Small Research Community Research Articles

Forests high on CO2: A glimpse into how scientists study the biochemical machinery of forest ecosystems

Are forests across the planet storing more carbon as a result of rising atmospheric carbon dioxide (CO2) concentration? In this text, I propose to reflect on the work of researchers who are asking that very question. The focus is on a particular approach called free-air CO2 enrichment (FACE) experiments, in which forests in their local environment are subjected to a CO2 concentration higher than in the ambient air, to test the CO2 fertilization hypothesis. This hypothesis predicts that forests store more carbon in those conditions. FACE studies held the promise of establishing cause–effect relations and transcending the here and now. They emerged in the United States in the late 1980s, at a time when ecology scaled up to make itself relevant to the then nascent Earth System science. FACE experiments in forests are now conducted in Australia, the United Kingdom, and Brazil, and their results are closely scrutinized by a small research community. The text, first, presents the engineering feat that underpins FACE experiments in forests and discuss two problems highlighted by scientists because they impede hasty generalization from the data: the timescale needed to witness forests change and the spatial heterogeneity of forest soils. It then shows how scientists contend with their incomplete understanding of forest ecosystems as they bring together computer models and empirical data to build consensus around the sources of epistemic uncertainty. To conclude, I propose to rework the idea of “the macroscope” to conceptualize what scientists do when they seek to study forests as complex, layered, multi-scale systems. I wish to capture how researchers, who willingly endorse a planetary gaze, problematize their own predicament. This, as I suggest, has to do with the immanence of forests in the world.

National cross-disciplinary research ethics and integrity study: methodology and results from Estonia

While empirical studies of research ethics and integrity are increasingly common, few have aimed at national scope, and even fewer at current results from Central and Eastern Europe. This article introduces the results of the first national research integrity survey in Estonia, which included all research-performing organisations in Estonia, was inclusive of all disciplines and all levels of experience. A web-based survey was developed and carried out in Estonia with a call sent to all accredited Estonian research institutions. The results indicate that the vast majority (89%) of respondents consider research ethics and integrity issues important and view falsification, fabrication, and plagiarism (FFPs) as the most severe forms of misconduct. Self-reporting of FFPs is generally comparable to levels published in other studies (6.2%). Gift authorship (41%) and hampering the work of a colleague (32%) were problematic practices most noticed among colleagues. At the same time, two of the noticed questionable research practices (QRPs) – salami-slicing and misuse of research funding – were seen as less severe, hinting at the existence of counter-norms that career advancement rules and structural factors like funding policies may encourage. The availability of research ethics and integrity guidelines was considered good. Ethical aspects of studying potentially stigmatising data in a very small research community are discussed in the article and results are analysed through counter-norms and normative dissonance frames.

Safeguarding Access to 500 Years of Biodiversity Data: Sustainability planning for the Biodiversity Heritage Library

The Biodiversity Heritage Library (BHL) is the world’s largest open access digital library for biodiversity literature and archives. Headquartered at Smithsonian Libraries and Archives (SLA), BHL is a global consortium of research institutions working together to build and maintain a critical piece of biodiversity data infrastructure. BHL provides free access to over 60 million pages of biodiversity content from the 15th–21st centuries. BHL works with the biodiversity community to develop tools and services to facilitate greater access, interoperability, and reuse of content and data. Through taxonomic intelligence tools developed by Global Names Architecture, BHL has indexed more than 230 million instances of taxonomic names throughout its collection, allowing researchers to locate publications about specific taxa. BHL also works to bring historical literature into the modern network of scholarly research by retroactively assigning DOIs (digital object identifiers) and making this historical content more discoverable and trackable. Biodiversity databases such as the Catalogue of Life, International Plant Names Index, Tropicos, World Register of Marine Species, and iNaturalist, rely on literature housed in BHL. Locked within its 60 million pages are valuable species occurrence data and observations from expeditions. To make this data FAIR (findable, accessible, interoperable, and reusable), BHL and its partners are working on a data pipeline to transform textual content into actionable data that can be deposited into data aggregators such as the Global Biodiversity Information Facility (GBIF). BHL’s shared vision began in 2006 among a small community of passionate librarians, technologists, and biodiversity researchers. Uniting as a consortium, BHL received grant funding to build and launch its digital library. BHL partners received additional grant funding for further technical development and targeted digitization projects. When initial grant funding ended in 2012, BHL established an annual dues model for its Members and Affiliates to help support central BHL operating expenses and technical development. This dues model continues today, along with in-kind contributions of staff time from Members and Affiliates. Significant funding is also provided by the Smithsonian in the form of an annual U.S. federal allocation, endowment funds, and SLA cost subvention, to host the technical infrastructure and Secretariat staff. BHL also relies on user donations to support its program. Though BHL has diversified funding streams over the years, it relies heavily on a few key institutions to cover operating costs. Though these institutions have overarching open access, research, and sustainability goals, priorities and resources to achieve these goals shift over time. Without long-term commitments, institutions may choose to prioritize new projects over established programs. Many BHL contributors have experienced funding loss for digitization projects, reducing the rate at which new content is added to BHL. Further loss of funding for central staff and technical infrastructure would reduce BHL from a data-rich technology project to an unsupported and deprecated platform. Without a long-term commitment to maintain and improve the technical infrastructure, BHL’s termination would result in countless broken links from biodiversity databases, library catalogs, Wikidata, and other aggregators across the web; detrimental impact on existing third-party projects relying on BHL citation and species data; and the elimination of more equitable and free access to biodiversity knowledge. To continue its mission, BHL must increase and improve its data integration with the wider biodiversity infrastructure and secure a sustainable future. Securing that future will require external expertise to diversify funding sources, re-engage support from existing partners, and identify new stakeholders for support. During the founding discussions of BHL, stakeholders agreed that the only way to do biodiversity science globally is through collaboration. One institution could not lead alone. Going forward, this imperative must also include collaborative funding models. Partnering with initiatives such as the Global Biodata Coalition (GBC) can lead to a stronger and more resilient biodiversity infrastructure. With ongoing collaboration, innovation, and an unwavering commitment to open access, BHL will continue to transform research on a global scale and provide researchers with the tools they need to study, explore, and conserve life on Earth.

Challenges for Implementing FAIR Digital Objects with High Performance Workflows

Challenges for Implementing FAIR Digital Objects with High Performance Workflows

Women’s Writing, 1660–1830: Feminism and Futures, ed. Jennie Batchelor and Gillian Dow.

<i>Women’s Writing, 1660–1830: Feminism and Futures</i>, ed. Jennie Batchelor and Gillian Dow.

Gaps in health research related to sex work: an analysis of Canadian health research funding

ABSTRACT Public health is tasked with addressing the urgent global priority of promoting the health and human rights of adults engaged in sex work and research is critical to support this endeavor. ‘What’ is studied, ‘how’ research is done, and ‘who’ is centered in this research is reflected in how research funding is allocated. In this article, we interrogate funding allocation for sex work-related health research in Canada. Drawing on critical perspectives aimed at illustrating how stigma operates in society, we examine operating grants (N = 64) awarded by the federal health research funding agency between 2003 and 2020. We find that sex workers’ health is problematized disproportionately in a street marketplace context that centers on HIV and sexually transmitted infections. Limited work attends to the socio-structural context of sex work and instead perpetuates stigmatizing narratives about sex work. Public health intervention studies are rare, presenting a barrier for implementing and evaluating evidence-based health promotion strategies. Notably, the research projects were conducted by a small number of highly networked, geographically clustered researchers, illustrating gaps in research that considers the complexity of sex work. We propose that it is essential to consider funding as a process that may be limiting the range of health issues being addressed and privileging a small community of researchers, which can inadvertently serve to worsen health inequities among some sex work communities. Researchers and funding bodies may draw on this analysis to inform a research agenda that meaningfully supports the health, safety, and well-being of sex workers in Canada and globally.

Why cross and mix disciplines and methodologies?: Multiple meanings of Interdisciplinarity and pluralism in ecological economics

Ecological Economists disagree much about their field and its relationship to mainstream economics and to policy. One reason for these disagreements is that the field pursues multiple goals under the headings of “interdisciplinarity” and “transdisciplinarity.” At least four distinct goals may be pursued under these labels; brainstorming and borrowing for novel combinations of ideas, building new sub-disciplines at the juncture of existing disciples, bringing multiple fields into methodological and theoretical coherence, and involving science in solving social problems. The latter two draw the most controversy. Ecological Economists desire reforming Economics and other social sciences by integrating theories from ecology and physics, but there are multiple means of doing so. Likewise, many seek to create new ways for academic knowledge to be better utilized in public decision-making, but perspectives differ here as well. These represent fundamentally different axes of disagreement but are not always treated as such. Ecological Economics continues to contain a broad range of perspectives, some contradictory, for a rather small research community.

The role of team science in the future of male contraception†.

Efforts to develop a male contraceptive method beyond condoms and vasectomy have been on-going for nearly 70 years. During this time, there have been ebbs and modest flows of resources available to support product development, but not at a level sufficient to carry research efforts through to market. The small community of researchers that have continued to pursue the development of male contraceptives is comprised of dedicated scientists who have a great deal of knowledge and experience to offer. While collaboration has been an organic outcome of limited resources, competing research objectives and geographically diverse locations have made consistent and sustained progress challenging, particularly for those working in the earliest stages of developing nonhormonal, reversible male contraceptive methods. While the past decade has seen an increase in funding to the field, the levels are still modest when placed in the context of actual costs to bring products to market. In addition, there are challenges still to be identified given that there is no regulatory precedent for these products. These challenges present an excellent use case for the application of design-thinking or human centered design, as a means of generating novel solutions. By engaging those with deep technical expertise in the field of male contraception as well as thought leaders from other fields of practice, design-thinking offers an opportunity to identify potential strategies, including nontraditional approaches, capable of driving the product development process forward, in a faster and more efficient manner.

What citation patterns reveal about reading research and practice in academic libraries

Purpose At the turn of the twenty-first century, academic libraries revived their tradition of working with readers, which resulted in a surge of publications in this area. However, the nature and thematic coverage of these publications has not changed dramatically in the past 18 years, signaling little advancement in the reach and scope of this professional activity. This paper aims to address the following research problem: What do citation patterns reveal about reading research and practice in academic libraries and do they point to interdisciplinary research and the presence of an evidence base or do they carry a mark of an inward disciplinary orientation? Design/methodology/approach This is a qualitative exploratory study, also involving descriptive statistics, that uses bibliographic and citation analysis as a method. Findings The study discovers a disconnect between the diversity of interdisciplinary research cited in the published work on reading in academic libraries and the sameness of respective professional practices; it describes a relatively small community of reading researchers in academic libraries, emerging as leaders who can change the direction and scope of reading practices; and it highlights a preference of academic librarians for relying on interdisciplinary knowledge about reading over building on the readers’ advisory experience of public librarians. Originality/value Translating the incredible wealth of interdisciplinary reading knowledge possessed by academic librarians into practical applications promises to advance and diversify reading practices in academic libraries. One method that could aid in this effort is more intentional learning from the readers’ advisory practices of public librarians.

A quick guide for student-driven community genome annotation.

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms and usually have minor or major errors. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions.

Adaptive Approach for Intelligent Web to Enhance Business Intelligence Applications

The World Wide Web (WWW) has grown quickly in the past two decades from a small research community to the biggest and most popular infrastructure for communication, information dissemination, search, social interaction and commerce. The continuous growth in size and use of the WWW creates a need for methods to process these wicked volumes of data. Web Intelligence (WI), as a research direction, has a broad agenda to deal with the issues that arise around the WWW phenomenon. WI corresponds to research and development to explore the fundamental roles, artificial intelligence and advanced information technology on the web-empowered systems, services, and activities. In this context, WI is concerning of mining in web data and user behaviors. This creates a demand for using mining technologies to search large volume of data for gaining hidden knowledge. This hidden knowledge helps in gaining competitive advantages, better customers’ relationships, and even fraud detection. Achieving the intelligence to the web enhances Business Intelligence (BI) for the enterprises. Web Usage Mining (WUM) and Web Opinion Mining (WOM) are considered a leading mining approaches in mining the user behavior and reviews. Most of previous studies depended in building intelligent web on mining and analyzing user’s profiles or opinions separately. This becomes not fair enough and cause of limitations. This limitations could be narrowed if both of user preferences and opinions are considered in building recommendations. The paper proposes a framework for achieving the intelligence via using WUM and WOM. The proposed framework would contribute in solving the problem. The paper also surveys the background of using the intelligent web as an approach to enhance the Business Intelligence (BI) applications

“Useful Information Turned into Something Useless”: Archival Silences, Imagined Records, and Suspicion of Mediated Information in the JFK Assassination Collection

The controversies, beliefs, and arguments surrounding the assassination of John F. Kennedy in November 1963 are classics in the canon of conspiracy theories. In October and November 2017, a large cache of documents was declassified and made available to the public through the National Archives and Records Administration’s (NARA) website. A small community of researchers coalesced soon after on reddit.com. When these users encounter silences, they often react to them with a certain level of suspicion towards NARA, its archivists, or the originating institution. I call this suspicion of mediated information. It is entangled with, and comes about as a result of, the notoriety and contested nature of the JFK assassination and its aftermath, the strength of the impossible archival imaginary and the imagined records associated with the JFK Assassination collection, and the nature of the archival silences in the online JFK Assassination Collection. Archivists, particularly those working with collections of conspiratorial significance (the MK-ULTRA documents, collections having to do with UFOs, etc.), should be aware of these sorts of reasoning patterns and how they affect use of the collection and user attitudes towards the collecting institution. The first section of this paper introduces the JFK Assassination Collection, the second goes through the canon of scholarship on conspiracy theories, outlining the new notion of suspicion of mediated information. In section three, I present my theoretical framework—rooted in the notion of Michel-Rolphe Trouillot’s “archival silences,” and Anne Gilliland and Michelle Caswell’s imagined records and impossible archival imaginaries. Section four outlines method, and section five consists of data and discussion. This paper constitutes preliminary research into the area, and will be built upon in later research.

Editorial challenges in a small scientific community: Study of Croatian editors

This article presents results from a study of 74 Social Science Croatian journal editors that asked about challenges encountered during their work, with a special focus on peer review processes. The study used an online questionnaire with 19 questions. The findings confirmed many logistics challenges and peer review‐related problems associated mostly with substandard work of the reviewers; author misconduct, especially plagiarism; and multiple submission of articles. The findings show similar problems to other regions of the world, and some problems discovered in this study demonstrate unique problems encountered within a small research community. The discovered problems call for changes and new editorial procedures.

The Precarious State of Famine Research

In 2017 famine struck yet again. While famine continues to haunt many fragile countries, the paper reveals a faltering scholarly interest in famine research, particularly within the research tradition of development studies. Today, the research field is rather dominated by the research traditions of history and economics. Interestingly, the steepest decline in scholarly attention to famine coincided with Amartya Sen being awarded the Nobel Prize in Economics in 1998 in part for his work on famine. The paper points to three characteristics of famine research that might account for this rather puzzling development: (i) the field of contemporary famine research exhibits limited interest in theory-building; (ii) the field is impeded by inaccessibility to key research sites; and (iii) the field is weakened by a small and dispersed research community. The paper suggests remedies that might address these obstacles to contemporary famine research in development studies. To facilitate more theoretical development, scholars could engage with the recent call for a criminalisation of famine, and the broader field of disaster research could be used as an institutional catalyst for scholars of famine.

How researchers perceive research misconduct in biomedicine and how they would prevent it: A qualitative study in a small scientific community

ABSTRACTThe aim of our study has been to use a qualitative approach to explore the potential motivations and drivers for unethical behaviors in biomedicine and determine the role of institutions regarding those issues in a small scientific community setting.Three focus groups were held---two with doctoral students and one with active senior researchers. Purposive sampling was used to reach participants at different stages of their scientific careers. Participants in all three focus groups were asked the same questions regarding the characteristics and behaviors of ethical/unethical scientists, ethical climate, role, and responsibility of institutions; they were also asked to suggest ways to improve research integrity. The data analysis included coding of the transcripts, categorization of the initial codes, and identification of themes and patterns.Three main topics were derived from the focus groups discussions. The first included different forms of unethical behaviors including increasing research “waste,” non-publication of negative results, authorship manipulation, data manipulation, and repression of collaborators. The second addressed the factors influencing unethical behavior, both external and internal, to the researchers. Two different definitions of ethics in science emerged; one from the categorical perspective and the other from the dimensional perspective. The third topic involved possible routes for improvement, one from within the institution through the research integrity education, research integrity bodies, and quality control, and the other from outside the institution through external supervision of institutions.Based on the results of our study, research misconduct in a small scientific community is perceived to be the consequence of the interaction of several social and psychological factors, both general and specific, for small research communities. Possible improvements should be systematic, aiming both for improvements in work environment and personal awareness in research ethics, and the implementation of those changes should be institutional responsibility.

Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels.

SummaryThe application of genomics in crops has the ability to significantly improve genetic gain for agriculture. Many marker‐dense tools have been developed, but few have seen broad adoption in plant genomics due to issues of significant variations of genome size, levels of ploidy, single nucleotide polymorphism (SNP) frequency and reproductive habit. When combined with limited breeding activities, small research communities and scant sequence resources, the suitability of popular systems is often suboptimal and routinely fails to effectively balance cost‐effectiveness and sample throughput. Genotyping‐by‐sequencing (GBS) encompasses a range of protocols including resequencing of the transcriptome. This study describes a skim GBS‐transcriptomics (GBS‐t) approach developed to be broadly applicable, cost‐effective and high‐throughput while still assaying a significant number of SNP loci. A range of crop species with differing levels of ploidy and degree of inbreeding/outbreeding were chosen, including perennial ryegrass, a diploid outbreeding forage grass; phalaris, a putative segmental allotetraploid outbreeding forage grass; lentil, a diploid inbreeding grain legume; and canola, an allotetraploid partially outbreeding oilseed. GBS‐t was validated as a simple and largely automated, cost‐effective method which generates sufficient SNPs (from 89 738 to 231 977) with acceptable levels of missing data and even genome coverage from c. 3 million sequence reads per sample. GBS‐t is therefore a broadly applicable system suitable for many crops, offering advantages over other systems. The correct choice of subsequent sequence analysis software is important, and the bioinformatics process should be iterative and tailored to the specific challenges posed by ploidy variation and extent of heterozygosity.

Does small equal predatory? Analysis of publication charges and transparency of editorial policies in Croatian open access journals.

IntroductionWe approach the problem of "predatory" journals and publishers from the perspective of small scientific communities and small journals that may sometimes be perceived as "predatory". Among other characteristics of "predatory" journals two most relevant are their business model and the quality of the editorial work.Materials and methodsWe analysed 444 Croatian open access (OA) journals in the Hrčak (portal of Croatian scientific journals) digital journal repository for the presence of article processing charges as a business model and the transparency of editorial policies.ResultsThe majority of journals do not charge authors or require submission or article processing charges, which clearly distinguishes them from “predatory” journals. Almost all Hrčak OA journals have publicly available information on editorial boards, including full names and affiliations, and detailed contact information for the editorial office at the Hrčak website. The journal names are unique and cannot be easily confused with another journal or intend to mislead about the journal’s origin. While most journals provide information on peer review process, many do not provide guidelines for reviewers or other editorial and publication ethics standards.ConclusionIn order to clearly differentiate themselves from predatory journals, it is not enough for journals from small research communities to operate on non-commercial bases, but also to have transparent editorial policies.

Applications of genotyping by sequencing in aquaculture breeding and genetics.

Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.

Computational Imaging for Cultural Heritage: Recent developments in spectral imaging, 3-D surface measurement, image relighting, and X-ray mapping

Because art is inherently visual, the use of imaging has long been an important way to understand its structure, form, and history. Recently, new ways of engaging with objects from our shared cultural heritage are possible with advances in computation and imaging that allow scientists to analyze art noninvasively, historians to pose new social questions about the art, and the public to explore and interact with art in ways never before possible. There is a rich history in applying image processing techniques to conventional photographic images of works of art, many of which have been highlighted in previous special issues of IEEE Signal Processing Magazine (e.g., the 2008 and 2015 July issues). Building on these contributions, this article comprises a survey of techniques where computation is central to the image acquisition process. Known as computational imaging, the methods being pioneered in this field are increasingly relevant to cultural heritage applications because they leverage advances in image processing, acquisition, and display technologies that make scientific data readily comprehensible to a broad cohort of nontechnical researchers interested in understanding the visual content of art. Presently, only a small research community undertakes computational imaging of cultural heritage. Here we aim to introduce this growing new field to a larger research community by discussing: 1) the historic background of imaging of art, 2) the burgeoning present day community of researchers interested in computational imaging in the arts, and finally, 3) our vision for the future of this new field.

The fungus living among us

By now, most of us have made peace with the fact that we are host to a complicated extended family of bacteria whose trillion-plus members give us vitamins, help us digest food, protect us from pathogens, and only rarely turn virulent on us. But what about the fungus among us? “Wherever there are bacteria, there’s fungus as well,” says Mahmoud Ghannoum, a microbiologist at Case Western Reserve University. “If you just focus on bacteria, then you are ignoring an important part of the story.” “Fungi have often been ignored,” adds Thomas Auchtung, who studies what he calls “phylogenetically underappreciated forms of life” at Baylor College of Medicine. “And because they’ve been totally ignored, we’re not sure how important they are.” Auchtung and Ghannoum are part of a small community of researchers trying to untangle the role that fungi, a group that includes yeasts and molds, play alongside the larger population