bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Mutation in PLA2G6 Gene in a Patient with Infantile Neuroaxonal Dystrophy
Authors: Veerapandiyan Aravindhan , Chaudhari Amit , Aravindhan Akilandeswari , Hayes-Rosen Caroline 
Published: November 2016

AbstractInfantile neuroaxonal dystrophy (INAD) is an autosomal recessive disorder that causes psychomotor regression. Clinicopathological features include truncal hypotonia followed by spastic quadriparesis, strabismus, nystagmus, cerebellar ataxia, bulbar dysfunction, and cerebellar atrophy. INAD is associated with a variety of mutations in the PLA2G6 gene that encodes the group VI calcium-independent phospholipase A2 protein which is important in cell membrane homeostasis. Defects in this protein cause axonal dystrophy. We report a 2-year-old boy with INAD who was found to have a novel deletion c.1019_1025del7 leading to a frame shift in the PLA2G6 gene. We suggest that this change may be an addition to the array of mutations causing INAD.
Graphical Function Mapping as a New Way to Explore Cause-and-Effect Chains
Authors: Evans Mary Anne 
Published: November 2016

Abstract
Graphical function mapping provides a simple method for improving communication within interdisciplinary research teams and between scientists and nonscientists. This article introduces graphical function mapping using two examples and discusses its usefulness. Function mapping projects the outcome of one function into another to show the combined effect. Using this mathematical property in a simpler, even cartoon-like, graphical way allows the rapid combination of multiple information sources (models, empirical data, expert judgment, and guesses) in an intuitive visual to promote further discussion, scenario development, and clear communication.
El mapeo gráfico-funcional ofrece un método simple para mejorar la comunicación hacia el interior de los grupos de investigación interdisciplinaria, así como también entre los científicos y los no científicos. En este artículo se introduce el mapeo gráfico-funcional, usando dos ejemplos y se discute su utilidad. El mapeo funcional proyecta el resultado de una función en otra para mostrar el efecto combinado. El uso de esta propiedad matemática traducido de una manera gráfica sencilla, incluso caricaturizada, permite una rápida combinación de múltiples fuentes de información (modelos, datos empíricos, juicios expertos y tanteos) dentro de un contexto visual intuitivo que promueve la discusión, el desarrollo de escenarios y una comunicación más eficiente.
La fonction de mapping graphique fournit une méthode simple pour améliorer la communication au sein des équipes de recherche interdisciplinaires et entre scientifiques et non-scientifiques. Cet article présente la fonction de mapping graphique à l'aide de deux exemples et discute de son utilité. La fonction de mapping graphique projette le résultat d'une fonction dans un autre pour en montrer l'effet combiné. L'utilisation de cette propriété mathématique de manière graphique simple, même caricaturale, permet la combinaison rapide de multiples sources d'information (modèles, données empiriques, jugement d'expert, et suppositions) dans un visuel intuitif pour promouvoir davantage la discussion, l'élaboration de scénarios, et une communication claire.
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
Authors: Fortin Jean-Philippe , Triche Timothy J. , Hansen Kasper D 
Published: November 2016

Abstract

Summary
The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC (‘EPIC’) array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 (‘450k’) and EPIC platforms. We introduce the single-sample Noob (ssNoob) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data.

Availability and Implementation
The minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project.

Supplementary information
Supplementary data are available at Bioinformatics online.
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm
Authors: Fresno Cristóbal , González Germán Alexis , Merino Gabriela Alejandra , Flesia Ana Georgina , Podhajcer Osvaldo Luis , Llera Andrea Sabina , Fernández Elmer Andrés 
Published: November 2016

AbstractMotivationThe PAM50 classifier is used to assign patients to the highest correlated breast cancer subtype irrespectively of the obtained value. Nonetheless, all subtype correlations are required to build the risk of recurrence (ROR) score, currently used in therapeutic decisions. Present subtype uncertainty estimations are not accurate, seldom considered or require a population-based approach for this context.ResultsHere we present a novel single-subject non-parametric uncertainty estimation based on PAM50’s gene label permutations. Simulations results (n = 5228) showed that only 61% subjects can be reliably ‘Assigned’ to the PAM50 subtype, whereas 33% should be ‘Not Assigned’ (NA), leaving the rest to tight ‘Ambiguous’ correlations between subtypes. The NA subjects exclusion from the analysis improved survival subtype curves discrimination yielding a higher proportion of low and high ROR values. Conversely, all NA subjects showed similar survival behaviour regardless of the original PAM50 assignment. We propose to incorporate our PAM50 uncertainty estimation to support therapeutic decisions.Availability and ImplementationSource code can be found in ‘pbcmc’ R package at Bioconductor.Supplementary informationSupplementary data are available at Bioinformatics online.
Adaptive full-order and reduced-order observers for one-sided Lur'e systems with set-valued mappings
Authors: Shi Min-Jie , Huang Jun , Chen Liang , Yu Lei 
Published: November 2016

AbstractThis article proposes an adaptive observer design method for one-sided Lipschitz Lur'e differential inclusion systems with unknown parameters. First, under some assumptions, we design an adaptive full-order observer for the system. Then, under the same assumptions, a reduced-order observer is proved to be valid. Finally, we simulate an example to show the effectiveness of the presented method under the background of rotor system.
Historical Durability of Resistance to Wheat Diseases in Kansas
Authors: Bockus William W. , De Wolf Erick D. , Gill Bikram S. , Jardine Douglas J. , Stack James P. , Bowden Robert L. , Fritz Allan K. , Martin T. Joe 
Published: November 2016

In Kansas, estimated annual losses from wheat diseases averaged 16% from 1976 through 1988; however, losses have declined to 10% in recent years. This decline is mainly due to emphasis on developing cultivars with resistance to important diseases. Data from annual KSU extension publications were used to track disease ratings over time for individual wheat cultivars to eight diseases to draw inferences on the durability of deployed resistance. The duration of durability of resistance to leaf rust has been short for some cultivars but moderate for others. Conversely, the duration of durability of resistance to stem and stripe rusts has been long, although a recent virulence shift in the stripe rust pathogen indicates only moderate duration. Duration of durability of resistance toward tan spot, Septoria tritici blotch, wheat soilborne mosaic, and wheat spindle streak mosaic has been long. Resistance to wheat streak mosaic has been of long duration in some cultivars but others have shown only moderate duration of durability. The effort by breeders to produce cultivars with resistance to diseases in Kansas has resulted in an annual savings of about $58 million. Just as important as the incorporation of resistance into those cultivars is the moderate to long duration of durability of the resistance contributing to effective management of these diseases. Accepted for publication 22 June 2011. Published 2 August 2011.
Estimating Population Densities of Root Lesion Nematodes, Pratylenchus spp., from Soil Samples Using Dual Active and Passive Assays
Authors: MacGuidwin Ann E. , Bender Breann E. 
Published: November 2016

Root lesion nematodes are versatile parasites that move freely between root and soil habitats. Most laboratories conduct separate assays for soil or root tissue, using time-of-year as the selecting factor. We used a dual assay that simultaneously extracts nematodes from soil and root fragments in soil samples to identify the value of soil versus root tests using 920 research samples collected 1 April to 15 May, and 853 clinic samples collected year round. Nematodes were recovered from both soil and root fragments regardless of the time of year or origin of the sample. When the data were summarized by cohort, the mean percentage of nematodes recovered from root fragments was 65% for the research samples, 59% for clinic samples submitted 1 March to 15 June, 56% for clinic samples submitted 16 June to 31 July, and 49% for clinic samples submitted after 1 August. Both the incidence and population density of root lesion nematodes was underestimated if only the soil or only the root fraction was considered, indicating the need for testing methods that consider both habitats. The variability among samples for the distribution of nematodes between root and soil habitats was high, negating the option of running one assay and using a constant scaling factor to account for the other. Accepted for publication 30 October 2012. Published 20 November 2012.
The neural basis of precise visual short-term memory for complex recognisable objects
Authors: Veldsman Michele , Mitchell Daniel J. , Cusack Rhodri 
Published: November 2016

AbstractRecent evidence suggests that visual short-term memory (VSTM) capacity estimated using simple objects, such as colours and oriented bars, may not generalise well to more naturalistic stimuli. More visual detail can be stored in VSTM when complex, recognisable objects are maintained compared to simple objects. It is not yet known if it is recognisability that enhances memory precision, nor whether maintenance of recognisable objects is achieved with the same network of brain regions supporting maintenance of simple objects.We used a novel stimulus generation method to parametrically warp photographic images along a continuum, allowing separate estimation of the precision of memory representations and the number of items retained. The stimulus generation method was also designed to create unrecognisable, though perceptually matched, stimuli, to investigate the impact of recognisability on VSTM. We adapted the widely-used change detection and continuous report paradigms for use with complex, photographic images.Across three functional magnetic resonance imaging (fMRI) experiments, we demonstrated greater precision for recognisable objects in VSTM compared to unrecognisable objects. This clear behavioural advantage was not the result of recruitment of additional brain regions, or of stronger mean activity within the core network. Representational similarity analysis revealed greater variability across item repetitions in the representations of recognisable, compared to unrecognisable complex objects. We therefore propose that a richer range of neural representations support VSTM for complex recognisable objects.
Starting from the end: what to do when restricted data is released
Authors: Teperek Marta , Morgan Rhys , Ellefson Michelle , Kingsley Danny 
Published: November 2016

SummaryRepository managers can never be one hundred percent sure of the security ofhosted research data. Even assuming that human errors and technical faults will never happen, repositories can be subject to hacking attacks. Therefore, repositories accepting personal/sensitive data (or other forms of restricted data) should have workflows in place with defined procedures to be followed should things go wrong and restricted data is inappropriately released. In this paper wewill report on our considerations and procedures when restricted data from ourinstitution was inappropriately released.
Standard Issue: Copy number heterogeneity of JC virus standards discovered through next-generation sequencing
Authors: Greninger Alexander L. , Bateman Allen C. , Atienza Ederlyn E. , Wendt Sharon , Jerome Keith R. , Cook Linda 
Published: November 2016

AbstractQuantitative PCR is a diagnostic mainstay of clinical virology, and accurate quantitation of viral load among labs requires the use of international standards. However, the use of multiple passages of viral isolates to obtain sufficient material for international standards may result in genomic changes that complicate their use as quantitative standards. We performed next-generation sequencing to gain single-nucleotide resolution and relative copy number of JC virus (JCV) clinical standards. Strikingly, the WHO international standard and ExactTMv1/v2 prototype standards for JCV showed 8-fold and 4-fold variation in genomic coverage between different loci in the viral genome, respectively, due to large deletions in the large T-antigen region. No such variation was seen for a clinical sample with high copy-number of JCV nor a plasmid control. Intriguingly, several of the JCV standards sequenced in this study with large T-antigen deletions were cultured in cell lines immortalized using SV40 T-antigen, suggesting the possibility of trans-complementation in cell culture. Using a cut-off of 2% variant allele fraction for junctional reads to define the presence of a strain, 11 different strains were present in the WHO standard. In summary, targeting of different regions of the same international standard could result in up to an 8-fold difference in quantitation. We recommend the use of next-generation sequencing to validate standards in clinical virology.
Identifying Migrant Origins Using Genetics, Isotopes, and Habitat Suitability
Authors: Ruegg Kristen C. , Anderson Eric C. , Harrigan Ryan J. , Paxton Kristina L. , Kelly Jeff , Moore Frank , Smith Thomas B. 
Published: November 2016

AbstractIdentifying migratory connections across the annual cycle is important for studies of migrant ecology, evolution, and conservation. While recent studies have demonstrated the utility of high-resolution SNP-based genetic markers for identifying population-specific migratory patterns, the accuracy of this approach relative to other intrinsic tagging techniques has not yet been assessed.Here, using a straightforward application of Bayes' Rule, we develop a method for combining inferences from high-resolution genetic markers, stable isotopes, and habitat suitability models, to spatially infer the breeding origin of migrants captured anywhere along their migratory pathway. Using leave-one-out cross validation, we compare the accuracy of this combined approach with the accuracy attained using each source of data independently.Our results indicate that when each method is considered in isolation, the accuracy of genetic assignments far exceeded that of assignments based on stable isotopes or habitat suitability models. However, our joint assignment method consistently resulted in small, but informative increases in accuracy and did help to correct misassignments based on genetic data alone. We demonstrate the utility of the combined method by identifying previously undetectable patterns in the timing of migration in a North American migratory songbird, the Wilson's warbler.Overall, our results support the idea that while genetic data provides the most accurate method for tracking animals using intrinsic markers when each method is considered independently, there is value in combining all three methods. The resulting methods are provided as part of a new computationally-efficient R-package, GIAIH, allowing broad application of our statistical framework to other migratory animal systems.
Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast
Authors: Cheng Jun , Maier Kerstin C. , Avsec Žiga , Rus Petra , Gagneur Julien 
Published: November 2016

ABSTRACTThe stability of mRNA is one of the major determinants of gene expression. Although a wealth of sequence elements regulating mRNA stability has been described, their quantitative contributions to half-life are unknown. Here, we built a quantitative model forSaccharomyces cerevisiaebased on functional mRNA sequence features that explains 60% of the half-life variation between genes and predicts half-life at a median relative error of 30%. The model revealed a new destabilizing 3’UTR motif, ATATTC, which we functionally validated. Codon usage proves to be the major determinant of mRNA stability. Nonetheless, single-nucleotide variations have the largest effect when occurring on 3’UTR motifs or upstream AUGs. Analyzing mRNA half-life data of 34 knockout strains showed that the effect of codon usage not only requires functional decapping and deadenylation, but also the 5’-to-3’ exonuclease Xrn1, the non-sense mediated decay genes, but not no-go decay. Altogether, this study quantitatively delineates the contributions of mRNA sequence features on stability in yeast, reveals their functional dependencies on degradation pathways, and allows accurate prediction of half-life from mRNA sequence.
Intimate partner violence, fatherhood, and co-parenting of men in residential substance misuse treatment
Authors: Rubenstein Batya , Stover Carla Smith 
Published: November 2016

Purpose
The purpose of this paper is to examine the role of co-parenting, childhood experiences, and satisfaction with fathering in a sample of men in a long-term residential drug rehabilitation program.

Design/methodology/approach
A paper and pencil survey was completed by 128 men between the ages of 18 and 68 (M age=30.42 years) in a court ordered residential rehabilitation center for drug misuse. Of the 128 respondents, 40.625 percent (n=52) were fathers and completed a longer survey to assess their co-parenting relationships.

Findings
The percentage of men with positive role models did not differ between the fathers and non-fathers, with 40.4 percent of fathers having had a positive role model growing up, χ2(1, n=127)=0.54, p=0.816. Fathers were more likely to report witnessing IPV between their parents during childhood than non-fathers, χ2(1, n=125)=4.7888, p=0.029. Linear regression models examining factors associated with co-parenting agreement and exposure to conflict were significant, but witnessing IPV as a child was the only significant individual predictor.

Practical implications
Exposure to IPV in childhood was a common experience for fathers in residential treatment for substance misuse. Fathers reported significant problems in their co-parenting relationships indicating a need for fatherhood and co-parenting focused services available within residential treatment programs.

Originality/value
There is little research about fathers with co-occurring histories of substance misuse and IPV in residential treatment. This paper is the first to examine co-parenting in this specific population.
Toward a scholarship of peace leadership
Authors: McIntyre Miller Whitney 
Published: November 2016

Purpose
The purpose of this paper is to discuss the phenomenon of peace leadership, an emerging sub-area of leadership studies.

Design/methodology/approach
This literature review discusses peace leadership scholarly work specifically identified as such by its authors, and therefore does not include literature potentially viewed as informing the broader discussion of peace leadership.

Findings
The peace leadership specific scholarly literature discussed herein includes work on the traits, characteristics, and practices of peace leaders; peace leader role and responsibilities; and the connective and collective nature of peace leadership.

Originality/value
Discussion of the literature concludes a proposed definition of peace leadership and with three suggestions for ways to continue to build peace leadership scholarship including: empirical studies, theoretical and conceptual model creation, and ongoing informed discussions, and in itself contributes to the emerging conversation of peace leadership.
Linking demands to work-family conflict through boundary strength
Authors: Furtado Liliane , Sobral Filipe , Peci Alketa 
Published: November 2016

Purpose
The purpose of this paper is to propose and test a model to examine how the active management of work-family boundary strength acts as behavioral mechanism through which role-based factors – role demands and role identity – influence the conflict experienced by individuals.

Design/methodology/approach
Three studies were conducted to examine the proposed model. Studies 1 and 2 used an experimental design to test the causal effects of role demands on the strength of work and family boundaries, whereas Study 3 surveyed 389 working professionals to test the interactional and mediating effects of the model variables on inter-role conflict.

Findings
Results suggest that increasing demands in one domain weaken the boundary strength around the cross-domain to make resource drain possible, which, in turn, increases the conflict experienced in that domain; moreover, results show that work identity reinforces the weakening of the boundary strength at home caused by increasing work demands.

Research limitations/implications
The study of boundary management decisions as an underlying mechanism through which individuals’ role-based factors affect work-family conflict (WFC) can offer new insights into how to manage increasing work-family responsibilities.

Practical implications
This study findings can help individuals to cope with role demands and organizations to promote a culture that supports work-family balance.

Originality/value
This paper advances WFC research by examining alternative mechanisms through which role demands influence WFC. Methodologically, the research improves on past studies by bringing together experimental and correlational designs.
Surface acting as a mediator between personality and attitudes
Authors: Andrews Martha C. , Kacmar K. Michele , Valle Matthew 
Published: November 2016

PurposeThe purpose of this paper is to explore surface acting as a mediator in the relationships between perceptions of organizational politics and personality, with stress, turnover intentions, and job satisfaction.Design/methodology/approachData were obtained via survey from 276 working adults, and responses were subjected to structural equation modeling to confirm the measurement model and test hypotheses.FindingsSurface acting was found to mediate the relationships between perceptions of organizational politics and intent to turnover and satisfaction, and between proactive personality and intent to turnover and satisfaction. No mediating effect for surface acting was found between agreeableness and the outcomes.Practical implicationsIndividual differences and situational contingencies do affect surface acting in the workplace, and individual work-related outcomes. Managers need to be aware of personality characteristics and situational contexts that impact surface acting in organizations to help understand the effects of potential divergent attitudes and behaviors on employee outcomes.Originality/valuePrevious research examining surface acting assessed behavior in light of employee-customer interactions. This research extends the study of surface acting by examining the mediating role of surface acting among new predictors including organizational politics, proactive personality, and agreeableness with stress, turnover intentions, and job satisfaction.