cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31167913.v1
title: Experimentally acquired low-light micro-PIV images of CO2 flows under transcritical and supercritical conditions

description: This experimentally acquired dataset consists of a series of µPIV-like low-light image sequences of fluorescent particles. The particles were recorded using a high-speed CCD camera and were imaged through a microchannel with flowing carbon dioxide across a range of high-pressure, transcritical conditions inducing optical distortions, so-called speckles. An important feature is that each optically corrupted image sequence is paired with a speckle-free ground-truth of an identical particle pattern. Additionally, the dataset is accompanied by thermodynamic metadata in the form of csv-files for each image.The dataset is designed to support the development, validation, and benchmarking of image reconstruction algorithms under realistic experimental conditions. This can be utilised to drive the advancement of novel data-driven approaches, but also to further develop conventional image reconstruction techniques.<b>Data Structure</b>The dataset is organised in a hierarchical directory structure designed to provide a clear and traceable mapping between thermodynamic conditions, image data, and associated metadata. At the top level, the data are grouped into individual directories corresponding to sequences. Each sequence represents a distinct experimental protocol (e.g. wall-heater or pre-heater operation) with a unique particle pattern and is listed in the extended operating-point table provided in: <i>03_additional_data/operating_points_full.csv. </i>Within each sequence directory, sub-directories are organised by operating point. Each operating point corresponds to a unique combination of boundary conditions. Each operating-point directory contains:Ten consecutively recorded image pairs in TIFF formatA comma-separated values (CSV) file containing the associated metadata for each imageThe image naming convention follows the format: <i>SeqXX_OPXX_imgXXX.tif </i>where <i>SeqXX</i> identifies the thermodynamic sequence, <i>OPXX</i> the operating point, and <i>imgXXX</i> the chronological order of acquisition. This filename also serves as the unique image identifier used throughout the dataset. The CSV metadata file links each image identifier to the recorded thermodynamic state variables. All values are reported in SI units. The same folder structure exists for both:raw_images: unprocessed camera outputprocessed_images: images after application of a 99% histogram stretch, as described in the accompanying publicationThe directory <i>03_additional_data</i> further contains reference image data acquired from fluorescent particles deposited on a simple glass slide. These images can be used to compute particle size distributions and to benchmark the optical and adhesive properties of the particle–adhesive solution independently of the microfluidic experiments.A Jupyter notebook is included with the dataset to demonstrate representative analysis workflows and to support reproducibility. The notebook is located in <i>03_additional_data/02_code/ </i>and is written entirely in Python.
DOI: 10.5061/dryad.q573n5tmf
title: Energetic constraints on body-size niches in a resource-limited marine environment

description: Body size of life on Earth spans many orders of magnitude, and with it
 scales the energetic requirements of organisms.  Thus, changes in
 environmental energy should impact community body-size distributions in
 predictable ways by reshaping ecological and niche dynamics. We examine
 how carbon, oxygen, and temperature, three energetic drivers, impact
 community size-based assembly in deep-sea bivalves. We demonstrate that
 body-size distributions are influenced by multiple energetic
 constraints.  Relaxation in these constraints leads to an
 expansion of body-size niche space through the addition of novel large
 size classes, increasing the standard deviation and mean of the body-size
 distribution. With continued Anthropogenic increases in temperature and
 reductions in carbon availability and oxygen in most ocean basins, our
 results point to possible radical shifts in invertebrate body size with
 the potential to impact ecosystem function.
DOI: 10.57903/uj/3vhyyq
title: Proteomic raw datasets for liver sinusoidal endothelial cells (LSECs) isolated from C57BL/6J mice and cultured human aortic endothelial cells (HAECs)

description: The purpose of collecting the data set was to explore the repertoire and relative abundance of proteins involved in the function and structure of murine primary LSECs and human-derived cultured HAECs. Data were obtained using an untargeted LC-MS/MS-based methodology.
DOI: 10.5061/dryad.hhmgqnkjx
title: Data from: It’s all about food: Environmental factors cause species-specific dispersal

description: Dispersal is a vital component of the life- history of nearly all
 organisms. The ability to disperse determines the distribution and
 abundance of a species and thus its community dynamic at different sites.
 The scientific challenge is to design standardized laboratory experiments
 that not only record the effects of single factors but also includes the
 multi-causal nature of dispersal. Here we tested the effect of the
 environmental factors density, food availability and predation and the
 combinations thereof on the dispersal of five free- living nematode
 species by performing experiments in two-patched systems. We hypothesized
 that emigration is generally positively correlated with the intrinsic rate
 of natural increase and would decrease with increasing food availability
 and increase both with the presence of a predator and at higher initial
 population densities. These predictions were tested both using
 single-species tests with laboratory cultures as well as using intact
 natural nematode communities to investigate whether environmental factors
 determine the composition of dispersing species. The results of our study
 revealed a positive correlation between dispersal and intrinsic growth
 ability, whereas the studied nematode species differed in their dispersal
 patterns, both under control conditions and in response to bottom-up,
 top-down, and density dependent stimuli. Despite the species- specific
 differences in dispersal behavior in response to the environmental
 factors, the availability of food appeared as the main driver. This was
 especially pronounced regarding a natural nematode community. Our
 experiments emphasize the central role of food availability in spatial
 structuring nematode communities.
DOI: 10.5061/dryad.n8pk0p2xz
title: Multifaceted DNA metabarcoding of bat guano

description: DNA sequences from multiple different loci recovered as part of
 multifaceted DNA metabarcoding (MDM) of guano samples collected from two
 bat communities. One community was located in New York, USA, and the other
 in Arizona, USA. Data classes recovered from each guano sample (individual
 scat) using DNA included bat species, bat sex (multiple zinc-finger gene
 primer sets), arthropod diet items (16S and 18S rRNA loci), bat parasites
 (16S and 18S rRNA loci), and, depending on bat community, exposure to
 Pseudogymnoascus destructans (white-nose syndrom pathogen) or plant diet
 (trnH-psbA, 18S rRNA loci). 
description: The archived data sets include all sequences used for making
 species, sex, or other determinations. All other sequence data, including
 raw sequence reads <em>may</em> be available upon request from
 the corresponding author.
DOI: 10.5061/dryad.00000005r
title: Cognitive flexibility supports the development of cumulative cultural learning in children

description: The scale of cumulative cultural evolution (CCE), the improvement of
 cultural traits over generations via social transmission, is widely
 believed to be one of humans’ most defining characteristics. Our capacity
 to build upon others' knowledge, skills, and technologies has
 produced the most diverse and complex technological repertoire on the
 planet. Despite growing interest in the field of CCE, the cognitive
 underpinnings supporting its development remain relatively understudied.
 In this study, we examined the role that cognitive flexibility plays in
 supporting cumulative cultural learning by studying U.S. children’s (N =
 167, 3-5-year-olds) propensity to relinquish an inefficient solution to a
 problem in favor of a more efficient alternative. We also examined whether
 children would resist reverting back to earlier versions and omit
 redundant actions from previous behaviors. In contrast to previous work
 with chimpanzees, most children who first learned to solve a puzzlebox in
 a highly inefficient way switched to an observed, more efficient
 alternative. However, over multiple task interactions, 85% of children who
 did switch also reverted back to the original, inefficient method.
 Moreover, almost all children in a control condition (who first learned
 the efficient method before observing the inefficient method) switched to
 the inefficient method. This suggests that children were keen to explore
 an alternative modeled solution but were overall conservative in reverting
 to their first-learned method across subsequent task interactions. We
 discuss these findings in the context of their implications for the
 cognitive ontogeny of CCE.
DOI: 10.6078/d13t40
title: Auxiliary supplementary material for the study on plant diversity relationships with satellite-detected phenological variability in USA wetlands at a national scale

description: This  dataset contains auxiliary data and supporting information
 for the research article by Iryna Dronova, Sophie Taddeo, and Kendall
 Harris "Plant diversity reduces satellite-observed phenological
 variability in wetlands at a national scale" for Science Advances
 (provisionally accepted in May 2022). It includes one Excel spreadsheet
 document with the main variables used in the study analyses
 (Data_S1_Regression_Dataset_v5_31_2022.xslx) and two ZIP files containing
 supporting information about two of those variables created in the custom
 way: phenological variability (PhenoVariability; workflow
 in Data_S2_Code_for_Custom_Variables.zip) and variation in land
 surface temperature (Var_LST; workflow
 in Data_S3_Code_for_Variability_LST.zip). The main purpose of
 this dataset is to share the study's variables used in statistical
 analyses. The relevant variables are compiled in the Excel spreadsheet
 (Data_S1_Regression_Dataset_v5_31_2022.xslx), where each entry corresponds
 to an individual wetland site surveyed by the National Wetland Condition
 Assessment (NWCA) by the U.S. Environmental Protection Agency in 2011. A
 unique identifier (UID) of each wetland site is included to allow users to
 link to other NWCA databases for additional already published information
 if desired (NWCA database is available at the following website under
 Wetlands 2011 category:
 https://www.epa.gov/national-aquatic-resource-surveys/data-national-aquatic-resource-surveys). Two supporting ZIP files (Data_S2_Code_for_Custom_Variables.zip and Data_S3_Code_for_Variability_LST.zip) contain README files, codes and code input data to allow for reproducibility of the custom-created variables that have been generated in this study and are not available in other databases. 
description: This dataset includes three files listed in the Supplementary
 Materials document of the publication as follows:  S1:
 Data_S1_Regression_Dataset_v5_31_2022.xslx: plant diversity and wetland
 site variables for 1138 wetland sites used in this study’s statistical
 analyses. S2:
 Data_S2_Code_for_Custom_Variables.zip: a Zip file containing a README
 explanatory text file, two Matlab codes for estimating measures of
 phenological variability and its two custom-derived covariates and two
 input data files required to run the codes: the dataset original 2002-2019
 series of Normalized Difference Vegetation Index computed from wetland
 sites for MOD09Q1.006 product and the dataset with site names.
 S3:
 Data_S3_Code_for_Variability_LST.zip: a Zip file containing a README_LST
 explanatory text file, two Matlab codes for estimating variability in land
 surface temperature (LST) from MOD11A2.006 Terra Land Surface Temperature
 and Emissivity 8-Day Global 1km product, and required input
 files.
description: Please refer to README_Master file with the information on README
 instructions and explanations for specific files in this
 dataset.
DOI: 10.6084/m9.figshare.31077541
title: Tyrosol effectively improves spermatogenesis recovery by S100A9/TLR4/NF-κB pathway in busulfan-induced oligozoospermia mice

description: <b>Background: </b>Oligozoospermia is a prevalent clinical manifestation of male infertility. It has been provided to be bound up with testicular inflammation and oxidative stress. The phenolic compound 2-(4-hydroxyphenyl) ethanol, chemically designated as tyrosol (Tyr), has been widely distributed in multiple botanical sources, such as olive oil, <i>Rhodiola</i>, and other plants. Given its anti‑inflammatory and antioxidant properties, Tyr shows potential as a pharmacological candidate for oligozoospermia. This research investigated the phenotype and molecular pathways associated with Tyr in mice.<b>Methods:</b> Fifty‑six‑day‑old mice were randomly assigned to six groups: a normal group, a model group, a hydroxytyrosol (HT) group, and three Tyr groups (10 mg/kg, 30 mg/kg, and 50 mg/kg). All groups except the normal group underwent a single does busulfan administration (30 mg/kg) via intraperitoneal injection to induce oligozoospermia. After a two‑week observation period, the HT and Tyr groups were treated orally with their respective medications for four weeks. Blood, testes, epididymides, and sperm samples were then collected for further analysis.<b>Results: </b>Tyr effectively reversed the mice symptom of oligozoospermia, as demonstrated by increased testis weight, improved sperm concentration, and restored testicular histomorphology. In addition, Tyr normalized serum sex hormone levels and testicular oxidative indices. Moreover, it reduced testicular inflammation by decreasing IL‑6 and TNF‑α expression, likely through modulation of the S100A9/TLR4/NF‑κB pathway.<b>Conclusions:</b> Tyr significantly ameliorated oligozoospermia in mice through S100A9/TLR4/NF-κB pathway, suggesting that it may represent a promising therapeutic option for patients with this condition.
DOI: 10.6084/m9.figshare.31077541.v5
title: Tyrosol effectively improves spermatogenesis recovery by S100A9/TLR4/NF-κB pathway in busulfan-induced oligozoospermia mice

description: <b>Background: </b>Oligozoospermia is a prevalent clinical manifestation of male infertility. It has been provided to be bound up with testicular inflammation and oxidative stress. The phenolic compound 2-(4-hydroxyphenyl) ethanol, chemically designated as tyrosol (Tyr), has been widely distributed in multiple botanical sources, such as olive oil, <i>Rhodiola</i>, and other plants. Given its anti‑inflammatory and antioxidant properties, Tyr shows potential as a pharmacological candidate for oligozoospermia. This research investigated the phenotype and molecular pathways associated with Tyr in mice.<b>Methods:</b> Fifty‑six‑day‑old mice were randomly assigned to six groups: a normal group, a model group, a hydroxytyrosol (HT) group, and three Tyr groups (10 mg/kg, 30 mg/kg, and 50 mg/kg). All groups except the normal group underwent a single does busulfan administration (30 mg/kg) via intraperitoneal injection to induce oligozoospermia. After a two‑week observation period, the HT and Tyr groups were treated orally with their respective medications for four weeks. Blood, testes, epididymides, and sperm samples were then collected for further analysis.<b>Results: </b>Tyr effectively reversed the mice symptom of oligozoospermia, as demonstrated by increased testis weight, improved sperm concentration, and restored testicular histomorphology. In addition, Tyr normalized serum sex hormone levels and testicular oxidative indices. Moreover, it reduced testicular inflammation by decreasing IL‑6 and TNF‑α expression, likely through modulation of the S100A9/TLR4/NF‑κB pathway.<b>Conclusions:</b> Tyr significantly ameliorated oligozoospermia in mice through S100A9/TLR4/NF-κB pathway, suggesting that it may represent a promising therapeutic option for patients with this condition.
DOI: 10.6084/m9.figshare.31077541.v6
title: Tyrosol effectively improves spermatogenesis recovery by S100A9/TLR4/NF-κB pathway in busulfan-induced oligozoospermia mice

description: <b>Background: </b>Oligozoospermia is a prevalent clinical manifestation of male infertility. It has been provided to be bound up with testicular inflammation and oxidative stress. The phenolic compound 2-(4-hydroxyphenyl) ethanol, chemically designated as tyrosol (Tyr), has been widely distributed in multiple botanical sources, such as olive oil, <i>Rhodiola</i>, and other plants. Given its anti‑inflammatory and antioxidant properties, Tyr shows potential as a pharmacological candidate for oligozoospermia. This research investigated the phenotype and molecular pathways associated with Tyr in mice.<b>Methods:</b> Fifty‑six‑day‑old mice were randomly assigned to six groups: a normal group, a model group, a hydroxytyrosol (HT) group, and three Tyr groups (10 mg/kg, 30 mg/kg, and 50 mg/kg). All groups except the normal group underwent a single does busulfan administration (30 mg/kg) via intraperitoneal injection to induce oligozoospermia. After a two‑week observation period, the HT and Tyr groups were treated orally with their respective medications for four weeks. Blood, testes, epididymides, and sperm samples were then collected for further analysis.<b>Results: </b>Tyr effectively reversed the mice symptom of oligozoospermia, as demonstrated by increased testis weight, improved sperm concentration, and restored testicular histomorphology. In addition, Tyr normalized serum sex hormone levels and testicular oxidative indices. Moreover, it reduced testicular inflammation by decreasing IL‑6 and TNF‑α expression, likely through modulation of the S100A9/TLR4/NF‑κB pathway.<b>Conclusions:</b> Tyr significantly ameliorated oligozoospermia in mice through S100A9/TLR4/NF-κB pathway, suggesting that it may represent a promising therapeutic option for patients with this condition.
DOI: 10.57707/fmi-b2share.2cfwt-ym267
title: Data and code for the manuscript "Mapping the dependence of BC radiative forcing on emission region and season" by Petri Räisänen et al. (submitted to ACP)

description: This dataset presents results from experiments, in which the dependence of black carbon (BC) radiative forcing on emission location and season has been systematically evaluated with the NorESM1-Happi climate model. Also provided are GrADS scripts and fortran programs employed to generate the results in the manuscript (Räisänen et al. 2022, submitted to ACP) in which these data are used. A related resource (a fortran-based tool for estimating the BC global-mean radiative forcing and associated temperature response based on the region and annual or monthly BC emission rates given by the user) is provided at https://doi.org/10.5281/zenodo.6461647 (Räisänen 2022).

REFERENCE FOR THE MANUSCRIPT:
Räisänen, P., Merikanto, J., Makkonen, R., Savolahti, M., Kirkevåg, A., Sand, M., Seland, Ø., and Partanen, A.-I.: Mapping the dependence of BC
radiative forcing on emission location and season, Atmos. Chem. Phys., submitted, 2022

REFERENCE FOR THE TOOL AVAILABLE AT ZENODO:
Räisänen, Petri: BC radiative forcing and climate response tool, version 1.0.0, Zenodo (code), https://doi.org/10.5281/zenodo.6461647, 2022.
description: NorESM1-Happi (Graff et al., https://doi.org/10.5194/esd-10-569-2019) was run at a horizontal resolution of ca. 1.9 x 2.5 deg (144 x 96 grid points) with 26 levels in the vertical. The model was run for years 2012-2017, and data is provided for 2013-2017. The experiments used prescribed sea surface temperature and sea ice. The model aerosol scheme was run in an offline mode, which means that the meteorological conditions are not influenced by the assumed aerosol emissions. This allowed for an essentially noise-free evaluation of the radiative forcing (RF) associated with changed BC emissions. To investigate how the BC RF depends on emission region and season, a very large number of experiments (960) was made, in which a fixed BC emission rate (1.E-12 kg m-2 s-1) was assumed separately for 192 regions (ca. 11.4 x 30 deg latitude-longitude boxes) and for five seasonal distributions of emissions. Evaluation of the methodology given in the manuscript showed that this approach works reasonably well for the BC direct RF and for the  RF due to BC in snow, but not for the BC indirect effects on clouds. It should also be understood that NorESM1-Happi, like any climate model, is subject to model-specific biases that may influence the derived BC RF.
description: The contents of the data files are described in the file "README_data.txt". The contents of the file containing code "fortran_programs_and_GrADS_scripts.zip" are described in "README_code.txt" as well as in README files included in the zip file.
The terms of use for the data and the code are given in the files "License_data.txt" and "License_code.txt", respectively.
DOI: 10.5061/dryad.s4mw6m98f
title: Data from: Experimental insect suppression causes loss of induced, but not constitutive, resistance in Solanum carolinense

description: Spatiotemporal variation in herbivory is a major driver of intraspecific
 variation in plant defense. Comparatively little is known, however, about
 how changes in herbivory regime affect the balance of constitutive and
 induced resistance, which are often considered alternative defensive
 strategies. Here, we investigated how nearly a decade of insect herbivore
 suppression affected constitutive and induced resistance in horsenettle
 (Solanum carolinense), a widespread herbaceous perennial. We allowed
 replicated horsenettle populations to respond to the presence or absence
 of herbivores by applying insecticide to all plants in half of 16 field
 plots. Horsenettle density rapidly increased in response to insecticide
 treatment, and this effect persisted for at least four years after the
 cessation of herbivore suppression. We subsequently grew half-sibling
 families from seeds collected during and shortly after insecticide
 treatment in a common garden and found strong effects of insect
 suppression on induced resistance. Feeding trials in field mesocosms with
 false Colorado potato beetles (Leptinotarsa juncta), a common specialist
 herbivore, revealed that multi-year herbivore suppression drove rapid
 attenuation of induced resistance: offspring of plants from
 insect-suppression plots exhibited a near-complete loss of induced
 resistance to beetles, while those from control plots incurred ~70% less
 damage after experimental induction. Plants from insect-suppression plots
 also had ~40% greater constitutive resistance than those from control
 plots, although this difference was not statistically significant. We
 nonetheless detected a strong trade-off between constitutive and induced
 resistance across families. In contrast, the constitutive expression of
 trypsin inhibitors (TI), an important chemical defense trait in
 horsenettle, was reduced by 20% in the offspring of plants from
 insect-suppression plots relative to those from control plots. However,
 TIs were induced to an equal extent whether or not insect herbivores had
 been historically suppressed. While several defense and performance traits
 (prickle density, TI concentration, resistance against false Colorado
 potato beetles and flea beetles, biomass, and seed mass) varied markedly
 across families, no traits exhibited significant pairwise correlations.
 Overall, our results indicate that, while the divergent responses of
 multiple defense traits to insect suppression led to comparatively small
 changes in overall constitutive resistance, they significantly reduced
 induced resistance against false Colorado potato beetle.