cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j81dm
title: Data from: Forest management adaptation to climate change: a Cornelian dilemma between drought resistance and soil macro-detritivore functional diversity

description: 1. Global warming induces new constraints on forest ecosystems and
 requires forest management adaptation. The reduction in stand density is
 currently debated as a potential tool to face increasing summer drought
 risk by improving forest resistance to climate change-induced tree
 mortality. However, few studies have yet assessed the impacts of this
 management change on soil biodiversity. 2. We conducted a large-scale,
 multi-site assessment of the response of soil macro-detritivore
 assemblages and soil functioning to experimental manipulations of stand
 density. A total of 33 stands were studied covering a wide gradient of
 stand density, that is stand basal area from 2·5 to 43·7 m2 ha−1, stand
 age, that is 18–171 years old, and local abiotic context. 3. We observed
 contrasting responses as a function of both taxonomic and functional
 groupings. Exploratory analysis using causal diagrams, that is path
 analysis, highlights that these changes were mainly related to alterations
 in understorey vegetation, microclimatic and soil pH conditions. The
 response of soil macro-detritivore assemblages to stand density
 manipulation was consistent over the gradient of stand ages. 4. Among the
 litter-dwelling macro-detritivores, millipede abundance and diversity
 decreased with stand density reduction, while woodlice and epigeic
 earthworms were unaffected. Further, a shift in soil-dwelling earthworm
 community composition was observed in mull stands. Endogeic earthworm
 abundance showed a sharp increase with stand density reduction, which
 translated into an increase in soil respiration. In contrast, anecic
 earthworm abundance decreased and was strongly associated with a decline
 of the rate of forest floor turnover. 5. Synthesis and applications. Our
 study provides strong evidence that reductions of stand density will have
 substantial impacts on soil macro-detritivore assemblages and cascading
 effects on soil functioning, particularly in mull stands. Managing stand
 density of oak forests at an intermediate level, that is 25 m2 ha−1,
 appears to be best to optimize the trade-off between improving forest
 resistance to climate change and ensuring the conservation of functional
 diversity to preserve forest ecosystem functioning and stability.
description: Soil macro-detritivore
 assemblage abundance and diversity, environmental variables and soil
 processes dataFile includes data about
 the abundance and diversity of soil macro-detritivore assemblages and
 their functional groups, i.e. litter transformers (Diplopoda, Isopoda and
 epigeic earthworms) and soil engineers (anecic and endogeic earthworms),
 on each experimental plots. It also includes plots characteristics,
 environmental variables used in the path analysis, soil processes data and
 abundance data for each species.Henneron_et_al._JPE_2015_Dataset.xlsx
DOI: 10.6084/m9.figshare.31155184
title: Supplementary Material for: Malignant progression of SEGA-imitating fibrous meningioma in a child carrying a germline CHEK2 mutation

description: Background:
The subependymal giant cell astrocytoma (SEGA) predominantly occurs in patients with tuberous sclerosis. Here, we present an unusual aggressive transformation of SEGA-imitating fibrous meningioma in a child carrying a germline CHEK2 mutation

Methods:
This case study was conducted at a tertiary pediatric oncology center in accordance with current diagnostic and therapeutic standards. Tumor classification followed WHO CNS5 criteria and was complemented by genome-wide DNA methylation profiling. Comprehensive molecular workup included germline and somatic whole-exome sequencing, copy-number analysis, and RNA-sequencing;

Results:
An 8.5-year-old girl presented with an intraventricular tumor initially diagnosed as SEGA based on imaging and partial resection histology. Treatment with an mTOR inhibitor led to four years of stability before rapid progression and death due to postoperative brain edema. Re-examination of both specimens revealed transformation into an aggressive anaplastic meningioma, while the initial lesion was reclassified as fibrous meningioma.
Whole-exome and microarray analyses excluded germline TSC1/TSC2 defects but identified a pathogenic germline CHEK2 variant (c.1466del, p.Asn489ThrfsTer23). Somatic alterations involving NF1, and TP53 were found in the primary tumor.

Conclusions:
Constitutional CHEK2 mutations combined with somatic NF1 defect may have promoted the malignant progression of SEGA-imitating fibrous meningioma and its favorable initial response to mTOR inhibitors.
DOI: 10.6084/m9.figshare.31155184.v1
title: Supplementary Material for: Malignant progression of SEGA-imitating fibrous meningioma in a child carrying a germline CHEK2 mutation

description: Background:
The subependymal giant cell astrocytoma (SEGA) predominantly occurs in patients with tuberous sclerosis. Here, we present an unusual aggressive transformation of SEGA-imitating fibrous meningioma in a child carrying a germline CHEK2 mutation

Methods:
This case study was conducted at a tertiary pediatric oncology center in accordance with current diagnostic and therapeutic standards. Tumor classification followed WHO CNS5 criteria and was complemented by genome-wide DNA methylation profiling. Comprehensive molecular workup included germline and somatic whole-exome sequencing, copy-number analysis, and RNA-sequencing;

Results:
An 8.5-year-old girl presented with an intraventricular tumor initially diagnosed as SEGA based on imaging and partial resection histology. Treatment with an mTOR inhibitor led to four years of stability before rapid progression and death due to postoperative brain edema. Re-examination of both specimens revealed transformation into an aggressive anaplastic meningioma, while the initial lesion was reclassified as fibrous meningioma.
Whole-exome and microarray analyses excluded germline TSC1/TSC2 defects but identified a pathogenic germline CHEK2 variant (c.1466del, p.Asn489ThrfsTer23). Somatic alterations involving NF1, and TP53 were found in the primary tumor.

Conclusions:
Constitutional CHEK2 mutations combined with somatic NF1 defect may have promoted the malignant progression of SEGA-imitating fibrous meningioma and its favorable initial response to mTOR inhibitors.
DOI: 10.6084/m9.figshare.31155187
title: Supplementary Material for: Crescentic IgM κ MIDD with Thrombotic Microangiopathy in Waldenström’s Macroglobulinemia: A Rare and Aggressive MGRS Presentation: A Case Report and Literature Review

description: Introduction: Monoclonal immunoglobulin deposition disease (MIDD) is a rare monoclonal gammopathy of renal significance (MGRS) characterized by linear, non-organized deposition of immunoglobulin fragments along glomerular, tubular, and vascular basement membranes. While light and heavy chain MIDDs are more frequently reported, IgM-associated MIDD is exceedingly rare, with only a few cases documented.
Case Presentation: We report a 71-year-old man who presented with seronegative rapidly progressive glomerulonephritis (RPGN) and sub-nephrotic-range proteinuria. Initial serologies were negative for autoimmune and infectious causes. A monoclonal workup revealed an IgM κ paraprotein, prompting further evaluation. Kidney biopsy demonstrated diffuse crescentic glomerulonephritis (81%), linear IgM κ deposits, and arteriolar thrombotic microangiopathy (TMA). Bone marrow studies confirmed lymphoplasmacytic lymphoma with an MYD88 L265P mutation, consistent with Waldenström’s macroglobulinemia (WM).
Conclusion: This case represents the first reported instance of IgM κ MIDD presenting with both crescentic GN and TMA in the setting of WM, defining a uniquely aggressive dual-injury renal phenotype. It highlights the diagnostic challenge of seronegative RPGN, in which MIDD should be included in the differential diagnosis. The case underscores the importance of integrated histopathology and hematologic genomics in identifying rare MGRS entities, recognizing that severe kidney injury may evolve rapidly despite appropriate management.
DOI: 10.5061/dryad.q7274
title: Data from: Using playback of territorial calls to investigate mechanisms of kin discrimination in red squirrels

description: Kin recognition can facilitate kin selection and may have played a role in
 the evolution of sociality. Red squirrels (Tamiasciurus hudsonicus) defend
 territories using vocalizations known as rattles. They use rattles to
 discriminate kin, though the mechanism underlying this ability is unknown.
 Our objective was to distinguish between the mechanisms of prior
 association, where animals learn the phenotypes of kin they associate with
 early in life, and phenotype matching/recognition alleles, where animals
 use a template to match phenotypes, thereby allowing them to recognize kin
 without an association early in life. We used audio playbacks to measure
 the responses of squirrels to rattles from familiar kin, unfamiliar kin,
 and non-kin. Initial analyses revealed that red squirrels did not
 discriminate between familiar and unfamiliar kin, but also did not
 discriminate between kin and non-kin, despite previous evidence indicating
 this capability. Post hoc analyses showed that a squirrel’s propensity to
 rattle in response to playback depended on an interaction between
 relatedness and how the playback stimuli had been recorded. Red squirrels
 discriminated between rattles from close kin (r = 0.5) and rattles from
 non-kin (r &lt; 0.125) when the rattles were recorded from provoked
 squirrels. Squirrels did not exhibit kin discrimination in response to
 unsolicited rattles. Once we accounted for how the stimuli had been
 recorded, we found no difference in the responses to familiar and
 unfamiliar kin. Our study suggests that kin discrimination by red
 squirrels may be context dependent.
description: Shonfield et al playback
 trial data fileThis data file contains
 data from playback trials conducted in the field on red squirrels in
 Kluane, Yukon. This data file contains the details of each playback trial,
 including location, date, subject squirrel info, playback stimulus info,
 and response of the subject squirrel.
DOI: 10.6084/m9.figshare.31155187.v1
title: Supplementary Material for: Crescentic IgM κ MIDD with Thrombotic Microangiopathy in Waldenström’s Macroglobulinemia: A Rare and Aggressive MGRS Presentation: A Case Report and Literature Review

description: Introduction: Monoclonal immunoglobulin deposition disease (MIDD) is a rare monoclonal gammopathy of renal significance (MGRS) characterized by linear, non-organized deposition of immunoglobulin fragments along glomerular, tubular, and vascular basement membranes. While light and heavy chain MIDDs are more frequently reported, IgM-associated MIDD is exceedingly rare, with only a few cases documented.
Case Presentation: We report a 71-year-old man who presented with seronegative rapidly progressive glomerulonephritis (RPGN) and sub-nephrotic-range proteinuria. Initial serologies were negative for autoimmune and infectious causes. A monoclonal workup revealed an IgM κ paraprotein, prompting further evaluation. Kidney biopsy demonstrated diffuse crescentic glomerulonephritis (81%), linear IgM κ deposits, and arteriolar thrombotic microangiopathy (TMA). Bone marrow studies confirmed lymphoplasmacytic lymphoma with an MYD88 L265P mutation, consistent with Waldenström’s macroglobulinemia (WM).
Conclusion: This case represents the first reported instance of IgM κ MIDD presenting with both crescentic GN and TMA in the setting of WM, defining a uniquely aggressive dual-injury renal phenotype. It highlights the diagnostic challenge of seronegative RPGN, in which MIDD should be included in the differential diagnosis. The case underscores the importance of integrated histopathology and hematologic genomics in identifying rare MGRS entities, recognizing that severe kidney injury may evolve rapidly despite appropriate management.
DOI: 10.5281/zenodo.18383840
title: 7-Tage-Inzidenz der COVID-19-Fälle in Deutschland

description: Im Datensatz "7-Tage-Inzidenz der COVID-19-Fälle in Deutschland" des Robert Koch-Instituts werden die täglich aktualisierten COVID-19-Inzidenzen auf Bundes-, Landes- und Landkreisebene basierend auf den Meldungen nach dem Infektionsschutzgesetz (IfSG) bereitgestellt. Die 7-Tage-Inzidenz wird definiert als Anzahl gemeldeter Fälle der letzten sieben Tage pro 100.000 Einwohner:innen und differenziert nach Altersgruppen und Regionen. Die Datenverarbeitung erfolgt vollständig elektronisch über das Deutsche Elektronische Melde- und Informationssystem (DEMIS).
DOI: 10.5061/dryad.1v154
title: Data from: Multilocus phylogenetics of new world milkweed vines (Apocynaceae, Asclepiadoideae, Gonolobinae)

description: Subtribe Gonolobinae of the cosmopolitan family Apocynaceae is diverse and
 represents the largest radiation of milkweeds in the New World (~500
 species). The largest genus, Matelea, is an amalgam that was united
 largely by a perceived lack of discrete morphological variation,
 particularly in floral structures. Using plastid and nuclear DNA
 sequences, we estimate a phylogeny of Gonolobinae using four chloroplast
 loci and three cloned nuclear regions. We investigate monophyly of Matelea
 and other established and provisional genera via a series of hypothesis
 tests. We find variable support and considerable conflict among the gene
 trees. Despite this, our data confirm the paraphyly of Matelea while
 Gonolobus and other segregate genera receive some support as monophyletic
 assemblages. We attribute conflicting signal in our data primarily to
 incomplete lineage sorting, a likely result of rapid radiation. Ancestral
 character reconstructions of growth form, fruit, and corolla morphology
 reveal a woody twining growth form to be plesiomorphic with one to two
 transitions to an herbaceous, non-twining growth form followed by one
 putative reversal to the woody twining growth form in the subtribe.
 Plesiomorphic states for fruit ornamentation and corolla shape are less
 clear and these characters exhibit high levels of homoplasy. This study is
 one of the most comprehensive phylogenies of gonoloboid milkweeds to date
 and the first to sample multiple nuclear loci and include allelic data.
description: McDonnellEtal_Gonolobinae_nexusfilesContains four alignment files, 3 nuclear (IIL1, GLU, and TRA2) and 2 plastid (2 locus dataset including concatenated rpl16 and trnC-rpoB regions and 4 locus dataset including concatenated rpl16, trnC-rpoB, trnL-F, rps16 regions).
DOI: 10.5061/dryad.1t4n5
title: Data from: Global genetic analysis reveals the putative native source of the invasive termite, Reticulitermes flavipes, in France

description: Biological invasions are recognized as a major threat to both natural and
 managed ecosystems. Phylogeographic and population genetic analyses can
 provide information about the geographical origins and patterns of
 introduction and explain the causes and mechanisms by which introduced
 species have become successful invaders. Reticulitermes flavipes is a
 North American subterranean termite that has been introduced into several
 areas, including France where introduced populations have become invasive.
 To identify likely source populations in the USA and to compare the
 genetic diversity of both native and introduced populations, an extensive
 molecular genetic study was undertaken using the COII region of mtDNA and
 15 microsatellite loci. Our results showed that native northern US
 populations appeared well differentiated from those of the southern part
 of the US range. Phylogenetic analysis of both mitochondrial and nuclear
 markers showed that French populations probably originated from
 southeastern US populations, and more specifically from Louisiana. All of
 the mtDNA haplotypes shared between the United States and France were
 found in Louisiana. Compared to native populations in Louisiana, French
 populations show lower genetic diversity at both mtDNA and microsatellite
 markers. These findings are discussed along with the invasion routes of R.
 flavipes as well as the possible mechanisms by which French populations
 have evolved after their introduction.
description: genotypedataMicrosatellite data of the 170 workers of Reticulitermes flavipes genotyped.
DOI: 10.5061/dryad.jq5g627
title: Data from: The search for loci under selection: trends, biases and progress

description: Detecting genetic variants under selection using FST outlier analysis (OA)
 and environmental association analyses (EAA) are popular approaches that
 provide insight into the genetic basis of local adaptation. Despite the
 frequent use of OA and EAA approaches and their increasing attractiveness
 for detecting signatures of selection, their application to field-based
 empirical data have not been synthesized. Here, we review 66 empirical
 studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We
 report trends and biases across biological systems, sequencing methods,
 approaches, parameters, environmental variables and their influence on
 detecting signatures of selection. We found striking variability in both
 the use and reporting of environmental data and statistical parameters.
 For example, linkage disequilibrium among SNPs and numbers of unique SNP
 associations identified with EAA were rarely reported. The proportion of
 putatively adaptive SNPs detected varied widely among studies, and
 decreased with the number of SNPs analyzed. We found that genomic sampling
 effort had a greater impact than biological sampling effort on the
 proportion of identified SNPs under selection. OA identified a higher
 proportion of outliers when more individuals were sampled, but this was
 not the case for EAA. To facilitate repeatability, interpretation and
 synthesis of studies detecting selection, we recommend that future studies
 consistently report geographic coordinates, environmental data, model
 parameters, linkage disequilibrium, and measures of genetic structure.
 Identifying standards for how OA and EAA studies are designed and reported
 will aid future transparency and comparability of SNP-based selection
 studies and help to progress landscape and evolutionary genomics.
description: Table S1 - Full data
 set.Data was collected by
 reading papers associated with environmental association analyses. Data
 includes location, species, methods used, genetic parameters of data sets
 reviewed, and analytical parameters of the analyses.Table
 S1_data.xlsxR code for mixed-effects
 linear modelsThe R code used to
 create the figures and estimate regressions of the data
 set.Ahrens
 et al 2018_MolEcol_review.R
DOI: 10.5061/dryad.2226v8m
title: Data from: Reliable species distributions are obtainable with sparse, patchy and biased data by leveraging over species and data types

description: 1. New methods for species distribution models (SDMs) utilise
 presence‐absence (PA) data to correct the sampling bias of presence‐only
 (PO) data in a spatial point process setting. These have been shown to
 improve species estimates when both data sets are large and dense.
 However, is a PA data set that is smaller and patchier than hitherto
 examined able to do the same? Furthermore, when both data sets are
 relatively small, is there enough information contained within them to
 produce a useful estimate of species’ distributions? These attributes are
 common in many applications. 2. A stochastic simulation was conducted to
 assess the ability of a pooled data SDM to estimate the distribution of
 species from increasingly sparser and patchier data sets. The simulated
 data sets were varied by changing the number of presence‐absence sample
 locations, the degree of patchiness of these locations, the number of PO
 observations, and the level of sampling bias within the PO observations.
 The performance of the pooled data SDM was compared to a PA SDM and a PO
 SDM to assess the strengths and limitations of each SDM. 3. The pooled
 data SDM successfully removed the sampling bias from the PO observations
 even when the presence‐absence data was sparse and patchy, and the PO
 observations formed the majority of the data. The pooled data SDM was, in
 general, more accurate and more precise than either the PA SDM or the PO
 SDM. All SDMs were more precise for the species responses than they were
 for the covariate coefficients. 4. The emerging SDM methodology that pools
 PO and PA data will facilitate more certainty around species’ distribution
 estimates, which in turn will allow more relevant and concise management
 and policy decisions to be enacted. This work shows that it is possible to
 achieve this result even in relatively data‐poor regions.
description: Species
 ListSpecies
 list for Dryad.csv
DOI: 10.5061/dryad.tr16k
title: Data from: Virulence evolution of a generalist plant virus in a heterogeneous host system

description: Modelling virulence evolution of multihost parasites in heterogeneous host
 systems requires knowledge of the parasite biology over its various hosts.
 We modelled the evolution of virulence of a generalist plant virus,
 Cucumber mosaic virus (CMV) over two hosts, in which CMV genotypes differ
 for within-host multiplication and virulence. According to knowledge on
 CMV biology over different hosts, the model allows for inoculum flows
 between hosts and for host co-infection by competing virus genotypes,
 competition affecting transmission rates to new hosts. Parameters of
 within-host multiplication, within-host competition, virulence and
 transmission were determined experimentally for different CMV genotypes in
 each host. Emergence of highly virulent genotypes was predicted to occur
 as mixed infections, favoured by high vector densities. For most simulated
 conditions, evolution to high virulence in the more competent Host 1 was
 little dependent on inoculum flow from Host 2, while in Host 2, it
 depended on transmission from Host 1. Virulence evolution bifurcated in
 each host at low, but not at high, vector densities. There was no evidence
 of between-host trade-offs in CMV life-history traits, at odds with most
 theoretical assumptions. Predictions agreed with field observations and
 are relevant for designing control strategies for multihost plant viruses.
description: Melon_BiomassThis file contains data on growth of melon plants (mg dry weight) infected by CMV with or without satRNAs (semicolon delimited format). Table 5 in Betancourt, et al., (2011) Journal of General Virology, 92, 1930–1938.Tomato_BiomassThis file contains data on growth of tomato plants (mg dry weight) infected by CMV with or without satRNAs (semicolon delimited format). Data was used to estimate virulence parameters according to Escriu et al. 2003 (Evolution 57, 755-765).Melon_VaccThis file contains data on CMV viral accumulation (µg virus/g tissue fresh weight) on melon plants infected by CMV with or without satRNAs (semicolon delimited format). Data was used to estimate CMV transmissibility and transmission parameters according to the experimetal regression of CMV transmissibility (F) on viral accumulation (V): F= 0,127707+0,000208373V (R^2=0.7680, P&lt;0.0001), see Betancourt, et al., 2011. (Journal of General Virology, 92, 1930–1938).Tomato_VacThis file contains data on CMV viral accumulation (µg virus/g tissue fresh weight) on tomato plants infected by CMV with or without satRNAs (semicolon delimited format). Data was used to estimate CMV transmissibility and transmission parameters according to Escriu et al. 2003 (Evolution 57, 755-765) and Escriu et al. 2000 (Phytopathology 90, 1068-1072).