diversity of functions for this family. In addition, we show that TRM1 interacts in vivo with TON1 and is able to target TON1 to cortical microtubules via its C-terminal TON1 interaction motif. Interestingly, three motifs of TRMs are found in CAP350, a human centrosomal protein interacting with FOP, and the C-terminal M2 motif of CAP350 is responsible for FOP recruitment at the centrosome. Moreover, we found that TON1 can interact with the human CAP350 M2 motif in yeast. Taken together, our results suggest conservation of eukaryotic centrosomal components in plant cells.
TheYABBYGeneTONGARI-BOUSHI1Is Involved in Lateral Organ Development and Maintenance of Meristem Organization in the Rice Spikelet
Authors: Tanaka Wakana , Toriba Taiyo , Ohmori Yoshihiro , Yoshida Akiko , Kawai Arata , Mayama-Tsuchida Tomoko , Ichikawa Hiroaki , Mitsuda Nobutaka , Ohme-Takagi Masaru , Hirano Hiro-Yuki 
Published: January 2012

AbstractThe meristem initiates lateral organs in a regular manner, and proper communication between the meristem and the lateral organs ensures the normal development of plants. Here, we show that mutation of the rice (Oryza sativa) gene TONGARI-BOUSHI1 (TOB1) results in pleiotropic phenotypes in spikelets, such as the formation of a cone-shaped organ instead of the lemma or palea, the development of two florets in a spikelet, or premature termination of the floret meristem, in addition to reduced growth of the lemma or palea and elongation of the awn. These phenotypes seem to result from not only failure in growth of the lateral organs, but also defects in maintenance and organization of the meristem. For example, the cone-shaped organ develops as a ring-like primordium from an initial stage, suggesting that regulation of organ initiation in the meristem may be compromised. TOB1 encodes a YABBY protein, which is closely related to FILAMENTOUS FLOWER in Arabidopsis thaliana, and is expressed in the lateral organ primordia without any patterns of polarization. No TOB1 expression is detected in the meristem, so TOB1 may act non–cell autonomously to maintain proper meristem organization and is therefore likely to play an important role in rice spikelet development.
Culinary tourism in Córdoba (Spain)
Authors: López‐Guzmán Tomás , Sánchez‐Cañizares Sandra 
Published: January 2012

PurposeGastronomy has become one of the key factors in the development and promotion of tourism, and offers the opportunity for certain locations to become specialised in culinary tourism. This paper aims to analyse the kind of tourist whose reason for travelling to a certain destination is to enjoy the local cuisine. In this case, the destination is Córdoba (Spain).Design/methodology/approachA list of restaurants and eating establishments offering dishes typical of Córdoba was compiled. A questionnaire was designed with the aim of analysing and defining tourists' opinions of Córdoba's cuisine. This questionnaire was filled out by a random sample of tourists in one of ten different restaurants. Of these ten establishments, four were classified as restaurants, three as tabernas, and three as a mixture of both restaurant and taberna. In each restaurant, the questionnaire was distributed randomly among Spanish and foreign tourists in the city on a daily basis. A total of 213 questionnaires was obtained. The fieldwork was carried out in October and November 2009. The tabling and analysis of the data obtained was carried out through the development of an appropriate database. The results were obtained using uni‐variant and bi‐variant analysis techniques (contingency tables, chi‐square contrasts and correlations).FindingsThe results of the study reflect the high level of education of the tourists surveyed, the length of their stay, the high percentage of foreign tourists, and the high level of satisfaction with both the local cuisine and with other tourist attractions Córdoba has to offer.Practical implicationsThe results imply that there is scope for developing food tourism products which would attract such tourists and could be used to promote Córdoba as a centre for culinary tourism.Originality/valueThis paper is one of the first studies on culinary tourism to be carried out in an important destination for cultural tourism in Europe, namely the city of Córdoba. This paper also tries to create a profile of the “food tourist”, a tourist whose primary motivation for visiting a given location is to explore the local cuisine.
Perceived risks and benefits of nanotechnology applied to the food and packaging sector in México
Authors: López‐Vázquez Esperanza , Brunner Thomas A. , Siegrist Michael 
Published: January 2012

PurposeNanotechnology has great potential in the food industry. The goal of this study is to identify food applications that are more likely and food applications that are less likely to be accepted by the public.Design/methodology/approachThe study was conducted in México and was a replica of a study conducted in Switzerland. Another goal is to compare the acceptance ratings of citizens from a highly developed European country to the ratings of citizens from a less developed country. Face‐to‐face interviews were conducted in three different places in México, which yieldedN=378 datasets.FindingsAffect and perceived control are important factors influencing risk and benefit perceptions. Applications that can be consumed are perceived as more controllable than applications related to the packaging or external use. The results are similar but not identical to the findings from Switzerland.Research limitations/implicationsA convenience sample was used that was clearly more highly educated than the average population. One should be cautious when generalizing the findings.Practical implicationsIt is important to pay attention to public views regarding new technologies in the food business during the product development stage to avoid some of the pitfalls that GM technology had.Originality/valueThis is the first study to analyze perceptions of nanotechnology applications in a less developed country. Emerging countries often do not have regulations that are as strong as those of developed countries; therefore, analyzing these markets is important, too.
Access to healthy food in Nantes, France
Authors: Shaw Hillary 
Published: January 2012

PurposeThe purpose of this paper is to investigate access to grocery retailing in Nantes, France.Design/methodology/approachThe spatial distribution of all grocery retailers in Nantes was mapped. Socio‐demographic data as supplied by INSEE was mapped for Nantes, and these data used to determine areas of poor access to healthy food, e.g. fresh fruit and vegetables retailing.FindingsThere are six areas of Nantes which appear to have both poor physical access to grocery retailing and a socio‐demographic profile which suggests people living there may have difficulties in travelling to remote shops. These six areas generally do not coincide with the officially‐recognised ZUS deprived areas of Nantes.Research limitations/implicationsData on obesity and related medical conditions were absent from INSEE, limiting the analysis that could be performed. The data were also liable to errors such as MAUP and ecological fallacy; however, the spatial detail was sufficient for meaningful conclusions to be drawn.Practical implicationsPrevious food and dietary research in France has concentrated on economic factors mediating diet. There has been less research on spatial access to food and any correlations with areas of poverty or areas with other populations, e.g. pensioners, who may find travel to remote shops difficult. This research investigates these spatial linkages. Officially‐recognised areas of poverty in Nantes (ZUS areas) are not the areas presenting the most problematical physical access to healthy food retailing, therefore research based on financial aspects alone may miss some areas of difficult food access.Originality/valueThe spatial patterns of food access in Nantes, and the implications for targeting research and policy initiatives to these areas, have not previously been researched.
Nutritional quality and safety of wheat‐soy composite flour chapattis
Authors: Issa Khan Muhammad , Muhammad Anjum Faqir , Pasha Imran , Sameen Ayesha , Nadeem Muhammad 
Published: January 2012

PurposeUnleavened bread (chapatti and roti) is the staple diet of people in the Indo‐Pak region, utilizing almost 90 percent of the wheat produced in the region. To improve the nutrition of chapattis, normally legume flour is used in the region. The purpose of the current study is to assess the nutritional quality and safety of chapattis supplemented with soy flour.Design/methodology/approachWheat and soybean were procured and soy flour was prepared. Trypsin inhibitor contents and mineral contents of different flour and chapattis prepared were determined. Chapattis were prepared from different flour blends and whole wheat flour. To assess the quality and acceptability, the chapattis were presented to a panel of judges and the sensory evaluation was carried out for color, taste, aroma, chew ability, folding ability and overall acceptability characteristics. The data obtained for each parameter were subjected to statistical analysis to determine the level of significance.FindingsThe phytic acid and trypsin content were higher in un‐autoclaved soy flour supplement composite flour. The defattening of soy flour also increases the level of these anti‐nutrients in chapattis. The phytate and trypsin content of composite flour decreased as a result of baking. The protein, fiber and ash contents of composite flour increased while moisture content and nitrogen free extracts (NFE) decreased by the addition of soy flour. Mineral contents of chapattis except Mn increased by the incorporation of soy flour. The chapattis were found acceptable by the panel of judges at 10 percent replacement level of whole wheat flour by soy flour.Practical implicationsThe results of the study indicate that 10 percent supplementation of soy flour in wheat flour was found acceptable by consumers as it did not affect the sensory attribute. For improved nutrition and to combat protein energy malnutrition, chapattis flour can be supplemented with soy flour.Originality/valueThe soy supplementation of wheat flour will improve the nutritional quality of the chapatti flour as soy flour is rich in high‐quality protein and mineral. The anti‐nutritional can be minimized or inactivated by autoclaving the soybean.