Ten simple rules for responsible big data research

Unlocking ground-based imagery for habitat mapping

Fine-grained environmental data across large extents are needed to resolve the processes that impact species communities from local to global scales. Ground-based images (GBIs) have the potential to capture habitat complexity at biologically relevant spatial and temporal resolutions. Moving beyond existing applications of GBIs for species identification and monitoring ecological change from repeat photography, we describe promising approaches to habitat mapping, leveraging multimodal data and computer vision. We illustrate empirically how GBIs can be applied to predict distributions of species at fine scales along Street View routes, or to automatically classify and quantify habitat features. Further, we outline future research avenues using GBIs that can bring a leap forward in analyses for ecology and conservation with this underused resource.

Ten simple rules for managing laboratory information

Information is the cornerstone of research, from experimental (meta)data and computational processes to complex inventories of reagents and equipment. These 10 simple rules discuss best practices for leveraging laboratory information management systems to transform this large information load into useful scientific findings.

Multi-lingual multi-platform investigations of online trade in jaguar parts

We conducted research to understand online trade in jaguar parts and develop tools of utility for jaguars and other species. Our research took place to identify potential trade across 31 online platforms in Spanish, Portuguese, English, Dutch, French, Chinese, and Vietnamese. We identified 230 posts from between 2009 and 2019. We screened the images of animal parts shown in search results to verify if from jaguar; 71 posts on 12 different platforms in four languages were accompanied by images identified as definitely jaguar, including a total of 125 jaguar parts (50.7% posts in Spanish, 25.4% Portuguese, 22.5% Chinese and 1.4% French). Search effort varied among languages due to staff availability. Standardizing for effort across languages by dividing number of posts advertising jaguars by search time and number of individual searches completed via term/platform combinations changed the proportions the rankings of posts adjusted for effort were led by Portuguese, Chinese, and Spanish. Teeth were the most common part; 156 posts offered at least 367 teeth and from these, 95 were assessed as definitely jaguar; 71 of which could be linked to a location, with the majority offered for sale from Mexico, China, Bolivia, and Brazil (26.8, 25.4, 16.9, and 12.7% respectively). The second most traded item, skins and derivative items were only identified from Latin America: Brazil (7), followed by Peru (6), Bolivia (3), Mexico (2 and 1 skin piece), and Nicaragua and Venezuela (1 each). Whether by number of posts or pieces, the most commonly parts were: teeth, skins/pieces of skins, heads, and bodies. Our research took place within a longer-term project to assist law enforcement in host countries to better identify potential illegal trade and presents a snapshot of online jaguar trade and methods that also may have utility for many species traded online.

United in Big Data? Exploring scholars' opinions on academic-industry partnership and the use of corporate data in digital behavioral research

The growing amount of data produced through digital technologies holds great promise for advancing behavioral research. Scholars worldwide now have the chance to access an incredible amount of personal information, thanks to the digital trace users continuously leave behind them. Private corporations play a crucial role in this scenario as the leading collectors of data on users, thus creating new incentives for partnerships between academic institutions and private companies. Due to the concerns that academic-company partnerships might raise and the ethical issues connected with Big Data research, our study explores the challenges and opportunities associated with the academic use of corporate data. We conducted 39 semi-structured interviews with academic scholars (professors, senior researchers, and postdocs) involved in Big Data research in Switzerland and the United States. We also investigated their opinions on using corporate data for scholarly research. Researchers generally showed an interest in using corporate data; however, they coincidentally shared ethical reservations towards this practice, such as threats to research integrity and concerns about a lack of transparency of companies' practices. Furthermore, participants mentioned issues of scholarly access to corporate data that might both disadvantage the academic research community and create issues of scientific validity. Academic-company partnerships could be a positive development for the advancement of scholarly behavioral research. However, strategies should be implemented to appropriately guide collaborations and appropriate use of corporate data, like implementing updated protocols and tools to govern conflicts of interest and the institution of transparent regulatory bodies to ensure adequate oversight of academic-corporate research collaborations.

Using smartphone-GPS data to quantify human activity in green spaces

Cities are growing in density and coverage globally, increasing the value of green spaces for human health and well-being. Understanding the interactions between people and green spaces is also critical for biological conservation and sustainable development. However, quantifying green space use is particularly challenging. We used an activity index of anonymized GPS data from smart devices provided by Mapbox (www.mapbox.com) to characterize human activity in green spaces in the Greater Toronto Area, Canada. The goals of our study were to describe i) a methodological example of how anonymized GPS data could be used for human-nature research and ii) associations between park features and human activity. We describe some of the challenges and solutions with using this activity index, especially in the context of green spaces and biodiversity monitoring. We found the activity index was strongly correlated with visitation records (i.e., park reservations) and that these data are useful to identify high or low-usage areas within green spaces. Parks with a more extensive trail network typically experienced higher visitation rates and a substantial proportion of activity remained on trails. We identified certain land covers that were more frequently associated with human presence, such as rock formations, and find a relationship between human activity and tree composition. Our study demonstrates that anonymized GPS data from smart devices are a powerful tool for spatially quantifying human activity in green spaces. These could help to minimize trade-offs in the management of green spaces for human use and biological conservation will continue to be a significant challenge over the coming decades because of accelerating urbanization coupled with population growth. Importantly, we include a series of recommendations when using activity indexes for managing green spaces that can assist with biomonitoring and supporting sustainable human use.

Ten quick tips for sequence-based prediction of protein properties using machine learning

The ubiquitous availability of genome sequencing data explains the popularity of machine learning-based methods for the prediction of protein properties from their amino acid sequences. Over the years, while revising our own work, reading submitted manuscripts as well as published papers, we have noticed several recurring issues, which make some reported findings hard to understand and replicate. We suspect this may be due to biologists being unfamiliar with machine learning methodology, or conversely, machine learning experts may miss some of the knowledge needed to correctly apply their methods to proteins. Here, we aim to bridge this gap for developers of such methods. The most striking issues are linked to a lack of clarity: how were annotations of interest obtained; which benchmark metrics were used; how are positives and negatives defined. Others relate to a lack of rigor: If you sneak in structural information, your method is not sequence-based; if you compare your own model to "state-of-the-art," take the best methods; if you want to conclude that some method is better than another, obtain a significance estimate to support this claim. These, and other issues, we will cover in detail. These points may have seemed obvious to the authors during writing; however, they are not always clear-cut to the readers. We also expect many of these tips to hold for other machine learning-based applications in biology. Therefore, many computational biologists who develop methods in this particular subject will benefit from a concise overview of what to avoid and what to do instead.

Big data and development sociology: An overview and application on governance and accountability through digitalization in Tanzania

The digital revolution and the widespread use of the internet have changed many realms of empirical social science research. In this paper, we discuss the use of big data in the context of development sociology and highlight its potential as a new source of data. We provide a brief overview of big data and development research, discuss different data types, and review example studies, before introducing our case study on active citizenship in Tanzania which expands on an Oxfam-led impact evaluation. The project aimed at improving community-driven governance and accountability through the use of digital technology. Twitter and other social media platforms were introduced to community animators as a tool to hold national and regional key stakeholders accountable. We retrieve the complete Twitter timelines up to October 2021 from all ~200 community animators and influencers involved in the project (over 1.5 million tweets). We find that animators have started to use Twitter as part of the project, but most have stopped tweeting in the long term. Employing a dynamic difference-in-differences design, we also do not find effects of Oxfam-led training workshops on different aspects of animators' tweeting behavior. While most animators have stopped using Twitter in the long run, a few have continued to use social media to raise local issues and to be part of conversations to this day. Our case study showcases how (big) social media data can be part of an intervention, and we end with recommendations on how to use digital data in development sociology.

A concentric circles view of health data relations facilitates understanding of sociotechnical challenges for learning health systems and the role of federated data networks

The ability to use clinical and research data at scale is central to hopes for data-driven medicine. However, in using such data researchers often encounter hurdles–both technical, such as differing data security requirements, and social, such as the terms of informed consent, legal requirements and patient and public trust. Federated or distributed data networks have been proposed and adopted in response to these hurdles. However, to date there has been little consideration of how FDNs respond to both technical and social constraints on data use. In this Perspective we propose an approach to thinking about data in terms that make it easier to navigate the health data space and understand the value of differing approaches to data collection, storage and sharing. We set out a socio-technical model of data systems that we call the “Concentric Circles View” (CCV) of data-relationships. The aim is to enable a consistent understanding of the fit between the local relationships within which data are produced and the extended socio-technical systems that enable their use. The paper suggests this model can help understand and tackle challenges associated with the use of real-world data in the health setting. We use the model to understand not only how but why federated networks may be well placed to address emerging issues and adapt to the evolving needs of health research for patient benefit. We conclude that the CCV provides a useful model with broader application in mapping, understanding, and tackling the major challenges associated with using real world data in the health setting.

Diversifying the genomic data science research community

Over the past 20 years, the explosion of genomic data collection and the cloud computing revolution have made computational and data science research accessible to anyone with a web browser and an internet connection. However, students at institutions with limited resources have received relatively little exposure to curricula or professional development opportunities that lead to careers in genomic data science. To broaden participation in genomics research, the scientific community needs to support these programs in local education and research at underserved institutions (UIs). These include community colleges, historically Black colleges and universities, Hispanic-serving institutions, and tribal colleges and universities that support ethnically, racially, and socioeconomically underrepresented students in the United States. We have formed the Genomic Data Science Community Network to support students, faculty, and their networks to identify opportunities and broaden access to genomic data science. These opportunities include expanding access to infrastructure and data, providing UI faculty development opportunities, strengthening collaborations among faculty, recognizing UI teaching and research excellence, fostering student awareness, developing modular and open-source resources, expanding course-based undergraduate research experiences (CUREs), building curriculum, supporting student professional development and research, and removing financial barriers through funding programs and collaborator support.

Building a culture of responsible neurotech: Neuroethics as socio-technical challenges

Scientists around the globe are joining the race to achieve engineering feats to read, write, modulate, and interface with the human brain in a broadening continuum of invasive to non-invasive ways. The expansive implications of neurotechnology for our conception of health, mind, decision-making, and behavior has raised social and ethical considerations that are inextricable from neurotechnological progress. We propose "socio-technical" challenges as a framing to integrate neuroethics into the engineering process. Intentionally aligning societal and engineering goals within this framework offers a way to maximize the positive impact of next-generation neurotechnologies on society.

Considerations for an integrated population health databank in Africa: lessons from global best practices

Background: The rising digitisation and proliferation of data sources and repositories cannot be ignored. This trend expands opportunities to integrate and share population health data. Such platforms have many benefits, including the potential to efficiently translate information arising from such data to evidence needed to address complex global health challenges. There are pockets of quality data on the continent that may benefit from greater integration. Integration of data sources is however under-explored in Africa. The aim of this article is to identify the requirements and provide practical recommendations for developing a multi-consortia public and population health data-sharing framework for Africa.

Methods: We conducted a narrative review of global best practices and policies on data sharing and its optimisation. We searched eight databases for publications and undertook an iterative snowballing search of articles cited in the identified publications. The Leximancer software © enabled content analysis and selection of a sample of the most relevant articles for detailed review. Themes were developed through immersion in the extracts of selected articles using inductive thematic analysis. We also performed interviews with public and population health stakeholders in Africa to gather their experiences, perceptions, and expectations of data sharing.

Results: Our findings described global stakeholder experiences on research data sharing. We identified some challenges and measures to harness available resources and incentivise data sharing.  We further highlight progress made by the different groups in Africa and identified the infrastructural requirements and considerations when implementing data sharing platforms. Furthermore, the review suggests key reforms required, particularly in the areas of consenting, privacy protection, data ownership, governance, and data access.

Conclusions: The findings underscore the critical role of inclusion, social justice, public good, data security, accountability, legislation, reciprocity, and mutual respect in developing a responsive, ethical, durable, and integrated research data sharing ecosystem.

Data Integration Challenges for Machine Learning in Precision Medicine

A main goal of Precision Medicine is that of incorporating and integrating the vast corpora on different databases about the molecular and environmental origins of disease, into analytic frameworks, allowing the development of individualized, context-dependent diagnostics, and therapeutic approaches. In this regard, artificial intelligence and machine learning approaches can be used to build analytical models of complex disease aimed at prediction of personalized health conditions and outcomes. Such models must handle the wide heterogeneity of individuals in both their genetic predisposition and their social and environmental determinants. Computational approaches to medicine need to be able to efficiently manage, visualize and integrate, large datasets combining structure, and unstructured formats. This needs to be done while constrained by different levels of confidentiality, ideally doing so within a unified analytical architecture. Efficient data integration and management is key to the successful application of computational intelligence approaches to medicine. A number of challenges arise in the design of successful designs to medical data analytics under currently demanding conditions of performance in personalized medicine, while also subject to time, computational power, and bioethical constraints. Here, we will review some of these constraints and discuss possible avenues to overcome current challenges.

Ethics and governance for internet-based conservation science research

Internet-based research is increasingly important for conservation science and has wide-ranging applications and contexts, including culturomics, illegal wildlife trade, and citizen science. However, online research methods pose a range of ethical and legal challenges. Online data may be protected by copyright, database rights, or contract law. Privacy rights may also restrict the use and access of data, as well as ethical requirements from institutions. Online data have real-world meaning, and the ethical treatment of individuals and communities must not be marginalized when conducting internet-based research. As ethics frameworks originally developed for biomedical applications are inadequate for these methods, we propose that research activities involving the analysis of preexisting online data be treated analogous to offline social science methods, in particular, nondeceptive covert observation. By treating internet users and their data with respect and due consideration, conservationists can uphold the public trust needed to effectively address real-world issues.

Modeling Ethics: Approaches to Data Creep in Higher Education

Though rapid collection of big data is ubiquitous across domains, from industry settings to academic contexts, the ethics of big data collection and research are contested. A nexus of data ethics issues is the concept of creep, or repurposing of data for other applications or research beyond the conditions of original collection. Data creep has proven controversial and has prompted concerns about the scope of ethical oversight. Institutional review boards offer little guidance regarding big data, and problematic research can still meet ethical standards. While ethics seem concrete through institutional deployment, I frame ethics as produced. Informed by my ethnographic research at a large public university in the U.S., I explore ethics through two models: ethics as institutional procedures and ethics as acts and intentions. The university where I conducted fieldwork is the development grounds for a predictive model that uses student data to anticipate academic success. While students consent to data collection, the circumstances of consent and the degree to which they are informed are not so apparent, as many data are a product of creep. Drawing from interviews and participant observation with administrators, data scientists, developers, and students, I examine data ethics, from a larger institutional model to everyday enactments related to data creep. After demonstrating the limits of such models, I propose a remodeling of ethics that draws on recent works on data, justice, and refusal to pose generative questions for rethinking ethics in institutional contexts.

The Challenges of Big Data for Research Ethics Committees: A Qualitative Swiss Study

Big data trends in health research challenge the oversight mechanism of the Research Ethics Committees (RECs). The traditional standards of research quality and the mandate of RECs illuminate deficits in facing the computational complexity, methodological novelty, and limited auditability of these approaches. To better understand the challenges facing RECs, we explored the perspectives and attitudes of the members of the seven Swiss Cantonal RECs via semi-structured qualitative interviews. Our interviews reveal limited experience among REC members with the review of big data research, insufficient expertise in data science, and uncertainty about how to mitigate big data research risks. Nonetheless, RECs could strengthen their oversight by training in data science and big data ethics, complementing their role with external experts and ad hoc boards, and introducing precise shared practices.

Meaningful measures of human society in the twenty-first century

Science rarely proceeds beyond what scientists can observe and measure, and sometimes what can be observed proceeds far ahead of scientific understanding. The twenty-first century offers such a moment in the study of human societies. A vastly larger share of behaviours is observed today than would have been imaginable at the close of the twentieth century. Our interpersonal communication, our movements and many of our everyday actions, are all potentially accessible for scientific research; sometimes through purposive instrumentation for scientific objectives (for example, satellite imagery), but far more often these objectives are, literally, an afterthought (for example, Twitter data streams). Here we evaluate the potential of this massive instrumentation-the creation of techniques for the structured representation and quantification-of human behaviour through the lens of scientific measurement and its principles. In particular, we focus on the question of how we extract scientific meaning from data that often were not created for such purposes. These data present conceptual, computational and ethical challenges that require a rejuvenation of our scientific theories to keep up with the rapidly changing social realities and our capacities to capture them. We require, in other words, new approaches to manage, use and analyse data.

Getting into the engine room: a blueprint to investigate the shadowy steps of AI ethics

Enacting an AI system typically requires three iterative phases where AI engineers are in command: selection and preparation of the data, selection and configuration of algorithmic tools, and fine-tuning of the different parameters on the basis of intermediate results. Our main hypothesis is that these phases involve practices with ethical questions. This paper maps these ethical questions and proposes a way to address them in light of a neo-republican understanding of freedom, defined as absence of domination. We thereby identify different types of responsibility held by AI engineers and link them to concrete suggestions on how to improve professional practices. This paper contributes to the literature on AI and ethics by focusing on the work necessary to configure AI systems, thereby offering an input to better practices and an input for societal debates.

Understanding changes in park visitation during the COVID-19 pandemic: A spatial application of big data

In the spring of 2020, the COVID-19 pandemic changed the daily lives of people around the world. In an effort to quantify these changes, Google released an open-source dataset pertaining to regional mobility trends-including park visitation trends. Changes in park visitation are calculated from an earlier baseline period for measurement. Park visitation is robustly linked to positive wellbeing indicators across the lifespan, and has been shown to support wellbeing during the COVID-19 pandemic. Therefore, this dataset offers vast application potential, containing aggregated information from location data collected via smartphones worldwide. However, empirical analysis of these data is limited. Namely, the factors influencing reported changes in mobility and the degree to which these changes can be directly attributable to COVID-19 remain unknown. This study aims to address these gaps in our understanding of the changes in park visitation, the causes of these changes (e.g., safer-at-home orders, amount of COVID-19 cases per county, climate, etc.) and possible impacts to wellbeing by constructing and testing a spatial regression model. Results suggest that elevation and latitude serve as primary influences of reported changes in park visitation from the baseline period. Therefore, it is surmised that Google's reported changes in park-related mobility are only partially the function of COVID-19.

Exploring human-nature interactions in national parks with social media photographs and computer vision

Understanding the activities and preferences of visitors is crucial for managing protected areas and planning conservation strategies. Conservation culturomics promotes the use of user-generated online content in conservation science. Geotagged social media content is a unique source of in situ information on human presence and activities in nature. Photographs posted on social media platforms are a promising source of information, but analyzing large volumes of photographs manually remains laborious. We examined the application of state-of-the-art computer-vision methods to studying human-nature interactions. We used semantic clustering, scene classification, and object detection to automatically analyze photographs taken in Finnish national parks by domestic and international visitors. Our results showed that human-nature interactions can be extracted from user-generated photographs with computer vision. The different methods complemented each other by revealing broad visual themes related to level of the data set, landscape photogeneity, and human activities. Geotagged photographs revealed distinct regional profiles for national parks (e.g., preferences in landscapes and activities), which are potentially useful in park management. Photographic content differed between domestic and international visitors, which indicates differences in activities and preferences. Information extracted automatically from photographs can help identify preferences among diverse visitor groups, which can be used to create profiles of national parks for conservation marketing and to support conservation strategies that rely on public acceptance. The application of computer-vision methods to automatic content analysis of photographs should be explored further in conservation culturomics, particularly in combination with rich metadata available on social media platforms.

Using culturomics and social media data to characterize wildlife consumption

Wildlife provides food, medicine, clothing, and other necessities for humans, but overexploitation can disrupt the sustainability of wildlife resources and severely threaten global biodiversity. Understanding the characteristics of consumer behavior is helpful for wildlife managers and policy makers, but the traditional survey methods are laborious and time-consuming. In contrast, culturomics may more efficiently identify the features of wildlife consumption. As a case study of the culturomics approach, we examined tiger bone wine consumption in China based on social media and Baidu search engine data. Tiger bone wine is one of the most purchased tiger products; its consumption is closely related to tiger poaching, which greatly threatens wild tiger survival. We searched a popular social media website for the term "tiger bone wine" and focused on posts that were originally created from 1 January 2012 to 31 December 2018. We filtered and classified posts related to the purchase, sale, or consumption of tiger bone wine and extracted information on providers, consumption motivations, year of production, and place of origin of the tiger bone wines based on the texts and photos of these posts. We found 756 posts related to tiger bone wine consumption, 113 of which mentioned providers of tiger bone wine, including friends (53%), elder relatives (37%), peer relatives (7%), and others (3%). Out of the 756 posts, 266 indicated the motivations of tiger bone wine consumption. Tiger bone wines were consumed as a tonic (34%), medicine (23%), game product (30%), and a symbol of wealth (28%). Some posts indicated ≥2 consumption motivations. These findings were consistent with the search queries from Baidu index. Such information could help develop targeted strategies for tiger conservation. The culturomics approach illustrated by our study is a rapid and cost-efficient way to characterize wildlife consumption.

Ethical Issues in Consent for the Reuse of Data in Health Data Platforms

Data platforms represent a new paradigm for carrying out health research. In the platform model, datasets are pooled for remote access and analysis, so novel insights for developing better stratified and/or personalised medicine approaches can be derived from their integration. If the integration of diverse datasets enables development of more accurate risk indicators, prognostic factors, or better treatments and interventions, this obviates the need for the sharing and reuse of data; and a platform-based approach is an appropriate model for facilitating this. Platform-based approaches thus require new thinking about consent. Here we defend an approach to meeting this challenge within the data platform model, grounded in: the notion of 'reasonable expectations' for the reuse of data; Waldron's account of 'integrity' as a heuristic for managing disagreement about the ethical permissibility of the approach; and the element of the social contract that emphasises the importance of public engagement in embedding new norms of research consistent with changing technological realities. While a social contract approach may sound appealing, however, it is incoherent in the context at hand. We defend a way forward guided by that part of the social contract which requires public approval for the proposal and argue that we have moral reasons to endorse a wider presumption of data reuse. However, we show that the relationship in question is not recognisably contractual and that the social contract approach is therefore misleading in this context. We conclude stating four requirements on which the legitimacy of our proposal rests.

Towards an educational data literacy framework: enhancing the profiles of instructional designers and e-tutors of online and blended courses with new competences

In the era of digitalization of learning and teaching processes, Educational Data Literacy (EDL) is highly valued and is becoming essential. EDL is conceptualized as the ability to collect, manage, analyse, comprehend, interpret, and act upon educational data in an ethical, meaningful, and critical manner. The professionals in the field of digitally supported education, i.e., Instructional Designers (IDs) and e-Tutors (eTUTs) of online and blended courses, need to be ready to inform their decisions with educational data, and face the upcoming data-related challenges; they need to update and enhance their profiles with relevant competences. This paper proposes a framework for EDL competence profiles of IDs/eTUTs and evaluates the proposal with the participation of worldwide professionals (N = 210) with experience in digitally supported education. The evaluation aims at validating the proposal and assesses (a) the current EDL-readiness of IDs/eTUTs; and (b) the extent to which the framework captures and describes the essential EDL competences. The findings indicate that professionals are not EDL-competent yet, but the proposed dimensions and related competences are offering a solid approach to support EDL development.

Understanding changes in park visitation during the COVID-19 pandemic: A spatial application of big data

In the spring of 2020, the COVID-19 pandemic changed the daily lives of people around the world. In an effort to quantify these changes, Google released an open-source dataset pertaining to regional mobility trends-including park visitation trends. Changes in park visitation are calculated from an earlier baseline period for measurement. Park visitation is robustly linked to positive wellbeing indicators across the lifespan, and has been shown to support wellbeing during the COVID-19 pandemic. Therefore, this dataset offers vast application potential, containing aggregated information from location data collected via smartphones worldwide. However, empirical analysis of these data is limited. Namely, the factors influencing reported changes in mobility and the degree to which these changes can be directly attributable to COVID-19 remain unknown. This study aims to address these gaps in our understanding of the changes in park visitation, the causes of these changes (e.g., safer-at-home orders, amount of COVID-19 cases per county, climate, etc.) and possible impacts to wellbeing by constructing and testing a spatial regression model. Results suggest that elevation and latitude serve as primary influences of reported changes in park visitation from the baseline period. Therefore, it is surmised that Google's reported changes in park-related mobility are only partially the function of COVID-19.

Second-Generation Digital Health Platforms: Placing the Patient at the Center and Focusing on Clinical Outcomes

Artificial intelligence (AI) digital health systems have drawn much attention over the last decade. However, their implementation into medical practice occurs at a much slower pace than expected. This paper reviews some of the achievements of first-generation AI systems, and the barriers facing their implementation into medical practice. The development of second-generation AI systems is discussed with a focus on overcoming some of these obstacles. Second-generation systems are aimed at focusing on a single subject and on improving patients' clinical outcomes. A personalized closed-loop system designed to improve end-organ function and the patient's response to chronic therapies is presented. The system introduces a platform which implements a personalized therapeutic regimen and introduces quantifiable individualized-variability patterns into its algorithm. The platform is designed to achieve a clinically meaningful endpoint by ensuring that chronic therapies will have sustainable effect while overcoming compensatory mechanisms associated with disease progression and drug resistance. Second-generation systems are expected to assist patients and providers in adopting and implementing of these systems into everyday care.

First do no harm: An exploration of researchers' ethics of conduct in Big Data behavioral studies

Research ethics has traditionally been guided by well-established documents such as the Belmont Report and the Declaration of Helsinki. At the same time, the introduction of Big Data methods, that is having a great impact in behavioral research, is raising complex ethical issues that make protection of research participants an increasingly difficult challenge. By conducting 39 semi-structured interviews with academic scholars in both Switzerland and United States, our research aims at exploring the code of ethics and research practices of academic scholars involved in Big Data studies in the fields of psychology and sociology to understand if the principles set by the Belmont Report are still considered relevant in Big Data research. Our study shows how scholars generally find traditional principles to be a suitable guide to perform ethical data research but, at the same time, they recognized and elaborated on the challenges embedded in their practical application. In addition, due to the growing introduction of new actors in scholarly research, such as data holders and owners, it was also questioned whether responsibility to protect research participants should fall solely on investigators. In order to appropriately address ethics issues in Big Data research projects, education in ethics, exchange and dialogue between research teams and scholars from different disciplines should be enhanced. In addition, models of consultancy and shared responsibility between investigators, data owners and review boards should be implemented in order to ensure better protection of research participants.

Twelve quick steps for genome assembly and annotation in the classroom

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.

Next-generation visitation models using social media to estimate recreation on public lands

Outdoor and nature-based recreation provides countless social benefits, yet public land managers often lack information on the spatial and temporal extent of recreation activities. Social media is a promising source of data to fill information gaps because the amount of recreational use is positively correlated with social media activity. However, despite the implication that these correlations could be employed to accurately estimate visitation, there are no known transferable models parameterized for use with multiple social media data sources. This study tackles these issues by examining the relative value of multiple sources of social media in models that estimate visitation at unmonitored sites and times across multiple destinations. Using a novel dataset of over 30,000 social media posts and 286,000 observed visits from two regions in the United States, we compare multiple competing statistical models for estimating visitation. We find social media data substantially improve visitor estimates at unmonitored sites, even when a model is parameterized with data from another region. Visitation estimates are further improved when models are parameterized with on-site counts. These findings indicate that while social media do not fully substitute for on-site data, they are a powerful component of recreation research and visitor management.

Health Forums and Twitter for Dementia Research: Opportunities and Considerations

BACKGROUND/OBJECTIVES

Social media platforms are promising sources for large quantities of participant-driven research data and circumvent some common challenges when conducting dementia research. This study provides a summary of key considerations and recommendations about using these platforms as research tools for dementia.

DESIGN

Mixed methods.

SETTING

Alzheimer's Society's online Dementia Talking Point forum from inception to April 17, 2018, and Twitter in February and March 2018.

PARTICIPANTS

All users of Dementia Talking Point who posted in subforums labeled "I have dementia" and "I care for a person with dementia," and Twitter users whose posts contained the keywords "dementia," "Alzheimer," or "Alzheimer's."

MEASUREMENTS

We quantified the average daily number of dementia-related posts on each platform and number of words per post. Guided by a codebook, we conducted thematic content analysis of 5% of the 15,513 posts collected from Dementia Talking Point, and 10% of the 25,948 comprehensible posts from Twitter containing "dementia," "Alzheimer," or "Alzheimer's." We also summarized research-relevant characteristics inherent to platforms and posts.

RESULTS

On average, Dementia Talking Point provided less than two new daily dementia-related posts with 213.5 to 241.5 words, compared with 7,883 new daily Twitter posts with 14.5 words. Persons with dementia (PWDs) commonly shared dementia-related concerns (75.7%), experiences (68.6%), and requests for, as well as offers of, information and support (44.3% and 38.6%, respectively). Caregivers commonly shared caregiving experience (67.0%) and requests for information and support (52.5%). Most common dementia-related Twitter posts were derogatory use of the term dementia (14.5%), advocacy, fundraising, and awareness (11.6%), and research dissemination (8.0%). Recommendations about these platforms' unique technical and ethical considerations are outlined.

CONCLUSIONS

Understanding the priorities of PWDs and their caregivers remains important to understand how clinicians can best support them. This study will help clinicians and researcher to better leverage online health forums and Twitter for such dementia-related information.

Discussions of miscarriage and preterm births on Twitter

BACKGROUND

Experiences typically considered private, such as, miscarriages and preterm births are being discussed publicly on social media and Internet discussion websites. These data can provide timely illustrations of how individuals discuss miscarriages and preterm births, as well as insights into the wellbeing of women who have experienced a miscarriage.

OBJECTIVES

To characterise how users discuss the topic of miscarriage and preterm births on Twitter, analyse trends and drivers, and describe the perceived emotional state of women who have experienced a miscarriage.

METHODS

We obtained 291 443 Twitter postings on miscarriages and preterm births from January 2017 through December 2018. Latent Dirichlet Allocation (LDA) was used to identify major topics of discussion. We applied time series decomposition methods to assess temporal trends and identify major drivers of discussion. Furthermore, four coders labelled the emotional content of 7282 personal miscarriage disclosure tweets into the following non-mutually exclusive categories: grief/sadness/depression, anger, relief, isolation, annoyance, and neutral.

RESULTS

Topics in our data fell into eight groups: celebrity disclosures, Michelle Obama's disclosure, politics, healthcare, preterm births, loss and anxiety, flu vaccine and ectopic pregnancies. Political discussions around miscarriages were largely due to a misunderstanding between abortions and miscarriages. Grief and annoyance were the most commonly expressed emotions within the miscarriage self-disclosures; 50.6% (95% confidence interval [CI] 49.1, 52.2) and 16.2% (95% CI 15.2, 17.3). Postings increased with celebrity disclosures, pharmacists' refusal of prescribed medications and outrage over the high rate of preterm births in the United States. Miscarriage disclosures by celebrities also led to disclosures by women who had similar experiences.

CONCLUSIONS

This study suggests that increase in discussions of miscarriage on social media are associated with several factors, including celebrity disclosures. Additionally, there is a misunderstanding of the potential physical, emotional and psychological impacts on individuals who lose a pregnancy due to a miscarriage.

Evolution and impact of bias in human and machine learning algorithm interaction

Traditionally, machine learning algorithms relied on reliable labels from experts to build predictions. More recently however, algorithms have been receiving data from the general population in the form of labeling, annotations, etc. The result is that algorithms are subject to bias that is born from ingesting unchecked information, such as biased samples and biased labels. Furthermore, people and algorithms are increasingly engaged in interactive processes wherein neither the human nor the algorithms receive unbiased data. Algorithms can also make biased predictions, leading to what is now known as algorithmic bias. On the other hand, human's reaction to the output of machine learning methods with algorithmic bias worsen the situations by making decision based on biased information, which will probably be consumed by algorithms later. Some recent research has focused on the ethical and moral implication of machine learning algorithmic bias on society. However, most research has so far treated algorithmic bias as a static factor, which fails to capture the dynamic and iterative properties of bias. We argue that algorithmic bias interacts with humans in an iterative manner, which has a long-term effect on algorithms' performance. For this purpose, we present an iterated-learning framework that is inspired from human language evolution to study the interaction between machine learning algorithms and humans. Our goal is to study two sources of bias that interact: the process by which people select information to label (human action); and the process by which an algorithm selects the subset of information to present to people (iterated algorithmic bias mode). We investigate three forms of iterated algorithmic bias (personalization filter, active learning, and random) and how they affect the performance of machine learning algorithms by formulating research questions about the impact of each type of bias. Based on statistical analyses of the results of several controlled experiments, we found that the three different iterated bias modes, as well as initial training data class imbalance and human action, do affect the models learned by machine learning algorithms. We also found that iterated filter bias, which is prominent in personalized user interfaces, can lead to more inequality in estimated relevance and to a limited human ability to discover relevant data. Our findings indicate that the relevance blind spot (items from the testing set whose predicted relevance probability is less than 0.5 and who thus risk being hidden from humans) amounted to 4% of all relevant items when using a content-based filter that predicts relevant items. A similar simulation using a real-life rating data set found that the same filter resulted in a blind spot size of 75% of the relevant testing set.

Foundational Practices of Research Data Management

The importance of research data has grown as researchers across disciplines seek to ensure reproducibility, facilitate data reuse, and acknowledge data as a valuable scholarly commodity. Researchers are under increasing pressure to share their data for validation and reuse. Adopting good data management practices allows researchers to efficiently locate their data, understand it, and use it throughout all of the stages of a project and in the future. Additionally, good data management can streamline data analysis, visualization, and reporting, thus making publication less stressful and time-consuming. By implementing foundational practices of data management, researchers set themselves up for success by formalizing processes and reducing common errors in data handling, which can free up more time for research. This paper provides an introduction to best practices for managing all types of data.

COVID-19 is spatial: Ensuring that mobile Big Data is used for social good

The mobility restrictions related to COVID-19 pandemic have resulted in the biggest disruption to individual mobilities in modern times. The crisis is clearly spatial in nature, and examining the geographical aspect is important in understanding the broad implications of the pandemic. The avalanche of mobile Big Data makes it possible to study the spatial effects of the crisis with spatiotemporal detail at the national and global scales. However, the current crisis also highlights serious limitations in the readiness to take the advantage of mobile Big Data for social good, both within and beyond the interests of health sector. We propose two strategical pathways for the future use of mobile Big Data for societal impact assessment, addressing access to both raw mobile Big Data as well as aggregated data products. Both pathways require careful considerations of privacy issues, harmonized and transparent methodologies, and attention to the representativeness, reliability and continuity of data. The goal is to be better prepared to use mobile Big Data in future crises.