cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.nncb8f
title: Occurrence Download

description: A dataset containing 36448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Streptomyces Waksman & Henrici, 1943"
 ]
}

 The dataset includes 36448 records from 425 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016084-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15255458
title: Ghost in the Machine: Evidence for Non-Random Errors During Direct RNA Nanopore Sequencing Due to Post-Translocated RNA Folding

description: Datasets used to generate the figures within the manuscript
DOI: 10.5281/zenodo.15255459
title: Ghost in the Machine: Evidence for Non-Random Errors During Direct RNA Nanopore Sequencing Due to Post-Translocated RNA Folding

description: Datasets used to generate the figures within the manuscript
DOI: 10.18739/a2n87319h
title: Radium and radon in massive ice, groundwater, seawater, and sediments in the Northwest Territories, Canada, 2019

description: Rapid warming in the Arctic is degrading permafrost and massive ice deposits, which releases solutes previously trapped in ice and frozen soils into groundwater, rivers, and the coastal ocean. Radium (Ra) and radon (Rn) isotopes are enriched in groundwaters and may therefore have utility as tracers for the delivery of permafrost-derived solutes to the ocean, particularly if massive ice- or permafrost- derived meltwaters have a distinct isotopic ratio. Radioactive (radium, radon) and stable (oxygen-18) isotopes were measured in massive ice, permafrost, groundwater, surface waters, and sediments on Tuktoyaktuk Island and Peninsula Point in the Northwest Territories, Canada, with the goal of identifying the isotopic signature of the massive ice endmember. To our knowledge, this is the first dataset that reports radium and radon activities in massive ice deposits.
DOI: 10.5281/zenodo.15579040
title: In Silico Analysis of the Mechanisms of Maribavir-Induced Inhibition and Drug Resistance Mutations in pUL97 Kinase Structure Predicted with AlphaFold2

description: atompLDDT score_pUL97_kinase.pdf: Predicted local distance difference test for the pUL97 kinase structure predicted with AlphaFold2.predicted_aligned_error_pUL97_kinase.json: Predicted aligned error for the pUL97 kinase structure predicted with AlphaFold2.
DOI: 10.5281/zenodo.15579041
title: In Silico Analysis of the Mechanisms of Maribavir-Induced Inhibition and Drug Resistance Mutations using the pUL97 Kinase Structure Predicted with AlphaFold2

description: atompLDDT score_pUL97_kinase.pdf: Predicted local distance difference test for the pUL97 kinase structure predicted with AlphaFold2.predicted_aligned_error_pUL97_kinase.json: Predicted aligned error for the pUL97 kinase structure predicted with AlphaFold2.
DOI: 10.5281/zenodo.15579508
title: In Silico Analysis of the Mechanisms of Maribavir-Induced Inhibition and Drug Resistance Mutations in pUL97 Kinase Structure Predicted with AlphaFold2

description: atompLDDT score_pUL97_kinase.pdf: Predicted local distance difference test for the pUL97 kinase structure predicted with AlphaFold2.predicted_aligned_error_pUL97_kinase.json: Predicted aligned error for the pUL97 kinase structure predicted with AlphaFold2.
DOI: 10.5061/dryad.j3tx95x89
title: The effect of precursor speciation on the growth of scorodite in an atmospheric scorodite synthesis

description: In this study, we propose a growth pathaway of scorodite in an atmospheric
 scorodite synthesis. Scorodite is a non-direct product, which is
  derived from the transformation of its precursor, ferrihydrite
 or poorly crystalline ferric arsenate. Different precursor speciation
 leads to different crystallinity and morphology of synthesized scorodite.
 At 10 and 20 g·L-1 initial arsenic concentration, the precursor of
 scorodite is identified as ferrihydrite. At 10 g·L-1 initial arsenic
 concentrtaion, low arsenic concentrtaion is unfavourable to the complex
 between arsenate and ferrihydrite, inhibiting the transformation of
 ferrihydrite into scorodite. The synthesized scorodite is 1-3 μm in size.
 At 20 g·L-1 initial arsenic concentration, higher arsenic concentration
 favours the complex between arsenate and ferrihydrite. The transformation
 process is accessible. Large scorodite in the particle size of 5-20 μm
 with excellent crystallinity is obtained. However, the increasing initial
 arsenic concentration is not always a positive force for the growth of
 scorodite. When initial arsenic concentrtaion increases to 30 g·L-1,
 Fe(O,OH)6  octahedron preferentially connects to As(O,OH)4
 tetrahedron. Poorly crystalline ferric arsenate rather than ferrihydrite
 is produced. Even poorly crystalline ferric arsenate can also transform to
 crystalline scorodite, its transformation process is much slower than
 ferrihydrite. Therefore, incomplete developed scorodite with poor
 crystallinity is obtained.
DOI: 10.5061/dryad.j3tx95x8b
title: Structure parameter optimization and bearing limit analysis of the expansion unit of three-roller tube expander

description: According to the performance requirements of expansion tools in bellows
 mechanical expansion process, this paper studies and analyzes the critical
 technical issues for the structure design of three-roller tube expander.
 It is indicated that the expansion unit structure is the main influencing
 factor for the performance of three-roller tube expander. The major design
 parameters and key parts of the expansion unit structure of 12 1/4"
 three-roller tube expander was optimized by theoretical analysis and
 finite element numerical simulation method. The bearing limit of
 three-roller tube expander was also studied by numerical simulation
 method. Results from study show that the required expansion force
 increases when the taper angle of the roller outer surface gets larger,
 taking the axial expansion force as the quantitative indicators. It is
 suggested that the roller tape angle of the expansion unit should be in
 the range of 9-12 ° considering the proper length of the roller and the
 un-self-locking tube expansion process. The required expansion force of
 the bellows first decreases and then increases when the gage length of the
 expansion unit becomes longer. The optimal value of the gage length is
 50mm considering the proper length of the roller. Multiple sets of needle
 roller bearing are adopted to improve the bearing system loading capacity
 of expansion unit. In order to improve the loading capacity and abrasive
 wear resistance capacity of the thrust bearing, polycrystalline diamond is
 used as the wear-resistant material on the friction surface of the sliding
 trust bearing. The reliability of the tube expander under various working
 conditions is verified according to the bearing limit analysis of the tube
 expander.
description: Calculated by numerical simulation. 
description: We would not need to know anything to use this dataset. There are
 not any missing values.
DOI: 10.5061/dryad.gb5mkkwk3
title: Development and validation of a postoperative delirium prediction model for patients admitted to an intensive care unit in China: a prospective study

description: Objectives: We aimed to develop and validate a postoperative delirium
 (POD) prediction model for patients admitted to the intensive care unit
 (ICU). Design: A prospective study was conducted. Setting: The study was
 conducted in the surgical, cardiovascular surgical, and trauma surgical
 ICUs of an affiliated hospital of a medical university in Heilongjiang
 Province, China. Participants: This study included 400 patients (≥18 years
 old) admitted to the ICU after surgery. Primary and secondary outcome
 measures: The primary outcome measure was postoperative delirium
 assessment during ICU stay. Results: The model was developed using 300
 consecutive ICU patients and was validated using 100 patients from the
 same ICUs. The model was based on five risk factors: Physiological and
 Operative Severity Score for the Enumeration of Mortality and Morbidity;
 acid-base disturbance; and history of coma, diabetes, or hypertension. The
 model had an area under the receiver operating characteristics curve of
 0.852 (95% confidence interval: 0.802–0.902), Youden index of 0.5789,
 sensitivity of 70.73%, and specificity of 87.16%. The Hosmer-Lemeshow
 goodness of fit was 5.203 (P = 0.736). At a cut-off of 24.5%, the
 sensitivity and specificity were 71% and 69%, respectively. Conclusions:
 The model, which used readily available data, exhibited high predictive
 value regarding risk of intensive care unit postoperative delirium
 (ICU-POD) at admission. Use of this model may facilitate better
 implementation of preventive treatments and nursing measures.
DOI: 10.5281/zenodo.18393786
title: SentinelSphere-post_workshop_responses_aggregated.csv
DOI: 10.5281/zenodo.18393784
title: SentinelSphere-post_workshop_responses_aggregated.csv
DOI: 10.5061/dryad.1jwstqjqb
title: Depth inversion with a 3D structure influences brightness perception

description: Whether or not depth perception influences brightness and/or lightness
 perception has been repeatedly discussed, and some studies have emphasized
 its importance. In addition, a small number of studies have empirically
 tested and shown the effect of depth inversion, such as seen in the Mach
 card illusion, on perceived lightness, and they interpreted such results
 in terms of lightness constancy. However, how perceived brightness changes
 contingent on depth inversion remains unexplained. Therefore, this study
 used the matching method to examine changes in brightness perception when
 depth inversion is observed. We created and used a three-dimensional (3D)
 concave object, composed of three sides made of card stock, which could be
 perceived as having two different shapes in 3D; it could be perceived as a
 horizontal concave object, corresponding to its actual physical structure,
 and as a convex standing object, similar in shape to a building.
 Participants observed this object as both a concave object and as a convex
 object, and judged the brightness of its surfaces during each observation.
 Our results show that the perception of the brightness of the object’s
 surfaces clearly changed depending on the perception of depth. When the
 object was seen as convex, one part of the surface was perceived as darker
 than when the object was seen as concave, but the other part of the
 surface remained unchanged. Here we discuss the relationship between depth
 perception and brightness perception in terms of perceptual organization.
DOI: 10.5061/dryad.3r2280gbp
title: Parasite-mediated selection in a natural metapopulation of Daphnia magna

description: Parasite-mediated selection varying across time and space in
 metapopulations is expected to result in host local adaptation and the
 maintenance of genetic diversity in disease-related traits. However,
 non-adaptive processes like migration and extinction-(re)colonization
 dynamics might interfere with adaptive evolution. Understanding how
 adaptive and non-adaptive processes interact to shape genetic variability
 in life-history and disease-related traits can provide important insights
 into their evolution in subdivided populations. Here we investigate
 signatures of spatially fluctuating, parasite-mediated selection in a
 natural metapopulation of Daphnia magna. Host genotypes from infected and
 uninfected populations were genotyped at microsatellite markers, and
 phenotyped for life-history and disease traits in common garden
 experiments. Combining phenotypic and genotypic data a QST-FST-like
 analysis was conducted to test for signatures of parasite mediated
 selection. We observed high variation within and among populations for
 phenotypic traits, but neither an indication of host local adaptation nor
 a cost of resistance. Infected populations have a higher gene diversity
 (Hs) than uninfected populations and Hs is strongly positively correlated
 with fitness. These results suggest a strong parasite effect on reducing
 population level inbreeding. We discuss how stochastic processes related
 to frequent extinction-(re)colonization dynamics as well as host and
 parasite migration impede the evolution of resistance in the infected
 populations. We suggest that the genetic and phenotypic patterns of
 variation are a product of dynamic changes in the host gene pool caused by
 the interaction of colonization bottlenecks, inbreeding, immigration,
 hybrid vigor, rare host genotype advantage and parasitism. Our study
 highlights the effect of the parasite in ameliorating the negative fitness
 consequences caused by the high drift load in this metapopulation.
DOI: 10.15468/dl.wqm8pq
title: Occurrence Download

description: A dataset containing 276 records in GBIF matching the query:
SELECT
 '417' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey 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 decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 80.58977051167653
 AND decimalLongitude &lt;= 89.91112128543796
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 276 records were derived from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001902-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wpzgmsbgq
title: Examining patterns in opioid prescribing for non-cancer-related pain in Wales: preliminary data from a retrospective cross-sectional study using large datasets

description: Objectives: To examine trends in strong opioid prescribing in a
 primary care population in Wales and identify if factors such as age,
 deprivation and recorded diagnosis of depression or anxiety may have
 influenced any changes noted. Design: Trend, cross-sectional and
 longitudinal analyses of routine data from the Primary Care General
 Practice database and accessed via the Secure Anonymised Information
 Linkage (SAIL) databank. Setting: A total of 345 Primary
 Care practices in Wales. Participants: Anonymised records of
 1,223,503 people aged 18 or over, receiving at least one opioid pre-
 scription between 1 January 2005 and 31 December 2015 were analysed.
 People with a cancer diagnosis (10.1%) were excluded from the detailed
 analysis. Results: During the study period, 26,180,200 opioid
 prescriptions were issued to 1,223,503 individuals (55.9% female, 89.9%
 non-cancer diagnoses). The greatest increase in annual prescribing was in
 the 18–24 age group (10,470%), from 0.08 to 8.3 prescriptions/1000
 population, although the 85+ age group had the highest
 prescribing rates across the study period (from 149.9 to 288.5
 prescriptions/1000 popu- lation). The number of people with recorded
 diagnoses of depression or anxiety and prescribed strong opioids increased
 from 1.2 to 5.1 people/1000 population (328%). The increase was 366.9% in
 areas of highest deprivation compared to 310.3 in the least. Areas of
 greatest deprivation had more than twice the rate of strong opioid
 prescribing than the least deprived areas of Wales.
 Conclusion: The study highlights a large increase in strong
 opioid prescribing for non-cancer pain, in Wales between 2005 and 2015.
 Population groups of interest include the youngest and oldest adult age
 groups and people with depression or anxiety particularly if living in the
 most deprived communities. Based on this evidence, development of a Welsh
 national guidance on safe and rational prescribing of opioids in chronic
 pain would be advisable to prevent further escalation of these medicines.
description: Data extracted from the Secure Anonymised Information Linkage
 databank (SAIL). SQL code used to extract annualised totals for each
 subset of data. Excel and SPSS25 used to analyse data
 using descriptive statistical methods. Excel used to
 produce trend graphs and totals.
description: No missing data.
DOI: 10.5061/dryad.7wm37pvng
title: Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter

description: Marine sponges are set to become more abundant in many near-future
 oligotrophic environments, where they play crucial roles in nutrient
 cycling. Of high importance is their mass turnover of dissolved organic
 matter (DOM), a heterogeneous mixture that constitutes the largest
 fraction of organic matter in the ocean and is recycled primarily by
 bacterial mediation. Little is known however about the mechanism that
 enables sponges to incorporate large quantities of DOM in their nutrition,
 unlike most other invertebrates. Here, we examine the cellular capacity
 for direct processing of DOM, and the fate of the processed matter, inside
 a dinoflagellate-hosting bioeroding sponge that is prominent on
 Indo-Pacific coral reefs. Integrating transmission electron microscopy
 with nanoscale secondary ion mass spectrometry, we track 15N- and
 13C-enriched DOM over time at the individual cell level of an intact
 sponge holobiont. We show initial high enrichment in the filter-feeding
 cells of the sponge, providing visual evidence of their capacity to
 process DOM through pinocytosis without mediation of resident bacteria.
 Subsequent enrichment of the endosymbiotic dinoflagellates also suggests
 sharing of host nitrogenous wastes. Our results shed light on the
 physiological mechanism behind the ecologically important ability of
 sponges to cycle DOM via the recently described sponge loop.
description: Data Table 1 <br> Nitrogen and carbon isotopic ratios and
 enrichment levels (∆δ values above 0h background) of five individual areas
 of interest (AOI) in the photosymbiotic bioeroding sponge <em>Cliona
 orientalis </em>after a pulse of DO<sup>15</sup>N and
 DO<sup>13</sup>C. AOI in the outer sponge body were (I)
 Dinoflagellate symbionts=S, (II) Cytoplasm of dinoflagellate-hosting
 sponge cells=Hs and (III) nearby outer-layer mesohyl cells or
 intercellular areas=Mo. AOI in the inner sponge body were (IV)
 Choanocytes=C and (V) nearby inner-layer mesohyl cells and intercellular
 space=Mi. Inner-body AOI displayed in Figure 1 of the main article (1b, f
 and j) are marked with an asterisk (*), while outer-body AOI displayed in
 Figure 2 (2b, f and j) are marked with a double asterisk (**).
DOI: 10.5061/dryad.v9s4mw6qf
title: Genetic admixture despite ecological segregation in a North African sparrow hybrid zone (Aves, Passeriformes, Passer domesticus x Passer hispaniolensis)

description: Under different environmental conditions hybridization between the same
 species might result in different patterns of genetic admixture.
 Particularly, species pairs with large distribution ranges and long
 evolutionary history may have experienced several independent
 hybridization events over time in different zones of overlap. In birds,
 the diverse hybrid populations of the house sparrow (Passer domesticus)
 and the Spanish sparrow (P. hispaniolensis) provide a striking example.
 Throughout their range of sympatry, these two species do not regularly
 interbreed, however a stabilized hybrid form (P. italiae) exists on the
 Italian Peninsula and on several Mediterranean islands. The spatial
 distribution pattern on the Eurasian continent strongly contrasts the
 situation in North Africa, where house sparrows and Spanish sparrows occur
 in close vicinity of phenotypically intermediate populations across a
 broad mosaic hybrid zone. In this study, we investigate patterns of
 divergence and admixture among the two parental species, stabilized and
 non-stabilized hybrid populations in Italy and Algeria based on a
 mitochondrial marker, a sex-chromosomal marker and 12 microsatellite loci.
 In Algeria, despite strong spatial and temporal separation of urban
 early-breeding house sparrows and hybrids and rural late-breeding Spanish
 sparrows, we found strong genetic admixture of mitochondrial and nuclear
 markers across all study populations and phenotypes. That pattern of
 admixture in the North African hybrid zone is strikingly different from i)
 the Iberian area of sympatry where we observed only weak asymmetrical
 introgression of Spanish sparrow nuclear alleles into local house sparrow
 populations, and ii) from the very homogenous Italian sparrow population
 where the mitogenome of one parent (P. domesticus) and the Z-chromosomal
 marker of the other parent (P. hispaniolensis) is fixed. The North African
 sparrow hybrids provide a further example of enhanced hybridization along
 with recent urbanization and anthropogenic land-use changes in a mosaic
 landscape.
DOI: 10.5061/dryad.f1vhhmgsb
title: The role of low-grade inflammation in ME/CFS (Myalgic Encephalomyelitis/Chronic Fatigue Syndrome) - associations with symptoms

description: Background Patients with Myalgic Encephalomyelitis/Chronic Fatigue
 Syndrome (ME/CFS) often present with a range of flu-like symptoms
 resembling sickness behavior as well as widespread pain and concentration
 deficits. The aim of this study was to explore the association between
 inflammatory markers previously shown to be related to fatigue severity in
 ME/CFS and common ME/CFS symptoms post-exertional fatigue, impaired
 cognitive processing, musculoskeletal pain and recurrent flu-like
 symptoms, and the moderating effect of sex on these associations. Methods
 53 adult patients diagnosed with ME/CFS at a specialist clinic were
 included in the study. Fasting blood plasma was analyzed using the Olink
 Proseek Multiplex Inflammation panel (β-NGF, CCL11, CXCL1, CXCL10, IL-6,
 IL-7, IL-8, IL-10, IL-18, TGF-α ,TGF-β-1 and SCF) and BioRad Human
 Cytokine Type 1 assay (TNF-α). Participants rated the average severity of
 symptoms (0-10) based on the 2011 International Consensus Criteria of
 ME/CFS during a structured clinical interview. Associations between
 inflammatory markers and symptom severity were analyzed using bivariate
 correlations and moderated regression analyses bootstrapped with 5000
 repetitions. Results and conclusions Only β-NGF was associated with the
 fatigue severity measure. However, higher levels of CCL11, CXCL10, IL-7,
 TNF-α and TGF-β-1 were significantly associated with higher levels of
 impaired cognitive processing and musculoskeletal pain, and sex was a
 significant moderator for CXCL10, IL-7 and TGF-β-1. Future studies should
 investigate the relationship between inflammatory markers and key symptoms
 in ME/CFS in a longitudinal design in order to explore if and for whom
 low-grade inflammation may contribute to illness development.