cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57707/fmi-b2share.e39g1-g5k58
title: Fluxes and plant diversity data in urban grasslands

description: Files that were used in Justine et al.'s manuscript (2023), entitled 'Lawns and meadows in urban green space - A comparison from perspectives of greenhouse gas, drought resilience and plant functional types'. CO2, CH4 and N2O fluxes, C/N content in soil and plant diversity were measured in urban grasslands around Helsinki Metropolitan Area. At four of the study sites including a mesic meadow, a dry meadow, an irrigated lawn and a non-irrigated lawn, total ecosystem respiration, GPP, green cover and plant diversity were intensively recorded (about every two weeks from May-November) from 2021-2022. Twelve other sites (6 control lawns and 6 meadows) belonging to the Lawns into Meadows experiment were studied from 2020-2022, they also provide crucial data (respiration, CH4 and N2O and plant functional type proportions) about conversion from a lawn into a meadow. 
Compared to the previous dataset, some changes were made:
 - 00_READ_ME: descriptions were improved and figures/tables updated 
 - 01_COCARBON_Flux_data: gas slope and NMRSE were added
 - 02_LIM_Flux_data: gas slope and NMRSE were added
 - ex-07_LIM_Plants&flux: discarded because of redundancy (in addition, one tree proportion value was missing)
 - 08_Soil_CN_data: added to the folder
 - 09_various_soil_characteristics: added to the folder
DOI: 10.57707/fmi-b2share.r60ga-s1j34
title: Fluxes and plant diversity data in urban grasslands

description: Files that were used in Justine et al.'s manuscript (2023), entitled 'Lawns and meadows in urban green space - A comparison from perspectives of greenhouse gas, drought resilience and plant functional types'. CO2, CH4 and N2O fluxes, C/N content in soil and plant diversity were measured in urban grasslands around Helsinki Metropolitan Area. At four of the study sites including a mesic meadow, a dry meadow, an irrigated lawn and a non-irrigated lawn, total ecosystem respiration, GPP, green cover and plant diversity were intensively recorded (about every two weeks from May-November) from 2021-2022. Twelve other sites (6 control lawns and 6 meadows) belonging to the Lawns into Meadows experiment were studied from 2020-2022, they also provide crucial data (respiration, CH4 and N2O and plant functional type proportions) about conversion from a lawn into a meadow. 
Compared to the previous dataset, some changes were made:
 - 00_READ_ME: descriptions were improved and figures/tables updated 
 - 01_COCARBON_Flux_data: gas slope and NMRSE were added
 - 02_LIM_Flux_data: gas slope and NMRSE were added
 - ex-07_LIM_Plants&flux: discarded because of redundancy (in addition, one tree proportion value was missing)
 - 08_Soil_CN_data: added to the folder
 - 09_various_soil_characteristics: added to the folder
DOI: 10.25338/b83s70
title: Automated protein-protein structure prediction of the T cell receptor-peptide major histocompatibility complex

description: The T Cell Receptor (TCR) recognition of a peptide-major
 histocompatibility complex (pMHC) is a crucial component of the adaptive
 immune response. The identification of TCR-pMHC pairs is a significant
 bottleneck in the implementation of TCR immunotherapies and may be
 augmented by computational methodologies that accelerate the rate of TCR
 discovery.  The ability to computationally design TCRs to a
 target pMHC will require an automated integration of next-generation
 sequencing, homology modeling, molecular dynamics (MD), and TCR ranking.
 We present a generic pipeline to evaluate patient-specific, sequence-based
 TCRs to a target pMHC. The most expressed TCRs from 16 colorectal cancer
 patients are homology modeled to target the CEA peptide using Modeller and
 ColabFold. Then, these TCR-pMHC structures are compared by performing an
 automated molecular dynamics equilibration. We find that Colabfold
 generates starting configurations that require, on average, an ~2.5X
 reduction in simulation time to equilibrate TCR-pMHC structures compared
 to Modeller. In addition, there are differences between equilibrated
 structures generated by Modeller and ColabFold.  Moreover, we
 identify TCR ranking criteria that may be used to prioritize TCRs for
 evaluation of in vitro immunogenicity.
description: The ".gro" files are molecular structure formatted
 files and can be viewed with any standard molecular viewing software
 (e.g., Pymol, VMD, Chimera, etc.). Information on the ".gro"
 file format can be found at the following link: https://manual.gromacs.org/archive/5.0.3/online/gro.html#:~:text=Files%20with%20the%20gro%20file,as%20in%20the%20sample%20below.
DOI: 10.13144/lil-0358
title: Budget des familles (BDF) - 1974

description: L'enquête "Budget de famille" réalisée par l'Insee en 1974 a pour objectif central l'étude des dépenses (montant et nature) et des ressources des ménages.Toutes les dépenses (alimentation, habillement, transports, vacances, épargne, logement) sont enregistrées. Cependant en raison de contraintes budgétaires, l'enquête "Budget de famille" est regroupée à l'enquête "Alimentaire", mais l'essai n'est pas concluant et seuls les résultats de la partie alimentaire sont fiables.
DOI: 10.5061/dryad.95x69p8nj
title: Optimization data for determination of varenicline through its reaction with erythrosine

description: Varenicline is used along with education and counseling to help people
 stop smoking. Erythrosine B, the food additive has been recently
 investigated as a fluorescent dye for the determination of drugs. Herein,
 two new facile methods were examined for varenicline, the smoking
 cessation aid using this fluorochrome. In the first method; the
 fluorescence of erythrosine B was quenched by increasing concentrations of
 varenicline through ion-pair complex formation. This linear response was a
 basis for the spectrofluorimetric method for varenicline quantitation in
 pure and dosage forms. The quenching is correlated with the concentration
 linearly over the range of 0.4-4.0 μg/mL at 550 nm after excitation at 528
 nm with a correlation coefficient of 0.9993. Different parameters were
 investigated to reach the optimal conditions with highest sensitivity and
 repeatability. The second method is depending on measuring the formed
 complex spectrophotometrically at 550 nm over the range of 1.0-10.0 μg/mL
 with excellent correlation coefficient of 0.9999. This ion-pair complex
 was measured at pH=4 using Britton Robinson buffer. The suggested methods
 were validated in consistent with ICH guidelines, with acceptable results.
 The procedures were utilized to test the uniformity of content of Champix
 tablets. By comparing to previous spectroscopic method; there was no
 significant difference as revealed from the calculated student t-test and
 variance ratio F test values.
DOI: 10.5281/zenodo.18399837
title: OnlineResource1_LiveStreamingCommerceSurveyData.xlsx

description: This repository contains the anonymized dataset generated by a survey and analyzed in the study entitled “Impulse Buying as a Socio-Technical Source of Symbolic Meaning in Live-Streaming Commerce”. The data were collected from active live-streaming commerce users in Indonesia and used to examine socio-technical mechanisms underlying impulse buying behavior. The dataset includes all variables used in the empirical analysis and is provided for transparency and replication purposes. No personally identifiable information is included.
DOI: 10.5061/dryad.d7wm37q3v
title: Data from: A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks

description: Ticks are the most important vectors of zoonotic disease-causing pathogens
 in North America and Europe. Many tick species are expanding their
 geographic range. Although correlational evidence suggests that climate
 change is driving the range expansion of ticks, experimental evidence is
 necessary to develop a mechanistic understanding of ticks’ response to a
 range of climatic conditions. Previous experiments used simulated
 microclimates, but these protocols require hazardous salts or expensive
 laboratory equipment to manipulate humidity. We developed a novel, safe,
 stable, convenient, and economical method to isolate individual ticks and
 manipulate their microclimates. The protocol involves placing individual
 ticks in plastic tubes, and placing six tubes along with a commercial
 two-way humidity control pack in an airtight container. We successfully
 used this method to investigate how humidity affects survival and
 host-seeking (questing) behavior of three tick species: the lone star tick
 (Amblyomma americanum), American dog tick (Dermacentor variabilis), and
 black-legged tick (Ixodes scapularis). We placed 72 adult females of each
 species individually into plastic tubes and separated them into three
 experimental relative humidity (RH) treatments representing distinct
 climates: 32% RH, 58% RH, and 84% RH. We assessed the survival and
 questing behavior of each tick for 30 days. In all three species,
 survivorship significantly declined in drier conditions. Questing height
 was negatively associated with RH in Amblyomma, positively associated with
 RH in Dermacentor, and not associated with RH in Ixodes. The frequency of
 questing behavior increased significantly with drier conditions for
 Dermacentor but not for Amblyomma or Ixodes. This report demonstrates an
 effective method for assessing the viability and host-seeking behavior of
 tick vectors of zoonotic diseases under different climatic conditions.
DOI: 10.5281/zenodo.18399838
title: OnlineResource1_LiveStreamingCommerceSurveyData.xlsx

description: This repository contains the anonymized dataset generated by a survey and analyzed in the study entitled “Impulse Buying as a Socio-Technical Source of Symbolic Meaning in Live-Streaming Commerce”. The data were collected from active live-streaming commerce users in Indonesia and used to examine socio-technical mechanisms underlying impulse buying behavior. The dataset includes all variables used in the empirical analysis and is provided for transparency and replication purposes. No personally identifiable information is included.
DOI: 10.25338/b8006r
title: Influence of crop field size on pest densities, pesticide use, and crop yield

description: Increasing diversity on farms can enhance many key ecosystem services to
 and from agriculture, and natural control of arthropod pests is often
 presumed to be among them.  The expectation that increasing the
 size of monocultural crop plantings exacerbates the impact of pests is
 common throughout the agroecological literature.  Here, we share
 five data sets, describing 14 pest species, 5 crops (cotton in California,
 citrus in California, potatoes in Peru, grapes in Spain, and olives in
 Spain), and 20,000 field-years of observations, that allow us to quantify
 the impact of field size on pest densities, pesticide applications, and
 crop yield. 
description: Data were collected by farmers, farm staff, or private pest
 control advisors in commercial agriculture (subsistence agriculture for
 Peru only).  Detailed methods on sampling are described in the companion
 paper ("Testing a tenet of agroecology: do larger field sizes
 exacerbate insect pest problems?").
description: Metadata are included with each data file, explaining the meaning
 of all variables.
DOI: 10.5061/dryad.f4qrfj6zf
title: A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)

description: Whole genome duplication events are notably widespread in plants and this
 poses particular challenges for phylogenetic inference in allopolyploid
 lineages, i.e. lineages that result from the merging of two or more
 diverged genomes after interspecific hybridization. The nuclear genomes
 resulting from allopolyploidization contain homologous gene copies from
 different evolutionary origins called homoeologs, whose orthologs must be
 sorted out in order to reconstruct the evolutionary history of polyploid
 clades. In this study, we propose a methodological approach to resolve the
 phylogeny of allopolyploid clades focusing on mesopolyploid genomes, which
 experienced some level of genome reshuffling and gene fractionation across
 their subgenomes. To illustrate our methodological framework, we applied
 it to a clade belonging to the model Brassicaceae plant family, the
 Brassiceae tribe, that experienced a mesohexaploidy event. The dataset
 analysed consists of both publically available genomic sequences and new
 transcriptomic data according to taxa. The present methodology requires a
 well-annotated reference genome, for which the identification of the
 parental subgenome fragments has been performed (e.g. Brassica rapa and
 Brassica oleracea). Focusing on fully retained genes (i.e., genes for
 which all homoeologous gene copies inherited from the parental lineages
 are still present in the reference genome), the method constructs
 multilabelled gene trees that allow subsequent assignment of each gene
 copy to its diploid parental lineage. Once the orthologous copies are
 identified, genes from the same parental origin are concatenated and
 tree-building methods are used to reconstruct the species tree. This
 method allows resolving the phylogenetic relationships (i) among extant
 species within a mesopolyploid clade, (ii) among the parental lineages of
 a mesopolyploid lineage, and (iii) between the parental lineages and
 closely related extant species. We report here the first well-resolved
 nuclear-based phylogeny of the Brassiceae tribe.
DOI: 10.5061/dryad.k98sf7m83
title: A genetically isolated dingo population in western Victoria, Australia, reveals greater structuring of the Australian dingo

description: The Australian dingo is a relatively recent anthropogenic addition to the
 Australian fauna, which spread rapidly across the continent and has since
 widely interbred with modern dogs. Genetic studies of dingoes have given
 rise to speculation about their entry to the continent and subsequent
 biogeographic effects, but few studies of their contemporary population
 structure have been conducted. Here we investigated the dingo ancestry and
 population structure of free-living dogs in western Victoria and
 contrasted it with a wider southern Australian sample. We wished to
 determine whether their geographic isolation was mirrored in genetic
 isolation. To address this question, we analysed genetic data using
 Bayesian clustering and discriminant analysis of principal components, and
 summarised genetic diversity at the population and individual levels. Upon
 finding low genetic diversity in western Victoria, we tested for a recent
 genetic bottleneck. The broader southern Australia sample (n=1,138)
 comprised mostly hybrid animals, with ~30% dingoes. All western Victorian
 individuals (n= 59) appeared to be hybrids with high dingo ancestry. The
 population showed no evidence of admixture with other populations and no
 recent bottleneck. Based upon our characterisation of this unusual
 mainland population, we sound caution for future studies assuming
 homogeneity of dingoes across the continent.
description: Tissue specimens were
 collected opportunistically from deceased dogs by individuals involved in
 wildlife management and research in Victoria, New South Wales, and South
 Australia and submitted to ongoing research projects by PJSF and DS from
 2007 to the present. Dog ear tissue specimens were stored in ~3 mL
 Longmire buffer until DNA extraction. Extractions were performed using
 Qiagen DNeasy blood and tissue kit (Qiagen Inc. CA, USA) with the
 recommended protocol. Extracts were amplified at 34 microsatellite markers
 in seven multiplexed PCRs.
DOI: 10.5061/dryad.44j0zpcgz
title: Comparative physiology of canopy tree leaves in evergreen and deciduous forests in lowland Thailand

description: The major forest types in lowland Thailand and its adjacent parts in
 Southeast Asia with the distinct dry season are the mixed deciduous forest
 (MDF), dry dipterocarp forest (DDF) and dry evergreen forest (DEF). We
 report the first comprehensive data set in leaf physiology of canopy trees
 in these three forest types and clarify adaptive functional differences of
 woody plants among three forests. Unlike temperate forests, the forest
 variations in leaf mass per area (LMA) were related to nutrient use
 strategies (less vs. more conservative) associated with soil nutrients
 rather than with leaf phenology (evergreen vs. deciduous). In the
 interspecific variations within each forest, Amax in MDF and DEF was
 limited by foliar phosphate, whereas that in DDF was limited by foliar
 nitrogen. The close association between leaf physiology and soil
 properties suggests that climate change and increasing human impacts will
 disrupt this association, leading to forest degradation and dysfunction.
description: In this study, we obtained the
 ecophysiological characteristics of top canopy leaves in almost all canopy
 tree species
 in three different forest
 types: including (1) mixed deciduous forest (MDF), (2) dry dipterocarp
 (deciduous) forest (DDF), and (3) dry evergreen forest (DEF), in Thailand.
 Here
 we obtained 21
 physiological traits in the top/sunlit leaves of canopy trees in 107, 65
 and 51 tree species in MDF, DEF and DDF, respectively. In this inventory, approximately 70%, 95% and
 95% of canopy tree species which consist of MDF, DEF and DDF were covered,
 respectively.
DOI: 10.5061/dryad.w0vt4b8v2
title: Population structure and genetic variance among local populations of an non-native earthworm species in Minnesota, USA

description: A variety of human activities have been identified as driving factors for
 the release and spread of invasive earthworm species in North America.
 Population genetic markers can help to identify locally relevant
 anthropogenic vectors and provide insights into the processes of
 population dispersal and establishment. We sampled the invasive European
 earthworm species Lumbricus terrestris at nine sites and several bait
 shops within the metropolitan area of Minneapolis-St. Paul in Minnesota,
 USA. We used microsatellite markers to infer genetic diversity and
 population structure, and 16S rDNA to address multiple introduction
 events, including bait dumping, which is a common source of L. terrestris
 introductions into the wild. Our results indicate multiple introductions
 but not from current bait dumping. Overall, genetic structure was low and
 earthworms &gt;5000 m apart were genetically differentiated, except
 for one sampling location, indicating jump-dispersal followed by
 population establishment. Further, earthworms at one location north of
 Minneapolis established from one or few founder individuals, suggesting
 that earthworm invasions are ongoing. We therefore encourage further
 monitoring of earthworm populations using molecular markers, in order to
 disentangle the different human-related vectors contributing to the spread
 of earthworms and their establishment, which is essential to develop
 adequate management strategies.
DOI: 10.5061/dryad.vt4b8gtvb
title: A 130-year global inventory of methane emissions from livestock: trends, patterns, and drivers

description: Livestock contributes approximately one-third of global anthropogenic
 methane (CH4) emissions. Quantifying the spatial and temporal variations
 of these emissions is crucial for climate change mitigation. Although
 country-level information is reported regularly through national
 inventories and global databases, spatially-explicit quantification of
 century-long dynamics of CH4 emissions from livestock has been poorly
 investigated. Using the Tier 2 method adopted from the 2019 Refinement to
 2006 IPCC guidelines, we estimated CH4 emissions from global livestock at
 a spatial resolution of 0.083° (~ 9 km at the equator) during the period
 1890−2019. We find that global CH4 emissions from livestock increased from
 31.8 [26.5−37.1] (mean [minimum−maximum of 95% confidence interval) Tg CH4
 yr-1 in 1890 to 131.7 [109.6−153.7] Tg CH4 yr-1 in 2019, a fourfold
 increase in the past 130 years. The growth in global CH4 emissions mostly
 occurred after 1950 and was mainly attributed to the cattle sector. Our
 estimate shows faster growth in livestock CH4 emissions as compared to the
 previous Tier 1 estimates and is ~20% higher than the estimate from
 FAOSTAT for the year 2019. Regionally, South Asia, Brazil, North Africa,
 China, the United States, Western Europe, and Equatorial Africa shared the
 majority of the global emissions in the 2010s. South Asia, tropical
 Africa, and Brazil have dominated the growth in global CH4 emissions from
 livestock in the recent three decades. Changes in livestock CH4 emissions
 were primarily associated with changes in population and national income
 and were also affected by the policy, diet shifts, livestock productivity
 improvement, and international trade. The new geospatial information on
 the magnitude and trends of livestock CH4 emissions identifies emission
 hotspots and spatial-temporal patterns, which will help to guide
 meaningful CH4 mitigation practices in the livestock sector at both local
 and global scales.
DOI: 10.5061/dryad.2rbnzs7qs
title: Data from: Neurotransmitter content heterogeneity within an interneuron class shapes inhibitory transmission at a central synapse

description: Neurotransmitter content is deemed the most basic defining criterion for
 neuronal classes, contrasting with the intercellular heterogeneity of many
 other molecular and functional features. Here we show, in the adult mouse
 brain, that neurotransmitter content variegation within a neuronal class
 is a component of its functional heterogeneity. Most Golgi cells (GoCs),
 the well-defined class of cerebellar interneurons inhibiting granule cells
 (GrCs), contain cytosolic glycine, accumulated by the neuronal transporter
 GlyT2, and GABA in various proportions. To assess the functional
 consequence of this neurotransmitter variation, we paired GrCs recordings
 with optogenetic stimulations of single GoCs, which preserve the
 intracellular transmitter mixture. We show that the strength and decay
 kinetics of GrCs IPSCs, which are entirely mediated by GABAA receptors are
 negatively correlated to the presynaptic expression of GlyT2 by GoCs. We
 isolate a slow spillover component of GrCs inhibition that is also
 affected by the expression of GlyT2, leading to a 56 % decrease in
 relative charge. Acute manipulations of cytosolic GABA and glycine supply
 recapitulate the modulation of IPSC charge, supporting the hypothesis that
 presynaptic loading of glycine negatively impact the GABAergic
 transmission in mixed interneurons through a competition for vesicular
 filling. Our results suggest that heterogeneity of neurotransmitter supply
 within the GoC class may provide a presynaptic mechanism to tune the gain
 of the stereotypic granular layer microcircuit, thereby expanding the
 realm of possible dynamic behavior.
description: The dataset is composed of electrophysiological recording
 acquired at 20 kHz of cerebellar granule cells during optogenetic
 stimulation of targeted presynaptic Golgi cell (inhibitory interneuron) or
 electrically stimulated Golgi cells axons at 10 Hz in continue.Both types
 of recordings correspond to the optogenetic (Figure 1 - 4) and
 pharmacological (Figure 5) experiment presented in our research article.
 Data has been processed with Python 2.7. Analysis details are mentioned in
 the materials and methods section of the article. 
description: Average traces are in text format (*.txt).
 Variables quantify from traces are available in *.txt  by group
 (GlyT2(-) or GlyT2(+)) corresponding to the neurochemical subpopulation of
 Golgi cell. Variables for each cell are available in
 *.npy, a numpy document that can be load, read and modify using Python as
 follow : &gt;import numpy as np
 &gt;data = np.load('PATH') or
 np.loadtxt('PATH')