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Supplemental information for McClelland et al. (2020). Management of cover crops in temperate climates influences soil organic carbon stocks – A meta-analysis
<p>All supplemental information for McClelland et al. (2020). Management of cover crops in temperate climates influences soil organic carbon stocks – A meta-analysis. </p>
Efficacy of treatments for polycystic ovarian syndrome management in adolescents: a systematic review and network meta-analysis
<p><span>Limited evidence on treatment options for polycystic ovarian syndrome (PCOS) has led to considerable variation in healthcare practices. We aimed to compare the effects of metformin and/or oral contraceptive pills (OCPs) in combination with pioglitazone, spironolactone, flutamide, and lifestyle interventions among adolescents aged 11-19 years with PCOS.<b> </b>Literature searches were performed in Medline, Embase, and the Cochrane Central Register of Controlled Trials from database inception through December 2018, with no language restriction. Two reviewers screened titles and abstracts, assessed full text eligibility, and extracted information from eligible trials. Evidence was synthesized through network meta-analyses (NMA) using Bayesian random-effects approach. We identified 37 RCTs, in which 2400 patients were randomized. NMA showed no statistically important difference among all interventions to improve menstrual regulation, or body mass index. Moderate quality evidence showed hirsutism scores were reduced by multiple interventions that included single and combination medications namely; lifestyle intervention, metformin, OCP, spironolactone, pioglitazone, metformin-OCP, metformin-spironolactone, metformin-flutamide, against placebo. Moderate quality evidence showed OCP results in more dysglycaemia compared to metformin (odds ratio 2.98; 95%credible interval 1.02, 8.96), no intervention resulted in dysglycaemia reduction. In conclusion,<b> </b>metformin and OCP as monotherapy or in combination with other interventions compared to placebo can reduce hirsutism scores, but none of these medications lead to effective menstrual cycle regulation or weight reduction. However, the use of OCP leads to worse cardiometabolic risk factors. Further research into new treatment options is urgently needed. </span></p>
Larger pollinators deposit more pollen on stigmas across multiple plant species – a meta-analysis
<p>Abstract</p> <p><b>1.</b> Many insect species provide essential pollination services. However, the amount of pollen deposited onto a stigma when visiting a flower ("single visit pollen deposition", SVD) can vary greatly among taxa depending on morphological traits of pollinators. Further, SVD is commonly measured using one of two methods ('static': waiting for an insect to visit a flower present on plant, and 'active': removing the flower and presenting it to a flower visitor) that may also differ in their effectiveness.</p> <p><b>2.</b> To gain a more comprehensive understanding of how SVD compares among pollinators, we conducted a hierarchical meta-analysis using data from 28 studies identified by a systematic review. These contained SVD data for 94 bee and 33 fly taxa (hereafter "wild pollinators"), across 30 plant species from which we included 127 observations. In the analysis of each study, we used the western honey bee (<i>Apis mellifera</i>) as a comparator species.</p> <p><b>3.</b> Wild pollinators deposited more pollen onto stigmas per single visit than honeybees, and those with larger body deposited significantly more pollen than smaller ones. Of the two methodological approaches to assess SVD, 'static' versus 'active', we found no significant difference regarding the amount of deposited pollen.</p> <p><b>4.</b> <i>Synthesis and applications. </i>Our meta-analysis highlights the breadth of wild pollinators that contribute to pollination effectiveness via their delivery of pollen to many crop and non-crop plant species. However, just 25% of the observations assessed the amount of pollen deposited by fly species. Our findings point to the need to further quantify the pollination effectiveness of non-bee pollinators as studies have largely focused on managed and wild bee species.</p>
A global, cross-system meta-analysis of polychlorinated biphenyl biomagnification
<p><span><span><span><span><span><span><span><span><span><span><span>Studies evaluating the mechanisms underpinning the biomagnification of polychlorinated biphenyls (PCBs), a globally prevalent group of regulated persistent organic pollutants, commonly couple chemical and stable isotope analyses to identify bioaccumulation pathways. <span><span>Due to </span></span>analytical costs constraining the taxonomic and geographic scope, sample size, and the range of compounds analyzed for most studies, and <span><span>study-to-study variation in methodologies and analytical resolution, </span></span>how PCBs biomagnify at food web, regional, and global scales remains uncertain. To overcome these constraints, we compiled diet (stable isotopes) and lipid-normalized PCB data from peer-reviewed studies reporting both values and used complementary analyses to evaluate the relative importance of global key PCB drivers and assess ecosystem- and ocean-wide biomagnification trends of sum total PCB concentrations (PCB<sub>ST</sub>), and the concentrations of seven individual PCB congeners, and their sum (PCB<sub>å7</sub>). We discovered that the number of congeners analyzed, region, and class were the most important factors predicting PCB<sub>ST</sub>, while, similarly, region, class and feeding location were the best predictors of PCB<sub>å7</sub> and all seven congeners. In addition, biomagnification analyses revealed that PCB<sub>ST</sub>, PCB<sub>Σ7</sub> and the seven individual PCBs all demonstrate a higher propensity for biomagnification in marine relative to freshwater food webs and within the Atlantic Ocean relative to the Pacific. We further found that some congeners exhibiting relatively high trophic magnification factors (TMFs) in the Atlantic exhibited low TMFs in the Pacific (such as PCB 118), while the order of individual congener TMFs relative to one another remained consistent across marine and freshwater ecosystems. Our analyses demonstrate that novel insights regarding PCB concentrations across taxonomic, food webs, regional and global scales can be gleaned by leveraging existing data to overcome analytical constraints. </span></span></span></span></span></span></span></span></span></span></span></p>
Supplementary material 3 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2a
Supplementary material 7 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2e
Supplementary material 8 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2f
Supplementary material 4 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2b
Supplementary material 6 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2d
Supplementary material 1 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Tables S1–S6
Figure 9 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 9 Box plots of a length (bases) and b GC (%) content of ITS1 and ITS2 sequences for each one of the main lineages (Clades/Clusters) of the genus Ganoderma. The size of each box represents 50% of the values, the black horizontal line within each box indicates the median, the 'x' represents the average value, the error bars represent interquartile ranges and circles indicate outliers.
Supplementary material 5 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2c
Figure 8 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 8 Box plots of aITS sequence similarity (%) and b genetic distances (p-values) within (intra) and between (inter) Ganoderma species for each one of the main lineages (Clades/Clusters) of the genus, as well as pairwise comparisons between selected species. The size of each box represents 50% of the values, the black horizontal line within each box indicates the median, the 'x' represents the average value, the error bars represent interquartile ranges and circles indicate outliers. The red-dotted horizontal line, transversing the plots, represents the value levels accepted in this study for proposing new phylogenetic species.
Figure 6 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 6 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clades B, C and D. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of the tree) and geographic origin of the respective material (the latter appears in different fonts colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 5 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 5 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clade A, Cluster A.3. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of the tree) and geographic origin of the respective material (the latter appears in different fonts colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 7 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 7 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clade E. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of tree) and geographic origin of the respective material (the latter appears in different fonts colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 4 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 4 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clade A, Clusters A.1 and A.2. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of tree) and geographic origin of the respective material (the latter appears in different font colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 3 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 3 Summary tree of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2). Thick lines represent ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95. Clades and Clusters within the tree appear as presented in Table 1 and Suppl. material 1: Table S2. Species names correspond to those inferred in this study. Scale bar: 0.01 nucleotide substitutions per site.
Figure 2 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 2 Basidiomes of Ganoderma spp. amongst those collected and analysed in this study (specimens codes appear in parantheses; Suppl. material 1: Table S1) aG. lucidum (A1180) bG. carnosum (DD1243) cG. resinaceum (2012-0077) dG. adspersum (2010-0015) eG. applanatum (DD2119) fG. pfeifferi (DD2118).
Figure 1 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 1 a Initial labelling of 3908 Ganoderma sequences analysed in the present study: numbers in parentheses correspond to sequences deposited under the particular name in GenBank/ENA/DDBJ and UNITE, while species names appear underlined when ITS sequences derive from type material b final assigment of 3908 Ganoderma sequences to 80 species and six distinct groups as a result of the phylogenetic analyses performed in this study: numbers in parentheses correspond to the number of sequences grouped within each taxon (data deriving from Table 1 and Suppl. material 1: Tables S2, S4).
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.