cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z8w9ghxdr
title: Density-dependent patterns of multivariate selection on sperm motility and morphology in a broadcast spawning mussel

description: Sperm cells exhibit extraordinary phenotypic variation, both among taxa
 and within individual species, yet our understanding of the adaptive value
 of sperm trait variation across multiple contexts is incomplete. For
 species without the opportunity to choose mating partners, such as sessile
 broadcast spawning invertebrates, fertilisation depends on gamete
 interactions, which in turn can be strongly influenced by local
 environmental conditions that alter the concentration of sperm and eggs.
 However, the way in which such environmental factors impact phenotypic
 selection on functional gamete traits remains unclear in most systems.
 Here, we analyse patterns of linear and nonlinear multivariate selection
 under experimentally altered local sperm densities (densities within the
 capture zone of eggs) on a range of functionally important sperm traits in
 the broadcast spawning marine mussel, Mytilus galloprovincialis.
 Specifically, we assay components of sperm motility and morphology across
 two fertilisation environments that simulate either sperm limitation (when
 there are too few sperm to fertilise all available eggs), or sperm
 saturation (when there are many more sperm than required for
 fertilisation, and the risk of polyspermy and embryonic failure is
 heightened). Our findings reveal that the strength, form, and targets of
 selection on sperm depend on the prevailing fertilisation environment. In
 particular, our analyses revealed multiple significant axes of nonlinear
 selection on sperm motility traits under sperm limitation, but only
 significant negative directional selection on flagellum length under sperm
 saturation. These findings highlight the importance of local sperm
 densities in driving the adaptation of sperm phenotypes, particularly
 those related to sperm motility, in broadcast spawning invertebrates.
description: ID = male ID; Block = block number; Treatment: H (high density
 fertilisation treatment) or L (low density fertilisation treatment); Fert:
 number of normally developed embryos out of 200; motilecount = number of
 motile sperm tracked; ALH = amplitude of lateral head movement;
 BCF = beat-cross frequency; LIN = linearity; STR = straightness;
 VAP = average-path velocity; VCL = curvilinear velocity;
 VSL = straight-line velocity; PM = percentage of motile sperm in sample;
 HW AVE = average sperm head width; AC AVE = average length of acrosomal
 cap; HL AVE = average sperm head length; FL AVE = average sperm flagellum
 length; TL AVE = total sperm length. Some individuals
 are missing values for either sperm motility or morphological measurements
 and were removed from analayses.
DOI: 10.5061/dryad.k6djh9w7w
title: CT slices of three Protoceratopsian skulls and example slices of other Gobi Desert vertebrates

description: This is a image dataset for deep learning studies. The main dataset
 comprises labeled CT slices from 3 protoceratopsian dinosaur skulls
 discovered from the Gobi Desert, Mongolia. The fossil specimens are now in
 the Division of Paleontology, American Museum of Natural History, New
 York, NY, USA. Inside the folders named after specimen number (i.e.
 IGM100-1021), there are six sub-folders comprising labeled or unlabled CT
 slice images of the specimen from three directions: axial, coronal, and
 sagittal. Each direction should contain all the information to reconstruct
 the entire specimen. The other folder named Gobi Vert comprise CT slices,
 but not enough to reconstruct the original specimens, of multiple
 vertebrate fossils also discovered from the Gobi Desert, Mongolia. The
 specimen number and taxa are noted in the image names.
description: The CT scans were done in either the Department of Earth
 & Planetary Sciences, Yale University, USA or the American Museum
 of Natural History. The segmentation was done by authors, then labelled
 images are exported as the groundtruth for deep learning training. The
 detail of the dataset is following: 
 Specimen number Taxa Dimension Voxel size (μm) Selected slices (training+testing) IGM 100/3654 <i>Protoceratops</i> 1228*1902*1042 21.43 2059+885 IGM 100/3655 <i>Protoceratops</i> 1362*1731*1193 21.44 3047+1239 IGM 100/1021 Protoceratopsia 768*1784*1533 22.74 2880+1205 However, users are free to divide training, testing, and validating dataset as they need. 
description: The dataset comprises three rarely preserved embryonic
 protoceratopsian dinosaurs skulls, thus the morphological information
 embedded are also important for paleontological studies. The slices
 included here are enough to reconstruct the entire morphology of these
 embryonic skulls, therefore, if anyone would like to study the morphology
 of these fossils, please ask the consent from the correspondence author
 Congyu Yu cyu@amnh.org.
DOI: 10.25338/b8n058
title: A novel intramandibular joint facilitates feeding versatility in the sixbar distichodus

description: The intramandibular joint (IMJ) is a secondary point of movement between
 the two major bones of the lower jaw. It has independently evolved in
 several groups of teleost fishes, each time representing a departure from
 related species in which the mandible functions as a single structure
 rotating only at the quadratomandibular joint (QMJ). In this study, we
 examine kinematic consequences of the IMJ novelty in a freshwater
 characiform fish, the herbivorous Distichodus sexfasciatus. We combine
 traditional kinematic approaches with trajectory-based analysis of motion
 shapes to compare patterns of prey capture movements during substrate
 biting, the fish&[prime]s native feeding mode, and suction of prey
 from the water column. We find that the IMJ enables complex jaw motions
 and contributes to feeding versatility by allowing the fish to modulate
 its kinematics in response to different prey and to various scenarios of
 jaw-substrate interaction. Implications of the IMJ include
 context-dependent movements of lower versus upper jaws, enhanced lower jaw
 protrusion, and the ability to maintain contact between the teeth and
 substrate throughout the jaw closing or biting phase of the motion. The
 IMJ in D. sexfasciatus appears to be an adaptation for removing attached
 benthic prey, consistent with its function in other groups that have
 evolved the joint. This study builds on our understanding of the role of
 the IMJ during prey capture and provides insights into broader
 implications of the innovative trait.
DOI: 10.7280/d1vh7w
title: Effects of the VACES particle concentrator on secondary organic aerosol and ambient particle composition

description: The effects of concentrating particles using the Versatile Aerosol
 Concentration Enrichment System (VACES) were investigated with a focus on
 the organic particle composition.  The VACES uses water
 condensation to grow particles and allow enrichment in particle
 concentrations by virtual impaction, followed by diffusion drying to
 remove excess liquid water.  Aerosol mass spectrometry was used
 to compare the submicron organic composition before and after the VACES
 for laboratory-generated secondary organic aerosol (SOA) from ozonolysis
 of α-pinene as well as ambient particles.  Size distributions
 were retained after the VACES for both types of samples.  SOA
 particles showed evidence of high molecular weight compounds forming after
 enrichment, suggesting that some oligomerization occurs during the water
 condensation and/or evaporation stages, but with only slight changes in
 the elemental composition.  Oligomerization was also observed for
 ambient particles, especially those with higher O/C in the accumulation
 mode.  Ambient ultrafine particles with low O/C were not as
 efficiently enriched.  Such composition changes in the organic
 fraction may be relevant to other methodologies where particles are grown
 through water uptake and then dried, as well as to atmospheric processes
 involving water uptake and evaporation.  In the context of
 particle mass, the extent of oligomerization is small.  However,
 given the widespread use of particle concentrators in health effects and
 particle composition studies, whether this impacts interpretation of
 health effects and particle composition data when using particle
 concentrators needs further exploration.
DOI: 10.5061/dryad.c2fqz619m
title: Relative species abundance successfully predicts nestedness and interaction frequency of monthly pollination networks in an alpine meadow

description: Plant-pollinator networks have been repeatedly reported as cumulative ones
 that are described with &gt;1 years observations. However, such
 cumulative networks are composed of pairwise interactions recorded at
 different periods, and thus may not be able to reflect the reality of
 species interactions in nature (e.g., early-flowering plants typically do
 not compete for shared pollinators with late-flowering plants, but they
 are assumed to do so in accumulated networks). Here, we examine the
 monthly sampling structure of an alpine plant-pollinator bipartite network
 over a two-year period to determine whether relative species abundance and
 species traits better explain the network structure of monthly networks
 than yearly ones. Although community composition and species abundance
 varied from one month to another, the monthly networks (as well as the
 yearly networks described with annual pooled data) had a highly nested
 structure, in which specialists directly interact with generalist
 partners. Moreover, relative species abundance predicted the nestedness in
 both the monthly and yearly networks and accounted for a statistically
 significant percentage of the variation (i.e., 20%-44%) in the pairwise
 interactions of monthly networks, but not yearly networks. The combination
 of relative species abundance and species traits (but not species traits
 only) showed a similar prediction power in terms of both network
 nestedness and pairwise interaction frequencies. Considering the
 previously recognized structural pattern and associated mechanisms of
 plant-pollinator networks, we propose that relative species abundance may
 be an important factor influencing both nestedness and interaction
 frequency of pollination networks.
DOI: 10.7488/ds/7980
title: Individual calf nemabiome test results and metadata
title: Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in Kenya

description: Gastrointestinal nematodes (GIN) are of major concern in dairy farming, particularly in smallholder systems, because of their impact on the health of the calves and later on their productivity. These infections often occur as co-infections, which can complicate their prevention and treatment. The aim of this study was to conduct fecal egg counts (FEC), genetically identify GIN species, assess species diversity, and identify associated risk factors for GIN infections in dairy calves. Fecal samples were collected from 532 dairy calves across 289 small holder dairy farms. Species identification was achieved through deep amplicon sequencing of the Internal Transcribed Spacer-2 rDNA locus (ITS-2) of first-stage larvae (L1). The mean eggs per gram (EPG) was 62.0 ± 93.0. Most of the calves 64.2% had lowintensity infections (&lt;50 EPG), 28.6% had medium-intensity infections (50–200 EPG), and 7.2% had high-intensity infections (&gt;200 EPG). Next Generation Sequencing analysis identified nine GIN species, with Cooperia punctata (27.8%), Haemonchus placei (26.3%), and Haemonchus contortus (23.6%) being the most prevalent. Co-infections were common, accounting for 69.5% of all infections, with two (40.1%), three (26.9%), and four-species combinations (19.8%) predominating. Male calves showed a significant association with both increased FEC and smaller heart girth, while FEC decreased with age. H. placei and C. punctata were associated with increased FEC, whereas Ostertagia ostertagi (14.5%) and Trichostrongylus colubriformis (8.0%) were associated with decreased heart girth. Calves managed under pasture systems had higher odds of co-infection. This study reveals that GIN infections are highly prevalent in dairy calves, with co-infections being common, and that GIN burden is significantly influenced by calf age, sex, and management system. The Nemabiome tool offers a promising approach to assessing GIN burden and guiding the selection of anthelmintic protocols as part of sustainable farming strategies in tropical regions.
description: This dataset is the test results from 579 calves sampled as part of a larger study on smallholder dairy cattle in Kenya. The data capture the key animal features such as age sex etc plus the results of screening for gastrointestinal nematodes using the nemabiome tool (a sequence based unbiased tool).
DOI: 10.5061/dryad.hx3ffbgg1
title: Locally adapting generic rubrics for the implementation of outcome-based medical education: A mixed-methods approach

description: Background Rubrics are frequently used to assess competencies in
 outcome-based education (OBE). The implementation of assessment systems
 using rubrics is usually realised through years of involvement in projects
 with various stakeholders. However, for countries or specialities new to
 OBE, faster and more simplified processes are required. In March 2019,
 Japan introduced nine competencies and generic rubrics of competencies for
 medical residents. We explored the local adaptation of these generic
 rubrics and its consequences for assessors. Results A locally adapted
 assessment system was developed and implemented in seven months. The
 scores of the generic rubrics and the adapted assessment tool completed by
 the supervising doctors showed good correlations in some items as opposed
 to others, assessed mainly with other tools. Participant interviews
 revealed that local adaptation decreased their cognitive load leading to
 consistent ratings, increased writing of comments, and promoting
 reflection on instruction. Conclusions This adaptation process is a
 feasible way to begin the implementation of OBE. Local adaptation has
 advantages over direct use of generic rubrics.
description: The study followed three steps. First, we locally adapted the
 generic rubrics. This was followed by conducting mixed-method research to
 explore the effect of the local adaptation. In step two, we examined the
 correlations between the scores in the locally adapted assessment sheets
 for supervising doctors, and the generic rubrics. In step three, we
 conducted interviews with supervising doctors. The study was conducted in
 the General Internal Medicine Department of Nagoya University, Japan. In
 the first step, doctors in the Medical Education Center and other medical
 departments, clerks, and residents participated. Supervising doctors in
 the General Internal Medicine Department participated in the second and
 third steps.
DOI: 10.5061/dryad.9s4mw6mj3
title: Effects of cold or warm ischemia and ex-vivo lung perfusion on the release of damage associated molecular patterns and inflammatory cytokines in experimental lung transplantation

description: Lung transplantation (LTx) is associated with sterile inflammation,
 possibly related to the release of damage associated molecular patterns
 (DAMPs) by injured allograft cells. We have measured cellular damage and
 the release of DAMPs and cytokines in an experimental model of LTx after
 cold or warm ischemia and examined the effect of pretreatment with ex-vivo
 lung perfusion (EVLP).
DOI: 10.5281/zenodo.18378569
title: ASSETS_D2.3_UniBZ_Bozen BolzanoTranscriptions

description: This dataset contains the fully anonymised interview transcripts collected for Deliverable 2.3 of the ASSETS project, which investigates the regulatory and policy context of the social economy.

The transcripts derive from qualitative interviews with key stakeholders, including policymakers, public officials, representatives of social economy organisations, and other relevant actors at different governance levels. The interviews explore existing legal frameworks, public policies, institutional arrangements, and regulatory barriers and opportunities affecting the development and sustainability of the social economy.

All transcripts have been fully anonymised in accordance with ethical requirements and data protection regulations. The dataset supports the qualitative analysis presented in Deliverable D5 and aims to enhance transparency, reusability, and comparability for future research on social economy governance, policy design, and institutional ecosystems.
DOI: 10.5281/zenodo.18378570
title: ASSETS_D2.3_UniBZ_Bozen BolzanoTranscriptions

description: This dataset contains the fully anonymised interview transcripts collected for Deliverable 2.3 of the ASSETS project, which investigates the regulatory and policy context of the social economy.

The transcripts derive from qualitative interviews with key stakeholders, including policymakers, public officials, representatives of social economy organisations, and other relevant actors at different governance levels. The interviews explore existing legal frameworks, public policies, institutional arrangements, and regulatory barriers and opportunities affecting the development and sustainability of the social economy.

All transcripts have been fully anonymised in accordance with ethical requirements and data protection regulations. The dataset supports the qualitative analysis presented in Deliverable D5 and aims to enhance transparency, reusability, and comparability for future research on social economy governance, policy design, and institutional ecosystems.
DOI: 10.5061/dryad.fn2z34tw5
title: Hypoxia-induced predation refuge for northern quahogs (Mercenaria mercenaria) in a temperate estuary

description: Oxygen depletion in estuaries and coastal waters is often associated with
 reduced biodiversity, coastal dead zones, and the loss of important
 ecosystem services. However, some species can benefit from low oxygen
 conditions due to the indirect effects these conditions have on trophic
 relationships. In Narragansett Bay, Rhode Island, U.S.A., northern quahogs
 (Mercenaria mercenaria) reach their highest densities in the areas of the
 Bay most prone to oxygen depletion. One line of evidence suggests that
 suboxic events (hypoxia and anoxia) can aid quahogs by excluding
 predators. Here, we analyze data from long-term surveys of water quality
 and quahog abundances to test whether a hypoxia-induced predation refuge
 is strong enough to explain quahog population dynamics in Narragansett
 Bay. We found that quahog cohorts were larger when they had been exposed
 to low oxygen conditions as juveniles, consistent with the predation
 refuge hypothesis. However, cohort size was also strongly associated with
 location and year settled, suggesting that a predation refuge is but one
 of a suite of factors influencing M.
 mercenaria populations.
description: Methods can be found in the associated publication.
description: The R script (MercenariaHypoxia_GalliganEtAl_12.20.21.R) should
 process the raw data files and reproduce all results and
 figures. You will need to set the working
 directory yourself. You will also need to create a
 file structure within the working directory as follows: 
 Folder: raw.data 
 Dredge_Data_Cleaned_7312020.rds
 Dredge_Data_Sizes_Cleaned_11062020.rds 
 Note: these .rds files can be accessed using the load command in
 R, but may not work with the standard readRDS command
 Subfolder: nbfsmn 
 All *.csv files (naming convention is bb.yyyy.csv)
 
 Please see the README file associated with this
 dataset for additional details. If any issues arise, please contact Bryan
 P. Galligan, S.J. (bgalligan@luc.edu).
DOI: 10.5061/dryad.d7wm37q2t
title: Glycosmis albicarpa (Rutaceae: Clauseneae), a new species from southern Western Ghats, India

description: A new species, Glycosmis albicarpa Sujana & Vadhyar from
 Kanyakumari wildlife sanctuary of southern Western Ghats, India is
 described and illustrated. It differs from all other species of Glycosmis
 by the short and broadly lanceolate leaves, short (3–5 mm long) peduncles,
 clawed petals and broadly ovoid white fruits. The description is
 complemented with color photographs, micromorphology of pollen and seed
 under SEM.
description: Phtography and basic editing using Photoshop.
DOI: 10.5061/dryad.7m0cfxpw5
title: Assessing the anticancer effects of Metformin

description: Metformin is an anti-hyperglycemic biguanide drug that is widely used as
 the first-line prescription for managing type 2 Diabetes Mellitus (T2DM).
 Research suggests metformin use helps control T2DM which is one of the
 many risk factors for cancer and is proposed to have multiple antagonistic
 actions against cancer cells. Suggested biological means that metformin
 utilizes include AMPK-driven cascades involving two pathways, a direct and
 an indirect one. This leads to a decrease in the mechanistic activity of
 rapamycin (mTOR), folate level, c-MYC, NF-B, and also increases P53
 phosphorylation. These cascades will also decrease cyclin D1, reactive
 oxygen species (ROS), and increase mTOR Complex1 (mTORC1) concentrations,
 apoptosis, and autophagy. Some researchers suggest metformin also exerts
 anti-inflammatory effects through reducing Interleukins-6 (IL6) and 8
 (IL8), inhibition of protein translation via LKB1, increasing expression
 of GPD1 which suppresses cancer by inhibiting mitochondria and inducing
 cell apoptosis, and inhibiting leptin while increasing adiponectin
 production. There is also evidence of possible suppressive effects on
 overexpressed signals in some cancers, such as Notch1/Hes1, STAT3, and
 HER2+ which ultimately could increase survival rates in cancer patients.
 Our goal is to explore the mechanisms in which metformin can act as an
 anticancer drug and assess the effect of metformin on various types of
 malignancies. We retrospectively studied 266 cancer patients diagnosed in
 2018 – 2019 in King Fahd Hospital of the University (KFHU). This
 population was furtherly divided into non-diabetic and diabetic cancer
 patients and the latter group into those who received metformin and those
 who did not. The results showed the statistical significance of metformin
 use on the cancer grade at diagnosis that favourably influences the
 morbidity/mortality. Metformin might have an anti-cancer effect on the
 grade of cancer at the time of diagnosis regardless of its dosage, and
 this might improve the prognosis of malignancy.
description: Retrospectively studied 266 cancer patients diagnosed in 2018 –
 2019 in King Fahd Hospital of the University (KFHU). Patients with
 malignancies have been divided into diabetic and non-diabetic groups. The
 diabetic group is further divided into Metformin users and non-metformin
 users. For each patient, the data is collected pertaining to the age at
 which his/her malignancy was first diagnosed, the tumour stage (e.g. TNM
 & other systems used in KFHU), the tumor histological grade, the
 course of the disease along the treatment protocols followed and the
 follow-ups. Patients with malignancies and without diabetes are considered
 as the overall control group. The record of all risk factors, including
 body mass index (BMI) and physical activity are collected. All relevant
 and available medication history and procedures are recorded.
DOI: 10.15468/dl.yqvrq7
title: Occurrence Download

description: A dataset containing 2015 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Ficus elastica"
 ]
}

 The dataset includes 2015 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003020-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.