bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling
Authors: Borrill Philippa , Harrington Sophie A. , Simmonds James , Uauy Cristobal 
Published: October 2018

AbstractSenescence is a tightly regulated developmental programme which is coordinated by transcription factors. Identifying these transcription factors in crops will provide opportunities to tailor the senescence process to different environmental conditions and regulate the balance between yield and grain nutrient content. Here we use ten time points of gene expression data alongside gene network modelling to identify transcription factors regulating senescence in polyploid wheat. We observe two main phases of transcription changes during senescence: early downregulation of housekeeping and metabolic processes followed by upregulation of transport and hormone related genes. We have identified transcription factor families associated with these early and later waves of differential expression. Using gene regulatory network modelling alongside complementary publicly available datasets we identified candidate transcription factors for controlling senescence. We validated the function of one of these candidate transcription factors in senescence using wheat chemically-induced mutants. This study lays the ground work to understand the transcription factors which regulate senescence in polyploid wheat and exemplifies the integration of time-series data with publicly available expression atlases and networks to identify candidate regulatory genes.
Genome wide association study of hippocampal subfield volume in PTSD cases and trauma-exposed controls
Authors: Morey Rajendra A. , Garrett Melanie E. , Stevens Jennifer S. , Clarke Emily , Haswell Courtney C. , van Rooij Sanne J.H. , Fani Negar , Lori Adriana ,   VA Mid-Atlantic MIRECC Workgroup, Marx Christine E. , Beckham Jean C. , McCarthy Gregory , Hauser Michael A. , Ashley-Koch Allison E. 
Published: October 2018

ABSTRACTBehavioral, structural, and functional neuroimaging have implicated the hippocampus as a critical brain region in PTSD pathogenesis. We conducted a GWAS of hippocampal subfield volumes in a sample of recent military veteran trauma survivors (n=157), including some with PTSD (n=66). Covariates in our analysis included lifetime PTSD diagnosis, sex, intracranial volume, genomic estimates of ancestry, and childhood trauma. Interactions between genetic variants and lifetime PTSD or childhood trauma were interrogated for SNPs with significant main effects. Several genetic associations surpassed correction for multiple testing for several hippocampal subfields, including fimbria, subiculum, cornu ammonis-1(CA1), and hippocampal amygdala transition area (HATA). One association replicated in an independent cohort of civilians with PTSD (rs12880795 inTUNARwith L-HATA volume,p=3.43 × 10-7in the discovery andp=0.0004 in the replication cohort). However, the most significant association in the discovery data set was between rs6906714 inLINC02571and R-fimbria volume (p=5.99 ×10-8,q=0.0056). Interestingly, the effect of rs6906714 on R-fimbria volume increased with childhood trauma (G*E interactionp=0.022). In addition to variants in long intergenic non-coding RNAs (lincRNAs), we identified SNPs associated with hippocampal subfield volume, which are also quantitative trait loci (QTLs) for genes involved in RNA editing of glutamate receptor subunits (GluRs), oxidative stress, and autoimmune disorders. Genomic regions, some with putative regulatory roles, influence the volume of hippocampal subfields. Neuroimaging phenotypes may offer important insight into the genetic architecture and neurobiological pathways relevant to PTSD, as well as in the identification of potential biomarkers and drug targets for PTSD.
baRcodeR with PyTrackDat: Open-source labelling and tracking of biological samples for repeatable science
Authors: Wu Yihan , Lougheed David R. , Lougheed Stephen C. , Moniz Kristy , Walker Virginia K. , Colautti Robert I. 
Published: October 2018

AbstractRepeatable experiments with accurate data collection and reproducible analyses are fundamental to the scientific method but may be difficult to achieve in practice. Several flexible, open-source tools developed for the R and Python coding environments aid the reproducibility of data wrangling and analysis in scientific research. In contrast, analogous tools are generally lacking for earlier stages, such as systematic labelling and processing of field samples with hierarchical structure (e.g. time points of individuals from multiple lines or populations) or curating heterogenous data collected by different researchers over several years. Such tools are critical for modern research given trends toward globally distributed collaborators using higher-throughput technologies. As a step toward improving repeatability of methods for the collection of biological samples, and curation of biological data, we introduce the R packagebaRcodeRand thePyTrackDatpipeline in Python. ThebaRcodeRpackage provides tools for generating biologically informative, hierarchical labels with digitally encoded 2D barcodes that can be printed and scanned using low-cost commercial hardware. ThePyTrackDatpipeline integrates withbaRcodeRoutput to build a web interface for sample management and tracking along with data collection and curation. We briefly describe the application of principles frombaRcodeRandPyTrackDatin three large research projects, which demonstrate their value to (i) help document sampling methods, (ii) facilitate collaboration and (iii) reduce opportunities for human errors and omissions that could otherwise propagate through downstream data analysis to compromise biological inference.
Cell confinement reveals a branched-actin independent circuit for neutrophil polarity
Authors: Graziano Brian R. , Town Jason P. , Nagy Tamas L. , Fošnarič Miha , Penič Samo , Iglič Aleš , Kralj-Iglič Veronika , Gov Nir , Diz-Muñoz Alba , Weiner Orion D. 
Published: October 2018

ABSTRACTMigratory cells use distinct motility modes to navigate different microenvironments, but it is unclear whether these modes rely on the same core set of polarity components. To investigate this, we disrupted Arp2/3 and WAVE complex, which assemble branched actin networks that are essential for neutrophil polarity and motility in standard adherent conditions. Surprisingly, confinement rescues polarity and movement of neutrophils lacking these components, revealing a processive bleb-based protrusion program that is mechanistically distinct from the branched actin-based protrusion program but shares some of the same core components and underlying molecular logic. We further find that the restriction of protrusion growth to one site does not always respond to membrane tension directly, as previously thought, but may rely on closely linked properties such as local membrane curvature. Our work reveals a hidden circuit for neutrophil polarity and indicates that cells have distinct molecular mechanisms for polarization that dominate in different microenvironments.
Exploring multimodal writing in secondary English classrooms: a literature review
Authors: Nash Brady 
Published: October 2018

PurposeThis paper aims to explore recent research (2007-2017) on the implementation of multimodal writing instruction in secondary English courses. It seeks to highlight the varied ways in which theoretical conceptions of multimodality have been implemented in writing instruction and the impacts of these implementations on students' experiences in classrooms.Design/methodology/approachThe author used a keyword search of relevant academic databases to identity articles within the search parameters. This was followed by bibliographic branching to identify additional articles and two rounds of open coding to identify themes for analysis.FindingsThe literature revealed a diversity of approaches to incorporating multimodal writing in classrooms; teachers mixed modalities within assignments, paired writing in print with multimodal composition and redesigned entire units or courses around multimodality. Studies showed the impact of multimodality on student learning through shifts in conceptions of communication, increases in student engagement, composition for real audiences and an increased role for students’ interests and identities.Practical implicationsThis review has implications for teachers and researchers interested in developing multimodal writing curricula. It highlights the specific ways in which multimodal writing can be incorporated into instruction and the changes in student learning that result from this shift.Originality/valueWhile theoretical writing on multimodality is abundant, multiple researchers have noted the difficulty of finding research on classroom implementations of multimodality (Howell et al., 2017; Smith, 2017). This review is intended to address this difficulty by contributing to a body of literature that teachers and scholars can draw on as they conceptualize and design multimodal writing experiences for students in the future.
Improving stability in physical human–robot interaction by estimating human hand stiffness and a vibration index
Authors: Bian Feifei , Ren Danmei , Li Ruifeng , Liang Peidong 
Published: October 2018

Purpose
The purpose of this paper is to eliminate instability which may occur when a human stiffens his arms in physical human–robot interaction by estimating the human hand stiffness and presenting a modified vibration index.

Design/methodology/approach
Human hand stiffness is first estimated in real time as a prior indicator of instability by capturing the arm configuration and modeling the level of muscle co-contraction in the human’s arms. A time-domain vibration index based on the interaction force is then modified to reduce the delay in instability detection. The instability is confirmed when the vibration index exceeds a given threshold. The virtual damping coefficient in admittance controller is adjusted accordingly to ensure stability in physical human–robot interaction.

Findings
By estimating the human hand stiffness and modifying the vibration index, the instability which may occur in stiff environment in physical human–robot interaction is detected and eliminated, and the time delay is reduced. The experimental results demonstrate significant improvement in stabilizing the system when the human operator stiffens his arms.

Originality/value
The originality is in estimating the human hand stiffness online as a prior indicator of instability by capturing the arm configuration and modeling the level of muscle co-contraction in the human’s arms. A modification of the vibration index is also an originality to reduce the time delay of instability detection.
The homicide circumplex: a new conceptual model and empirical examination
Authors: DeLisi Matt , Drury Alan , Elbert Michael 
Published: October 2018

PurposeHomicide is the most severe form of crime and one that imposes the greatest societal costs. The purpose of this paper is to introduce the homicide circumplex, a set of traits, behaviors, psychological and psychiatric features that are associated with greater homicidal ideation, homicidal social cognitive biases, homicide offending and victimization, and psychopathology that is facilitative of homicide.Design/methodology/approachUsing the data from a near population of federal supervised release offenders from the Midwestern USA, ANOVA, multinomial logistic, Poisson and negative binomial regression models were developed.FindingsGreater homicidal ideation is associated with homicide offending, attempted homicide offending and attempted homicide victimization and predicted by gang activity, alias usage, antisocial personality disorder and intermittent explosive disorder. These behavioral disorders, more extensive criminal careers, African American status and gang activity also exhibited significant associations with dimensions of the homicide circumplex.Originality/valueDeveloping behavioral profiles of offenders that exhibit homicidal ideation and behaviors are critical for identifying clients at greatest risk for lethal violence. The homicide circumplex is an innovation toward the goal that requires additional empirical validation.
Ritual as assemblage: feast of sacrifice experiences of Turkish consumers
Authors: Torlak Ömer , Özmen Müjdat , Tiltay Muhammet Ali , İşlek Mahmut Sami , Ay Ufuk 
Published: October 2018

Purpose
The purpose of this paper is to theorize and empirically investigate the formation of consumer’s consumption ritual experiences and discourses associated with Feast of Sacrifice.

Design/methodology/approach
The authors have approached the data from assemblage theory perspective. By use of ethnographic participant observation and in-depth interviews, seven themes are uncovered and discussed: meaning of Qurban, preparation of the ritual, Qurban choice, meat, Qurban ritual, marketplace and framing of discourses.

Findings
This study provides a theoretical development in which it depicts that assemblage theory can be used in the context of religious rituals such as the Feast of Sacrifice. This suggests that parts forming the social phenomena include different meanings and functions in different assemblages to the ritual, which has a structure with a particular process, roles and content scenario. This implies that even the most structured social phenomena as religious rituals can be accepted as social assemblage where every individual experiences his/her own ritual with the parts that have ever-changing material and expressive roles.

Originality/value
This study will contribute to the literature on religious rituals and practices through viewing ritual as an assemblage including material and expressive features as well as human and non-human actors. Besides, this study aims to find out whether there is a constant consumer and the concept of ritual by focusing on buying experiences of consumer in Feast of Sacrifice in Turkey.
Professional resistance against competitive public procurement in Iran
Authors: Sepehri Mehran , Qadiri Mohsen 
Published: October 2018

Purpose
This study aim to examine the roots of professional resistance of procurement in Iran. Public procurement (PP) contracts, in developing countries, hide the structural problems of governmental management because of the lack of bureaucratic processes.

Design/methodology/approach
A two-phase qualitative study offers contextual and critical understandings on why Iranian PP experts, who are aware of the philosophies behind internationally endorsed principles, prefer to resist against the use of those principles. They help, unexpectedly, their traditionalist companions to resolve the difficulties of the PP contracts by the use of local methods and routines.

Findings
Evidence, from in-depth interviews with procurements professionals in Iran Oil industry, provides four specific themes of “professional disorder,” “anti-internationalism,” “resistance mentality” and “politicized procurement.” A preemptive resistance is characterized to guarantee that the national benefits in Iran are preferred over the international economic interests.

Originality/value
Iran has been in isolation due to political sanctions, for two decades. There are many diverse political and social reasons for resistance against professional public procurement.
A dynamic differential oligopoly game with sticky price and advertising
Authors: Raoufinia Marjan , Baradaran Vahid , Shahrjerdi Reza 
Published: October 2018

PurposeThe purpose of this study is to analyze comparatively the properties of open-loop and closed-loop equilibria in a dynamic oligopoly model with price dynamics and reflexive behavior of market agents.Design/methodology/approachTo consider dynamic competitive markets, the authors focus on a differential game theory in oligopolistic structures, using analytical models to illustrate how advertising effort, good differentiation and price stickiness interact simultaneously in the open-loop and the closed-loop Nash equilibria. The comparative assessment of these equilibria obtains some significant results.FindingsAn optimization model that enriches the continuous time is presented. Under the open-loop and the closed-loop, Nash equilibrium showed an increase in the total output, advertising in price stickiness and promotional efficiency, while there was a decrease in product differentiation and advertising promotional efficiency. However, the open-loop equilibrium levels are larger than the closed-loop equilibrium. Under the closed-loop information, the long-run equilibrium was faster than the opened-loop in a dynamic oligopoly. The graphical illustration was used to present the behavior of the model parameters.Practical implicationsThis study helps managers to choose an appropriate price and advertising adjustment to maximize profit. The obtained results may help firms to make the smart decision and may provide managers the valuable tool for making decisions in the competitive market environments.Originality/valueThis is a first attempt to analyze a dynamic oligopoly in the differentiated market environment. It considers a joint action of the output and advertising in shaping the closed-loop and the open-loop equilibria with N competitors in a dynamic competitive setting.
Impact of Barrett's esophagus surveillance on the prognosis of esophageal adenocarcinoma: A meta‐analysis
Authors: Ding Yu E , Li Yue , He Xing Kang , Sun Lei Min 
Published: October 2018

ObjectiveWhether endoscopic surveillance would improve the outcomes of esophageal adenocarcinoma in patients previously diagnosed with Barrett's esophagus remains unclear. This meta‐analysis aimed to assess the survival advantages of endoscopic surveillance for patients with Barrett's esophagus.MethodsDatabases including PubMed, the Web of Science, and the Cochrane Library were examined systematically from their inception to July 2017, for articles related to the survival outcomes of esophageal adenocarcinoma in patients with Barrett's esophagus under endoscopic surveillance. Adjusted hazard estimates were adopted to determine overall results with 95% confidence intervals (CIs), using the fixed‐effect model. We conducted subgroup and sensitivity analyses using the “metan” command in Stata software to assess the stability of the overall results. Begg's test, Egger's test and the funnel plot were used to evaluate the presence of publication bias.ResultsA total of eight studies (two case‐control and six cohort studies) were finally included in our current study. Compared with patients with esophageal adenocarcinoma that was not detected by surveillance, a significant 29% reduction in mortality from esophageal adenocarcinoma was observed among patients under endoscopic surveillance (adjusted hazard ratio [HR] 0.71, 95% CI 0.66–0.77). This effect was presented in both the USA (adjusted HR 0.71, 95% CI 0.65–0.78) and Europe (adjusted HR 0.71, 95% CI 0.60–0.83). We found no evidence of publication bias.ConclusionsOur meta‐analysis supports the concept that endoscopic surveillance for patients with Barrett's esophagus could improve the prognosis of esophageal adenocarcinoma. More well‐designed prospective studies are needed to confirm this association.
Gendered Geographies of Elimination: Decolonial Feminist Geographies in Latin American Settler Contexts
Authors: Zaragocin Sofia 
Published: October 2018

AbstractGendered geographies of elimination further settler colonialism's influence on conceptual discussions in human geography on contemporary forms of the place‐based death of indigenous peoples. Through work stemming from scholarship on the gendering of settler colonialism, this paper adds to narratives on place annihilation and dispossession of indigenous territory tied to the slow death of racialised, gendered and sexualised populations. Building on incipient reflections in geography with settler colonialism, I explore the geographic implications from the perspective of Epera women, indigenous women belonging to a trinational ethnicity experiencing elimination along the Ecuador–Colombia borderland from the perspective of decolonial feminist geography frameworks. I claim that attrition implied in settler colonialism's logic of elimination is a territorial project demonstrated in place‐based elimination and gendered embodied elimination.
Myelin water imaging to detect demyelination and remyelination and its validation in pathology
Authors: Laule Cornelia , Moore G.R. Wayne 
Published: October 2018

AbstractDamage to myelin is a key feature of multiple sclerosis (MS) pathology. Magnetic resonance imaging (MRI) has revolutionized our ability to detect and monitor MS pathology in vivo. Proton density, T1 and T2 can provide qualitative contrast weightings that yield superb in vivo visualization of central nervous system tissue and have proved invaluable as diagnostic and patient management tools in MS. However, standard clinical MR methods are not specific to the types of tissue damage they visualize, and they cannot detect subtle abnormalities in tissue that appears otherwise normal on conventional MRIs. Myelin water imaging is an MR method that provides in vivo measurement of myelin. Histological validation work in both human brain and spinal cord tissue demonstrates a strong correlation between myelin water and staining for myelin, validating myelin water as a marker for myelin. Myelin water varies throughout the brain and spinal cord in healthy controls, and shows good intra‐ and inter‐site reproducibility. MS plaques show variably decreased myelin water fraction, with older lesions demonstrating the greatest myelin loss. Longitudinal study of myelin water can provide insights into the dynamics of demyelination and remyelination in plaques. Normal appearing brain and spinal cord tissues show reduced myelin water, an abnormality which becomes progressively more evident over a timescale of years. Diffusely abnormal white matter, which is evident in 20%–25% of MS patients, also shows reduced myelin water both in vivo and postmortem, and appears to originate from a primary lipid abnormality with relative preservation of myelin proteins. Active research is ongoing in the quest to refine our ability to image myelin and its perturbations in MS and other disorders of the myelin sheath.
Group income and individual preferences for redistribution
Authors: Quattrociocchi Jeff 
Published: October 2018

AbstractThis paper empirically examines the relationship between group income and an individual's preferences for redistribution. First, I develop a theoretical framework where an individual's identity is strengthened by the status of their group. Then, utilizing data from the US General Social Survey, I find evidence that the average incomes of one's ethnic and religious groups are negatively correlated with one's preferences for redistribution. Controlling for household income and a number of other individual‐level characteristics and additional controls, I find that a standard deviation increase in the average income of one's social groups correlates to a weakening of an individual's preferences for redistribution by 7% to 8%. This result is robust to the inclusion of rich controls and alternate measures of group status as well as a number of robustness checks, such as sample restrictions and the use of additional data.