cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4f4qrfjhx
title: Data from: Phosphorus storage and utilization strategies of two bloom-forming freshwater cyanobacteria

description: The inter-relationships between cellular phosphorus (P) storage, dissolved
 inorganic P (DIP) uptake affinity, alkaline phosphatase activity (APA),
 and dissolved inorganic nitrogen (DIN) concentrations were studied in two
 ubiquitous diazotrophic freshwater cyanobacteria, Raphidiopsis raciborskii
 (six strains) and Chrysosporum ovalisporum (two strains). DIP uptake
 kinetics were measured using rates of incorporation of the radio-isotope,
 33P, and APA as a proxy for DOP-ester utilization. The study showed that
 DIP uptake of individual strains followed Michaelis-Menten kinetics
 (modified in our study to incorporate cellular P quotas), but differed
 with DIN and P availability, and between growth stages. High-affinity DIP
 uptake and APA were activated below a P quota threshold of ~0.01 µg P µg-1
 C across the species and strains. C. ovalisporum had significantly higher
 APA and P quotas (per unit C and cell) but lower uptake affinity than R.
 raciborskii. Demand for DIP by C.ovalisporum increased when N fixation
 occurred, but typically not for R.raciborskii. Our results indicate that
 cyanobacterial species and strains differ in their strategies to P
 limiting conditions, and highlight the interplay between N and P.
 Physiological adaptations like APA and diazotrophy of cyanobacteria
 adapting to low-DIP and/or DIN conditions, may occur simultaneously and
 drive species dominance in oligotrophic environments.
description: We collected all the data from
 laboratory culture experiments on two diazotrophic cyanobacteria,
 <em>Raphidiopsis raciborskii</em> (six strains) and
 <em>Chrysosporum ovalisporum</em> (two strains), in response
 to different DIN and P availabilities.
 Dissolved inorganic P
 (DIP) uptake affinity,
 alkaline phosphatase activity (APA), photosynthetic yield, optical
 density at 750 nm wavelength (OD750), cell count (cell volume, number),
 cellular nutrient concentrations (carbon, N, and P), dissolved inorganic N
 and P (ammonium, nitrite/nitrate, phosphate) were measured over the
 duration of the experiments. We used R package
 <em>“segmented</em>” to run segment regression analysis to
 determine the threshold of cellular P quotas where there was an abrupt
 change in DIP uptake affinity and APA. We used MATLAB and high
 performancing computer (HPC) to run Monte Carlo simulations to determine
 the best fit of uptake kinetics, i.e., maximum uptake rates and half
 saturation constant of DIP uptake, in response to a given external DIP
 supply.
description: Codes are written in R and Matlab.
 Input files can be .csv files for the R codes, and .xlsx files for
 Matlab.
DOI: 10.5281/zenodo.18403631
title: Cellular and molecular landscapes of human tendons across the lifespan revealed by spatial and single-cell transcriptomics

description: Abstract

Tendon injuries are common and often heal poorly. While developing tendons heal without scarring, this capacity declines with age, yet the underlying cellular transitions remain poorly defined. Here, we integrate histological, single-nucleus, single-cell, and spatial transcriptomic profiling of human Achilles and quadriceps tendons across embryonic, foetal, and adult stages, including ruptured adult tendons. We identify seven embryonic progenitor states that give rise to three distinct tendon-associated fibrillar, connective tissue, and chondrogenic lineages. These populations diversify during development and occupy distinct spatial niches, adopting specialised roles in matrix synthesis, tissue remodelling, and mechanical adaptation. While non-fibroblast populations remain transcriptionally stable with age, fibroblasts undergo marked reprogramming, shifting to homeostatic or injury-responsive states. In ruptured adult tendons, a subset of fibroblasts partially reactivates developmental programs but remains transcriptionally distinct from their regenerative counterparts. These findings define the cellular architecture of human tendon development and ageing and reveal lineage-specific targets for therapeutic repair.

Data description

This dataset comprises the 10X Visium spatial transcriptomics data from human fetal Achilles (Dev16126_Ach_EnthMB) and Quadriceps (Dev16126_Quad_MB and Dev16126_Quad_MB2) tendons. For each sample this dataset contains:



cellranger filtered_feature_bc_matrix

spatial files, including Loupe files


Methods:

Foetal Achilles (N=1) and quadriceps tendons (N=2) (Table S1) were dissected from both legs of a single 20 pcw foetus and flash frozen in liquid nitrogen. In preparation for spatial transcriptomics (ST), the samples were cut to ≤0.65 cm² to fit the 10x Genomics Visium ST slide regions. We were able to retain enthesis-to-MTJ as well as adjacent muscle tissue regions for both types of tendons. The samples were embedded in cold OCT mounting medium (VWR) on dry ice and cut longitudinally into 10 μm sections, which were then fixed and stained with H&E to verify tissue morphology and suitability. The sections were prepared for sequencing according to the 10X Genomics recommended protocols using the Visium Gene Expression Slide and Reagent Kit alongside a Dual Index Kit TT Set A. Libraries were sequenced using Illumina NextSeq500 (paired-end) at a depth of 54,000 (Quad2 tendon), 74,000 (Ach) and 119,000 (Quad1) mean reads per spot. The data and images were processed with SpaceRanger (v1.3.1; 10X Genomics) using default settings and mapped to the GRCh38 reference genome.
DOI: 10.5281/zenodo.18403632
title: Cellular and molecular landscapes of human tendons across the lifespan revealed by spatial and single-cell transcriptomics

description: Abstract

Tendon injuries are common and often heal poorly. While developing tendons heal without scarring, this capacity declines with age, yet the underlying cellular transitions remain poorly defined. Here, we integrate histological, single-nucleus, single-cell, and spatial transcriptomic profiling of human Achilles and quadriceps tendons across embryonic, foetal, and adult stages, including ruptured adult tendons. We identify seven embryonic progenitor states that give rise to three distinct tendon-associated fibrillar, connective tissue, and chondrogenic lineages. These populations diversify during development and occupy distinct spatial niches, adopting specialised roles in matrix synthesis, tissue remodelling, and mechanical adaptation. While non-fibroblast populations remain transcriptionally stable with age, fibroblasts undergo marked reprogramming, shifting to homeostatic or injury-responsive states. In ruptured adult tendons, a subset of fibroblasts partially reactivates developmental programs but remains transcriptionally distinct from their regenerative counterparts. These findings define the cellular architecture of human tendon development and ageing and reveal lineage-specific targets for therapeutic repair.

Data description

This dataset comprises the 10X Visium spatial transcriptomics data from human fetal Achilles (Dev16126_Ach_EnthMB) and Quadriceps (Dev16126_Quad_MB and Dev16126_Quad_MB2) tendons. For each sample this dataset contains:



cellranger filtered_feature_bc_matrix

spatial files, including Loupe files


Methods:

Foetal Achilles (N=1) and quadriceps tendons (N=2) (Table S1) were dissected from both legs of a single 20 pcw foetus and flash frozen in liquid nitrogen. In preparation for spatial transcriptomics (ST), the samples were cut to ≤0.65 cm² to fit the 10x Genomics Visium ST slide regions. We were able to retain enthesis-to-MTJ as well as adjacent muscle tissue regions for both types of tendons. The samples were embedded in cold OCT mounting medium (VWR) on dry ice and cut longitudinally into 10 μm sections, which were then fixed and stained with H&E to verify tissue morphology and suitability. The sections were prepared for sequencing according to the 10X Genomics recommended protocols using the Visium Gene Expression Slide and Reagent Kit alongside a Dual Index Kit TT Set A. Libraries were sequenced using Illumina NextSeq500 (paired-end) at a depth of 54,000 (Quad2 tendon), 74,000 (Ach) and 119,000 (Quad1) mean reads per spot. The data and images were processed with SpaceRanger (v1.3.1; 10X Genomics) using default settings and mapped to the GRCh38 reference genome.
DOI: 10.5061/dryad.280gb5mv3
title: Data for: Hidden non-collinear spin-order induced topological surface states

description: Rare-earth monopnictides are a family of materials simultaneously
 displaying complex magnetism, strong electronic correlation, and
 topological band structure. The recently discovered emergent arc-like
 surface states in these materials have been attributed to the
 multi-wave-vector antiferromagnetic order, yet the direct experimental
 evidence has been elusive. Here we report the observation of non-collinear
 antiferromagnetic order with multiple modulations using spin-polarized
 scanning tunneling microscopy. Moreover, we discover a hidden
 spin-rotation transition of single-to-multiple modulations 2 K below the
 Neel temperature. The hidden transition coincides with the onset of the
 surface state splitting observed by our angle-resolved photoemission
 spectroscopy measurements. Single modulation gives rise to a band
 inversion with induced topological surface states in a local momentum
 region while the full Brillouin zone carries trivial topological indices,
 and multiple modulation further splits the surface bands via non-collinear
 spin tilting, as revealed by our calculations. The direct evidence of the
 non-collinear spin order in NdSb not only clarifies the mechanism of the
 emergent topological surface states but also opens up a new paradigm of
 control and manipulation of band topology with magnetism.
description: The STM data was collected by Omicron LT-STM at 4K. MTRX files
 were exported to the IgorPro files with the software Vernissage. Data
 analysis was performed on IgorPro. The figures are plotted with Origin and
 arranged in Adobe Illustrator.
description: Use Vernissage to open the head file ending with
 "_0001.mtrx" and inspect the data contained within. The data can
 be exported as IgorPro files and further analyzed in IgorPro.
 IPF files are IgorPro procedures for data analysis.
description: # Data for: Hidden non-collinear spin-order induced topological surface
 states ## Description of the data and file structure There are three files
 in the dataset: Dataset.zip, filter.ipf, and DriftCorrection.ipf.
 filter.ipf is the IgorPro procedure for filtering out high-frequency noise
 of topographic images.\ DriftCorrection.ipf is the IgorPro procedure for
 drift correction of topographic images by the Lawler-Fujita algorithm. The
 dataset.zip contains folders arranged by the figures in the article
 "Hidden non-collinear spin-order induced topological surface
 states" to be published in Nature Communications. Each folder
 contains the STM raw data for plotting the STM images in the corresponding
 figure. Please refer to the article for a more detailed description of the
 data and methods.
DOI: 10.15472/2fcitm
title: Desarrollo de la especie Masdevallia ignea en dos ambientes del Jardín Botánico José Celestino Mutis - 2025

description: Evaluación del desarrollo de Masdevallia ignea en dos ambientes contrastantes del Jardín Botánico José Celestino Mutis a través de medidas morfológicas (número de hojas, estado fitosanitario) y reproductivas (número de inflorescencias y frutos). Se tomaron 200 medidas durante junio y octubre de 2025.
DOI: 10.7284/164464
title: Multiplexed data collected during research cruise AE2413 using a BIOS METOC instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/164465
title: Multiplexed data collected during research cruise AE2413 using a BIOS METOC instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.gqnk98stm
title: Data from: Allometric brain reduction in an insular, dwarfed population of black-tailed deer

description: Insular populations of mammals have been shown to undergo drastic
 morphological changes relative to mainland counterparts, and these
 adaptations can provide insight into the evolutionary effects of predation
 and competition. Selection has been shown to favor more energetically
 efficient body plans in insular mammals, even when this entails the
 reduction of anti-predator defenses, but few studies have focused on
 morphological effects within the same species. Previous research has
 established that insular large mammals tend to reduce in body size, and
 that size reduction may not scale isometrically across all body parts. The
 brain has been a particular subject of interest due to its high energy
 requirements. Here, we report that an extant, dwarfed island population of
 black-tailed deer (Odocoileus hemionus columbianus) exhibits significantly
 reduced brain mass relative to body mass in comparison to their mainland
 conspecifics, with brain mass 4.9% smaller in the island population for a
 given body mass. Further, in the dwarfed population, orbital area was 4.1%
 smaller for a given body mass, but this reduction was not significant.
 Foramina magna reduced isometrically. In resource-limited insular
 environments, negative allometry of the brain is consistent with
 predictions of reduced investment in energetically costly organs. This
 study is, to our knowledge, the first to examine the morphological effects
 of insularity on brain size in two conspecific populations, and these
 findings suggest that selection toward reduced brain size may act
 relatively quickly after isolation.
DOI: 10.7284/164466
title: Multiplexed data collected during research cruise AE2413 using a BIOS METOC instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.stqjq2c7s
title: Data from: Trait-dependent associations between early- and late-life reproduction in a wild mammal

description: Early- versus late-life trade-offs are a central prediction of
 life-history theory that are expected to shape the evolution of ageing.
 While ageing is widely observed in wild vertebrates, evidence that
 early–late trade-offs influence ageing rates remains limited. Vertebrate
 reproduction is a complex, multi-stage process, yet few studies have
 examined how different aspects of early-life reproductive allocation shape
 late-life performance and ageing. Here, we use longitudinal data from a
 36-year study of wild Soay sheep to show that early-life reproduction
 predicts late-life reproductive performance in a trait-dependent manner.
 Females that started breeding earlier showed more rapid declines in annual
 fecundity with age, consistent with a trade-off. However, age-related
 declines in offspring first-year survival and birth weight were not
 associated with early-life reproduction. Selective disappearance was
 evident in all three late-life reproductive measures, with longer-lived
 females having higher average performance. Our results provide mixed
 support for early–late reproductive trade-offs and show that the way
 early-life reproduction shapes late-life performance and ageing can differ
 among reproductive traits.
DOI: 10.7284/164467
title: Multiplexed data collected during research cruise AE2413 using a BIOS METOC instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/164390
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE2413 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/164468
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE2413 using a SeaBird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/164463
title: Singlebeam Echosounder data collected during research cruise AE2413 using a Knudsen 3260 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6076/d11c7p
title: ASTRAL-Pro: Quartet-based species-tree inference despite paralogy

description: Phylogenetic inference from genome-wide data (phylogenomics) has
 revolutionized the study of evolution because it enables accounting for
 discordance among evolutionary histories across the genome. To this end,
 summary methods have been developed to allow accurate and scalable
 inference of species trees from gene trees. However, most of these
 methods, including the widely used ASTRAL, can only handle single-copy
 gene trees and do not attempt to model gene duplication and gene loss. As
 a result, most phylogenomic studies have focused on single-copy genes and
 have discarded large parts of the data. Here, we first propose a measure
 of quartet similarity between single-copy and multicopy trees that
 accounts for orthology and paralogy. We then introduce a method called
 ASTRAL-Pro (ASTRAL for PaRalogs and Orthologs) to find the species tree
 that optimizes our quartet similarity measure using dynamic programming.
 By studying its performance on an extensive collection of simulated data
 sets and on real data sets, we show that ASTRAL-Pro is more accurate than
 alternative methods.
description: The data are all simulated data generated using Simphy and
 analyzed using a pipeline explained in the paper, including gene tree
 estimation, species tree estimation using various methods.
DOI: 10.5061/dryad.fxpnvx0xn
title: Raw data for: Sex and population differences underlie variation in reproductive success in a warming environment

description: Current rising temperatures are threatening biodiversity. It is therefore
 crucial to understand how climate change impacts male and female fertility
 and whether evolutionary responses can help in coping with heat stress. We
 use experimental evolution to study male and female fertility during
 real-time evolution of two historically differentiated populations
 of Drosophila subobscura under different thermal selection
 regimes for 23 generations. We aim to (1) tease apart sex-specific
 differences in fertility after exposure to warming conditions during
 development, (2) test whether thermal selection can enhance fertility
 under thermal stress, and (3) address the role of historically distinct
 genetic backgrounds. Contrary to expectations, heat stress during
 development had a higher negative impact on female fertility than on male
 fertility. We did not find clear evidence for enhanced fertility in males
 or females evolving under warming conditions. Population history had a
 clear impact on fertility response under thermal stress, particularly in
 males with those from lower latitudes presenting better performance than
 their higher latitude counterparts. We show that the impact of thermal
 stress on fertility varies between traits, sexes and genetic backgrounds.
 Incorporating these several levels of variation is crucial for a deeper
 understanding of how fertility evolves under climate change.
description: This dataset includes the raw data for the article accepted for
 publication in Evolution (EVO-23-0043): "<em>Sex and population
 differences underlie variation in reproductive success in a warming
 environment</em>.” Data correspond to a phenotypic assay performed
 on experimental populations after 23 generations of evolution in different
 thermal selection regimes. Assay included populations from 2 thermal
 selection regimes (warming vs controls, each three fold replicated). Adult
 reproductive performance (Fecundity, productivity and juvenile viability)
 under warming conditions (peak temperature of 29.4ºC) was assessed for
 couples (1 male + 1 female) of the different experimental populations in
 which either the male, the female or both were exposed to those same
 warming conditions during the developmental stage. Raw data are the
 individual data from each assayed couple from a given experimental
 population. Please see the accompanying README.md file for details on data
 description and structure.
DOI: 10.6076/d1wk5r
title: Data for: Weighting by gene tree uncertainty improves accuracy of quartet-based species trees

description: Phylogenomic analyses routinely estimate species trees using methods that
 account for gene tree discordance. However, the most scalable species tree
 inference methods, which summarize independently inferred gene trees to
 obtain a species tree, are sensitive to hard-to-avoid errors introduced in
 the gene tree estimation step. This dilemma has created much debate on the
 merits of concatenation versus summary methods and practical obstacles to
 using summary methods more widely and to the exclusion of concatenation.
 The most successful attempt at making summary methods resilient to noisy
 gene trees has been contracting low support branches from the gene trees.
 Unfortunately, this approach requires arbitrary thresholds and poses new
 challenges. Here, we introduce threshold-free weighting schemes for the
 quartet-based species tree inference, the metric used in the popular
 method ASTRAL. By reducing the impact of quartets with low support or long
 terminal branches (or both), weighting provides stronger theoretical
 guarantees and better empirical performance than the unweighted ASTRAL.
 Our simulations show that weighting improves accuracy across many
 conditions and reduces the gap with concatenation in conditions with low
 gene tree discordance and high noise. On empirical data, weighting
 improves congruence with concatenation and increases support. Together,
 our results show that weighting, enabled by a new optimization algorithm
 we introduce, improves the utility of summary methods and can reduce the
 incongruence often observed across analytical pipelines.
description: - Data are generated using simulations for three out of the four
 archives; see README and the paper for details - From a
 previous publication (https://doi.org/10.1016/j.cub.2018.08.041) for the dogs dataset
DOI: 10.7910/dvn/iakp6p
title: Caracteristicas de informates y sus organizaciones

description: De acuerdo al protocolo de anonimización aprobado por el Comité de Ética de la Pontificia Universidad Católica del Perú, este Dataset contiene 3 archivos. Secundaria-P (en formatos XLSX, TXT y CSV) contiene los detalles anonimizados de las personas que actuaron como informantes. Secundaria-O (en formatos XLSX, TXT y CSV) contiene los datos de las organizaciones a las que pertenecen las personas informantes. El documento en PDF contiene tablas que sintetizan la información procedente de los otros dos archivos.