cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qnk98sffp
title: Data from: Bi-channel image registration and deep-learning segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain

description: We have developed an open-source software called BIRDS (bi-channel image
 registration and deep-learning segmentation) for the mapping and analysis
 of 3D microscopy data and applied this to the mouse brain. The BIRDS
 pipeline includes image pre-processing, bi-channel registration, automatic
 annotation, creation of a 3D digital frame, high-resolution visualization,
 and expandable quantitative analysis. This new bi-channel registration
 algorithm is adaptive to various types of whole-brain data from different
 microscopy platforms and shows dramatically improved registration
 accuracy. Additionally, as this platform combines registration with neural
 networks, its improved function relative to other platforms lies in the
 fact that the registration procedure can readily provide training data for
 network construction, while the trained neural network can efficiently
 segment incomplete/defective brain data that is otherwise difficult to
 register. Our software is thus optimized to enable either minute-timescale
 registration-based segmentation of cross-modality, whole-brain datasets or
 real-time inference-based image segmentation of various brain regions of
 interest. Jobs can be easily submitted and implemented via a Fiji plugin
 that can be adapted to most computing environments.
description: Brain 3,4 and 5 were obtained with LSFM and each dataset
 encompassed ~700 Gigavoxels ( ~10000×8000×5000), with an isotropic voxel
 size of 1 μm<sup>3</sup>.  8-week-old Thy-GFP-M mice
 (RRID:IMSR_JAX:007788) and the brain tissue was first clarified with
 uDISCO protocol<sup>42</sup> before imaging. Brain 3 and 4
 were acquired using a custom-built Bessel plane illumination microscope, a
 type of LSFM modality employing non-diffraction thin Bessel light-sheet.
 Brain 5 was whole-brain 3D image of a Thy-GFP-M mice acquired using a
 lab-built selective plane illumination microscope
 (SPIM)<sup>20</sup>, another LSFM modality combining Gaussian
 light-sheet with multi-view image acquisition/fusion.
description: The resolution was download to 20*20*20 μm3.
DOI: 10.5068/d1wd55
title: Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery

description: The unicellular green alga Chlamydomonas reinhardtii is
 a choice reference system for the study of photosynthesis and chloroplast
 metabolism, cilium assembly and function, lipid and starch metabolism, and
 metal homeostasis. Despite decades of research, the functions of thousands
 of genes remain largely unknown, and new approaches are needed to
 categorically assign genes to cellular pathways. Growing collections of
 transcriptome and proteome data now allow a systematic approach based on
 integrative co-expression analysis. We used a dataset comprising 518 deep
 transcriptome samples derived from 58 independent experiments to identify
 potential co-expression relationships between genes. We visualized
 co-expression potential with the R package corrplot, to easily
 assess co-expression and anti-correlation between genes. We extracted
 several hundred high-confidence genes at the intersection of multiple
 curated lists involved in cilia, cell division, and photosynthesis,
 illustrating the power of our method. Surprisingly, Chlamydomonas
 experiments retained a significant rhythmic component across the
 transcriptome, suggesting an underappreciated variable during sample
 collection, even in samples collected in constant light. Our results
 therefore document substantial residual synchronization in batch cultures,
 contrary to assumptions of asynchrony. We provide step-by-step protocols
 for the analysis of co-expression across transcriptome data sets from
 Chlamydomonas and other species to help foster gene function discovery
description: For Chlamydomonas, the data set consists of 518 RNA-seq samples
 derived from 58 independent experiments, most published.
 For Arabidospis, the data sets were downloaded from the AtGenExpress project site (http://jsp.weigelworld.org/AtGenExpress/resources/), and collated into a single file that consisted of 34 Arabidopsis accessions, 16 sets of etiolated seedlings exposed to various light treatments, 36 sets of seedlings exposed to pathogens, 13 cell culture samples, 68 sets each for shoots and roots exposed to various abiotic stresses, 79 developmental samples (72 from shoots or leaves, 7 from roots), and 18 sets each for leaves and roots subjected to iron deficiency, with controls included. 
description: For Chlamydomonas, all genes were retained, and the data
 normalized by calculating the log2(FPKM+1). For
 Arabidopsis, control probes were removed manually prior to
 normalization.
DOI: 10.3886/e244701
title: Botswana Combination Prevention Project (BCPP) - Public Release Data

description: The Botswana Combination Prevention Project (BCPP) was a research project conducted by the Botswana Ministry of Health (MOH), Harvard School of Public Health/Botswana Harvard AIDS Institute Partnership (BHP), and the U.S. Centers for Disease Control and Prevention (CDC). BCPP was a community randomized trial that examined the impact of prevention interventions on HIV incidence in 15 intervention and 15 control communities. The interventions included extensive HIV testing, linkage to care, and universal treatment services. To reduce HIV incidence in the intervention communities, the UNAIDS 90-90-90 goals were used: 90% of HIV-positive persons know their status; 90% of persons who know status are to be on ART; 90% of persons on ART are to be virally suppressed. The BCPP study is composed of 2 interlocking protocols: Evaluation Protocol and Intervention Protocol. The Evaluation Protocol of the BCPP evaluated the primary endpoint (HIV incidence), as well as some key related secondary endpoints. This protocol focused on the Baseline Household Survey; the HIV Incidence Cohort; and an End of Study Survey. The Intervention Protocol of the BCPP implemented the combination prevention (CP) intervention package in CPCs and measures the uptake of these interventions (expanded HIV testing and counselling, strengthened male circumcision, and expanded HIV Care and Treatment).
DOI: 10.5061/dryad.m63xsj41c
title: Slab metamorphism and interface earthquakes in Peru: implications for along-strike fluid content and seismotectonic variation

description: Evidenced by a typically shallow subducted thick mid-ocean ridge basalt
 (MORB) layer that dominates the subducting Nazca plate and a significant
 lack of arc magmatism, the Peruvian megathrust remain enigmatic in thermal
 regime and petrological metamorphism. Thermally controlled slab
 dehydration in the incoming plate may facilitate fluids release and
 migration which possibly causes fault instability and seismic and aseismic
 slips. We find that (1) the eclogitization of the MORB layer and the
 harzburgitization of the ultramafic layer, and the subsequent dehydration
 embrittlement probably affect interface seismicity in Peru; (2) the
 subduction of the Nazca Ridge separates southern Peru from north-central
 Peru, leading to a MORB-dominant oceanic lithosphere beneath Peru
 associated with an aseismic interface at depth and a lack of arc
 magmatism; (3) slab dehydration of &gt;0.01 wt%/km accompanied by
 temperatures of 300-600°C possibly affect the occurrence of earthquakes
 and slips distributed on the hydrated interface. The along-strike fluid
 content variation possibly interprets the forearc seismotectonic
 segmentation associated with pore fluid pressure variation on megathrusts.
DOI: 10.3886/e244701v1
title: Botswana Combination Prevention Project (BCPP) - Public Release Data

description: The Botswana Combination Prevention Project (BCPP) was a research project conducted by the Botswana Ministry of Health (MOH), Harvard School of Public Health/Botswana Harvard AIDS Institute Partnership (BHP), and the U.S. Centers for Disease Control and Prevention (CDC). BCPP was a community randomized trial that examined the impact of prevention interventions on HIV incidence in 15 intervention and 15 control communities. The interventions included extensive HIV testing, linkage to care, and universal treatment services. To reduce HIV incidence in the intervention communities, the UNAIDS 90-90-90 goals were used: 90% of HIV-positive persons know their status; 90% of persons who know status are to be on ART; 90% of persons on ART are to be virally suppressed. The BCPP study is composed of 2 interlocking protocols: Evaluation Protocol and Intervention Protocol. The Evaluation Protocol of the BCPP evaluated the primary endpoint (HIV incidence), as well as some key related secondary endpoints. This protocol focused on the Baseline Household Survey; the HIV Incidence Cohort; and an End of Study Survey. The Intervention Protocol of the BCPP implemented the combination prevention (CP) intervention package in CPCs and measures the uptake of these interventions (expanded HIV testing and counselling, strengthened male circumcision, and expanded HIV Care and Treatment).
DOI: 10.15468/dl.jyxh6e
title: Occurrence Download

description: A dataset containing 807 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dalhousiea africana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 807 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002761-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vq83bk3rq
title: Shift of seed mass and fruit type spectra along longitudinal gradient: High water availability and growth allometry

description: CE1 Propagule traits vary among biomes along geographical gradients such
 as longitude, but the mechanisms that underlie these variations
 remain unclear. This study aims to explore seed mass variation
 patterns of different biome types along a longitudinal gradient
 and their underlying variation mechanisms by involving an
 in-depth analysis on the variation of seed mass, fruit type
 spectra, growth forms and dispersal mode spectra in Inner Mongolia and
 northeastern China. Plant community characterization and seed
 collection were conducted in 26 sites spreading over five
 vegetation types and covering 622 species belonging to 66
 families and 298 genera. We found there are significantly
 declining trends for mean seed mass, vertebrate-dispersed species
 richness and fleshy-fruited species richness along a
 longitudinal gradient from forests to desert grasslands. However,
 we also found the lowest average seed mass and the smallest
 proportion of species dispersed by vertebrates occurring at
 typical grasslands in the five biomes. The variations of average
 seed mass display high congruence CE2 with transition of
 growth form spectra. The selection for these propagule attributes
 is driven mainly by climatic factors such as precipitation,
 temperature, soil moisture and evaporation, as well as by
 internal biotic factors such as growth forms, canopy coverage
 and leaf area. A hypothesis was provided that environmental
 factors and botanical traits that favor greater water
 availability lead to emergence (or speciation) of species with
 large seeds or fleshy fruits with high water content. Due to
 greater water availability and increasing leaf area, much more
 photosynthate (photosynthesis production) and allometric growth then
 ultimately increase the biome average seed mass from west to east.
 Phylogenetic signal or diversity are not found to be
 significantly involved in the effect on the patterns. A novel
 mechanistic framework and mathematical model are provided to expound seed
 variation among species or biomes.
description: Please see the README document ("README_Dataset_Seed mass
 for species in Inner Mongolia) and the accompanying published article: Yu
 SL, Wang GX, Katz O, Li DF, Wang QB, Yue M., Liu CR. 2021. Shift of seed
 mass and fruit type spectra along longitudinal gradient: high water
 availability and growth allometry. Biogeoscience 18: 655-667. Published.
 DOI: 10.1007/bg-2019-479.
DOI: 10.5061/dryad.stqjq2c2q
title: Genotypes of Italian free-ranging dogs

description: Domestication has greatly changed the social and reproductive behavior of
 dogs relative to that of wild members of the genus Canis, which typically
 exhibit social monogamy and extended parental care. Unlike a typical grey
 wolf pack that consists of a single breeding pair and their offspring from
 multiple seasons, a group of free-ranging dogs (FRDs) can include multiple
 breeding individuals of both sexes. To understand the consequences of this
 shift in reproductive behavior, we reconstructed the genetic pedigree of
 an FRD population and assessed the kinship patterns in social groups,
 based on genome-wide SNP genotypes. Consistent with behavioral
 observations, the mating system of the study population was characterized
 by polygynandry. Instead of the discreet family units observed in wolves,
 FRDs were linked by a network of kinship relationships that
 spread across packs. However, we also observed reproduction of
 the same male-female pairs in multiple seasons, retention of adult
 offspring in natal packs and dispersal between neighboring packs –
 patterns in common with wolves. Although monogamy is the predominant
 mating system in wolves, polygyny and polyandry are occasionally observed
 in response to increased food availability. Thus, polygynandry of domestic
 dogs was likely influenced by the shift in ecological niche from an apex
 predator to a human commensal.
description: The samples were genotyped at 360K SNP (single nucleotide
 polymorphisms) loci, using Axiom Canine HD Genotyping Array (Thermo
 Scientific). We used Plink1.9
 software for the filtering of the SNP loci. We removed loci
 that were invariable for the analyzed population or showed very low
 variability (Minor Allele Frequency &lt;0.01), as well as loci having
 more than 20% missing data for the study population. We
 removed from the analysis two individuals with more than 10% missing
 data. The data can be open using Plink software or a text editor.
description: Missing values are marked as 0.
DOI: 10.5061/dryad.n8pk0p2tr
title: Nematodes community composition and environmental parameters, Eastern Antarctic Peninsula

description: This study provides a snapshot of the largely understudied meiobenthic and
 nematode communities in the Prince Gustav Channel and Duse Bay. We
 compared five stations sampled at different water depths along the shelf
 and investigated their meiobenthic community structure. We approached
 nematode biodiversity comparing traditional taxonomic identification and
 high throughput sequencing (HTS), with the use of Amplicon Sequence
 Variants (ASVs). Additionally, we characterized the environment by primary
 production proxies, grain size and seasonal ice conditions. Our
 results suggest that the availability of organic matter and its freshness
 are responsible for the high densities found at all depths. However,
 potential factors influencing the high local and regional variability of
 meiofauna density and biodiversity are less clear. A bathymetric transect
 consisting of three stations in Duse Bay (200 m, 500 m and 1000 m depth)
 showed increasing pigment concentrations in the first centimeters of the
 sediment vertical profile with increasing water depth, whereas the
 meiofauna densities showed the opposite trend. The deepest station of Duse
 Bay seems to function as a sink for fine material as supported by the
 higher silt fraction and higher organic matter concentrations. When
 comparing the two basins in the Prince Gustav Channel (1000 m and 1250 m)
 and the one in Duse Bay (1000 m), differences in terms of environmental
 variables, meiofaunal densities and composition were observed. The deepest
 basin in Prince Gustav Channel is located further South (closer to the
 highly unstable Larsen area), and marked differences with the other basins
 suggest that it might be experiencing different conditions as a result of
 its presence near the summer ice margin and its more elongated topography.
 Both, the shallowest and the deepest stations showed the highest number of
 unique sequences, suggesting a more biodiverse nematode assemblage. The
 morphological identification did not show significant differences in the
 biodiversity of all stations which suggests that molecular approaches can
 be more efficient for biodiversity studies. However the lack of
 reference sequences in online databases is still an important issue to
 consider as it potentially leads to underestimations of biodiversity and
 functional traits.
DOI: 10.15468/dl.u7uc6v
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Gymnascella dankaliensis"
 ]
}

 The dataset includes 116 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002759-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2jm63xsns
title: Data from: The allometry of sound frequency bandwidth in songbirds

description: Theory predicts that allometric constraints on sound production should be
 stronger for the lower frequencies of vocalizations than for their higher
 frequencies, which could originate an allometry for sound frequency
 bandwidth, but this was never tested. Using song recordings of ca. 1000
 passerine species (from &gt;75% passerine genera), we show a
 significantly steeper allometry for the lower than the higher song
 frequencies, resulting in a positive allometry of frequency bandwidth:
 larger species can use wider bandwidths than smaller species. The
 bandwidth allometry exists in songbirds (oscines), but not non-oscine
 passerines, indicating that it emerges from a combination of physical
 constraint and the evolved behavior of oscines: unlike the narrow
 bandwidths of most non-oscine songs, the learned songs of oscines often
 use wide bandwidths that can be limited by both the lower and upper limits
 of sound frequency production. This bandwidth allometry has implications
 for several research topics in acoustic communication.
DOI: 10.5061/dryad.ns1rn8prv
title: Root and chemical traits

description: Many studies have quantified the functional variation of fine root traits
 to understand the overarching trade-off between maximizing resource
 acquisition or conservation (root economics spectrum -RES-). However, we
 know remarkably less on how plant strategies along the RES are actually
 constrained by the amount of photosynthates required to construct roots
 (i.e. construction costs, CC) or how belowground interactions with
 symbiotic organisms modify root trait patterns and their relationships
 with CC. Our main aim was to quantify CC of fine roots (&lt;2 mm) and
 their underlying components (carbon, minerals and organic nitrogen
 concentrations) in 60 Mediterranean woody species with contrasting
 symbiotic association types (ectomycorrhizas, arbuscular and ericoid
 mycorrhizas and N-fixing bacteria). We examined (1) if the covariation
 among fine root traits along the RES was related to the intrinsic cost of
 producing roots and if this relationship was dependent on the type of root
 symbiosis; (2) if the relationship of each CC component with the RES was
 dependent on the type of root symbiosis; and (3) whether soil water and
 nutrient availability determined differences in CC across sites. According
 to the RES hypothesis, fine root traits showed a main covariation trend
 (acquisition vs. conservation), defined by the first PCA axis, which also
 segregated species by their two main contrasting symbiotic types
 (arbuscular and ectomycorrhizal). We found a positive relationship between
 root CC and the RES (i.e. PCA axis 1) and, interestingly, slopes differed
 among symbiotic types, in response to the different role of each specific
 CC component. In addition, independently of symbiotic type, root CC
 decreased linearly with soil nutrient availability and quadratically with
 plant water availability. Synthesis. Our study demonstrates that woody
 plants display different functional strategies in their root CC, related
 with their position on the RES, and that CC differ among symbiotic groups.
 The influence of the root CC components across species varied among
 symbiotic associations, pointing to a trade-off between structural and
 metabolic compounds. Root CC were also strongly modulated by soil resource
 availability (nutrients and water). This study highlights that root CC are
 fundamental to better understand belowground resource use strategies.
DOI: 10.5061/dryad.wpzgmsbm8
title: Data from: Upland rush management advocated by agri-environment schemes increases predation of artificial wader nests

description: Farmland birds, including breeding waders, have declined across Europe.
 One frequently advocated strategy to facilitate population recovery is
 using agri-environment schemes (AES) to improve vegetation structure. A
 key example is cutting dense rush Juncus to open the sward which aims to
 increase the abundance of wading birds, for example by improving foraging
 conditions. Effects on breeding success are, however, unknown. This is a
 critical knowledge gap as high nest and chick predation rates are a key
 driver of wader declines. For wader species that nest across a range of
 sward structures, e.g. Eurasian curlew Numenius arquata and common snipe
 Gallinago gallinago, converting denser swards to more open ones may reduce
 opportunities for nest concealment and thus increase predation risk. Due
 to the difficulties of locating large numbers of wader nests, we assess
 rush management impacts on nest predation risk using artificial wader
 nests (n = 184) in two upland areas of England, using fields in which rush
 is managed according to AES prescriptions (treatment; n = 21) or
 un-managed (control; n = 22) fields. Daily nest predation rates (DPRs)
 were twice as high in treatment (0.064 day-1) than control fields (0.027
 day-1). Within treatment fields, DPRs were twice as high for nests in cut
 rush patches (0.108 day-1) than in uncut rush (0.055 day-1). Modelling
 links higher DPRs associated with rush cutting to the resultant shorter
 and less dense vegetation. Our results highlight the need to assess how
 AES prescriptions that alter vegetation structure impact all aspects of
 the target species’ fitness and thus determine population recovery.
 Studies using real wader nests should test whether AES rush management
 inadvertently creates an ecological trap by altering vegetation structure,
 and identify the sward structure and configuration that optimises
 trade-offs between foraging conditions and nest predation risk.
description: <strong>Artificial wader nest data
 </strong> ArtificialNestData.xlsx
 Dataset for analyses of daily nest predation rates of artificial
 waders nests in treatment fields with rush management and control fields
 without rush management. Each row is an individual nest. Metadata is
 available in a second sheet in the ArtificialNestData.xlsx file. The mean
 number of corvids and the mean number of avian predators were calculated
 from the AvianPredData.xlsx file.  <strong>Avian
 predator survey data</strong>
 AvianPredData.xlsx Dataset for analyses of
 avian predator abundance. Each row is an individual visit to a field with
 the number of avian predators observed. The sum of the number of corvids
 and the sum of the number of avian predators are provided. Metadata is
 available in a second sheet in the AvianPredData.xlsx file.