cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12123705
title: Supplementary Material for: Nonsurgical Treatments for Extramammary Paget Disease: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> Surgery is commonly regarded as the mainstay of treatment of extramammary Paget disease (EMPD)<b><i>;</i></b> however, nonsurgical approaches have gained popularity in recent years. <b><i>Objectives:</i></b> To review the published evidence for the efficacy and safety of nonsurgical modes of therapy for EMPD. <b><i>Methods:</i></b> A systematic review and meta-analysis of nonsurgical EMPD treatments was performed. The primary outcome was complete response (CR); secondary outcomes were clinical regression by ≥50%, adverse events, and recurrence rate. <b><i>Results:</i></b> The systematic review included 43 observational studies (341 patients; 7 prospective cohort studies, 19 retrospective cohort studies, and 17 cases series) evaluating 5 treatment modalities. Imiquimod (13 studies, 110 patients) administered at variable doses ranging from daily to twice weekly for 2–56 weeks demonstrated CR of 54% (95% CI, 40–67%; <i>I</i><sup>2</sup> = 37%) and had a satisfactory safety profile. In 14 heterogeneous studies (122 patients) evaluating photodynamic therapy (PDT), only 36% (95% CI, 22–53%; <i>I</i><sup>2</sup> = 52%) of patients achieved CR. Radiotherapy (12 studies, 67 patients) showed CR of 97%, but was associated with local and systemic side effects. Ablative lasers and topical fluorouracil and calcipotriene lacked adequate evidence of efficacy. <b><i>Conclusions:</i></b> Imiquimod and radiotherapy are the most appropriate nonsurgical modalities for EMPD treatment given their good efficacy and safety profile. PDT has limited efficacy but may be appropriate in selected clinical settings.
DOI: 10.6084/m9.figshare.12123660
title: Long-term population monitoring of a territorial forest raptor species

description: Census data on a non-invasive long-term monitoring programme of booted eagle: nest and territorial occupancy, productivity, individuals’ identification as well as the colour polymorphism of booted eagle.
DOI: 10.6084/m9.figshare.12123654
title: Supplementary Material for: Carcinoid Heart Disease: Prognostic Value of 5-Hydroxyindoleacetic Acid Levels and Impact on Survival: A Systematic Literature Review

description: <b><i>Background:</i></b> Carcinoid heart disease (CHD) can develop in patients with carcinoid syndrome (CS), itself caused by overproduction of hormones and other products from some neuroendocrine tumours. The most common hormone is serotonin, detected as high 5-hydroxyindoleacetic acid (5-HIAA). This systematic literature review summarises current literature on the impact of CHD on survival, and the relationship between 5-HIAA levels and CHD development, progression, and mortality. <b><i>Methods:</i></b> MEDLINE, Embase, Cochrane databases, and grey literature were searched using terms for CHD, 5-HIAA, disease progression, and mortality/survival. Eligible articles were non-interventional and included patients with CS and predefined CHD and 5-HIAA outcomes. <b><i>Results:</i></b> Publications reporting on 31 studies were included. The number and disease states of patients varied between studies. Estimates of CHD prevalence and incidence among patients with a diagnosis/symptoms indicative of CS were 3–65% and 3–42%, respectively. Most studies evaluating survival found significantly higher mortality rates among patients with versus without CHD. Patients with CHD reportedly had higher 5-HIAA levels; median urinary levels in patients with versus without CHD were 266–1,381 versus 67.5–575 µmol/24 h. Higher 5-HIAA levels were also found to correlate with disease progression (median progression/worsening-associated levels: 791–2,247 µmol/24 h) and increased odds of death (7% with every 100 nmol/L increase). <b><i>Conclusions:</i></b> Despite the heterogeneity of studies, the data indicate that CHD reduces survival, and higher 5-HIAA levels are associated with CHD development, disease progression, and increased risk of mortality; 5-HIAA levels should be carefully managed in these patients.
DOI: 10.6084/m9.figshare.12123654.v1
title: Supplementary Material for: Carcinoid Heart Disease: Prognostic Value of 5-Hydroxyindoleacetic Acid Levels and Impact on Survival: A Systematic Literature Review

description: <b><i>Background:</i></b> Carcinoid heart disease (CHD) can develop in patients with carcinoid syndrome (CS), itself caused by overproduction of hormones and other products from some neuroendocrine tumours. The most common hormone is serotonin, detected as high 5-hydroxyindoleacetic acid (5-HIAA). This systematic literature review summarises current literature on the impact of CHD on survival, and the relationship between 5-HIAA levels and CHD development, progression, and mortality. <b><i>Methods:</i></b> MEDLINE, Embase, Cochrane databases, and grey literature were searched using terms for CHD, 5-HIAA, disease progression, and mortality/survival. Eligible articles were non-interventional and included patients with CS and predefined CHD and 5-HIAA outcomes. <b><i>Results:</i></b> Publications reporting on 31 studies were included. The number and disease states of patients varied between studies. Estimates of CHD prevalence and incidence among patients with a diagnosis/symptoms indicative of CS were 3–65% and 3–42%, respectively. Most studies evaluating survival found significantly higher mortality rates among patients with versus without CHD. Patients with CHD reportedly had higher 5-HIAA levels; median urinary levels in patients with versus without CHD were 266–1,381 versus 67.5–575 µmol/24 h. Higher 5-HIAA levels were also found to correlate with disease progression (median progression/worsening-associated levels: 791–2,247 µmol/24 h) and increased odds of death (7% with every 100 nmol/L increase). <b><i>Conclusions:</i></b> Despite the heterogeneity of studies, the data indicate that CHD reduces survival, and higher 5-HIAA levels are associated with CHD development, disease progression, and increased risk of mortality; 5-HIAA levels should be carefully managed in these patients.
DOI: 10.6084/m9.figshare.12123660.v1
title: Long-term population monitoring of a territorial forest raptor species

description: Census data on a non-invasive long-term monitoring programme of booted eagle: nest and territorial occupancy, productivity, individuals’ identification as well as the colour polymorphism of booted eagle.
DOI: 10.6084/m9.figshare.12123579
title: Comtrade PPE data

description: Comtrade data on imports and exports of personal protective equipment, specifically gloves and masks
DOI: 10.6084/m9.figshare.12123522
title: LPR2018data_public.csv

description: Data are available for use in accordance with the data policy: https://livingplanetindex.org/documents/data_agreement.pdf.<br><br>Time series of population abundance data for vertebrate species spanning years between 1970 and 2014. These data were used in the Living Planet Report 2018. Confidential records that cannot be shared have been removed from this data set. A beta version of the code used in calculation of the Living Planet Index using this data set can be found here https://github.com/Zoological-Society-of-London/rlpi.
DOI: 10.6084/m9.figshare.12123579.v1
title: Comtrade PPE data

description: Comtrade data on imports and exports of personal protective equipment, specifically gloves and masks
DOI: 10.6084/m9.figshare.12123522.v1
title: LPR2018data_public.csv

description: Time series of population abundance data for vertebrate species spanning years between 1970 and 2014. These data were used in the Living Planet Report 2018. Confidential records that cannot be shared have been removed from this data set. A beta version of the code used in calculation of the Living Planet Index using this data set can be found here https://github.com/Zoological-Society-of-London/rlpi. Data are available for use in accordance with the data policy: https://livingplanetindex.org/documents/data_agreement.pdf.
DOI: 10.5522/04/12123354
title: Two-photon imaging of neurons in mouse superior colliculus (Matlab files)

description: These data contain activity (in form of calcium traces) of single neurons in superior colliculus (SC) of mouse. Mice were able to run on a floating ball. Running speed and pupil size were recorded simultaneously. Mice were presented with full-field, drifting, sinusoidal gratings (“gratings”), uniform gray screens (“grayScreen”), or black and white squares on gray background (“noise”). See Schröder et al. (2020) for details on methods.<br>See readme.rtf for description of data.
DOI: 10.5522/04/12123354.v1
title: Two-photon imaging of neurons in mouse superior colliculus

description: These data contain activity (in form of calcium traces) of single neurons in superior colliculus (SC) of mouse. Mice were able to run on a floating ball. Running speed and pupil size were recorded simultaneously. Mice were presented with full-field, drifting, sinusoidal gratings (“gratings”), uniform gray screens (“grayScreen”), or black and white squares on gray background (“noise”). See Schröder et al. (2020) for details on methods.<br>See readme.rtf for description of data.
DOI: 10.6084/m9.figshare.12123210
title: Table S1-4.xlsx

description: Table S1-S4.
DOI: 10.6084/m9.figshare.12123210.v1
title: Table S1-4.xlsx

description: Table S1-S4.
DOI: 10.6084/m9.figshare.12123189
title: Total-evidence phylogeny and divergence times of Vermilingua (Mammalia: Pilosa)

description: Vermilingua is a peculiar group of xenarthran placental mammals with well-established phylogenetic relationships based on morphological and molecular data, but until now, no combined analysis of those data types. Here we perform the first total-evidence phylogenetic analysis of Vermilingua and estimate divergence times for living and fossil anteaters with a tip-dating approach, using the Fossilized Birth-Death model in a Bayesian framework. Using combined analyses, we recovered as monophyletic the two families, Cyclopedidae and Myrmecophagidae, as in previous studies, although our revised morphological data alone do not support the monophyly of Cyclopedidae. We show how the combination of molecular and morphological data indirectly affects the position and support for fossil taxa even though molecular datasets do not contain direct information for them. The estimated divergence times of <i>Palaeomyrmidon</i> and <i>Protamandua</i> are much older than the ages of those fossils, reinforcing the scarcity of the vermilinguan fossil record. In addition, we obtained evidence that the extinct <i>Neotamandua</i> is an ancestor of the extant <i>Myrmecophaga</i>, not a sister taxon as in previous studies, that did not incorporate the possibility of anagenetic evolution between fossil and living taxa.
DOI: 10.6084/m9.figshare.12123192
title: New insights into the phylogeny of the dark-spored Myxomycetes (Amoebozoa: Conosa: Myxogastria: Fuscisporidia) and polyphyly of the genus <i>Stemonitis</i>

description: About a thousand described species of Myxomycetes, colloquially named slime moulds, are present in most terrestrial habitats. Molecular environmental sampling has revealed that a significant proportion of sequences could not be assigned to known species, with some specific groups showing a high hidden diversity. One such group included <i>Stemonitis</i> and allied genera, with only a few closely related reference sequences from known species and many distantly related sequences from environmental sampling. To improve the phylogeny and help define genera in this lineage, we provided nine new small-subunit ribosomal RNA gene sequences of <i>Stemonitis</i> and allied genera, along with microscopy observations. We showed that the genus <i>Stemonitis</i> is polyphyletic, clearly separated into two groups, with the main distinguishing feature being spore ornamentation. The first group included the type species <i>Stemonitis fusca</i>, and was characterized by reticulated spores, while the second contained species with warted spores (e.g. <i>S. flavogenita</i> and <i>S. axifera</i>) and many undetermined environmental sequences. In addition, we show that the related genera <i>Stemonitopsis</i>, <i>Stemonaria</i> and <i>Symphytocarpus</i> were polyphyletic and that their circumscription was based on inconsistent characteristics. Instead, representatives of these genera clustered into the two clades according to their spore ornamentation. Our study provides a first insight into the genetic diversity of <i>Stemonitis</i> and allied genera, and proposes spore ornamentation as an evolutionary informative feature to distinguish genera in this group.
DOI: 10.6084/m9.figshare.12123192.v1
title: New insights into the phylogeny of the dark-spored Myxomycetes (Amoebozoa: Conosa: Myxogastria: Fuscisporidia) and polyphyly of the genus <i>Stemonitis</i>

description: About a thousand described species of Myxomycetes, colloquially named slime moulds, are present in most terrestrial habitats. Molecular environmental sampling has revealed that a significant proportion of sequences could not be assigned to known species, with some specific groups showing a high hidden diversity. One such group included <i>Stemonitis</i> and allied genera, with only a few closely related reference sequences from known species and many distantly related sequences from environmental sampling. To improve the phylogeny and help define genera in this lineage, we provided nine new small-subunit ribosomal RNA gene sequences of <i>Stemonitis</i> and allied genera, along with microscopy observations. We showed that the genus <i>Stemonitis</i> is polyphyletic, clearly separated into two groups, with the main distinguishing feature being spore ornamentation. The first group included the type species <i>Stemonitis fusca</i>, and was characterized by reticulated spores, while the second contained species with warted spores (e.g. <i>S. flavogenita</i> and <i>S. axifera</i>) and many undetermined environmental sequences. In addition, we show that the related genera <i>Stemonitopsis</i>, <i>Stemonaria</i> and <i>Symphytocarpus</i> were polyphyletic and that their circumscription was based on inconsistent characteristics. Instead, representatives of these genera clustered into the two clades according to their spore ornamentation. Our study provides a first insight into the genetic diversity of <i>Stemonitis</i> and allied genera, and proposes spore ornamentation as an evolutionary informative feature to distinguish genera in this group.
DOI: 10.6084/m9.figshare.12123186
title: Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus <i>Carpetania</i> (Oligochaeta, Hormogastridae)

description: Research on cryptic species complexes has reached a consensus on the necessity of integrating multiple sources of evidence. Reduced representation library techniques such as Genotyping-by-Sequencing (GBS) have proven useful to study these groups. Both integrative taxonomy and genome-wide single nucleotide polymorphism (SNP) data remain to be widely applied to earthworms, an animal group with widespread presence of cryptic diversity. The genus <i>Carpetania</i> (formerly the <i>Hormogaster elisae</i> species complex) was found to contain six deeply divergent genetic lineages and some inconspicuous morphological differentiation based on a handful of Sanger-sequenced markers. Marchán et al. (submitted) delimited three well-supported species-level clades on the basis of a genome-wide SNP dataset and geometric morphometric analyses, highlighting the necessity of a formal taxonomic description of these taxa. In this work, further analyses are applied to the SNP data and a thorough morphological study is performed in order to provide an integrative description of two new species and to redescribe <i>Carpetania elisae</i>. Species-specific SNPs are identified and used as diagnostic characters, and genome-wide and cytochrome oxidase C subunit 1 (COI) genetic distances are compared finding a strong correlation between them. The taxonomic description of these three cryptic species provides a useful tool to include them effectively in ecological studies and biodiversity conservation actions. www.zoobank.org/urn:lsid:zoobank.org:act:19CC41D7-BD25-4337-BED5-CDB04CAFB537 www.zoobank.org/urn:lsid:zoobank.org:act:206EE090-4AF5-4D12-82CA-F4A6494E90D4 www.zoobank.org/urn:lsid:zoobank.org:pub:2797FDDF-EA3D-4347-96C6-E632DC26CDA3
DOI: 10.6084/m9.figshare.12123189.v1
title: Total-evidence phylogeny and divergence times of Vermilingua (Mammalia: Pilosa)

description: Vermilingua is a peculiar group of xenarthran placental mammals with well-established phylogenetic relationships based on morphological and molecular data, but until now, no combined analysis of those data types. Here we perform the first total-evidence phylogenetic analysis of Vermilingua and estimate divergence times for living and fossil anteaters with a tip-dating approach, using the Fossilized Birth-Death model in a Bayesian framework. Using combined analyses, we recovered as monophyletic the two families, Cyclopedidae and Myrmecophagidae, as in previous studies, although our revised morphological data alone do not support the monophyly of Cyclopedidae. We show how the combination of molecular and morphological data indirectly affects the position and support for fossil taxa even though molecular datasets do not contain direct information for them. The estimated divergence times of <i>Palaeomyrmidon</i> and <i>Protamandua</i> are much older than the ages of those fossils, reinforcing the scarcity of the vermilinguan fossil record. In addition, we obtained evidence that the extinct <i>Neotamandua</i> is an ancestor of the extant <i>Myrmecophaga</i>, not a sister taxon as in previous studies, that did not incorporate the possibility of anagenetic evolution between fossil and living taxa.
DOI: 10.6084/m9.figshare.12123186.v1
title: Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus <i>Carpetania</i> (Oligochaeta, Hormogastridae)

description: Research on cryptic species complexes has reached a consensus on the necessity of integrating multiple sources of evidence. Reduced representation library techniques such as Genotyping-by-Sequencing (GBS) have proven useful to study these groups. Both integrative taxonomy and genome-wide single nucleotide polymorphism (SNP) data remain to be widely applied to earthworms, an animal group with widespread presence of cryptic diversity. The genus <i>Carpetania</i> (formerly the <i>Hormogaster elisae</i> species complex) was found to contain six deeply divergent genetic lineages and some inconspicuous morphological differentiation based on a handful of Sanger-sequenced markers. Marchán et al. (submitted) delimited three well-supported species-level clades on the basis of a genome-wide SNP dataset and geometric morphometric analyses, highlighting the necessity of a formal taxonomic description of these taxa. In this work, further analyses are applied to the SNP data and a thorough morphological study is performed in order to provide an integrative description of two new species and to redescribe <i>Carpetania elisae</i>. Species-specific SNPs are identified and used as diagnostic characters, and genome-wide and cytochrome oxidase C subunit 1 (COI) genetic distances are compared finding a strong correlation between them. The taxonomic description of these three cryptic species provides a useful tool to include them effectively in ecological studies and biodiversity conservation actions. www.zoobank.org/urn:lsid:zoobank.org:act:19CC41D7-BD25-4337-BED5-CDB04CAFB537 www.zoobank.org/urn:lsid:zoobank.org:act:206EE090-4AF5-4D12-82CA-F4A6494E90D4 www.zoobank.org/urn:lsid:zoobank.org:pub:2797FDDF-EA3D-4347-96C6-E632DC26CDA3
DOI: 10.6084/m9.figshare.12123165
title: The complex effect of heterogeneity and isolation in determining alpha and beta orchid diversity on islands in the Aegean archipelago

description: Knowledge of factors determining the distribution of plants on islands is of crucial importance in island biogeography. Here the drivers and mechanisms that best explain α- and β-diversity of orchids in the Aegean Archipelago were explored. The analyses were based on (a) matrix of the total number of orchid taxa recorded on each island, and (b) matrix containing the number of grid cells of each island in which each orchid has been recorded. Based on these matrices, generalized linear models (GLMs) were then used to determine the most important factors (geographical, climatic, geological) associated with orchid richness. Generalized dissimilarity modelling (GDM) was used to explore whether there are specific patterns in β-diversity and to evaluate contributions to individual factors to these patterns. To investigate the similarity of the Aegean islands in terms of their orchid flora, a β-diversity abundance matrix was analyzed using non-metric multidimensional scaling ordination method. GLM analysis revealed that maximum elevation, index of bioclimatic breadth (IBB), neighbour index (NI), island area, and the percentage of granite, limestone and quartz at each island were the best predictors of orchid α-diversity. Maximum elevation, habitat heterogeneity, IBB and island area were positively associated with α-diversity, whereas neighbour index and the percentage of granite, limestone and quartz at each island were negatively associated. Maximum elevation, NI, habitat heterogeneity and geographical distance were the best predictors of orchid turnover across the Aegean islands, whereas IBB, granite and limestone were less important. The NMDS ordination revealed that islands are structured from the southernmost to the northernmost, in a way that in general conforms to the phytogeographical division of the Aegean Archipelago. The drivers that account for the patterns in α- and β-diversity were associated with differences in the degrees of isolation and heterogeneity (climatic and habitat) of the islands. Among the predictors, elevation and IBB proved to be better surrogates of habitat heterogeneity than island area.