cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b2rbnzsff
title: Data from: Native shade trees aid bird conservation in tea plantations in southern India

description: In the Western Ghats, India, we study how different intensities of tea
 cultivation influence birds. We compared bird communities in conventional
 monoculture tea and mixed-shade tea plantations, both of which use
 agrochemicals, with organic tea plantations, a rainforest fragment, and
 continuous rainforest within the Anamalai Tiger Reserve. In 225 point
 count surveys, overall bird species richness and abundance were lowest in
 conventional tea and up to 33% higher in organic tea. Mixed-shade tea had
 40% higher species richness (including 15 canopy and 4 shrub and
 mid-storey species – primarily frugivores, nectarivores and insectivores),
 and 83% higher bird abundance than conventional tea, with a greater
 proportion of forest-affiliated birds and similarity in species
 composition with forest sites. The rainforest fragment and continuous
 rainforest had a higher proportion, richness and abundance of
 forest-affiliated birds and fewer open-country birds, unlike tea
 plantations where the pattern was reversed. Habitat associations of 62
 bird species in indicator species analysis revealed similar patterns. Thus
 organic tea is better than conventional tea for birds, but mixed-shade tea
 is even better, although still poorer than forests. Retaining or promoting
 native shade trees in tea plantations will increase bird diversity and
 abundance, including of forest-affiliated species and support
 landscape-level bird conservation.
description: Details are available in the paper: Raman, T.
 R. S., Gonsalves, C., Jeganathan, P. and Mudappa, D.  (2021) Native shade
 trees aid bird conservation in tea plantations in southern India.
 <em>Current Science</em> 121(2): 294-305. doi:
 10.18520/cs/v121/i2/294-305. Supplementary Table 1
 (Table S1, URL:
 https://www.currentscience.ac.in/Volumes/121/02/0294-suppl.pdf) is also
 made available here. Dataset:<br> The dataset
 includes 3 data files in comma-delimited format (CSV) and 2 text files of
 R code (analysis code in R statistical and programming environment:
 http://r-project.org). Details of the content of each
 of the following CSV data files are provided in the Readme.txt file
 included with the dataset:<br> 1) teabirds.csv (bird
 dataset)<br> 2) sphabt.csv (bird species list with habit and habitat
 categorisation)<br> 3) dat_with_guilds.csv (bird dataset with
 dietary guild categorisation)<br> 4) teabirdsanalysis.Rmd (bird data
 analysis R code)<br> 5) guildanalysis.R (guild data analysis R
 code)
DOI: 10.5061/dryad.59zw3r276
title: Data from: Genomic region associated with run-timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

description: Conserving life history variation is a stated goal of many management
 programs, but the most effective means by which to accomplish this are
 often far from clear. Early, premature migrating and late, mature
 migrating forms of Chinook salmon face unequal pressure from natural and
 anthropogenic forces. These forces may result in the diminishment of
 migration variation in some stocks because migration timing is known to be
 highly heritable. Genomic regions of chromosome 28 are known to be
 strongly associated with migration variation in adult Chinook salmon, but
 it remains unclear whether there is consistent association among the
 diverse populations of Chinook salmon. Therefore, application of
 this association for management may be premature. We examined the
 association of genetic variation in 28 markers on chromosome 28 surveyed
 with high-throughout genotyping (GT-seq) with individual run timing
 characteristics gleaned from passive integrated transponder recordings of
 over 5,000 Chinook salmon from the three phylogeographic lineages that
 inhabit the Columbia River Basin. Despite the strong genetic differences
 among them, the three lineages exhibited very similar genetic variants in
 the chromosome 28 region and moderate to strong association of these
 variants and run timing phenotypes. This is particularly notable for the
 interior stream-type lineage, which exhibits an earlier and more
 constrained migration of fish than the other lineages and which are
 exclusively premature when they enter freshwater. In both interior
 stream-type and interior-ocean type Chinook salmon, heterozygotes of the
 most strongly associated linkage groups are largely intermediate to
 homozygotes in migration timing, and while we make no robust conclusions
 about dominance, results indicate codominance or marginal partial
 dominance of the early migrating allele. Our results lend support to the
 cautious utilization of chromosome 28 variation in tracking and predicting
 run timing in these Chinook salmon.
DOI: 10.5061/dryad.prr4xgxm6
title: Modulation of fracture healing by the transient accumulation of senescent cells

description: Senescent cells have detrimental effects across tissues with aging but may
 have beneficial effects on tissue repair, specifically on skin wound
 healing. However, the potential role of senescent cells in fracture
 healing has not been defined. Here, we performed an in silico analysis of
 public mRNAseq data and found that senescence and senescence-associated
 secretory phenotype (SASP) markers increased during fracture healing. We
 next directly established that the expression of senescence biomarkers
 increased markedly during murine fracture healing. We also identified
 cells in the fracture callus that displayed hallmarks of senescence,
 including distension of satellite heterochromatin and telomeric DNA
 damage; the specific identity of these cells, however, requires further
 characterization. Then, using a genetic mouse model (Cdkn2aLUC) containing
 a Cdkn2aInk4a-driven luciferase reporter, we demonstrated transient in
 vivo senescent cell accumulation during callus formation. Finally, we
 intermittently treated young adult mice following fracture with drugs that
 selectively eliminate senescent cells (‘senolytics’, Dasatinib plus
 Quercetin), and showed that this regimen both decreased senescence and
 SASP markers in the fracture callus and significantly accelerated the time
 course of fracture healing. Our findings thus demonstrate that senescent
 cells accumulate transiently in the murine fracture callus and, in
 contrast to the skin, their clearance does not impair but rather improves
 fracture healing.
DOI: 10.6084/m9.figshare.30456320
title: Datasets for "Simultaneous thermal and large field-of-view two-photon imaging enables optimization of signal-to-noise"

description: Datasets for "Simultaneous thermal and large field-of-view two-photon imaging enables optimization of signal-to-noise"<br>Unfortunately, due to the 20GB limit, only a portion of the dataset can be shared.
DOI: 10.5061/dryad.xpnvx0kfn
title: Data supplement for: Agreement of analytical and simulation-based estimates of the required land depth in climate models

description: Many current-generation climate models have land components that are too
 shallow. Under climate change conditions, the long-term warming trend at
 the surface propagates deeper into the ground than the commonly used
 3-10m. Shallow models alter the terrestrial heat storage and distribution
 of temperatures in the subsurface, influencing the simulated
 land-atmosphere interactions. Previous studies focusing on annual
 timescales suggest that deeper models are required to match
 subsurface-temperature observations and the classic analytical heat
 conduction solution. However, for a systematic investigation of land-model
 deepening in the frame of anthropogenic climate change, the classic
 analytical solution is inaccurate because it does not mimic the timescale
 and amplitude of the simulated warming trend. This study intends to bridge
 the gap between analytical and simulation-based estimates of the
 subsurface thermodynamic state by adapting the classic analytical
 framework to mimic long-term anthropogenic warming. The analysis shows
 that a land-model depth of at least 170m is recommended for a proper
 simulation of the post-1850 ground climate, which differs up to 30% from
 the estimate of the classic approach. Compared to previous studies, this
 provides an accurate estimate of the required land model depth for
 long-term climate-change simulations and indicates the relative bias in
 insufficiently deep land models.
description: See Readme File
DOI: 10.6084/m9.figshare.30456320.v2
title: Datasets for "Simultaneous thermal and large field-of-view two-photon imaging enables optimization of signal-to-noise"

description: Datasets for "Simultaneous thermal and large field-of-view two-photon imaging enables optimization of signal-to-noise"<br>Unfortunately, due to the 20GB limit, only a portion of the dataset can be shared.
DOI: 10.6084/m9.figshare.30456320.v1
title: Datasets for "Simultaneous thermal and large field-of-view two-photon imaging enables optimization of signal-to-noise"

description: Datasets for "Simultaneous thermal and large field-of-view two-photon imaging enables optimization of signal-to-noise"<br>Unfortunately, due to the 20GB limit, only a portion of the dataset can be shared.
DOI: 10.5061/dryad.ksn02v749
title: Optimal test-assisted quarantine strategies for COVID-19

description: Objective: To evaluate the effectiveness of SARS-CoV-2 testing on
 shortening the duration of quarantines for COVID-19 and to identify the
 most effective choices of testing schedules. Design: We performed
 extensive simulations to evaluate the performance of quarantine strategies
 when one or more SARS-CoV-2 tests were administered during the quarantine.
 Simulations were based on statistical models for the transmissibility and
 viral loads of SARS-CoV-2 infections and the sensitivities of available
 testing methods. Sensitivity analyses were performed to evaluate the
 impact of perturbations in model assumptions on the outcomes of optimal
 strategies. Results: We found that SARS-CoV-2 testing can effectively
 reduce the length of a quarantine without compromising safety. A single
 RT-PCR test performed before the end of quarantine can reduce quarantine
 duration to 10 days. Two tests can reduce the duration to 8 days, and
 three highly sensitive RT-PCR tests can justify a 6-day quarantine. More
 strategic testing schedules and longer quarantines are needed if tests are
 administered with less sensitive RT-PCR tests or antigen tests. Shorter
 quarantines can be utilized for applications that tolerate a residual
 post-quarantine transmission risk comparable to a 10-day quarantine.
 Conclusions: Testing could substantially reduce the length of isolation,
 reducing the physical and mental stress caused by lengthy quarantines.
 With increasing capacity and lowered costs of SARS-CoV-2 tests,
 test-assisted quarantines could be safer and more cost-effective than
 14-day quarantines and warrant more widespread use.
description: The dataset consists of PQTR (post-quarantine transmission
 risk) and observed test sensitivity for test-assisted quarantine
 strategies with different duration and test strategies, under the
 assumption of either mixed and simultaneous onset of infection. PQTR is
 calculated as the occurrence of failures (infecting others after released
 from quarantine) of at least 500K (mostly 1M) replicate simulations using
 the simulation model described in the manuscript.
description: The dataset is in EXCEL format. Users can open it and search for
 interested quarantine strategies using the filter feature of
 EXCEL.
DOI: 10.6084/m9.figshare.31166053
title: Additional file 8 of Synonymous and non-synonymous variants at splice junctions can disrupt splicing and are frequently linked to disease associated loss of function genes

description: Supplementary Material 8. Table S4 Gene-wise total count of variants per exon at donor and acceptor splice sites
DOI: 10.6084/m9.figshare.31166053.v1
title: Additional file 8 of Synonymous and non-synonymous variants at splice junctions can disrupt splicing and are frequently linked to disease associated loss of function genes

description: Supplementary Material 8. Table S4 Gene-wise total count of variants per exon at donor and acceptor splice sites
DOI: 10.6084/m9.figshare.31166056
title: Additional file 9 of Synonymous and non-synonymous variants at splice junctions can disrupt splicing and are frequently linked to disease associated loss of function genes

description: Supplementary Material 9. Table S5 Gene-wise summary of total variants per exon at the splice junction
DOI: 10.6084/m9.figshare.31166056.v1
title: Additional file 9 of Synonymous and non-synonymous variants at splice junctions can disrupt splicing and are frequently linked to disease associated loss of function genes

description: Supplementary Material 9. Table S5 Gene-wise summary of total variants per exon at the splice junction
DOI: 10.5061/dryad.wh70rxwnf
title: Simulation of sheared granular layers activated by fluid pressurization

description: Fluid pressurization of critically stressed sheared zones can trigger slip
 mechanisms at play in many geological rupture processes, including
 earthquakes or landslides. The increasing fluid pressure reduces the
 effective stress, giving possibility to the shear zone to reactivate.
 Nonetheless, the mechanisms that dictate the mode of slip, from aseismic
 steady creep to seismic dynamic rupture, remain poorly understood. By
 using discrete element modeling, we simulate pore-pressure-step creep test
 experiments on a sheared granular layer under a sub-critical stress state.
 The goal is to investigate the micromechanical processes at stake during
 fluid induced reactivation. The global simulated response is consistent
 with both laboratory and in situ experiments. In particular, the
 progressive increase of pore pressure promotes slow steady slip at
 sub-critical stress states (creep), and fast accelerated dynamic slip once
 the critical strength is overcome (rupture). The analyses of both global
 and local quantities show that these two emergent slip behaviors correlate
 to characteristic deformation modes: diffuse deformation during creep, and
 highly localized deformation during rupture. Our results suggest that the
 fabric of pressurized shear zones controls their emergent slip behavior.
 In particular, rupture results from grain rotations initiating from
 overpressure induced unlocking of interparticle contacts mostly located
 within the shear band, which, as a consequence, acts as a roller bearing
 for the surrounding bulk.
description: The first script prepares a sheared sample that represents a
 fault. The second script starts the fluid injection
 test and collects data. The raw data contain
 information of boundary stresss, contact stress, displacements of the
 sample during the fluid injection.
DOI: 10.6084/m9.figshare.31166080
title: Additional file 1 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.31166080.v1
title: Additional file 1 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.31166083
title: Additional file 2 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.31166083.v1
title: Additional file 2 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.31166086
title: Additional file 3 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.31166086.v1
title: Additional file 3 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.31166089
title: Additional file 4 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 4.
DOI: 10.6084/m9.figshare.31166089.v1
title: Additional file 4 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 4.
DOI: 10.5061/dryad.3ffbg79hv
title: Rates of attraction of cane toad tadpoles to chemicals

description: Chemical cues produced by late-stage embryos of the cane toad (Rhinella
 marina) attract older conspecific larvae, which are highly cannibalistic
 and can consume an entire clutch. To clarify the molecular basis of this
 attraction response, we presented captive tadpoles with components present
 in toad eggs. As previously reported, attractivity arises from the
 distinctive toxins (bufadienolides) produced by cane toads, with some
 toxins (e.g., bufagenins) much stronger attractants than others (e.g.,
 bufotoxins). Extracts of frozen toad parotoid glands (rich in bufagenins)
 were more attractive than were fresh MeOH extracts of the parotoid
 secretion (rich in bufotoxins), and purified marinobufagin was more
 effective than marinobufotoxin. Cardenolide aglycones (e.g.,
 digitoxigenin) were active attractors, whereas C-3 glycosides (e.g.,
 digoxin, oubain) were far less effective. A structure-activity
 relationship study revealed that tadpole attractant potency strongly
 correlated with Na+/K+ ATPase inhibitory activity, suggesting that
 tadpoles monitor and rapidly react to perturbations to Na+/K+ ATPase
 activity.
DOI: 10.6084/m9.figshare.31166092
title: Additional file 5 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 5.
DOI: 10.6084/m9.figshare.31166092.v1
title: Additional file 5 of Cutting through the clones: genomic strategies for core collection development in moso bamboo

description: Supplementary Material 5.
DOI: 10.6084/m9.figshare.31166101
title: Additional file 1 of 3-M syndrome: evolution of the phenotype over time

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.31166101.v1
title: Additional file 1 of 3-M syndrome: evolution of the phenotype over time

description: Supplementary Material 1
DOI: 10.5281/zenodo.18397095
title: Dataset from Gut Microbial Community Structure, Metabolic Signature, and Resistome in Dyslipidemia: Implications for Cardiovascular Disease Management

description: Dataset from Gut Microbial Community Structure, Metabolic Signature, and Resistome in Dyslipidemia: Implications for Cardiovascular Disease Management
DOI: 10.5281/zenodo.13846612
title: Dataset from Gut Microbial Community Structure, Metabolic Signature, and Resistome in Dyslipidemia: Implications for Cardiovascular Disease Management

description: Dataset from Gut Microbial Community Structure, Metabolic Signature, and Resistome in Dyslipidemia: Implications for Cardiovascular Disease Management
DOI: 10.5061/dryad.qjq2bvqg8
title: Reevaluating the species status of the southern ghost pipe, Monotropa brittonii (Ericaceae)

description: Relationships among members of Ericaceae subfamily Monotropoideae have
 been notoriously difficult to resolve due to convergent evolution in these
 parasitic plants. All species in this subfamily are fully
 mycoheterotrophic, meaning they obtain nutrients by parasitizing fungi
 rather than through photosynthesis. Here, we examine relationships and
 host specificity in one of the most widespread species in this subfamily,
 Monotropa uniflora L. We use several lines of evidence to investigate
 whether there is support for recognizing a segregate, M. brittonii Small,
 as distinct. Based on molecular and morphological analysis of Monotropa
 collected throughout their range in the United States, we find two
 distinct lineages, one of which corresponds morphologically and
 geographically to Small’s M. brittonii. We identified several
 morphological characters that differ between the two species. We also
 observed a high degree of fungal host specificity in M. brittonii, which
 appear to parasitize almost exclusively Lactifluus subgenus Lactariopsis
 section Albati. Additionally, M. brittonii were primarily collected from
 Florida scrub, which are xeric, shrub-dominated habitats that differ
 substantially from the mesic forests where M. uniflora typically
 occur. Based on these molecular, morphological, and ecological
 differences, we support recognition of M. brittonii as distinct from M.
 uniflora.
DOI: 10.5061/dryad.69p8cz926
title: Data from: Earthquake-spawning faults in the Seoul metropolitan area and their seismic implications

description: Quaternary faults run across the Seoul metropolitan area that is the
 highest population region in the Korean Peninsula. Active fault
 identification and seismic hazard potential assessment are
 crucial for public safety. Densely-deployed permanent and
 temporal seismic stations enabled us to detect micro to small
 earthquakes, allowing us to identify earthquake-spawning faults in
 Seoul metropolitan area. The source parameters of 455 earthquakes
 in 2004-2020 are refined. The Gutenberg-Richter b value is 0.94.
 Dominant focal depths are 4-15 km. The focal mechanism solutions
 of 64 earthquakes are determined using seismic-wave polarities
 and amplitude ratios. Strike-slip earthquakes are dominant in the
 region. Earthquakes are clustered around the Chugaryeong fault
 system. The dominant strikes of fault planes range from
 N20◦E-N45◦E in the northern and southern Seoul metropolitan
 areas, suggesting branch fault development locally. The earthquakes
 in middle-northern Seoul present N-S directional strike-slip
 motions at depths ∼7.5 km along the Chugaryeong fault. The
 spatial earthquake distribution and fault-plane orientations
 suggest near-vertical continuous faults subparallel with
 Chugaryeong fault, being seismically active.
description: This data
 set is concerned with the article "Earthquake-spawning faults in the
 Seoul metropolitan area and seismic implications" submitted to Earth
 and Space Science by Tae-Kyung Hong, Dongchan Chung, Junhyung Lee,
 Seongjun Park, Byeongwoo Kim, and Woohan Kim in 2021. 
 The full event list and 1-D velocity model analyzed in the
 article are provided. The event information to produce Figure 15 in the
 article is also included. All data files are given in the ASCII
 format. Please see the detailed information in the file
 "README" included in the zip file.
DOI: 10.6084/m9.figshare.31166103
title: Additional file 1 of HUBMet: an integrative database and analytical platform for human blood metabolites and metabolite-protein associations

description: Additional file 1: Table S1. List of the 49 publications used for blood metabolite list compilation. Table S2. List of 3,950 metabolites included in HUBMet, with HUBMet ID, common name, and category. Table S3. The metabolite-protein associations curated in HUBMet with validated evidence level and validation results based on an independent dataset. Table S4. Metabolite-protein network analysis results, including centrality measurements, functional annotations, and enrichment analysis results of metabolites and proteins within each community. Table S5. Tissue relevance analysis results for metabolite-tissue pairs with high reliability. Table S6. Statistical results for the case study in HUBMet. Table S7. Kappa scores of all the available metabolite sets in HUBMet.