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      Between darkness and light: spring habitats provide new perspectives for modern researchers on groundwater biology

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      PeerJ
      PeerJ Inc.
      Seepage, Source, Shallow subterranean habitats, Adaptation, Subterranean biology, Cave

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          Abstract

          Springs are interfaces between groundwater and surface habitats and may play an important role in the study of subterranean animals. In this systematic evidence review and meta-analysis, we explore whether observations of stygobionts in springs are relevant and more common than observations of epigean animals in groundwater. We searched the Web of Science database for papers on groundwater fauna and spring fauna. For each paper we found, we recorded whether the paper reported the occurrence of typical stygobionts in springs, of surface animals in groundwater, or of the same taxa in both habitats. If so, we recorded how many such species were reported. We also recorded the scientific discipline of each study and the year of publication. Our search yielded 342 papers. A considerable number of these papers reported stygobionts in springs: 20% of papers dealing with groundwater fauna and 16% of papers dealing with spring fauna reported the occurrence of stygobionts in spring habitats. Both the number of papers that mentioned stygobionts in springs, and the number of stygobiont species that were documented in springs, were higher than equivalent measures for the occurrence of surface fauna underground. We also detected a positive relationship between year of publication and the number of reports of stygofauna in springs. To broaden the insights from biological research on underground environments, we suggest that springs should be considered not only as simple sampling points of stygobionts but also as core stygobiont habitats.

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          glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling

          Count data can be analyzed using generalized linear mixed models when observations are correlated in ways that require random effects. However, count data are often zero-inflated, containing more zeros than would be expected from the typical error distributions. We present a new package, glmmTMB, and compare it to other R packages that fit zero-inflated mixed models. The glmmTMB package fits many types of GLMMs and extensions, including models with continuously distributed responses, but here we focus on count responses. glmmTMB is faster than glmmADMB, MCMCglmm, and brms, and more flexible than INLA and mgcv for zero-inflated modeling. One unique feature of glmmTMB (among packages that fit zero-inflated mixed models) is its ability to estimate the Conway-Maxwell-Poisson distribution parameterized by the mean. Overall, its most appealing features for new users may be the combination of speed, flexibility, and its interface’s similarity to lme4. The R journal, 9 (2) ISSN:2073-4859
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            Evaluations of the uptake and impact of the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) Statement and extensions: a scoping review

            Background The PRISMA Statement is a reporting guideline designed to improve transparency of systematic reviews (SRs) and meta-analyses. Seven extensions to the PRISMA Statement have been published to address the reporting of different types or aspects of SRs, and another eight are in development. We performed a scoping review to map the research that has been conducted to evaluate the uptake and impact of the PRISMA Statement and extensions. We also synthesised studies evaluating how well SRs published after the PRISMA Statement was disseminated adhere to its recommendations. Methods We searched for meta-research studies indexed in MEDLINE® from inception to 31 July 2017, which investigated some component of the PRISMA Statement or extensions (e.g. SR adherence to PRISMA, journal endorsement of PRISMA). One author screened all records and classified the types of evidence available in the studies. We pooled data on SR adherence to individual PRISMA items across all SRs in the included studies and across SRs published after 2009 (the year PRISMA was disseminated). Results We included 100 meta-research studies. The most common type of evidence available was data on SR adherence to the PRISMA Statement, which has been evaluated in 57 studies that have assessed 6487 SRs. The pooled results of these studies suggest that reporting of many items in the PRISMA Statement is suboptimal, even in the 2382 SRs published after 2009 (where nine items were adhered to by fewer than 67% of SRs). Few meta-research studies have evaluated the adherence of SRs to the PRISMA extensions or strategies to increase adherence to the PRISMA Statement and extensions. Conclusions Many studies have evaluated how well SRs adhere to the PRISMA Statement, and the pooled result of these suggest that reporting of many items is suboptimal. An update of the PRISMA Statement, along with a toolkit of strategies to help journals endorse and implement the updated guideline, may improve the transparency of SRs. Electronic supplementary material The online version of this article (10.1186/s13643-017-0663-8) contains supplementary material, which is available to authorized users.
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              The cave environment.

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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                26 July 2021
                2021
                : 9
                : e11711
                Affiliations
                [1 ]Department of Environmental Science and Policy, Università degli Studi di Milano , Milano, Lombardia, Italy
                [2 ]Parco Regionale del Monte Barro, Laboratorio di Biologia Sotterranea “Enrico Pezzoli” , Galbiate, Italy
                Author information
                http://orcid.org/0000-0001-6071-8194
                Article
                11711
                10.7717/peerj.11711
                8320523
                34395066
                9de88a67-4bd8-4b33-ad42-1aa2afdeba51
                © 2021 Manenti and Piazza

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 13 April 2021
                : 10 June 2021
                Funding
                Funded by: University of Milan
                Funded by: APC
                The University of Milan supported the publication fee through the APC initiative. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Ecology
                Zoology
                Freshwater Biology

                seepage,source,shallow subterranean habitats,adaptation,subterranean biology,cave

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