Large-scale Collaborative Projects Research Articles

Causal inference can lead us to modifiable mechanisms and informative archetypes in sepsis.

Medical progress is reflected in the advance from broad clinical syndromes to mechanistically coherent diagnoses. By this metric, research in sepsis is far behind other areas of medicine-the word itself conflates multiple different disease mechanisms, whilst excluding noninfectious syndromes (e.g.,trauma, pancreatitis) with similar pathogenesis. New technologies, both for deep phenotyping and data analysis, offer the capability to define biological states with extreme depth. Progress is limited by a fundamental problem: observed groupings of patients lacking shared causal mechanisms are very poor predictors of response to treatment. Here, we discuss concrete steps to identify groups of patients reflecting archetypes of disease with shared underlying mechanisms of pathogenesis. Recent evidence demonstrates the role of causal inference from host genetics and randomised clinical trials to inform stratification analyses. Genetic studies can directly illuminate drug targets, but in addition they create a reservoir of statistical power that can be divided many times among potential patient subgroups to test for mechanistic coherence, accelerating discovery of modifiable mechanisms for testing in trials. Novel approaches, such as subgroup identification in-flight in clinical trials, will improve efficiency. Within the next decade, we expect ongoing large-scale collaborative projects to discover and test therapeutically relevant sepsis archetypes.

Decentralized Mixed Effects Modeling in COINSTAC.

Performing group analysis on magnetic resonance imaging (MRI) data with linear mixed-effects (LME) models is challenging due to its large dimensionality and inherent multi-level covariance structure. In addition, as large-scale collaborative projects become commonplace in neuroimaging, data must increasingly be stored and analyzed from different locations. In such settings, substantial overhead can occur in terms of data transfer and coordination between participating research groups. In some cases, data cannot be pooled together due to privacy or regulatory concerns. In this work, we propose a decentralized LME model to perform a large-scale analysis of data from different collaborations without data pooling. This method is efficient as it overcomes the hurdles of data sharing and has lower bandwidth and memory requirements for analysis than the centralized modeling approach. We evaluate our model using features extracted from structural magnetic resonance imaging (sMRI) data. Results highlight gray matter reductions in the temporal lobe/insula and medial frontal regions in schizophrenia, consistent with prior studies. Our analysis also demonstrates that decentralized LME models achieve similar performance compared to the models trained with all the data in one location. We also implement the decentralized LME approach in COINSTAC, an open source, decentralized platform for federating neuroimaging analysis, providing an easy to use tool for dissemination to the neuroimaging community.

Developing shared understanding through online interdisciplinary collaboration: Reflections from a research project on better integration of health outcomes in future urban development practice

Collaborative working has gained widespread recognition in policy and practice. However, there is less research on the process of doing collaborative research in practice than there is on the epistemological, theoretical, and methodological aspects of such work. In this paper, we address this gap by offering reflections on our practical experience of online interdisciplinary collaboration as part of a wider research project on future urban development practice. We sought to develop a shared understanding of the systems of urban development decision-making. We utilise two established frameworks of interdisciplinarity to reflect on our experience and offer practical recommendations that can help facilitate such work carried out remotely by early career researchers from diverse academic backgrounds. In so doing, our paper offers fresh insights on some of the common issues in interdisciplinary collaboration and on developing shared understanding and intellectual coherence through productive online interactions. As research is evolving to tackle complex problems that require a holistic understanding, our paper contributes to developing replicable methods for remotely conducted interdisciplinary work in the early phases of large-scale collaborative projects.

HBM4EU from the Coordinator's perspective: lessons learnt from managing a large-scale EU project.

We discuss some important management issues of the Human Biomonitoring Initiative (HBM4EU) from the perspective of the Coordinator that may be valuable for the design and management of similar projects. As a large-scale international collaborative project, HBM4EU comprised 118 institutions from 30 countries and the European Environment Agency and had a budget of about €74 million. It has set up an innovative cooperative network of national and EU authorities and scientific institutions at the science-policy interface. A project of this scale raises major management challenges and requires transparent, efficient, and well-organized administrative and scientific steering structures. We present four major points: First, prior to the beginning of the project, the Consortium Agreement needs to be well elaborated to prevent conflicts during the project lifetime. Second, a strong role for national and EU policy-making authorities in the administrative governance structure enhances the interest of recipients of project results. Third, large-scale international collaborative projects need an elaborate and well-financed scientific governance structure. Fourth, a differentiation of funding rates among project activities threatens to create conflicts. HBM4EU provides a prototype for EU funded large-scale projects targeting future policies for realizing the Green Deal and Zero Pollution Ambition in the field of chemicals, health, and environment.

The DIMA Network: Bridging boundaries via shared scientific interests

Abstract The DIMA Network (Developing Innovative Multi-proxy Analyses – in Siberia and the Russian Far East (SRFE)) started from a small nucleus of palaeoenvironmental researchers in the UK and SRFE at a workshop in 2008 and currently includes researchers from over 25 institutions. The mutual interest in creating long-term records of environmental change was rekindled during workshops in Magadan (2018), Tomsk (2018) and Southampton (2019). These events were organised to connect researchers from the UK and SRFE with these aims: (1) provide training in new techniques and methods, (2) facilitate knowledge transfer about local sites and conditions, (3) stimulate large-scale collaborative projects across SRFE and (4) inspire a new generation of palaeoenvironmental researchers.

Street-level collaborative governance for urban regeneration: How were conflicts resolved at grassroot level?

ABSTRACT Urban regeneration is one of the most important public administration issues facing modern cities. While abundant studies have focused on the state-led or market-based governance modes of large urban regeneration projects, relatively fewer studies investigate the collaborative governance mode, especially on the numerous street-level small-scale regeneration projects. Street-level small-scale regeneration projects directly touch on citizens’ life and impact governance effectiveness at grassroot level. This paper studies dynamics of collaborative governance of a street-level regeneration that can balance multiple regeneration objectives and successfully address conflicts and tensions inherent in such projects. Our findings are significant in confirming the applicability of the basic tenets of collaborative governance in grassroot level and pointing out some key differences between large-scale collaborative governance projects and street-level small-scale projects in how governance effectiveness could be achieved through different stakeholders’ interactions in urban regeneration.

SketchUp and Sketchfab: Tools for Teaching with 3D

SketchUp and Sketchfab: Tools for Teaching with 3D

Large-Scale Collaborative Research Projects in Theatre and Performance Studies: Resources, Politics, and Ethics in the Margins of Europe during the COVID-19 Pandemic

Staging National Abjection: Theatre and Politics in Turkey and Its Diasporas is a research project funded by the European Research Council's Starting Grants program. Building on the initial insights of the project, the authors study collaboration as a performative process. They analyze the promises and risks involved in large-scale collaborative research projects and how they unfold in the context of Turkish academia and the COVID-19 pandemic. The authors examine how they manage their responsibilities to fellow members of their research team, to other members of Turkish academia, to the minoritarian communities they work with, and to the broader public who funds their research. Finally, they discuss how they work toward collective care and empowerment while negotiating the demands of globalized neoliberal academia as well as the oppressive sociopolitical environment in Turkey and explore the limits of their scholarly and ethical endeavors.

Laypeople Can Predict Which Social-Science Studies Will Be Replicated Successfully

Large-scale collaborative projects recently demonstrated that several key findings from the social-science literature could not be replicated successfully. Here, we assess the extent to which a finding’s replication success relates to its intuitive plausibility. Each of 27 high-profile social-science findings was evaluated by 233 people without a Ph.D. in psychology. Results showed that these laypeople predicted replication success with above-chance accuracy (i.e., 59%). In addition, when participants were informed about the strength of evidence from the original studies, this boosted their prediction performance to 67%. We discuss the prediction patterns and apply signal detection theory to disentangle detection ability from response bias. Our study suggests that laypeople’s predictions contain useful information for assessing the probability that a given finding will be replicated successfully.

Managing Oil Palm Plantations More Sustainably: Large-Scale Experiments Within the Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) Programme

Conversion of tropical forest to agriculture results in reduced habitat heterogeneity, and associated declines in biodiversity and ecosystem functions. Management strategies to increase biodiversity in agricultural landscapes have therefore often focused on increasing habitat complexity; however, the large-scale, long-term ecological experiments that are needed to test the effects of these strategies are rare in tropical systems. Oil palm (Elaeis guineensis Jacq.)—one of the most widespread and important tropical crops—offers substantial potential for developing wildlife-friendly management strategies because of its long rotation cycles and tree-like structure. Although there is awareness of the need to increase sustainability, practical options for how best to manage oil palm plantations, for benefits to both the environment and crop productivity, have received little research attention. In this paper we introduce the Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) Programme: a long-term research collaboration between academia and industry in Sumatra, Indonesia. The BEFTA Programme aims to better understand the oil palm agroecosystem and test sustainability strategies. We hypothesise that adjustments to oil palm management could increase structural complexity, stabilise microclimate, and reduce reliance on chemical inputs, thereby helping to improve levels of biodiversity and ecosystem functions. The Programme has established four major components: (1) assessing variability within the plantation under business-as-usual conditions; (2) the BEFTA Understory Vegetation Project, which tests the effects of varying herbicide regimes; (3) the Riparian Ecosystem Restoration in Tropical Agriculture (RERTA) Project, which tests strategies for restoring riparian habitat; and (4) support for additional collaborative projects within the Programme landscape. Across all projects, we are measuring environmental conditions, biodiversity, and ecosystem functions. We also measure oil palm yield and production costs, in order to assess whether suggested sustainability strategies are feasible from an agronomic perspective. Early results show that oil palm plantation habitat is more variable than might be expected from a monoculture crop, and that everyday vegetation management decisions have significant impacts on habitat structure. The BEFTA Programme highlights the value of large-scale collaborative projects for understanding tropical agricultural systems, and offers a highly valuable experimental set-up for improving our understanding of practices to manage oil palm more sustainably.

Biomagnetic biomarkers for dementia: A pilot multicentre study with a recommended methodological framework for magnetoencephalography

IntroductionAn increasing number of studies are using magnetoencephalography (MEG) to study dementia. Here we define a common methodological framework for MEG resting-state acquisition and analysis to facilitate the pooling of data from different sites. MethodsTwo groups of patients with mild cognitive impairment (MCI, n = 84) and healthy controls (n = 84) were combined from three sites, and site and group differences inspected in terms of power spectra and functional connectivity. Classification accuracy for MCI versus controls was compared across three different types of MEG analyses, and compared with classification based on structural MRI. ResultsThe spectral analyses confirmed frequency-specific differences in patients with MCI, both in power and connectivity patterns, with highest classification accuracy from connectivity. Critically, site acquisition differences did not dominate the results. DiscussionThis work provides detailed protocols and analyses that are sensitive to cognitive impairment, and that will enable standardized data sharing to facilitate large-scale collaborative projects.

GcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.

Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities. A variety of large-scale collaborative projects are being conducted to encompass samples from diverse environments and habitats. This change has resulted in enormous demands for long-term data maintenance and capacity for data analysis. The Global Catalogue of Metagenomics (gcMeta) is a part of the ‘Chinese Academy of Sciences Initiative of Microbiome (CAS-CMI)’, which focuses on studying the human and environmental microbiome, establishing depositories of samples, strains and data, as well as promoting international collaboration. To accommodate and rationally organize massive datasets derived from several thousands of human and environmental microbiome samples, gcMeta features a database management system for archiving and publishing data in a standardized way. Another main feature is the integration of more than ninety web-based data analysis tools and workflows through a Docker platform which enables data analysis by using various operating systems. This platform has been rapidly expanding, and now hosts data from the CAS-CMI and a number of other ongoing research projects. In conclusion, this platform presents a powerful and user-friendly service to support worldwide collaborative efforts in the field of meta-omics research. This platform is freely accessible at https://gcmeta.wdcm.org/.

Buddhist Sculpture Studies of Hwang Su-young and Chin Hong-sup

When we look back on the accomplishments of Hwang Su-young and Chin Hong-sup on the 100th anniversary of their births, their achievements show where Korean art history began and how it arrived to the present. This study examines their works on Buddhist sculptures. Hwang and Chin’s early researches were mainly centred on excavation and analysis of primary sources, but their academic achievements thereafter are mesmerizing. They planned large-scale collaborative research projects, for example on the Silla Five Sacred Mountains and the Three Mountains of Gyeongju, to obtain more specific and specialized information on Buddhist sculptures, and continued further research. They also paid attention to inscriptions and written documents, collecting them for studies of sculptures. Their preliminary research were published into introductory surveys and catalogues that provided foundations for Buddhist sculpture studies. However, they recognized their limitations by stating that, “though we have written a history of sculptures, its main focus is on works from Three Kingdoms Dynasty and Unified Silla, and offers only brief introductions to major works. Research on Korea sculptures must begin from these preliminary writings and make progress over a long period of time.” Their works did not include dating by comparison with Chinese Buddhist sculptures or iconographical analysis, and though some interests were expressed about the sculptures of Goryeo and Joseon, they were not developed into full-depth research. This, of course, originates from the academic limitations of the time. They also took responsibilities in administrations for cultural heritage that includes Buddhist sculptures. In the 1960s, as the Korean society became more stable, Hwang and Chin took active parts in various works that were related to cultural heritages. Designated surveys for preservation, consultations for repair work, administrative works for museums, and improving public awareness of cultural heritage are some examples of their extensive endeavours. It is apparent that they felt a sense of duty towards their roles and worked with dedication. Moreover, these administrative works likely supported their academic competence as well. Two scholars’ area of expertise encompassed not only individual research but also publication, administrative works that contributed to the fast improvement of social understanding of cultural heritage-related studies. They were devoted scholars who carried out their duties that the era had put before them, the best they can, in their capacity and position. Their extensive field research is an example that today’s scholars must learn from above all else. Buddhist sculpture studies have made great progress and became specialized into specific fields, but tends to depend too heavily on historiography. Individual field research is vital but there are also opportunities such as designated surveys, catalogue compilation of National Treasure and Treasures, and research projects. As the age of major excavation or discovery are past, and as few Buddhist sculptures are designated for research, there are only few opportunities for first-hand experience for researchers. Today, national-scale compilation works are only made by some national institutions such as museums, the National Institute of Cultural Heritage, and Buddhism-related research institutions. These projects are important processes through which young scholars can enhance their learning, meaning that more prolific research or compilation projects are needed.

Recommender systems, cultural heritage applications, and the way forward

Abstract Modern recommender systems appeared during the last decade of the 20th century and have already proven their importance in tackling with information overload and content or services personalisation in the modern big-data world. This is markedly suggested by their adoption by major industry parties in a wide variety of domains. The application of recommender systems in the Cultural Heritage domain has appeared relatively recently, particularly during the advent of the 21st century. Nevertheless, a large number of works appeared in the scientific literature, driven primarily from large-scale cultural heritage collaborative projects. This paper presents a review of the current recommender system approaches, including some basic mathematical formalism, and focuses on recommender system applications in Cultural Heritage, to identify the advantages, the benefits and prospects, the disadvantages and pitfalls. The paper discusses the diversity and some common assumptions in the reviewed works, outlines some proposals for future development, and takes a position on the way forward.

Emo, love and god: making sense of Urban Dictionary, a crowd-sourced online dictionary.

The Internet facilitates large-scale collaborative projects and the emergence of Web 2.0 platforms, where producers and consumers of content unify, has drastically changed the information market. On the one hand, the promise of the ‘wisdom of the crowd’ has inspired successful projects such as Wikipedia, which has become the primary source of crowd-based information in many languages. On the other hand, the decentralized and often unmonitored environment of such projects may make them susceptible to low-quality content. In this work, we focus on Urban Dictionary, a crowd-sourced online dictionary. We combine computational methods with qualitative annotation and shed light on the overall features of Urban Dictionary in terms of growth, coverage and types of content. We measure a high presence of opinion-focused entries, as opposed to the meaning-focused entries that we expect from traditional dictionaries. Furthermore, Urban Dictionary covers many informal, unfamiliar words as well as proper nouns. Urban Dictionary also contains offensive content, but highly offensive content tends to receive lower scores through the dictionary’s voting system. The low threshold to include new material in Urban Dictionary enables quick recording of new words and new meanings, but the resulting heterogeneous content can pose challenges in using Urban Dictionary as a source to study language innovation.

Adaptation to Climate Change in Panchase Mountain Ecological Regions of Nepal

Rural mountain communities in developing countries are considered particularly vulnerable to environmental change, including climate change. Forests and agriculture provide numerous ecosystem goods and services (EGS) to local communities and can help people adapt to the impacts of climate change. There is however poor documentation on the role of EGS in people’s livelihood and adaptation practices. This study in the rural Panchase Mountain Ecological Region of Nepal identifies practices being used to adapt to a changing environment through key informant interviews and focus group discussions. At the household level, livelihood diversification, changes in cropping patterns and farming practices, use of multipurpose plant species and income-generation activities were identified as adaptation strategies. Among major strategies at the community level were community forestry-based climate adaptation plans of action for forest and water resource management. Landscape-level adaptation strategies were large-scale collaborative projects and programs, such as Ecosystem-based Adaptation and Chitwan Annapurna Landscape conservation; which had implications at both the local and landscape-level. A proper blending and integration of adaptation strategies from individual households through to the community and to the landscape level is needed for implementing effective adaptation in the region.

Beyond antiquarianism. A review of current theoretical issues in German-speaking prehistoric archaeology

AbstractWhereas German-speaking archaeology (GSA) has long been understood as generally uninterested in theoretical debates, the situation has taken a most interesting development since the year 2000. Archaeologists tried to escape the general decline of the small university disciplines by getting more and more involved in the overarching research questions of cultural studies and in large-scale collaborative projects. The necessity of integrating a clear theoretical and methodological approach for a successful proposal and the subsequent research changed the significance of theoretical discussions. As a consequence, theme-oriented research has developed which aims at addressing overarching themes in the cultural and social sciences. We have chosen five of the most prominent themes in German-speaking archaeology – self-reflexivity, identities, space, cultural encounter and knowledge transfer – as well as material culture, and shed light on their theoretical conceptualization and methodological implementation in recent publications. Despite the lack of dominant schools of thinking, its strong rootedness in the evaluation of empirical sources, and its close link to the discipline of history, current GSA can contribute to the overall theoretical discourse of the discipline.

Barriers and facilitators experienced in collaborative prospective research in orthopaedic oncology: A qualitative study.

ObjectivesAs tumours of bone and soft tissue are rare, multicentre prospective collaboration is essential for meaningful research and evidence-based advances in patient care. The aim of this study was to identify barriers and facilitators encountered in large-scale collaborative research by orthopaedic oncological surgeons involved or interested in prospective multicentre collaboration.MethodsAll surgeons who were involved, or had expressed an interest, in the ongoing Prophylactic Antibiotic Regimens in Tumour Surgery (PARITY) trial were invited to participate in a focus group to discuss their experiences with collaborative research in this area. The discussion was digitally recorded, transcribed and anonymised. The transcript was analysed qualitatively, using an analytic approach which aims to organise the data in the language of the participants with little theoretical interpretation.ResultsThe 13 surgeons who participated in the discussion represented orthopaedic oncology practices from seven countries (Argentina, Brazil, Italy, Spain, Denmark, United States and Canada). Four categories and associated themes emerged from the discussion: the need for collaboration in the field of orthopaedic oncology due to the rarity of the tumours and the need for high level evidence to guide treatment; motivational factors for participating in collaborative research including establishing proof of principle, learning opportunity, answering a relevant research question and being part of a collaborative research community; barriers to participation including funding, personal barriers, institutional barriers, trial barriers, and administrative barriers and facilitators for participation including institutional facilitators, leadership, authorship, trial set-up, and the support of centralised study coordination.ConclusionsOrthopaedic surgeons involved in an ongoing international randomised controlled trial (RCT) were motivated by many factors to participate. There were a number of barriers to and facilitators for their participation. There was a collective sense of fatigue experienced in overcoming these barriers, which was mirrored by a strong collective sense of the importance of, and need for, collaborative research in this field. The experiences were described as essential educational first steps to advance collaborative studies in this area. Knowledge gained from this study will inform the development of future large-scale collaborative research projects in orthopaedic oncology.Cite this article: J. S. Rendon, M. Swinton, N. Bernthal, M. Boffano, T. Damron, N. Evaniew, P. Ferguson, M. Galli Serra, W. Hettwer, P. McKay, B. Miller, L. Nystrom, W. Parizzia, P. Schneider, A. Spiguel, R. Vélez, K. Weiss, J. P. Zumárraga, M. Ghert. Barriers and facilitators experienced in collaborative prospective research in orthopaedic oncology: A qualitative study. Bone Joint Res 2017;6:–314. DOI: 10.1302/2046-3758.65.BJR-2016-0192.R1.

How to manage large-scale collaborative genomics research projects?

How to manage large-scale collaborative genomics research projects?

Durkheim with Data: The Database of Religious History

This article introduces a new online, quantitative encyclopedia of religious cultural history, the Database of Religious History (DRH). The DRH aims to systematically collect information on past religious groups from around the world in a standardized form, providing a novel digital humanities resource for the religious studies community, a forum for scholarly debates, a pedagogical aid, and a platform for testing hypotheses about religious change over space and time. We employ the DRH project as a lens through which to view some larger intellectual issues surrounding the comparative study of religion, the role of functionalism and “big data” in the study of religion, the challenges of large-scale collaborative projects, and the future of science-humanities integration.