bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resistance to malaria through structural variation of red blood cell invasion receptors
Authors: Leffler Ellen M. , Band Gavin , Busby George B.J. , Kivinen Katja , Si Le Quang , Clarke Geraldine M. , Bojang Kalifa A. , Conway David J. , Jallow Muminatou , Sisay-Joof Fatoumatta , Bougouma Edith C. , Mangano Valentina D. , Modiano David , Sirima Sodiomon B. , Achidi Eric , Apinjoh Tobias O. , Marsh Kevin , Ndila Carolyne M. , Peshu Norbert , Williams Thomas N. , Drakeley Chris , Manjurano Alphaxard , Reyburn Hugh , Riley Eleanor , Kachala David , Molyneux Malcolm , Nyirongo Vysaul , Taylor Terrie , Thornton Nicole , Tilley Louise , Grimsley Shane , Drury Eleanor , Stalker Jim , Cornelius Victoria , Hubbart Christina , Jeffreys Anna E. , Rowlands Kate , Rockett Kirk A. , Spencer Chris C.A. , Kwiatkowski Dominic P. ,   Malaria Genomic Epidemiology Network
Published: October 2016

AbstractPlasmodium falciparuminvades human red blood cells by a series of interactions between host and parasite surface proteins. Here we analyse whole genome sequence data from worldwide human populations, including 765 new genomes from across sub-Saharan Africa, and identify a diverse array of large copy number variants affecting the host invasion receptor genesGYPAandGYPB. We find that a nearby reported association with severe malaria is explained by a complex structural variant that involves the loss ofGYPBand gain of two hybrid genes, each with a GYPB extracellular domain and GYPA intracellular domain. This variant reduces the risk of severe malaria by 40% and has recently risen in frequency in parts of Kenya. We show that the structural variant encodes the Dantu blood group antigen, and therefore a serologically distinct red cell phenotype. These findings demonstrate that structural variation of red blood cell invasion receptors is associated with natural resistance toP. falciparummalaria.
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
Authors: Stein-O’Brien Genevieve L , Carey Jacob L , Lee Wai-shing , Considine Michael , Favorov Alexander V , Flam Emily , Guo Theresa , Li Sijia , Marchionni Luigi , Sherman Thomas , Sivy Shawn , Gaykalova Daria A , McKay Ronald D , Ochs Michael F , Colantuoni Carlo , Fertig Elana J 
Published: October 2016

AbstractSummaryNon-negative Matrix Factorization (NMF) algorithms associate gene expression with biological processes (e.g., time-course dynamics or disease subtypes). Compared with univariate associations, the relative weights of NMF solutions can obscure biomarkers. Therefore, we developed a novel PatternMarkers statistic to extract genes for biological validation and enhanced visualization of NMF results. Finding novel and unbiased gene markers with PatternMarkers requires whole-genome data. However, NMF algorithms typically do not converge for the tens of thousands of genes in genome-wide profiling. Therefore, we also developed Genome-Wide CoGAPS Analysis in Parallel Sets (GWCoGAPS), the first robust whole genome Bayesian NMF using the sparse, MCMC algorithm, CoGAPS. This software contains analytic and visualization tools including a Shiny web application, patternMatcher, which are generalized for any NMF. Using these tools, we find granular brain-region and cell-type specific signatures with corresponding biomarkers in GTex data, illustrating GWCoGAPS and patternMarkers ascertainment of data-driven biomarkers from whole-genome data.AvailabilityPatternMarkers & GWCoGAPS are in the CoGAPS Bioconductor package (3.5) under the GPL license.Contactgsteinobrien@jhmi.edu;ccolantu@jhmi.edu;ejfertig@jhmi.edu
A simple molecular mechanism explains multiple patterns of cell-size regulation
Authors: Delarue Morgan , Weissman Daniel , Hallatschek Oskar 
Published: October 2016

AbstractIncreasingly accurate and massive data have recently shed light on the fundamental question of how cells maintain a stable size trajectory as they progress through the cell cycle. Microbes seem to use strategies ranging from a pure sizer, where the end of a given phase is triggered when the cell reaches a critical size, to pure adder, where the cell adds a constant size during a phase. Yet the biological origins of the observed spectrum of behavior remain elusive. We analyze a molecular size-control mechanism, based on experimental data from the yeastS. cerevisiae, that gives rise to behaviors smoothly interpolating between adder and sizer. The size-control is obtained from the titration of a repressor protein by an activator protein that accumulates more rapidly with increasing cell size. Strikingly, the size-control is composed of two different regimes: for small initial cell size, the size-control is a sizer, whereas for larger initial cell size, is is an imperfect adder. Our model thus indicates that the adder and critical size behaviors may just be different dynamical regimes of a single simple biophysical mechanism.
Quantitative Modeling and Automated Analysis of Meiotic Recombination
Authors: White Martin A. , Wang Shunxin , Zhang Liangran , Kleckner Nancy 
Published: October 2016

AbstractMany morphological features, in both physical and biological systems, exhibit spatial patterns that are specifically characterized by a tendency to occur with even spacing (in one, two or three dimensions). The positions of crossover (CO) recombination events along meiotic chromosomes provides an interesting biological example of such an effect (1–3). In general, mechanisms that explain such patterns may (a) be mechanically-based, (b) occur by a reaction-diffusion mechanism in which macroscopic mechanical effects are irrelevant, or (c) involve a combination of both types of effects. We have proposed that meiotic CO patterns arise by a mechanical mechanism, have developed mathematical expressions for such a process based on a particular physical system with analogous properties (the so-called “beam-film model”), and have shown that the beam-film model can very accurately explain experimental CO patterns as a function of the values of specific defined parameters (4–7). Importantly, the mathematical expressions of the beam-film model can apply quite generally to any mechanism, whether it involves mechanical components or not, as long as its logic and component features correspond to those of the beam-film system (3; below). Furthermore, via its various parameters, the beam-film model discretizes the patterning process into specific components. Thus, the model can be used to explore the theoretically predicted effects of various types of changes in the patterning process. Such predictions can expand detailed understanding of the bases for various biological effects (e.g. 2, 5). We present here a new MATLAB program that implements the mathematical expressions of the beam-film model with increased robustness and accessibility as compared to programs presented previously. As in previous versions, the presented program permits both: (i) simulation of predicted CO positions along chromosomes of a test population; and (ii) easy analysis of CO positions, both for experimental data sets and for data sets resulting from simulations. The goal of the current presentation is to make these approaches more readily accessible to a wider audience of researchers. Also, the program is easily modified, and we encourage interested users to make changes to suit their specific needs. A link to the program is available on the Kleckner laboratory web site:http://projects.iq.harvard.edu/kleckner_lab.
A better career environment for women: developing a blueprint for individuals and organisations
Authors: Holton Viki , Dent Fiona Elsa 
Published: October 2016

Purpose
The purpose of this paper is to explore the findings from empirical research conducted with women managers about their careers and to propose a template or blueprint for how individuals and organisations might create a better career environment for women.

Design/methodology/approach
This paper draws on a research study that included interviews with 20 senior women managers from a range of sectors and countries and a self-completion survey questionnaire completed by 1,402 women.

Findings
The paper illustrates the difficulties that women continue to face in the workplace and how terms such as leadership, management and team leader may be gender biased. There is a need for employers and for individuals to consider a variety of different approaches to help create a more positive career environment for women.

Research limitations/implications
The findings have implications for career development structures and talent management processes within organisations. They also would be useful for professional associations.

Practical implications
The template proposed offers a useful guide to help organisations reflect on possible gender bias in career development structures.

Originality/value
This paper adds to the understanding of the issues that women managers face and highlight the practical changes employers could make to help address these issues.
Exploring the value co-creation process on guided tours (the ‘AIM-model’) and the experience-centric management approach
Authors: Zátori Anita 
Published: October 2016

PurposeThe purpose of the paper was to explore the influence of the experience-centric approach and the concept of co-creation on service design and provision and to analyze the process of on-site experience co-creation between provider and consumer, particularly, how tour providers and tour guides enhance and support the process of co-creation.Design/methodology/approachThe study reviews the literature on experience-centric approach and value co-creation, discusses personal resources and experience-centric service design as resources for co-creation. It analyzes primary data from 33 interviews and 28 observations of 11 sightseeing tour providers.FindingsThe methods and tools of tour providers’ service design were explored and evaluated whether they fit the criteria of the concept of co-creation and experience-centric approach. The findings show that small-group tour providers use the concept of co-creation to the biggest extent, followed by alternative tour providers. The study also analyzed what types of service designs support a co-creative service provision. Three steps were identified as steps to support and realize experience and value co-creation from the side of the service provider. Based on the empirical results, the attention-involve-make discover (AIM) model was created, which proposes that the process of value and experience co-creation happens by provoking attention, by engaging and involving and, finally, by making consumers to discover.Originality/valueThe originality of the paper lies in the creation of the AIM-model illustrating the on-site co-creation process in the context of guided tours, which can further be tested in other fields and areas.
Reframing “building back better” for post-disaster housing design: a community perspective
Authors: Rahmayati Yenny 
Published: October 2016

Purpose
This study aims to reframe the common concept of post-disaster reconstruction “building back better”, especially in the context of post-disaster housing design.

Design/methodology/approach
An Aceh post-tsunami housing reconstruction project is used as a case study with qualitative methodology through in-depth interviews of selected respondents.

Findings
The study findings have shown that the term “building back better” is not a familiar term for housing recipients. Whichever different personal background post-disaster survivors come from, whether they are housewife, civil servant, fisherman, university student, businessman or a professional, none have ever heard this phrase. All found it hard to understand the term. This study argues that the “building back better” concept is good in policy but not working in practice. As a result, housing recipients not only were dissatisfied with their new houses but also found that the new housing configurations profoundly altered their traditional way of life. In light of these findings, the paper argues that the concept of “building back better” needs to be reframed to take account of the cultural individual and communal needs and wants of post-disaster survivors.

Research limitations/implications
This study discusses only one aspect of post-disaster reconstruction that is the design of housing reconstruction.

Practical implications
Results from this study provide a practical contribution for reconstruction actors especially designers, architects and planners. It helps them to reconsider the common concepts they have used for post-disaster reconstruction processes particularly in designing housing reconstruction projects.

Originality/value
This study focuses on the question of how tsunami survivors in Aceh reacted to the design of their new post-tsunami houses and what they had done themselves to make their homes a better and nicer place to live within their own cultural needs. This study also sought to understand what motivated the opinions the respondents had about the design of housing reconstruction after the tsunami in Aceh generally. In addition, the study investigated whether survivors knew the phrase and the credo of “building back better” in a post-disaster context.
Autonomous evacuation and local community
Authors: Kakimoto Ryuji , Yamada Fumihiko 
Published: October 2016

Purpose
The Aso area of Kumamoto Prefecture and the western part of Oita Prefecture in Japan experienced heavy rainfall from midnight until morning on 12 July 2012. Flooding and landslides caused by this torrential rain killed 31 people and injured 11. This paper aims to analyze a time series of flood risk perception and evacuation behavior, and to identify factors that promote effective autonomous evacuation.

Design/methodology/approach
A time series of flood risk perception and evacuation behavior following the 2012 flood was developed and systematically analyzed. Differences between the data sets (compiled from survey data) for the evacuated group and the non-evacuated group were statistically evaluated. Then, an evacuation behavior model was developed to simulate which households would be likely to evacuate in different scenarios. The relationship between disaster prevention and activities of a local community were also statistically assessed.

Findings
This study concludes that an assessment of river conditions and evacuation advice from fellow local community members are the factors that most strongly influence and promote autonomous evacuation. This study also revealed that the everyday activities of a local community have the potential to foster effective disaster prevention and emergency responses if they promote the building of relationships between community members.

Originality/value
The research focused on actual decision-making and autonomous evacuation behavior. Whereas previous studies were limited to the analysis of activities of disaster prevention on a normal day, this study proved that the usual activity level in local community activities and relationships significantly affected evacuation behavior.
An international comparative analysis of local hazard mitigation plan evaluation for flood
Authors: Kim Hwayoung , Kakimoto Ryuji 
Published: October 2016

Purpose
This research aims to identify the qualitative differences between local hazard mitigation plan (LHMP) of the developing country when compared to those of developed countries. It also seeks to demonstrate the relative importance of public private partnership and the need for PPs to be integrated into LHMP because they help to create strong LHMP, thereby making communities will become more resilient to not only floods but also other natural disasters. It focuses on the components of hazard mitigation from a developed country perspective and how these influence the contents/focus of the LHMP especially when compared to those of a developing country.

Design/methodology/approach
Based on official information such as population, climate and major threat that has faced, research sites were selected. Each LHMP can be downloaded from the official city websites, except Korea. Through plan evacuation protocols the LHMP for each city – USA (Baltimore), Japan (Kumamoto) and Korea (Pohang) – were assessed three times by the research team. Plans were evaluated using a plan coding evacuation process.

Findings
The LHMP of the developing country did not contain maps illustrating to the people who are exposed to flood and evacuation routes and who are vulnerable (both economically and physically), when compared with the developed countries plan. However, quicker response because of simple political hierarchy can be possible in Japan and Korea when compared to the USA, which has three different tiers of political governments – federal, State and Local government – though Korea is a developing country.

Originality/value
In recent times, pre-disaster response, which is a proactive approach to natural disasters, is an emerging issue rather than post disaster response because of sustainable and resilient ideas of the locals that have repeatedly suffered from natural hazards. This study compares LHMPs of each country to better understand strengths and weakness, as well as to identify strategies that will enhance the quality of mitigation plan for the developed country and developing country. It is hoped that this study will inform and augment existing literature by assisting underdeveloped and developing countries suffering from floods with the preparation of their LHMPs based on the suggestion of this research.
Alternative dispute resolution in Palestine: the myth and dilemma of construction mediation
Authors: Besaiso Haytham , Fenn Peter , Emsley Margaret 
Published: October 2016

Purpose
This paper aims to investigate the use of alternative dispute resolution (ADR) techniques in the Palestinian construction industry. It also seeks to identify some of the drivers and barriers to the greater use of particular ADR techniques.

Design/methodology/approach
In this study, 12 semi-structured in-depth interviews were conducted with senior ADR practitioners comprising nine construction professionals, two eminent lawyers and a retired judge.

Findings
This research has explored the practices of mediation, adjudication and expert evaluation in the Palestinian construction industry and has identified deficiencies in implementation and the roles that the cultural and legal contexts play in this. The research findings cast some doubt on the results of previous studies asserting the widespread use of construction mediation.

Originality/value
This paper contributes to knowledge by bringing new insight into the practice of particular ADR techniques in the Palestinian construction industry and in identifying challenges to the more widespread adoption of these ADR techniques. This paper exposes the myth of the popularity of construction mediation and the dilemma to the use of mediation brought by the social construction and conceptualisation of the mediator’s role.
Ready for the future? A survey on open access with scientists from the French National Research Center (CNRS)
Authors: Schöpfel Joachim , Ferrant Coline , André Francis , Fabre Renaud 
Published: October 2016

Purpose
This paper aims to present empirical evidence on the opinion and behaviour of French scientists (senior management level) regarding open access (OA) to scientific and technical information.

Design/methodology/approach
The results are part of a nationwide survey on scientific information and documentation with 432 directors of French public research laboratories conducted by the French National Research Center (CNRS) in 2014.

Findings
The CNRS senior research managers (laboratory directors) globally share the positive opinion towards OA revealed by other studies with researchers from the UK, Germany, the USA and other countries. However, they are more supportive of open repositories (green road) than of OA journal publishing (gold). The response patterns reveal a gap between generally positive opinions about OA and less supportive behaviours, principally publishing articles with article processing charges (APCs). A small group of senior research managers does not seem to be interested in green or gold OA and reluctant to self-archiving and OA publishing. Similar to other studies, the French survey confirms disciplinary differences, i.e. a stronger support for self-archiving of records and documents in HAL by scientists from Mathematics, Physics and Informatics than from Biology, Earth Sciences and Chemistry; and more experience and positive feelings with OA publishing and payment of APCs in Biology than in Mathematics or in Social Sciences and Humanities. Disciplinary differences and specific French factors are discussed, in particular in the context of the new European policy in favour of Open Science.

Originality/value
For the first time, a nationwide survey was conducted with the senior research management level from all scientific disciplines. The response rate was high (>30 per cent), and the results provide good insight into the real awareness, support and uptake of OA by senior research managers who provide both models (examples for good practice) and opinion leadership.
Looking beyond place branding: the emergence of place reputation
Authors: Bell Fraser 
Published: October 2016

Purpose
As place branding is reaching an impasse in terms of its development with numerous shortcomings being uncovered, this commentary suggests that the practice can be repositioned as part of the more comprehensive notion of place reputation. By building on the idea of corporate reputation and embryonic evidence of its application to geographical entities, this paper aims to argue for a more substantial translation of this concept to cities and regions.

Design/methodology/approach
This idea was investigated through empirical work in English second-tier cities, specifically concerning semi-structured interviews with local and regional stakeholders on the topic of place reputation conducted in 2014.

Findings
The empirical work found that place branding and place reputation can remain complimentary to one another, are entwined and are problematic to disentangle. This discovered that place branding is not as effective when used in isolation, and the concept benefits from the support of a more comprehensive reputation management strategy. In addition, this study found that the idea of reputational capital is a key theory for the development of reputation, allowing this broad notion to be tackled in terms of audiences, domains and sectors.

Originality/value
Moreover, this commentary constitutes a novel piece of research, and this is achieved by exploring gaps in both interdisciplinary place branding and corporate literatures of reputation being applied to place. This is addressed from a relational economic geography perspective, with the support of reputational capital which has links to Pierre Bourdieu’s (1986) Forms of Capital, this seeks to raise issues and add value to current place branding debates.