cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.4ndsm7
title: Occurrence Download

description: A dataset containing 44027 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bycanistes bucinator (Temminck, 1824))",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 44027 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000362-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jfvepe
title: Occurrence Download

description: A dataset containing 54004 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation)",
 "Issue is one of (Geodetic datum assumed WGS84, Coordinate rounded, Continent derived from coordinates, The taxon ID was not used in backbone matching)",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (04fd2e13-6881-4e5c-9dd1-8fdd9ab993c1, d2519a48-9ed7-4e86-8692-338cfc214629, def3224b-b19e-4280-92bb-fee4c7f6180d, 1e9400fa-ce73-4737-9eaa-f25df148945c, b8323864-602a-4a7d-9127-bb903054e97d, d3978a37-635a-4ae3-bb85-7b4d41bc0b88)",
 "TaxonKey is Mytilus trossulus A.Gould, 1850",
 "Year 2000-2024"
 ]
}

 The dataset includes 54004 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000361-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24139067
title: Measurement properties of assessment instruments of quality of life in people with spinal cord injury: A systematic review

description: A spinal cord injury or disease (SCI/D) is a devastating condition that affects all areas of a person’s life, including quality of life (QoL). Assessing this construct using clinical instruments with adequate measurement properties is fundamental for an effective multi-professional treatment. To identify the clinical instruments for assessing the QoL that present the best recommendation for use in people with SCI based on their measurement properties. The overall methodology was conducted according to Consensus-based Standards for the selection of health Measurement Instruments (COSMIN) systematic review guidance and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. A literature search was conducted up to March 2023 on MEDLINE/PubMed, Web of Science, Scopus, CINAHL, and Embase databases. Seventy-seven studies were included in this review, and 49 instruments were identified. The overall methodological quality of all studies ranged from insufficient to sufficient, and the level of evidence ranged from very low to high confidence. Twenty-six instruments may have the potential to be recommended, and the other 23 should not be recommended. None of the QoL instruments can be highly recommended as the most suitable instrument for the construct and population of interest. The generic instruments SF-36, SF-12, QWB, WHOQOL-DIS, WHOQOL-BREF, QLI-SCI, QOLP-PD, LS Questions, Lisat-9, and BRFSS are the clinical instruments that have the best measurement properties tested and have the potential to be the current best recommendation for assessing QoL in individuals with SCI.
DOI: 10.6084/m9.figshare.24139067.v1
title: Measurement properties of assessment instruments of quality of life in people with spinal cord injury: A systematic review

description: A spinal cord injury or disease (SCI/D) is a devastating condition that affects all areas of a person’s life, including quality of life (QoL). Assessing this construct using clinical instruments with adequate measurement properties is fundamental for an effective multi-professional treatment. To identify the clinical instruments for assessing the QoL that present the best recommendation for use in people with SCI based on their measurement properties. The overall methodology was conducted according to Consensus-based Standards for the selection of health Measurement Instruments (COSMIN) systematic review guidance and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. A literature search was conducted up to March 2023 on MEDLINE/PubMed, Web of Science, Scopus, CINAHL, and Embase databases. Seventy-seven studies were included in this review, and 49 instruments were identified. The overall methodological quality of all studies ranged from insufficient to sufficient, and the level of evidence ranged from very low to high confidence. Twenty-six instruments may have the potential to be recommended, and the other 23 should not be recommended. None of the QoL instruments can be highly recommended as the most suitable instrument for the construct and population of interest. The generic instruments SF-36, SF-12, QWB, WHOQOL-DIS, WHOQOL-BREF, QLI-SCI, QOLP-PD, LS Questions, Lisat-9, and BRFSS are the clinical instruments that have the best measurement properties tested and have the potential to be the current best recommendation for assessing QoL in individuals with SCI.
DOI: 10.6084/m9.figshare.28195520
title: Pediatric health and life domain priorities: A national survey of people with spinal cord injury and their parents and caregivers

description: No information is available regarding priorities for pediatric-onset spinal cord injury (SCI). This study described the Health and Life (H&L) domain priorities of youth with pediatric-onset SCI and their parents/caregivers living in Spain. A cross-sectional survey. Two SCI rehabilitation centers. Sixty participants, youth with pediatric-onset SCI (n = 26) and parents/caregivers (n = 34). Not applicable. Median overall priorities calculated on the basis of importance, unhappiness, and research measured with a new survey of pediatric H&L domains and rated using a 5-point Likert Scale. A total of 60 surveys were received providing information on 35 individuals with SCI: 2-7-year-olds (25.7%), 8-12-year-olds (22.9%), 13-17-year-olds (31.4%), and 18-25-year-olds (20.0%). The top three overall H&L priorities reported by parents/caregivers of 2-12-year-olds were “parenthood expectations” (84%), “leg/foot movement” (83%), and “bladder” function (83%), compared to “dressing/undressing” (78%), “walking/ability to move” (77%) and “bladder” function (77%) rated for 13-25-year-olds. “Sit-to-stand” (79%), “leg/foot movement” (78%) and “arm/hand movement” (77%) were reported as priorities by 13-25-year-olds. The 13-25-year-olds highlighted “sit-to-stand” (100%), “eating/drinking” (54%), and “physical function” (94%) as their top unhappiness, importance, and research priorities, respectively. Significant differences between tetraplegia and paraplegia were found in “mobility in the community” (unhappiness item) for 13-25-years-old. Health domains were considered the top overall H&L priorities by parents/caregivers of 13-25-year-olds, compared to life domains reported for their 2-12-year-olds. This survey will aid rehabilitation professionals to engage stakeholders to implement a comprehensive SCI management program for the pediatric population.
DOI: 10.6084/m9.figshare.22341830
title: Effects of robot-assisted gait training on cardiopulmonary function and lower extremity strength in individuals with spinal cord injury: A systematic review and meta-analysis

description: Robot-assisted gait training (RAGT) has been increasingly adopted in many rehabilitation facilities for walking function and activity in individuals with spinal cord injury (SCI). However, the effectiveness of RAGT on lower extremity strength and cardiopulmonary function, especially static pulmonary function, have not been clearly outlined. Determine the effect of RAGT on cardiopulmonary function and lower extremity strength in SCI survivors. Eight databases were systematically searched for randomized controlled trials comparing RAGT with conventional physical therapy or other non-robotic therapies for survivors with SCI. Study selection required lower extremity strength decline after SCI at baseline. The overall effects of RAGT were calculated using a meta-analytic method. Begg’s test was used to assess the risk of publication bias. The pooled analysis demonstrated that RAGT may have a positive effect for individuals with SCI on lower extremity strength enhancing (<i>n</i> = 408; standardized mean difference [SMD]  =  0.81; 95% confidence interval [CI] = 0.14–1.48) and cardiopulmonary endurance(<i>n</i> = 104; standardized mean difference [SMD]  =  2.24; 95% confidence interval [CI] = 0.28–4.19). However, no significant effect was established on static pulmonary function. No publication bias was observed according to the Begg’s test. RAGT may be a useful technique for improving lower limb strength and cardiovascular endurance in SCI survivors. The usefulness of RAGT in enhancing static pulmonary function was not demonstrated by the study. However, these results should be interpreted with caution, given the low number of selected studies and subjects. Clinical studies with large sample sizes will be necessary in the future.
DOI: 10.6084/m9.figshare.22341830.v1
title: Effects of robot-assisted gait training on cardiopulmonary function and lower extremity strength in individuals with spinal cord injury: A systematic review and meta-analysis

description: Robot-assisted gait training (RAGT) has been increasingly adopted in many rehabilitation facilities for walking function and activity in individuals with spinal cord injury (SCI). However, the effectiveness of RAGT on lower extremity strength and cardiopulmonary function, especially static pulmonary function, have not been clearly outlined. Determine the effect of RAGT on cardiopulmonary function and lower extremity strength in SCI survivors. Eight databases were systematically searched for randomized controlled trials comparing RAGT with conventional physical therapy or other non-robotic therapies for survivors with SCI. Study selection required lower extremity strength decline after SCI at baseline. The overall effects of RAGT were calculated using a meta-analytic method. Begg’s test was used to assess the risk of publication bias. The pooled analysis demonstrated that RAGT may have a positive effect for individuals with SCI on lower extremity strength enhancing (<i>n</i> = 408; standardized mean difference [SMD]  =  0.81; 95% confidence interval [CI] = 0.14–1.48) and cardiopulmonary endurance(<i>n</i> = 104; standardized mean difference [SMD]  =  2.24; 95% confidence interval [CI] = 0.28–4.19). However, no significant effect was established on static pulmonary function. No publication bias was observed according to the Begg’s test. RAGT may be a useful technique for improving lower limb strength and cardiovascular endurance in SCI survivors. The usefulness of RAGT in enhancing static pulmonary function was not demonstrated by the study. However, these results should be interpreted with caution, given the low number of selected studies and subjects. Clinical studies with large sample sizes will be necessary in the future.
DOI: 10.6084/m9.figshare.28195520.v1
title: Pediatric health and life domain priorities: A national survey of people with spinal cord injury and their parents and caregivers

description: No information is available regarding priorities for pediatric-onset spinal cord injury (SCI). This study described the Health and Life (H&L) domain priorities of youth with pediatric-onset SCI and their parents/caregivers living in Spain. A cross-sectional survey. Two SCI rehabilitation centers. Sixty participants, youth with pediatric-onset SCI (n = 26) and parents/caregivers (n = 34). Not applicable. Median overall priorities calculated on the basis of importance, unhappiness, and research measured with a new survey of pediatric H&L domains and rated using a 5-point Likert Scale. A total of 60 surveys were received providing information on 35 individuals with SCI: 2-7-year-olds (25.7%), 8-12-year-olds (22.9%), 13-17-year-olds (31.4%), and 18-25-year-olds (20.0%). The top three overall H&L priorities reported by parents/caregivers of 2-12-year-olds were “parenthood expectations” (84%), “leg/foot movement” (83%), and “bladder” function (83%), compared to “dressing/undressing” (78%), “walking/ability to move” (77%) and “bladder” function (77%) rated for 13-25-year-olds. “Sit-to-stand” (79%), “leg/foot movement” (78%) and “arm/hand movement” (77%) were reported as priorities by 13-25-year-olds. The 13-25-year-olds highlighted “sit-to-stand” (100%), “eating/drinking” (54%), and “physical function” (94%) as their top unhappiness, importance, and research priorities, respectively. Significant differences between tetraplegia and paraplegia were found in “mobility in the community” (unhappiness item) for 13-25-years-old. Health domains were considered the top overall H&L priorities by parents/caregivers of 13-25-year-olds, compared to life domains reported for their 2-12-year-olds. This survey will aid rehabilitation professionals to engage stakeholders to implement a comprehensive SCI management program for the pediatric population.
DOI: 10.15468/dl.wf3agj
title: Occurrence Download

description: A dataset containing 1378 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is one of (New Zealand fish and squid distributions from research bottom trawls 1964-2008, Marine biological observation data from coastal and offshore surveys around New Zealand, iNaturalist Research-grade Observations, Catch data from New Zealand research trawls since 2008)",
 "Issue is one of (Coordinate rounded, Geodetic datum assumed WGS84, Continent derived from coordinates, The taxon ID was not used in backbone matching)",
 "OccurrenceStatus is Present",
 "TaxonKey is Perna canaliculus (Gmelin, 1791)",
 "Year 2000-2024"
 ]
}

 The dataset includes 1378 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000365-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13617404
title: BGC-Argo Satellite matchup to compute variability in the Chl:C ratio of phytoplankton.

description: This dataset provides matchups between BGC-Argo and MODIS satellites (both atmospheric and ocean color products). This dataset allows users to compare the variability of the Chlorophyll(Chl)  to Phytoplankton Carbon ratio from BGC-Argo floats depending on the light in the mixed layer and link to information obtained from satellites about cloud coverage. 

Quality control previously performed on this dataset and matchup criteria are described in the associated publication

Here are some of the column headers detailed for clarity:

Columns 1-24 represent data from the BGC-Argo floats:



dt: Datetime in datenum format.

region : Longhurst Region

biomes: Biomes according to Fay & McKinley, 2014 (with West Mediterranean biome 18 and East Mediterranean biome 19)

zenith : Sun zenith angle at time of surfacing 

kd_490_Xing : Downwelling diffuse attenuation coefficient at 490nm from Xing et al.,2021 method. 

PAR_0_Argo : PAR(0-) right below the surface also from Xing et al., 2021 

chla : Median chlorophyll from fluorescence in the mixed layer (corrected for Non-Photochemical Quenching)

Z_iso : Depth of the 0.415 mol/quanta/m-2/d-1 isolume. 

Zeu : Euphotic depth, 1% of surface light

Eg_Argo : Median light level in the mixed layer, bounded by the surface and the mld_mat depth

MLD : Mixed layer depth, determined using the 0.03 density criteria

bbp_XXX : Backscattering at a specific wavelength

Cphyto : Median Phytoplankton Carbon in the mixed layer. Computed from Bbp following Graff et al, 2015

F_indiv : Calibration factor for Chlorophyll fluorescence according to the method described in Xing et al, 2011. 

F_median : Median Correction factor for all the float F in a biome

F_std: Standard deviation of above. 

Chl_cor : Chla from floats corrected using the F_median factor according to Xing et al., 2011. 

ratio_cor: Chl_cor /Cphyto.


Columns 25-42 have products from matchups with ocean-color MODIS files:



sat_dt : Datetime of satellite overpass in the datenum format. 

chlor_a : Satellite chl obtained from NASA's OBPG hybrid algorithm.

Ratio_Chl_sat: Ratio of satellite chlorophyll (chlor_a) over BGC-Argo corrected Chl (Chl_cor)

PAR:  Satellite PAR above the surface (0+)

PAR_minus : Satellite PAR propagate right below the surface (0-)


Eg_daily is the daily hourly median light in the mixed layer computed as PAR_minus * (Eg_Argo/PAR_0_argo)/24.

Columns 44-48 have products from matchups with atmospheric MODIS files: 



a_lat, a_lon, a_dt: Same as above but for the atmospheric file

COT: Cloud optical thickness

Confident Cloudy: Number of pixels (Out of 25) with the Confident Cloudy flag.
DOI: 10.15468/dl.9659hy
title: Occurrence Download

description: A dataset containing 106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diuraphis noxia (Mordvilko, 1913)",
 "Country is United States of America",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 106 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000367-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.58053/mapbiomas/jwwejp
title: Destaques do módulo de Degradação da vegetação nativa do Brasil - MapBiomas Degradação Beta (1986-2021)

description: Documento com os principais destaques do módulo de Degradação da vegetação nativa no Brasil de 1986 a 2021
DOI: 10.15468/dl.tp5ngc
title: Occurrence Download

description: A dataset containing 8526844 records in GBIF matching the query:
SELECT "year", GBIF_EEARGCode( 1000, decimalLatitude, decimalLongitude, COALESCE(coordinateUncertaintyInMeters, 1000) ) AS eeaCellCode, classKey, class, familyKey, family, COUNT(*) AS occurrences, MIN(COALESCE(coordinateUncertaintyInMeters, 1000)) AS minCoordinateUncertaintyInMeters, MIN(GBIF_TemporalUncertainty(eventDate)) AS minTemporalUncertainty FROM occurrence WHERE occurrenceStatus = 'PRESENT' AND countrycode = 'BE' AND "year" &gt;= 1900 AND hasCoordinate = TRUE AND familyKey IS NOT NULL AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE') AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE') AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID') AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH') AND (LOWER(identificationVerificationStatus) NOT IN ( 'unverified', 'unvalidated', 'not validated', 'under validation', 'not able to validate', 'control could not be conclusive due to insufficient knowledge', 'uncertain', 'unconfirmed', 'unconfirmed - not reviewed', 'validation requested' ) OR identificationVerificationStatus IS NULL)AND classKey IN (126, 131, 137, 139, 148, 151, 179, 183, 186, 194, 196, 199, 203, 205, 206, 212, 216, 220, 225, 229, 232, 244, 245, 252, 255, 256, 270, 281, 282, 307, 327, 328, 354, 356, 359, 360, 361, 365, 367, 7073593, 7228684, 7742773, 7774442, 7947184, 8179345, 9273948, 10689325, 11133537, 11418114, 11493978, 11545536, 11592253)AND coordinateUncertaintyInMeters &lt;= 10000GROUP BY "year", eeaCellCode, classKey, class, familyKey, family ORDER BY "year" DESC, eeaCellCode ASC, familyKey ASC;

 The dataset's 8526844 records were derived from 297 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000346-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14680163
title: Deaminase-mediated chromatin accessibility profiling with single-allele resolution

description: Binding of transcription factors (TFs) at gene regulatory elements controls cellular epigenetic state and gene expression. Current genome-wide chromatin profiling approaches have inherently limited resolution, complicating assessment of TF occupancy and co-occupancy, especially at individual alleles. In this work, we introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), which harnesses a double-stranded DNA cytosine deaminase (Ddd) enzyme to stencil TF binding locations within accessible chromatin regions. We optimize bulk and single-cell ACCESS-ATAC protocols and develop computational methods to show that the increased resolution compared with ATAC-seq improves the accuracy of TF binding site prediction. We use ACCESS-ATAC to perform genome-wide allelic occupancy and co-occupancy imputation for 64 TFs each in HepG2 and K562, revealing that the propensity of a majority of TFs to co-occupy nearby motifs oscillates with a period approximating the helical turn of DNA. Altogether, ACCESS-ATAC expands the resolution and capabilities of bulk and single-cell epigenomic profiling.
DOI: 10.5281/zenodo.14680164
title: Deaminase-mediated chromatin accessibility profiling with single-allele resolution

description: Binding of transcription factors (TFs) at gene regulatory elements controls cellular epigenetic state and gene expression. Current genome-wide chromatin profiling approaches have inherently limited resolution, complicating assessment of TF occupancy and co-occupancy, especially at individual alleles. In this work, we introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), which harnesses a double-stranded DNA cytosine deaminase (Ddd) enzyme to stencil TF binding locations within accessible chromatin regions. We optimize bulk and single-cell ACCESS-ATAC protocols and develop computational methods to show that the increased resolution compared with ATAC-seq improves the accuracy of TF binding site prediction. We use ACCESS-ATAC to perform genome-wide allelic occupancy and co-occupancy imputation for 64 TFs each in HepG2 and K562, revealing that the propensity of a majority of TFs to co-occupy nearby motifs oscillates with a period approximating the helical turn of DNA. Altogether, ACCESS-ATAC expands the resolution and capabilities of bulk and single-cell epigenomic profiling.
DOI: 10.5281/zenodo.14680777
title: Deaminase-mediated chromatin accessibility profiling with single-allele resolution

description: Binding of transcription factors (TFs) at gene regulatory elements controls cellular epigenetic state and gene expression. Current genome-wide chromatin profiling approaches have inherently limited resolution, complicating assessment of TF occupancy and co-occupancy, especially at individual alleles. In this work, we introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), which harnesses a double-stranded DNA cytosine deaminase (Ddd) enzyme to stencil TF binding locations within accessible chromatin regions. We optimize bulk and single-cell ACCESS-ATAC protocols and develop computational methods to show that the increased resolution compared with ATAC-seq improves the accuracy of TF binding site prediction. We use ACCESS-ATAC to perform genome-wide allelic occupancy and co-occupancy imputation for 64 TFs each in HepG2 and K562, revealing that the propensity of a majority of TFs to co-occupy nearby motifs oscillates with a period approximating the helical turn of DNA. Altogether, ACCESS-ATAC expands the resolution and capabilities of bulk and single-cell epigenomic profiling.