cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.34tmpg4p7
title: The missing link in biogeographic reconstruction: Accounting for lineage extinction rewrites history

description: Aim In the most widely used family of methods for ancestral range
 estimation (ARE), dispersal, speciation and extirpation events are
 estimated from information on extant lineages. However, this approach
 fails to consider the geographic distribution of extinct species and their
 position on the phylogenetic tree, an omission that could compromise
 reconstruction. Here, we present a method that models the geographic
 distribution of extinct species and we quantify the potential inaccuracy
 in ancestral range estimation when extinction rates are above zero.
 Location Global applications, with an example from the Americas. Taxon All
 taxa, with an example from hummingbirds (Amazilia). Methods Methods
 capable of explicitly modelling extinct branches along with their
 reconstructed geographic information (GeoSSE) have been overlooked in ARE
 analysis, perhaps due to the inherent complexity of implementation. We
 develop a user-friendly platform, which we term LEMAD (Lineage Extinction
 Model of Ancestral Distribution) that generalizes the likelihood described
 in GeoSSE for any number of areas and under several sets of geographic
 assumptions. We compare LEMAD and extinction-free approaches using
 extensive simulations under different macroevolutionary scenarios. We
 apply our method to revisit the historical biogeography
 of Amazilia hummingbirds. Results We find that
 accounting for the lineages removed from a tree by extinction improves
 reconstructions of ancestral distributions, especially when rates of
 vicariant speciation are higher than rates of in situ speciation, and when
 rates of extinction and range evolution are high. Rates of in situ and
 vicariant speciation are accurately estimated by LEMAD in all scenarios.
 North America as the most likely region for the common ancestor of
 hummingbirds. Main conclusions Methods that neglect lineage extinction are
 less likely to accurately reconstruct true biogeographic histories of
 extant clades. Our findings on an empirical dataset reconcile the Eurasian
 origin of Amazilia with biogeographic reconstructions
 when lineage extinction is considered.
description: Data were collected from McGuire et al. 2014 and Ornelas et al.
 2014. Please see the paper for more details. I include
 R scripts to run lemad analysis. Please first install R package LEMAD
 from: https://github.com/leonelhalsina/lemad
DOI: 10.5061/dryad.t4b8gtj5c
title: Research data of Env38 protein functions in SVCV infection in zebrafish

description: Endogenous retroviruses (ERVs) are the relics of ancient retroviruses
 occupying a substantial fraction of vertebrate genomes. However, knowledge
 about the functional association of ERVs with cellular activities remains
 limited. Recently, we have identified approximately 3,315 ERVs from
 zebrafish at genome-wide level, among which 421 ERVs were actively
 expressed in response to the infection of Spring viraemia of carp virus
 (SVCV). These findings demonstrated the previously unrecognized activity
 of ERVs in zebrafish immunity, thereby making zebrafish an attractive
 model organism for deciphering the interplay among ERVs, exogenous
 invading viruses, and host immunity. In the present study, we investigated
 the functional role of an envelope protein (Env38) derived from an
 ERV-E5.1.38-DanRer element in zebrafish adaptive immunity against SVCV in
 view of its strong responsiveness to SVCV infection. This Env38 is a
 glycosylated membrane protein mainly distributed on MHC-II+
 antigen-presenting cells (APCs). By performing blockade and
 knockdown/knockout assays, we found that the deficiency of Env38 markedly
 impaired the activation of SVCV-induced CD4+ T cells and thereby led to
 the inhibition of IgM+/IgZ+ B cell proliferation, IgM/IgZ Ab production,
 and zebrafish defense against SVCV challenge. Mechanistically, Env38
 activates CD4+ T cells by promoting the formation of pMHC-TCR-CD4
 complex via cross-linking MHC-II and CD4 molecules between APCs
 and CD4+ T cells, wherein the surface subunit (SU) of Env38
 associates with the second immunoglobin domain of CD4 (CD4-D2) and the
 first α1 domain of MHC-IIα (MHC-IIα1). Notably, the expression and
 functionality of Env38 were strongly induced by zebrafish IFNφ1,
 indicating that env38 acts as an IFN-stimulating gene (ISG) regulated by
 IFN signaling. To the best of our knowledge, this study is the first to
 identify the involvement of an Env protein in host immune defense against
 an exogenous invading virus by promoting the initial activation of
 adaptive humoral immunity. It improved the current understanding of the
 cooperation between ERVs and host adaptive immunity.
DOI: 10.5061/dryad.jwstqjqd7
title: Data For: Ornamentation diversified faster than eco-morphology across Nearctic dragonflies

description: A major goal of biology is to understand the origins and maintenance of
 phenotypic differences between closely related species. Eco-morphology and
 ornamentation are two phenotypic dimensions along which co-existing
 species often diverge, yet theory makes contrasting predictions about how
 these phenotypes diversify relative to each other. Some theory predicts
 that intense, idiosyncratic sexual selection will cause more pronounced
 divergence in ornamentation than in eco-morphology. Other theory predicts
 that the ability of condition-dependent ornaments to signal local
 specialization will result in different species evolving similar ornaments
 but very divergent eco-morphology. Here, we evaluated these conflicting
 predictions in Nearctic Libelluloidea dragonflies by testing if the
 diversification of a condition-dependent ornament, male wing melanization,
 was slower and less pronounced between closely related species than the
 diversification of two key eco-morphological traits, body size and
 relative wing size. Our results show that male wing melanization evolved
 much faster than either body size or relative wing size. Furthermore, in
 contrast to the patterns for either eco-morphological trait, the
 best-supported models of diversification in male wing melanization
 indicate that the majority of divergence arose between the most closely
 related species. These results reveal that the primary axis of divergence
 between closely related Libelluloidea dragonflies is ornamentation rather
 than eco-morphology. Our study therefore suggests that evolutionary
 responses to disparate reproductive demands may be fundamental to the
 persistence and co-existence of closely related species.
description: Data on species' traits was gathered from field guides (body
 size, relative wing size) and measured from citizen-science observations
 (male wing melanization)
description: R
DOI: 10.5061/dryad.fj6q573z9
title: Comparative observational study of gastric content in women scheduled for caesarean section or operative hysteroscopy: The ECHOCESAR study

description: Objective: There is a large literature concerning the estimation of
 gastric content in third-trimester pregnant women but their conclusions
 remain contradictory. Our objective was to compare gastric content in
 pregnant women and in non-pregnant ones using gastric ultrasound. Design:
 An observational two centres study was designed. Methods: The antral
 cross-sectional area (CSA) in the semi-recumbent position (SRP), primary
 outcome, and in the right lateral position (RLD) were measured in pregnant
 women scheduled for a caesarean section (CS group) or non-pregnant women
 who underwent hysteroscopy (HS group) just before surgery. Perlas'
 score was also evaluated. Results: One hundred and twenty-six patients
 were analysed, 61 patients in the CS group and 65 in the HS group. Antral
 CSA, measured in the SRP, was greater in the CS group than in the HS group
 (350 mm2 [236 - 415] vs 247 mm2 [180 - 318]; (P=0.001). This difference
 remained significant when the analysis was adjusted for fasting duration
 (P&lt;0.001) or anxiety (P=0.001) or both (P&lt;0.001). Among
 secondary outcomes, Perlas scores did not differ between groups (P=0.860).
 Concordance between antral CSA, categorised as corresponding to an empty
 or full stomach, and Perlas score was very poor. Conclusions: Our results
 bring arguments to consider that individuals among pregnant women could
 have a delayed gastric emptying and support performing a gastric
 ultrasound in term pregnant patients prior to general anaesthesia.
description: eCRF
DOI: 10.15468/dl.hzuesa
title: Occurrence Download

description: A dataset containing 82987 species occurrences available in GBIF matching the query:
{
 "PublishingOrg" : [
 "is fd70f580-4ce2-11db-b80e-b8a03c50a862"
 ]
}

 The dataset includes 82987 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003277-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ns1rn8pww
title: Data for: Species richness and assemblages of bats along a forest elevational transect in Papua New Guinea

description: Over the past decades, elevational gradients have become a powerful tool
 with which to understand the underlying cause(s) of biodiversity. The Mt.
 Wilhelm elevational transect is one such example, having been used to
 study the birds, insects, and plants of Papua New Guinea (PNG). However, a
 survey of mammals from this forest elevational transect was lacking. We
 thus aimed to investigate patterns in the community structure and species
 richness of bats (Chiroptera) along the transect, link the species to
 available regional data, and explain the observed patterns by including
 environmental characteristics. Bat assemblages were surveyed between 200 m
 and a timberline at 3,700 m a.s.l. at eight study sites separated by 500 m
 in elevation. We conducted mist-netting and acoustic surveys to detect and
 identify species at each site. Regional data were compiled to compare
 local with regional diversity. Finally, biotic (i.e., food availability,
 habitat features) and abiotic (i.e., mean daily temperature) factors were
 included in our analyses to disentangle the ecological drivers underlying
 bat diversity. Results revealed that species richness decreases with
 ascending elevation and was best explained by a corresponding decrease in
 temperature. We observed both turnover and nestedness of the species
 composition at regional scale whereas turnover was dominant at local
 scale. Extensions and shifts of bat elevational ranges were also found in
 Mt. Wilhelm. Consequently, despite that the study was restricted to one
 mountain in PNG, it demonstrates how basic inventory surveys can be used
 to address ecological questions in other similar and undisturbed tropical
 mountains.
description: The environmental data comes from measurements conducted in
 previous surveys (Sam et al. 2019) along the Mt. Wilhelm
 transect. The Mt.Wilhelm data compiled all the bat
 species captured and recorded during this study along the Mt. Wilhelm
 transect. The regional data compiled the distribution
 of the bat species described as present in Central Range and Sepik-Ramu
 Basin in Bonaccorso (1998).
DOI: 10.5061/dryad.stqjq2c6j
title: Data from: Identification of a minority population of LMO2+ breast cancer cells that integrate into the vasculature and initiate metastasis.

description: Metastasis is responsible for the majority of breast cancer-related
 deaths, however, identifying the cellular determinants of metastasis has
 remained challenging. Here, we identified a minority population of
 immature THY1+/VEGFA+ tumor epithelial cells in human breast tumor
 biopsies that display angiogenic features and are marked by the expression
 of the oncogene, LMO2. Higher abundance of LMO2+ basal cells correlated
 with tumor endothelial content and predicted poor distant recurrence-free
 survival in patients. Using MMTV-PyMT/Lmo2CreERT2 mice, we demonstrated
 that Lmo2 lineage-traced cells integrate into the vasculature and have a
 higher propensity to metastasize. LMO2 knockdown in human breast tumors
 reduced lung metastasis by impairing intravasation, leading to a reduced
 frequency of circulating tumor cells. Mechanistically, we find that LMO2
 binds to STAT3 and is required for STAT3 activation by TNFα and IL6.
 Collectively, our study identifies a population of metastasis-initiating
 cells with angiogenic features and establishes the LMO2-STAT3 signaling
 axis as a therapeutic target in breast cancer metastasis.
description: <strong>Brief overview</strong>
 Please find enclosed in this repository two main
 folders: (1) 'data', which contains raw and
 processed data used for the genomic analysis done in the manuscript
 including original scRNA-seq data from our laboratory and publicly
 available scRNA-seq data from other labs, and (2)
 'scripts', which contains the code and scripts used to generate
 the results shown in the figures. Please reach out directly to us if you
 have any questions about the data and scripts enclosed here for the
 manuscript.
description: All data are stored as tab-delimited text files that can be
 opened with any spreadsheet software program. All code was written in
 either R or bash.
DOI: 10.5061/dryad.k3j9kd5bc
title: Analysis table of optimal preparation conditions of expanded graphite

description: The environmentally friendly preparation of sulfur-free expanded graphite
 (EG) remains a great challenge. A large amount of strong acids and strong
 oxidants were used in the preparation of expandable graphite, resulting in
 environmental pollution problems. Herein, a novel and green preparation
 method for sulfur-free expanded graphite (EG) has been developed.
 Sulfur-free EG was fabricated using natural flake graphite (NFG), sodium
 perchlorate (NaClO4), and oxalic acid (C2H2O4) as raw materials. The
 electrochemical oxidation method was applied to prepare sulfur-free
 expandable graphite, and microwave irradiation technology was adopted to
 prepare sulfur-free EG. The optimum weight ratio was as follows:
 NFG:NaClO4:C2H2O4 = 1.5:10:2. The anodic oxidation occurred under a
 constant current density of 47 mA/cm2, and the intercalation reaction
 lasted for 60 min at ambient temperature. The largest expanded volume (EV)
 of sulfur-free EG was 290 mL/g. The FTIR spectrum proved that the ClO4−
 and COO− groups had entered the graphite layers. The SEM images showed
 that the graphite layers were completely opened, and the pore structure
 was clearly observed. The sulfur-free EG prepared by the method does not
 cause environmental pollution and has broad application prospects.
description: A certain amount of
 sulfur-free expandable graphite was weighed, and the EV was measured using
 a 150 mL graduated cylinder after expansion. The EV of the EG was
 calculated by the following equation: EV = V/M (mL/g).
 The higher expansion volume indicates
 that the more expanded graphite is obtained.
description: .xlsx format
DOI: 10.5061/dryad.x3ffbg7ns
title: International comparison of cross-disciplinary integration in industry 4.0: A co-authorship analysis using academic literature databases

description: In innovation strategy, a type of Schumpeterian competitive strategy in
 business administration, "intra-individual diversity" has
 attracted attention as one factor for creating innovation. In this study,
 we redefine "framework for identifying researchers' areas of
 expertise" as "a framework for quantifying intra-individual
 diversity among researchers. Note that diversity here refers to authorship
 of articles in multiple research fields. The application of this framework
 then made it possible to visualize organizational diversity by
 accumulating the intra-individual diversity of researchers and to discuss
 the innovation strategy of the organization. The analysis in this study
 discusses how countries are promoting research on the topics of artificial
 intelligence (AI), big data, and Internet of Things (IoT) technologies,
 which are at the core of Industry 4.0, from an innovation perspective.
 Note that Industry 4.0 is a technological framework that aims to “improve
 the efficiency of all social systems,” “create new industries,” and
 “increase intellectual productivity.”  For the analysis, we used
 19-year bibliographic data (2000–2018) from the top 20 countries in terms
 of the number of papers in AI, big data, and IoT technologies. As the
 results, this study classified the styles of cross-disciplinary fusion
 into four patterns in AI and three patterns in big data. This study did
 not consider the results in IoT because of only small differences between
 countries. Furthermore, regional differences in the style of
 cross-disciplinary fusion were also observed, and the global innovation
 patterns in Industry 4.0 were classified into seven categories. In Europe
 and North America, the cross-disciplinary integration style was similar to
 that between the United States, Germany, the Netherlands, Spain, England,
 Italy, Canada, and France. In Asia, the cross-disciplinary fusion style
 was similar between China, Japan, and South Korea.
description: We used the bibliographic data of Web of Science (WoS) core
 collection, one of the biggest bibliographic databases from 2000 to 2018.
 The analysis of the visualization organizational diversity used data from
 2018; studies on AI, big data, and IoT have been continuously increasing,
 reaching 3,133, 5,155, and 4,662 related papers in 2018, respectively. The
 23 Essential Science Indicators Subject Areas in the Web of Science Core
 Collection were used for the article specialties. This data was generated
 from the "Web of Science Categories” using a conversion table
 (Thomson Reuters Community, 2012).
description: The dataset consists of 60 CSV files ( Top 20 countries in number
 of papers on AI, Big Data, and IoT technologies) which can be used with a
 variety of software. The data format consists of three
 parts: source node, target note, and number of edge connections. For
 example, it can be imported into Cytoscape (https://cytoscape.org/) to display a network diagram.
DOI: 10.15468/dl.spbqhu
title: Occurrence Download

description: A dataset containing 1339 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Enterolobium cyclocarpum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1339 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003286-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r4xgxd2gw
title: Data for: From southern Africa and beyond: historical biogeography of a monocotyledonous bulbous geophyte

description: Aim Low taxon sampling and taxonomic uncertainties still obscure our
 evolutionary knowledge of many taxa, especially widespread lineages across
 diverse landscapes. Of particular interest are those lineages inhabiting
 seasonal and arid landscapes, which showcase unique distributional
 patterns that hint at fascinating histories. Using the most comprehensive
 sampling to date of a widespread bulbous monocot, we hypothesize two
 independent dispersals to Madagascar, and that vicariance due to
 Miocene-driven aridification contracted a once-widespread distribution
 between Africa and Eurasia. Location Sub-Saharan Africa, Madagascar,
 Eurasia Taxon Ledebouriinae (Scilloideae, Asparagaceae) Methods Using the
 Angiosperms353 probe set for 195 taxa (86 ingroup taxa), we perform
 phylogenetic reconstruction using IQ-Tree, and we infer age estimates
 using penalized likelihood as implemented in treePL. Capitalizing on our
 broad geographic sampling, which includes African, Malagasy, and Eurasian
 taxa, we use ‘BioGeoBEARS’ to reconstruct ancestral ranges and investigate
 the role of vicariance and dispersal.  Results The Ledebouriinae
 originated within the past ~30 myr in southeastern sub-Saharan Africa,
 with the major subclades arising soon thereafter. Although long-distance
 dispersal cannot be fully ruled out, we argue that vicariance was the
 major process responsible for the current distribution
 of Ledebouria in Eurasia. We recover two
 distinct Ledebouria groups that overlap in eastern Africa, but
 are divided into mostly northern and southern clades with divergent
 biogeographical histories, each showing an independent dispersal to
 Madagascar. A similar north-south split is seen in Drimiopsis.
 Additionally, we recover a complex biogeographic history in the
 predominantly sub-Saharan African Ledebouria clade, with a rapid radiation
 at ~14 mya. Main conclusions The expansion of seasonal rainfall and
 aridity in sub-Saharan Africa, coupled with orogenic activity, may have
 fostered the diversification of the Ledebouriinae and many subclades.
 Miocene-driven aridification may have caused fragmentation of a once
 widespread distribution that led to their occurrence in Eurasia.
DOI: 10.15468/dl.96tw5t
title: Occurrence Download

description: A dataset containing 483533 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Salix cinerea"
 ]
}

 The dataset includes 483533 records from 1768 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003214-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57703/ce-c7twj
title: R32 - FAMU-FSU College of Engineering Submission

description: Scanning white light interferometry measurements using Bruker Countour GT a 5x, 20x, and 50x magnification.
DOI: 10.24414/rob-euref-cako00hrv
title: GNSS data of CAKO00HRV, Cakovec, Croatia

description: Permanent GNSS station dataset as daily RINEX files
DOI: 10.5281/zenodo.15282792
title: Models generated by AlphaFold3 used for CASP16 predictions

description: Elofsson and AF3-server predictions for CASP16




Organisation


The file Targets.MD contains comments about predictions and choices made for each target



Code


in bin/ all scripts used during the predictions are made available



Targets


All submitted targets for Elofsson (#241) and AF3-server (#304) can be found in targets/ (gzipped)



Scores


The file scores.csv contains all the pTM/ipTM/Ranking_confidence values for all models generated. In most cases the highest ranking_confidence score relates to the Elofsson prediction. and the fold_XYYYY_summary_confidences_0 related to the prediction submitted as the AF3-server. However, for large targets and round 0 models this is not always the case. Note also that for round 1 models often round 0 models are submitted. Due to space limitations

 

Please also examine the git repository for this project

 

 https://github.com/ElofssonLab/casp16/

 

Paper available here

https://doi.org/10.1101/2025.04.10.648174
DOI: 10.5281/zenodo.15282793
title: Models generated by AlphaFold3 used for CASP16 predictions

description: Elofsson and AF3-server predictions for CASP16




Organisation


The file Targets.MD contains comments about predictions and choices made for each target



Code


in bin/ all scripts used during the predictions are made available



Targets


All submitted targets for Elofsson (#241) and AF3-server (#304) can be found in targets/ (gzipped)



Scores


The file scores.csv contains all the pTM/ipTM/Ranking_confidence values for all models generated. In most cases the highest ranking_confidence score relates to the Elofsson prediction. and the fold_XYYYY_summary_confidences_0 related to the prediction submitted as the AF3-server. However, for large targets and round 0 models this is not always the case. Note also that for round 1 models often round 0 models are submitted. Due to space limitations

 

Please also examine the git repository for this project

 

 https://github.com/ElofssonLab/casp16/

 

Paper available here

https://doi.org/10.1101/2025.04.10.648174
DOI: 10.34740/kaggle/dsv/12019250
title: Peer-to-Peer Boliviano (BOB) Exchange Data