bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transit-amplifying cells coordinate changes in intestinal epithelial cell-type composition
Authors: Sanman Laura E. , Chen Ina W. , Bieber Jake M. , Steri Veronica , Hann Byron , Wu Lani F. , Altschuler Steven J. 
Published: November 2019

AbstractRenewing tissues have the remarkable ability to continually produce both proliferative progenitor and specialized differentiated cell-types. How are complex milieus of microenvironmental signals interpreted to coordinate tissue cell-type composition? Here, we develop a high-throughput approach that combines organoid technology and quantitative imaging to address this question in the context of the intestinal epithelium. Using this approach, we comprehensively survey enteroid responses to individual and paired perturbations to eight epithelial signaling pathways. We uncover culture conditions that enrich for specific cell-types, including Lgr5+ stem and enteroendocrine cells. We analyze interactions between perturbations and dissect mechanisms underlying an unexpected mutual antagonism between EGFR and IL-4 signals. Finally, we show that, across diverse perturbations, modulating proliferation of transit-amplifying cells also consistently changes the composition of differentiated secretory and absorptive cell-types. This property is conserved in vivo and can arise from differential amplification of secretory and absorptive progenitor cells. Taken together, the observations highlight an underappreciated role for transit-amplifying cells in which proliferation of these short-lived progenitors provides a lineage-based mechanism for tuning differentiated cell-type composition.
The flexible N-terminus of BchL protects its [4Fe-4S] cluster in oxygenic environments and autoinhibits activity
Authors: Corless Elliot , Saad Imran Syed Muhammad , Watkins Maxwell B. , Origanti Sofia , Bacik John-Paul , Kitelinger Robert , Soffe Mark , Danyal Karamatullah , Seefeldt Lance C. , Bennett Brian , Ando Nozomi , Antony Edwin 
Published: November 2019

AbstractThe dark-operative protochlorophyllide oxidoreductase (DPOR) enzyme contains two [4Fe-4S]- containing component proteins (BchL and BchNB) that assemble in an ATP-dependent fashion to coordinate electron transfer and reduction of protochlorophyllide to chlorophyllide. Photosynthesis generates an oxygenic environment that is non-optimal for [Fe-S] clusters and we here present an elegant evolutionarily conserved mechanism in BchL to protect its [4Fe-4S] cluster. We present a crystal structure of BchL in the nucleotide-free form with an ordered N-terminus that shields the [4Fe-4S] cluster at the docking interface between BchL and BchNB. Amino acid substitutions that perturb the shielding of the [4Fe-4S] cluster produce an unstable, but hyper-active enzyme complex, suggesting a role for the N-terminus in both auto-inhibition and enzyme stability. Upon ATP binding, a patch of amino acids, Asp-Phe-Asp (‘DFD patch’), situated at the mouth of the BchL ATP-binding pocket promotes inter-subunit cross stabilization of the two subunits and relieves the auto-inhibition by the N-terminus. A linked BchL dimer with one defective ATP-binding site does not support substrate reduction, illustrating that nucleotide binding to both subunits is a prerequisite for the inter-subunit cross stabilization. We propose that ATP-binding produces a conformational compaction of the BchL homodimer leading to a release of the flexible N-terminus from blocking the [4Fe-4S] cluster and promotes complex formation with BchNB to drive electron transfer. The auto-inhibitive feature and release mechanism appear unique to DPOR and is not found in the structurally similar nitrogenase.
Mesmerize: a dynamically adaptable user-friendly analysis platform for 2D & 3D calcium imaging data
Authors: Kolar Kushal , Dondorp Daniel , Zwiggelaar Jordi Cornelis , Høyer Jørgen , Chatzigeorgiou Marios 
Published: November 2019

AbstractCalcium imaging is an increasingly valuable technique for understanding neural circuits, neuroethology, and cellular mechanisms. The analysis of calcium imaging data presents challenges in image processing, data organization, analysis, and accessibility. Tools have been created to address these problems independently, however a comprehensive user-friendly package does not exist. Here we present “Mesmerize”, an efficient, expandable and user-friendly analysis platform, which uses a Findable, Accessible, Interoperable and Reproducible (FAIR) system to encapsulate the entire analysis process, from raw data to interactive visualizations for publication. Mesmerize provides a user-friendly graphical interface to state-of-the-art analysis methods for signal extraction & downstream analysis. We demonstrate the broad scientific scope of Mesmerize’s applications by analyzing neuronal datasets from mouse and a volumetric zebrafish dataset. We also applied contemporary time-series analysis techniques to analyze a novel dataset comprising neuronal, epidermal, and migratory mesenchymal cells of the protochordate Ciona intestinalis.
Detection of somatic structural variants from short-read next-generation sequencing data
Authors: Gong Tingting , Hayes Vanessa M , Chan Eva KF 
Published: November 2019

AbstractSomatic structural variants (SVs) play a significant role in cancer development and evolution, but are notoriously more difficult to detect than small variants from short-read next-generation sequencing (NGS) data. This is due to a combination of challenges attributed to the purity of tumour samples, tumour heterogeneity, limitations of short-read information from NGS, and sequence alignment ambiguities. In spite of active development of SV detection tools (callers) over the past few years, each method has inherent advantages and limitations. In this review, we highlight some of the important factors affecting somatic SV detection and compared the performance of eight commonly used SV callers. In particular, we focus on the extent of change in sensitivity and precision for detecting different SV types and size ranges from samples with differing variant allele frequencies and sequencing depths of coverage. We highlight the reasons for why some SV callers perform well in some settings but not others, allowing our evaluation findings to be extended beyond the eight SV callers examined in this paper. As the importance of large structural variants become increasingly recognised in cancer genomics, this paper provides a timely review on some of the most impactful factors influencing somatic SV detection and guidance on selecting an appropriate SV caller.
Phylogenetic reconstruction based on synteny block and gene adjacencies
Authors: Drillon Guénola , Champeimont Raphaël , Oteri Francesco , Fischer Gilles , Carbone Alessandra 
Published: November 2019

AbstractGene order can be used as an informative character to reconstruct phylogenetic relationships-between species independently from the local information present in gene/protein sequences.PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches.PhyChro performance isevaluatedon two datasets of 13 vertebrates and 21 yeast genomes by using up to 130 000 and 179 000 breakpoints respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared to other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in less than 15 min.AvailabilityPhyChro will be freely available under the BSD license after publicationContactalessandra.carbone@lip6.fr
Evolutionary branching of function-valued traits under constraints
Authors: Ito Hiroshi C. 
Published: November 2019

AbstractSome evolutionary traits are described by scalars and vectors, while others are described by continuous functions on spaces (e.g., shapes of organisms, resource allocation strategies between growth and reproduction along time, and effort allocation strategies for continuous resource distributions along resource property axes). The latter are called function-valued traits. This study develops conditions for candidate evolutionary branching points, referred to as CBP conditions, for function-valued traits under simple equality constraints, in the framework of adaptive dynamics theory (i.e., asexual reproduction and rare mutation are assumed). CBP conditions are composed of conditions for evolutionary singularity, strong convergence stability, and evolutionary instability. The CBP conditions for function-valued traits are derived by transforming the CBP conditions for vector traits into those for infinite-dimensional vector traits.
China’shukousystem and city economic growth: from the aspect of rural–urban migration
Authors: Zhang Kunling , Chen Chunlai , Ding Jian , Zhang Zhinan 
Published: November 2019

PurposeThe purpose of this paper is to evaluate the economic impacts of China’shukousystem and propose the possible direction for future reform.Design/methodology/approachThe study develops a framework to incorporate thehukousystem into the economic growth model. Using prefecture city-level panel data covering 241 cities over the period 2004–2016 and applying the fixed effects and instrumental variable regression techniques, the authors investigated empirically the impacts of thehukousystem on city economic growth.FindingsThe study provides three main findings. First, the city sector conditionally benefits from labour mobility deregulation that allows migrants to work in cities. Second, thehukousystem has different impacts on economic growth among cities with different sizes and administrative levels. Third, to offset the costs of providing exclusive public services to the migrants, the big or high-administrative-level cities can use their high-valuedhukouto attract the high-skilled migrants, but the small- or low-administrative-level cities do not have this advantage.Practical implicationsThis study suggests that the key for furtherhukousystem reform is how to deal with thehukou–welfare binding relationship.Originality/valueThe authors developed a theoretical framework and conducted an empirical analysis on the direct relationship between thehukousystem and economic growth to reveal the mechanism of how does thehukousystem influence the city economic growth and answer the question of why is thehukousystem reform so hard in China. The framework also sheds some lights on explaining the success and failure of thehukousystem reforms in the past 40 years.
The Buyout at Tru-Foods For You
Authors: Ronnie Linda 
Published: November 2019

Learning outcomes
Learning outcomes are as follows: to appreciate the people challenges imbedded in an acquisition; to assess and analyse the impact of an acquisition process; to propose appropriate strategies for managing an acquisition; to explore the advantages and disadvantages of mergers and acquisitions; to describe the main reasons for the failure of M&As.

Case overview/synopsis
Often mergers and acquisitions fail because of the inability to either manage or consider organisational and people management issues. It has also been acknowledged that during a process of extreme change or transition, such as a merger and acquisition (M&A), employees view the past as a time of safety and security with the future appearing as uncertain and confused. This teaching case study highlights these challenges and the change processes imbedded in an acquisition. The acquiring firm is Marshall Foods, a well-established branded continental distribution company with a strong emphasis on nutritional whole food products based in South Africa, and the target firm is Tru-Foods For You, a small Cape Town online company that sold natural and organic foods. The case study explores the challenges faced by the Tru-Foods For You owner and staff as a result of the acquisition process. The case describes the background to the acquisition, the processes during this phase and the resultant outcomes.

Complexity academic level
Business students who are studying at postgraduate or MBA level and executive short courses in strategy and change management.

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 11: Strategy.
The Pransky interview: Brian Carlisle, pioneer, robotics entrepreneur, President and Co-Founder of Precise Automation
Authors: Pransky Joanne 
Published: November 2019

Purpose
The following paper is a “Q&A interview” conducted by Joanne Pransky of Industrial Robot Journal as a method to impart the combined technological, business and personal experience of a prominent, robotic industry engineer-turned entrepreneur regarding his pioneering efforts in the industrial robot industry and the commercialization and challenges of bringing robotic inventions to market. This paper aims to discuss these issues.

Design/methodology/approach
The interviewee is Brian Carlisle, President and Co-founder of Precise Automation, a robot manufacturer that specializes in collaborative robots. Carlisle discusses the highlights of his 40-year career that led to groundbreaking innovations in small parts assembly and handling robots, along with some of the challenges. He also shares his thoughts on the future of the industry.

Findings
Brian Carlisle received his BS and MS degrees in Mechanical Engineering from Stanford University. After Stanford, Carlisle and colleague Dr Bruce Shimano worked for Vicarm, a three-person company started by robotics pioneer Victor Scheinman. Vicarm was sold to Unimation and Carlisle became Unimation’s Director of R&D where he and his team developed the PUMA™ series of electric robots and grew sales from $0 to $40m in five years. In 1983, Carlisle and Shimano co-founded Adept Technology and as its CEO for 20 years, Carlisle grew Adept to over $100m in robot sales. In 2004, Carlisle co-founded with Shimano, Precise Automation, and is the President and CEO.

Originality/value
Brian Carlisle is a pioneer of the small parts assembly and handling robot. He was one of the key members of the team that developed the PUMA™ robot for Unimation. The PUMA™ robot was the watershed product that launched the assembly robot business in the USA and Europe. At Adept, he led the design of the first Direct Drive SCARA Robot and under his helm, Precise Automation introduced the first commercially available collaborative robots. Carlisle was President of the Robotic Industries Association for three years, is the recipient of the Joseph Engelberger Award for Leadership in Robotics, and an elected IEEE Fellow. He has served on the Board of the National Coalition for Advanced Manufacturing, the Boards of the National Center for Manufacturing Science, the Automation Forum of NEMA and is a founding member of the National Electronics Manufacturing Initiative. He holds multiple patents for robot designs.
Evaluating complex transformation
Authors: Best Allan , Ong Narelle , Cooper Penny , Davison Carolyn , Coatta Katherine , Berland Alex , Herbert Carol , Mitton Craig , Millar John , Reichert Stephen , Cano Allison 
Published: November 2019

Purpose
The purpose of this paper is to present a detailed case study of the evaluation strategies of a complex, multi-faceted response to a public health emergency: drug-related overdose deaths. It sets out the challenges of evaluating such a complex response and how they were overcome. It provides a pragmatic example of the rationale and issues faced to address the what, the why and particularly the how of the evaluation.

Design/methodology/approach
The case study overviews British Columbia’s Provincial Response to the Overdose Public Health Emergency, and the aims and scope of its evaluation. It then outlines the conceptual approach taken to the evaluation, setting out key methodological challenges in evaluating large-scale, multi-level, multisectoral change.

Findings
The evaluation is developmental and summative, utilization focused and system informed. Defining the scope of the evaluation required a strong level of engagement with government leads, grantees and other evaluation stakeholders. Mixed method evaluation will be used to capture the complex pattern of relationships that have informed the overdose response. Working alongside people with drug use experience to both plan and inform the evaluation is critical to its success.

Originality/value
This case study builds on a growing literature on evaluating large-scale and complex service transformation, providing a practical example of this.
Making sense of external partnerships
Authors: Sahlin Susanne 
Published: November 2019

Purpose
The purpose of this paper is to examine principals’ sense-making of a school–university collaboration taking an institutional perspective on organizational change. The study’s context involves three schools in a collaboration focusing on leadership and school improvement with one university.

Design/methodology/approach
The study draws on findings from a qualitative case study that examined principals’ sense-making of this type of school–university collaboration. Data were collected over three years and consisted of semistructured interviews, meeting notes, field observations, field notes and document analysis. A qualitative content analysis was performed using the Atlas.ti 6.2 software tool.

Findings
The findings showed that mattering sense-making for the principals in this collaboration is related to the cultivation of collective participation and responsibility, the development of trust and improvement culture among actors, and the sense of moving towards research-based and collaborative learning-oriented practices in their schools.

Research limitations/implications
This study encountered several limitations that need to be addressed and recognized. First, the small number of cases in this multiple case study, as well as the specific social context, limits the possibilities for the generalization of the findings. Second, the study was not independently selected and the findings and analyses were linked to national and local contexts, which can be seen as a limitation and a strength. Nevertheless, this study provides in-depth information about the principals’ experiences and constructions of meaning as they helped lead a school–university collaboration in their schools. Finally, although the sample was small and not representative, the findings provided useful insights into and examples of how principals understand and interpret a school–university partnership in their schools’ improvement processes.

Originality/value
The findings provide an elaborated illustration of how intentional efforts to collaborate and develop the schools in a school–university partnership may affect the regulative, normative and cultural–cognitive aspects in schools.
Presenting the model in improving maintenance and excellence in organizational culture and reliability in Iran tile and ceramic industries
Authors: Pezeshkian Alireza , Hamidi Naser 
Published: November 2019

Purpose
In order to increase productivity and create added value in ceramic and tile industries of Iran, the role of physical assets including machinery, equipment and utilities is very important in these industries, and management of those take an important role. Organizational culture and its role in physical asset management implementation are very important in the Iran ceramic and tile industries. In these industries, there is a secret force called culture, which must be changed if the organization wants to grow up and improve physical assets management. The purpose of this paper is to identify organizational cultural, technical and reliability variables and structure of these variables in form of a combined structural model.

Design/methodology/approach
In order to present a structural combination model, a development model type, the mixed research method is used, and expert’s comments are also used. This model was implemented at Apadana Ceram Company, and its results, in comparison with previous models on physical assets, have shown that consideration of four culture elements can be of great help to reach an optimal point in maintenance and excellence.

Findings
In this paper, analysis of previous research studies, project documents and expert’s opinions in ceramic and tile industries have been used. In the presented model, special attention has been paid to organizational culture and its four elements including values, patterns, rituals and procedures and cultural infrastructure in order to achieve excellence and reach an optimal point in maintenance. Also, governing structure between organizational culture and technical and reliability variables was nominated, which could help companies in physical asset management. Furthermore, eight components of change management were expressed, which are important in order to implement this model.

Originality/value
This model with special consideration of four culture elements can be of great help to industries to reach an optimal point in maintenance and excellence.
Assessing the information waste in maintenance management processes
Authors: Marttonen-Arola Salla , Baglee David 
Published: November 2019

Purpose
Due to recent technological developments, many maintenance managers become overwhelmed by the vast amount of data available to support their decision making. The purpose of this paper is to discuss identifying and eliminating waste in information management processes through a value stream mapping (VSM)-based method.

Design/methodology/approach
A theoretical framework is constructed based upon a review of the previous academic literature. The application of the framework is demonstrated with an empirical case example of a maintenance information management process within a food manufacturing company.

Findings
The paper highlights existing examples of applying VSM in information management; however, the knowledge is fragmented and has not been extensively applied in a maintenance context. The case example shows that the suggested process offers a feasible method of mapping and evaluating the inherent waste in information management processes.

Originality/value
The paper summarizes the existing body of knowledge on lean information management in maintenance, and presents a theoretical framework on how VSM can be applied in the context. An empirical example is provided to show the method applied to a real industry case. The results will illustrate how the framework can support companies in identifying the waste and development potential in their maintenance information management.