cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.66t1g1k6h
title: Data from: Individual contribution to niche expansion in amphibians: A test of the niche variation hypothesis

description: The niche variation hypothesis (NVH) suggests that populations released
 from competition are able to expand their realized ecological niche (Van
 valen 1965; Bolnick et al. 2007). This increase in total niche width (TNW)
 can arise by i) increasing heterogeneity among individuals’ niche through
 individual specialization, i.e. inter-individual variation in resource
 use, (IS – Bolnick et al., 2002; 2003) occurring when different
 individuals of a population use a subset of the population’s resource
 pool, or ii) by expanding the niche of all individuals within the
 population (Bolnick et al. 2007). Although several morphological and
 phenotypical studies have confuted the NVH (e.g. Meiri et al. 2005), there
 is generally strong support for this hypothesis when behavioural or
 ecological traits are considered, and in particular when the trophic niche
 is measured at the individual level (Bolnick et al. 2007; Maldonado et
 al., 2017). In this study our primary aim is to corroborate the NVH,
 providing robust evidence for a significant and positive relationship
 between population TNW and IS in amphibian populations, at a global scale.
description: The dataset consists of two files:
   
 <strong>1)</strong>"<em>Data.csv</em>" -
 contains data used to perform the analysis and has 10
 variables:   
 <strong>Species_ID_NCBI_Taxonomy</strong> - ID of the species,
 following NCBI Taxonomy, used to produce phylogenetic tree on
 PhyloT <strong>Species_Name</strong> -
 Abbreviated species names 
 <strong>Family</strong> - Family of each species
 <strong>Order </strong>- Order of each
 family <strong>V</strong> -
 Inter-individual diet variation measure, as retrieved by published
 research or calculated from orgiginal data 
 <strong>TNW </strong>- Total niche width, as retrieved by
 published research or calculated from orgiginal data
 <strong>PopID </strong>- ID of the
 population <strong>Net_Primary_Productivity
 </strong>- Environmental predictor used in the analysis
 <strong>Annu_Days_Foraging_Activity </strong>-
 Environmental predictor used in the analysis 
 <strong>Species_Richness </strong>- Environmental predictor
 used in the analysis   
 <strong>2)</strong>"<em>Phylogenetic_tree.txt</em>" - text file containing the phylogenetic tree as obtained from PhyloT
DOI: 10.5061/dryad.cvdncjt89
title: Data for: Soil organic carbon contents of collected soil samples from China's black soil region

description: The long-term use of cropland and cropland reclamation from natural
 ecosystems led to soil degradation. This study investigated the effect of
 the long-term use of cropland and cropland reclamation from natural
 ecosystems on soil organic carbon (SOC) content and density over the past
 35 years. Altogether, 2140 topsoil samples (0–20 cm) were collected across
 Northeast China. Landsat images were acquired from 1985 to 2020 through
 Google Earth Engine, and the reflectance of each soil sample was extracted
 from the Landsat image that its time was consistent with sampling. The
 hybrid model that included two individual SOC prediction models for two
 clustering regions was built for accurate estimation after k-means
 clustering. The probability hybrid model, a combination between the hybrid
 model and classification probabilities of pixels, was introduced to
 enhance the accuracy of SOC mapping. Cropland reclamation results were
 extracted from the land cover time series dataset at a 5-year interval.
 Our study indicated that: (1) Long-term use of cropland led to a 3.07 g
 kg-1 and 6.71 Mg C ha-1 decrease in SOC content and density, respectively,
 and the decrease of SOC stock was 0.32 Pg over the past 35 years; (2)
 Nearly 64% of cropland had a negative change in terms of SOC content from
 1985 to 2020; (3) Cropland reclamation track changed from high to low SOC
 content, and almost no cropland was reclaimed on the ‘Black soils’ after
 2005; (4) Cropland reclamation from wetlands resulted in the highest
 decrease, and reclamation period of years 31–35 decreased when SOC density
 and SOC stock were 16.05 Mg C ha-1 and 0.005 Pg, respectively, while
 reclamation period of years 26–30 from forest witnessed SOC density and
 stock decreases of 8.33 Mg C ha-1 and 0.01 Pg, respectively. Our research
 results provide a reference for SOC change in the black soil region of
 Northeast China and can attract more attention to the area of the
 protection of ‘Black soils’ and natural ecosystems.
DOI: 10.5061/dryad.jm63xsjgw
title: Data for: Egg mimicry, not the sight of a common cuckoo, is the cue for parasitic egg rejection

description: Many studies have found that if hosts observe a brood parasite at their
 nest, they use it as a cue to reject parasitic eggs. However, most
 previous work has simulated brood parasitic events by exposing a stuffed
 parasite near a host’s nest. Responses to the presence of a real parasite
 have not yet been adequately studied under natural conditions. We
 therefore investigated whether great reed warblers (Acrocephalus
 arundinaceus) are more likely to reject a parasitic egg if they see a
 parasitizing common cuckoo (Cuculus canorus) at their nest than if the
 parasite approaches host nest unnoticed. Using video recordings of 70
 nests we showed that spotting a cuckoo at the nest did not increase
 rejection rate of parasitic eggs, even if hosts saw the cuckoo repeatedly.
 Hosts instead used the level of mimicry in background colour for cuckoo
 egg rejection. Since not every visit by the cuckoo leads to parasitism,
 seeing the brood parasite may not be a reliable enough cue for the host.
 Therefore, our results suggest that the sight of the brood parasite at the
 nest may not be as important as previously thought.
description: We video recorded natural
 common cuckoo (<em>Cuculus canorus</em>) parasitism at great
 reed warbler (<em>Acrocephalus arundinaceus</em>) nests and
 calculated mimicry of cuckoo eggs. Then we used generalised linear mixed
 models (GLMM) to investigate whether seeing the cuckoo female at the nest
 and cuckoo egg mimicry affect host rejection
 behaviour.
description: Microsoft Excel or any other program for opening .csv files and
 RStudio for further analyses.
DOI: 10.5281/zenodo.18382915
title: openff-2.2.0-rc1-alkanes-revert

description: Generated by yammbs-dataset-submission: https://github.com/openforcefield/yammbs-dataset-submission
DOI: 10.5281/zenodo.18382916
title: openff-2.2.0-rc1-alkanes-revert

description: Generated by yammbs-dataset-submission: https://github.com/openforcefield/yammbs-dataset-submission
DOI: 10.6076/d1m59n
title: Fast and accurate distance‐based phylogenetic placement using divide and conquer

description: Phylogenetic placement of query samples on an existing phylogeny is
 increasingly used in molecular ecology, including sample identification
 and microbiome environmental sampling. As the size of available reference
 trees used in these analyses continues to grow, there is a growing need
 for methods that place sequences on ultra-large trees with high accuracy.
 Distance-based placement methods have recently emerged as a path to
 provide such scalability while allowing flexibility to analyse both
 assembled and unassembled environmental samples. In this study, we
 introduce a distance-based phylogenetic placement method, APPLES-2, that
 is more accurate and scalable than existing distance-based methods and
 even some of the leading maximum-likelihood methods. This scalability is
 owed to a divide-and-conquer technique that limits distance calculation
 and phylogenetic placement to parts of the tree most relevant to each
 query. The increased scalability and accuracy enable us to study the
 effectiveness of APPLES-2 for placing microbial genomes on a data set of
 10,575 microbial species using subsets of 381 marker genes. APPLES-2 has
 very high accuracy in this setting, placing 97% of query genomes within
 three branches of the optimal position in the species tree using 50 marker
 genes. Our proof-of-concept results show that APPLES-2 can quickly place
 metagenomic scaffolds on ultra-large backbone trees with high accuracy as
 long as a scaffold includes tens of marker genes. These results pave the
 path for a more scalable and widespread use of distance-based placement in
 various areas of molecular ecology.
description: See README file for details. We include both simulated datasets
 and real datasets modeifed from the WoL resources. 
description: See the README file for links to tools, referenced here: https://github.com/balabanmetin/apples2-data
DOI: 10.5061/dryad.1ns1rn900
title: Data for: Sub-zero temperatures and large-scale weather patterns induce tooth damage in Icelandic arctic foxes

description: Tooth damage in carnivores can reflect shifts in both diet and feeding
 habits, and in large carnivores it is associated with increased bone
 consumption. Variation in tooth condition in Icelandic arctic foxes, a
 mesocarnivore, was recorded from 854 individual foxes spanning 29 years.
 We hypothesized that annual climatic variations, which can influence food
 abundance and accessibility, will influence tooth condition by causing
 dietary shifts toward less edible prey. We examined tooth condition in
 relation to four climatic predictors: mean annual winter temperature,
 indices of both the El Niño anomaly and North Atlantic subpolar gyre
 (SPG), and the number of rain-on-snow days (ROS). We found unequivocal
 evidence for a strong effect of annual climate on tooth condition. Teeth
 of Icelandic foxes were in better condition when winter temperatures were
 higher, when the SPG was more positive, and when the number of ROS was
 low. We also found a substantial subregional effect with foxes from
 northeastern Iceland having lower tooth damage than those from two western
 sites. Contradicting our original hypothesis that foxes from northeastern
 Iceland, where foxes are known to scavenge on large mammal remains (e.g.,
 sheep and horses), would show the highest tooth damage, we suggest that
 western coastal sites exhibited greater tooth damage because cold winter
 temperatures lowered the availability of seabirds, causing a shift in diet
 toward abrasive marine subsidies (e.g., bivalves) and frozen beach wrack.
 Our study shows that monitoring tooth breakage and wear can be a useful
 tool for evaluating the impact of climate on carnivore populations and
 that climate change may influence the condition and fitness of carnivores
 in complex and potentially conflicting ways.
description: We used the extensive
 collection of arctic fox lower mandibles, collected initially by the late
 Pall Hersteinsson, and now stored in the Icelandic Institute of Natural
 History. We recorded
 missing teeth from both the left and right mandibles (dentary bones) of
 each individual. The canine teeth were missing from all mandibles because
 they were extracted for age determination. Often, some of the incisors,
 the first premolar (PM1), and/or the third molar (M3) were also missing.
 Therefore, we focused on teeth that were most often present (PM2-PM4 and
 M1-M2), ten teeth in total. We examined every tooth for breakage and
 cracks, and calculated the fraction of damaged teeth in each specimen
 (i.e., out of ten teeth). We also scored the level of wear in the focal
 ten teeth using a five-stage wear score that ranged from minimal wear
 (stage 1) to heavy wear (stage 5).
DOI: 10.5061/dryad.dz08kps2t
title: Tn-seq wig files for wild-type and ΔrecG library replicates

description: Maintaining the integrity of the genome is of utmost importance for cell
 division and propagation. In Escherichia coli, the RecG protein has been
 implicated in processing branched recombination intermediates during DNA
 repair processes, but the primary cellular role(s) of RecG and the repair
 pathways in which it acts have been difficult to define. To gain
 additional insight into RecG function, we employed transposon sequencing
 (Tn-seq) to identify recG genetic interactions and reveal complementary or
 redundant functions. The strongest hits from the screen were the dam,
 uvrD, rnhA, radA, and rep genes. The conditional importance of these five
 genes in cells lacking recG was confirmed using a plasmid-based assay,
 revealing synthetic lethal interactions for most double deletion strains.
 Several of the synthetic lethal gene combinations (with uvrD, rep, and
 radA; but not rnhA or dam) were suppressed by deletion of recF or recO,
 indicating that their genetic relationships involved roles in
 post-replication gap repair. Additionally, loss of the RecG/SSB
 interaction phenocopied a recG deletion when combined with dam, uvrD,
 radA, or rnhA deletions but not with rep. The results reinforce the idea
 of RecG as a general genome guardian. Its varied genetic interactions
 reflect critical roles in several different repair contexts, where RecG
 alleviates toxic DNA intermediates.
description: Can use MochiView of IGV to view gene insertion profiles.
description: # Tn-seq data wig files for wild-type and *recG E. coli* K12 MG1655
 library replicate samples --- Tn-seq libraries were created in triplicate
 for wild-type MG1655 *E. coli* and *E. coli* lacking the *recG* gene.
 Libraries were sequenced using Illumina NGS technology and raw sequencing
 data was analyzed to map transposon insertions to genes in each library
 replicate. ## Description of the data and file structure These files
 provide the number of insertion sequencing reads present at each
 chromosomal location from each dataset. The files can be viewed as
 transposon insertion profiles for genes or intergenic regions in programs
 such as MochiView and IGV. ## Sharing/Access information The data shared
 here is part of a manuscript that has been submitted to the Journal of
 Bacteriology. Raw sequencing data can be found here:
DOI: 10.15468/dl.e4xgzp
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sida rhombifolia",
 "Country is Samoa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 16 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025694-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/2hcgwn
title: Replication Data for: Following Through on an Intention to Vote: Present Bias and Turnout

description: Many citizens express an intention to vote but then fail to follow through on their motivation. It is well known that impulsiveness contributes to unsound behaviors with adverse individual consequences like smoking, overeating, and undersaving. I apply these findings and theory to political participation and argue that present bias is also likely to limit collective behaviors. Those who desire to act are challenged by impulsiveness in following through on their motivation. In a nationally-representative survey merged to administrative records, those with present bias are around 10 points less likely to vote. Importantly, those with present bias are less likely to vote even after expressing pre-election intention to do so. Along with a formal decision-theoretic model of turnout with present bias, the results provide a new framework to reason about the choice to vote, an alternative interpretation of the over-report of turnout, and have implications for policy approaches to promote individual action in the public interest.
DOI: 10.7910/dvn/bnioh3
title: A10_18320.jpg

description: Link to OCHRE database: &lt;a href = 'http://pi.lib.uchicago.edu/1001/org/ochre/92aa9126-ffa2-4cd0-b35e-649c3218f4bb'&gt;http://pi.lib.uchicago.edu/1001/org/ochre/92aa9126-ffa2-4cd0-b35e-649c3218f4bb
DOI: 10.7910/dvn/qbuc7p
title: A17_33719.jpg

description: Link to OCHRE database: &lt;a href = 'http://pi.lib.uchicago.edu/1001/org/ochre/cc20cbd5-0aba-486d-b230-0c51916ed1c7'&gt;http://pi.lib.uchicago.edu/1001/org/ochre/cc20cbd5-0aba-486d-b230-0c51916ed1c7
DOI: 10.7910/dvn/w0k9bf
title: Replication Data for: Fish farmers’ perceptions, impacts and adaptation on/of/to climate change in Africa (The case of Egypt and Nigeria)

description: Perception is the bed rock to really apprehend the assertiveness and interpretations of the farmers which are the grass root receptors or benefactors of the effects of climate change. Individual perception and knowledge on climate change varies according to geographical location, occupation, political and socio-economics, ecological, cultural background of the entity. Empirical observations and climate models both indicate that global climate and ocean conditions have been changing over the last 100 years and will likely change more rapidly in the future. Fish production and supply in Africa could not meet up with the demand of the consumers as a result of financial constraints, low capital investment, high cost of fish stocking and feeding, dry season, pollution and climate change. This research therefore, assesses the fish farmers’ perceptions, impacts and adaptation on/of/to climate change in Africa, using Egypt and Nigeria as archetypal examples. It also annotates the precautionary measures taken by the fish farmers to ameliorate the negative impacts of climate change in the continent. KoboCollect method was used to design relevant questions and analyzed the fish farmers’ responses. The results revealed that climate change has both positive and negative impacts on African aquaculture and it is believe that aquaculture is a way of adapting to the adverse effect of climate change on fisheries. 93% of the fish farmers in Africa have the ideal of climate change, 64% believe that the change will linger and persevere in the next 10–20 years. In Nigeria, 61% of the respondents relied on stream and river while in Egypt, 99% of the fish farmers cultured their fish on earthen ponds and depend on the use of agricultural drainage water. Fish production could not meet up with the demand of the consumers in Nigeria as a result of pending constraints unlike Egypt which has achieved the scale of aquaculture expansion compare to other African countries. It is therefore, expedient that efforts should be geared towards regional and continental integration in order to encourage aquaculture practices in other part of Africa and climate change investment should be encouraged.
DOI: 10.7910/dvn/x09j1m
title: A98_9677.jpg

description: Link to OCHRE database: &lt;a href = 'http://pi.lib.uchicago.edu/1001/org/ochre/237a79e6-cadf-c952-a128-f8bc723803e9'&gt;http://pi.lib.uchicago.edu/1001/org/ochre/237a79e6-cadf-c952-a128-f8bc723803e9
DOI: 10.15468/dl.dgjz8s
title: Occurrence Download

description: A dataset containing 43177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphipoda",
 "HasCoordinate is true",
 "Depth is greater than 3000m"
 ]
}

 The dataset includes 43177 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017603-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/meerd1
title: A10_18094.JPG

description: Link to OCHRE database: &lt;a href = 'http://pi.lib.uchicago.edu/1001/org/ochre/acc03eb6-dd04-47ae-b8dd-7d20a38613d6'&gt;http://pi.lib.uchicago.edu/1001/org/ochre/acc03eb6-dd04-47ae-b8dd-7d20a38613d6
DOI: 10.7910/dvn/bjybvf
title: Measurement of Southeast Asian Countries' Capabilities and Capacity for Harnessing the Ocean Economy: A Dataset Development for ASEAN's Blue Economic Posture

description: In the new global economy, Blue Economy has become a central issue, including for Southeast Asian Countries regarding its potentials as key drivers of economic growth and innovation. ASEAN member countries has declared to commit on taking the lead on the regional cooperation in relation to the Blue Economy through ASEAN Leaders’ Declaration on the Blue Economy, last 26 October 2021, in Brunei Darussalam. Besides the economic opportunities, Blue Economy has responsibilities to carry out due to the need to ensure ocean sustainability and rules-based ocean governance. Previous studies on the topic in general, have reported some issues such as (1) Blue Economy complexity and diversity on stakeholders’ and policymakers’ perspectives and perceptions, (2) contested narratives between the economic growth and development vis-à-vis ocean resources environmental protection, and (3) the urge to strengthen regional centrality and unity in term of commitments on achieving the goals. This study aims to identify ASEAN member countries capacities and capabilities regarding the Blue Economy implementations. We developed ASEAN Blue Economy Dataset using numbers of official and reputable macro-economic and political-security data which are related to established and emerging sectors of Blue Economy. By using the data and indices generated from the dataset, we measured ASEAN ‘Blue Economic Posture’ to quantify and portray ASEAN’s trajectory to actualize sustainable ocean economy in term of capacity building and potential cooperation initiatives.
DOI: 10.7910/dvn/ce4zng
title: Writings of the 19c missionaries in China

description: 1033 records of writings of the 19c missionaries in China. Source: Memorials of Protestant missionaries to the Chinese
DOI: 10.7910/dvn/grvr99
title: Replication Data for: Retaining Political Talent: A Candidate-Centered Theory of Primary Adoption

description: Why do party leaders constrain their own power and allow the use of primary elections? I develop a model of intraparty politics and electoral competition in which an ambitious officeseeker reevaluates her party affiliation after her party chooses a nomination rule. The model shows that, in settings in which the linkages between politicians and parties are weak, party leaders adopt primaries in order to keep potential defectors from pursuing their individual ambitions outside of the party. The main theoretical result shows that only parties that are electorally strong ex ante can use primaries as a strategy to hold their parties together. Thus, in contrast to an extensive literature that links the use of primaries to electorally weak parties, this model posits the existence of a positive relationship between the use of primaries and a party’s electoral strength. Analysis of legislative and gubernatorial nominations in Mexico provides strong support for the model’s expectations.
description: This dataset underwent an independent verification process that replicated the tables and figures in the primary article. For the supplementary materials, verification was performed solely for the successful execution of code. The verification process was carried out by the Odum Institute for Research in Social Science at the University of North Carolina at Chapel Hill. 
<br>
The associated article has been awarded Open Materials and Open Data Badges. Learn more about the Open Practice Badges from the Center for Open Science.<br>