bluuebunny/crossref_metadata_2025_split huggingface dataset:
T helper cells modulate intestinal stem cell renewal and differentiation
Authors: Biton Moshe , Haber Adam L. , Beyaz Semir , Rogel Noga , Smillie Christopher , Shekhar Karthik , Schnell Alexandra , Chen Zuojia , Wu Chuan , Ordovas-Montanes Jose , Alvarez David , Herbst Rebecca H. , Tirosh Itay , Burgin Grace , Dionne Danielle , Xifaras Michael E. , Zhang Mei , Shalek Alex K. , Andrian Ulrich H. von , Graham Daniel B. , Rozenblatt-Rosen Orit , Shi Hai Ning , Kuchroo Vijay , Yilmaz Omer , Regev Aviv , Xavier Ramnik J. 
Published: November 2017

AbstractIn the small intestine, a cellular niche of diverse accessory cell types supports the rapid generation of mature epithelial cell types through self-renewal, proliferation, and differentiation of intestinal stem cells (ISCs). However, not much is known about interactions between immune cells and ISCs, and it is unclear if and how immune cell dynamics affect eventual ISC fate or the balance between self-renewal and differentiation. Here, we used single-cell RNA-seq (scRNA-Seq) of intestinal epithelial cells (IECs) to identify new mechanisms for ISC–immune cell interactions. Surprisingly, MHC class II (MHCII) is enriched in two distinct subsets of Lgr5+ crypt base columnar ISCs, which are also distinguished by higher proliferation rates. Using co-culture of T cells with intestinal organoids, cytokine stimulations, and in vivo mouse models, we confirm that CD4+ T helper (Th) cells communicate with ISCs and affect their differentiation, in a manner specific to the Th subtypes and their signature cytokines and dependent on MHCII expression by ISCs. Specific inducible knockout of MHCII in intestinal epithelial cells in mice in vivo results in expansion of the ISC pool. Mice lacking T cells have expanded ISC pools, whereas specific depletion of Treg cells in vivo results in substantial reduction of ISC numbers. Our findings show that interactions between Th cells and ISCs mediated via MHCII expressed in intestinal epithelial stem cells help orchestrate tissue-wide responses to external signals.
The Brain Dynamics Toolbox for Matlab
Authors: Heitmann Stewart , Aburn Matthew J , Breakspear Michael 
Published: November 2017

AbstractNonlinear dynamical systems are increasingly informing both theoretical and empirical branches of neuroscience. The Brain Dynamics Toolbox provides an interactive simulation platform for exploring such systems in MATLAB. It supports the major classes of differential equations that arise in computational neuroscience: Ordinary Differential Equations, Delay Differential Equations and Stochastic Differential Equations. The design of the graphical interface fosters intuitive exploration of the dynamics while still supporting scripted parameter explorations and large-scale simulations. Although the toolbox is intended for dynamical models in computational neuroscience, it can be applied to dynamical systems from any domain.
Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution
Authors: Kittelmann Sebastian , Buffry Alexandra D. , Franke Franziska A. , Almudi Isabel , Yoth Marianne , Sabaris Gonzalo , Couso Juan Pablo , Nunes Maria D. S. , Frankel Nicolás , Gómez-Skarmeta José Luis , Pueyo-Marques Jose , Arif Saad , McGregor Alistair P. 
Published: November 2017

AbstractConvergent phenotypic evolution is often caused by recurrent changes at particular nodes in the underlying gene regulatory networks (GRNs). The genes at such evolutionary ‘hotspots’ are thought to maximally affect the phenotype with minimal pleiotropic consequences. This has led to the suggestion that if a GRN is understood in sufficient detail, the path of evolution may be predictable. The repeated evolutionary loss of larval trichomes among Drosophila species is caused by the loss of shavenbaby (svb) expression. svb is also required for development of leg trichomes, but the evolutionary gain of trichomes in the ‘naked valley’ on T2 femurs in Drosophila melanogaster is caused by the loss of microRNA-92a (miR-92a) expression rather than changes in svb. We compared the expression and function of components between the larval and leg trichome GRNs to investigate why the genetic basis of trichome pattern evolution differs in these developmental contexts. We found key differences between the two networks in both the genes employed, and in the regulation and function of common genes. These differences in the GRNs reveal why mutations in svb are unlikely to contribute to leg trichome evolution and how instead miR-92a represents the key evolutionary switch in this context. Our work shows that variability in GRNs across different developmental contexts, as well as whether a morphological feature is lost versus gained, influence the nodes at which a GRN evolves to cause morphological change. Therefore, our findings have important implications for understanding the pathways and predictability of evolution.Author SummaryA major goal of biology is to identify the genetic cause of organismal diversity. Convergent evolution of traits is often caused by changes in the same genes – evolutionary ‘hotspots’. shavenbaby is a ‘hotspot’ for larval trichome loss in Drosophila, however microRNA-92a underlies the gain of leg trichomes. To understand this difference in the genetics of phenotypic evolution, we compared the expression and function of genes in the underlying regulatory networks. We found that the pathway of evolution is influenced by differences in gene regulatory network architecture in different developmental contexts, as well as by whether a trait is lost or gained. Therefore, hotspots in one context may not readily evolve in a different context. This has important implications for understanding the genetic basis of phenotypic change and the predictability of evolution.
Complementary, Semi-automated Methods for Creating Multi-dimensional, PEG-based Biomaterials
Authors: Brooks Elizabeth A. , Jansen Lauren E. , Gencoglu Maria F. , Yurkevicz Annali M. , Peyton Shelly R. 
Published: November 2017

ABSTRACTTunable biomaterials that mimic selected features of the extracellular matrix (ECM), such as its stiffness, protein composition, and dimensionality, are increasingly popular for studying how cells sense and respond to ECM cues. In the field, there exists a significant trade-off for how complex and how well these biomaterials represent thein vivomicroenvironment, versus how easy they are to make and how adaptable they are to automated fabrication techniques. To address this need to integrate more complex biomaterials design with high-throughput screening approaches, we present several methods to fabricate synthetic biomaterials in 96-well plates and demonstrate that they can be adapted to semi-automated liquid handling robotics. These platforms include 1) glass bottom plates with covalently attached ECM proteins, and 2) hydrogels with tunable stiffness and protein composition with either cells seeded on the surface, or 3) laden within the three-dimensional hydrogel matrix. This study includes proof-of-concept results demonstrating control over breast cancer cell line phenotypes via these ECM cues in a semi-automated fashion. We foresee the use of these methods as a mechanism to bridge the gap between high-throughput cell-matrix screening and engineered ECM-mimicking biomaterials.
Tracking wakefulness as it fades: micro-measures of Alertness
Authors: Jagannathan Sridhar R. , Nassar Alejandro E. , Jachs Barbara , Pustovaya Olga V. , Bareham Corinne A. , Bekinschtein Tristan A. 
Published: November 2017

AbstractA major problem in psychology and physiology experiments is drowsiness: around a third of participants show decreased wakefulness despite being instructed to stay alert. In some non-visual experiments participants keep their eyes closed throughout the task, thus promoting the occurrence of such periods of varying alertness. These wakefulness changes contribute to systematic noise in data and measures of interest. To account for this omnipresent problem in data acquisition we defined criteria and code to allow researchers to detect and control for varying alertness in electroencephalography (EEG) experiments. We first revise a visual-scoring method developed for detection and characterization of the sleep-onset process, and adapt the same for detection of alertness levels. Furthermore, we show the major issues preventing the practical use of this method, and overcome these issues by developing an automated method based on frequency and sleep graphoelements, which is capable of detecting micro variations in alertness. The validity of the automated method was verified by training and testing the algorithm using a dataset where participants are known to fall asleep. In addition, we tested generalizability by independent validation on another dataset. The methods developed constitute a unique tool to assess micro variations in levels of alertness and control trial-by-trial retrospectively or prospectively in every experiment performed with EEG in cognitive neuroscience.
Histone deacetylation promotes transcriptional silencing at facultative heterochromatin
Authors: Watts Beth Rosina , Wittmann Sina , Wery Maxime , Gautier Camille , Kus Krzysztof , Heo Dong-Hyuk , Kilchert Cornelia , Morillon Antonin , Vasiljeva Lidia 
Published: November 2017

AbstractIt is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains. Indeed, mutation of class I/II HDACs leads to increased transcription of meiotic genes and accumulation of their mRNAs. Mechanistic dissection of the pho1 gene where, in response to phosphate, transient facultative heterochromatin is established by overlapping lncRNA transcription shows that the Clr3 HDAC contributes to silencing independently of SHREC, but in an lncRNA-dependent manner. We propose that HDACs promote facultative heterochromatin by establishing alternative transcriptional silencing.
Behavioural insights into benefits claimants’ training
Authors: Gloster Rosie , Buzzeo Jonathan , Cox Annette , Bertram Christine , Tassinari Arianna , Schmidtke Kelly Ann , Vlaev Ivo 
Published: November 2017

PurposeThe purpose of this paper is to explore the behavioural determinants of work-related benefits claimants’ training behaviours and to suggest ways to improve claimants’ compliance with training referrals.Design/methodology/approachQualitative interviews were conducted with 20 Jobcentre Plus staff and training providers, and 60 claimants. Claimants were sampled based on whether or not they had been mandated to training and whether or not they subsequently participated. Along with general findings, differences between these groups are highlighted.FindingsClaimants’ behaviours are affected by their capabilities, opportunities, and motivations in interrelated ways. Training programmes should appreciate this to better ensure claimants’ completion of training programmes.Originality/valueWhilst past papers have largely examined a limited number of factors that affect claimants’ training behaviours, this report offers a synchronised evaluation of all the behavioural factors that affect claimants’ training behaviours.
AI empowered context-aware smart system for medication adherence
Authors: Wu Qiong , Zeng Zhiwei , Lin Jun , Chen Yiqiang 
Published: November 2017

Purpose
Poor medication adherence leads to high hospital admission rate and heavy amount of health-care cost. To cope with this problem, various electronic pillboxes have been proposed to improve the medication adherence rate. However, most of the existing electronic pillboxes use time-based reminders which may often lead to ineffective reminding if the reminders are triggered at inopportune moments, e.g. user is sleeping or eating.

Design/methodology/approach
In this paper, the authors propose an AI-empowered context-aware smart pillbox system. The pillbox system collects real-time sensor data from a smart home environment and analyzes the user’s contextual information through a computational abstract argumentation-based activity classifier.

Findings
Based on user’s different contextual states, the smart pillbox will generate reminders at appropriate time and on appropriate devices.

Originality/value
This paper presents a novel context-aware smart pillbox system that uses argumentation-based activity recognition and reminder generation.
Complex crowdsourcing task allocation strategies employing supervised and reinforcement learning
Authors: Cui Lizhen , Zhao Xudong , Liu Lei , Yu Han , Miao Yuan 
Published: November 2017

Purpose
Allocation of complex crowdsourcing tasks, which typically include heterogeneous attributes such as value, difficulty, skill required, effort required and deadline, is still a challenging open problem. In recent years, agent-based crowdsourcing approaches focusing on recommendations or incentives have emerged to dynamically match workers with diverse characteristics to tasks to achieve high collective productivity. However, existing approaches are mostly designed based on expert knowledge grounded in well-established theoretical frameworks. They often fail to leverage on user-generated data to capture the complex interaction of crowdsourcing participants’ behaviours. This paper aims to address this challenge.

Design/methodology/approach
The paper proposes a policy network plus reputation network (PNRN) approach which combines supervised learning and reinforcement learning to imitate human task allocation strategies which beat artificial intelligence strategies in this large-scale empirical study. The proposed approach incorporates a policy network for the selection of task allocation strategies and a reputation network for calculating the trends of worker reputation fluctuations. Then, by iteratively applying the policy network and reputation network, a multi-round allocation strategy is proposed.

Findings
PNRN has been trained and evaluated using a large-scale real human task allocation strategy data set derived from the Agile Manager game with close to 500,000 decision records from 1,144 players in over 9,000 game sessions. Extensive experiments demonstrate the validity and efficiency of computational complex crowdsourcing task allocation strategy learned from human participants.

Originality/value
The paper can give a better task allocation strategy in the crowdsourcing systems.
A study on MCIN model in intelligent clothing industry
Authors: Nan Yixuan , Liu Yi , Shen Jianping , Chai Yueting 
Published: November 2017

Purpose
This paper aims to study the material conscious information network (MCIN) to present new models of clothing products and persons and propose new crowd-designing patterns to reconstruct an improved supply–demand relationship in clothing industry.

Design/methodology/approach
This paper aims to study the MCIN to present new models of clothing products and persons and propose new crowd-designing patterns to reconstruct an improved supply–demand relationship in clothing industry.

Findings
At last, this paper implements a prototype system of novel e-commerce platform based on the CDCI to illustrate the effectiveness and soundness of the CDCI modeling.

Originality/value
Different from most related works just focusing on the physiology dimension in the matching of customer and clothing, this paper proposes that the dimension of physiology, character, knowledge and experience should be synthetically considered.
Town centre cooperation: changing perception of property owners
Authors: Håkansson Johan , Lagin Madelen , Wennström Johanna 
Published: November 2017

Purpose
The purpose of this paper is to investigate if, and how, different stakeholders perceive property owners (PO) have changed their activities in a town centre after increased competition, and if this has led to a different perception of the PO’ stakeholder group.

Design/methodology/approach
A comparative follow-up case study is conducted through semi-structured interviews on changes in the town centre management (TCM) stakeholders’ perceptions of the role, benefit, and contribution of PO. The interviews are carried out before and after the establishment of a big-box retailer, which makes it possible to analyse possible changes in the perceptions in relation to the overall role of the PO when retail competition increases.

Findings
A limited number of PO and local authorities have started working more strategically and proactively by creating a time-restricted alliance that goes beyond the work of the TCM organisation. Although the activities of the PO have increased, this is not fully understood by everyone in the town centre, especially the retailers.

Research limitations/implications
In comparison with other studies, this study clearly indicates that the property owner plays a key strategic role in enabling town centre development. This role is broader than what the original TCM literature suggests and is based on the aspects of resource coordination and distribution.

Practical implications
In order to create the opportunity to develop a town centre in the long run, it is of strategic importance that the PO are in agreement with the development plans. In addition, it is necessary to consider those members who should be part of the strategic alliance.

Originality/value
By conducting a comparative follow-up case study, the authors are able to contribute with a deeper understanding of how stakeholders’ perceptions change over time. The authors extend the current literature by showing that the PO are a key stakeholder due to their organisational resources and their ability to facilitate town centre development.
Idea-generation communities: when should host firms intervene?
Authors: Ponnamma Divakaran Pradeep Kumar 
Published: November 2017

Purpose
The purpose of this paper is to explore when, why and to what extent firms should intervene in firm-hosted idea-generation communities, and to develop a framework for firm-intervention.

Design/methodology/approach
A single case-study is conducted in a highly successful firm-hosted idea-generation community called Dell IdeaStorm, whereby the netnographic approach is applied.

Findings
The findings indicate that, overall, firm-participation is minimal and passive, and varies according to the three stages of the idea lifecycle in the community, such as ideation stage – here firm-participation is limited to acknowledgement of new ideas, checking for redundancy, managing search tool and profanity filtering; discussion and development stage – here firm-participation is more active by providing feedback and clarification when needed, troubleshooting, asking for additional input on an idea, etc.; and completion stage – here a firm intervenes to screen and select the most promising ideas for implementation and also provides status updates on ideas.

Originality/value
This study contributes by developing a new framework for firm-participation, which is useful for the early diagnosis of community issues in idea generation. The framework is also a tactical tool which can be used to guide community managers in selecting the correct moderation approach, depending on the specific stage in the idea lifecycle.
Managing brand identity strategy: how professional football wins the game
Authors: Blumrodt Jens , Huang-Horowitz Nell C. 
Published: November 2017

Purpose
While research on brand identity is abundant, an area that is less explored is whether an organisation’s communication about itself directly translates to key stakeholders’ perception of that organisation. The purpose of this study is to explore whether certain Web-based communication strategies are more effective in aligning organisations’ communicated identity (CI) with their perceived identity (PI).

Design/methodology/approach
This study uses a mixed-methods design in the context of professional football league clubs. The CI was determined through an analysis of the clubs websites (n = 20), and PI was investigated through interviews with spectators (n = 244). Both CI and PI were operationalised using image categories.

Findings
Three main strategies of identity communication are observed. The results show that the strategy focusing on product-related categories leads to discrepancy. WBC with non-product related categories and benefits shows better CI-PI alignment. The study also found that clubs emphasising their CI as local, engaged in community and family-friendly are more likely to achieve greater alignment.

Practical implications
The quality of the brand identity depends on the discrepancy or congruence of brand image categories. Best practices are observed for brands having largely updated WBC of all categories, attitudes and engagement in the community.

Originality/value
The interrelated nature of brand identity communication and perception makes it necessary to empirically test how the two may be bridged with one. The developed concepts provide insight into which strategies better contribute to a consistent, coherent brand identity.
Expanding the scope of affect: taxonomy construction for emotions, tones, and associations
Authors: Spiteri Louise , Pecoskie Jen 
Published: November 2017

PurposeThe purpose of this paper is to provide an examination of emotional experiences, particularly how they are situated in the readers’ advisory (RA) literature and the literatures from a variety of outside disciplines in order to create taxonomies of affect from this context.Design/methodology/approachThe approach of this study is twofold. First, this work reviews the literature on affect in Library and Information Science (LIS) and ancillary disciplines in order to understand the definition of affect. Second, using extant taxonomies and resources noted from the literature review, taxonomies are created for three aspects of affect: emotions, tones, and associations.FindingsThis paper contextualises and defines affect for the LIS discipline. Further, a result of the work is the creation of three taxonomies through an RA lens by which affective experiences can be classified. The resulting three taxonomies focus on emotion, tone, and associations.Practical implicationsThe taxonomies of emotion, tone, and associations can be applied to the practical work of bibliographic description, helping to expand access and organisation through an affective lens. These taxonomies of affect could be used by readers’ advisors to help readers describe their desired reading experiences. As the taxonomies have been constructed from an RA perspective, and can be applied to the RA literature, they could expand the understanding of RA theory, especially that of appeal.Originality/valueThis study furthers the exploration of affect in LIS and provides tangible taxonomies of affect for the LIS discipline in an RA context, which have not been previously produced.