cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dz08kps02
title: Potential areas of groundwater discharge, Humboldt River Basin, Nevada

description: Potential areas of groundwater discharge were delineated for the Humboldt
 River Basin to estimate groundwater evapotranspiration from phreatophyte
 vegetation, the primary component of natural groundwater discharge in the
 region. The boundary that defines the potential area of groundwater
 discharge represents the maximum spatial extent of groundwater discharge
 by phreatophyte vegetation, and areas within this boundary may discharge
 little to no groundwater where bare soil or sparse vegetation is the
 primary land cover. The boundaries are based on the original delineations
 of phreatophyte vegetation published in Reconnaissance Series Reports and
 Water Resource Bulletins for the state, which have also been included in
 this database with the filename
 "Historical_recon_and_wrb_phreatophyte_boundaries.shp".
description: Potential areas of groundwater discharge by
 phreatophyte vegetation were delineated based on a combination of
 previously published phreatophyte boundary maps and datasets, digital
 elevation model (DEM), gSSURGO soils data (USDA, 2017), high resolution
 aerial imagery of the NAIP, Landsat land surface temperature and
 vegetation indices, USGS and NDWR groundwater level data, and field
 investigations. These boundaries were further refined and divided
 into ET Units consisting of playa/bare
 soil, phreatophyte shrubland, meadow, riparian, and
 cropland.
DOI: 10.5061/dryad.9s4mw6mjc
title: A simple method reveals minimum time required to quantify steady-rate metabolism and net cost of transport for human walking

description: The U-shaped net cost of transport (COT) curve of walking has helped
 scientists understand the biomechanical basis that underlies energy
 minimization during walking. However, to produce an individual’s net COT
 curve, data must be analyzed during periods of steady-rate metabolism.
 Traditionally, studies analyze the last few minutes of a 6–10 min trial,
 assuming that steady-rate metabolism has been achieved. Yet, it is
 possible that an individual achieves steady rates of metabolism much
 earlier. However, there is no consensus on how to objectively quantify
 steady-rate metabolism across a range of walking speeds. Therefore, we
 developed a simple slope method to determine the minimum time needed for
 humans to achieve steady rates of metabolism across slow to fast walking
 speeds.We hypothesized that a shorter time window could be used to produce
 a net COT curve that is comparable to the net COT curve created using
 traditional methods. We analyzed metabolic data from 21 subjects who
 completed several 7 min walking trials ranging from 0.50 to 2.00 m s−1. We
 partitioned the metabolic data for each trial into moving 1, 2 and 3 min
 intervals and calculated their slopes. We statistically compared these
 slope values with values derived from the last 3 min of the 7 min trial,
 our ‘gold’ standard comparison. We found that a minimum of 2 min is
 required to achieve steady-rate metabolism and that data from 2–4 min
 yields a net COT curve that is not statistically different from the one
 derived from experimental protocols that are generally accepted in the
 field.
description: Please refer to the following publication for a description of
 methods for data collection and data processing: Adeyeri et al. 2022.
 "A simple method reveals minimum time required to quantify
 steady-rate metabolism and net cost of transport for human walking"
 in the Journal of Experimental Biology.
description: Microsoft Excel and Notepad.
DOI: 10.25338/b8cd2s
title: Data From: Broad- and fine-scale structure across the distribution of the Relict Dace (Relictus solitarius) in the Great Basin Desert, USA

description: The Relict Dace is a small cyprinid and the only species in its genus,
 Relictus. It is naturally distributed in four drainage basins of central
 Nevada - Butte Valley, Ruby Valley, Steptoe Valley and Goshute Valley. The
 species has experienced periods of isolation and connection within these
 four basins since the late Pliocene, with the last 100 years characterized
 by anthropogenic disturbance. To better inform conservation actions, we
 investigated range-wide and intra-basin genetic structure and diversity
 and conducted Fst outlier tests using RAD-sequencing. We found high levels
 of genetic structure and four main lineages on a broad scale corresponding
 primarily to geography, and on a very fine scale (&lt;1km) within
 drainage basins. Signatures of selection in the form of outlier loci were
 documented in multiple locations across the range.  Our results
 provide baseline data for conservation efforts and highlight the degree of
 fine-scale genetic structuring that may be present in fishes of the Great
 Basin that are now restricted to small, isolated habitats, particularly
 wetland complexes. We caution against assuming that geographic distance is
 a proxy for genetic similarity in Great Basin fishes, encourage thorough
 genetic sampling, and note that broad-scale genetic surveys can overlook
 fine-scale genetic structure.
description: See associated paper. In short, RAD libraries followed the protocol described in Ali et al. (2016) using the restriction enzyme Sbf1. Pooled libraries were sequenced on an Illumina HiSeq4000 with paired end 150 bp sequencing.
DOI: 10.5519/qd.8izzkvam
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (11685 records)
DOI: 10.5061/dryad.sbcc2fr87
title: Barley fasciated ear genes determine inflorescence meristem size and grain yield

description: In flowering plants, the inflorescence meristem (IM) provides founder
 cells to form successive floral meristems, the precursors of fruits or
 seeds. Hence, the activity and developmental progression of IM are
 critical for yield production in cereal crops. IM size is positively
 associated with spikelet number in some major cereals, like rice (Oryza
 sativa) and maize (Zea mays). However, the relationship and regulatory
 mechanism between IM size and grain yield remain unknown in Triticeae
 tribe. Here, we report that IM size has a negative correlation with yield
 traits in barley (Hordeum vulgare), and three FASCIATED EAR (FEA)
 orthologs, HvFEA2, HvFEA3, and HvFEA4, regulates IM size and spike
 development and ultimately affect the grain yield. All three HvFEAs are
 highly expressed in developing spikes, and loss-of-function mutants
 exhibit enlarged IM size, shortened spike length and decreased spikelet
 number, which leads to the reduced grain yield. We further reveal that
 HvFEA4 potentially targets to multiple pathways during reproductive
 development, including transcriptional control, phytohormones signaling
 and redox status. Our findings uncover the roles of barley FEA genes in
 limiting IM size and promoting spikelet formation, which provides insights
 into yield improvement by manipulating IM activity.
DOI: 10.5061/dryad.np5hqbzvq
title: Dataset for: Short flowers for long tongues: functional specialization in a nocturnal pollination network of an asclepiad in long-tongued hawkmoths (Biotropica)

description: Since Darwin, very long and narrow floral tubes have been known to
 represent the main floral morphological feature for specialized
 long-tongued hawkmoth pollination. However, specialization may be driven
 by other contrivances instead of floral tube morphology. Asclepiads are
 plants with a complex floral morphology where primary hawkmoth pollination
 had never been described. We detailed here the intricate pollination
 mechanism of the South American asclepiad Schubertia grandiflora, where
 functional specialization on long-tongued hawkmoth pollinators occurs
 despite the short floral tube of this species. We studied two plant
 populations in the Brazilian Cerrado and recorded floral visitors using
 different approaches, such as light-trapped hawkmoths for pollen analysis,
 direct field observations, and IR motion-activated cameras. Finally, using
 a community-level approach we applied an ecological network analysis to
 identify the realized pollinator niche of S. grandiflora among the
 available niches in the pollinator community. Throughout a period of 17
 years, long-tongued hawkmoths were consistently recorded as the main
 floral visitors and the only effective pollinators of S. grandiflora.
 Flowers rely on highly modified corona and gynostegium, and enlarged
 nectar chambers, to drive visitors and pollination mechanism. Despite
 relatively short-tube, network analysis placed S. grandiflora in the
 module including exclusively long-tongued hawkmoth pollinators and the
 most phenotypically specialized sphingophilous plants in the community.
 These results represent the first example of functional specialization in
 long-tongued hawkmoths in an asclepiad species. However, this
 specialization is uncoupled from the long floral tubes historically
 associated with the sphingophily syndrome.
description: See methods in Amorim et al. (2022) Short flowers for long
 tongues: functional specialization in a nocturnal pollination network of
 an asclepiad in long-tongued hawkmoths (Biotropica).
description: All data are available.
DOI: 10.5061/dryad.c866t1g8q
title: Convergent evolution of barnacles and molluscs sheds lights in origin and diversification of calcareous shell and sessile lifestyle

description: The calcareous shell and sessile lifestyle are the representative
 phenotypes of many molluscs, which happen to be present in barnacles, a
 group of unique crustaceans. The origin of these phenotypes is unclear,
 but it may be embodied in the convergent genetics of such distant groups
 (interphylum). Herein, we perform comprehensive comparative genomics
 analysis in barnacles and molluscs, and reveal a genome-wide strong
 convergent molecular evolution between them, including coexpansion of
 biomineralisation and organic matrix genes for shell formation, and
 origination of lineage-specific orphan genes for settlement. Notably, the
 expanded biomineralisation gene encoding alkaline phosphatase evolves a
 novel, highly conserved motif that may trigger the origin of barnacle
 shell formation. Unlike molluscs, barnacles adopt novel organic matrices
 and cement proteins for shell formation and settlement, respectively, and
 their calcareous shells have potentially originated from the cuticle
 system of crustaceans. Therefore, our study corroborates the idea that
 selection pressures driving convergent evolution may strongly act in
 organisms inhabiting similar environments regardless of phylogenetic
 distance. The convergence signatures shed light on the origin of the shell
 and sessile lifestyle of barnacles and molluscs. In addition, notable
 nonconvergence signatures are also present and may contribute to
 morphological and functional specificities.
DOI: 10.6084/m9.figshare.31167946
title: <b>MM-MCD：</b>Multiple Myeloma Bone Marrow Smear Analysis Dataset

description: Multiple Myeloma Bone Marrow Smear AnalysisMM-MCD is a large-scale, high-resolution, expert-annotated dataset tailored for multi-cell segmentation and fine-grained classification in multiple myeloma (MM) bone marrow smear analysis, addressing the gap of insufficiently diverse and context-rich datasets in hematological AI research. It includes about 20000 publicly available 1024×1024 pixel whole-smear images (with a full collection of 20,000 images for five-fold cross-validation) acquired under standardized clinical conditions, featuring rigorous annotations for 49 distinct bone marrow cell categories spanning plasma cell subtypes, erythroid, myeloid, lymphoid, monocytic, and megakaryocytic lineages—generated via independent labeling, cross-review, and senior hematologist adjudication with Cohen’s Kappa coefficient &gt; 0.85 to ensure high reliability. Provided in the widely compatible COCO format with predefined 8:2 training-validation splits and detailed metadata, MM-MCD preserves the spatial context and cellular heterogeneity of real-world MM bone marrow smears (including dense cell distributions, overlapping cells, and staining variability), outperforming existing MM-focused datasets that only target plasma cells by covering the entire hematopoietic microenvironment. Intended for non-commercial research and educational use, this dataset serves as a robust foundation for developing clinically relevant computer-aided diagnosis (CAD) systems, facilitating advancements in automated bone marrow morphology analysis while supporting fair and reproducible model benchmarking.
DOI: 10.6084/m9.figshare.31167946.v1
title: <b>MM-MCD：</b>Multiple Myeloma Bone Marrow Smear Analysis Dataset

description: Multiple Myeloma Bone Marrow Smear AnalysisMM-MCD is a large-scale, high-resolution, expert-annotated dataset tailored for multi-cell segmentation and fine-grained classification in multiple myeloma (MM) bone marrow smear analysis, addressing the gap of insufficiently diverse and context-rich datasets in hematological AI research. It includes 2000 publicly available 1024×1024 pixel whole-smear images (with a full collection of 20,000 images for five-fold cross-validation) acquired under standardized clinical conditions, featuring rigorous annotations for 49 distinct bone marrow cell categories spanning plasma cell subtypes, erythroid, myeloid, lymphoid, monocytic, and megakaryocytic lineages—generated via independent labeling, cross-review, and senior hematologist adjudication with Cohen’s Kappa coefficient &gt; 0.85 to ensure high reliability. Provided in the widely compatible COCO format with predefined 8:2 training-validation splits and detailed metadata, MM-MCD preserves the spatial context and cellular heterogeneity of real-world MM bone marrow smears (including dense cell distributions, overlapping cells, and staining variability), outperforming existing MM-focused datasets that only target plasma cells by covering the entire hematopoietic microenvironment. Intended for non-commercial research and educational use, this dataset serves as a robust foundation for developing clinically relevant computer-aided diagnosis (CAD) systems, facilitating advancements in automated bone marrow morphology analysis while supporting fair and reproducible model benchmarking.
DOI: 10.6084/m9.figshare.31167946.v2
title: <b>MM-MCD：</b>Multiple Myeloma Bone Marrow Smear Analysis Dataset

description: Multiple Myeloma Bone Marrow Smear AnalysisMM-MCD is a large-scale, high-resolution, expert-annotated dataset tailored for multi-cell segmentation and fine-grained classification in multiple myeloma (MM) bone marrow smear analysis, addressing the gap of insufficiently diverse and context-rich datasets in hematological AI research. It includes about 20000 publicly available 1024×1024 pixel whole-smear images (with a full collection of 20,000 images for five-fold cross-validation) acquired under standardized clinical conditions, featuring rigorous annotations for 49 distinct bone marrow cell categories spanning plasma cell subtypes, erythroid, myeloid, lymphoid, monocytic, and megakaryocytic lineages—generated via independent labeling, cross-review, and senior hematologist adjudication with Cohen’s Kappa coefficient &gt; 0.85 to ensure high reliability. Provided in the widely compatible COCO format with predefined 8:2 training-validation splits and detailed metadata, MM-MCD preserves the spatial context and cellular heterogeneity of real-world MM bone marrow smears (including dense cell distributions, overlapping cells, and staining variability), outperforming existing MM-focused datasets that only target plasma cells by covering the entire hematopoietic microenvironment. Intended for non-commercial research and educational use, this dataset serves as a robust foundation for developing clinically relevant computer-aided diagnosis (CAD) systems, facilitating advancements in automated bone marrow morphology analysis while supporting fair and reproducible model benchmarking.
DOI: 10.5061/dryad.vx0k6djtm
title: Chromosome-level genome of Capitulum mitella reveals an ancient whole-genome duplication event and intertidal adaptation of barnacles

description: Barnacles are the only sessile crustaceans inhabiting intertidal zone, an
 extremely stressful environment for sessile organisms. Herein, we report
 the chromosome-level genome of a stalked barnacle, Capitulum mitella,
 which is a dominant intertidal cirripede of the west Pacific Ocean coast.
 After comprehensive comparative genomic analyses, it is the first time to
 find an ancient whole-genome duplication (WGD) event that preceded the
 divergence of Lepadomorpha and Sessilia approximately 237 million years
 ago. The retained duplicated genes of WGD are primarily enriched in many
 environmental information processing pathways, shedding light on its
 adaptive evolution of intertidal sessile life. In addition, transcriptomic
 and metabolomic sequencing and analyses of C. mitella indicated that the
 upregulation of some expanded anti-stress factors and accumulation of
 acyl-carnitines help barnacles adapt to stressful intertidal conditions.
 Therefore, this study provides a valuable resource for understanding the
 unique intertidal adaptation mechanism of sessile crustaceans and reveals
 novel WGD events in invertebrates.
DOI: 10.5061/dryad.7wm37pvvz
title: Absorptive roots drive a larger microbial carbon pump efficacy than transport roots in alpine coniferous forests

description: Root activity creates a unique microbial hotspot in the rhizosphere and
 profoundly regulates soil carbon (C) dynamics, but empirical assessments
 of the soil microbial carbon pump (MCP, the iterative accumulation of
 necromass after microbial anabolism) and associated ecological
 consequences on soil C storage based on insight of the rhizosphere are
 still neglected, especially for different root functional modules. We
 assessed the soil MCP efficacy (i.e., the contribution of microbial
 necromass to SOC) by investigating the divergent contribution of microbial
 necromass based on amino sugar extrapolations to soil organic C (SOC) in
 the rhizosphere of two root functional modules (i.e., absorptive roots and
 transport roots) and the bulk soil in an alpine coniferous forest. The
 results showed that the MCP efficacy in both rhizosphere and bulk soil was
 more than 50%, suggesting that microbial necromass plays a key role in SOC
 formation. More importantly, absorptive roots drove a greater MCP efficacy
 (56%) in the rhizosphere than transport roots (51%). Synthesis. These
 observations suggest that the microbial necromass is a major contributor
 to SOC storage in both rhizosphere and bulk soil in alpine coniferous
 forests. The magnitude of the contribution of microbial necromass to
 rhizosphere SOC depends on root functional differentiation. Our study
 provides novel and direct empirical evidence for the active soil MCP
 functions in SOC sequestration from the perspective of the rhizosphere.
DOI: 10.5061/dryad.p8cz8w9s6
title: Data from: Demographic correction – a tool for inference from individuals to populations

description: Estimation of responses of organisms to their environment using
 experimental manipulations, and comparison of such responses across sets
 of species, is one of the primary tools in ecology research. The most
 common approach is to compare response of a single life stage of species
 to an environmental factor and use this information to draw conclusions
 about population dynamics of these species. Such approach ignores the fact
 that interspecific fitness differences measured at a single life stage are
 not directly comparable and cannot be extrapolated to lifetime fitness of
 individuals and thus species’ population dynamics. Comparison of one life
 stage only while omitting demographic information can strongly bias
 conclusions, both in experimental studies with a few species, and in large
 comparative studies. We illustrate the effect of this omission using both
 an exaggerated fictitious example, and biological data on congeneric
 species differing in their demography. We are showing, taking simple
 assumptions, that different demography can completely revert conclusions
 reached by a comparison based on an experiment focusing on a single life
 stage. We show that a "demographic correction", namely
 translating observed effects into differences in outcomes of demographic
 models, is a solution to this problem. It requires turning the detected
 effects from the experiment into changes of transition probabilities of
 projection matrix models. Although such solution is limited by the low
 number of species with demographic data available, we believe that
 existing data (and data likely to be collected in the near future) permit
 at least approximate handling of this problem.
description: This dataset contains selected projection matrices from Janovský
 and Herben 2020 (see Related Works) and R code for analyses
 (examples).
DOI: 10.5061/dryad.83bk3j9t5
title: Stratigraphic column of the Xiazhen Formation with the 18 stromatoporoid-bearing intervals (clathrodictyid stromatoporoids)

description: Clathrodictyids are the most abundant stromatoporoids in the Upper
 Ordovician Xiazhen Formation (middle to upper Katian) of South China. A
 total of nine species belonging to four clathrodictyid genera are
 identified in the formation, including Clathrodictyon idense (Webby and
 Banks, 1976), Clathrodictyon cf. Cl. microundulatum (Nestor, 1964),
 Clathrodictyon cf. Cl. mammillatum  (Schmidt, 1858),
 Clathrodictyon megalamellatum Jeon n. sp., Clathrodictyon plicatum (Webby
 and Banks, 1976), Ecclimadictyon nestori Webby, 1969, Ecclimadictyon
 undatum (Webby and Banks, 1976), Camptodictyon amzassensis (Khalfina,
 1960) and Labyrinthodictyon cascum (Webby and Morris, 1976). The
 clathrodictyid fauna in the Xiazhen Formation is very similar to those
 from both New South Wales and Tasmania, although the latter two Australian
 regions do not share any common clathrodictyid species during the Late
 Ordovician. The paleobiogeographic pattern indicates that the northward
 drift of South China resulted in a favorable environment for the migration
 of clathrodictyids from other peri-Gondwanan terranes to South China.
 Also, these peri-Gondwanan clathrodictyid species hosted various
 endobionts, representing a variety of paleoecological interactions. The
 high abundance and species-level diversity of clathrodictyid species
 presumably increased the substrate availability of suitable host taxa,
 judging from the diverse intergrowth associations between clathrodictyids
 and other benthic organisms. These paleoecological interactions between
 stromatoporoid and other organisms are known from the Late Ordovician and
 became more abundant and widespread in the Siluro–Devonian. Overall, the
 Late Ordovician clathrodictyid assemblage in South China demonstrates one
 of the highest species-level diversities among all peri-Gondwanan terranes
 and represents a precursor of the complex, clathrodictyid-dominanted
 communities of later metazoan reefs during the Great Ordovician
 Biodiversification Event.