cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xksn02vdf
title: Supplemental material from: A population-based prevalence of myotonic dystrophy type 1

description: Objective: To determine whether the genetic prevalence of the CTG
 expansion in the DMPK gene associated with myotonic
 dystrophy (DM1) in an unbiased cohort is higher than previously reported
 population estimates, ranging from 5-20 per 100,000 individuals. Methods:
 This study used a cross-sectional cohort of de-identified dried blood
 spots (DBS) from the newborn screening program in the state of New York,
 taken from consecutive births from 2013-2014. Blood spots were
 screened for the CTG repeat expansion in the DMPK gene
 using triplet-repeat primed PCR and melt curve analysis. Melt
 curve morphology was assessed by four blinded reviewers to identify
 samples with possible CTG expansion. Expansion of the CTG repeat
 was validated by PCR fragment sizing using capillary electrophoresis for
 samples classified as positive or premutation to confirm the
 result. Prevalence was calculated as the number of samples with
 CTG repeat size ≥50 repeats compared to the overall
 cohort.   Results: Out of 50,382 consecutive
 births, there were 24 with a CTG repeat expansion ≥50, consistent with a
 diagnosis of DM1. This represents a significantly higher DM1
 prevalence of 4.76 per 10,000 births (95%CI 2.86, 6.67) or 1 in every
 2,100 births. There were an additional 96 samples (19.1 per
 10,000 or 1 in 525 births) with a CTG expansion in
 the DMPK gene in the premutation range (CTG)35-49.
 Conclusions: The prevalence of individuals with CTG repeat expansions
 in DMPK is up to five times higher than previous
 reported estimates. This suggests DM1, with multisystemic
 manifestations, is likely underdiagnosed in practice.
DOI: 10.5061/dryad.gxd2547jg
title: Code for: Same-sex sexual behaviour and selection for indiscriminate mating

description: File provides Mathematica code to replicate the analyses of "Same-sex
 sexual behaviour and selection for indiscriminate mating" by Lerch
 and Servedio. All figures from the manuscript (and its supplement) can be
 obtained by running the code. Comments for the code is provided for the
 "Additive death" section with other sections presented in
 parallel.
DOI: 10.5061/dryad.qrfj6q5d7
title: Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"

description: Trait-based ecology suggests that abiotic filtering is the main mechanism
 structuring the regional species pool in different subsets of
 habitat-specific species. At more local spatial scales, other ecological
 processes may add on giving rise to complex patterns of functional
 diversity (FD). Understanding how assembly processes operating on the
 habitat-specific species pools produce the locally observed plant
 assemblages is an ongoing challenge. Here, we evaluated the importance of
 different processes to community assembly in an alpine fellfield,
 assessing its effects on local plant trait FD. Using classical
 randomization tests and linear mixed models, we compared the observed FD
 with expectations from three null models that hierarchically incorporate
 additional assembly constraints: stochastic null models (random assembly),
 independence null models (each species responding individual and
 independently to abiotic environment), and co-occurrence null models
 (species responding to environmental variation and to the presence of
 other species). We sampled species composition in 115 quadrats across 24
 locations in the central Pyrenees (Spain) that differed in soil
 conditions, solar radiation and elevation. Overall, the classical
 randomization tests were unable to find differences between the observed
 and expected functional patterns, suggesting that the strong abiotic
 filters that sort out the flora of extreme regional environments blur any
 signal of other local processes. However, our approach based on linear
 mixed models revealed the signature of different ecological processes. In
 the case of seed mass and leaf thickness, observed FD significantly
 deviated from the expectations of the stochastic model, suggesting that
 fine-scale abiotic filtering and facilitation can be behind these
 patterns. Our study highlights how the hierarchical incorporation of
 ecological additional constraints may shed light on the dim signal left by
 local assembly processes in alpine environments.
description: The folder contains: a)
 NullAssemblagesSimulation - R source code to:<br>         1)
 estimate the occurrence probability of each specie based on hierarchically
 increasingly complex null models<br>         2) simulate the null
 assemblages <br>         3) compare the observed and expected
 functional diversity (RAO). Generation of Standardized Effect Sizes
 (SES).<br>         4) test for significance based on i)
 randomization tests and ii) generalized linear mixed models
 <br> b) DataSets.Rdata - R file containing the datasets of
 vegetation cover, functional traits and predictor variables. 
 c) DataSets.xlsx - Excel file containing sheets with the metadata
 and the datasets of vegetation cover, functional traits and predictor
 variables.
DOI: 10.5061/dryad.8931zcrnz
title: Results from: Angiogenic property of silk fibroin scaffolds with adipose-derived stem cells on chick chorioallantoic membrane

description: Angiogenesis is a key step in tissue regeneration and repair. Biomaterials
 that allow or promote angiogenesis are thus beneficial. In this study,
 angiogenic properties of salt-leached silk fibroin (SF) scaffolds seeded
 with human adipose stem cells (hADSCs) were studied using chick
 chorioallantoic membrane (CAM) as a model. The hADSC-seeded SF scaffolds
 (SF-hADSC) with porosity of 77.34 ± 6.96 % and pore diameter of 513.95 ±
 4.99 µm were implanted on CAM of chick embryos that were on embryonic day
 8 (E8) of development. The SF-hADSC scaffolds induced a spoke-wheel
 pattern of capillary network indicative of angiogenesis, which was evident
 since E11. Moreover, ingrowth of blood vessels into the scaffolds was seen
 in histological sections. The unseeded scaffolds induced the same extent
 of angiogenesis later on E14. In contrast, the control group could not
 induce angiogenesis to the same extent even as late. In vitro cytotoxicity
 tests and in vivo angioirritative study reaffirmed the biocompatibility of
 the scaffolds. This work highlighted that the biocompatible SF-hADSC
 scaffolds accelerates angiogenesis, and hence they can be a promising
 biomaterial for regeneration of tissues that require angiogenesis.
description:
DOI: 10.5061/dryad.hmgqnk9f2
title: Inter-group relationships influence territorial defence in mountain gorillas

description: 1. Many species show territoriality, in which territory owners have
 exclusive or priority use of a region. In humans, tolerance of others
 within our space also depends greatly on our social relationships with
 them. This has been hypothesised as one potential driver of the evolution
 of long-term, inter-group relationships, through enabling shared access of
 resources and easing disputes over space. 2. However, extremely little is
 known about the importance of social relationships between neighbouring
 groups in non-humans for how space is used and shared. 3. Using 16 years
 of data on the simultaneous movement and interaction patterns of 17
 mountain gorilla groups, we investigated how the occurrence of aggressive
 and affiliative behaviour during inter-group encounters was influenced by
 both their social and spatial context. 4. We found evidence of territorial
 defence, with rates of aggression increasing towards the centre of home
 ranges. Groups which had previously split from each other showed higher
 levels of affiliation during encounters with each other and experienced
 lower levels of aggression when within the other’s peripheral home range.
 However, encounters within core areas of the home range consistently
 elicited higher aggression, regardless of the groups’ history. Our
 findings indicate that not only are the social relationships between
 groups retained after they split from one another, but that these
 relationships enable groups to access certain areas with a reduced risk of
 aggression. 5. This suggests that reduced aggression when accessing areas
 within neighbours’ home ranges may be an advantage for the maintenance of
 inter-group relationships and a potential driver in the evolution of
 long-term, post-dispersal relationships and complex multi-level societies.
DOI: 10.5061/dryad.3bk3j9kh3
title: A neural circuit for flexible control of persistent behavioral states

description: To adapt to their environments, animals must generate behaviors that are
 closely aligned to a rapidly changing sensory world. However, behavioral
 states such as foraging or courtship typically persist over long time
 scales. It remains unclear how neural circuits generate persistent
 behavioral states while maintaining flexibility to switch states when the
 context changes. Here, we elucidate the architecture of a circuit
 controlling the choice between roaming and dwelling foraging states in C.
 elegans. Through ensemble-level calcium imaging in freely-moving animals,
 we identify stable, circuit-wide activity patterns corresponding to each
 state. Mutual inhibition between two neuromodulatory systems underlies the
 persistence and mutual exclusivity of the opposing network states. We
 identify a sensory processing neuron that transmits information about food
 odors to both the roaming and dwelling circuits, biasing the animal
 towards different states in different contexts. These findings reveal a
 circuit architecture that enables flexible, sensory-driven control of
 persistent behavioral states.
DOI: 10.15468/dl.zj2eab
title: Occurrence Download

description: A dataset containing 440 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Castanospermum australe",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 440 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002574-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jm63xsj84
title: Supplementary material for: Long branch attraction biases in phylogenetics

description: Long branch attraction is a prevalent form of bias in phylogenetic
 estimation but the reasons for it are only partially understood. We argue
 here that it is largely due to differences in the sizes of the model
 spaces corresponding to different trees. Trees with long branches together
 allow much more flexible internal branch-length parameter estimation.
 Consequently, although each tree has the same number of parameters, trees
 with long branches together have larger effective model spaces. The
 problem of long branch attraction becomes particularly pronounced with
 partitioned data. Formulation of tree estimation as model selection leads
 us to propose bootstrap bias corrections as cross-checks on estimation
 when long branches end up being estimated together.
DOI: 10.5281/zenodo.18393124
title: Transient morphogenetic constraints organize self-assembling axon neighborhoods for robust yet flexible wiring

description: Transient morphogenetic constraints organize self-assembling axon neighborhoods for robust yet flexible wiring

Overview

This repository provides data supporting the study of constrained stochastic assembly in the C. elegans nerve ring. It includes embryonic morphogenetic imaging, curated EM-derived neurite contact and spatial domain datasets, and agent-based innervation simulation outputs and intermediate processed data used in all analyses. Source code for agent-based simulations and figure generation is maintained in a companion GitHub repository (https://github.com/cabrittin/constrained-innervation-abm/), with versioned releases archived for reproducibility. Documentation specifies data formats, software dependencies, and instructions for reproducing the analyses and simulations.

Data Organization (Conceptual Structure)

Conceptually, the datasets are organized into the following categories:- Embryonic imaging data used to identify rosettes, corridor cells and pioneer axon trajectories.   - EM-derived neurite contact, spatial domain datasets and neighborhood metrics.  - Agent-based simulation outputs  

Due to file size constraints, datasets are provided as individually downloadable files and compressed archives rather than a nested directory structure.

File Manifest



exemplar_embryo_rosette_corridor_id.tar.bz2: Exemplar embryo used to identify rosettes and corridor cells; includes raw embryo image and associated AceTree lineage file

abm_sim_model54.tar.bz2: ABM simulations for local self-organizing model 54; raw simulation data used for Fig. 5E-M and Fig. S9

abm_sim_model58.tar.bz2: ABM simulations for local self-organizing model 58; raw simulation data used for Fig. 6A,B,C,F,G,H; Fig. 7A-E; Fig. S9

abm_sim_model65.tar.bz2: ABM simulations for local self-organizing model 65; raw simulation data used for Fig. 7F 

abm_sim_pi_models.tar.bz2: ABM simulations for positionally informed models 66, 67, 68; ABM simulations for positionally informed negative control; raw simulation data used for Fig. S7B 


Code Availability

Source code for agent-based simulations, data processing, and figure generation is hosted in a companion GitHub repository:

GitHub: https://github.com/cabrittin/constrained-innervation-abm/

Versioned releases of the codebase are archived via Zenodo for long-term reproducibility.

Reproducibility

Documentation in the GitHub repository specifies:- Software dependencies- Execution instructions- Scripts to reproduce figures and analyses

Processed datasets in this repository correspond to the analyses reported in the manuscript.

Citation

Citation for this dataset will be updated upon manuscript publication.

Zenodo DOI: 10.5281/zenodo.18393124

License

Data are released under the CC-BY 4.0 License, unless otherwise noted.Code is released under the MIT License (see GitHub repository).

Contact

For questions, contact:Christopher Brittin (corresponding author)
DOI: 10.5061/dryad.w9ghx3fn0
title: Stan code from: Branching networks can have opposing influences on genetic variation in riverine metapopulations

description: Aim: Fractal networks, represented by branching complexity in rivers, are
 ubiquitous in nature. In rivers, the number of either distal (e.g., in
 headwater streams) or confluent (e.g., in mainstems) locations can be
 increased along with their branching complexity. Distal- or
 confluent-spatial locations can result in fewer or greater corridor
 linkages that can alter genetic divergence at the metapopulation scale.
 These mechanisms underlying the resulting genetic structuring remain
 poorly understood at the metapopulation scale, particularly in terms of
 the roles of species-specific dispersal traits. The objective of this
 study is to mechanistically understand how branching complexity can
 simultaneously influence genetic divergence in opposite directions.
 Location: Northeastern Japan Methods: To evaluate the integrated
 influences of network complexity and species dispersal on genetic
 divergence among populations at the catchment scale, we modelled
 metapopulation genetic dynamics under a Bayesian inference framework by
 adapting empirical genetic data from four macroinvertebrate species.
 Simulations were then performed using empirical and virtual
 species-characteristics on virtual river networks. Results: Our simulation
 experiments showed that both greater landscape connectivity (resulting
 from shorter watercourse distance) and greater isolation of distal
 locations occurred in the more-branched river networks. These two spatial
 features have negative and positive influences on genetic divergence, with
 their relative importance varying among different species and dispersal
 characteristics. Specifically, genetic divergence at the metapopulation
 scale increased for species having higher downstream-biased dispersal but
 decreased for species having higher upstream-biased dispersal. Distal
 populations (e.g., in headwaters) have higher genetic independence when
 downstream-biased asymmetry is higher. Main conclusions: We found a strong
 association between species dispersal and evolutionary processes such as
 gene flow and genetic drift. This association mediates the pervasive
 influences of branching complexity on genetic-divergence in the
 metapopulation. It also highlights the importance of considering species
 dispersal-patterns when developing management strategies in the face of
 rapid environmental-change scenarios.
DOI: 10.7280/d1f973
title: Permeability of H2 in ice Ih

description: Reconstructions of paleoatmospheric H2 using polar firn air and ice cores
 would lead to a better understanding of the H2 biogeochemical cycle and
 how it is influenced by climate change and human activity. H2 is a small,
 highly diffusive molecule, and its mobility in the ice matrix must be
 accounted for when intepreting polar firn air and ice core measurements.
 Previous work on the mobility of H2 in ice has focused on warm (272-273
 K), high pressure systems that are not directly comparable to conditions
 in polar ice sheets. In this study, the permeability,
 diffusivity, and solubility of H2 are determined experimentally in ice Ih
 at temperatures relevant to polar ice sheets (199-253 K). The data are
 reported as the optimized diffusivity (m2 s-1), solubility (mol m-3 Pa-1),
 and permeability (mol m-1 s-1 Pa-1) for each of 17 experiments using two
 different samples of ice. Optimized values are reported with
 their ±1σ uncertainties. The temperature (K) for each experiment
 is also reported. 
description: This study was carried out using a “block degassing” method. This
 involves exposing a block of ice to a pure H<sub>2</sub>
 atmosphere for several hours, then replacing the H<sub>2</sub>
 with air and<br> monitoring the H<sub>2</sub> outgassing
 as a function of time. The measurements were analyzed using 3-dimensional
 finite difference diffusion model of the block of ice. The model
 diffusivity and solubility were varied across a wide range of possible
 values. Reported diffusivities and solubilities are the values which
 minimized the sum of the squared residuals between modeled and measured
 rates of H<sub>2</sub> outgassing. For more detailed methods,
 see Patterson & Saltzman (2021).
DOI: 10.5061/dryad.s1rn8pk5q
title: Data from: Asymmetries affecting aggressive contests between solitary parasitoids: the effect of host species

description: Conflicts in animals are usually resolved based on asymmetries, where
 contest winners are often those that value a resource the most and/or
 those who have the greatest potential to retain it. In parasitoid wasps,
 contests between females determine which individual exploits hosts for
 offspring production. Previous studies on solitary parasitoids rarely
 considered the role of biotic factors generating phenotypic variation that
 could influence the strength of asymmetries. Some parasitoid species
 parasitize host species of various sizes, producing offspring that vary
 considerably in size and potentially fighting ability. In this study, we
 reared the egg endoparasitoid Telenomus podisi (Hymenoptera: Scelionidae)
 on two host species to measure the effect of body size on contest
 resolution and how it interacts with ownership and resource value
 asymmetries. Our results showed that ownership status best predicts final
 contest outcome when similar sized wasps fight over hosts. The frequency
 and outcomes of individual fights structuring contests were better
 explained by the difference in the number of eggs laid in the hosts by
 each female at a given time. When contestants varied in body size, larger
 intruders frequently dislodged small owners regardless of ownership and
 resource value asymmetries. These results imply that body size is an
 important factor to consider in solitary parasitoid contests and that it
 can overshadow the effects of other asymmetries. Our study suggests that
 host community diversity could have a direct effect on parasitoid contests
 and that biotic communities, through their effects on animal phenotypes,
 may play an underrated role in contest resolution.
DOI: 10.5061/dryad.rbnzs7h9b
title: Data and code for: River noise alters orb-weaving spider abundance, web size, and prey capture

description: Novel anthropogenic noise has received considerable attention in
 behavioral ecology, but natural acoustic environments have largely been
 ignored as ecological niche axes. In riparian sites, within an arid
 sagebrush steppe ecosystem, we use a natural range of acoustic
 environments along with experimentally broadcasted whitewater river noise
 to test our hypothesis that river noise is an important niche axis. We
 show that orb-weaving spiders (Araneidae and Tetragnathidae) are more
 abundant in high sound level environments, but do not seem to be affected
 by the background noise spectrum. We explore multiple hypotheses for these
 patterns, such as loss of vertebrate predators and increased prey capture,
 and then assess how web-building behavior and body condition may be
 altered. Here, we demonstrate that river noise has the potential to alter
 spider abundance and behavior.
DOI: 10.5061/dryad.g4f4qrfnr
title: Weighted haltere and imposed haltere stroke reduction tethered flying Drosophila kinematics

description: In the true flies (Diptera) the hind wings have evolved into specialized
 mechanosensory organs known as halteres, which are sensitive to gyroscopic
 and other inertial forces. Together with the fly’s visual system, the
 halteres direct head and wing movements through a suite of equilibrium
 reflexes that are crucial to the fly’s ability to maintain stable flight.
 As in other animals (including humans), this presents challenges to the
 nervous system as equilibrium reflexes driven by the inertial sensory
 system must be integrated with those driven by the visual system in order
 to control an overlapping pool of motor outputs shared between the two of
 them. Here, we introduce an experimental paradigm for reproducibly
 altering haltere stroke kinematics and use it to quantify multisensory
 integration of wing and gaze equilibrium reflexes. We show that
 multisensory wing-steering responses reflect a linear superposition of
 individual haltere-driven and visually-driven responses, but that
 multisensory gaze responses follow a non-linear integration logic.
description: Video recordings of flying, tethered
 <em>Drosophila</em> were made using two synchronized
 high-speed cameras (TS3 or IL5, Fastec) at 1000 or 2000FPS. These captured
 the left and right aspects of each fly. Haltere and wing stroke
 joint-angle timeseries were produced using the DeepLabCut
 (https://github.com/DeepLabCut/) and/or DLTdv
 (http://biomech.web.unc.edu/dltdv/) software packages. Body axis length
 and haltere bulb cross-sectional area were estimated using custom MATLAB
 scripts. Concurrent recordings were made with an
 industrial camera (Chameleon3, FLIR) at 100FPS. Head yaw and wing
 downstroke envelope timeseries were produced using the flyalyzer
 (https://github.com/michaelrauscher/flyalyzer) software package.
description: Kinematics data provided in MATLAB .mat format, along with
 accompanying scripts to produce figures for the associated publication.
 README files outline data for weighted haltere experiments
 (BulbWeightData), imposed haltere stroke reduction experiments
 (MagPulseData), and a large control dataset of kinematics from untreated
 flies flying in a magnetic field of varying polarity and magnitude
 (UntreatedData). Also included are several redistributable software
 packages used in accompanying analysis code.