cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rbnzs7h84
title: Genome-wide association results from: Transcriptomic stratification of late-onset Alzheimer’s cases reveals novel genetic modifiers of disease pathology

description: Late-Onset Alzheimer’s disease (LOAD) is a common, complex genetic
 disorder well-known for its heterogeneous pathology. The genetic
 heterogeneity underlying common, complex diseases poses a major challenge
 for targeted therapies and the identification of novel disease-associated
 variants. Case-control approaches are often limited to examining a
 specific outcome in a group of heterogenous patients with different
 clinical characteristics. Here, we developed a novel approach to define
 relevant transcriptomic endophenotypes and stratify decedents based on
 molecular profiles in three independent human LOAD cohorts. By integrating
 post-mortem brain gene co-expression data from 2114 human samples with
 LOAD, we developed a novel quantitative, composite phenotype that can
 better account for the heterogeneity in genetic architecture underlying
 the disease. We used iterative weighted gene co-expression network
 analysis (WGCNA) to reduce data dimensionality and to isolate gene sets
 that are highly co-expressed within disease subtypes and represent
 specific molecular pathways. We then performed single variant association
 testing using whole genome-sequencing data for the novel composite
 phenotype in order to identify genetic loci that contribute to disease
 heterogeneity. Distinct LOAD subtypes were identified for all three study
 cohorts (two in ROSMAP, three in Mayo Clinic, and two in Mount Sinai Brain
 Bank). Single variant association analysis identified a genome-wide
 significant variant in TMEM106B (p-value &lt; 5´10-8, rs1990620G) in
 the ROSMAP cohort that confers protection from the inflammatory LOAD
 subtype. Taken together, our novel approach can be used to stratify LOAD
 into distinct molecular subtypes based on affected disease pathways.
description: Whole-genome sequencing data and transcriptomic data (RNA-Seq)
 were collected from three independent human cohorts - ROSMAP, Mayo, and
 MSBB - made available by the AMP-AD consortium
 (https://adknowledgeportal.synapse.org/). Gene co-expression modules were
 derived that stratified Alzheimer's disease cases into transcriptomic
 subtypes. Summary phenotypes from each module and subtype scores were
 scanned for genome-wide associations using EMMAX software. Details on data
 processing and analysis are in the linked publication.
description: This data package includes the complete results of the
 genome-wide association analyses published in the associated manuscript,
 as generated by EMMAX. See the README file and the linked publication for
 further details.
DOI: 10.5281/zenodo.17479395
title: Demonstration of a family of X-ray dark-field retrieval approaches on a common set of samples

description: Experimental data, along with retrieved dark-field and phase-retrieved transmission images of carbon-sphere samples, obtained using various imaging techniques and dark-field retrieval algorithms.

 

Full namuscript: (IUCr) Demonstration of a family of X-ray dark-field retrieval approaches on a common set of samples
DOI: 10.5281/zenodo.17479396
title: Demonstration of a family of X-ray dark-field retrieval approaches on a common set of samples

description: Experimental data, along with retrieved dark-field and phase-retrieved transmission images of carbon-sphere samples, obtained using various imaging techniques and dark-field retrieval algorithms.

 

Full namuscript: (IUCr) Demonstration of a family of X-ray dark-field retrieval approaches on a common set of samples
DOI: 10.5061/dryad.x69p8czfg
title: Data from: Demographic history and genomic diversity and divergence in blue tit populations across heterogeneous environments

description: Understanding the genomic processes underlying local adaptation is a
 central aim of modern evolutionary biology. This task requires identifying
 footprints of local selection but also estimating spatio-temporal
 variation in population demography and variation in recombination rate and
 diversity along the genome. Here, we investigated these parameters in blue
 tit populations inhabiting deciduous versus evergreen
 forests and insular versus mainland areas, in the
 context of a previously described strong phenotypic differentiation.
 Neighboring population pairs of deciduous and evergreen habitats were
 weakly genetically differentiated (FST = 0.004 on average),
 nevertheless with a statistically significant effect of habitat type on
 the overall genetic structure. This low differentiation was consistent
 with the strong and long-lasting gene flow between populations,
 inferred by demographic modeling. In turn, insular and mainland
 populations were moderately differentiated (FST = 0.08 on
 average), in line with the inference of moderate ancestral migrations,
 followed by isolation since the end of the last glaciation. Effective
 population sizes were overall large, yet smaller on the island than on the
 mainland. Weak and non-parallel footprints of divergent selection between
 deciduous and evergreen populations were consistent with their high
 connectivity and the probable polygenic nature of local adaptation in
 these habitats. In turn, stronger footprints of divergent selection were
 identified between long isolated insular versus mainland
 birds, and were more often found in regions of low recombination as
 expected from theory. Lastly, we identified a genomic inversion on the
 mainland, spanning 2.8Mb. These results provide insights into the
 demographic history and genetic architecture of local adaptation in blue
 tit populations at multiple geographic scales.
DOI: 10.5061/dryad.dv41ns1vh
title: Data from: Experience counts: the role of female age in morning incubation and brooding behavior in relation to temperature

description: Reproductive experience can impact how individuals allocate time and
 energy to reproduction and generate differences in reproductive behavior
 that leads to experience dependent variation in reproductive success. In
 order to understand if individual variation in parental behavior is
 related to environmental temperature and breeding experience, we observed
 the timing and duration of the first morning off bout in a wild, open cup
 nesting passerine bird during the incubation and early nestling period. We
 compared incubation behaviors and nest temperature of inexperienced
 (second year = first breeding season) and experienced (after second year)
 female hooded warblers Setophaga citrina. Females left the nest earlier on
 colder mornings suggesting an energetic constraint due to the long
 overnight on bout during colder temperatures. During incubation, females
 increased the duration of the first morning off bout with increasing
 temperature. Similarly, during the early nestling period, experienced
 females had shorter off bout duration on colder mornings and increased
 duration with warmer temperatures. In contrast, inexperienced females
 increased off bout duration with colder morning temperatures. Experienced
 females maintained higher nest temperatures and higher minimum nest
 temperatures compared to inexperienced females. We also found evidence
 that experienced females nested in microhabitats with higher minimum
 morning temperature which may buffer older females from colder daily
 extremes and enable older females to maintain higher nest temperatures.
 While we found no relationship between incubation and brooding behaviors
 and fledging success, the proportion of the clutch that hatched was
 positively related to minimum nest temperature. The ability of experienced
 females to maintain higher minimum nest temperatures and to adjust
 brooding behaviors during colder mornings is a potential mechanism that
 has consequences for nestling condition in a wild population. Our results
 highlight the need to examine experience related parental care behaviors
 in responding to environmental variation.
DOI: 10.5061/dryad.zcrjdfn7v
title: Data from: Trait evolution and historical biogeography shape assemblages of annual killifish

description: Aim: Different species assemblages of annual killifish possess replicated
 body size distributions yet have unique sets of species in each area of
 endemism. Here, we use models of trait evolution and historical
 biogeography to discover how size variation originated and has been
 restructured. Location: South America. Taxon: Austrolebias
 (Cyprinodontiformes). Methods: We sampled 63 individuals from 26
 Austrolebias species. Using phylogenetic trees (BEAST2), data on
 environmental variables at sampling locations and size data we compare
 different models for trait evolution (SURFACE, l1OU) of body size and
 niche traits. We model the historical biogeography of the areas of
 endemism (BioGeoBEARS) and use both analyses in combination to reconstruct
 the history of four species assemblages. Results: We present new
 phylogenetic trees for Austrolebias and use them to show that large size
 principally arose within a single area driven by a shifted selection
 optimum for a subset of the species in that area. We suggest that
 ecological interactions triggered size divergence and that this
 large-bodied lineage subsequently spread to two other areas. A second
 assemblage may have been shaped by adaptation to a new environment without
 an associated increase in size divergence. A third assemblage, which has
 the smallest size range and the most recent origin, is phylogenetically
 clustered and we found no evidence of environmental filtering. Main
 conclusions: Assemblage similarity in Austrolebias is the result of
 contrasting ecological, evolutionary and historical processes. Modelling
 trait evolution together with historical biogeography can help to
 disentangle the complex histories of multispecies assemblages. This
 approach provides context to commonly used tests investigating the role of
 ecological processes from phylogenetic data and generates new testable
 hypotheses on the processes that generated trait diversity and assemblage
 similarity.
DOI: 10.5061/dryad.hhmgqnkdc
title: Self-organised criticality models

description: Complex biological systems are considered to be controlled using feedback
 mechanisms. Reduced systems modelling has been effective to describe these
 mechanisms, but this approach does not sufficiently encompass the
 required complexity that is needed to understand how localised
 control in a biological system can provide global stable states.
 Self-Organised Criticality (SOC) is a characteristic property of locally
 interacting physical systems, which readily emerges from changes to its
 dynamic state due to small nonlinear perturbations. These small changes in
 the local states, or in local interactions, can greatly affect the total
 system state of critical systems. It has long been conjectured that SOC is
 cardinal to biological systems, that show similar critical dynamics, and
 also may exhibit near power-law relations. Rate Control of Chaos (RCC)
 provides a suitable robust mechanism to generate SOC systems, which
 operates at the edge of chaos. The bio-inspired RCC method requires only
 local instantaneous knowledge of some of the variables of the system, and
 is capable of adapting to local perturbations. Importantly, connected RCC
 controlled oscillators can maintain global multi-stable states, and
 domains where power-law relations may emerge. The network of oscillators
 deterministically stabilises into different orbits for different
 perturbations, and the relation between the perturbation and amplitude can
 show exponential and power-law correlations. This can be considered to be
 representative of a basic mechanism of protein production and control,
 that underlies complex processes such as homeostasis. Providing feedback
 from the global state, the total system dynamic behaviour can be boosted
 or reduced. Controlled SOC can provide much greater understanding of
 biological control mechanisms, that are based on distributed local
 producers, with remote consumers of biological resources, and globally
 defined control.
description: These euqation files match the EuNeurone numerical simulation
 software. It can use different fixed step integration algorithms for the
 numerical integration of an entire set of equations. The Eq files contain
 the equation code, which is byte compiled for real time computation.
 External data can be presented to the models using a socket
 implementation. A client is provided that demonstrate this mechanism. This
 can be used to feed numerical models with real data.
 Code is available at Github, but needs to be custom build by the
 user due to the dependencies.
 https://github.com/biodynamical/euneurone
description: Models are descibred as sets of differential equations with
 initial values, and parameters. These are parsed and compiled by the
 EuNeurone software for integration.
DOI: 10.5061/dryad.xsj3tx9bt
title: Data from: Redescription and phylogenetic affinities of the caimanine Eocaiman cavernensis (Crocodylia, Alligatoroidea) from the Eocene of Argentina

description: Caimaninae is one of the few crocodylian lineages that still has living
 representatives. Today, most of its six extant species are restricted to
 South and Central America. However, recent discoveries revealed a more
 complex evolutionary history, with a fossil record richer than previously
 thought and a possible North American origin. Among the oldest caimanines
 is Eocaiman cavernensis, from the Eocene of Patagonia, Argentina. It was
 described by George G. Simpson in the 1930s, representing the first
 caimanine reported for the Paleogene. E. cavernensis has then been
 ubiquitous in phylogenetic studies on the group, but a more detailed
 morphological description and revision of the taxon was lacking. Here, we
 present a reassessment of E. cavernensis, based on first-hand examination
 and micro-computed tomography of the holotype, and reinterpret different
 aspects of its morphology. We explore the phylogenetic affinities of E.
 cavernensis and other caimanines using parsimony and Bayesian inference
 approaches. Our results provide evidence for a monophyletic Eocaiman genus
 within Caimaninae, even though some highly incomplete taxa (including the
 congeneric Eocaiman itaboraiensis) represent significant sources of
 phylogenetic instability. We also found Culebrasuchus mesoamericanus as
 sister to all other caimanines and the North American globidontans (i.e.
 Brachychampsa and closer relatives) outside Caimaninae. A time-calibrated
 tree, obtained using a fossilised birth-death model, shows a possible
 Campanian origin for the group (76.97±6.7 Ma), which is older than the age
 estimated by studies using molecular data, and suggests that the earliest
 cladogenetic events of caimanines took place rapidly and across the K-Pg
 boundary.
DOI: 10.5061/dryad.nvx0k6dpd
title: A practical approach to measuring the biodiversity impacts of land conversion

description: 1. Further progress in reducing biodiversity loss relies on the improved
 quantification of the connections between drivers of habitat loss and
 subsequent biodiversity impacts. To this end, biodiversity impact metrics
 should be able to report linked trends in specific human activities and
 changes in biodiversity state, accounting for both the ecology of
 different species, and the cumulative effects of historical habitat
 losses. These characteristics are not currently captured within a single
 metric. 2. Here we develop a globally applicable methodological framework
 that uses freely and publicly available datasets to quantify the relative
 impacts of anthropogenic activities on biodiversity. We use
 species-specific habitat suitability models to link specific land uses to
 ensuing changes in the likelihood that local populations of those species
 will persist. To illustrate our approach we assess the impacts of soy
 expansion and other land uses within the Brazilian Cerrado on over 2,000
 species of amphibians, birds, mammals and plants for three periods between
 2000 and 2014. 3.  Our results showed that mammals and plants
 suffered the greatest overall reduction of suitable habitat. However,
 among endemic and near-endemic species – which face greatest risk of
 global extinction from habitat conversion in the Cerrado – birds and
 mammals were the most affected groups. While conversion of natural
 vegetation to grassland and planted pastures were together responsible for
 most of the biodiversity impact of recent changes, soy expansion (via
 direct conversion of natural vegetation) had the greatest impact per unit
 area. The total biodiversity impact of recent land-use change was
 concentrated in the southern states of the Cerrado -Minas Geráis, Goiás
 and Mato Grosso - but the impact on biodiversity of production of soy was
 greatest within the agricultural frontiers of Bahía and Piauí. 4. The
 flexibility of our approach to examine linkages between biodiversity loss
 and specific human activities has clear potential to better characterise
 the pathways by which habitat loss drivers operate. Its capacity to
 incorporate species-specific ecological needs, through a globally
 applicable methodology, can improve the tangibility of biodiversity loss
 assessments.
DOI: 10.5061/dryad.mcvdncjxp
title: Age, tissue, genotype and virus infection regulate Wolbachia levels in Drosophila

description: The bacterial symbiont Wolbachia can protect insects against viral
 pathogens, and the varying levels of antiviral protection are correlated
 with the endosymbiont load within the insects. To understand why Wolbachia
 strains differ in their antiviral effects, we investigated the factors
 controlling Wolbachia density in five closely related strains in their
 natural Drosophila hosts. We found that Wolbachia density varied greatly
 across different tissues and between flies of different ages, and these
 effects depended on the host-symbiont association. Some endosymbionts
 maintained largely stable densities as flies aged while others increased,
 and these effects in turn depended on the tissue being examined. Measuring
 Wolbachia rRNA levels in response to viral infection, we found that viral
 infection itself also altered Wolbachia levels, with FHV causing
 substantial reductions in symbiont loads late in the infection. This
 effect, however, was virus-specific as DCV had little impact on Wolbachia
 in all of the five host systems. Since viruses have strong tissue tropisms
 and antiviral protection is thought to be cell autonomous, these effects
 are likely to affect the virus-blocking phenomenon. However, we were
 unable to find any evidence of a correlation between Wolbachia and viral
 titers within the same tissues. We conclude that Wolbachia levels within
 flies are regulated in a complex host-symbiont-virus dependent manner and
 this trinity is likely to influence the antiviral effects of Wolbachia.
DOI: 10.5061/dryad.6q573n5w9
title: Data from: Decreased bioefficacy of long-lasting insecticidal nets and the resurgence of malaria in Papua New Guinea

description: Papua New Guinea (PNG) has the highest malaria transmission outside of
 Africa. Long-lasting insecticidal nets (LLINs) are believed to have helped
 to reduce average malaria prevalence in PNG from 15.7% in 2008 to 1% in
 2014. Since 2015 malaria indicators in PNG have risen significantly. In
 the present study, we observed a drastically decreased bioefficacy of
 unused LLINs with manufacturing dates between 2013 and 2019 collected from
 villages and LLIN distributors in PNG. Specifically, of the tested n=167
 LLINs manufactured between 2013 and 2019 only 16% achieved ≥ 80%
 24h-mortality or ≥ 95% 60 min-knockdown in cone
 bioassays conducted with pyrethroid susceptible Anopheles farauti
 mosquitoes. In contrast, all (100%, n=25) LLINs with manufacturing dates
 between 2007 and 2012 achieved ≥ 80% 24h-mortality or ≥ 95% 60
 min-knockdown. This difference was extremely statistically significant. We
 hypothesise that decreased bioefficacy of LLINs has contributed to the
 malaria resurgence in PNG.
description: This dataset is the result of cone bioassays on unused and used
 long-lasting insecticidal nets using Anopheles farauti mosquitoes. The
 assays were conducted at the Papua New Guinea Institute of Medical
 Research. Please refer to the manuscript methods section for detailed
 information on the methods employed in this study. Data are presented in
 the form of an excel spreadsheet.
DOI: 10.5061/dryad.t4b8gthzp
title: Orchelimum vulgare microbiome nutrient data

description: Understanding what conditions alter insect gut microbial communities is
 important for management and conservation of insect herbivores like
 grasshoppers and katydids. This dataset represents the constituents of the
 gut microbiome of the common meadow katydid, Orchelimum vulgare (n=13),
 when subjected to added nutrients. The objective was to identify whether
 or not there would be shifts in characteristic microbial groups or changes
 in levels of community diversity when nitrogen and phosphorus or sodium
 were added to the host environment.  Katydids were harvested and
 processed and their gut microbiome subsequently sequenced to identify
 microbial taxa present in the host.
description: Individual specimens of the common meadow katydid
 <em>Orchelimum vulgare </em>were collected from a coastal tall
 grass prairie in Texas. This prairie had been divided into treatment plots
 recieving added sodium and added nitrogen and phophorus.  Some plots
 recieved no added nutrients.  The treatments were as follows: added sodium
 only (Sodium), added nitrogen and phosphorus only (NP), both added sodium
 and added nitrogen and phosphorus (NPNA), and no added nutrients (None). 
 No katydid was collected from the same plot.  There were a total of 13
 individuals: Sodium (n=4), NP (n=3), NPNA (n=3), None (n=3).
 Each individual was dissected and the entire gut was removed. The
 DNA was extracted from the gut after homogenization and lysis. DNA was
 sent for 16s sequencing of the V3-V4 region and the ITS2 region. 
 Bacterial and fungal communities were characterized using the Greenegenes
 database (gg_13_8).