bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Cytoplasmic Interactions in the Collective Polarization of Tissues and its Interplay with Cellular Geometry
Authors: Shadkhoo Shahriar , Mani Madhav 
Published: March 2018

AbstractPlanar cell polarity (PCP), the ability of a tissue to polarize coherently over multicellular length scales, provides the directional information that guides a multitude of developmental processes at cellular and tissue levels. While it is manifest that cells utilize both intra-cellular and intercellular mechanisms, how they couple together to produce the collective response remains an active area of investigation. Exploring a phenomeno-logical reaction-diffusion model, we predict a crucial, and novel, role for cytoplasmic interactions in the large-scale correlations of cell polarities. We demonstrate that finite-range (i.e. nonlocal) cytoplasmic interactions are necessary and sufficient for the robust and long-range polarization of tissues — even in the absence of global cues — and are essential to the faithful detection of weak directional signals. Strikingly, our model re-capitulates an observed influence of anisotropic tissue geometries on the orientation of polarity. In order to facilitate a conversation between theory and experiments, we compare five distinct classes ofin silicomutants with experimental observations. Within this context, we propose quantitative measures that can guide the search for the participant molecular components, and the identification of their roles in the collective polarization of tissues.
Alanine tRNA translate environment into behavior inCaenorhabditis elegans
Authors: Fernandes De Abreu Diana Andrea , Salinas-Giegé Thalia , Drouard Laurence , Remy Jean-Jacques 
Published: March 2018

AbstractCaenorhabditis elegansnematodes produce and maintain imprints of attractive chemosensory cues to which they are exposed early in life. Early odor-exposure increases adult chemo-attraction to the same cues. Imprinting is transiently or stably inherited, depending on the number of exposed generations.We show here that the Alanine tRNA (UGC) plays a central role in regulatingC. eleganschemo-attraction. Naive worms fed on tRNAAla(UGC) purified from odor-experienced worms, acquire odor-specific imprints.Chemo-attractive responses require the tRNA-modifying Elongator complex sub-units 1 (elpc-1) and 3 (elpc-3) genes.elpc-3deletions impair chemo-attraction, which is fully restored by wild-type tRNAAla(UGC) feeding. A stably inherited decrease of odor-specific responses ensues from early odor-exposition ofelpc-1deletion mutants.tRNAAla(UGC) may adopt various chemical forms to mediate the cross-talk between innately-programmed and environment-directed chemo-attractive behavior.
TBtools - an integrative toolkit developed for interactive analyses of big biological data
Authors: Chen Chengjie , Chen Hao , Zhang Yi , Thomas Hannah R. , Frank Margaret H. , He Yehua , Xia Rui 
Published: March 2018

AbstractThe rapid development of high-throughput sequencing (HTS) techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 100 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools, with a new plotting engine (“JIGplot”) developed to maximum their interactive ability, which allows quick point-and-click modification to almost every graphic feature.TBtools is a platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer. It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.
Deep proteomic analysis of chicken erythropoiesis
Authors: Leduc Marjorie , Gautier Emilie-Fleur , Guillemin Anissa , Broussard Cédric , Salnot Virginie , Lacombe Catherine , Gandrillon Olivier , Guillonneau François , Mayeux Patrick 
Published: March 2018

AbstractIn contrast to mammalian erythroid cells that lost their nucleus at the end of the differentiation process, circulating chicken erythrocytes, like erythrocytes of most other non-mammalian vertebrates, are nucleated although their nucleus is believed to be transcriptionally silent. This major difference suggests that the erythroid differentiation process is likely to present both similarities and differences in mammals compared to other vertebrates. Since proteins are the major cellular effectors, analysis of the proteome is more prone to reflect true differences than analysis of the pattern of mRNA expression. We have previously reported the evolution of the proteome of human erythroid cells throughout their differentiation process. Here we report the analysis of the proteome of chicken erythroblasts during their terminal differentiation. We used the T2EC cellular model that allows to obtain homogenous populations of immature erythroblasts. Induction of their terminal differentiation led to their maturation and the possibility to obtain cells at different differentiation stages. Mass spectrometry analysis of these cell populations allowed the absolute quantification of 6167 proteins throughout the terminal differentiation process. Beside many proteins with similar expression patterns between chicken and human erythroblasts, like SLC4A1 (Band3), GATA1 or CD44, this analysis also revealed that other important proteins like Kit or other GATA transcription factors exhibit fully different patterns of expression.
Topovectorial mechanisms control the juxtamembrane proteolytic processing of Nrf1 to remove its N-terminal polypeptides during maturation of the CNC-bZIP factor
Authors: Xiang Yuancai , Halin Josefin , Fan Zhuo , Hu Shaofan , Wang Meng , Qiu Lu , Zhang Zhengwen , Mattjus Peter , Zhang Yiguo 
Published: March 2018

ABSTRACTThe topobiological behaviour of Nrf1 dictates its post-translational modification and its ability to transactivate target genes. Here, we have elucidated that topovectorial mechanisms control the juxtamembrane processing of Nrf1 on the cyto/nucleoplasmic side of endoplasmic reticulum (ER), whereupon it is cleaved and degraded to remove various lengths of its N-terminal domain (NTD, also refold into a UBL module) and acidic domain-1 (AD1) to yield multiple isoforms. Notably, an N-terminal ∼12.5-kDa polypeptide of Nrf1 arises from selective cleavage at an NHB2-adjoining region within NTD, whilst other longer UBL-containing isoforms may arise from proteolytic processing of the protein within AD1 around PEST1 and Neh2L degrons. The susceptibility of Nrf1 to proteolysis is determined by dynamic repositioning of potential UBL-adjacent degrons and cleavage sites from the ER lumen through p97-driven retrotranslocation and -independent pathways into the cyto/nucleoplasm. These repositioned degrons and cleavage sites within NTD and AD1 of Nrf1 are coming into theirbona fidefunctionality, thereby enabling it to be selectively processed by cytosolic DDI-1/2 proteases and also degradedvia26S proteasomes. The resultant proteolytic processing of Nrf1 gives rise to a mature ∼85-kDa CNC-bZIP transcription factor, which regulates transcriptional expression of cognate target genes. Furthermore, putative ubiquitination of Nrf1 is not a prerequisite necessary for involvement of p97 in the client processing. Overall, the regulated juxtamembrane proteolysis (RJP) of Nrf1, though occurring in close proximity to the ER, is distinctive from the mechanism that regulates the intramembrane proteolytic (RIP) processing of ATF6 and SREBP1.
Temperature-dependent estimation of Gibbs energies using an updated group contribution method
Authors: Du Bin , Zhang Zhen , Gruber Sharon , Yurkovich James T. , Palsson Bernhard O. , Zielinski Daniel C. 
Published: March 2018

AbstractReaction equilibrium constants determine the mass action ratios necessary to drive flux through metabolic pathways. Group contribution methods offer a way to estimate reaction equilibrium constants at wide coverage across the metabolic network. Here, we present an updated group contribution method with: 1) additional curated thermodynamic data used in fitting; and 2) capabilities to calculate equilibrium constants as a function of temperature. We first collected and curated aqueous thermo-dynamic data, including reaction equilibrium constants, enthalpies of reaction, Gibbs free energies of formation, enthalpies of formation, entropies change of formation of compounds, and proton and metal ion binding constants. We further estimated magnesium binding constants for 618 compounds using a linear regression model validated against measured data. Next, we formulated the calculation of equilibrium constants as a function of temperature and calculated necessary parameters, including standard entropy change of formation (ΔfS∘) and standard entropy change of reaction (ΔrS∘), using a model based on molecular properties. The median absolute errors in estimating ΔfS∘and ΔrS∘were 0.010 kJ/K/mol and 0.018 kJ/K/mol, respectively. The efforts here fill in gaps for thermodynamic calculations under various conditions, specifically different temperatures and metal ion concentrations. These results support the study of thermodynamic driving forces underlying the metabolic function of organisms living under diverse conditions.
Not so sterile after all: The endomicrobiome of plerocercoids of the cestode parasiteSchistocephalus solidusand changes to the microbiome of its Threespine Stickleback host
Authors: Hahn Megan , Dheilly Nolwenn 
Published: March 2018

AbstractDespite the growing recognition of the role of bacteria in animal biology, the microbiome of parasites remains largely unexplored. In particular, the presence of bacteria in tapeworms has never been investigated and parasites that exit the intestine would be considered sterile. We characterized for the first time the microbiome of a tapeworm.Schistocephalus solidusplerocercoids, collected from the body cavity of its stickleback host, were found to harbor a complex microbiome. The most abundant and the most prevalent bacteria wasPolynucleobacter sp.. In addition,S. solidusinfection was associated significant changes in the stickleback host gut microbiome with an increase in microbial load and changes in diversity and composition. Finally, the same bacteria were often found inS. solidusand the stomach and intestine of the corresponding hosts, a result that highlights the importance of characterizing the microbiome of host tissues and parasites from the same individuals to assess the potential for horizontal transmission of microbes. This study clearly emphasizes the need for further characterization of the microbiome of a broad range of parasites and for studies to determine the ecological, evolutionary and functional role that microbes play in host-parasite interactions.
Processing of Auditory Novelty Across the Cortical Hierarchy: An Intracranial Electrophysiology Study
Authors: Nourski Kirill V. , Steinschneider Mitchell , Rhone Ariane E. , Kawasaki Hiroto , Howard Matthew A. , Banks Matthew I. 
Published: March 2018

AbstractUnder the predictive coding hypothesis, specific spatiotemporal patterns of cortical activation are postulated to occur during sensory processing as expectations generate feedback predictions and prediction errors generate feedforward signals. Establishing experimental evidence for this information flow within cortical hierarchy has been difficult, especially in humans, due to spatial and temporal limitations of non-invasive measures of cortical activity. This study investigated cortical responses to auditory novelty using the local/global deviant paradigm, which engages the hierarchical network underlying auditory predictive coding over short (‘local deviance’; LD) and long (‘global deviance’; GD) time scales. Electrocorticographic responses to auditory stimuli were obtained in neurosurgical patients from regions of interest (ROIs) including auditory, auditory-related and prefrontal cortex. LD and GD effects were assayed in averaged evoked potential (AEP) and high gamma (70-150 Hz) signals, the former likely dominated by local synaptic currents and the latter largely reflecting local spiking activity. AEP LD effects were distributed across all ROIs, with greatest percentage of significant sites in core and non-core auditory cortex. High gamma LD effects were localized primarily to auditory cortex in the superior temporal plane and on the lateral surface of the superior temporal gyrus (STG). LD effects exhibited progressively longer latencies in core, non-core, auditory-related and prefrontal cortices, consistent with feedforward signaling. The spatial distribution of AEP GD effects overlapped that of LD effects, but high gamma GD effects were more restricted to non-core areas. High gamma GD effects had shortest latencies in STG and preceded AEP GD effects in most ROIs. This latency profile, along with the paucity of high gamma GD effects in the superior temporal plane, suggest that the STG plays a prominent role in initiating novelty detection signals over long time scales. Thus, the data demonstrate distinct patterns of information flow in human cortex associated with auditory novelty detection over multiple time scales.
The Bake Collective – making a delicious difference
Authors: Karmali Zoha A. , Galliara Meena , Srivastava Manjari 
Published: March 2018

Subject area
Social Entrepreneurship.

Study level/applicability
This case study can be used on the module on introduction to social entrepreneurship for postgraduate students specializing in Social Entrepreneurship or Social Work.

Case overview
This case explores the difference between social entrepreneurship and idealism. It captures the journey of Charlene Vaz and Kavita Gonsalves, two passionate young women, who formed “The Bake Collective” (TBC). Kavita and Charlene are both full-time employees, who spend their weekends and evenings running TBC and through bake sells raise funds for supporting social causes. The women have been able to get a teacher hired for differently abled children, provide water purifiers to victims of the Nepal earthquake, furnish a classroom in a school for less privileged children and provide teaching material for schools in over 400 villages in the State of Maharashtra in India. The case highlights the power of volunteering for a cause that can result in developing a social enterprise. It helps to unfold the steps undertaken to kick-start the cause as well as the risks involved in the start-up stage. It also discusses the measures that can be taken to mitigate the risks in the start-up phase and the ways by which social entrepreneurs can scale and grow their programme.

Expected learning outcomes
From this case, students will learn about the factors that lead to the germination of a social enterprise and identify characteristics of social entrepreneurs. They will be able to understand critical factors required to sustain start-up enterprises. The case will also enable students to explore systems and processes that need to be designed to sustain the start-up phase. Further, the case will help students to brainstorm on growth strategies for social enterprises.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 3: Entrepreneurship.
Preparing future-ready graduates through experiential entrepreneurship
Authors: de Villiers Scheepers Margarietha Johanna , Barnes Renee , Clements Michael , Stubbs Alix Jayne 
Published: March 2018

PurposeThe purpose of this paper is to propose an experiential entrepreneurship work-integrated learning (EE WIL) model recognising that the development of an entrepreneurial mindset enables graduates to manage their careers in uncertain labour markets. The model shows how students develop relationships with their professional community, and not only a few employers.Design/methodology/approachThe pedagogical underpinning of the conceptual model, attributes associated with the entrepreneurial mindset and relationships between the student, professional community and university are explained, and illustrated through a case study at the University of the Sunshine Coast.FindingsThe EE WIL model enables students to develop agency through structured engagement with a professional community, facilitating the development of bridging social capital. Bonding social capital can be developed through intense, sustained interaction between students and their professional community.Practical implicationsWIL curricula should be scaffolded and directed towards developing sustained interaction and information sharing, underpinned by professional community norms. This approach enables students to develop an aligned professional identity and emotional attachment to the professional community. The experiential development of an entrepreneurial mindset enables students to solve career challenges, by viewing these as opportunities. Professional communities and universities both share the responsibilities of preparing the future graduate workforce.Originality/valueThe conceptual model draws on effectual entrepreneurship pedagogy and contributes to the WIL literature, showing that an entrepreneurial mindset can be cultivated experientially through an intensive, emotional and authentic learning experience.
Perceived value of internship experience: a try before you leap
Authors: Bhattacharya Sonali , Neelam Netra 
Published: March 2018

Purpose
The purpose of this paper is to examine how internship value is manifested in the context of a business school. The authors have examined the internship experience in terms of experiential learning and employability. Specifically, the authors investigate the factors that determine internship at four phases: design, conduct, evaluation and feedback.

Design/methodology/approach
The authors have applied a mixed method approach. In all, 110 students of a busines school were first surveyed on their expectation, motivation and level of preparation through a self-administered questionnaire before internship. Based on the survey result, eight of these students were interviewed in details about internship expectations from industry, the selection process for internship, communications or exchanges between intern and companies prior to internship and perceived industry expectation from interns. At the next phase, authors used a qualitative research approach by conducting semi-structured, in-depth interviews with 14 interns and their mentors after internship period. They were interviewed on design, conduct, evaluation and feedback process of the internship. Interviews tried capture what kind of leader-member exchange led to satisfactory internship experience and outcome from view of both inter and mentor.

Findings
The authors find that at various stages of internship program quality of mentor – intern exchanges (as defined by leadership exchange theory), and task characteristics as indicated by autonomy, task variety, task significance and performance feedback determine intern’s performance. An intern’s performance is antecedent to an intern’s and a mentor’s satisfaction and overall internship value. The authors also found that intrinsic capability of intern such as critical thinking ability and learning orientation result in enhanced value of internship experience. The proposed models, postulate that at designing stage, lower the level of communication from employers, higher the feeling of ambiguity and lower the perceived internship value in terms of experiential learning and perceived employability. Feeling of ambiguity is moderated by existence of prior work experience of interns. At conduction stage, mentor-intern exchange is directly related to flexibility in structure of the program and inversely related to dependency on peer learning. Mentor-intern exchange also related to mentor and intern’s learning value. However, the learning value is moderated by learning orientation of the intern.

Originality/value
The authors have tried the summer internship experience from the perspective of interns and mentors. This is the uniqueness of the research.
Housing delivery to the low income in Botswana
Authors: Kampamba Johnson , Kachepa Simon , Nkwae Boipuso , Matlhogojane Ntombi Godiraone , Outule Tuelo 
Published: March 2018

Purpose
The purpose of this study is to evaluate the housing delivery to the low income through the Self Help Housing Agency (SHHA) in Gaborone, Botswana.

Design/methodology/approach
Data were collected through the use of questionnaire, interviews, records searches and observations using the mixed-method approach to establish why people sale houses. Proportionate and simple random sampling was used to obtain a sample size of 93 plots for both new SHHA areas and old SHHA areas at 90 per cent confidence level. For each plot, data pertaining to plot allocation, plot ownership, exchange of ownership over the years were collected.

Findings
The findings revealed that the programme has been hit by challenges emanating from the low-income group selling their houses to middle-income group which is predominant in the area thus leading to gentrification. It was also established that the number of sales in SHHA areas were increasing as evidenced from the transfers that were taking place. This could be influenced by the increasing demand for housing due to a growing population in Gaborone. The findings also revealed that demand is one of the determinants of rising prices, thus an incentive to the low-income group to sell their houses at higher prices.

Research limitations/implications
The implication of these findings is that the low income will be displaced and might become homeless in future thus creating an opportunity for illegal settlements to develop.

Originality/value
The study has provided a context in which housing delivery to the low-income group can be safe guarded.
Religious literacy for responding to violence and abuse involves the capacity to go beyond stereotypes
Authors: Crisp Beth R. , Epstein Sarah , Afrouz Rojan , Taket Ann 
Published: March 2018

Purpose
There is an increasing recognition that health and social care professionals require the knowledge and skills to negotiate religious beliefs and cultures but as yet there is little understanding as to what this entails. The purpose of this paper is to explore what religious literacy means in regard to protecting children from sexual assault in Australia’s Jewish community and Muslim women who experience domestic violence.

Design/methodology/approach
Drawing on two ongoing research studies, this paper provides an overview of the diverse perspectives found in the literature on child sexual assault in Jewish communities and Muslim women’s experiences and responses to domestic violence.

Findings
Individual and community attitudes and responses to child sexual assault and domestic violence do not fit stereotypes either within or beyond religious communities. Hence, educating for religious literacy needs to ensure stereotypes are recognised as undue simplifications of the truth, and failure to understand this can result in harm. Furthermore, religious literacy is important for health and social care workers if they are to effectively engage with the leadership of religious communities to change community attitudes.

Originality/value
This paper draws together common issues around the need for religious literacy when working with Jewish and Muslim communities in addressing issues of abuse and violence.