Using machine learning to advance synthesis and use of conservation and environmental evidence

Cheng, Samantha H.; Augustin, Caitlin; Bethel, Alison; Gill, David; Anzaroot, Sam; Brun, J; DeWilde, B.; Minnich, R. C.; Garside, Ruth; Masuda, Yuta J.; Miller, Daniel C.; Wilkie, David; Wongbusarakum, Supin; McKinnon, Madeleine C.

doi:10.1111/cobi.13117

Cited by 95 publications

(70 citation statements)

References 8 publications

(10 reference statements)

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“…We also included all references from the bibliographies of the two previous systematic reviews on CO-BSI in Africa and Asia (25,26). Endnote was used to remove duplicates, and a final deduplicated data set was uploaded to an online systematic review tool for abstract and full-text screening (91).…”

Section: Methodsmentioning

confidence: 99%

A Systematic Review and Meta-analysis of the Prevalence of Community-Onset Bloodstream Infections among Hospitalized Patients in Africa and Asia

Marchello

Dale

Pisharody

et al. 2019

Antimicrob Agents Chemother

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Community-onset bloodstream infections (CO-BSI) are major causes of severe febrile illness and death worldwide. In light of new data and the growing problem of antimicrobial resistance (AMR) among pathogens causing BSI, we undertook a systematic review of hospital-based studies of CO-BSI among patients hospitalized with fever. Without restriction to language or country, we searched PubMed, Web of Science, and Scopus for prospective hospital-based studies of culture-confirmed CO-BSI among febrile inpatients. We determined by study the prevalence of BSI among participants, the pathogens responsible for BSI, and the antimicrobial susceptibility patterns of pathogens causing BSI, according to place and time. Thirty-four (77.3%) of 44 eligible studies recruited 29,022 participants in Africa and Asia combined. Among participants in these two regions, the median prevalence of BSI was 12.5% (range, 2.0 to 48.4%); of 3,220 pathogens isolated, 1,119 (34.8%) were Salmonella enterica, 425 (13.2%) Streptococcus pneumoniae, and 282 (8.8%) Escherichia coli. Antimicrobial susceptibility testing was reported in 16 (36.4%) studies. When isolates collected prior to 2008 were compared to those collected in the period of 2008 through 2018, the proportions of typhoidal Salmonella and Staphylococcus aureus isolates resistant to several clinically relevant antimicrobials increased over time, while S. pneumoniae susceptibility was stable. CO-BSI remain a major cause of severe febrile illness among hospitalized patients in Africa and Asia, with S. enterica, S. pneumoniae, and E. coli predominating. There is a concerning increase in AMR among serious infections caused by community-onset pathogens. Ongoing surveillance is needed to inform empirical management and strategies to control AMR.

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Section: Methodsmentioning

confidence: 99%

A Systematic Review and Meta-analysis of the Prevalence of Community-Onset Bloodstream Infections among Hospitalized Patients in Africa and Asia

Marchello

Dale

Pisharody

et al. 2019

Antimicrob Agents Chemother

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“…Despite progress in the use of machine learning to help automate abstract screening [70,71], we concluded this technology is not sufficiently developed to have been applicable without further testing. Innovative methods are much needed, particularly as the size and scope of maps and reviews continue to increase [72,73].…”

Section: Efficiency In the Review Processmentioning

confidence: 99%

Absence of evidence for the conservation outcomes of systematic conservation planning around the globe: a systematic map

et al. 2018

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Background: Systematic conservation planning is a discipline concerned with the prioritisation of resources for biodiversity conservation and is often used in the design or assessment of terrestrial and marine protected area networks. Despite being an evidence-based discipline, to date there has been no comprehensive review of the outcomes of systematic conservation plans and assessments of the relative effectiveness of applications in different contexts. To address this fundamental gap in knowledge, our primary research question was: what is the extent, distribution and robustness of evidence on conservation outcomes of systematic conservation planning around the globe?Methods: A systematic mapping exercise was undertaken using standardised search terms across 29 sources, including publication databases, online repositories and a wide range of grey literature sources. The review team screened articles recursively, first by title only, then abstract and finally by full-text, using inclusion criteria related to systematic conservation plans conducted at sub-global scales and reported on since 1983. We sought studies that reported outcomes relating to natural, human, social, financial or institutional outcomes and which employed robust evaluation study designs. The following information was extracted from included studies: bibliographic details, background information including location of study and broad objectives of the plan, study design, reported outcomes and context. Results:Of the approximately 10,000 unique articles returned through our searches, 1209 were included for full-text screening and 43 studies reported outcomes of conservation planning interventions. However, only three studies involved the use of evaluation study designs which are suitably rigorous for inclusion, according to best-practice guidelines. The three included studies were undertaken in the Gulf of California (Mexico), Réunion Island, and The Nature Conservancy's landholdings across the USA. The studies varied widely in context, purpose and outcomes. Study designs were non-experimental or qualitative, and involved use of spatial landholdings over time, stakeholder surveys and modelling of alternative planning scenarios. Conclusion:Rigorous evaluations of systematic conservation plans are currently not published in academic journals or made publicly available elsewhere. Despite frequent claims relating to positive implications and outcomes of these planning activities, we show that evaluations are probably rarely conducted. This finding does not imply systematic conservation planning is not effective but highlights a significant gap in our understanding of how, when and why it may or may not be effective. Our results also corroborate claims that the literature on systematic conservation planning is dominated by methodological studies, rather than those that focus on implementation and outcomes, and support the case that this is a problematic imbalance in the literature. We emphasise the need for academics and practitioners to publish the...

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“…Following the completion of all searches, these will be imported into Colandr (a product of a collaborative partnership between the Science for Nature and People Partnership Evidence-Based Conservation working group, DataKind, and Conservation International-https ://www.colan drapp .com/) to allow screening by multiple screeners. Colandr provides a platform for all systematic mapping requirements, from title and abstract screening to meta-data extraction, and applies machine learning and natural language processing algorithms to sort articles according to relevance which can reduce the time taken to screen compared with traditional methods [25]. An exercise to measure inter-rater agreement using Cohen's kappa [26] will be undertaken before title, abstract and full-text screening and meta-data extraction [27].…”

Section: Screening Processmentioning

confidence: 99%

What do we know about the impacts of the Marine Stewardship Council seafood ecolabelling program? A systematic map protocol

et al. 2018

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Background: Voluntary sustainability standards and eco-labels are market-based mechanisms used to encourage producers and consumers toward environmental sustainability. The Marine Stewardship Council (MSC) is one such program which aims to improve the state of the world's oceans and promote a sustainable seafood market. Now in its 21st year, with approximately 14% of global fisheries landings certified, there is growing evidence of the program's impacts (direct and indirect) on factors from fisheries management and consumer awareness to coastal communities' livelihoods and international law. To better understand the program as a whole, the proposed systematic map will collate and describe published research on the environmental, social and economic effects of the MSC program, and indicate the prevalence of disciplines or topics and study designs in this literature. Areas considered of greater interest, knowledge gaps, and future research priorities will be identified. Methods:This systematic map protocol describes how research regarding the MSC will be searched, identified and described. All research on the MSC and its effects (direct and indirect) will be included. The review is not limited to effects on certified fisheries but will include those on supply chain companies, socio-economics of coastal communities, governments, biological populations and ecosystems, NGOs and other stakeholders impacted by or potentially influenced by the MSC. The search scope includes studies from MSC's foundation in 1997 to the present. To identify studies, pre-determined inclusion and exclusion criteria will be used at the title, abstract and full text levels. In addition to the use of bibliographic databases and internet search engines, the authors will call for and search for grey-literature. The final systematic map will be presented in a descriptive report detailing the focus, extent, and occurrence of research on the MSC's impacts, taking special care to map the disciplines focused on the programme and the study design of research.

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Using machine learning to advance synthesis and use of conservation and environmental evidence

Abstract: Article impact statement: Machine learning optimizes processes of systematic evidence synthesis and improves its utility for evidence‐based conservation.

Cited by 95 publications

References 8 publications

A Systematic Review and Meta-analysis of the Prevalence of Community-Onset Bloodstream Infections among Hospitalized Patients in Africa and Asia

A Systematic Review and Meta-analysis of the Prevalence of Community-Onset Bloodstream Infections among Hospitalized Patients in Africa and Asia

Absence of evidence for the conservation outcomes of systematic conservation planning around the globe: a systematic map

What do we know about the impacts of the Marine Stewardship Council seafood ecolabelling program? A systematic map protocol

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