bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dietary daidzein, but not genistein, has a hypocholesterolemic effect in non-ovariectomized and ovariectomized female Sprague-Dawley rats on a cholesterol-free diet
Authors: Bhattarai Keshab , Adhikari Sudhashree , Fujitani Mina , Kishida Taro 
Published: July 2017

AbstractWe compared the effects of two major isoflavones, daidzein and genistein, on lipid metabolism in rats. Daidzein (150 mg/kg diet), genistein (150 mg/kg diet), daidzein and genistein (1:1, 300 mg/kg diet), or control diets were fed to 4 groups of 6-week-old ovariectomized (Ovx) and non-Ovx Sprague Dawley rats for 4 weeks. Dietary daidzein, but not genistein, reduced serum and hepatic total cholesterol levels significantly relative to that by the control group, regardless of whether the rats had undergone ovariectomy. Genistein did not exhibit any physiological effects on lipid levels, but did affect genes involved in cholesterol metabolism. These results indicate that daidzein and genistein may influence lipid regulation via differing modes of action.
A short synthetic chimeric sequence harboring matrix attachment region/PSAR2 increases transgene expression in Chinese hamster ovary cells
Authors: Li Qin , Wang Wen , Guo Xiao , Jia Yan-Long , Wang Yan-Fang , Wang Tian-Yun 
Published: July 2017

Abstract
A chimeric DNA fragment containing an interferon-beta matrix attachment region (MAR) and an immunoglobulin MAR (PSAR2) was synthesized. PSAR2 was cloned into the upstream or downstream region of an enhanced green fluorescent protein (eGFP) expression cassette in a eukaryotic vector, which was then transfected into CHO cells. The results showed that PSAR2 did not effectively increase transgene expression when it was cloned into the upstream region of the eGFP expression cassette. However, when inserted downstream of the eGFP expression cassette, PSAR2-enhanced transient transgene expression and significantly increased the numbers of stably transfected cells compared with the control vector. Additionally, PSAR2 significantly increased eGFP copy numbers as compared with the control vector. PSAR2 could significantly enhance transgene expression in CHO cells according to the position in the vector and increased transgene copy numbers. We found a short chimeric sequence harboring two MARs effectively increased transgene expression in CHO cells.
Phylotyper: in silico predictor of gene subtypes
Authors: Whiteside Matthew D , Gannon Victor P J , Laing Chad R 
Published: July 2017

Abstract

Summary
Whole genome sequencing (WGS) is being adopted in public health for improved surveillance and outbreak analysis. In public health, subtyping has been used to infer phenotypes and distinguish bacterial strain groups. In silico tools that predict subtypes from sequences data are needed to transition historical data to WGS-based protocols. Phylotyper is a novel solution for in silico subtype prediction from gene sequences. Designed for incorporation into WGS pipelines, it is a general prediction tool that can be applied to different subtype schemes. Phylotyper uses phylogeny to model the evolution of the subtype and infer subtypes for unannotated sequences. The phylogenic framework in Phylotyper improves accuracy over approaches based solely on sequence similarity and provides useful contextual feedback.

Availability and implementation
Phylotyper is a python and R package. It is available from: https://github.com/superphy/insilico-subtyping.

Supplementary information
Supplementary data are available at Bioinformatics online.
FRB as products of accretion disc funnels
Authors: Katz J. I. 
Published: July 2017

Abstract
The repeating FRB 121102, the only fast radio burst (FRB) with an accurately determined position, is associated with a variable persistent radio source. I suggest that an FRB originates in the accretion disc funnels of black holes. Narrowly collimated radiation is emitted along the wandering instantaneous angular momentum axis of accreted matter. This emission is observed as a fast radio burst when it sweeps across the direction to the observer. In this model, in contrast to neutron star (pulsar, RRAT or SGR) models, repeating FRBs do not have underlying periodicity and are co-located with persistent radio sources resulting from their off-axis emission. The model is analogous, on smaller spatial, lower mass and accretion rate and shorter temporal scales, to an active galactic nucleus (AGN), with FRB corresponding to blazars in which the jets point towards us. The small inferred black hole masses imply that FRBs are not associated with galactic nuclei.
Systematic Review of Costs and Effects of Self-Management Interventions for Chronic Musculoskeletal Pain: Spotlight on Analytic Perspective and Outcomes Assessment
Authors: Hernon Marian J. , Hall Amanda M. , O’Mahony James F. , Normand Charles , Hurley Deirdre A. 
Published: July 2017

AbstractBackgroundEvidence for the cost-effectiveness of self-management interventions for chronic musculoskeletal pain (CMP) lacks consensus, which may be due to variability in the costing methods employed.PurposeThe purposes of the study were to identify how costs and effects have been assessed in economic analysis of self-management interventions for CMP and to identify the effect of the chosen analytical perspective on cost-effectiveness conclusions.Data SourcesFive databases were searched for all study designs using relevant terms.Study SelectionTwo independent researchers reviewed all titles for predefined inclusion criteria: adults (≥18 years of age) with CMP, interventions with a primary aim of promoting self-management, and conducted a cost analysis.Data ExtractionDescriptive data including population, self-management intervention, analytical perspective, and costs and effects measured were collected by one reviewer and checked for accuracy by a second reviewer.Data SynthesisFifty-seven studies were identified: 65% (n = 37) chose the societal perspective, of which 89% (n = 33) captured health care utilization, 92% (n = 34) reported labor productivity, 65% (n = 24) included intervention delivery, and 59% (n = 22) captured patient/family costs. Types of costs varied in all studies. Eight studies conducted analyses from both health service and societal perspectives; cost-effectiveness estimates varied with perspective chosen, but in no case was the difference sufficient to change overall policy recommendations.LimitationsChronic musculoskeletal pain conditions where self-management is recommended, but not as a primary treatment, were excluded. Gray literature was excluded.ConclusionSubstantial heterogeneity in the cost components captured in the assessment of self-management for CMP was found; this was independent of the analytic perspective used. Greater efforts to ensure complete and consistent costings are required if reliable cost-effectiveness evidence of self-management interventions is to be generated and to inform the most appropriate perspective for economic analyses in this field.
Cross-Sectional Relationships of Physical Activity and Sedentary Behavior With Cognitive Function in Older Adults With Probable Mild Cognitive Impairment
Authors: Falck Ryan S. , Landry Glenn J. , Best John R. , Davis Jennifer C. , Chiu Bryan K. , Liu-Ambrose Teresa 
Published: July 2017

Abstract

Background
Mild cognitive impairment (MCI) represents a transition between normal cognitive aging and dementia and may represent a critical time frame for promoting cognitive health through behavioral strategies. Current evidence suggests that physical activity (PA) and sedentary behavior are important for cognition. However, it is unclear whether there are differences in PA and sedentary behavior between people with probable MCI and people without MCI or whether the relationships of PA and sedentary behavior with cognitive function differ by MCI status.

Objective
The aims of this study were to examine differences in PA and sedentary behavior between people with probable MCI and people without MCI and whether associations of PA and sedentary behavior with cognitive function differed by MCI status.

Design
This was a cross-sectional study.

Methods
Physical activity and sedentary behavior in adults dwelling in the community (N = 151; at least 55 years old) were measured using a wrist-worn actigraphy unit. The Montreal Cognitive Assessment was used to categorize participants with probable MCI (scores of &lt;26/30) and participants without MCI (scores of ≥26/30). Cognitive function was indexed using the Alzheimer Disease Assessment Scale-Cognitive-Plus (ADAS-Cog Plus). Physical activity and sedentary behavior were compared based on probable MCI status, and relationships of ADAS-Cog Plus with PA and sedentary behavior were examined by probable MCI status.

Results
Participants with probable MCI (n = 82) had lower PA and higher sedentary behavior than participants without MCI (n = 69). Higher PA and lower sedentary behavior were associated with better ADAS-Cog Plus performance in participants without MCI (β = −.022 and β = .012, respectively) but not in participants with probable MCI (β &lt; .001 for both).

Limitations
This study was cross-sectional and therefore could not establish whether conversion to MCI attenuated the relationships of PA and sedentary behavior with cognitive function. The diagnosis of MCI was not confirmed with a physician; therefore, this study could not conclude how many of the participants categorized as having probable MCI would actually have been diagnosed with MCI by a physician.

Conclusions
Participants with probable MCI were less active and more sedentary. The relationships of these behaviors with cognitive function differed by MCI status; associations were found only in participants without MCI.
Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins
Authors: Harmon Tyler S. , Holehouse Alex S. , Rosen Michael K. , Pappu Rohit V. 
Published: July 2017

AbstractMany intracellular membraneless bodies appear to form via reversible phase transitions of multivalent proteins. Two relevant types of phase transitions aresol-gel transitions(gelation) andphase separation plus gelation. Gelation refers to the formation of a system spanning molecular network. This can either be enabled by phase separation or it can occur independently. Despite relevance for the formation and selectivity of compositionally distinct protein and RNA assemblies, the determinants of gelation as opposed to phase separation plus gelation remain unclear. Here, we focus on linear multivalent proteins that consist of interaction domains that are connected by disordered linkers. Using results from computer simulations and theoretical analysis we show that the lengths and sequence-specific features of disordered linkers determine the coupling between phase separation and gelation. Thus, the precise nature of phase transitions for linear multivalent proteins should be biologically tunable through genetic encoding of or post-translational modifications to linker sequences.
Intraclass correlation: improved modeling approaches and applications for neuroimaging
Authors: Chen Gang , Taylor Paul A. , Haller Simone P. , Kircanski Katharina , Stoddard Joel , Pine Daniel S. , Leibenluft Ellen , Brotman Melissa A. , Cox Robert W. 
Published: July 2017

AbstractIntraclass correlation (ICC) is a reliability metric that gauges similarity when, for example, entities are measured under similar, or even the same, well-controlled conditions, which in MRI applications include runs/sessions, twins, parent/child, scanners, sites, etc. The popular definitions and interpretations of ICC are usually framed statistically under the conventional ANOVA platform. Here, we provide a comprehensive overview of ICC analysis in its prior usage in neuroimaging, and we show that the standard ANOVA framework is often limited, rigid, and inflexible in modeling capabilities. These intrinsic limitations motivate several improvements. Specifically, we start with the conventional ICC model under the ANOVA platform, and extend it along two dimensions: first, fixing the failure in ICC estimation when negative values occur under degenerative circumstance, and second, incorporating precision information of effect estimates into the ICC model. These endeavors lead to four modeling strategies: linear mixed-effects (LME), regularized mixed-effects (RME), multilevel mixed-effects (MME), and regularized multilevel mixed-effects (RMME). Compared to ANOVA, each of these four models directly provides estimates for fixed effects as well as their statistical significances, in addition to the ICC estimate. These new modeling approaches can also accommodate missing data as well as fixed effects for confounding variables. More importantly, we show that the MME and RMME approaches offer more accurate characterization and decomposition among the variance components, leading to more robust ICC computation. Based on these theoretical considerations and model performance comparisons with a real experimental dataset, we offer the following general-purpose recommendations. First, ICC estimation through MME or RMME is preferable when precision information (i.e., weights that more accurately allocate the variances in the data) is available for the effect estimate; when precision information is unavailable, ICC estimation through LME or the RME is the preferred option. Second, even though the absolute agreement version, ICC(2,1), is presently more popular in the field, the consistency version, ICC(3,1), is a practical and informative choice for whole-brain ICC analysis that achieves a well-balanced compromise when all potential fixed effects are accounted for. Third, approaches for clear, meaningful, and useful result reporting in ICC analysis are discussed. All models, ICC formulations, and related statistical testing methods have been implemented in an open source program3dICC, which is publicly available as part of the AFNI suite. Even though our work here focuses on the whole brain level, the modeling strategy and recommendations can be equivalently applied to other situations such as voxel, region, and network levels.
Detecting violation of business constraints in declarative process execution: a case study
Authors: Lam Vitus S.W. 
Published: July 2017

Purpose
Declarative process modelling is a constraint-centric approach that treats business rules as first-class citizens in business process models. Augmenting the declarative process modelling technique with capability to detect the constraint violations during business process execution is of crucial importance. The purpose of this paper is to contribute to the modelling of business rules through a repository of pattern-oriented templates.

Design/methodology/approach
The semantics of the business rule templates is underpinned by linear temporal logic (LTL). Automated temporal reasoning is then conducted for determining whether process executions adhere to the business rules through the utilisation of the Logics Workbench (LWB). An application of the methodological framework is illustrated by a realistic case study on degree requirements verification.

Findings
To access the practicality of the approach, the case study of this paper is based on the verification of degree requirements, which is different from the domain area of the case study in the author’s prior work. The findings indicated that the temporal framework could be applied to the declarative process modelling in a consistent and efficient manner.

Originality/value
This paper is an extended version of the author’s earlier study. More details on the LTL and LWB are provided in the current study. The author introduces 17 new business rule templates and illustrates the utilisation of the new templates via a case study that belongs to a different domain area.
Learning from students behind the fence: a critical book club with incarcerated youth
Authors: Bemiss Elizabeth McCall , Doyle Jennifer L. , Styslinger Mary Elizabeth 
Published: July 2017

PurposeThis paper aims to explore alternative literacy instruction with incarcerated youth, add to the body of existing literature documenting the literacy of those incarcerated and investigate the construction of book clubs through a critical lens.Design/methodology/approachThis qualitative case study answered the following research questions: What can a critical book club reveal about the literacy lives of these incarcerated youth? What can we learn from incarcerated youth through a critical book club? Data were collected through participant observation and in-depth interviews and analyzed using a critical literacy framework.FindingsFindings indicate students used text connections to critically reflect on selves and schools. They questioned issues of power, particularly the power of literacy in their own lives as well as the power of schools, teachers and curriculum. The paper concludes with the authors’ critical reflection on both the findings and process which results in implications for future book clubs in settings with incarcerated youth.Social implicationsAs educators, administrators and community members living in the “age of incarceration” (Hill, 2013), there is a social responsibility to design curriculum and pedagogy that expands instruction in correctional facilities.Originality/valueThe need for expanded literacy instruction in juvenile detention centers has been widely documented and supported; however, conventional methods of teaching literacy are not always successful for youth who may not have had positive experiences with traditional schooling. This study expands and explores literacy instruction with incarcerated youth through book clubs, an alternative literacy structure which challenges traditional curricula, pedagogical practices and culturally irrelevant texts which often contribute to the alienation and disempowerment of many students. Book clubs can facilitate new understandings through a critical lens.
Conceptualising and enacting the critical imagination through a critical writing pedagogy
Authors: Mendelowitz Belinda 
Published: July 2017

Purpose
Imagination in critical literacy research is usually referred to as a taken for granted concept that is seldom theorised, leaving the assumptions unchecked that everyone has a shared understanding of imagination. This paper aims to challenge critical literacy researchers to rethink the relationship between criticality and imagination and its implication for a critical writing pedagogy. It aims to synthesise the imagination and criticality in the context of critical literacy, both theoretically and empirically and in doing so to illustrate what form a critical writing pedagogy that foregrounds the critical imagination might take.

Design/methodology/approach
This argument is illustrated through analysing two sets of data that contain embodied enactments of contested gender issues across different modes and genres. Data from student teachers’ embodied enactments of contested gender issues and from their writing on these issues were analysed thematically.

Findings
A crucial aspect of the critical imagination entails creating pedagogical spaces that mobilise affect and empathy alongside criticality. Embodied literacy work across different modes and genres can play a significant role in facilitating the critical imagination by enabling students to enact, perform and immerse themselves in different discourses, ultimately generating new insights and ways of seeing.

Research limitations/implications
Data was drawn from a relatively small sample of 30 assignments in the context of teacher education in South Africa. More empirical research needs to be conducted across a wider range of contexts.

Practical implications
The paper provides a theoretical framework and practical ideas for implementing a critical writing pedagogy that foregrounds the critical imagination and thus could be used in both teacher education contexts and school literacy classrooms.

Originality/value
This paper challenges critical literacy researchers to rethink the relationship between criticality and imagination and its implication for a critical writing pedagogy.
Regional patient safety and quality leaders aim to reduce disparities in healthcare with collaborative approach
Authors: Veit Kelly Renee 
Published: July 2017

Purpose
Washington Patient Safety Coalition (WPSC) brings individuals and healthcare organizations together to identify and work on patient safety priorities. It holds bi-annual strategic planning sessions to assess program effectiveness around current organizational goals and to develop new goals. The purpose of this paper is to describe how WPSC members came to identify health disparities as a priority, and what they did to integrate this into organizational strategy.

Design/methodology/approach
For the 2015 strategic planning session, WPSC staff used 2012-2015 internal activities records to conduct a SWOT analysis. The author conducted stakeholder and member “Sensing Surveys” and framed action items on two underlying considerations: first, positioning of the members within the patient safety landscape, taking into account where the members are most “touching” the issue of disparity and are most appropriately positioned to act as change agents and, second, WPSC is not an established content expert in health disparities.

Findings
The author focused the efforts on assisting the Governor’s Interagency Council in promoting Culturally and Linguistically Appropriate Services standards. This Council helps to drive policy, but not necessarily operationalizing it. WPSC has ability to fulfill that role; the membership is comprised of organizational leaders, those positioned to operationalize the Council’s disparity interventions. The WPSC saw an opportunity to partner the efforts, bridging gaps between policy and operational action.

Practical implications
This viewpoint shows the power of a small collaboration interested in broadening awareness of a complex issue.

Originality/value
Health disparities are complex and multifaceted. Within the Seattle area there were many organizations committed to working on this topic, each with their unique value add to the issue.
The pre-eminence of patient safety in health care governance
Authors: MacVane Phipps Fiona 
Published: July 2017

Purpose
The purpose of this paper is to identify a common theme linking the articles in this issue of IJHG. The review editor elucidates on this topic while presenting key findings from the articles which comprise the current issue.

Design/methodology/approach
The design is a general review describing the articles under review while expanding on the subject matter through reference to other authors.

Social implications
The Review provides readers with a brief overview of the current articles enabling them to select the ones which reflect their needs or interests.

Originality/value
IJHG is the only Emerald journal providing a Review section of this type.