cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/b354cde1-8cc6-4b29-a1b2-e21fa3e412e9
title: Development and molecular barcoding of Terebellidae polychaetes from Rothera Research Station, Antarctic Peninsula, Antarctica

description: This dataset set describes the developmental stages and the molecular barcoding of Terebellidae larvae identified from diver-collected samples on 2021-04-22 in Ryder Bay near Rothera Research Station, Antarctic Peninsula, Antarctica. Photographs were collected at seven stages across the larval development. Development was captured from the trochophore stage where the polychaete larvae were bound in mucus to the free swimming planktonic metatrochophore to the nectochaete stage. Molecular barcoding was performed using the 18S rRNA gene at the British Antarctic Survey.

Funding: 
This study was funded by core funding to UKRI NERC-BAS.
description: Egg samples were collected on 2021-04-22 from Troval dive site, Ryder Bay, using SCUBA. Specimens were maintained in ambient water temperature during transit from the dive site to the Aquarium. Egg samples were transferred into a through-flow aquarium tank where they remained for seven months. 

Specimens were checked each week and photographed upon noticeable changes in their development. In the Bonner Laboratory aquarium, a subsample of the egg mass was pipetted from the mucus mass and transferred to a petri dish. A portable dissection microscope (Meiji EMZ-TR) was temporarily installed in the aquarium. 

Photographs were collected using a simple system of aligning an Olympus TG4 camera in the lens viewer, in the absence of a suitable aquarium microscope with a fitted camera.
Samples were quickly returned to the aquarium tank.

Molecular barcoding using the 18SrRNA gene was performed to identify the larvae. Briefly DNA was extracted from the larvae using the DNeasy Blood and Tissue kit (Qiagen) according to manufacturer's instructions. Amplification of a 560bp fragment of the 18S rRNA was performed using the primers NSF4 (CTGGTTGATYCTGCCAGT) and NSR581 (ATTACCGCGGCTGCTGGC) and 2x MyTaq HS Readymix (Meridian Biosciences) according to manufacturer's instructions. PCR cycling conditions were as follows: 95 degrees C for 5 mins, the 35 cycles of 95 degrees C for 20 secs; 60 degrees C for 20 secs; 72 degrees C for 30 secs and a final extension of 72 degrees C for 10 mins. The PCR product was Sanger sequenced by Source Bioscience (UK). Blast sequence similarity searching revealed that it was highly likely that these larvae were an uncharacterised Terebellidae species. In the absence of any associated adults for detailed taxonomy, more detailed identification to species level was not possible. The 18SrRNA sequence is available from NCBI under Accession number PP908343.
DOI: 10.5281/zenodo.12800546
title: A unified intensity of the magnetic field in the protoplanetary disk from the Winchcombe meteorite

description: Alternating field demagentisation data for the Winchcombe meteorite, published in 'A unified intensity of the magnetic field in the protoplanetary disk from the Winchcombe meteorite' (2023) Meteoritics and Planetary Science, 59, 1194-1215, 10.1111/maps.14079
DOI: 10.5281/zenodo.12800547
title: A unified intensity of the magnetic field in the protoplanetary disk from the Winchcombe meteorite

description: Alternating field demagentisation data for the Winchcombe meteorite, published in 'A unified intensity of the magnetic field in the protoplanetary disk from the Winchcombe meteorite' (2023) Meteoritics and Planetary Science, 59, 1194-1215, 10.1111/maps.14079
DOI: 10.6084/m9.figshare.26356507
title: R code for combined effects of thermal environment and gene regulation on metabolic enzyme activities of major metabolic tissues in a winter-breeding amphibian

description: Coding.R: R code used for data analysis in this study.
DOI: 10.57745/4g5imm
title: mapdo_metrics.gpkg

description: Base de données au format SIG
DOI: 10.57745/sinia0
title: attributes.tab

description: Descriptif des attributs
DOI: 10.6084/m9.figshare.25664443
title: Global research landscape on the contribution of <i>de novo</i> mutations to human genetic diseases over the past 20 years: bibliometric analysis

description: As the contribution of <i>de novo</i> mutations (DNMs) to human genetic diseases has been gradually uncovered, analyzing the global research landscape over the past 20 years is essential. Because of the large and rapidly increasing number of publications in this field, understanding the current landscape of the contribution of DNMs in the human genome to genetic diseases remains a challenge. Bibliometric analysis provides an approach for visualizing these studies using information in published records in a specific field. This study aimed to illustrate the current global research status and explore trends in the field of DNMs underlying genetic diseases. Bibliometric analyses were performed using the Bibliometrix Package based on the R language version 4.1.3 and CiteSpace version 6.1.R2 software for publications from 2000 to 2021 indexed under the Web of Science Core Collection (WoSCC) about DNMs underlying genetic diseases on 17 September 2022. We identified 3435 records, which were published in 731 journals by 26,538 authors from 6052 institutes in 66 countries. There was an upward trend in the number of publications since 2013. The USA, China, and Germany contributed the majority of the records included. The University of Washington, Columbia University, and Baylor College of Medicine were the top-producing institutions. Evan E Eichler of the University of Washington, Stephan J Sanders of the Yale University School of Medicine, and Ingrid E Scheffer of the University of Melbourne were the most high-ranked authors. Keyword co-occurrence analysis suggested that DNMs in neurodevelopmental disorders and intellectual disabilities were research hotspots and trends. In conclusion, our data show that DNMs have a significant effect on human genetic diseases, with a noticeable increase in annual publications over the last 5 years. Furthermore, potential hotspots are shifting toward understanding the causative role and clinical interpretation of newly identified or low-frequency DNMs observed in patients.
DOI: 10.6084/m9.figshare.25664443.v1
title: Global research landscape on the contribution of <i>de novo</i> mutations to human genetic diseases over the past 20 years: bibliometric analysis

description: As the contribution of <i>de novo</i> mutations (DNMs) to human genetic diseases has been gradually uncovered, analyzing the global research landscape over the past 20 years is essential. Because of the large and rapidly increasing number of publications in this field, understanding the current landscape of the contribution of DNMs in the human genome to genetic diseases remains a challenge. Bibliometric analysis provides an approach for visualizing these studies using information in published records in a specific field. This study aimed to illustrate the current global research status and explore trends in the field of DNMs underlying genetic diseases. Bibliometric analyses were performed using the Bibliometrix Package based on the R language version 4.1.3 and CiteSpace version 6.1.R2 software for publications from 2000 to 2021 indexed under the Web of Science Core Collection (WoSCC) about DNMs underlying genetic diseases on 17 September 2022. We identified 3435 records, which were published in 731 journals by 26,538 authors from 6052 institutes in 66 countries. There was an upward trend in the number of publications since 2013. The USA, China, and Germany contributed the majority of the records included. The University of Washington, Columbia University, and Baylor College of Medicine were the top-producing institutions. Evan E Eichler of the University of Washington, Stephan J Sanders of the Yale University School of Medicine, and Ingrid E Scheffer of the University of Melbourne were the most high-ranked authors. Keyword co-occurrence analysis suggested that DNMs in neurodevelopmental disorders and intellectual disabilities were research hotspots and trends. In conclusion, our data show that DNMs have a significant effect on human genetic diseases, with a noticeable increase in annual publications over the last 5 years. Furthermore, potential hotspots are shifting toward understanding the causative role and clinical interpretation of newly identified or low-frequency DNMs observed in patients.
DOI: 10.6084/m9.figshare.26207163
title: Exploring the evidence for mitochondrial dysfunction and genetic abnormalities in the etiopathogenesis of tropical ataxic neuropathy

description: Tropical ataxic neuropathy (TAN) is characterised by ataxic polyneuropathy, degeneration of the posterior columns and pyramidal tracts, optic atrophy, and sensorineural hearing loss. It has been attributed to nutritional/toxic etiologies, but evidence for the same has been equivocal. TAN shares common clinical features with inherited neuropathies and mitochondrial disorders, it may be hypothesised that genetic abnormalities may underlie the pathophysiology of TAN. This study aimed to establish evidence for mitochondrial dysfunction by adopting an integrated biochemical and multipronged genetic analysis. Patients (<i>n</i> = 65) with chronic progressive ataxic neuropathy with involvement of visual and/or auditory pathways underwent deep phenotyping, genetic studies including mitochondrial DNA (mtDNA) deletion analysis, mtDNA and clinical exome sequencing (CES), and respiratory chain complex (RCC) assay. The phenotypic characteristics included dysfunction of visual (<i>n</i> = 14), auditory (<i>n</i> = 12) and visual + auditory pathways (<i>n</i> = 29). Reduced RCC activity was present in 13 patients. Mitochondrial DNA deletions were noted in five patients. Sequencing of mtDNA (<i>n</i> = 45) identified a homoplasmic variant (<i>MT-ND6)</i> and a heteroplasmic variant (<i>MT-COI</i>) in one patient each. CES (<i>n</i> = 45) revealed 55 variants in nuclear genes that are associated with neuropathy (<i>n</i> = 27), deafness (<i>n</i> = 7), ataxia (<i>n</i> = 4), and mitochondrial phenotypes (<i>n</i> = 5) in 36 patients. This study provides preliminary evidence that TAN is associated with a spectrum of genetic abnormalities, including those associated with mitochondrial dysfunction, which is in contradistinction from the prevailing hypothesis that TAN is related to dietary toxins. Analysing the functional relevance of these genetic variants may improve the understanding of the pathogenesis of TAN.
DOI: 10.6084/m9.figshare.26207163.v1
title: Exploring the evidence for mitochondrial dysfunction and genetic abnormalities in the etiopathogenesis of tropical ataxic neuropathy

description: Tropical ataxic neuropathy (TAN) is characterised by ataxic polyneuropathy, degeneration of the posterior columns and pyramidal tracts, optic atrophy, and sensorineural hearing loss. It has been attributed to nutritional/toxic etiologies, but evidence for the same has been equivocal. TAN shares common clinical features with inherited neuropathies and mitochondrial disorders, it may be hypothesised that genetic abnormalities may underlie the pathophysiology of TAN. This study aimed to establish evidence for mitochondrial dysfunction by adopting an integrated biochemical and multipronged genetic analysis. Patients (<i>n</i> = 65) with chronic progressive ataxic neuropathy with involvement of visual and/or auditory pathways underwent deep phenotyping, genetic studies including mitochondrial DNA (mtDNA) deletion analysis, mtDNA and clinical exome sequencing (CES), and respiratory chain complex (RCC) assay. The phenotypic characteristics included dysfunction of visual (<i>n</i> = 14), auditory (<i>n</i> = 12) and visual + auditory pathways (<i>n</i> = 29). Reduced RCC activity was present in 13 patients. Mitochondrial DNA deletions were noted in five patients. Sequencing of mtDNA (<i>n</i> = 45) identified a homoplasmic variant (<i>MT-ND6)</i> and a heteroplasmic variant (<i>MT-COI</i>) in one patient each. CES (<i>n</i> = 45) revealed 55 variants in nuclear genes that are associated with neuropathy (<i>n</i> = 27), deafness (<i>n</i> = 7), ataxia (<i>n</i> = 4), and mitochondrial phenotypes (<i>n</i> = 5) in 36 patients. This study provides preliminary evidence that TAN is associated with a spectrum of genetic abnormalities, including those associated with mitochondrial dysfunction, which is in contradistinction from the prevailing hypothesis that TAN is related to dietary toxins. Analysing the functional relevance of these genetic variants may improve the understanding of the pathogenesis of TAN.
DOI: 10.25345/c5kp7v33g
title: MassIVE MSV000095415 - Cancer in Heart fAilure: characteriziNg the association with a dual epidemioloGical and Experimental approach - CHANGE study
title: The proteomic analysis described in this study was performed on EVs extracted from plasma of GISSI-HF cases and controls and from pooled plasma of sham mice or mice subjected to LV ligation. Proteomic analyses were performed by means of a label free shotgun platform, consisting of an Eksigent nanoLC-Ultra 2D System configured in trap-elute mode coupled to an Orbitrap Exploris120 mass spectrometer equipped with Easy Spray ion source.
DOI: 10.17894/ucph.fea7386b-099c-4655-bf8d-d84fa681a6b6
title: Raw sequencing reads, hybpiper output and reference sequences for paper - From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?
DOI: 10.25781/kaust-13tx8
title: Green turtle tracking leads the discovery of seagrass blue carbon resources

description: Locations of seagrass sites extracted from studies carried out in the Red Sea
DOI: 10.25781/kaust-mmpr3
title: Cavitation dataset (related to: arXiv:2311.13425v2)

description: The present dataset is related to the research activity described in: https://doi.org/10.48550/arXiv.2311.13425. The first file contains the results of an experimental campaign to estimate the cavitation threshold for a 24 kHz transducer in water.
The second file shows the results coming from the application of an acoustic analogy to the experiments (impulsive cavitation in a tube hit by a mallet) conducted by Pan et al. [https://doi.org/10.1073/pnas.1702502114].
DOI: 10.25345/c5fx74906
title: MassIVE MSV000095416 - PANORAMA_Test_Batch 5_Breath data
title: Test for the analysis of data of PANORAMA project - testing untargeted data on a small subset
DOI: 10.15468/dl.urakqe
title: Occurrence Download

description: A dataset containing 670 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Amaranthus retroflexus L."
 ]
}

 The dataset includes 670 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033816-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ztfwmh
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Habenaria eustachya Rchb.f."
 ]
}

 The dataset includes 178 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033817-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12742956
title: (simulated Data:) Detecting interactions in high dimensional data using Cross Leverage Scores
title: Simulated data and intermediate results

description: We upload the data according to the paper "Detecting interactions in high dimensional data using Cross Leverage Scores" (Teschke et al., 2024) which we submitted at the Biometrical Journal. The data is also being uploaded on behalf of the paper's co-authors, Katja Ickstadt and Alexander Munteanu.

Furthermore we upload some Intermediate results, because calculations takes very long time and need lots of memory. You can therefore use them for further insights.

For details of the simulation, we refer to Teschke et al. (2024).
DOI: 10.5281/zenodo.12742957
title: (simulated Data:) Detecting interactions in high dimensional data using Cross Leverage Scores
title: Simulated data and intermediate results

description: We upload the data according to the paper "Detecting interactions in high dimensional data using Cross Leverage Scores" (Teschke et al., 2024) which we submitted at the Biometrical Journal. The data is also being uploaded on behalf of the paper's co-authors, Katja Ickstadt and Alexander Munteanu.

Furthermore we upload some Intermediate results, because calculations takes very long time and need lots of memory. You can therefore use them for further insights.

For details of the simulation, we refer to Teschke et al. (2024).
DOI: 10.5281/zenodo.12800617
title: Data and Code for "Detecting context-dependence in the expression of life history tradeoffs"

description: This repository hosts the data, R scripts, and Stan models needed to reproduce results and figures from the article Detecting context-dependence in the expression of life history tradeoffs.

See the README file for a description of the different files contained in this repository.
DOI: 10.5281/zenodo.12800618
title: Data and Code for "Detecting context-dependence in the expression of life history tradeoffs"

description: This repository hosts the data, R scripts, and Stan models needed to reproduce results and figures from the article Detecting context-dependence in the expression of life history tradeoffs.

See the README file for a description of the different files contained in this repository.
DOI: 10.6084/m9.figshare.24556459.v1
title: The implementation of a virtual field trip to aid geological interpretation within an undergraduate volcanology course

description: Geological skills such as interpreting outcrops are often taught during fieldwork. However, recent advancements in digital technologies and the demand for more inclusive and accessible learning has provided an opportunity to teach these skills in virtual field trips (VFT). The Iceland VFT was developed to teach students about volcanic features and processes in Iceland and help students develop geological skills within a third-year, classroom-based, physical volcanology course. To determine the effectiveness of the VFT at aiding the development of student interpretation skills, we calculated the learning gains from an applied sketching exercise administered pre- and post- VFT, where students were asked to sketch a photograph of a lava flow outcrop and interpret flow shape and features from a range of different perspectives. The largest learning gains were for lava flow interpretation in map-view (0.40) followed by lava flow interpretation in side-view (0.31). Student responses to a post-VFT evaluation exercise indicate that the instructional/360 videos and the 3D landscape and rock models allowed students to spatially explore volcanic features within the landscape which aided their ability to interpret what the lava flow outcrop within the applied sketching exercise might look like in multiple perspectives. We conclude that the VFT supported students’ geological interpretation of lava flows and recommend that virtual fieldtrips with interactive spatially challenging exercises can be used to improve students’ conceptual understanding of content delivered in lectures and laboratories as well as preparation or reinforcement of fieldwork.
DOI: 10.6084/m9.figshare.24556459
title: The implementation of a virtual field trip to aid geological interpretation within an undergraduate volcanology course

description: Geological skills such as interpreting outcrops are often taught during fieldwork. However, recent advancements in digital technologies and the demand for more inclusive and accessible learning has provided an opportunity to teach these skills in virtual field trips (VFT). The Iceland VFT was developed to teach students about volcanic features and processes in Iceland and help students develop geological skills within a third-year, classroom-based, physical volcanology course. To determine the effectiveness of the VFT at aiding the development of student interpretation skills, we calculated the learning gains from an applied sketching exercise administered pre- and post- VFT, where students were asked to sketch a photograph of a lava flow outcrop and interpret flow shape and features from a range of different perspectives. The largest learning gains were for lava flow interpretation in map-view (0.40) followed by lava flow interpretation in side-view (0.31). Student responses to a post-VFT evaluation exercise indicate that the instructional/360 videos and the 3D landscape and rock models allowed students to spatially explore volcanic features within the landscape which aided their ability to interpret what the lava flow outcrop within the applied sketching exercise might look like in multiple perspectives. We conclude that the VFT supported students’ geological interpretation of lava flows and recommend that virtual fieldtrips with interactive spatially challenging exercises can be used to improve students’ conceptual understanding of content delivered in lectures and laboratories as well as preparation or reinforcement of fieldwork.
DOI: 10.6084/m9.figshare.24970172.v1
title: A citizen science approach to teaching climate change in introductory-level undergraduate general science courses

description: Hundreds of thousands of undergraduates enroll in general education science courses to fulfill university core requirements. However, many of these lecture-based courses fail to foster high-level data literacy skills. This work details the design, implementation, and analysis of a new climate change-based classroom activity for college students that pairs data interpretation with participation in an online citizen science project called Floating Forests (http://floatingforests.org). We pilot tested our activity in introductory geoscience and biology courses at six universities (∼1,500 students) during the 2020–2021 academic year. Additionally, we developed and validated a survey to assess how engagement with our activity impacted students’ self-reported changes across four factors: (1) perceptions of the impacts of climate change, (2) data literacy self-efficacy, (3) beliefs about the value of citizen science, and (4) beliefs about science engagement. In a pre- to post-test comparison, students who utilized our activity in their courses showed statistically significant increases (<i>p</i> &lt; 0.05) across all four factors. These results highlight the potential benefit of implementing data-driven, citizen science-based activities in introductory-level undergraduate courses.
DOI: 10.6084/m9.figshare.24970172
title: A citizen science approach to teaching climate change in introductory-level undergraduate general science courses

description: Hundreds of thousands of undergraduates enroll in general education science courses to fulfill university core requirements. However, many of these lecture-based courses fail to foster high-level data literacy skills. This work details the design, implementation, and analysis of a new climate change-based classroom activity for college students that pairs data interpretation with participation in an online citizen science project called Floating Forests (http://floatingforests.org). We pilot tested our activity in introductory geoscience and biology courses at six universities (∼1,500 students) during the 2020–2021 academic year. Additionally, we developed and validated a survey to assess how engagement with our activity impacted students’ self-reported changes across four factors: (1) perceptions of the impacts of climate change, (2) data literacy self-efficacy, (3) beliefs about the value of citizen science, and (4) beliefs about science engagement. In a pre- to post-test comparison, students who utilized our activity in their courses showed statistically significant increases (<i>p</i> &lt; 0.05) across all four factors. These results highlight the potential benefit of implementing data-driven, citizen science-based activities in introductory-level undergraduate courses.