Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens

Pea-comb is a dominant mutation in chickens that drastically reduces the size of the comb and wattles. It is an adaptive trait in cold climates as it reduces heat loss and makes the chicken less susceptible to frost lesions. Here we report that Pea-comb is caused by a massive amplification of a duplicated sequence located near evolutionary conserved non-coding sequences in intron 1 of the gene encoding the SOX5 transcription factor. This must be the causative mutation since all other polymorphisms associated with the Pea-comb allele were excluded by genetic analysis. SOX5 controls cell fate and differentiation and is essential for skeletal development, chondrocyte differentiation, and extracellular matrix production. Immunostaining in early embryos demonstrated that Pea-comb is associated with ectopic expression of SOX5 in mesenchymal cells located just beneath the surface ectoderm where the comb and wattles will subsequently develop. The results imply that the duplication expansion interferes with the regulation of SOX5 expression during the differentiation of cells crucial for the development of comb and wattles. The study provides novel insight into the nature of mutations that contribute to phenotypic evolution and is the first description of a spontaneous and fully viable mutation in this developmentally important gene

Predicting breast cancer response to neoadjuvant treatment using multi-feature MRI: results from the I-SPY 2 TRIAL.

Dynamic contrast-enhanced (DCE) MRI provides both morphological and functional information regarding breast tumor response to neoadjuvant chemotherapy (NAC). The purpose of this retrospective study is to test if prediction models combining multiple MRI features outperform models with single features. Four features were quantitatively calculated in each MRI exam: functional tumor volume, longest diameter, sphericity, and contralateral background parenchymal enhancement. Logistic regression analysis was used to study the relationship between MRI variables and pathologic complete response (pCR). Predictive performance was estimated using the area under the receiver operating characteristic curve (AUC). The full cohort was stratified by hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) status (positive or negative). A total of 384 patients (median age: 49 y/o) were included. Results showed analysis with combined features achieved higher AUCs than analysis with any feature alone. AUCs estimated for the combined versus highest AUCs among single features were 0.81 (95% confidence interval [CI]: 0.76, 0.86) versus 0.79 (95% CI: 0.73, 0.85) in the full cohort, 0.83 (95% CI: 0.77, 0.92) versus 0.73 (95% CI: 0.61, 0.84) in HR-positive/HER2-negative, 0.88 (95% CI: 0.79, 0.97) versus 0.78 (95% CI: 0.63, 0.89) in HR-positive/HER2-positive, 0.83 (95% CI not available) versus 0.75 (95% CI: 0.46, 0.81) in HR-negative/HER2-positive, and 0.82 (95% CI: 0.74, 0.91) versus 0.75 (95% CI: 0.64, 0.83) in triple negatives. Multi-feature MRI analysis improved pCR prediction over analysis of any individual feature that we examined. Additionally, the improvements in prediction were more notable when analysis was conducted according to cancer subtype

Theorizing the Process of Leaving: Turning Points and Trajectories in the Stages of Change

The Stages of Change Model (J. O. Prochaska & C. C. DiClemente, 1984) has been used to explore women\u27s process of leaving relationships involving intimate partner violence. Using a strengths-based approach, this study aims to build upon the model to further theorize the process of leaving. We conducted secondary data analysis of interviews with 19 mothers who left their abusive husbands. Turning points marked mothers\u27 movements from one stage of change to another, resulting in linear and nonlinear trajectories of leaving. All turning points were similar across cases except for the turning point between the stages of action and preparation. Consequently, 3 variations in the trajectories of leaving were found. The theoretical and practical implications for future work with abused mothers are discussed

Perceptions of Boundary Ambiguity in the Process of Leaving An Abusive Partner

The process of leaving an abusive partner has been theorized using the Stages of Change Model. Although useful, this model does not account for changes in relational boundaries unique to the process of leaving. Using family stress and feminist perspectives, this study sought to integrate boundary ambiguity into the Stages of Change Model. Boundary ambiguity is defined as a perception of uncertainty as to who is in or out of a family system (Boss & Greenberg, 1984). Twenty-five mothers who had temporarily or permanently left their abusers were interviewed. Data were analyzed using constructivist grounded theory methods. Results identify types, indicators of, and mothers\u27 responses to boundary ambiguity throughout the five stages of change. Most mothers and abusers fluctuated between physical and psychological presence and absence over multiple separations. The integration of boundary ambiguity into the Stages of Change Model highlights the process of leaving an abusive partner as systemic, fluid, and nonlinear

The Semantics of Metadata: Avalon Media System and the Move to RDF

The Avalon Media System (Avalon) provides access and management for digital audio and video collections in libraries and archives. The open source project is led by the libraries of Indiana University Bloomington and Northwestern University and is funded in part by grants from The Andrew W. Mellon Foundation and Institute of Museum and Library Services. Avalon is based on the Samvera Community (formerly Hydra Project) software stack and uses Fedora as the digital repository back end. The Avalon project team is in the process of migrating digital repositories from Fedora 3 to Fedora 4 and incorporating metadata statements using the Resource Description Framework (RDF) instead of XML files accompanying the digital objects in the repository. The Avalon team has worked on the migration path for technical metadata and is now working on the migration paths for structural metadata (PCDM) and descriptive metadata (from MODS XML to RDF). This paper covers the decisions made to begin using RDF for software development and offers a window into how Semantic Web technology functions in the real world

A Rights Expression Language for Federated Repositories

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014Posters, Demos and Developer "How-To's"We will reveal the most common characteristics found in twelve institutional repository deposit licenses and measure whether existing Rights Expression Languages (RELs) are suitable for expressing those characteristics in a machine-readable manner. The creation or adaptation of a REL to express repository and depositor rights and responsibilities is important, as repositories of scholarly content are increasingly included in federations that aggregate content but do not provide straightforward ways to deposit content.Konkiel, Stacy (Indiana University, United States of America)Liss, Jennifer A. (Indiana University, United States of America)Hardesty, Juliet L. (Indiana University, United States of America

Coparenting Relationships After Divorce: Variations by Type of Marital Violence and Fathers\u27 Role Differentiation

Using grounded theory methods, we examined coparenting relationships for 25 divorced mothers who experienced violence during their marriages. How well former husbands were able to differentiate, or keep separate, their parental and spousal roles emerged as central to coparenting dynamics and was partly related to type of marital violence. Linking differentiation to types of martial violence advances our theoretical understanding of variations in coparenting relationships after divorce. Results can be used to more effectively match divorcing parents with appropriate interventions

Lesbian/Bisexual Mothers and Intimate Partner Violence: Help Seeking in the Context of Social and Legal Vulnerability

Mothers in same-sex relationships face unique challenges when help seeking for intimate partner violence (IPV). Formal helping systems often invalidate their family relationships, leaving them vulnerable and distrustful when help seeking. To better understand their experiences, the authors interviewed 24 lesbian/bisexual mothers who were either in or had left abusive same-sex relationships. Increasing severity of violence, effects of violence on children and families, and being tired influenced their definitions of the situation. Decisions to seek formal help appeared to be influenced by their support from informal networks and perceived stigma related to the intersection of IPV and being lesbian or bisexual

Marital Violence and Co-parenting Quality After Separation

Research has identified multiple predictors of coparenting quality, but few studies have investigated how intimate partner violence (IPV) affects divorcing couples\u27 coparenting relationships. We addressed this question in a sample of 154 mothers with different marital IPV experiences. Mothers were recruited within 4 months of a divorce filing and completed two interviews 3 months apart. At Time 1, mothers reported on violence and coercive control during marriage, and postseparation behavioral (e.g., parental communication), emotional (e.g., anger), and intrusion (e.g., harassment) dynamics; at Time 2, they reported on coparenting quality (i.e., levels of support and conflict). In the overall sample, divorce and violence variables independently predicted coparenting quality. Mothers were then classified into three groups: no violence (NV; n = 74), situational couple violence (SCV; n = 46), or coercive controlling violence (CCV; n = 34). Of the 3, coparenting quality was lowest in the CCV group. While the SCV group was similar to the NV group on most divorce-related variables, the CCV group reported more hostility at separation and placed less importance on father-child relationships. Finally, patterns of association between study variables and coparenting quality showed some parallels between the SCV and NV groups. For CCV, postseparation harassment and fear were negatively associated with coparenting quality. Findings contribute to understanding predictors of coparenting quality and support the need for individualized assessments of divorce cases with attention to IPV dynamics

Collaborate, Automate, Prepare, Prioritize: Creating Metadata for Legacy Research Data

Data curation projects frequently deal with data that were not created for the purposes of long-term preservation and re-use. How can curation of such legacy data be improved by supplying necessary metadata? In this report, we address this and other questions by creating robust metadata for twenty legacy research datasets. We report on quantitative and qualitative metrics of creating domain-specific metadata and propose a four-prong framework of metadata creation for legacy research data. Our findings indicate that there is a steep learning curve in encoding metadata using the FGDC content standard for digital geospatial metadata. Our project also demonstrates that data curators who are handed research data “as is” and are tasked with incorporating such data into a data sharing environment can be very successful in creating descriptive metadata -- particularly, in conducting subject analysis and assigning keywords based on controlled vocabularies and thesauri. At the same time, they need to be aware of limitations in their efforts when it comes to structural and administrative metadata