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20,299 results for “Systematic”
Occupational Lyme Disease: A Systematic Review and Meta-Analysis
<p>Data used in meta-analysis</p>
Telomeres and anthropogenic disturbances in wildlife: a systematic review and meta-analysis
<p>Human-driven environmental changes are affecting wildlife across the globe. These challenges do not influence species or populations to the same extent and therefore, a comprehensive evaluation of organismal health is needed to determine their ultimate impact. Evidence suggests that telomeres (the terminal chromosomal regions) are sensitive to environmental conditions and have been posited as a surrogate for animal health and fitness. Evaluation of their use in an applied ecological context is still scarce. Here, using information from molecular and occupational biomedical studies, we aim to deliver ecologists and evolutionary biologists an accessible synthesis of the links between human disturbances and telomere length. In addition, we perform a systematic review and meta-analysis on studies measuring telomere length in wild/wild-derived animals facing anthropogenic disturbances. Despite the relatively small number of studies to date, our meta-analysis revealed a significant small negative association between disturbances and telomere length (-0.092 [-0.153, -0.030]; n= 28; k=159). Yet, our systematic review suggests that the use of telomeres as a biomarker to understand the anthropogenic impact on wildlife is limited. We propose some research avenues that will help to broadly evaluate their suitability: <i>i)</i> further causal studies on the link between human disturbances and telomeres; <i>ii)</i> investigating the organismal implications, in terms of fitness and performance, of a given telomere length in anthropogenically-disturbed scenarios; <i>iii)</i> better understanding of the underlying mechanisms of telomere dynamics. Future studies in these facets will help to ultimately determine their role as markers of health and fitness in wildlife facing anthropogenic disturbances.</p>
Adverse effects of remdesivir, hydroxychloroquine, and lopinavir/ritonavir when used for COVID-19: systematic review and meta-analysis of randomized trials
<p><strong>Background</strong>: To summarize specific adverse effects of remdesivir, hydroxychloroquine, and lopinavir/ritonavir in patients with COVID-19.</p> <p><strong>Methods</strong>: We searched 32 databases through 27 October 2020. We included randomized trials comparing any of the drugs of interest to placebo or standard care, or against each other. We conducted fixed-effects pairwise meta-analysis and assessed the certainty of evidence using the GRADE approach.</p> <p><strong>Results</strong>: We included 16 randomized trials which enrolled 8226 patients. For most interventions and outcomes the certainty of the evidence was very low to low except for gastrointestinal adverse effects from hydroxychloroquine, which was moderate certainty. Compared to standard care or placebo, low certainty evidence suggests that remdesivir may not have an important effect on acute kidney injury or cognitive dysfunction/delirium. Low certainty evidence suggests that hydroxychloroquine may increase the risk of cardiac toxicity (and cognitive dysfunction/delirium, whereas moderate certainty evidence suggests hydroxychloroquine probably increases the risk of diarrhoea (RD 106 more per 1000, 95% CI: 48 more to 175 more) and nausea and/or vomiting (RD 62 more per 1000, 95% CI: 23 more to 110 more) compared to standard care or placebo. Low certainty evidence suggests lopinavir/ritonavir may increase the risk of diarrhoea and nausea and/or vomiting compared to standard care or placebo.</p> <p><strong>Discussion</strong>: Hydroxychloroquine probably increases the risk of diarrhoea and nausea and/or vomiting and may increase the risk of cardiac toxicity and cognitive dysfunction/delirium. Lopinavir/ritonavir may increase the risk of diarrhoea and nausea and/or vomiting. Remdesivir may have no important effect on risk of acute kidney injury or cognitive dysfunction/delirium. These findings provide important information to support the development of evidence-based management strategies for patients with COVID-19.</p> <p><strong>Funding</strong>: This study was supported by the Canadian Institutes of Health Research (grant: VR4-172738)</p> <p><strong>Registration</strong>: Not registered in PROSPERO, protocol available in the supplementary material of BMJ 2020;370:m2980; http://dx.doi.org/10.1136/bmj.m2980.</p>
Parasitic trophic mode of plant host affects the extent of colonization, but does not induce systematic shifts in the composition of foliar endophytic assemblages in temperate meadow ecosystems
<p>1. Foliar endophytic bacteria and fungi are increasingly being recognized as important drivers of plant host phenotype – affecting a wide range of eco-physiological processes. However, we are still lacking fundamental ecosystem-level knowledge about the structure, function, and inter-species interactions in endophytic assemblages associated with plant hosts sharing a common life strategy or ecological specialization.</p> <p>2. In this study, we chose two groups of plants with contrasting physiology as model systems: parasites and their hosts. We assessed whether plant life history strategy, namely differences in nutrient acquisition and accumulation, plays a role in structuring above-ground microbiomes under field conditions.</p> <p>3. We focused on the structure, colonization extent, and potential function of foliar endophytic bacteria and fungi in three root hemiparasitic species (Orobanchaceae), one stem holoparasite (Convolvulaceae), and their potential host plants co-occurring in species-rich temperate grassland ecosystems. For this purpose, we combined next generation amplicon sequencing with quantitative real-time PCR, chemical analyses of leaf tissue, and, in the case of bacteria, functional predictions using information deposited in available databases.</p> <p>4. We found the foliar endophytic assemblages to be diverse, dominated by generalist taxa, but highly similar across all studied species. Despite of the highly contrasting leaf tissue chemistry in the parasitic and non-parasitic plant species, the parasitic trophic mode did not induce systematic shifts in the diversity, composition, or predicted biogeochemical function of the endophytic microbiomes under field conditions. However, compared to their potential hosts, leaves of both hemiparasitic and holoparasitic species harbored significantly lower fungal counts, estimated as <em>ß-actin</em> gene copies ng DNA<sup>-1</sup>, which suggests that parasitic plants may possess mechanisms to regulate the extent of colonization by endophytic fungi.</p>
GraphQL: A Systematic Mapping Study - Supplemental Material
<p><strong>GraphQL: A Systematic Mapping Study - Supplemental Material</strong></p> <p>As supplementary material, we add online appendices to the study, containing:</p> <table> <tbody> <tr> <td><strong>File</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>01 SMS-Study-Identification.xlsx</td> <td>Study identification process dataset</td> </tr> <tr> <td>02 SMS-GraphQL-Primary-Studies.pdf</td> <td>SMS primary study dataset</td> </tr> <tr> <td>03 SMS-GraphQL-Data-Extraction.xlsx</td> <td>Dataset of the data extraction from the SMS primary studies</td> </tr> </tbody> </table> <p> </p> <p><br> </p>
Database of Systematic review of the literature. Planning of ICT in educational centers
<pre>These documents include a database of RSL articles developed on strategic planning in the integration of ICT in educational centers.</pre>
Molecular systematics, species concepts and myrmecophytism in Cecropia (Cecropieae: Urticaceae): Insights from restriction-site associated DNA
<p><em>Cecropia</em> is a group of fast-growing pioneer trees that are important in forest regeneration and a common ant-plant mutualism in the Neotropics. To investigate the evolution of mutualism between <em>Cecropia</em> and associated ants a phylogenetic framework is necessary. <em>Cecropia</em> species are difficult to distinguish morphologically and conventional genetic markers are insufficiently variable to resolve phylogeny. Our study aimed to infer relationships in approximately half of the species in the genus using restriction site associated DNA (RAD) sequencing. RAD sequence data resolved and supported species level relationships, despite potential introgression based on D-statistic tests. Our results support a deeply divergent non-myrmecophytic clade including <em>C. sciadophylla </em>and African <em>Musanga</em>. Results from geographically widespread and morphologically heterogenous <em>C. obtusifolia</em> and <em>C. angustifolia</em> suggests that current synonymy lumps together genetically dissimilar lineages. Reconstruction of ant associations on the highly supported <em>Cecropia</em> phylogeny inferred equal probability of the ancestor of <em>Cecropia </em>being myrmecophytic or not. More intensive genetic study is needed to refine species concepts in <em>Cecropia</em>.</p>
Database outcomes systematic review on participatory restoration ecology scenarios
<p><span>Large-scale ecological </span>restoration is <span>crucial for effective </span>biodiversity conservation <span>and combating climate change. However, perspectives on the goals and values of restoration are highly diverse, as are the different approaches to restoration e.g., ranging from the restoration of cultural ecosystems to rewilding. We assess how the future of nature is envisioned in participatory scenarios, focusing on which elements of rewilding and nature contributions to people have been considered in scenario narratives across Europe. We use the Nature Futures Framework to study how different perspectives on the the relationship of people with nature are captured in participatory scenarios. We found that a range of material, regulating and non-materical benefits were well represented in participatory scenarios. The different ecological aspects of rewilding were also present in many participatory scenarios, but not as well represented as nature contributions to people. Nature as culture was the main perspective present in the scenarios, with expected highest positive impacts on non-material benefits and to a lessesr extent on regulating benefits. Nature for nature futures were associated with positive impacts on regulating benefits and negative impacts on material benefits, being the only type of future associate with positive impacts on all three components of rewilding. Nature for society futures were associated with moderate positive impacts on all three types of nature contributions to people. Business as usual futures were associate with negative impacts on regulating and non-material benefits and on all three components of rewilding. Our</span> results <span>also </span>highlight<span> two major gaps that should be addressed in participatory restoration planning and models. Firstly, there is a paucity of spatially explicit approaches, with most studies failing to transform the results of participatory scenario planning into model projections. Secondly, we found scenarios that explored co-benefits between multiple nature perspectives were overall missing from the literature.</span></p>
Data archive for the publication: Multi-variable compensated quantum yield measurements of upconverting nanoparticles with high dynamic range: a systematic approach
<p>The two compressed repositories contain raw and analysed data for the following publication on Optics Express: <strong><a href="https://doi.org/10.1364/OE.452874">Multi-variable compensated quantum yield measurements of upconverting nanoparticles with high dynamic range: a systematic approach</a></strong></p> <p>The code for processing and analysing these data is available on GitHub and it has its own DOI. </p> <p>To access the code and for instructions on how to run the it follow the link: <a href="https://github.com/Biophotonics-Tyndall/QY-System-paper">Biophotonics-Tyndall/QY-System-paper (github.com)</a>. </p>
FIG. 7 in Ontogenetic systematic characterisation of an endemic frog Rhacophorus malabaricus Jerdon, 1870 (Anura: Rhacophoridae) from Western Ghats, Kerala, India
FIG. 7. — Comparison of length-age ratio of tadpole of Rhacophorus malabaricus Jerdon, 1870.
FIG. 2. — Leafs hiding a in Ontogenetic systematic characterisation of an endemic frog Rhacophorus malabaricus Jerdon, 1870 (Anura: Rhacophoridae) from Western Ghats, Kerala, India
FIG. 2. — Leafs hiding a foam nest of Rhacophorus malabaricus Jerdon, 1870.
Supplementary material for "Language and User Requirements for Business Process Simulation - A Systematic Literature Review"
<p>This is ment as a supplementary material for the Publication "Language and User Requirements for Business Process Simulation - A Systematic Literature Review". It contains all sources that were used for the creation of the requirements broken down for each one.</p>
IoT-Enabled Smart Waste Management Systems for Smart Cities: A Systematic Review
<p>Data collected from primary studies.</p> <p>We 1) identified the main approaches and services that are applied in the city and SGB-level SWM systems, 2) listed sensors and actuators and analyzed their application in various types of SWM systems, 3) listed the direct and indirect stakeholders of the SWM systems, 4) identified the types of data shared between the SWM systems and stakeholders, and 5) identified the main promising directions and research gaps in the field of SWM systems.</p>
Fig. 1 in An overlooked case for a century: taxonomy and systematics of a new Iberian species of Eumerus Meigen, 1822 (Diptera, Syrphidae)
Fig. 1. Distribution map of E. colladoi sp. nov. in the Iberian Peninsula.
Systematic review and meta-analysis: water type and temperature affect environmental DNA decay metadata
<p>Environmental DNA (eDNA) has been used in a variety of ecological studies and management applications. The rate at which eDNA decays has been widely studied but at present it is difficult to disentangle study-specific effects from factors that universally affect eDNA degradation. To address this, a systematic review and meta-analysis was conducted on aquatic eDNA studies. Analysis revealed eDNA decayed faster at higher temperatures and in marine environments (as opposed to freshwater). DNA type (mitochondrial or nuclear) and fragment length did not affect eDNA decay rate, although a preference for < 200 bp sequences in the available literature means this relationship was not assessed with longer sequences (<em>e.g.</em> > 800 bp). At present, factors such as ultraviolet light, pH, and microbial load lacked sufficient studies to feature in the meta-analysis. Moving forward, we advocate researching these factors to further refine our understanding of eDNA decay in aquatic environments. This dryad entry contains the metadata which formed the basis for the meta-analysis.</p>
Revealing the Sustainability of Novel Food System Technologies: A systematic scoping review
<p>This repository contains the R- script and data files used to generate visualizations for a systematic scoping review on the sustainability of novel food system technologies. </p>
Systematics of the New World bats Eptesicus and Histiotus suggest trans-marine dispersal followed by Neotropical cryptic diversification
<p>Biodiversity can be boosted by colonization of new habitats, such as different continents and remote islands. Molecular studies have suggested that recently evolved organisms probably colonized already separated continents by dispersal, either via land bridge connections or crossing the ocean. Here we test the on-land and trans-marine dispersal hypotheses by evaluating possibilities of colonization routes over Bering land bridge and across the Atlantic Ocean in the cosmopolitan bat genus <em>Eptesicus</em> (Chiroptera, Vespertilionidae). Previous molecular studies have found New World <em>Eptesicus</em> more closely related to <em>Histiotus</em>, a Neotropical endemic lineage with enlarged ears, than to Old World <em>Eptesicus</em>. However, phylogenetic relationships within the New World group remained unresolved and their evolutionary history was unclear. Here we studied the systematics of New World <em>Eptesicus</em> and <em>Histiotus</em> using extensive taxonomic and geographic sampling, and genomic data from thousands of ultra-conserved elements (UCEs). We estimated phylogenetic trees using concatenation and multispecies coalescent. All analyses supported four major New World clades and a novel topology where <em>E. fuscus</em> and <em>Histiotus</em> are sister clades that together diverged from two sister clades of Neotropical <em>Eptesicus</em>. Intra-clade divergence suggested cryptic diversity that has been concealed by morphological features, especially in the Neotropics where taxonomic re-evaluations are warranted. Molecular dating estimated that Old World and New World clades diverged around 17 million years ago followed by radiation of major New World clades in the mid-Miocene, when climatic changes might have facilitated global dispersal and radiation events. Biogeographic ancestral reconstruction supported the Neotropical origin of the New World clades, suggesting a trans-Atlantic colonization route from North Africa to the northern Neotropics. We highlight that trans-marine dispersal may be more prevalent than currently acknowledged and may be an important first step to global biodiversification.</p>
Replication package: 40 Years of Designing Code Comprehension Experiments: A Systematic Mapping Study
<p>Replication package | 40 Years of Designing Code Comprehension Experiments: A Systematic Mapping Study</p>
Randomised trials in maternal and perinatal health in low- and middle-income countries from 2010 to 2019: A systematic scoping review
<p><strong>Objectives: </strong>To identify and map all trials in maternal health conducted in low- and middle-income countries (LMIC) over the 10-year period 2010-2019, to identify geographical and thematic trends, as well as compare to global causes of maternal death and pre-identified priority areas.</p> <p><strong>Design: </strong>Systematic scoping review.</p> <p><strong>Primary and secondary outcome measures: </strong>Extracted data included location, study characteristics and whether trials corresponded to causes of mortality and identified research priority topics.</p> <p><strong>Results: </strong>Our search identified 7,269 articles, 874 of which were included for analysis. Between 2010 and 2019, maternal health trials conducted in LMICs more than doubled (50 to 114). Trials were conducted in 61 countries – 231 trials (26.4%) were conducted in Iran. Only 225 trials (25.7%) were aligned with a cause of maternal mortality. Within these trials, pre-existing medical conditions, embolism, obstructed labour, and sepsis were all under-represented when compared with number of maternal deaths globally. Large numbers of studies were conducted on priority topics such as labour and delivery, obstetric haemorrhage, and antenatal care. Hypertensive disorders of pregnancy, diabetes, and health systems and policy – despite being high-priority topics – had relatively few trials.</p> <p><strong>Conclusion: </strong>Despite trials conducted in LMICs increasing from 2010 to 2019, there were significant gaps in geographical distribution, alignment with causes of maternal mortality, and known research priority topics. The research gaps identified provide guidance and insight for future research conducted in low-resource settings.</p>
Host plant specificity of the monarch butterfly Danaus plexippus: A systematic review and meta-analysis
<p>The preference-performance hypothesis explains host specificity in phytophagous insects, positing that host plants chosen by adults confer the greatest larval fitness. However, adults sometimes oviposit on plants supporting low larval success because the components of host specificity (adult preference, plant palatability, and larval survival) are non-binary and not necessarily correlated. Palatability (willingness to eat) is governed by chemical cues and physical barriers such as trichomes, while survival (ability to complete development) depends upon nutrition and toxicity. Absence of a correlation between the components of host specificity results in low-performance hosts supporting limited larval development. Most studies of specificity focus on oviposition behavior leaving the importance and basis of palatability and survival under-explored. We conducted a comprehensive review of 127 plant species that have been claimed or tested to be hosts for the monarch butterfly Danaus plexippus to classify them as non-hosts, low performance, or high performance. We performed a meta-analysis to test if performance status could be explained by the properties of neurotoxic cardenolides or trichome density. We also conducted a no-choice larval feeding experiment to identify the causes of low performance. We identified 34 high performance, 42 low performance, 33 non-hosts, and 18 species with unsubstantiated claims. Mean cardenolide concentration was greater in high- than low-performance hosts and a significant predictor of host status, suggesting possible evolutionary trade-offs in monarch specialization. Other cardenolide properties and trichome density were not significant predictors of host status. In the experiment, we found, of the 62% of larvae that attempted to eat low-performance hosts, only 3.5% survived to adult compared to 85% of those on the high-performance host, demonstrating that multiple factors affect larval host plant specificity. Our study is the first to classify all known host plants for monarchs and has conservation implications for this threatened species.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.