bluuebunny/crossref_metadata_2025_split huggingface dataset:
Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads
Authors: Zhang Kui , Zhi Degui 
Published: August 2013

Abstract
Motivation: Hidden Markov model, based on Li and Stephens model that takes into account chromosome sharing of multiple individuals, results in mainstream haplotype phasing algorithms for genotyping arrays and next-generation sequencing (NGS) data. However, existing methods based on this model assume that the allele count data are independently observed at individual sites and do not consider haplotype informative reads, i.e. reads that cover multiple heterozygous sites, which carry useful haplotype information. In our previous work, we developed a new hidden Markov model to incorporate a two-site joint emission term that captures the haplotype information across two adjacent sites. Although our model improves the accuracy of genotype calling and haplotype phasing, haplotype information in reads covering non-adjacent sites and/or more than two adjacent sites is not used because of the severe computational burden.
Results: We develop a new probabilistic model for genotype calling and haplotype phasing from NGS data that incorporates haplotype information of multiple adjacent and/or non-adjacent sites covered by a read over an arbitrary distance. We develop a new hybrid Markov Chain Monte Carlo algorithm that combines the Gibbs sampling algorithm of HapSeq and Metropolis–Hastings algorithm and is computationally feasible. We show by simulation and real data from the 1000 Genomes Project that our model offers superior performance for haplotype phasing and genotype calling for population NGS data over existing methods.
Availability: HapSeq2 is available at www.ssg.uab.edu/hapseq/.
Contact: dzhi@uab.edu or kzhang@uab.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors
Authors: Chawla Konika , Tripathi Sushil , Thommesen Liv , Lægreid Astrid , Kuiper Martin 
Published: August 2013

Abstract
Summary: Gene regulatory network assembly and analysis requires high-quality knowledge sources that cover functional aspects of the various components of the gene regulatory machinery. A multiplicity of resources exists with information about mammalian transcription factors (TFs); yet, only few of these provide sufficiently accurate classifications of the functional roles of individual TFs, or standardized evidence that would justify the information on which these functional classifications are based. We compiled the list of all putative TFs from nine different resources, ignored factors such as general TFs, mediator complexes and chromatin modifiers, and for the remaining factors checked the available literature for references that support their function as a true sequence-specific DNA-binding RNA polymerase II TF (DbTF). The results are available in the TFcheckpoint database, an exhaustive collection of TFs annotated according to experimental and other evidence on their function as true DbTFs. TFcheckpoint.org provides a high-quality and comprehensive knowledge source for genome-scale regulatory network studies.
Availability: The TFcheckpoint database is freely available at www.tfcheckpoint.org
Contact: martin.kuiper@ntnu.no
Supplementary information: Supplementary data are available at Bioinformatics online.
Analysis of base-pairing probabilities of RNA molecules involved in protein–RNA interactions
Authors: Iwakiri Junichi , Kameda Tomoshi , Asai Kiyoshi , Hamada Michiaki 
Published: August 2013

Abstract
Motivation: Understanding the details of protein–RNA interactions is important to reveal the functions of both the RNAs and the proteins. In these interactions, the secondary structures of the RNAs play an important role. Because RNA secondary structures in protein–RNA complexes are variable, considering the ensemble of RNA secondary structures is a useful approach. In particular, recent studies have supported the idea that, in the analysis of RNA secondary structures, the base-pairing probabilities (BPPs) of RNAs (i.e. the probabilities of forming a base pair in the ensemble of RNA secondary structures) provide richer and more robust information about the structures than a single RNA secondary structure, for example, the minimum free energy structure or a snapshot of structures in the Protein Data Bank. However, there has been no investigation of the BPPs in protein–RNA interactions.
Results: In this study, we analyzed BPPs of RNA molecules involved in known protein–RNA complexes in the Protein Data Bank. Our analysis suggests that, in the tertiary structures, the BPPs (which are computed using only sequence information) for unpaired nucleotides with intermolecular hydrogen bonds (hbonds) to amino acids were significantly lower than those for unpaired nucleotides without hbonds. On the other hand, no difference was found between the BPPs for paired nucleotides with and without intermolecular hbonds. Those findings were commonly supported by three probabilistic models, which provide the ensemble of RNA secondary structures, including the McCaskill model based on Turner’s free energy of secondary structures.
Contact: iwakiri@cb.k.u-tokyo.ac.jp or mhamada@cb.k.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
ArabidopsisBasic Helix-Loop-Helix Transcription Factors MYC2, MYC3, and MYC4 Regulate Glucosinolate Biosynthesis, Insect Performance, and Feeding Behavior
Authors: Schweizer Fabian , Fernández-Calvo Patricia , Zander Mark , Diez-Diaz Monica , Fonseca Sandra , Glauser Gaétan , Lewsey Mathew G. , Ecker Joseph R. , Solano Roberto , Reymond Philippe 
Published: August 2013

AbstractArabidopsis thaliana plants fend off insect attack by constitutive and inducible production of toxic metabolites, such as glucosinolates (GSs). A triple mutant lacking MYC2, MYC3, and MYC4, three basic helix-loop-helix transcription factors that are known to additively control jasmonate-related defense responses, was shown to have a highly reduced expression of GS biosynthesis genes. The myc2 myc3 myc4 (myc234) triple mutant was almost completely devoid of GS and was extremely susceptible to the generalist herbivore Spodoptera littoralis. On the contrary, the specialist Pieris brassicae was unaffected by the presence of GS and preferred to feed on wild-type plants. In addition, lack of GS in myc234 drastically modified S. littoralis feeding behavior. Surprisingly, the expression of MYB factors known to regulate GS biosynthesis genes was not altered in myc234, suggesting that MYC2/MYC3/MYC4 are necessary for direct transcriptional activation of GS biosynthesis genes. To support this, chromatin immunoprecipitation analysis showed that MYC2 binds directly to the promoter of several GS biosynthesis genes in vivo. Furthermore, yeast two-hybrid and pull-down experiments indicated that MYC2/MYC3/MYC4 interact directly with GS-related MYBs. This specific MYC–MYB interaction plays a crucial role in the regulation of defense secondary metabolite production and underlines the importance of GS in shaping plant interactions with adapted and nonadapted herbivores.
Corporate heritage, corporate heritage marketing, and total corporate heritage communications
Authors: Balmer John M.T. 
Published: August 2013

PurposeThe purpose of this paper is to advance the general understanding of the corporate heritage domain. The paper seeks to specify the requisites of corporate heritage and to introduce and explicate the corporate heritage marketing and total corporate heritage communications notions.Design/methodology/approachAs befits an opening article of the first special edition specifically devoted to corporate heritage, this article is largely conceptual in character and draws on the extant literature on corporate heritage brands and identities. In illuminating key points, it also makes reference to extant corporate heritage entities/brands.FindingsA provisional theory of corporate heritage sustainability is articulated, as is the enumeration of key corporate heritage traits. The notions of corporate heritage marketing and total corporate heritage communications are introduced and articulated. Key corporate heritage traits requisites encompass omni‐temporality; institution trait constancy; external/internal tri‐generational hereditary; augmented role identities; ceaseless multigenerational stakeholder utility and unremitting management tenacity. Corporate heritage marketing consists of eight dimensions: corporate heritage character/communications/covenant/conceptualisations/culture/constituencies/custodianship/context. Total corporate heritage communicates consists of primary/secondary/tertiary and legacy communications.Practical implicationsThe paper notes the need for assiduous management attention to be accorded to organisations with a bona‐fide corporate heritage. Managers are custodians – as are organisational members guardians – of a corporate heritage. Corporate heritage institutions because they aresui generisrequire distinct approachesvis‐à‐vistheir preservation and management.Social implicationsCorporate heritage identities and corporate heritage brands confer not only corporate but also temporal, territorial, social, cultural and ancestral identities to multi‐generational groups of customers and other stakeholders. As such, they are of importance not only as corporate entities but also as perennial social identities as well. This is of importance to policy makers, managers and owners of corporate heritage identities and corporate heritage brands.Originality/valueThe unveiling of corporate heritage marketing and of total corporate heritage communications perspective and the articulation of key corporate heritage entity traits is original and is of value to corporate communications/corporate marketing scholars and practitioners alike.
Adding dynamics to core competence concept applications
Authors: Ljungquist Urban 
Published: August 2013

PurposeThis paper seeks to enhance practical applications, by refining the original core competence concept to better fit dynamic environments.Design/methodology/approachThis paper combines theoretical research streams treating core competence and dynamic capability.FindingsThe original core competence concept cannot help managers with today's dynamic business environments. This paper theoretically reviews conceptions of core competence to enhance dynamism and better align theory and practice. The author concludes that a core competence could become more dynamic in three ways, by: balancing itself with the external environment and including external activities and processes; reducing path‐dependency influences; and carefully “orchestrating” resources, by guidance rather than control, to release the inherent potential of project teams.Research limitations/implicationsThe author rejuvenates a popular concept by including contemporary, more dynamic considerations; however, his propositions need to be tested empirically.Practical implicationsThree criteria are reformulated to match contemporary dynamism; these are also rephrased to better meet practical applications and take account of the internal sharing and transfer of competencies. This supplements the practitioner's toolbox for managing core competence in a company. For ideal core competence dynamism, managers should selectively incorporate external information and adapt external activities and processes, all to match the existing internal resource base.Originality/valueThis paper incorporates contemporary dynamics in an important strategy concept.
Well integrity assessment for CO2 injection
Authors: Asamoto Shingo , Le Guen Yvi , Poupard Olivier , Capra Bruno 
Published: August 2013

PurposeIn the carbon dioxide capture and storage (CCS) project, the integrity of CO2 injection wells plays a vital role in the long‐term safety of CO2 storage. The authors aim to practically investigate possible CO2 leakage of a CO2 injection well section during the injection operation and shut‐in by the thermomechanical FEM simulation. The application of numerical simulation to the CO2 injection well deep underground is the first step that will help in the quantitative evaluation of the mechanical risks.Design/methodology/approachThe injection of CO2 at a temperature different from those of the well and the surrounding geological formation is likely to cause different thermal deformations of constitutive well materials. This could lead to cement cracking and microannuli openings at the interfaces of different materials such as casing/cement and cement/rock. In this paper, the possibility and order of magnitude of cement cracking and microannuli creation in the cross section of the well are assessed from a numerical case study within a classical thermomechanical finite element model framework.FindingsThe possibility of compressive failure and tensile cracking in the cement of the studied wells due to CO2 injection is small unless a large casing eccentricity or an initial defect in the cement is present. Some microannuli openings are generated at interfaces cement/casing and/or cement/rock during the CO2 injection because of different thermal shrinkage of each material. However, the width is not important enough to cause significant CO2 leakage under the studied conditions. The use of “flexible” cement especially developed for oil well applications could mitigate the risk of cement cracking during CO2 injection.Originality/valueNumerous experimental studies on the chemical deterioration of the cement under severe conditions have been carried out. On the other hand, only a few investigations have focused on the mechanical behavior under thermal/pressure changes related to CO2 injection. In this paper, the quantitative analysis to investigate cement cracking and microannuli formation is achieved to help in the identification of possible mechanical defects to cause CO2 leakage. In addition, the discussion about the risk of the possible casing eccentricity and the application of flexible cement in the oil and gas field to CO2 injection well could be practically useful.
Higher technological education specialties and graduates’ vocational status and prospects
Authors: Kostoglou Vassilis , Vassilakopoulos Michael , Koilias Christos 
Published: August 2013

PurposeThe purpose of this paper is to focus on a thorough comparison of the broader specialties and subspecialties provided by Greek higher technological education, regarding the employment status and the vocational prospects of the corresponding graduates, and aims to identify and analyze the relevant existing differences.Design/methodology/approachOriginal empirical data were collected from 5,183 graduates of Technological Educational Institutes of higher education through a national survey using telephone interviews and a structured questionnaire. The stratified sample consisted of graduates originating from all nine different broader specialties (faculties) and 45 subspecialties (departments). Descriptive, bivariate and multivariate statistical analysis was used for the elaboration of the collected information.FindingsThe results showed that there are significant differences among the graduates of different specialties regarding some employment characteristics, such as professional status, type of employment, relevance between present work and Bachelor studies, and satisfaction from employment and wages. Additionally, the results identify distinguished clusters among certain broader specialties and subspecialties regarding graduates’ employment status and characteristics.Practical implicationsThe revealed existence of strong relationships between broader specialties/subspecialties and their graduates’ vocational prospects can offer justified advice/guidelines to secondary education graduates for applying to specialties presenting promising employment prospects.Originality/valueThis work, being one of the very few nation‐wide studies, reveals and highlights the most important higher education specialties regarding the vocational status and prospects of the corresponding graduates, providing a guideline for the selection of the subject of studies that leads to a more promising career.
A multi-objective antidisturbance robust filter for SINS/GPS navigation systems
Authors: LIU Jia , Zhang Yumin , Guo Lei , Gao Xiaoying 
Published: August 2013

Purpose
– A full-order multi-objective anti-disturbance robust filter for SINS/GPS navigation systems with multiple disturbances is designed. Generally, the unmodeled dynamics, the external environmental disturbance and the inertial apparatus random drift may exist simultaneously in an integrated navigation system, which can be classified into three type of disturbances, that is, the Gaussian noise, the norm bounded noise and the time correlated noise. In most classical studies, the disturbances in integrated navigation systems are classified as Gaussian noises or norm bounded noises, where the Kalman filtering or robust filtering can be employed, respectively. While it is not true actually, such assumptions may lead to conservative results. The paper aims to discuss these issues.

Design/methodology/approach
– The Gaussian noises, the norm bounded noises and the time correlated noises in the integrated navigation system are considered simultaneously in this contribution. As a result, the time correlated noises are augmented as a part of system state of the integrated navigation system error model, the relative integrated navigation problem can be transformed into a full-order multi-objective robust filter design problem for systems with Gaussian noises and norm bounded disturbances. Certainly, the errors of the time correlated noises are estimated and compensated for high precision navigation purpose. Sufficient conditions for the existence of the proposed filter are presented in terms of linear matrix inequalities (LMIs) such that the system stability is guaranteed and the disturbance attenuation performance is achieved.

Findings
– Simulations for SINS/GPS integrated navigation system given show that the proposed full-order multi-objective anti-disturbance filter, has stronger robustness and better precision when multiple disturbances exist, that is, the present algorithm not only can suppression the effect of white noises and norm bounded disturbance but also can estimate and compensate the modeled disturbance.

Originality/value
– The proposed algorithm has stronger anti-disturbance ability for integrated navigation with multiple disturbances. In fact, there exist multiple disturbances in integrated navigation system, so the proposed scheme has important significance in applications.
First‐generation college students: mentoring through social media
Authors: Ware Paige , Ramos Jose 
Published: August 2013

PurposeThis exploratory study aims to examine how online mentoring was provided through social media to support potential first‐generation Latino college students during their final year of high school and their transition into a two‐year or four‐year institution.Design/methodology/approachUsing a one‐year qualitative study design, data were collected through interviews, surveys, and archived interactions on Facebook. Discourse analysis was used to code for types of social, informational, and emotional support provided.FindingsFindings suggest that online mentoring through social media is a support system that the focal students turned to primarily for informational support, rather than for social or emotional support, and its impact seems to be contingent on the existence of conventional mentoring structures of high school counsellors, peers, and family.Practical implicationsHigh school counsellors and mentors in college outreach programs can leverage students’ presence in social media forums such as Facebook to help structure informational support (application deadlines, financial aid forms, contact information for college outreach) to help students prepare for and transition into college.Social implicationsThe visibility and amplification of information delivered through social media provides an untapped resource for assisting first‐generation college students in navigating the complex financial and logistical steps in transitioning to college. Its use as an additional tool for counsellors and mentors could increase matriculation and retention rates.OriginalityHigh school counsellors and directors of college outreach and mentoring programs could draw on findings in this paper when considering ways to integrate innovative approaches to providing mentoring support.
Determinants of antenatal care quality in Ghana
Authors: Atinga Roger A. , Baku Anita A. 
Published: August 2013

PurposeTo achieve Goal 5 of the MDGs, the Government of Ghana introduced the free maternal health service system to break financial barriers of access to maternal care services. In spite of this, facility‐based deliveries continue to be low due partly to poor quality of antenatal care that prevents pregnant women from giving birth in hospitals. The aim of this study is to examine factors shaping quality of antenatal care in selected public hospitals in the country.Design/methodology/approach363 expectant mothers were randomly selected for interview. Women who have previously received antenatal care in the health facilities for at least two occasions were interviewed. Multivariate logistic regression model were computed to examine correlates of antenatal care quality.FindingsThe odds of reporting quality of antenatal care as good was higher among women aged between 30 and 34 years. Similarly women with junior/senior high education were more likely to report antenatal care quality as good. Distance to the health facilities generally influence women perception of antenatal care quality but the relative odds of reporting quality of care as good attenuated with proximity to the health facility. Five factors (pleasant interaction with providers, privacy during consultation, attentiveness of providers, adequate facilities and availability of drugs) emerged as statistically significant in explaining antenatal care quality after controlling for selected demographic variables.Originality/valueResults of the study generally demonstrate the need to improve maternal services in public facilities to stimulate utilisation and facility‐based deliveries.
Toiling children in India: the gender dimension
Authors: Kumar Rajnish , Mitra Arup , Murayama Mayumi 
Published: August 2013

PurposeChild labour in several low‐income households is rather pursued for gaining experience and at times for meagre incomes, which are possibly spent on household food expenditure. The purpose of this paper is to estimate the incidence of child labour and identifies the factors which explain participation of the children in the labour market. It also focuses on some of the outcomes of labour market participation of the children.Design/methodology/approachBased on the primary survey of the slum households in four Indian cities this paper applies certain quantitative techniques to estimate child labour and the factors that explain their participation in the labour market.FindingsThough the contribution made by the child labour to the overall well‐being does not turn out to be substantial, without child labour these households would have been much worse off than the households which can afford not to have child labour. The probability of working is higher for a male child compared to a girl child. This is because the girl children are often engaged in household activities and even when they are engaged in income earning jobs they are shown as helpers. Parents' income as such may not be having a positive impact on child's education.Originality/valueThe study is based on a primary survey. It employs certain indirect methods to arrive at a more realistic estimate of the incidence of child labour. Besides, it focuses on the quantitative methods to identify the factors that explain child labour. Finally the policy implications are brought out.