cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.05qfttf6z
title: Automated and manual segmentation of the hippocampus in human infants

description: The hippocampus, critical for learning and memory, undergoes substantial
 changes early in life. Investigating the developmental trajectory of
 hippocampal structure and function requires an accurate method for
 segmenting this region from anatomical MRI scans. Although manual
 segmentation is regarded as the “gold standard” approach, it is laborious
 and subjective. This has fueled the pursuit of automated segmentation
 methods in adults. However, little is known about the reliability of these
 automated protocols in infants, particularly when anatomical scan quality
 is degraded by head motion or the use of shorter and quieter
 infant-friendly sequences. During a task-based fMRI protocol, we collected
 quiet T1-weighted anatomical scans from 42 sessions with awake infants
 aged 4–23 months. Two expert tracers first segmented the hippocampus in
 both hemispheres manually. The resulting inter-rater reliability (IRR) was
 only moderate, reflecting the difficulty of infant segmentation. We then
 used four protocols to predict these manual segmentations: average adult
 template, average infanBt template, FreeSurfer software, and Automated
 Segmentation of Hippocampal Subfields (ASHS) software. ASHS generated the
 most reliable hippocampal segmentations in infants, exceeding the manual
 IRR of experts. Automated methods thus provide robust hippocampal
 segmentations of noisy T1-weighted infant scans, opening new possibilities
 for interrogating early hippocampal development.
description: This dataset was collected with magnetic resonance imaging
 (MRI). Facial
 information has been stripped for anonymity. Brain scans were
 submitted to manual and automated approaches for segmenting the
 hippocampus. The resulting segmentations are included along with
 additional information and results. No direct idenitifers and no more than
 three indirect identifiers (age, sex, location) are included, in
 compliance with Dryad's human subjects information
 guidelines. Additional details are provided in the
 manuscript: Fel, J. T., Ellis, C. T., & Turk-Browne, N. B. (2023)
 Automated and manual segmentation of the hippocampus in human infants.
 Developmental Cognitive Neuroscience.
description: Please
 refer to the README for guidance on how to use the data.
DOI: 10.6086/d1367q
title: Vehicle trajectory data in Eco-friendly Cooperative Traffic Optimization (EcoTOp) system at signalized intersections

description: Surface transportation systems (e.g., arterial roadways with signalized
 intersections) are inherently inefficient, particularly at higher traffic
 volumes. In general, both the infrastructure (e.g., traffic signals) and
 the vehicles operate independently, with little coordination between them.
 Previous research has shown that implementing strategies that take
 advantage of infrastructure-to-vehicle communication can improve overall
 mobility and reduce environmental impacts, e.g., the Eco-Approach and
 Departure (EAD) application that takes advantage of communicating signal
 phase and timing information to the vehicles. In this research, we will
 build upon this past research to develop a new cooperative traffic
 operation approach that takes advantage of not only
 infrastructure-to-vehicle communications, but also
 vehicle-to-infrastructure communications. This effort integrates a dynamic
 traffic signalization algorithm together with EAD algorithm to achieve
 even greater traffic efficiency. The research was carried out in a
 high-fidelity simulation environment and shows upwards of 15% fuel savings
 and 85% reductions in waiting time. The dataset contain the vehicle
 trajectory of all CAVs and non-CAVs in the SUMO-based traffic simulation
 from all approaches, with vary penetratin rate at 0% (baseline), 20%, 50%,
 80% and 100%.
description: The dataset was collected from the
 trajectory output of SUMO, a micro-scopic traffic simulation software.
 Different scenarios under varying penetrations are tested, e.g. penetratin
 rate at 0% (baseline), 20%, 50%, 80% and 100%. The trajectory data are then archived as
 txt files.
description: The data were saved in txt files in
 the format of second-by-second trajectories. One can use any text editor
 to open it.
DOI: 10.5061/dryad.x0k6djhpx
title: Collybiopsis pakistanica (Omphalotaceae, Agaricales, Basidiomycota), a new mushroom species from Margalla Hills, Pakistan, and two new combinations

description: A new species, Collybiopsis pakistanica, from Margalla Hills National
 Park, Pakistan, is described based on micro-morphological and molecular
 phylogenetic analyses. This species is characterized by its milky white
 pileus, yellowish orange or light yellow to orange at central disc and
 margins, lacrymoid basidiospores, cheilocystidia with median construction,
 and broadly utriform and clavate to narrowly utriform pleurocystidia and
 epithelioid hymeniderm pileipellis. Its placement as a new taxon of
 Collybiopsis is confirmed by phylogenetic analyses of ITS and nrLSU
 sequences. Two new combinations, Collybiopsis ugandensis and Collybiopsis
 pleurocystidiata are also proposed as these species are transferred from
 Gymnopus.
DOI: 10.5061/dryad.d51c5b07b
title: Studies of Vietnamese pteridophyte flora 2

description: We reported nine fern species: Amblovenatum opulentum, Athyrium
 erythropodum, Haplopteris angustifolia, Hymenophyllum acanthoides,
 Hymenophyllum pachydermicum, Huperzia liangshanica, Microlepia smithii,
 Selaginella bisulcata, and Selaginella reticulata as indigenous to Vietnam
 based on our new collections and study of type materials and relevant
 references. We also described one new species Dryopteris huongii to
 accommodate its morphological distinctiveness from its congeneric species.
 We further investigated the phylogenetic relationships of the new species
 using three plastid DNA markers and the result shows it belongs to
 Acrorumohra clade, sister of D. gymnophylla.
DOI: 10.5061/dryad.hqbzkh1mc
title: Anthropogenic change decouples a freshwater predator’s density feedback

description: The datasets here were used to determine annual changes in anthropogenic
 environmental stressors, the prey-fish community, and the walleye
 population in Lake Erie and its western basin during 1969–2018. Here, we
 provide three datasets, which are used in the paper by Sinclair et al.
 titled: "Anthropogenic change decouples a freshwater predator’s
 density feedback". Each dataset is provided as a separate tab in a
 single Excel worksheet. The first dataset ("Environmental
 stressors") provides the annual values for nutrient inputs, water
 transparency, temperature, and commercial walleye harvest. The second
 dataset ("Prey-fish community") provides the annual
 catch-per-unit-effort (CPUE; individuals per trawl minute) for all fish
 species that tend to be found in walleye diets caught in Lake Erie's
 western basin during 1969–2018 in fall (September-October) trawl surveys
 conducted by the Ohio Department of Natural Resources - Division of
 Wildlife. The third dataset ("Walleye") provides the annual
 estimated size of the age-3+ walleye population, the number of walleye
 growing degree days, and the average lengths of age-1 and age-2 walleye
 caught in gill net surveys conducted in the western basin by the Ohio
 Department of Natural Resources - Division of Wildlife. A summary and
 explanation of each variable are also provided in the "Info"
 tab. Further information on how values were calculated is provided in the
 methods and supporting information of the associated article.
description: Please refer to the associated article for data collection
 methods.
description: Please refer to the associated article for information on
 variable transformations and data usage.
DOI: 10.5061/dryad.1vhhmgqxd
title: Predicting the density of zooplankton subsidy to a stream with multiple impoundments using water quality parameters

description: Damming a stream inserts a lentic system (an impoundment or reservoir)
 into a lotic system, changing downstream hydrological, biogeochemical, and
 ecological processes. One such ecological effect of damming is to create a
 resource subsidy of easily captured and consumed zooplankton, which are
 preyed upon by filter-feeders and visual predators.  The data
 included here were used to predict the density of lentic zooplankton
 subsidizing downstream habitats with water quality parameters as an
 alternative to microscopy.  We also used this data to detect
 three different water quality regimes (high conductivity, high-CDOM, and a
 remainder) that are associated with differences in the density of
 zooplankton.  This dataset is contained in two parts, both of
 which are focused on zooplankton density in the effluent of a series of
 tributary-impoundment reservoirs: 1) zooplankton density for a single
 summer season with water quality parameters and 2) zooplankton density for
 a series of three summers without water quality parameters.
description: The methods of data collection are given in more detail within
 the accompanying peer-reviewed article.  We sampled the effluent (outlet)
 of four different reservoirs on a weekly basis during the summer. 
 Zooplankton samples were obtained with a 63-micron zooplankton net. 
 Concurrent environmental (water quality) data was obtained using a
 multi-parameter sonde and hand-held instruments.  Most water-quality
 parameters were measured in the field but some were measured in the lab
 shortly after sampling.  The "zooplankton density" found in this
 dataset has been standardized to count/L.
DOI: 10.5061/dryad.cz8w9gj78
title: Soil microbial relative resource limitation exhibited contrasting seasonal patterns along an elevational gradient in Yulong snow mountain

description: 1. Microbial relative resource limitations represented by enzyme
 stoichiometry reflect the relationship between microbial nutrient
 requirements and nutrient status in soil, but the issue on whether
 alterations in environments along elevational gradients affect the
 magnitude of microbial relative resource limitations remains unresolved.
 2. Here, we examined seasonal patterns in microbial relative carbon (C)
 and phosphorus (P) limitations indicated by vector lengths and angles
 using relative proportional enzymatic activities and key controlling
 factors along an elevational gradient in the Yulong Snow Mountain. We also
 analyzed the relationships between microbial metabolic processes and
 microclimates (i.e., soil moisture and temperature), soil properties
 (i.e., pH and soil texture), and microbial attributes (i.e., microbial
 biomass and fungal: bacterial ratio). 3. We found that soil microbial
 relative C limitation decreased with increasing elevations, with lower
 levels observed in the dry season than in the wet season. In contrast,
 soil microbial relative P limitation varied significantly with elevations,
 with linearly increasing trends in wet seasons but unimodal trends in dry
 seasons. Meanwhile, we found higher relative C limitation in the
 coniferous forest but higher relative P limitation in the broad-leaved
 forest. Notably, soil microbial relative C limitation was primarily
 affected by the soil microenvironment (i.e., soil temperature) and
 substrate quantity (i.e., the ratio of soil dissolved organic C to
 available P), whereas soil microbial relative P limitation could be
 alleviated by increasing microbial relative C limitation combined with
 increasing soil pH. Additionally, the significant linear pattern of the C
 use efficacy with elevations was only observed in the wet seasons, which
 was directly influenced by soil microclimates and microbial relative C
 limitation. 4. Overall, our results provided important information for
 better understanding the essential role of microbial processes in the
 regulation of C and P cycling in vulnerable subtropical mountain
 ecosystems.
description:
DOI: 10.5061/dryad.sxksn0373
title: Exome sequencing of a hybrid pine species complex on the Qinghai-Tibetan Plateau

description: This study investigates the evolutionary history
 of Pinus densata on the Qinghai-Tibetan Plateau
 (QTP) and genomic heterogeneity across a zone of species transition to
 understand contemporary dynamics of selection and evolution of species
 barriers. We analyzed the genetic diversity in a range-wide collection
 of P. densata and representative populations of its
 progenitors P. tabuliformis and P. yunnanensis using 40,000 exome probe capture sequencing.
description: 268 individuals were exome sequenced and genotyped.
description: Dataset consists of genomic data
 generated in vcf format.
DOI: 10.5061/dryad.2fqz612t5
title: Using geometric morphometrics to determine the ‘fittest’ floral shape: a case study in large-flowered buzz-pollinated Melastomataceae

description: PREMISE Floral shape, i.e. the relative arrangement and position of floral
 organs, is critical in mediating fit with pollinators and maximizing
 conspecific pollen transfer. This seems particularly true for functionally
 specialized systems. To date, however, few studies have attempted to
 quantify flowers as the inherently three-dimensional structures that they
 are, and determine the effect of intraspecific shape variation on pollen
 transfer. We here address this research gap using a functionally
 specialized system, buzz pollination, where bees extract pollen through
 vibrations, as a model. Our study species, Meriania hernandoi
 (Melastomataceae), undergoes a natural floral shape change from
 pseudo-campanulate corollas with more actinomorphically-arranged stamens
 (first day) to open corollas with more zygomorphic stamens (second day)
 over anthesis, providing a natural experiment to test how variation in
 floral shape affects male and female fitness. METHODS In one population of
 M. hernandoi, we bagged 51 pre-anthetic flowers and exposed half of them
 to bee pollinators when they were in either stage of their shape
 transition. We then collected flowers, obtained 3D flower models through
 X-ray Computed Tomography for 3D geometric morphometrics, and counted the
 amount of pollen grains remaining per stamen (male fitness) and stigmatic
 pollen loads (female fitness). KEY RESULTS We found significantly higher
 male fitness in open flowers with zygomorphic androecia than in
 pseudo-campanulate flowers. Female fitness did not differ among floral
 shapes. CONCLUSIONS These results suggest that there is an ‘optimal’ shape
 for male fitness, while the movement of bees around the flower when
 buzzing the spread-out stamens results in sufficient pollen deposition
 regardless of floral shape.
description: Experimental field data on pollen removal from flowers and pollen
 deposition collected in Cosanga, Ecuador; flowers were exposed to
 pollinators for two hours, then flowers were collected in 70% ethanol, and
 subsequently micro-CT scanned in the laboratories of the University of
 Vienna. After CT scanning, stamens were removed from flowers for pollen
 counting using a liquid particle counter, and stigmas were sliced off
 flowers for counting stigmatic pollen loads under a fluorescence
 microscope. Flower shapes were captured through the placement of landmarks
 on 3D models of the respective flowers, using the software AMIRA, and then
 analyzed in R. See details in our manuscript.
DOI: 10.5683/sp3/4xl9w6
title: Male Genital Cancers AND Primary Care

description: The notes field contains the Ovid MEDLINE search for male genital cancers, primary care, and prevention/management. The file in this dataset contains the full MEDLINE (Ovid), Embase (Ovid), Scopus, CINAHL (Ebsco), Cochrane, and Global Index Medicus searches. Searches were conducted 2025-07-30 and 2025-07-31.
description: 1 exp Genital Neoplasms, Male/ 196158
2 exp Testicular Neoplasms/ 28500
3 exp "neoplasms, germ cell and embryonal"/ 417696
4 ((penile or penis or testic* or testis or testes or male genital* or male reproductive system* or prostat* or scrot* or seminal vesicle* or gonad* or vas deferens or epididymis) adj5 (cancer* or neoplas* or malignan* or tumo?r* or carcino* or sarcoma* or melanoma* or metasta* or disease* or adeno* or cyst* or lymphoma*)).tw,kf. 250884
5 ((urethra* and (penis or penile or male or men or man)) adj5 (cancer* or neoplas* or malignan* or tumo?r* or carcino* or sarcoma* or melanoma* or metasta* or disease* or adeno* or cyst* or lymphoma*)).tw,kf. 3590
6 seminoma*.tw,kf. 8473
7 nonseminoma*.tw,kf. 2534
8 non seminoma*.tw,kf. 2172
9 (germ* adj3 (tumo?r* or neoplas*)).tw,kf. 18646
10 (paget* adj2 disease*).tw,kf. 9065
11 (testi* adj2 choriocarcinoma*).tw,kf. 153
12 testi* teratoma*.tw,kf. 526
13 mesothelioma of the tunica vaginalis testis.tw,kf. 133
14 (epididymis adj3 tumo?r*).tw,kf. 268
15 (leydig cell adj3 (cancer* or tumo?r*)).tw,kf. 2045
16 sertoli cell tumo?r*.tw,kf. 819
17 TGCT*.tw,kf. 1591
18 ITGCN.tw,kf. 48
19 NSGCT*.tw,kf. 829
20 EMPD.tw,kf. 654
21 (SCC* adj3 (penis or penile)).tw,kf. 270
22 or/1-21 [Male Reproductive System Cancer] 699101
23 primary health care/ or "continuity of patient care"/ or patient-centered care/ 140874
24 exp General Practice/ 80512
25 primary care.tw,kf. 164769
26 (family doctor* or family physician* or family pract*).tw,kf. 31912
27 general practitioner*.tw,kf. 62560
28 nurs*.tw,kf. 587789
29 (health* professional* or health* worker* or health care professional* or health care worker*).tw,kf. 233240
30 or/23-29 [Primary Health Care] 1082786
31 exp Preventive Health Services/ 722473
32 Mass Screening/ 122214
33 disease management/ 44632
34 early diagnosis/ or "early detection of cancer"/ 76817
35 exp treatment outcome/ 1358921
36 prevent*.tw,kf. 2014871
37 manag*.tw,kf. 2092962
38 detect*.tw,kf. 3113864
39 screen*.tw,kf. 1142169
40 diagnos*.tw,kf. 3496244
41 or/31-40 [Prevention] 10941718
42 22 and 30 and 41 4635
DOI: 10.5061/dryad.9kd51c5nd
title: Complex hybridization between deeply diverged fish species in a disturbed ecosystem

description: Over the past two decades, researchers have documented the extent of
 natural hybridization between closely related species using genomic tools.
 Many species across the tree of life show evidence of past hybridization
 with their evolutionary relatives. In some cases, this hybridization is
 complex – involving gene flow between more than two species. While
 hybridization is common over evolutionary timescales, some researchers
 have proposed that it may be even more common in contemporary populations
 where anthropogenic disturbance has modified a myriad of aspects of the
 environments in which organisms live and reproduce. Here, we develop a
 flexible tool for local ancestry inference in hybrids derived from three
 source populations and describe a complex, recent hybridization event
 between distantly related swordtail fish lineages (Xiphophorus) and its
 potential links to anthropogenic disturbance.
description: The reference genomes were assembled as part of previous
 publications and were used for three-way
 <em>ancestryinfer</em> runs in Banerjee & Powell et
 al. The ancestry informative markers and parental
 counts were developed and used for <em>ancestryinfer</em> runs
 in Banerjee & Powell et al. Please see methods and supporting
 information of Banerjee & Powell et al. for information about
 developing ancestry informative sites and parental counts.
 Details for the <em>ancestryinfer</em> runs performed
 for Banerjee & Powell et al can be found at https://github.com/smbanerjee/Tlalica_three-way_hybrids and details for the program <em>ancestryinfer</em> can be found at https://github.com/Schumerlab/ancestryinfer. 
description: These files do not require specifc software to open or read.
DOI: 10.15468/dl.qmjmqy
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Arachnida and Myriapoda (Luomus)",
 "Geometry POLYGON((62.61855 69.27991,54.97074 64.50072,53.94246 56.74795,56.18847 54.6737,52.66428 51.50062,55.65675 50.57579,58.33264 51.13227,65.35765 54.29959,69.97679 61.29828,78.03199 73.66732,68.78393 74.01052,62.61855 69.27991))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010860-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wmyxw4
title: Occurrence Download

description: A dataset containing 3311 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Russian Federation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((62.61855 69.27991,54.97074 64.50072,53.94246 56.74795,56.18847 54.6737,52.66428 51.50062,55.65675 50.57579,58.33264 51.13227,65.35765 54.29959,69.97679 61.29828,78.03199 73.66732,68.78393 74.01052,62.61855 69.27991))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Araneae"
 ]
}

 The dataset includes 3311 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010858-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.asxtam
title: Occurrence Download

description: A dataset containing 5118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Parasteatoda tabulata (Levi, 1980), Coleosoma floridanum Banks, 1900, Howaia mogera (Yaginuma, 1972), Agelena orientalis C.L.Koch, 1837, Ostearius melanopygius (O.Pickard-Cambridge, 1880))"
 ]
}

 The dataset includes 5118 records from 243 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113124-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q573n5tnx
title: Effect of temperature in methanol conversion to dimethyl ether (DME) and light hydrocarbons with beta zeolite

description: Crystalline beta zeolite molecular sieve with SiO2/Al2O3 molar ratio of
 28.5 was synthesized by the hydrothermal crystallization method and
 examined for the methanol dehydration reaction. The micro-mesoporous beta
 zeolite was active between 250 and 450°C. Dimethyl ether (DME) was
 observed as the predominant product at all reaction temperatures, with a
 maximum selectivity of 47.9% at 300°C and a methanol turnover frequency
 (TOFMeOH) of 741.9 h-1. At increased reaction temperatures, the beta
 zeolite showed enhanced strong acid site fraction, promoting higher
 hydrocarbon formation following the olefin-based cycle. It was revealed
 that the crystallinity, porosity, and acidity of the beta zeolite change
 in the reaction environment. Amorphous carbon deposition occurred on beta
 zeolite, which involved the loss in crystallinity to some extent. The
 temperature increase showed a pore-broadening phenomenon at elevated
 temperature regions. The regeneration cycle test showed stable activity of
 regenerated beta zeolite for 280 h time-on-stream.
description: The dataset was collected by several characterization and
 activity test experiments for preparation of the submitted manuscript. All
 the data has been processed and analyzed by the authors of the manuscript.
 The shared data is in .xlx, .txt and .csv formats.