Dwarna : a blockchain solution for dynamic consent in biobanking

Dynamic consent aims to empower research partners and facilitate active participation in the research process. Used within the context of biobanking, it gives individuals access to information and control to determine how and where their biospecimens and data should be used. We present Dwarna—a web portal for ‘dynamic consent’ that acts as a hub connecting the different stakeholders of the Malta Biobank: biobank managers, researchers, research partners, and the general public. The portal stores research partners’ consent in a blockchain to create an immutable audit trail of research partners’ consent changes. Dwarna’s structure also presents a solution to the European Union’s General Data Protection Regulation’s right to erasure—a right that is seemingly incompatible with the blockchain model. Dwarna’s transparent structure increases trustworthiness in the biobanking process by giving research partners more control over which research studies they participate in, by facilitating the withdrawal of consent and by making it possible to request that the biospecimen and associated data are destroyed.peer-reviewe

The myth of reproducibility : a review of event tracking evaluations on Twitter

Event tracking literature based on Twitter does not have a state-of-the-art. What it does have is a plethora of manual evaluation methodologies and inventive automatic alternatives: incomparable and irreproducible studies incongruous with the idea of a state-of-the-art. Many researchers blame Twitter's data sharing policy for the lack of common datasets and a universal ground truth–for the lack of reproducibility–but many other issues stem from the conscious decisions of those same researchers. In this paper, we present the most comprehensive review yet on event tracking literature's evaluations on Twitter. We explore the challenges of manual experiments, the insufficiencies of automatic analyses and the misguided notions on reproducibility. Crucially, we discredit the widely-held belief that reusing tweet datasets could induce reproducibility. We reveal how tweet datasets self-sanitize over time; how spam and noise become unavailable at much higher rates than legitimate content, rendering downloaded datasets incomparable with the original. Nevertheless, we argue that Twitter's policy can be a hindrance without being an insurmountable barrier, and propose how the research community can make its evaluations more reproducible. A state-of-the-art remains attainable for event tracking research.peer-reviewe

An automatic participant detection framework for event tracking on twitter

Topic Detection and Tracking (TDT) on Twitter emulates human identifying developments in events from a stream of tweets, but while event participants are important for humans to understand what happens during events, machines have no knowledge of them. Our evaluation on football matches and basketball games shows that identifying event participants from tweets is a difficult problem exacerbated by Twitter’s noise and bias. As a result, traditional Named Entity Recognition (NER) approaches struggle to identify participants from the pre-event Twitter stream. To overcome these challenges, we describe Automatic Participant Detection (APD) to detect an event’s participants before the event starts and improve the machine understanding of events. We propose a six-step framework to identify participants and present our implementation, which combines information from Twitter’s pre-event stream and Wikipedia. In spite of the difficulties associated with Twitter and NER in the challenging context of events, our approach manages to restrict noise and consistently detects the majority of the participants. By empowering machines with some of the knowledge that humans have about events, APD lays the foundation not just for improved TDT.peer-reviewe

Capture it on video: Implementing a novel knowledge translation strategy as part of the Safe Motherhood Project, Jimma Zone, Ethiopia

This short report addresses videography as a novel knowledge translation tool in maternal, newborn and child health (MNCH) research, detailing the experiences of the Safe Motherhood Research Project in Ethiopia. The Safe Motherhood Research Project (2015-2020) studied the implementation and scale up of MNCH interventions in rural communities of Jimma Zone, Ethiopia. In 2018, a videography component was integrated into the project, including three major activities: producing a video documentary; delivering capacity building workshops for university students and staff; and donating video equipment to the Jimma University Institute of Health. These activities have increased the exposure of the research project to a broader audience and enabled university students and staff to undertake new videography projects. Challenges, lessons learned, and future opportunities are detailed in the hopes that other research teams can adopt videography to increase the exposure and impact of their research.   Ce court rapport aborde la vidéographie comme un nouvel outil d'application des connaissances dans la recherche sur la santé des mères et des enfants (SME), détaillant les expériences du Safe Motherhood Research Project en Éthiopie. Le projet de recherche (2015-2020) a étudié la mise en oeuvre et l'intensification des interventions de SME dans les communautés rurales de la zone de Jimma, en Éthiopie. En 2018, un élément vidéographie a été intégré au projet, comprenant trois activités majeures : la production d'un documentaire vidéo; organiser des ateliers de renforcement des capacités pour les étudiants et le personnel universitaires ; et en faisant don d'équipement vidéo à institut de la santé à l'Université Jimma. Ces activités ont accru l'exposition du projet de recherche à un public plus large et ont permis aux étudiants et au personnel universitaire d'entreprendre de nouveaux projets de vidéographie. Les défis, les leçons apprises et les opportunités futures sont détaillés dans l'espoir que d'autres équipes de recherche puissent utiliser la vidéographie pour augmenter la visibilité et l'impact de leur recherch

Longitudinal performance of senescence accelerated mouse prone-strain 8 (SAMP8) mice in an olfactory-visual water maze challenge

© 2018 Lam, Takechi, Albrecht, D’Alonzo, Graneri, Hackett, Coulson, Fimognari, Nesbit and Mamo. Morris water maze (MWM) is widely used to assess cognitive deficits in pre-clinical rodent models. Latency time to reach escape platform is frequently reported, but may be confounded by deficits in visual acuity, or differences in locomotor activity. This study compared performance of Senescence Accelerated Mouse Prone-Strain 8 (SAMP8) and control Senescence Accelerated Mouse Resistant-Strain 1 (SAMR1) mice in classical MWM, relative to performance in a newly developed olfactory-visual maze testing protocol. Performance indicated as the escape time to rescue platform for classical MWM testing showed that SAMP8 mice as young as 6 weeks of age did poorly relative to age-matched SAMR1 mice. The olfactory-visual maze challenge described better discriminated SAMP8 vs. SAMR1 mice than classical MWM testing, based on latency time measures. Consideration of the distance traveled rather than latency time in the classical MWM found no treatment effects between SAMP8 and SAMR1 at 40 weeks of age and the olfactory-visual measures of performance confirmed the classical MWM findings. Longitudinal (repeat) assessment of SAMP8 and SAMR1 performance at 6, 20, 30, and 40 weeks of age in the olfactory-visual testing protocol showed no age-associated deficits in SAMP8 mice to the last age end-point indicated. Collectively, the results from this study suggest the olfactory-visual testing protocol may be advantageous compared to classical MWM as it avoids potential confounders of visual impairment in some strains of mice and indeed, may offer insight into cognitive and behavioral deficits that develop with advanced age in the widely used SAMP8 murine model

Evaluation of Kenya’s readiness to transition from sentinel surveillance to routine HIV testing for antenatal clinic-based HIV surveillance

BACKGROUND: Sentinel surveillance for HIV among women attending antenatal clinics using unlinked anonymous testing is a cornerstone of HIV surveillance in sub-Saharan Africa. Increased use of routine antenatal HIV testing allows consideration of using these programmatic data rather than sentinel surveillance data for HIV surveillance. METHODS: To gauge Kenya’s readiness to discontinue sentinel surveillance, we evaluated whether recommended World Health Organization standards were fulfilled by conducting data and administrative reviews of antenatal clinics that offered both routine testing and sentinel surveillance in 2010. RESULTS: The proportion of tests that were HIV-positive among women aged 15–49 years was 6.2 % (95 % confidence interval [CI] 4.6–7.7 %] in sentinel surveillance and 6.5 % (95 % CI 5.1–8.0 %) in routine testing. The agreement of HIV test results between sentinel surveillance and routine testing was 98.0 %, but 24.1 % of specimens that tested positive in sentinel surveillance were recorded as negative in routine testing. Data completeness was moderate, with HIV test results recorded for 87.8 % of women who received routine testing. CONCLUSIONS: Additional preparation is required before routine antenatal HIV testing data can supplant sentinel surveillance in Kenya. As the quality of program data has markedly improved since 2010 a repeat evaluation of the use of routine antenatal HIV testing data in lieu of ANC sentinel surveillance is recommended

Modeling the interactions between river morphodynamics and riparian vegetation

The study of river-riparian vegetation interactions is an important and intriguing research field in geophysics. Vegetation is an active element of the ecological dynamics of a floodplain which interacts with the fluvial processes and affects the flow field, sediment transport, and the morphology of the river. In turn, the river provides water, sediments, nutrients, and seeds to the nearby riparian vegetation, depending on the hydrological, hydraulic, and geomorphological characteristic of the stream. In the past, the study of this complex theme was approached in two different ways. On the one hand, the subject was faced from a mainly qualitative point of view by ecologists and biogeographers. Riparian vegetation dynamics and its spatial patterns have been described and demonstrated in detail, and the key role of several fluvial processes has been shown, but no mathematical models have been proposed. On the other hand, the quantitative approach to fluvial processes, which is typical of engineers, has led to the development of several morphodynamic models. However, the biological aspect has usually been neglected, and vegetation has only been considered as a static element. In recent years, different scientific communities (ranging from ecologists to biogeographers and from geomorphologists to hydrologists and fluvial engineers) have begun to collaborate and have proposed both semiquantitative and quantitative models of river-vegetation interconnections. These models demonstrate the importance of linking fluvial morphodynamics and riparian vegetation dynamics to understand the key processes that regulate a riparian environment in order to foresee the impact of anthropogenic actions and to carefully manage and rehabilitate riparian areas. In the first part of this work, we review the main interactions between rivers and riparian vegetation, and their possible modeling. In the second part, we discuss the semiquantitative and quantitative models which have been proposed to date, considering both multi- and single-thread river

Healthcare Access and Quality Index based on mortality from causes amenable to personal health care in 195 countries and territories, 1990-2015 : a novel analysis from the Global Burden of Disease Study 2015

Background National levels of personal health-care access and quality can be approximated by measuring mortality rates from causes that should not be fatal in the presence of effective medical care (ie, amenable mortality). Previous analyses of mortality amenable to health care only focused on high-income countries and faced several methodological challenges. In the present analysis, we use the highly standardised cause of death and risk factor estimates generated through the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) to improve and expand the quantification of personal health-care access and quality for 195 countries and territories from 1990 to 2015. Methods We mapped the most widely used list of causes amenable to personal health care developed by Nolte and McKee to 32 GBD causes. We accounted for variations in cause of death certification and misclassifications through the extensive data standardisation processes and redistribution algorithms developed for GBD. To isolate the effects of personal health-care access and quality, we risk-standardised cause-specific mortality rates for each geography-year by removing the joint effects of local environmental and behavioural risks, and adding back the global levels of risk exposure as estimated for GBD 2015. We employed principal component analysis to create a single, interpretable summary measure-the Healthcare Quality and Access (HAQ) Index-on a scale of 0 to 100. The HAQ Index showed strong convergence validity as compared with other health-system indicators, including health expenditure per capita (r= 0.88), an index of 11 universal health coverage interventions (r= 0.83), and human resources for health per 1000 (r= 0.77). We used free disposal hull analysis with bootstrapping to produce a frontier based on the relationship between the HAQ Index and the Socio-demographic Index (SDI), a measure of overall development consisting of income per capita, average years of education, and total fertility rates. This frontier allowed us to better quantify the maximum levels of personal health-care access and quality achieved across the development spectrum, and pinpoint geographies where gaps between observed and potential levels have narrowed or widened over time. Findings Between 1990 and 2015, nearly all countries and territories saw their HAQ Index values improve; nonetheless, the difference between the highest and lowest observed HAQ Index was larger in 2015 than in 1990, ranging from 28.6 to 94.6. Of 195 geographies, 167 had statistically significant increases in HAQ Index levels since 1990, with South Korea, Turkey, Peru, China, and the Maldives recording among the largest gains by 2015. Performance on the HAQ Index and individual causes showed distinct patterns by region and level of development, yet substantial heterogeneities emerged for several causes, including cancers in highest-SDI countries; chronic kidney disease, diabetes, diarrhoeal diseases, and lower respiratory infections among middle-SDI countries; and measles and tetanus among lowest-SDI countries. While the global HAQ Index average rose from 40.7 (95% uncertainty interval, 39.0-42.8) in 1990 to 53.7 (52.2-55.4) in 2015, far less progress occurred in narrowing the gap between observed HAQ Index values and maximum levels achieved; at the global level, the difference between the observed and frontier HAQ Index only decreased from 21.2 in 1990 to 20.1 in 2015. If every country and territory had achieved the highest observed HAQ Index by their corresponding level of SDI, the global average would have been 73.8 in 2015. Several countries, particularly in eastern and western sub-Saharan Africa, reached HAQ Index values similar to or beyond their development levels, whereas others, namely in southern sub-Saharan Africa, the Middle East, and south Asia, lagged behind what geographies of similar development attained between 1990 and 2015. Interpretation This novel extension of the GBD Study shows the untapped potential for personal health-care access and quality improvement across the development spectrum. Amid substantive advances in personal health care at the national level, heterogeneous patterns for individual causes in given countries or territories suggest that few places have consistently achieved optimal health-care access and quality across health-system functions and therapeutic areas. This is especially evident in middle-SDI countries, many of which have recently undergone or are currently experiencing epidemiological transitions. The HAQ Index, if paired with other measures of health-systemcharacteristics such as intervention coverage, could provide a robust avenue for tracking progress on universal health coverage and identifying local priorities for strengthening personal health-care quality and access throughout the world. Copyright (C) The Author(s). Published by Elsevier Ltd.Peer reviewe

Measuring the health-related Sustainable Development Goals in 188 countries : a baseline analysis from the Global Burden of Disease Study 2015

Background In September, 2015, the UN General Assembly established the Sustainable Development Goals (SDGs). The SDGs specify 17 universal goals, 169 targets, and 230 indicators leading up to 2030. We provide an analysis of 33 health-related SDG indicators based on the Global Burden of Diseases, Injuries, and Risk Factors Study 2015 (GBD 2015). Methods We applied statistical methods to systematically compiled data to estimate the performance of 33 health-related SDG indicators for 188 countries from 1990 to 2015. We rescaled each indicator on a scale from 0 (worst observed value between 1990 and 2015) to 100 (best observed). Indices representing all 33 health-related SDG indicators (health-related SDG index), health-related SDG indicators included in the Millennium Development Goals (MDG index), and health-related indicators not included in the MDGs (non-MDG index) were computed as the geometric mean of the rescaled indicators by SDG target. We used spline regressions to examine the relations between the Socio-demographic Index (SDI, a summary measure based on average income per person, educational attainment, and total fertility rate) and each of the health-related SDG indicators and indices. Findings In 2015, the median health-related SDG index was 59.3 (95% uncertainty interval 56.8-61.8) and varied widely by country, ranging from 85.5 (84.2-86.5) in Iceland to 20.4 (15.4-24.9) in Central African Republic. SDI was a good predictor of the health-related SDG index (r(2) = 0.88) and the MDG index (r(2) = 0.2), whereas the non-MDG index had a weaker relation with SDI (r(2) = 0.79). Between 2000 and 2015, the health-related SDG index improved by a median of 7.9 (IQR 5.0-10.4), and gains on the MDG index (a median change of 10.0 [6.7-13.1]) exceeded that of the non-MDG index (a median change of 5.5 [2.1-8.9]). Since 2000, pronounced progress occurred for indicators such as met need with modern contraception, under-5 mortality, and neonatal mortality, as well as the indicator for universal health coverage tracer interventions. Moderate improvements were found for indicators such as HIV and tuberculosis incidence, minimal changes for hepatitis B incidence took place, and childhood overweight considerably worsened. Interpretation GBD provides an independent, comparable avenue for monitoring progress towards the health-related SDGs. Our analysis not only highlights the importance of income, education, and fertility as drivers of health improvement but also emphasises that investments in these areas alone will not be sufficient. Although considerable progress on the health-related MDG indicators has been made, these gains will need to be sustained and, in many cases, accelerated to achieve the ambitious SDG targets. The minimal improvement in or worsening of health-related indicators beyond the MDGs highlight the need for additional resources to effectively address the expanded scope of the health-related SDGs.Peer reviewe

Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015

Forouzanfar MH, Afshin A, Alexander LT, et al. Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015. LANCET. 2016;388(10053):1659-1724.Background The Global Burden of Diseases, Injuries, and Risk Factors Study 2015 provides an up-to-date synthesis of the evidence for risk factor exposure and the attributable burden of disease. By providing national and subnational assessments spanning the past 25 years, this study can inform debates on the importance of addressing risks in context. Methods We used the comparative risk assessment framework developed for previous iterations of the Global Burden of Disease Study to estimate attributable deaths, disability-adjusted life-years (DALYs), and trends in exposure by age group, sex, year, and geography for 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks from 1990 to 2015. This study included 388 risk-outcome pairs that met World Cancer Research Fund-defined criteria for convincing or probable evidence. We extracted relative risk and exposure estimates from randomised controlled trials, cohorts, pooled cohorts, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. We developed a metric that allows comparisons of exposure across risk factors-the summary exposure value. Using the counterfactual scenario of theoretical minimum risk level, we estimated the portion of deaths and DALYs that could be attributed to a given risk. We decomposed trends in attributable burden into contributions from population growth, population age structure, risk exposure, and risk-deleted cause-specific DALY rates. We characterised risk exposure in relation to a Socio-demographic Index (SDI). Findings Between 1990 and 2015, global exposure to unsafe sanitation, household air pollution, childhood underweight, childhood stunting, and smoking each decreased by more than 25%. Global exposure for several occupational risks, high body-mass index (BMI), and drug use increased by more than 25% over the same period. All risks jointly evaluated in 2015 accounted for 57.8% (95% CI 56.6-58.8) of global deaths and 41.2% (39.8-42.8) of DALYs. In 2015, the ten largest contributors to global DALYs among Level 3 risks were high systolic blood pressure (211.8 million [192.7 million to 231.1 million] global DALYs), smoking (148.6 million [134.2 million to 163.1 million]), high fasting plasma glucose (143.1 million [125.1 million to 163.5 million]), high BMI (120.1 million [83.8 million to 158.4 million]), childhood undernutrition (113.3 million [103.9 million to 123.4 million]), ambient particulate matter (103.1 million [90.8 million to 115.1 million]), high total cholesterol (88.7 million [74.6 million to 105.7 million]), household air pollution (85.6 million [66.7 million to 106.1 million]), alcohol use (85.0 million [77.2 million to 93.0 million]), and diets high in sodium (83.0 million [49.3 million to 127.5 million]). From 1990 to 2015, attributable DALYs declined for micronutrient deficiencies, childhood undernutrition, unsafe sanitation and water, and household air pollution; reductions in risk-deleted DALY rates rather than reductions in exposure drove these declines. Rising exposure contributed to notable increases in attributable DALYs from high BMI, high fasting plasma glucose, occupational carcinogens, and drug use. Environmental risks and childhood undernutrition declined steadily with SDI; low physical activity, high BMI, and high fasting plasma glucose increased with SDI. In 119 countries, metabolic risks, such as high BMI and fasting plasma glucose, contributed the most attributable DALYs in 2015. Regionally, smoking still ranked among the leading five risk factors for attributable DALYs in 109 countries; childhood underweight and unsafe sex remained primary drivers of early death and disability in much of sub-Saharan Africa. Interpretation Declines in some key environmental risks have contributed to declines in critical infectious diseases. Some risks appear to be invariant to SDI. Increasing risks, including high BMI, high fasting plasma glucose, drug use, and some occupational exposures, contribute to rising burden from some conditions, but also provide opportunities for intervention. Some highly preventable risks, such as smoking, remain major causes of attributable DALYs, even as exposure is declining. Public policy makers need to pay attention to the risks that are increasingly major contributors to global burden. Copyright (C) The Author(s). Published by Elsevier Ltd