bluuebunny/crossref_metadata_2025_split huggingface dataset:
RETINAL PHENOTYPE IN A CASE OF LCHAD/TFP DEFICIENCY WITH LATE-STAGE DIAGNOSIS
Authors: Knowles Jacob A. , Dimopoulos Ioannis S. , MacDonald Ian M. 
Published: March 2017

Purpose:
To report the retinal phenotype of a rare case of long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD)/trifunctional protein (TFP) deficiency diagnosed in his late 40s with ocular findings of diffuse chorioretinal atrophy and bilateral retinoschisis.

Methods:
An acylcarnitine profile assay revealed LCHAD/TFP deficiency in a 45-year-old man with a history of high myopia, bilateral decreased vision, episodic rhabdomyolysis, and peripheral neuropathy. Ocular findings were evaluated with spectral domain optical coherence tomography (Spectralis OCT; Heidelberg Engineering, Heidelberg, Germany) and color fundus photography.

Results:
Spectral domain optical coherence tomography revealed severe bilateral macular retinoschisis. Subretinal fibrosis was noted in the left temporal macula with an associated lamellar macular hole. Fundus photographs demonstrated diffuse, symmetric chorioretinal atrophy characteristic of end-stage retinopathy, as previously reported in younger patients. Myopic staphylomas were evident in the posterior pole of both eyes. A trial of topical dorzolamide for 3 months resulted in no change in the retinal profile.

Conclusion:
We report the retinal phenotype of a patient with LCHAD/TFP deficiency diagnosed later in life. To date, this is the oldest patient reported with LCHAD/TFP–associated retinopathy. Macular retinoschisis may represent a feature of the end-stage retinopathy due to the progressive myopia. The diagnosis of LCHAD/TFP deficiency should be considered in adult patients with a history rhabdomyolysis, neuropathy, and retinopathy, as they would not have undergone routine newborn screening before the late 90s.
Home-Based Psychoeducational Intervention for Breast Cancer Survivors
Authors: Şengün İnan Figen , Üstün Besti 
Published: March 2017

Background:
It is important to manage psychological distress and improve the quality of life (QOL) in patients after breast cancer treatment.

Objective:
The aim of this study was to evaluate the effects of a home-based, psychoeducational program on distress, anxiety, depression, and QOL in breast cancer survivors.

Methods:
The study was a single-group pretest and posttest quasi-experimental design. The data were collected using the Distress Thermometer, the Hospital Anxiety and Depression Scale, and the Turkish version of the World Health Organization Quality of Life Instrument, short form. The home-based, individual, face-to-face psychoeducational program was structured according to breast cancer survivors’ needs and the Neuman Systems Model.

Results:
A total of 32 Turkish breast cancer survivors participated in this study. There were statistically significant differences in the mean scores for distress, anxiety, and depression in the breast cancer survivors over 4 measurements. The mean scores for all subscales of the QOL at 6 months postintervention were significantly higher than the mean scores at baseline.

Conclusions:
The results indicated that the psychoeducational program may be effective in reducing distress, anxiety, and depression and in improving the QOL in breast cancer survivors.

Implications for Practice:
Psychoeducational programs may be effective and should be considered as part of the survivorship care for breast cancer survivors.
Pathway-Level Information ExtractoR (PLIER) for gene expression data
Authors: Mao Weiguang , Zaslavsky Elena , Hartmann Boris M. , Sealfon Stuart C. , Chikina Maria 
Published: March 2017

AbstractA major challenge in gene expression analysis is to accurately infer relevant biological insight, such as regulation of cell type proportion or pathways, from global gene expression studies. We present a general solution for this problem that outperforms available cell proportion inference algorithms, and is more widely useful to automatically identify specific pathways that regulate gene expression. Our method improves replicability and biological insight when applied to trans-eQTL identification.
Optimizing Pedigrees: Using a Biasing System to Determine Likely Inheritance Systems
Authors: Ang Justin 
Published: March 2017

AbstractPedigrees, though straightforward and versatile, lack the ability to tell us information about many individuals. Though numerical systems have been developed, there is currently no system to quantify the probability of a pedigree following certain inheritance systems. My system intends to fulfill that chasm by creating a flexible numerical system and testing it for variance. First, my system attempts to adapt inheritance system to known pedigree data. Then, it calculates the difference between the calculated values and the known pedigree data. It aggregates these values, then it uses a chi-squared analysis in order to determine the likelihood of said inheritance system. This is done for many different systems, until we have a general idea of which systems are probable and which are not.
Accuracies of univariate and multivariate genomic prediction models in African Cassava
Authors: Okeke Uche Godfrey , Akdemir Deniz , Rabbi Ismail , Kulakow Peter , Jannink Jean-Luc 
Published: March 2017

List of abbreviationsGSGenomic SelectionBLUPBest Linear Unbiased PredictionEBVsEstimated Breeding ValuesEGVsEstimated genetic ValuesGEBVsGenomic Estimated Breeding ValuesSNPsSingle Nucleotide polymorphismsGxEGenotype-by-environment interactionsGxEGenotype-by-environment interactionsGxGGene-by-gene interactionsGxGxEGene-by-gene-by-environment interactionsuTUnivariate single environment one-step modeluEUnivariate multi environment one-step modelMTMulti-trait single environment one-step modelMEMultivariate single trait multi environment modelAbstractBackgroundGenomic selection (GS) promises to accelerate genetic gain in plant breeding programs especially for long cycle crops like cassava. To practically implement GS in cassava breeding, it is useful to evaluate different GS models and to develop suitable models for an optimized breeding pipeline.MethodsWe compared prediction accuracies from a single-trait (uT) and a multi-trait (MT) mixed model for single environment genetic evaluation (Scenario 1) while for multi-environment evaluation accounting for genotype-by-environment interaction (Scenario 2) we compared accuracies from a univariate (uE) and a multivariate (ME) multi-environment mixed model. We used sixteen years of data for six target cassava traits for these analyses. All models for Scenario 1 and Scenario 2 were based on the one-step approach. A 5-fold cross validation scheme with 10-repeat cycles were used to assess model prediction accuracies.ResultsIn Scenario 1, the MT models had higher prediction accuracies than the uT models for most traits and locations analyzed amounting to 32 percent better prediction accuracy on average. However for Scenario 2, we observed that the ME model had on average (across all locations and traits) 12 percent better predictive power than the uE model.ConclusionWe recommend the use of multivariate mixed models (MT and ME) for cassava genetic evaluation. These models may be useful for other plant species.
Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer
Authors: Benítez-Páez Alfonso , Sanz Yolanda 
Published: March 2017

AbstractBackgroundThe miniaturised and portable DNA sequencer MinION™ has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION™ platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach.ResultsAfter compiling a robust database by parsing and extracting therrnbacterial region from more than 67,000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION™ device using R9 and R9.4 chemistries was sufficient to study two mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities.ConclusionsAlthough nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and long amplicon sequencing using the MinION™ MkIb DNA sequencer and R9 and R9.4 chemistries that help to overcome the main disadvantage of this portable sequencing platform. Furthermore, the nanopore sequencing library constructed with the last releases of pore chemistry (R9.4) and sequencing kit (SQK-LSK108) permitted to retrieve the higher level of 1D read accuracy sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimising base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information in near future. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems.
powsimR: Power analysis for bulk and single cell RNA-seq experiments
Authors: Vieth Beate , Ziegenhain Christoph , Parekh Swati , Enard Wolfgang , Hellmann Ines 
Published: March 2017

AbstractPower analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
GenomicDataCommons:a Bioconductor Interface to the NCI Genomic Data Commons
Authors: Morgan Martin T. , Davis Sean R. 
Published: March 2017

AbstractThe National Cancer Institute (NCI) Genomic Data Commons (Grossman et al. 2016,https://gdc.cancer.gov/) provides the cancer research community with an open and unified repository for sharing and accessing data across numerous cancer studies and projects via a high-performance data transfer and query infrastructure. TheBioconductorproject (Huber et al. 2015) is an open source and open development software project built on theRstatistical programming environment (R Core Team 2016). A major goal of theBioconductorproject is to facilitate the use, analysis, and comprehension of genomic data. TheGenomicDataCommons Bioconductorpackage provides basic infrastructure for querying, accessing, and mining genomic datasets available from the GDC. We expect thatBioconductordeveloper and bioinformatics community will build on theGenomicDataCommonspackage to add higher-level functionality and expose cancer genomics data to many state-of-the-art bioinformatics methods available inBioconductor.Availabilityhttps://bioconductor.org/packages/GenomicDataCommons&https://github.com/seandavi/GenomicDataCommons.
Effects of business maturity, experience, and size on farms economic vitality
Authors: Rusiana Hofner , Brewer Brady , Escalante Cesar 
Published: March 2017

Purpose
The purpose of this paper is to examine the relative financial strength and endurance of several paired classes of farmers according to business maturity (beginning versus mature farm businesses), farm operators’ age/experience (young versus older, more experienced farm operators), and farm size (small vs large farm businesses) by utilizing random-effects ordered logistic techniques.

Design/methodology/approach
This study uses a credit migration approach to analyze the factors that impact the probability of farm credit migration rates. An ordered logit model is used to assess the influence that factors have on a farm upgrading, staying same, or downgrading in credit rating.

Findings
Results show that increasing farm size will lead to a higher probability of class upgrades. Being a young farm operator, meanwhile, decreases this probability. Positive changes in money supply and farm real estate values were found to increase the likelihood of credit upgrades. Results also show trend reversal of credit risk movement, where upgrades (downgrades) are more likely to be followed by downgrades (upgrades).

Originality/value
With farms being dependent on capital for growth, knowing what factors affect the ability of a farm to obtain credit lends insight in the agricultural credit markets. This paper is also the first to assess the impacts of these factors on small farms which constitute 92 percent of farms in the USA per the US Department of Agriculture.
A bootstrap approach for pricing crop yield insurance
Authors: Xiao Yugu , Wang Ke , Porth Lysa 
Published: March 2017

Purpose
While crop insurance ratemaking has been studied for many decades, it is still faced with many challenges. Crop insurance premium rates (PRs) are traditionally determined only by point estimation, and this approach may lead to uncertainty because it is sensitive to the underwriter’s assumptions regarding the trend, yield distribution, and other issues such as data scarcity and credibility. Thus, the purpose of this paper is to obtain the interval estimate for the PR, which can provide additional information about the accuracy of the point estimate.

Design/methodology/approach
A bootstrap method based on the loss cost ratio ratemaking approach is proposed. Using Monte Carlo experiments, the performance of this method is tested against several popular methods. To measure the efficiency of the confidence interval (CI) estimators, the actual coverage probabilities and the average widths of these intervals are calculated.

Findings
The proposed method is shown to be as efficient as the non-parametric kernel method, and has the features of flexibility and robustness, and can provide insight for underwriters regarding uncertainty based on the width of the CI.

Originality/value
Comprehensive comparisons are conducted to show the advantage and the efficiency of the proposed method. In addition, a significant empirical example is given to show how to use the CIs to support ratemaking.
The impact of gender and culture on networking and venture creation
Authors: Kalafatoglu Tugba , Mendoza Xavier 
Published: March 2017

PurposeTo date, little research has been focused on the nature and dynamics of female entrepreneurial networking activity. Thus, the purpose of this paper is to examine how gender and culture affect business creation, how women perceive social capital, and how important their personal networks are for their businesses, especially in the context of patriarchal societies.Design/methodology/approachSemi-structured interviews were conducted with women entrepreneurs living and operating businesses in Turkey and in four countries of the Middle East and North African region, namely, Lebanon, Saudi Arabia, Morocco, and Egypt.FindingsThe results indicate that being a woman entrepreneur in a highly patriarchal society limits entrepreneurial activities due to culture and social norms. However, networking appears as the key factor for these women entrepreneurs to overcome the barriers that they face, such as access to capital, financial information, resources, and new business opportunities.Research limitations/implicationsThis study has limitations that tend to be commonly found in exploratory studies, so you cannot make generalizations. However, the findings lay the groundwork for future studies to examine the role of networking activity in female entrepreneurship in the context of patriarchal societies.Practical implicationsThe findings are helpful for policymakers and other social groups interested in improving the conditions for female entrepreneurship. Governments and other economic actors need to provide training in both management and networking skills, encourage local businesses and associations to provide their venues for networking opportunities, and also provide support to women business organizations.Social implicationsWomen’s entrepreneurship is growing, but still there is a scarcity of scholarly literature on the women entrepreneurs and their entrepreneurial activity.Originality/valueThis research provides empirical evidence of the nature and dynamics of female entrepreneurial networking activity in the context of patriarchal societies.
Applying cultural intelligence to religious symbols in multinationals
Authors: O’Sullivan Sharon L. 
Published: March 2017

Purpose
The purpose of this paper is to describe how religious symbols might impede employees’ motivational cultural intelligence (CQ) in some international contexts, and how multinational managers might employ this knowledge to respond in a manner that mitigates risks to knowledge sharing.

Design/methodology/approach
The paper uses several theories (e.g. CQ, social categorization, expectancy, and contact theories) to develop a conceptual model about the nature of the risk to employees’ motivational CQ. It then draws on models of acculturation to explore how multinational corporation managers might respond.

Findings
It is conjectured that the salience of religious-based value conflict, learned both vicariously and through direct experiences, will adversely impact motivational CQ, and that the introduction of religious symbols may exacerbate this relationship. A framework of possible interventions is offered, and each intervention approach is evaluated in terms of how it may mitigate or exacerbate the risks raised by the model.

Research limitations/implications
The proposed model requires empirical validation.

Practical implications
Multinationals are advised how (and why) to treat the preservation of motivational CQ as central to any intervention in the conflict over religious symbols.

Social implications
An uninformed response to controversy over religious symbols could impede knowledge sharing and potentially exacerbate broader societal tensions (UN Global Compact, 2013). Therefore, this paper addresses a clear socio-economic need.

Originality/value
Controversy over the use of religious symbols in the workplace has generated considerable international media attention, but has been neglected by cross-cultural management research.
The opportunity model of organizational commitment
Authors: Cicekli Elif , Kabasakal Hayat 
Published: March 2017

Purpose
The purpose of this paper is to determine the relationships between promotion, development, and recognition opportunities at work and organizational commitment, and whether these relationships are moderated by the job opportunities employees have in other organizations.

Design/methodology/approach
An opportunity model of organizational commitment is developed based on social exchange theory and several streams of opportunity research. Factor analyses and hierarchical multiple regression analyses are carried out to test the hypotheses using data from 550 white-collar employees.

Findings
The results of the analyses show that opportunities for development and recognition are predictors of organizational commitment, that job opportunities employees have in other organizations negatively moderate the relationship between recognition opportunity at work and organizational commitment, and that promotion opportunity does not predict organizational commitment.

Research limitations/implications
Future researchers could study the issue in the context of other cultures using data from multiple sources.

Practical implications
Employers who seek to increase their employees’ organizational commitment are advised to divert their energies from struggling to create promotion opportunities for their employees to creating opportunities for development and recognition.

Originality/value
The study explores the under-researched concept of opportunity at work and connects several streams of opportunity research by drawing on social exchange theory as a theoretical framework. The model is the first to address the effects of opportunity and alternative opportunities on organizational commitment.
The individual and organizational level effects of TQM practices on job satisfaction
Authors: Prajogo Daniel I. , Cooper Brian 
Published: March 2017

PurposeThe purpose of this paper is to examine the multi-level relationship between people-related total quality management (TQM) practices and employee job satisfaction. The authors draw upon organizational climate theory to hypothesize that TQM is related to job satisfaction at the individual employee level, as well as at the organizational level in the form of shared perceptions of TQM practices in the workplace.Design/methodology/approachMulti-level modelling was used to test the study hypotheses. The sample was drawn from 201 employees working in 23 organizations in Australia.FindingsThe findings show that people-related TQM practices are positively related to job satisfaction at both individual and organizational levels, with a stronger effect on employee attitudes observed at the organizational level.Research limitations/implicationsThe statistically significant multi-level relationship between people-related TQM practices and job satisfaction extends the findings of previous studies conducted only at the individual level; thus, supporting the sustainability of TQM as a management principle at a company-wide level.Practical implicationsThe findings broadly support the implementation of people-related TQM practices as part of a strategy of creating a “high performance” climate in organizations, which in turn, will likely to positively affect both individual and organizational performance.Social implicationsFrom a wider social perspective, the implementation of TQM practices as a company-wide initiative could facilitate greater corporate social responsibility of the organization. Such practices as training, involving, and empowering employees can promote social commitment by valuing employees as one important stakeholder.Originality/valueThis is the first empirical study to the best of the author’s knowledge that uses multi-level modelling to examine the relationship between TQM practices and employee attitudes such as job satisfaction.