cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5tb2rbp1k
title: Data from: Novel roles of chloroquine and hydroxychloroquine in Graves’ orbitopathy therapy by targeting orbital fibroblasts

description: Context: Graves’ orbitopathy (GO) causes infiltrative exophthalmos by
 inducing excessive proliferation, adipogenesis and glycosaminoglycan
 production in orbital fibroblasts (OFs). Interference with OF autophagy is
 a potential therapy for proptosis. Objectives: Here, we aimed to evaluate
 the effects of chloroquine (CQ) and hydroxychloroquine (HCQ), the
 autophagy inhibitors commonly used in clinical practice, on OFs.
 Design/Setting/Participants: OFs isolated from patients with GO (GO-OFs)
 or control persons (non-GO-OFs) were cultured in proliferation medium (PM)
 or subjected to differentiation medium (DM). OFs were treated with CQ or
 HCQ (0, 2, 5,10 μM), and subsequently examined in vitro. Main Outcome
 Measures: CCK-8, EdU incorporation and flow cytometry assays were used to
 assess cellular viability. Adipogenesis was assessed with Western blot
 analysis, real-time PCR, and Oil Red O staining. Hyaluronan production was
 determined by real-time PCR and ELISA. Autophagy flux was detected using
 RFP-GFP-LC3 fluorescent staining and Western blot analysis. Results:
 CQ/HCQ halted proliferation and adipogenesis in GO-OFs in a
 concentration-dependent manner through blockage of autophagy, which were
 not detected in non-GO-OFs. Besides, inhibitory effect of CQ/HCQ on
 hyaluronan secretion of GO-OFs was also concentration-dependent, mediated
 by downregulation of hyaluronan synthase 2 (HAS2) rather than
 hyaluronidases. Moreover, CQ (10 mM) induced GO-OFs apoptosis without
 aggravating oxidative stress. Conclusions: The antimalarials CQ/HCQ affect
 proliferation, adipogenesis and hyaluronan generation in GO-OFs by
 inhibiting autophagy, providing proof of concept that they can treat GO as
 autophagy inhibitors.
description: Supplemental figures 1-3
DOI: 10.25338/b8s90q
title: Underlying data for: Influence of temporally varying weatherability on CO2-climate coupling and ecosystem change in the late Paleozoic

description: This dataset contains the primary data used as input parameters in a
 mechanistic stomatal CO2 model (Franks et al., 2014 (Geophysical Research
 Letters)) and the Paleosol Barometer Uncertainty Quantifier (i.e., PBUQ;
 Breecker, 2013 (Geochemistry, Geophysics, Geosystems)), as well as
 age-adjusted CO2 data from Montañez et al., 2016 (Nature
 Geoscience). The stomatal parameters were measured by Richey et
 al., 2020 (Climate Of The Past) and the paleosol parameters are
 revised from Montañez et al., 2007 (Science). These input parameters and
 previous age-adjusted CO2 estimates were used to create
 a 40-Myr pCO2 record for the Late Paleozoic Ice
 Age (LPIA) and its Permian demise.
description: See main text and supplemental materials and methods
 from: Richey, J. D., Montañez, I. P., Goddéris, Y.,
 Looy, C. V., Griffis, N. P., and Dimichele, W. A.: Influence of temporally
 varying weatherability on CO<sub>2</sub>–climate coupling and
 ecosystem change in the late Paleozoic, Clim. Past., 16, 1759–1775,
 https://doi.org/10.5194/cp-16-1759-2020, 2020.
 Montañez, I. P., Tabor, N. J., Niemeier, D., DiMichele, W. A.,
 Frank, T. D., Fielding, C. R., Isbell, J. L., Birgenheier, L. P., and
 Rygel, M. C.: CO<sub>2</sub>-forced climate and vegetation
 instability during Late Paleozoic deglaciation, Science, 315, 87–91,
 https://doi.org/10.1126/science.1134207, 2007.
 Montañez, I. P., McElwain, J. C., Poulsen, C. J., White, J. D.,
 Dimichele, W. A., Wilson, J. P., Griggs, G., and Hren, M. T.: Climate,
 <em>p</em>CO<sub>2</sub> and terrestrial carbon
 cycle linkages during late Palaeozoic glacial-interglacial cycles, Nat.
 Geosci., 9, 824–828, https://doi.org/10.1038/ngeo2822, 2016.
description: Brief descriptions of the input parameters and
 their calculation/source is included in the data set. For more
 information, see Richey, J. D., Montañez, I. P., Goddéris, Y., Looy, C.
 V., Griffis, N. P., and Dimichele, W. A.: Influence of temporally varying
 weatherability on CO<sub>2</sub>–climate coupling and
 ecosystem change in the late Paleozoic, Clim. Past., 16, 1759–1775,
 https://doi.org/10.5194/cp-16-1759-2020, 2020.
DOI: 10.5061/dryad.tqjq2bvvm
title: Data from: Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study

description: How insect communities are assembled in nature remains largely unknown. In
 particular, whether habitat filtering or competition serves as the main
 mechanism in forming insect communities is rarely subject to an in-depth
 investigation. One bottleneck lies in the difficulty of species
 identification when dealing with a large number of diverse insects.
 However, High-Throughput Sequencing (HTS) technology coupled with classic
 DNA barcoding offers a great opportunity to infer community assembly for
 this speciose group. In this study, using 13,909 full-length barcodes
 obtained by Sanger sequencing or the SOAPBarcode metabarcoding method, we
 showed that competition was the main assembly mechanism for the moth
 communities studied in temperate forests of China. The two sequencing
 methods showed highly consistent results with regards to both diversity
 composition and community assembly mechanism. Significant phylogenetic
 signals and structure suggested that the focal moth communities were the
 result of the non-neutral assembly process, which was further confirmed by
 results of neutral assembly test that accounted for immigration and
 speciation rates. In conclusion, HTS coupled with a well-curated DNA
 barcode library can facilitate community assembly inferences, especially
 for speciose taxonomic groups.
description: Please see the published article and contact the author if
 unavailable.
description: Please see README files for specific information.
DOI: 10.5061/dryad.5tb2rbp1m
title: Information collected during the post-breeding season guides future breeding decisions in a migratory bird

description: Breeding habitat choice and investment decisions are key contributors to
 fitness in animals. Density of individuals is a well-known cue of habitat
 quality used for future breeding decisions, but accuracy of density cues
 decreases as individuals disperse from breeding sites. Used nests remain
 an available information source also after breeding season, but whether
 such information is used for breeding decisions is less well known. We
 experimentally investigated whether migratory, cavity-nesting pied
 flycatchers (Ficedula hypoleuca) prospect potential breeding sites after
 breeding season and use old nests as a cue for future breeding decisions.
 In late summer 2013, forest sites were assigned to four treatments: (1)
 sites including nest boxes with old nests of heterospecifics (tits), (2)
 sites including suitable but empty nest boxes, (3) sites with unsuitable
 nest boxes, or (4) sites without any nest boxes. In the following year, we
 investigated pied flycatcher habitat choice and reproductive investment
 according to these “past” cues while also controlling for additional
 information sources present during settlement. Flycatchers preferred sites
 where tits had been perceived to breed in the previous year, but only if
 great tits were also currently breeding in the site and had a relatively
 high number of eggs. Old flycatchers avoided sites previously treated with
 suitable but empty cavities, whereas young flycatchers preferred sites
 where tits had apparently bred in the previous year. Also egg mass, but
 not clutch size or clutch mass, was affected by the combination of past
 treatment information and current tit abundance.
description: Data set from an experiment in natural environment manipulating
 the availability of social information and breeding sites for a passerine
 bird, the pied flycatcher <em>Ficedula hypoleuca</em>.
 Experimental manipulation was conducted during the post-breeding season
 (period from chick fledging to autumn migration) in 2013 and the responses
 were observed during the next breeding season in 2014. The uploaded files
 include data for nest site (nest box) occupation analysis (edited for Cox
 regression) and data for timing of breeding (laying date of the first
 egg), reproductive investment (clutch size, mean egg mass, clutch mass)
 and success (brood size, fledgling number). For further details, please
 contact the authors.
DOI: 10.5061/dryad.zs7h44j5h
title: Data from: Transcriptome analysis of Drosophila melanogaster laboratory strains of different geographical origin after long-term laboratory maintenance

description: Positive selection may be the main factor of the between-population
 divergence in gene expression. Expression profiles of two Drosophila
 melanogaster laboratory strains of different geographical origin and
 long-term laboratory maintenance were analyzed using microchip arrays
 encompassing probes for 18,500 transcripts. The Russian strain D18 and the
 North American strain Canton-S were compared. A set of 223 known or
 putative genes demonstrated significant changes in expression levels
 between these strains. Differentially expressed genes were enriched in
 response to DDT (P=0.0014), proteolysis (P=2.285E-5), transmembrane
 transport (P=1.03E-4), carbohydrate metabolic process (P=0.0317), protein
 homotetramerization (P=0.0444), antibacterial humoral response (P=425E-4).
 The expression in subset of genes from different categories was verified
 by qRT-PCR. Analysis of transcript abundance between Canton-S and D18
 strains allowed to select several genes to estimate their participation in
 latitude adaptation. Expression of selected genes was analyzed in five D.
 melanogaster lines of different geographic origins by qRT-PCR and we found
 two candidate genes that may be associated with latitude adaptation in
 adult flies – smp-30 and Cda9. Quite possible that several alleles of
 these genes may be important for insect survival in the environments of
 global warming. It is interesting that the number of genes involved in
 local adaptation demonstrate expression level appropriate to their
 geographical origin even after decades of laboratory maintenance.
DOI: 10.5061/dryad.2jm63xskk
title: Age of European silver eels during a period of declining abundance in Norway

description: The European eel (Anguilla anguilla) is critically endangered throughout
 its range. Knowledge about age distribution of future spawners (silver
 eels) is essential to monitor the status and contribute to the recovery of
 this species. Determination of age in anguillid eels is challenging,
 especially in eels from the northern part of the distribution area where
 growth is slow and age at maturation can be up to 30 years or more. Eels
 from the river Imsa in Norway have been monitored since 1975 and this
 reference time-series has been used to assess the stock at the European
 level. Population dynamics in this catchment were analyzed during the late
 1980s by estimating ages on whole cleared otoliths. However, techniques
 for revealing annual increments on otoliths have evolved over the years
 sometimes yielding significant differences in age estimates. In this
 study, the historical otolith data were reanalyzed using a grinding and
 polishing method rather than reading the whole otolith. The new age
 estimates were considerably higher than the previous ones, sometimes by up
 to 29 years. Since the 1980s, mean age of silver eels only slightly
 increased (from 19 to 21 years in the 2010s). This was mainly due to the
 disappearance of younger silver eels (less than 15 years) in the 2010s.
 The new age estimates agreed with the steep decline in recruitment which
 occurred in the late 1980s in the Imsa catchment. Mean growth (30 mm y-1,
 min-max: 16 - 64 mm y-1) has not changed since the 1980s, although density
 in the catchment has decreased. Revealing and reading age of slow growing
 eels remain a challenge but adding a measure of otolith reading
 uncertainty may improve age data collection and contribute to recovery
 measures for this species.
description: See the manuscript for methods.
description: Missing values are identified with NA
DOI: 10.5061/dryad.3bk3j9kfz
title: Data from: Shading enhances plant species richness and diversity on an extensive green roof

description: Green roofs can promote biodiversity in urban areas. The extent to which
 green roofs stimulate plant diversity can depend on roof characteristics
 such as roof age, substrate depth and shading. We exploratively studied
 the vegetation on a Dutch green roof in 50 permanent plots (1 m2) over
 eight years (2012–2019) following roof construction. Plots were situated
 either on low substrate depth (6 cm light-weight extensive substrate) or
 high substrate depth (6 cm light-weight extensive substrate topped with 14
 cm native soil) and differed in the amount of shading received from a
 higher building floor. Increased substrate depth and shading additively
 increased plant species richness and plant diversity, with high shaded
 plots supporting on average 6.4 more plant species than low unshaded
 plots. Shading likely acts via reducing drought stress, whereas increasing
 substrate depth with native soil may also enhance plant diversity via
 addition of nutrients and native seeds. The vegetation composition on the
 roof was dynamic and changed over the years. Sedum acre was initially
 dominant but disappeared within the first years, whereas Sedum
 kamtschaticum increased and became dominant in the last years. Trifolium
 arvense was the most abundant forb species and was especially dominant
 three years after roof construction. We conclude that increased substrate
 depth and shading can promote plant species richness and diversity and
 recommend that both aspects are considered when green roofs are designed.
 Shading can be achieved by a stepped building architecture and by placing
 structures on the roof itself, such as solar panels on standards.
description: See the main article on how the data was collected.
description: The dataset consists of three tables:
 <em>Plots.csv</em> provides the plot characteristics
 (substrate depth and shading) of each of the 50 surveyed plots.
 <em>Years.csv</em> provides information on whether
 plots were surveyed and spring precipitation in each year. The
 precipitation data was obtained from the Royal Netherlands Meteorological
 Institute (KNMI) weather station in Deelen.
 <em>Survey_data</em> provides the cover of each plant
 species found in each plot in each year. Columns Plot_ID and Year are the
 identifiers to match the data with the tables <em>Plots.csv
 </em>and <em>Years.csv</em>, respectively.
   Update 28 September 2020: An error was found
 in the <em>Survey_data</em> file, which accidentily included
 data from the roof in the study and another roof. The file has been
 replaced by a correct file. The error was made when transferring the data
 to Dryad, and the correct dataset has been used for the
 analysis.
DOI: 10.5061/dryad.r7sqv9s85
title: Phylo-k-mers databases for SHERPAS

description: SHERPAS is a new program to identify novel recombinant sequences in a
 large collection of viral sequences, and to provide a first estimate of
 their recombinant structure. SHERPAS is much faster than other softwares
 for recombination detection; its main feature is the use of a pre-computed
 database of "phylogenetically-informed k-mers" (or
 phylo-k-mers). The computation of this phylo-k-mer database is a heavy
 computational step, but it only needs to be executed once for a given
 reference alignment. A phylo-k-mer database can be built from any
 reference alignment, and a phylogenetic tree built from that alignment,
 using RAPPAS2 (https://github.com/phylo42/rappas2). We propose here three
 ready-to-use databases, for three reference alignments: -An alignment of
 167 sequences of the pol region of the HIV genome, provided with the
 program SCUEAL, accessible at
 https://github.com/spond/SCUEAL/blob/master/data/pol2009.nex -An alignment
 of 339 sequence of the whole HBV genome, provided with the programm jpHMM,
 accessible at http://jphmm.gobics.de/download.html. -An alignment of 881
 sequences of the whole HIV genome, also provided with jpHMM, accessible at
 http://jphmm.gobics.de/download.html. For each of these alignments, we
 provide a .zip file containing three files: The phylo-k-mer database (.rps
 file), the reference phylogenetic tree used to build the database (.tree
 file), and a table associating each reference sequence to a strain of the
 virus (.csv file). The details of the construction of the database, the
 construction of the tree, as well as the origin of the information
 reported in the table, can be found in the Supplementary Materials
 associated with the original Bioinformatics publication.
description: <em>Structure of the dataset:</em>
 For the pol region of the HIV genome (167 reference
 sequences):<br>     pkDB-HIV-pol.zip<br>          
   DB_k10_o1.5.rps<br>             pol2009-GTRtree.tree<br>   
          ref-group.csv For the whole HBV genome (339
 reference sequences):<br>     pkDB-HBV-full.zip<br>           
  DB_k10_o1.5.rps<br>             HBV_tree.tree<br>           
  ref-group.csv For the whole HIV genome (881 reference
 sequences):<br>     pkDB-HIV-full.zip<br>           
  DB_k10_o1.5.rps<br>             HIV-alignment.tree<br>       
      ref-group.csv  
 <em>SHERPAS download and
 documentation:</em> https://github.com/phylo42/sherpas
DOI: 10.5281/zenodo.18395075
title: CLINICAL IMMUNOLOGICAL ALTERATIONS IN ENTEROBIASIS: A COMPREHENSIVE REVIEW
DOI: 10.5061/dryad.280gb5mmt
title: Data from: Rapid radiation in a highly diverse marine environment

description: Rapid diversification is often observed when founding species invade
 isolated or newly formed habitats that provide ecological opportunity for
 adaptive radiation. However, most of the Earth’s diversity arose in
 diverse environments where ecological opportunities appear to be more
 constrained. Here, we present a striking example of a rapid radiation in a
 highly diverse marine habitat. The hamlets, a group of reef fishes from
 the wider Caribbean, have radiated into a stunning diversity of color
 patterns but show low divergence across other ecological axes. Although
 the hamlet lineage is approximately 26 million years old, the radiation
 appears to have occurred within the last 10,000 generations in a burst of
 diversification that ranks among the fastest in fishes. As such, the
 hamlets provide a compelling backdrop to uncover the genomic elements
 associated with phenotypic diversification and an excellent opportunity to
 build a broader comparative framework for understanding the drivers of
 adaptive radiation. The analysis of 170 genomes suggests that color
 pattern diversity is generated by different combinations of alleles at a
 few large-effect loci. Such a modular genomic architecture of
 diversification has been documented before in Heliconius butterflies,
 capuchino finches and munia finches, three other tropical radiations that
 took place in highly diverse and complex environments. The hamlet
 radiation also occurred in a context of high effective population size,
 which is typical of marine populations. This allows for the accumulation
 of new variants through mutation and the retention of ancestral genetic
 variation, both of which appear to be important in this radiation.
DOI: 10.5281/zenodo.18395074
title: CLINICAL IMMUNOLOGICAL ALTERATIONS IN ENTEROBIASIS: A COMPREHENSIVE REVIEW
DOI: 10.5061/dryad.547d7wm55
title: Detecting shrub encroachment in semi-natural grasslands using UAS LiDAR

description: Shrub encroachment in semi-natural grasslands threatens local biodiversity
 unless management is applied to reduce shrub density. Dense vegetation of
 Cytisus scoparius homogenizes the landscape negatively affecting local
 plant diversity. Detecting structural change (e.g., biomass) is essential
 for assessing negative impacts of encroachment. Hence, exploring new
 monitoring tools to achieve this task is important for effectively
 capturing change and evaluating management activities. This study combines
 traditional field-based measurements with novel Light Detection and
 Ranging (LiDAR) observations from an Unmanned Aircraft System (UAS). We
 investigate the accuracy of mapping C. scoparius in three dimensions (3D)
 and of structural change metrics (i.e. biomass) derived from ultra-high
 density point-cloud data (&gt;1000 pts/m2). We utilized a 3D
 point-based classification to distinguish shrub genera based on their
 structural appearance (i.e. density, light penetration and surface
 roughness) in a semi-natural grassland in Denmark. From the identified C.
 scoparius individuals we related different volume metrics (mean, max and
 range) to measured biomass and quantified spatial variation in biomass
 change from 2017 to 2018. We obtained overall classification accuracies
 above 86% from point clouds of both seasons. Maximum volume explained
 77.4% of the variation in biomass. The spatial patterns revealed landscape
 scale variation in biomass change between autumn 2017 and spring 2018,
 with a notable decrease in some areas. Further studies are needed to
 disentangle the causes of the observed decrease, e.g., recent winter
 grazing and/or frost events. We present a workflow for processing
 ultra-high density spatial data obtained from a UAS LiDAR system to detect
 change in C. scoparius. We demonstrate that UAS LiDAR is a promising tool
 to map and monitor grassland shrub dynamics at the landscape scale with
 the accuracy needed for effective nature management. It is a new tool for
 standardized and non-biased evaluation of management activities initiated
 to prevent shrub encroachment.
description: <i>- </i>All data are associated to the processing of UAS-LiDAR point clouds in Mols with the following dates and dataset ID’s: 06-10-2017 à “Mols17” 23-04-2018 à “Mols18” - Groundtruth GNSS points are available as point shapefiles - Biomass measurements from harvested Cytisus scoparius individuals are available as spreadsheet. - Associated scripts for the Opals processing are available as batch files  
description: <i>Processing:</i> The LiDAR
 data were processed until step 1 following the
 workflow in Fig. 1 (described in <i>Madsen et al. (2019)</i>).
 Hence the data uploaded as .las files are already post-processed,
 georeferenced and filtered for noisy points.
   The full data overview are presented in the
 document "MolsLiDAR17-18_processed.doc" and if necessary, the
 raw data or other levels of processing can be made available upon
 request.