cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n8pk0p2zz
title: Data from: Bivalves from the Changhsingian (Upper Permian) Bellerophon Formation of the Dolomites (Italy): ancestors of the Lower Triassic post extinction benthic communities

description: The diverse shallow marine fossil assemblages from the Changhsingian
 Bellerophon Formation of the Dolomites record the late Palaeozoic marine
 life immediately before the end-Permian mass extinction. Here, based on
 the collection of c. 6500 bivalve specimens from different localities of
 the western Dolomites, we have taxonomically classified 26 species,
 including 10 new species, 3 new genera and 1 new family: Acharax
 frenademezi sp. nov., Bakevellia (Bakevellia) preromangica sp. nov.,
 Edmondia hautmanni sp. nov., Etheripecten stuflesseri sp. nov., Ladinomya
 fosteri gen. et sp. nov., Lovaralucina covidi gen. et sp. nov., Palaeolima
 badiotica sp. nov., Promytilus merlai sp. nov., Tambanella?
 stetteneckensis sp. nov., Volsellina carinata sp. nov., Gardenapecten gen.
 nov., Ladinomyidae fam. nov. The occurrence of three Eumorphotis species
 with a different and superimposed stratigraphic distribution led us to
 propose an upper Permian ‘lower Eumorphotis Zone’ in contrast to the
 already known Lower Triassic Eumorphotis Zone which is consequently
 renamed as ‘upper Eumorphotis Zone’. The ‘lower Eumorphotis Zone’ is
 divided, in ascending stratigraphic order, into E. praecurrens, E.
 striatocostata and E. lorigae subzones. A palaeoecological analysis of the
 bivalves contained in each sampled bed has allowed us to recognize 6
 biofacies and 4 ecofacies, based on richness, dominance and ecological
 lifestyle. The bivalves from Bellerophon Formation inhabited lagoonal to
 nearshore environments affected by stressed conditions, mostly represented
 by high temperatures, high salinity, shallow water depths, low oxygen and
 high terrigenous input. The upper Bellerophon Fm is characterized by
 increasing fully marine conditions, although the occurrence of eurytopic
 taxa still suggests stressed marine conditions.
description: The bivalves for this research
 have been collected from the following localities: Balest, Bulla II,
 Culatsch, Ruf da Piz and Jmueia da Insom in Gardena Valley and from Seres
 and Preroman in Badia Valley. For the studied sections, the fossiliferous
 beds were chosen for quantitative sampling of bivalves. Each sampling was
 performed until more than 100 specimens were obtained or until further
 sampling doesn't reveal new taxa. Some beds were sampled repeatedly
 until well-preserved specimens of some taxa have been obtained. The
 samples were taken to the preparation lab and there extracted with
 pneumatic air pen. In total, 2360 fossil-bearing samples with
 6515 specimens were collected. The minimum number of individuals (MNI) has
 been totaled by counting only the most numerous valves (left/right)
 together with the articulated specimens.
description: Excel or Open Office
DOI: 10.5061/dryad.41ns1rnj1
title: Multiple sequence alignments of newly reconstructed and published cervid and human mtDNA

description: Assigning prehistoric objects to specific individuals is usually
 impossible outside of burial contexts. Here we present a non-destructive
 method for gradually releasing DNA from ancient bone and tooth artifacts.
 Application of the method to an Upper Paleolithic deer tooth pendant from
 Denisova Cave (Russia) resulted in the recovery of DNA from both the deer
 and a female human individual. Genetic dates obtained from the deer and
 human mitochondrial genomes estimate the age of the pendant at
 approximately 20,000 to 24,000 years. Nuclear DNA from its presumed maker
 or wearer shows strong affinities to contemporaneous Ancient North
 Eurasian individuals previously found further east in Siberia. Our work
 opens up new possibilities for linking cultural and genetic records in
 prehistoric archaeology.
description: The non-destructive DNA extraction method described in the
 associated publication was used to recover DNA from a cervid tooth pendant
 found in the Upper Paleolithic layers of Denisova Cave. This DNA was
 converted into single-stranded libraries and enriched separately for human
 and cervid mitochondrial(mt) DNA via hybridization capture and sequenced.
 The human mtDNA capture resulted in 62-fold average coverage of the human
 mtDNA genome allowing for reconstruction of a near-complete mtDNA genome.
 This genome (DCP1 in Aligned_human_mtDNA.fst) was aligned to the revised
 Cambridge reference sequence with a selection of published ancient and
 present-day human mtDNA genomes. The cervid mtDNA capture resulted in
 635-fold coverage, also allowing for reconstruction of a mtDNA genome.
 This genome (DCP1 in Aligned_cervid_mtDNA.fst) was alighed to a waipiti
 mtDNA genome with selection of ancient waipiti mtDNA genomes. Each of
 these multiple sequence alignments was used for tree building and
 molecular branch shortening. Finally, the list of SNPs enriched for in the
 hybridization capture of human nuclear DNA (probeset referred to as
 "AA204") is also included. 
description: The two files are a multiple sequence alignment file and can be
 read in a text editor or any MSA viewing program (e.g. MEGA, Seaview,
 etc.). The SNP list is a tab-delimited file that can be read in a text
 editor.
DOI: 10.5061/dryad.rfj6q57f6
title: Source data for: Synthesis phylogeny of insects

description: The Holy Grail of an Insect Tree of Life can only be ‘discovered’ through
 extensive collaboration among taxon specialists, phylogeneticists, and
 centralized frameworks (such as TreeBase and Open Tree of Life), but an
 insufficient effort from stakeholders has so far hampered this promising
 approach. The resultant unavailability of synthesis phylogenies is an
 unfortunate situation given the numerous practical usages of phylogenies
 in the near-term against the backdrop of the ongoing biodiversity crisis.
 To redress this issue, we establish a new online hub that centralizes the
 collation of relevant phylogenetic data and provides the resultant
 synthesis molecular phylogenies. This is achieved through key developments
 in a proposed pipeline for the construction of a species-level insect
 phylogeny. The framework is demonstrated through the construction of a
 highly supported, species-comprehensive phylogeny of Diptera, built from
 integrated omics data, COI DNA barcodes, and a compiled database of over
 100 standardized, published Diptera phylogenies. Machine-readable forms of
 the phylogeny (and subsets thereof) are publically available at
 insectphylo.org, a new public repository for species-comprehensive
 phylogenies for biological research. 
description: Please see publication.
DOI: 10.5061/dryad.ngf1vhhxn
title: Data from: Influence of topography and the underlying surface of the Bohai Sea on wind and gust forecasts

description: Accurate gust forecasts can reduce potential threats to people’s lives and
 properties, but we need more reliable forecasting methods and models. A
 recent development is the meteorologically stratified gust factor (MSGF)
 model, which is more accurate in forecasting gusts than the previous gust
 factor model. The regional terrain and underlying surface both have
 crucial effects on the gust factor. We therefore combined observations
 from the China Meteorological Administration over the ocean surface and
 along the coast with the MSGF model to explore the influence of topography
 and the underlying surface on wind and gust forecasts. The regional
 terrain and underlying surface affected the peak gust climatologies, the
 mean wind speed, the mean prevailing wind direction and the gust factors.
 The topography and the underlying surface had different impacts in
 different ranges of the mean wind speed. The strong turbulence that causes
 changes in the gust factor under light winds is not initiated over rough
 underlying surfaces. When the mean wind speed is &gt;2.5 m s−1, the
 underlying surface influences both the wind speed and the gust factor. A
 rough underlying surface stimulates stronger turbulence and increases the
 gust speed and gust factor, whereas a smooth underlying surface directly
 increases the mean wind speed and the gust speed by different magnitudes
 to reduce the difference between them, thus decreasing the gust factor. We
 evaluated the ability of the MSGF model to forecast gusts and verified a
 method combining the products of a numerical model and the MSGF model in
 gust forecasts.
description: Please see the README document
 ("README.md") and the associated article: Ke Wang, Xinyu Lyu,
 Jing Huang, Meng Luo, Fei Xu. 2022. Influence of topography and the
 underlying surface of the Bohai Sea on wind and gust
 forecasts.<br>
DOI: 10.5061/dryad.2bvq83btn
title: Plant secondary metabolic responses to global climate change: A meta-analysis in medicinal and aromatic plants

description: Plant secondary metabolites (SMs) play crucial roles in plant-environment
 interactions and contribute greatly to human health. Global climate
 changes are expected to dramatically affect plant secondary metabolism,
 yet a systematic understanding of such influences is still lacking. Here,
 we employed medicinal and aromatic plants (MAAPs) as model plant taxa and
 performed a meta-analysis from 360 publications using 1828 paired
 observations to assess the responses of different SMs levels and the
 accompanying plant traits to elevated carbon dioxide (eCO2), elevated
 temperature (eT), elevated nitrogen deposition (eN), and decreased
 precipitation (dP). The overall results showed that phenolic and terpenoid
 levels generally respond positively to eCO2 but negatively to eN, while
 the total alkaloid concentration was increased remarkably by eN. By
 contrast, dP promotes the levels of all SMs, while eT exclusively exerts a
 positive influence on the levels of phenolic compounds. Further analysis
 highlighted the dependence of SM responses on different moderators such as
 plant functional types, climate change levels or exposure durations, mean
 annual temperature and mean annual precipitation. Moreover, plant phenolic
 and terpenoid responses to climate changes could be attributed to the
 variations in C/N ratio and total soluble sugar levels, while the
 trade-off supposition contributed to SM responses to climate changes other
 than eCO2. Taken together, our results predicted the distinctive SM
 responses to diverse climate changes in MAAPs, and allowed us to define
 potential moderators responsible for these variations. Further, linking SM
 responses to C-N metabolism and growth-defence balance provided biological
 understandings in terms of plant secondary metabolic regulation.
description: Peer-reviewed journal articles
 published online from January 1990 to March 2022 were searched using
 <em>Web of Science</em> (http://www.isiknowledge.com/), with
 the following terms: (global change OR climate change OR free-air carbon
 dioxide enrichment OR free-air CO<sub>2</sub> enrichment OR
 elevated carbon dioxide OR elevated CO<sub>2</sub> OR elevated
 atmospheric CO<sub>2</sub> OR CO<sub>2</sub>
 enrichment OR eCO<sub>2</sub> OR atmospheric
 CO<sub>2 </sub> enrichment OR elevated atmospheric carbon
 dioxide OR carbon dioxide enrichment OR [carbon dioxide] OR nitrogen
 deposition OR nitrogen addition OR nitrogen application OR nitrogen
 fertiliz* OR nitrogen nutrition OR N deposition OR N addition OR N
 application OR N fertiliz* OR N nutrition OR changing precipitation OR
 increased precipitation OR decreased precipitation OR drought OR water
 stress OR water addition OR warming OR elevated temperature OR climate
 warming OR elevated temperature OR increased temperature) AND (medicinal
 plant OR aromatic plants).
DOI: 10.5061/dryad.jwstqjqdb
title: Data from: HIF prolyl hydroxylase 2/3 deletion disrupts astrocytic integrity and exacerbates neuroinflammation

description: Astrocytes constitute the parenchymal border of the blood-brain barrier
 (BBB), modulate the exchange of soluble and cellular elements, and are
 essential for neuronal metabolic support. Thus, astrocytes critically
 influence neuronal network integrity. In hypoxia, astrocytes upregulate a
 transcriptional program that has been shown to boost neuroprotection in
 several models of neurological diseases. We investigated transgenic mice
 with astrocyte-specific activation of the hypoxia-response program by
 deleting the oxygen sensors, HIF prolyl-hydroxylase domains 2 and 3
 (Phd2/3). We induced Phd2/3 deletion in experimental autoimmune
 encephalomyelitis (EAE) in a therapeutic approach that led to an
 exacerbation of the disease mediated by massive immune cell infiltration.
 We found that Phd2/3-ko astrocytes, though expressing a neuroprotective
 signature, exhibited a gradual loss of gap-junctional Connexin-43 (Cx43),
 which was induced by vascular endothelial growth factor-alpha (Vegf-a)
 expression. These results provide mechanistic insights into astrocyte
 biology, their critical role in hypoxic states, and in chronic
 inflammatory CNS diseases.
description: By using TRAP (translating ribosome affinity purification) just
 actively translating mRNA from astrocytes of mice
 Aldh1l1-cre<sup>ERT2</sup>; Phd2<sup>fl/fl or
 wt/wt</sup>; Phd3<sup>fl/fl or wt/wt</sup>; L10a-eGFP
 was collected (spinal cord and brain stem), purified and sequenced at the
 HiSeq4000 system. For detailed protocol information please refer to
 Heiman et al., 2014 and Rosiewicz et
 al., 2020. Then raw fastq files were quality checked by FastQC, then rRNA
 content was filtered-out with SortMeRNA and finally aligned to mouse
 genome by Salmon.<br>
description: Salmon output data can be further analyzed by R based package
 DESeq2.
DOI: 10.5061/dryad.hhmgqnkkx
title: The benefit of augmenting open data with clinical data-warehouse EHR for forecasting SARS-CoV-2 hospitalizations in Bordeaux area, France

description: Objective The aim of this study was to develop an accurate regional
 forecast algorithm to predict the number of hospitalized patients and to
 assess the benefit of the Electronic Health Records (EHR) information to
 perform those predictions. Materials and Methods Aggregated data from
 SARS-CoV-2 and weather public database and data warehouse of the Bordeaux
 hospital were extracted from May 16, 2020, to January 17, 2022. The
 outcomes were the number of hospitalized patients in the Bordeaux Hospital
 at 7 and 14 days. We compared the performance of different data sources,
 feature engineering, and machine learning models. Results During the
 period of 88 weeks, 2561 hospitalizations due to COVID-19 were recorded at
 the Bordeaux Hospital. The model achieving the best performance was an
 elastic-net penalized linear regression using all available data with a
 median relative error at 7 and 14 days of 0.136 [0.063; 0.223] and 0.198
 [0.105; 0.302] hospitalizations, respectively. Electronic health records
 (EHRs) from the hospital data warehouse improved median relative error at
 7 and 14 days by 10.9% and 19.8%, respectively. Graphical evaluation
 showed remaining forecast error was mainly due to delay in slope shift
 detection. Discussion Forecast models showed overall good performance both
 at 7 and 14 days which was improved by the addition of the data from
 Bordeaux Hospital data warehouse. Conclusions The development of hospital
 data warehouses might help to get more specific and faster information
 than traditional surveillance systems, which in turn will help to improve
 epidemic forecasting at a larger and finer scale.
description: Aggregated data from 2020-05-16 to 2022-01-17 regarding Bordeaux
 Hospital EHR. Bordeaux hospital data warehouse was
 used, during the pandemic, to describe the current state of the epidemic
 at the hospital level on a daily basis. Those data were then used in the
 forecast model including: hospitalizations, hospital and ICU admission and
 discharge, ambulance service notes and emergency unit notes. Concepts
 related to COVID-19 were extracted from notes by dictionary-based
 approaches (e.g. cough, dyspnoea, covid-19). Dictionaries were manually
 created based on manual chart review to identify terms used by
 practitioners. Then, the number and proportion of ambulance service calls
 or hospitalization in emergency units mentioning concepts related to
 covid-19 were extracted. Due to different data acquisition mechanisms,
 there was a delay between the occurrence of events and the data
 acquisition. It was of 1 day for EHR data, 5 days for department
 hospitalizations and RT-PCR, 4 days for weather, 2 days for variants and 4
 days for vaccination. For the training and evaluation of the model, the
 chosen date was the date of data availability to mimic a real-time
 streaming forecast.
description: Data are stored in a .rdata file. Please use R
 (https://www.r-project.org/) software to open the data.
DOI: 10.5061/dryad.4qrfj6qdg
title: Data for: From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator

description: The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation
 around the world due to its coastal distribution. Information regarding
 population connectivity is crucial to evaluate its conservation status and
 local fishing impacts. In this study, we sampled 922 putative Bull Sharks
 from 19 locations in the first global assessment of population structure
 of this cosmopolitan species. Using a recently developed DNA-capture
 approach (DArTcap), samples were genotyped for 3,400 nuclear markers.
 Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were
 sequenced. Reproductive isolation was found between and across ocean
 basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West
 Pacific) with distinct island populations in Japan and Fiji. Bull Sharks
 appear to maintain gene flow using shallow coastal waters as dispersal
 corridors, whereas large oceanic distances and historical land-bridges act
 as barriers. Females tend to return to the same area for reproduction,
 making them more susceptible to local threats and an important focus for
 management actions. Given these behaviours, the exploitation of Bull
 Sharks from insular populations, such as Japan and Fiji, may instigate
 local decline that cannot readily be replenished by immigration, which can
 in turn affect ecosystem dynamics and functions. These data also supported
 the development of a genetic panel to ascertain the population of origin,
 which will be useful in monitoring the trade of fisheries products and
 assessing population-level impacts of this harvest.
description: A total of 922 putative Bull
 Shark samples (muscle or fin clip) were collected between 1980 and 2019
 from 19 different countries or water bodies (termed ‘sampling locations’)
 around the globe in all major ocean basin regions: the eastern Pacific
 (E-PAC), western Atlantic (W-ATL), eastern Atlantic (E-ATL), and the
 Indo-West Pacific. Initially,
 188 samples with a minimum of 10 samples per location were genotyped
 following the DArTseq approach (according to Feutry et al.,
 2017).
 Overall, 1,014 sample libraries, including 92
 technical replicates, were genotyped with the DArTcap
 protocol. The full
 mitochondrial genomes of 384 putative Bull
 Sharks from the
 E-ATL, IWP, and E-PAC were sequenced to investigate their matrilineal
 evolutionary history. 
description: Raw data are provided in Excell .csv file. Quality-filtered SNP
 data are provied as .Rdata. All analyses were performed in R 4.0.2, mainly
 using the following packges: radiator, adegenet, stratag, diveRsity, and
 rubias.
DOI: 10.5061/dryad.djh9w0w3q
title: Limited sex differences in plastic responses suggest evolutionary conservatism of thermal reaction norms: A meta-analysis in insects

description: Temperature has a profound effect on the growth and development of
 ectothermic animals. However, the extent to which ecologically-driven
 selection pressures can adjust thermal plastic responses in growth
 schedules is not well understood. Comparing temperature-induced plastic
 responses between sexes provides a promising but underexploited approach
 to evaluating the evolvability of thermal reaction norms: males and
 females share largely the same genes and immature environments but
 typically experience different ecological selection pressures. We proceed
 from the idea that substantial sex differences in plastic responses could
 be interpreted as resulting from sex-specific life-history optimization,
 whereas similarity among the sexes should rather be seen as evidence of an
 essential role of physiological constraints. In this study, we performed a
 meta-analysis of sex-specific thermal responses in insect development
 times, using data on 161 species with comprehensive phylogenetic and
 ecological coverage. As a reference for judging the magnitude of
 sex-specificity in thermal plasticity, we compared the magnitude of sex
 differences in plastic responses to temperature with those in response to
 diet. We show that sex-specific responses of development times to
 temperature variation are broadly similar. We also found no strong
 evidence for sex-specificity in thermal responses to depend on the
 magnitude or direction of sex differences in development time. Sex
 differences in temperature-induced plastic responses were systematically
 less pronounced than sex differences in responses induced by variations in
 larval diet. Our results point to the existence of substantial constraints
 on the evolvability of thermal reaction norms in insects as the most
 likely explanation. If confirmed, the low evolvability of thermal response
 is an essential aspect to consider in predicting evolutionary responses to
 climate warming.
description: This data set was collated from published papers reporting
 sex-specific data on insect development times measured in two or more
 temperature treatments. Methods for data acquiring, extracting, inclusion
 criteria, processing, and analysis are described in the paper's
 Material & Methods section.
description: Data are provided as csv-files, R scripts are provided for
 analyses. Researchers interested in the re-use of this data set and code
 are expected to contact the authors of the data set for
 collaboration.
DOI: 10.15468/dl.r3pyh9
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alma",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 71 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003308-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.