cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6t1g1jx33
title: Supplementary information for: NUMT PARSER: Automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera

description: Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of
 mtDNA genomes and affect the reliability of mtDNA datasets for
 phylogenetic and population genetic comparisons. Here, we present the
 program Numt Parser, which allows for the identification of DNA sequences
 that likely originate from numt pseudogene DNA. Sequencing reads are
 classified as originating from either numt or true cytoplasmic
 mitochondrial (cymt) DNA by direct comparison against cymt and numt
 reference sequences. Classified reads can then be parsed into cymt or numt
 datasets. We tested this program using whole genome shotgun-sequenced data
 from two ancient Cape lions (Panthera leo) because mtDNA is often the
 marker of choice for ancient DNA studies, and the genus Panthera is known
 to have numt pseudogenes. Numt Parser decreased sequence disagreements
 that were likely due to numt pseudogene contamination and equalized read
 coverage across the mitogenome by removing reads that likely originated
 from numts. We compared the efficacy of Numt Parser to two other
 bioinformatic approaches that can be used to account for numt
 contamination. We found that Numt Parser outperformed approaches that rely
 only on read alignment or Basic Local Alignment Search Tool (BLAST)
 properties, and was effective at identifying sequences that likely
 originated from numts while having minimal impacts on the recovery of cymt
 reads. Numt Parser therefore improves the reconstruction of true
 mitogenomes, allowing for more accurate and robust biological inferences.
description: Sequencing reads and alignments generated from ancient DNA of two
 Cape Lion (<em>Panthera leo melanochaitus</em>) samples. Raw
 reads were aligned to the <em>Panthera leo </em>mitochondrial
 reference (NCBI Accession KP202262.1) to obtain mitochondrial-specific reads. These mitochondrial reads were then processed using different methods (BLAST, SAMtools, Numt Parser) to identify and filter Numt-contaminant reads. See de Flamingh, et al. (2022) for additional information on the specific bioinformatic pipeline used and a description of the Numt Parser software.
description: Files in BAM format (.bam) are stored in binary and require the
 use of SAMtools
 for conversion. SAM (.sam) and FASTA (.fa) files are in text format and
 can be accessed using any text editor software (in either the command line
 or a graphical application).
DOI: 10.5061/dryad.v6wwpzh0q
title: Distinct Wolbachia localization patterns in oocytes of diverse host species reveal multiple strategies of maternal transmission

description: A broad array of endosymbionts radiate through host populations via
 vertical transmission, yet much remains unknown concerning the cellular
 basis, diversity and routes underlying this transmission strategy. Here we
 address these issues, by examining the cellular distributions
 of Wolbachia strains that diverged up to 50 million
 years ago in the oocytes of 18
 divergent Drosophila species. This analysis revealed
 three Wolbachia distribution patterns: 1) a tight
 clustering at the posterior pole plasm (the site of germline formation);
 2) a concentration at the posterior pole plasm, but with a significant
 bacteria population distributed throughout the oocyte; 3) and a
 distribution throughout the oocyte, with none or very few located at the
 posterior pole plasm. Examination of this latter class
 indicates Wolbachia accesses the posterior pole plasm
 during the interval between late oogenesis and the blastoderm formation.
 We also find that one Wolbachia strain in this class
 concentrates in the posterior somatic follicle cells that encompass the
 pole plasm of the developing oocyte. In contrast, strains in
 which Wolbachia concentrate at the posterior pole plasm
 generally exhibit no or few Wolbachia in the follicle
 cells associated with the pole plasm. Taken together, these studies
 suggest that for
 some Drosophila species, Wolbachia invade the germline from neighboring somatic follicle cells. Phylogenomic analysis indicates that closely related Wolbachia strains tend to exhibit similar patterns of posterior localization, suggesting that specific localization strategies are a function of Wolbachia-associated factors. Previous studies revealed that endosymbionts rely on one of two distinct routes of vertical transmission: continuous maintenance in the germline (germline-to-germline) or a more circuitous route via the soma (germline-to-soma-to-germline). Here we provide compelling evidence that Wolbachiastrains infecting Drosophila species maintain the diverse arrays of cellular mechanisms necessary for both of these distinct transmission routes. This characteristic may account for its ability to infect and spread globally through a vast range of host insect species.
DOI: 10.5281/zenodo.18401993
title: Area Measurements, Preservation Scores, and Bioerosion Drill Hole Sizes in Planktonic Foraminifera Exposed to Acid Solution over Time in a Controlled Experimental Setting

description: This dataset, provided as supplementary material, documents the dissolution susceptibility of Globigerinoides ruber (lumping G. ruber albus and G. elongatus) tests in relation to bioerosion drill holes. Sixty foraminiferal tests were extracted from a sample at 131 cm depth (20.8 ± 1.2 ka BP) in Core SAT-048A (29º11’S, 47º15’W, 1,542 mbsl). Core SAT-048A was collected from the slope of the Pelotas Basin (south brazilian continental margin) and donatd by the Brazilian National Petroleum Agency (ANP). For sample preparation see Frozza et al., 2020. Specimens were subjected to a dissolution experiment using a buffered acetic acid solution (pH 6.6). The dataset categorizes specimens into groups based on bioerosion levels, ranging from no drill holes (control) to four drill holes, to assess the impact of bioerosion on test preservation. Dissolution progression was monitored at hourly intervals until specimen destruction, and preservation was quantified using Absolute and Relative Preservation Scores (APS and RPS), as well as the two-dimensional projected area of the specimens. The experiment provides insights into the preservation dynamics of bioeroded foraminiferal tests under controlled dissolution conditions. The dataset includes images, size measurements, and preservation scores for each specimen, along with statistical analyses conducted using R. This data can aid in understanding dissolution impacts on the fossil record and bioerosion’s role in foraminiferal preservation.
description: Data Set S1. Projected test area (µm²) measurements of five specimens (2, 6, 8, 10, and 13) from the Control group across five iterations (T1–T5, UT for untreated areas)) of the digital shadow removal treatment applied to images taken at different dissolution time points (0-13 hours) in acid solution.

Data Set S2. Preservation scores assigned to 15 specimens from each bioerosion level group (C, I, III, IV). The Absolute Preservation Scores (APS), ranging from eight (best preservation) to zero (missing test). Relative Preservation Scores (RPS) reflect the preservation state relative to the initial state (Exp. Time = 0) prior to exposure.

Data Set S3. Test Area (µm²) of 15 specimens from each bioerosion level group (C, I, III, IV) over the exposure time in acid solution. Relative Preservation Areas (RPA) reflect the preserved area state relative to the initial state (Exp. Time = 0) prior to exposure.

Data Set S4. Areas (µm²) of bioerosion drill holes from three groups (I, III, and IV), measured prior to exposure to the acid solution.
DOI: 10.5281/zenodo.18401994
title: Area Measurements, Preservation Scores, and Bioerosion Drill Hole Sizes in Planktonic Foraminifera Exposed to Acid Solution over Time in a Controlled Experimental Setting

description: This dataset, provided as supplementary material, documents the dissolution susceptibility of Globigerinoides ruber (lumping G. ruber albus and G. elongatus) tests in relation to bioerosion drill holes. Sixty foraminiferal tests were extracted from a sample at 131 cm depth (20.8 ± 1.2 ka BP) in Core SAT-048A (29º11’S, 47º15’W, 1,542 mbsl). Core SAT-048A was collected from the slope of the Pelotas Basin (south brazilian continental margin) and donatd by the Brazilian National Petroleum Agency (ANP). For sample preparation see Frozza et al., 2020. Specimens were subjected to a dissolution experiment using a buffered acetic acid solution (pH 6.6). The dataset categorizes specimens into groups based on bioerosion levels, ranging from no drill holes (control) to four drill holes, to assess the impact of bioerosion on test preservation. Dissolution progression was monitored at hourly intervals until specimen destruction, and preservation was quantified using Absolute and Relative Preservation Scores (APS and RPS), as well as the two-dimensional projected area of the specimens. The experiment provides insights into the preservation dynamics of bioeroded foraminiferal tests under controlled dissolution conditions. The dataset includes images, size measurements, and preservation scores for each specimen, along with statistical analyses conducted using R. This data can aid in understanding dissolution impacts on the fossil record and bioerosion’s role in foraminiferal preservation.
description: Data Set S1. Projected test area (µm²) measurements of five specimens (2, 6, 8, 10, and 13) from the Control group across five iterations (T1–T5, UT for untreated areas)) of the digital shadow removal treatment applied to images taken at different dissolution time points (0-13 hours) in acid solution.

Data Set S2. Preservation scores assigned to 15 specimens from each bioerosion level group (C, I, III, IV). The Absolute Preservation Scores (APS), ranging from eight (best preservation) to zero (missing test). Relative Preservation Scores (RPS) reflect the preservation state relative to the initial state (Exp. Time = 0) prior to exposure.

Data Set S3. Test Area (µm²) of 15 specimens from each bioerosion level group (C, I, III, IV) over the exposure time in acid solution. Relative Preservation Areas (RPA) reflect the preserved area state relative to the initial state (Exp. Time = 0) prior to exposure.

Data Set S4. Areas (µm²) of bioerosion drill holes from three groups (I, III, and IV), measured prior to exposure to the acid solution.
DOI: 10.5061/dryad.prr4xgxqx
title: Dataset for: Exploring the legacy effect of biochar application on soil nitrous oxide emissions

description: This dataset contains data for exploring the legacy effects of biochar
 addition on soil nitrous oxide emissions and their effects on functional
 gene abundance associated with soil nitrogen cycling. The dataset contains
 two data files, one is a data table on the impact of biochar application
 on soil nitrous oxide emissions, which contains the coordinates of the
 study site, climate, basic physical and chemical properties of the soil,
 biochar characteristics and study duration, crop type and management. The
 other is the data table on the effect of biochar application on the
 abundance of functional genes related to soil nitrogen cycling, which
 contains information such as test site coordinates, climate, biochar
 characteristics, crop type and management. This data can be referenced and
 reused without any legal or ethical considerations.
description: We compiled and updated the
 datasets of several existing meta-analysis studies. The literature collection cut-off date is March
 2022. Our database contained only field and pot studies and excluded
 laboratory incubation experiments because of its underrepresentation of in
 situ environments. In addition, we referred to the search terms and
 screening criteria used in previous meta-analyses when updating the
 literature. In total, we obtained 747 pairs of observations from 96
 articles, of which 398 were for N<sub>2</sub>O emissions, 166
 were for genes related to ammonia oxidation processes, and 183 were for
 genes related to denitrification processes.
DOI: 10.15468/dl.rb2zy6
title: Occurrence Download

description: A dataset containing 2906 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gleditsia triacanthos",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2906 records from 255 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003405-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.70rxwdc2n
title: HIV-1 Subtypes of HIV-1 patients with virologic failure in different voluntary counseling testing and treatment centers in Khartoum State, Sudan, 2020

description: Background: Various HIV subtypes have evolved and play significant roles
 in the pathogenesis, progression, and response to treating human
 immunodeficiency virus. Method: One hundred and ten HIV-1 patients who
 attended different voluntary counseling testing and treatment centers in
 Khartoum state were included. Nested PCR was done for the Pol gene in
 plasma samples that showed virologic failure, and then successfully
 amplified samples were sequenced for HIV-1 ­­subtype’s identification.
 Result: Out of the total, 20 (18.2%) samples showed virologic failure, of
 them only 9 (45%) were successfully amplified and sequenced; of them,
 55.6% (5/9) belonged to subtype C, and only 11.1% (1/9) occurred at the
 frequency of each subtype A, D, G, and K. Conclusion: No relationship
 between HIV-1 subtypes and increased viral load were detected, although
 HIV-1 subtypes are still a strong predictor of disease progression.
description: <em>Dataset collection:</em> After
 explaining the study and its goal, all participants enrolled in this study
 were provided with written informed consent for guarantees of
 confidentiality. Data were obtained by direct interviewing questionnaire
 during sampling, and information on ART history was collected
 retrospectively on site from patient records.
 <em>Data processing:</em>
 Statistical tests were performed using SPSS version 23. The
 enumeration data were expressed with percentage (%), and frequencies and
 the difference between two groups were assessed with
 χ<sup>2</sup>-test. A value of P&lt;0.05 was taken as
 signiﬁcant.
DOI: 10.5061/dryad.1rn8pk0z4
title: Multi-stage sleep classification using photoplethysmographic sensor

description: The conventional approach to monitoring sleep stages requires placing
 multiple sensors on the patients, which is inconvenient for long-term
 monitoring and requires expert support. We propose a single sensor
 Photoplethysmographic (PPG) based automated multi-stage sleep
 classification. This experimental study recorded the PPG during the entire
 night's sleep of ten patients. Data analysis was performed to obtain
 82 features from the recordings, which were then classified against the
 sleep stages. The classification results using SVM with the polynomial
 kernel gave the overall accuracy of 84.66%, 79.62%, and 72.23% for two,
 three, and four-stage sleep classification. These results show that using
 only PPG; it is possible to conduct sleep stage monitoring. These findings
 open the opportunities for PPG-based wearable solutions for home-based
 automated sleep monitoring.
description: The PSG data were recorded for
 the night sleep duration of ten participants (9 male/ 1 female, age 43–75
 years). The length of sleep time ranged from 6.8 to 10.1 hours. All
 participants were volunteers and recruited from the out-patients at
 Charite Hospital, Berlin, Germany. All suffered sleep-disordered breathing
 and were free from a history of cardiac issues. The diagnosis was based on
 PSG outcomes and clinical symptoms. The research and data collection
 protocol was approved by the Charite Hospital Committee for Ethics in
 Human Research (2018), Berlin, Germany, and the experiments were conducted
 in accordance with the Helsinki declaration for ethical experiments,
 revised in 2013. Written consent was taken prior to the experiments. The
 demographic information of the subjects. Each PSG recording included
 two-channel EEG (channel C3-A2 and C4-A1), ECG, PPG, left and right EOG,
 leg movements, thoracic and abdominal wall expansion, arterial oxygen
 saturation SaO2, and oronasal airflow. According to the American Academy of Sleep
 Medicine (AASM) criteria, the PSG recordings were segmented into 30-second
 epochs, and an expert sleep physiologist labelled sleep
 stages.
description: Microsoft Excel or Matlab or Python.
DOI: 10.5061/dryad.k98sf7m9j
title: C and N stable isotope ratios in fishes from marine protected areas and areas open to fishing

description: Here, we assess whether fishery exploitation affects the trophic structure
 of carnivorous fishes. We censused fishes and analysed the stable isotope
 ratios of C and N of species targeted by fishermen in areas open to
 fishing and marine protected areas in the Mediterranean Sea and the
 north-eastern Atlantic Ocean. Results demonstrated a major impact of
 fishing on the biomass and the size structure of nektobenthic carnivorous
 fishes. However, those changes did not modify the diversity of the trophic
 resources used by the assemblage, the pattern of resource partitioning
 between species or the degree of trophic redundancy. These results add to
 recent evidence suggesting that marine protected areas implemented in
 fished seascapes may fail to restore the original structure of the food
 webs that once existed in pre-fished ecosystems, because regional
 decimation and extinction of highly mobile predators prevents recovering
 the original diversity of predators at local scales, even at no-take
 areas. If so, more strict local fishing regulations are unlikely to
 restore the original diversity of high trophic level carnivores and
 restoration goals should be reframed in terms of an objective that is less
 unrealistic than restoring the pre-fished condition while still recovering
 aspects of the historical trophic structure.
description: Fish were captures in shallow rocky bottoms of marine protected
 areas and areas open to fishing and the stable isotope ratios of C and N
 in muscle assessed.
DOI: 10.15468/dl.sudev5
title: Occurrence Download

description: A dataset containing 74114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thymallus thymallus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 74114 records from 157 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002622-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f67dhy
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is A survey of bdelloid rotifers from coastal ponds in Southern Norway"
 ]
}

 The dataset includes 67 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025689-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16911874
title: Underlying data - PMS of the EEN
DOI: 10.15468/dl.p7544p
title: Occurrence Download

description: A dataset containing 16872 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coltricia perennis"
 ]
}

 The dataset includes 16872 records from 323 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009993-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.83xn4b
title: Occurrence Download

description: A dataset containing 392 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leontodon longirostris",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 392 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009994-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v7gn2n
title: Occurrence Download

description: A dataset containing 12945 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cortinarius cinnamomeus"
 ]
}

 The dataset includes 12945 records from 270 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009996-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sgjvx6
title: Occurrence Download

description: A dataset containing 140 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leontodon tuberosus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 140 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009997-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w4h3cx
title: Occurrence Download

description: A dataset containing 387954623 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Magnoliopsida"
 ]
}

 The dataset includes 387954623 records from 14841 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009970-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18739/a22v2cc33
title: InSitu and Ground Penetrating Radar (GPR) Data on a Continuous Permafrost Hillslope in the Galbraith Lake Basin, 2022 - 2023

description: This dataset was used to identify the spatial distribution of subsurface ice content along a continuous permafrost hillslope in the Galbraith Lake Basin. This data set includes the raw Ground-Penetrating Radar (GPR) data taken on the hillslope in the summer of 2022 and 2023. It also includes relevant in situ measurements along each GPR line; Active layer thickness, soil moisture, water level (if applicable), vegetation, and coordinates of the end point of the GPR lines.
DOI: 10.48597/uabg-t8h4
title: Measurement of Aerosol light scattering at Whistler Mountain

description: Measurement of Aerosol light scattering at Whistler Mountain
DOI: 10.5281/zenodo.15579838
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250602v Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250602v Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.5281/zenodo.15579839
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250602v Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250602v Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract