cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17144592
title: Cell cycle–specific NEK2 interactome dataset

description: Proteomics analysis for cell cycle resolved Nek2 interaction dataset.
DOI: 10.5281/zenodo.17144593
title: Cell cycle–specific NEK2 interactome dataset

description: Proteomics analysis for cell cycle resolved Nek2 interaction dataset.
DOI: 10.5061/dryad.bnzs7h4g5
title: Chronic hyperadiponectinemia induced by transgenic overexpression increases plasma exosomes without significantly improving glucose and lipid metabolism

description: The fat-derived factor, adiponectin, is considered a salutary circulating
 factor. We recently demonstrated that native adiponectin binds T-cadherin
 and promotes intracellular biogenesis and secretion of the exosome.
 Exosomes play important roles in various aspects of
 homeostasis, including glucose and energy metabolism. However, it
 remains unclear whether and how the promotion of exosome production by
 adiponectin in vivo is beneficial for glucose and lipid metabolism. In the
 present study, overexpression of human adiponectin in mice resulted in an
 increased number of circulating exosomes, but it did not significantly
 improve glucose metabolism, change body weights, or change triglyceride
 clearance under a high-fat diet. Multiple small doses of streptozotocin
 increased blood glucose and decreased triglyceride clearance similarly in
 both wild-type and transgenic mice. Thus, these results indicated that
 human adiponectin overexpression in mice increases plasma exosomes but
 does not significantly influence glucose and lipid metabolism.
description: Methods are described in the published article: https://doi.org/10.1507/endocrj.EJ22-0665
DOI: 10.5061/dryad.tdz08kq3w
title: Raw motif mapping bedfile data and model training set class probabilities

description: Leveraging prior viral genome sequencing data to make predictions on
 whether an unknown, emergent virus harbors a ‘phenotype-of-concern’ has
 been a long-sought goal of genomic epidemiology. A predictive phenotype
 model built from nucleotide-level information alone is
 challenging with respect to RNA viruses due to the ultra-high
 intra-sequence variance of their genomes, even within closely related
 clades. We developed a degenerate k-mer method to accommodate this high
 intra-sequence variation of RNA virus genomes for modeling
 frameworks. By leveraging a taxonomy-guided ‘group-shuffle-split’
 cross validation paradigm on complete coronavirus assemblies from prior to
 October 2018, we trained multiple regularized logistic regression
 classifiers at the nucleotide k-mer level. We demonstrate the feasibility
 of this method by finding models accurately predicting withheld SARS-CoV-2
 genome sequences as human pathogens and accurately predicting withheld
 Swine Acute Diarrhea Syndrome coronavirus (SADS-CoV) genome sequences as
 non-human pathogens. Feature selection using L1 regularization identified
 several degenerate nucleotide predictor motifs with high model
 coefficients for the human pathogen class that were present across widely
 disparate clades of coronaviruses. However, these motifs differed in which
 genes they were present in, what specific codons were used to encode them,
 and what the translated amino acid motif was. This emphasizes the
 importance of a phenetic view of emerging pathogenic RNA viruses, as
 opposed to the canonical phylogenetic interpretations most commonly used
 to track and manage viral zoonoses. Applying our model to more recent
 Orthocoronavirinae genomes deposited since October 2018 yields a novel
 contextual view of pathogen potential across bat-related, canine-related,
 porcine-related, and rodent-related coronaviruses and critical adaptations
 which may have contributed to the emergence of the pandemic SARS-CoV-2
 virus. Finally, we discuss the next steps to achieve robust predictive
 ensembles and the utility of these models (and their associated predictor
 motifs) to novel biosurveillance protocols that substantially increase the
 ‘pound-for-pound’ information content of field-collected sequencing data
 and make a strong argument for the necessity of routine collection and
 sequencing of zoonotic viruses. 
description: The data was produced by hierarchically clustering K-mers to
 produce degenerate motifs that were then mapped back to the originating
 2276 coronavirus genomes they were drawn from. Class probabilities we
 produced by regularized logistic regression models fit for a human
 pathogen phenotype label applied to those input genomes.
description: tar, gzip. Files can be read using any text reader, and processed
 with bedtools compatible software.
DOI: 10.5281/zenodo.18402603
title: Supplementary_tables_Influence_microphytobenthos_acetate_nitrate_reduction_bacterial_diversity_intertidal_sediments_Seine_Estuary

description: Supplementary material from the study by Turrel et al.  examining the impact of acetate and microphytobenthos on nitrate reduction and bacterial diversity in intertidal sediments of the Seine Estuary.

Supplementary Table 1 : Nitrate Reduction Rate (NRR), Nitrite Production Rate (NiPR) and Ammonium Release Rate (ARR) mesured at the outlet of the FTRs

Supplementary Table 2 : Distribution of ASVs across samples and taxonomic classification

Supplementary Table 3 : MetaCyc Pathways predicted with PICRUSt2 along with their abundances across samples

Supplementary Table 4 : KEGG Orthologs predicted with PICRUSt2 along with their abundances across samples
DOI: 10.5281/zenodo.18402604
title: Supplementary_tables_Influence_microphytobenthos_acetate_nitrate_reduction_bacterial_diversity_intertidal_sediments_Seine_Estuary

description: Supplementary material from the study by Turrel et al.  examining the impact of acetate and microphytobenthos on nitrate reduction and bacterial diversity in intertidal sediments of the Seine Estuary.

Supplementary Table 1 : Nitrate Reduction Rate (NRR), Nitrite Production Rate (NiPR) and Ammonium Release Rate (ARR) mesured at the outlet of the FTRs

Supplementary Table 2 : Distribution of ASVs across samples and taxonomic classification

Supplementary Table 3 : MetaCyc Pathways predicted with PICRUSt2 along with their abundances across samples

Supplementary Table 4 : KEGG Orthologs predicted with PICRUSt2 along with their abundances across samples
DOI: 10.5061/dryad.9w0vt4bkw
title: Data from: Seasonality and growth in tropical freshwater ectotherm vertebrates: results from one-year experimentation in the African grey bichir, giraffe catfish, and the West African mud turtle

description: Growth in ectotherm vertebrates is strongly rhythmed by seasonal variation
 in environmental parameters. To track the seasonal variation in ancient
 times in a continental and tropical context, we aim to develop a method
 based on the use of the growth rate of fossil ectotherm vertebrates
 (actinopterygians and chelonians) influenced by seasonal environmental
 fluctuations they experienced in their lifetime. However, the impact of
 environmental parameters on growth, positive or negative, and its
 intensity, depends on the taxa considered and data are scarce for tropical
 species. For one year, an experiment was conducted to better understand
 the effect of seasonal variation in environmental parameters (food
 abundance, temperature, and photoperiod) on the somatic growth rate of
 three species of tropical freshwater ectotherm vertebrates: the fishes
 Polypterus senegalus and Auchenoglanis occidentalis and the turtle
 Pelusios castaneus. Mimicking seasonal shifts expected to be experienced
 by the animals in the wild, the experiment highlighted the preponderant
 effect of food abundance on the growth rate of those three species. Water
 temperature variation had a significant effect on the growth rate of Po.
 senegalus and Pe. castaneus. Moreover, the photoperiod demonstrated no
 significant effect on the growth of the three species. The duration of
 application of starvation or cool water conditions, ranging from 1 to 3
 months, did not affect the growth rate of the animals. However, Pe.
 castaneus showed a temporary sensitivity to the return of ad libitum
 feeding or of warm water, after a period of starvation or cool water, by a
 period of compensatory growth. Finally, this experiment revealed, in the
 three species, fluctuations in the growth rate under controlled and
 constant conditions. This variation, similar to the variation in
 precipitation and temperature observed in their native environment, could
 be linked to a strong effect of an internal rhythm controlling somatic
 growth rate.
description: All analyses were performed in R Version 4.2.2 (R Core Team,
 2022).
DOI: 10.5061/dryad.573n5tbc9
title: A theory of oligogenic adaptation of a quantitative trait

description: Rapid phenotypic adaptation is widespread in nature, but the underlying
 genetic dynamics remain controversial. Whereas population genetics
 envisages sequential beneficial substitutions, quantitative genetics
 assumes a collective response through subtle shifts in allele frequencies.
 This dichotomy of a monogenic and a highly polygenic view of adaptation
 raises the question of a middle ground, as well as the factors controlling
 the transition. Here, we consider an additive quantitative trait with
 equal locus effects under Gaussian stabilizing selection that adapts to a
 new trait optimum after an environmental change. We present an analytical
 framework based on Yule branching processes to describe how phenotypic
 adaptation is achieved by collective changes in allele frequencies at the
 underlying loci. In particular, we derive an approximation for the joint
 allele-frequency distribution at threshold levels of the trait mean as a
 comprehensive descriptor of the adaptive architecture. Depending on the
 model parameters, this architecture reproduces the well-known patterns of
 sequential, monogenic sweeps, or of subtle, polygenic frequency shifts.
 Between these endpoints, we observe oligogenic architecture types that
 exhibit characteristic patterns of partial sweeps. We find that a single
 compound parameter, the population-scaled background mutation rate Θbg, is
 the most important predictor of the type of adaptation, while selection
 strength, the number of loci in the genetic basis, and linkage only play a
 minor role.
description: The included raw data was generated by evolutionary
 (Wright-Fisher) simulations. The used C++ simulation scripts are included
 as source codes and compiled executables.<br><br>The raw data
 is processed, plotted and complemented with modeling results by Wolfram
 Mathematica scripts. The used code snippets are presented in Mathematica
 Notebooks.<br><br>We provide all code and data to recreate the
 figures in the publication.
description: Wolfram Research, Inc., Mathematica, Version 12.0, Champaign, IL
 (2019). For *.nb (Mathematica Notebooks) and *.mx (Wolfram Language MX
 files).<br><br>Executables and corresponding C++ code
 (Stroustrup, Bjarne. The C++ Programming Language. Reading, Mass.:
 Addison-Wesley, 1995; *.cpp) can be compiled with g++. We use the GNU
 Scientific Library (GSL).<br><br>Besides, the repository
 contains plain text files (*.csv, *.txt), Bash scripts (*.sh),
 OpenDocument Presentation (*.odp), vector graphics (*.pdf) and raster
 graphics (*.png).
DOI: 10.5061/dryad.n8pk0p30x
title: Niche breadth explains the range size of European-centred butterflies, but dispersal ability does not

description: Aim: The breadth of ecological niches and dispersal abilities have long
 been discussed as important determinants of species’ range sizes. However,
 studies directly comparing the relative effects of both factors are rare,
 taxonomically biased and revealed inconsistent results. Location: Europe.
 Time period: Cenozoic. Major taxa: Butterflies, Lepidoptera. Methods: We
 relate climate, diet, and habitat niche breadth and two indicators of
 dispersal ability, wingspan and a dispersal tendency index, to the global
 range size of 369 European-centred butterfly species. The relative effects
 of these five predictors and their variation across the butterfly
 phylogeny were assessed by means of phylogenetic generalized least squares
 models and phylogenetically weighted regressions, respectively. Results:
 Climate niche breadth was the most important single predictor, followed by
 habitat and diet niche breadth, while dispersal tendency and wingspan
 showed no relation to species’ range size. All predictors together
 explained 59% of the variation in butterfly range size. However, the
 effects of each predictor varied considerably across families and genera.
 Main conclusions: Range sizes of European-centred butterflies are strongly
 correlated with ecological niche breadth but apparently independent of
 dispersal ability. The magnitude of range size – niche breadth
 relationships is not stationary across the phylogeny and is often
 negatively correlated across the different dimensions of the ecological
 niche. This variation limits the generalizability of range size–trait
 relationships across broad taxonomic groups.
description: For details see the published manuscript.
description: Required software: Excel, R
DOI: 10.5061/dryad.9kd51c5nv
title: Data from: A re-evaluation of the effects of mechanical cockle dredging in the Dutch Wadden Sea

description: The three datasets are obtained directly from the papers we discuss or
 from their authors. The first two datasets concern recruitment of cockles
 and Balthic tellins at seven sites in the Wadden Sea. The third dataset
 contains data on dredging and suitability for knots at 272 1 km2 grid
 cells in the western Wadden Sea.
DOI: 10.5061/dryad.0rxwdbs4t
title: Data from: Geographic variation in the altitudinal migration patterns, body size, oxidative status and exploratory behavior in a neotropical bird

description: To cope with life in the mountains, populations of the same species can
 exhibit substantial variability in their altitudinal migration patterns
 and phenotypes in response to local weather conditions. Studying such
 variability can provide valuable insights into how local populations
 respond to environmental challenges, and this information can be useful
 for conservation efforts in mountain ecosystems. Here, we used δ2H values
 of feathers and blood to evaluate latitudinal variation in altitudinal
 migration patterns and its possible links with body size, oxidative
 status, and exploratory behavior in 86 individuals of rufous-collared
 sparrow (Zonotrichia capensis) that breed at low and high elevations in
 the center (~33°) and south (~38°) of Chile. Our results show that both
 altitudinal migration patterns and oxidative status were significantly
 influenced by the latitude of breeding sites, while exploratory behavior
 was associated with elevation. Notably, we found that fast-explorer birds
 inhabiting low elevations in central Chile displayed higher levels of
 oxidative damage than slow-explorer birds. These outcomes underscore the
 possibility of local adaptations in response to diverse local
 environmental conditions in the Andes. We discuss the implications of
 latitude, elevation, and environmental temperature in shaping the observed
 patterns and highlight the significance of identifying local adaptations
 in mountain birds for better predicting their response to climate change
 and other challenges stemming from anthropogenic activities.
description: # data z.capensis --- Summary of dataset contents: Description data set ##
 Description of the data and file structure The dataset comprised 72
 sexually mature individuals of the Zonotrichia capensis species, which
 were captured across four distinct study sites located in varying
 elevations and latitudes within Chile. The collected data included
 information such as bird identification (Id), study site location,
 genetically determined sex, morphometric measurements, and additional
 variables obtained from a novel environment test to characterize
 exploratory behavior. Furthermore, we obtained total antioxidant values
 (TAC), measures of oxidative damage (TBARS), and oxidative status
 (TBARS/TAC) from each individual. Additionally, we analyzed isotopic
 values of Deuterium present in both feathers and blood samples in some
 individuals. To ensure comparability of the isotopic data between these
 samples, we corrected blood values by adding +24ppm to the original
 Deuterium blood values. NA was used for missing data ## Software All
 analyses were performed in the R Studio statistical environment
 v.1.4.17.17 using the Base (version v.1.4.17.17), stats (version 3.6.2)
 and lme4 (version 1.1.-27.1) packages.
DOI: 10.5061/dryad.1c59zw40n
title: Data from: Postnatal administration of S-adenosylmethionine restores developmental AHR activation-induced deficits in CD8+ T cell function during influenza A virus infection

description: Abstract Developmental exposures can influence life-long health; yet,
 counteracting negative consequences is challenging due to poor
 understanding of cellular mechanisms. The aryl hydrocarbon receptor (AHR)
 binds many small molecules, including numerous pollutants. Developmental
 exposure to the signature environmental AHR ligand
 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) significantly dampens adaptive
 immune responses to influenza A virus (IAV) in adult offspring. CD8+
 cytotoxic T lymphocytes (CTL) are crucial for successful infection
 resolution, which depends on the number generated and the complexity of
 their functionality. Prior studies showed developmental AHR activation
 significantly reduced the number of virus-specific CD8+ T cells, but
 impact on their functions is less clear. Other studies showed
 developmental exposure was associated with differences in DNA methylation
 in CD8+ T cells. Yet, empirical evidence that differences in DNA
 methylation are causally related to altered CD8+ T cell function is
 lacking. The two objectives were to ascertain whether developmental AHR
 activation affects CTL function, and whether differences in methylation
 contribute to reduced CD8+ T cell responses to infection. Developmental
 AHR triggering significantly reduced CTL polyfunctionality, and modified
 the transcriptional program of CD8+ T cells. S-adenosylmethionine (SAM),
 which increases DNA methylation, but not Zebularine, which diminishes DNA
 methylation, restored polyfunctionality and boosted the number of
 virus-specific CD8+ T cells. These findings suggest that diminished
 methylation, initiated by developmental exposure to an AHR-binding
 chemical, contributes to durable changes in antiviral CD8+ CTL functions
 later in life. Thus, deleterious consequence of development exposure to
 environmental chemicals are not permanently fixed, opening the door for
 interventional strategies to improve health.
description: Any program that can open FCS files such as FlowJo, CellEngine,
 WinList, Flowlogic, or FCS Express. FCS files can also be read into R.
 Free software: Floreada.io, FCSalyzer, FACSanadu, Red Matter App,
 Cyflogic, Flowing Software, WinMDI.
DOI: 10.5061/dryad.dv41ns238
title: Spillover of chalkbrood fungi to native solitary bee species from non-native congeners

description: Introduced, managed bees such as mason bees (genus Osmia) can confer
 significant pollination benefits to agricultural systems, but a risk of
 introducing non-native species into new ecosystems is the co-introduction
 of pathogens along with them. Pathogen spillover to wild, native bees may
 then drive native bee species declines. This study examined prevalence of
 the chalkbrood-causing fungal genus Ascosphaera in the nests of both
 non-native and native mason bee species. We conducted large-scale
 trap-nesting and pan-trapping efforts across the Mid-Atlantic United
 States with community scientists. Using molecular methods, nests were
 screened for all known Ascosphaera species in which genetic sequences have
 been published. After finding Ascosphaera species first described in Asia,
 we compared their local prevalence with the local abundance of mason bees
 from Asia. Lastly, we compared the prevalence of co-introduced Ascosphaera
 species across sites with a variety of landcover profiles. Results
 indicate species originally described in Japan, Ascosphaera naganensis and
 Ascosphaera fusiformis, are now present in native Virginia mason bees,
 Osmia lignaria and Osmia georgica, with high prevalence of A. naganensis
 found in O. georgica. We also found that the declining native mason bee O.
 georgica experienced higher prevalence of non-native Ascosphaera spp. at
 sites with larger numbers of non-native O. cornifrons and O. taurus,
 perhaps indicating greater likelihood of spillover of these Ascosphaera
 species with greater sources of transmission. Lastly, when the proportion
 of agricultural landcover surrounding bee nests was high, there was
 significantly greater prevalence of non-native Ascosphaera in O.
 georgica compared to more natural landcover types. Synthesis and
 applications. Through community science programming, we documented species
 of Japanese chalkbrood fungi inside native mason bee nests in North
 America. Native mason bees encounter non-native fungi more frequently with
 increasing abundance of non-native mason bees. Agricultural landscapes may
 exacerbate spillover of non-native fungi for native mason bees. The use of
 non-native bee species in agriculture should involve monitoring native
 bees for pathogens in the surrounding area for detection of spillover and
 species declines.
description: Please refer to the "Methods" section of the associated
 article, as well as Appendix S1 of the Supporting Information, where you
 will find all information related to methodogy and data
 processing.
description: Please see the “Materials and Methods” section of the associated
 article, as well as Appendix S1 of the Supporting Information for details
 on how these data were collected and processed.
 Data_file01.csv contains data used for main analyses relating to
 Ascosphaera sequencing and landcover analysis. Data_file02.csv contains
 all collection data from pan traps, as described in Methods
 section. See README for variable
 definitions.
DOI: 10.25349/d91g8q
title: Processed data for: Co-registration of heading to visual cues in retrosplenial cortex

description: Spatial cognition depends on an accurate representation of orientation
 within an environment. Head direction cells in distributed brain regions
 receive a range of sensory inputs, but visual input is particularly
 important for aligning their responses to environmental landmarks. To
 investigate how population-level heading responses are aligned to visual
 input, we recorded from retrosplenial cortex (RSC) of head-fixed mice in a
 moving environment using two-photon calcium imaging. We show that RSC
 neurons are tuned to the animal's relative orientation in the
 environment, even in the absence of head movement. Next, we found that RSC
 receives functionally distinct projections from visual and thalamic areas,
 and contains several functional classes of neurons. While some functional
 classes mirror RSC inputs, a newly discovered class coregisters visual and
 thalamic signals. Finally, decoding analyses reveal unique contributions
 to heading from each class. Our results suggest an RSC circuit for
 anchoring heading representations to environmental visual landmarks.