cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f1vhhmgxr
title: Song varies with latitude, climate, and species richness in a Neotropical bird

description: Animals can encode information within acoustic signals, particularly, bird
 songs can be remarkably complex and can indicate individual identity and
 quality. Two main sets of hypotheses attempt to explain the evolution of
 increased birdsong complexity across large-scale geographic ranges: (1)
 larger acoustic space availability, and (2) greater sexual selection
 intensity, both of which would favor the evolution of more complex songs
 at higher latitudes, more seasonal and/or species-poor environments.
 However, few studies have assessed patterns of song complexity for birds
 with broad geographic ranges. Here, we determined patterns of song
 variation in the blue-black grassquit (Volatinia jacarina), considering
 metrics of song complexity, structure and performance. This Neotropical
 bird occurs from Mexico to Argentina and produces a monosyllabic song.
 Using recordings from online databases, we calculated song metrics, such
 as bandwidth, song rate, number of song components, and proportion of
 vibratos of this signal. We found that song features varied with latitude,
 climate seasonality, bird species richness and hemisphere. However,
 contrary to theoretical predictions, complexity mostly decreased with
 latitude and greater seasonality, while it was positively correlated with
 bird species richness. Proportion of vibratos was positively correlated
 with latitude and seasonality, and may be a feature under sexual selection
 in this species. Overall, our results did not support the main hypotheses
 proposed as explanations for song complexity. Our findings also highlight
 that song complexity does not vary uniformly among songbirds and song
 parameters, and future studies encompassing more species should clarify
 patterns and drivers of song variation across broad geographic dimensions.
description: Data on the blue-black grassquit song complexity,
 structure and performance were collected from recordings available in
 online databases from citizen science projects and audiovisual
 collections, i.e., Xeno-Canto (www.xeno-canto.org), Macaulay Library at
 the Cornell Lab of Ornithology
 (www.macaulaylibrary.org), WikiAves
 (www.wikiaves.com.br) and Fonoteca Neotropical Jacques Vielliard (FNJV)
 (www2.ib.unicamp.br/fnjv). We also collected climate and bird species
 richness data from online databases, such as WorldClim v2
 (www.worldclim.org) and BiodiversityMapping.org
 website. To calculate the
 acoustic metrics of the blue-black grassquit song, we inspected
 spectrograms of the recordings and selected the beginning and the end of
 up to three songs per recording, and we also selected uninterrupted song
 bouts from 15 s to 120 s. We used these selections to calculate different
 song metrics, using the Raven Pro 1.6 (Cornell Lab of Ornithology,
 www.ravensoundsoftware.com) and the R environment (i.e., <i>warbleR
 </i>package).
description: R codes for the statistical analyses of the manuscript:
 https://doi.org/10.5281/zenodo.5513930
DOI: 10.5061/dryad.dv41ns200
title: Monoclonal antibodies from humans with Mycobacterium tuberculosis exposure or latent infection recognize distinct arabinomannan epitopes

description: The surface polysacharide arabinomannan (AM) and related glycolipid
 lipoarabinomannan (LAM) play critical roles in tuberculosis pathogenesis.
 Human antibody responses to AM/LAM are heterogenous and knowledge of
 reactivity to specific glycan epitopes at the monoclonal level is limited,
 especially in individuals who can control M. tuberculosis infection. We
 generated human IgG mAbs to AM/LAM from B cells of two asymptomatic
 individuals exposed to or latently infected with M. tuberculosis. We here
 show that two of these mAbs have high affinity to AM/LAM, are
 non-competing, and recognize different glycan epitopes distinct from other
 anti-AM/LAM mAbs reported. Both mAbs recognize virulent M. tuberculosis
 and nontuberculous mycobacteria with marked differences, can be used for
 the detection of urinary LAM, and can detect M. tuberculosis and LAM in
 infected lungs. These mAbs enhance our understanding of the spectrum of
 antibodies to AM/LAM epitopes in humans and are valuable for tuberculosis
 diagnostic and research applications.
description: ELISA data contain optical densities read at 450nm from three
 experiments. Glycan array raw data have been provided
 and additional details can also be found on the NCBI Gene Expression Omnibus
 (GEO) database with accession number GSE180517.
 The BioLayer Interferometry (BLI) kinetics data provided were
 used to estimate values
 for the k<sub>on</sub> (association rate constant),
 k<sub>off</sub> (dissociation rate constant), and
 <em>K<sub>D,app</sub></em> (apparent equilibrium
 dissociation constant), we used a global data fitting 2:1 binding
 model. The BioLayer Interferometry (BLI)
 epitope binning data provided were used to estimate mAb competition in a
 two-phase experiment.
DOI: 10.5061/dryad.j6q573nfd
title: Individual-based eco-evolutionary models for understanding adaptation in changing seas

description: As climate change threatens species’ persistence, predicting the potential
 for species to adapt to rapidly changing environments is imperative for
 the development of effective conservation strategies. Eco-evolutionary
 individual-based models (IBMs) can be useful tools for achieving this
 objective. We performed a literature review to identify studies that apply
 these tools in marine systems. Our survey suggested that this is an
 emerging area of research fueled in part by developments in modeling
 frameworks that allow simulation of increasingly complex ecological,
 genetic, and demographic processes. The studies we identified illustrate
 the promise of this approach and advance our understanding of the capacity
 for adaptation to outpace climate change. These studies also identify
 limitations of current models and opportunities for further
 development. We discuss three main topics that emerged across
 studies: 1) effects of genetic architecture and non-genetic responses on
 adaptive potential; 2) capacity for gene flow to facilitate rapid
 adaptation; and 3) impacts of multiple stressors on persistence. Finally,
 we perform a set of simple simulations to demonstrate the approach and
 provide a framework for users to explore eco-evolutionary IBMs as tools
 for understanding adaptation in changing seas.
description: Connectivity probabilities for generating the connectivity matrix
 in Figure 1 (original data from Xue et al. 2008).
 Present surface temperature and projections based on CMIP5 of the
 IPCC (RCP 8.5) used in our SLiM simulations can be freely accessed
 at https://www.bio-oracle.org/ (model scripts are available here:
 https://github.com/QuentinRougemont/marine_IBM_paper).
DOI: 10.6086/d14h5c
title: NCST real world brake activity of heavy-duty vehicles

description: This study uses a heavy-duty test vehicle to investigate the braking
 activity of HDVs. Brake parameters such as brake fluid pressure and brake
 temperature were measured along with the brake activity so that the brake
 activity can be characterized along with brake parameters. Ambient
 temperature, location, and speed were also measured. Testing was done by
 using simulated driving in a chassis dynanometer as well as real-world on
 road tests.
DOI: 10.5061/dryad.5x69p8d3z
title: Data from: Functional attractors in microbial community assembly

description: For microbiome biology to become a more predictive science, we must
 identify which descriptive features of microbial communities are
 reproducible and predictable, which are not, and why. We address this
 question by experimentally studying parallelism and convergence in
 microbial community assembly in replicate glucose-limited habitats. Here,
 we show that the previously observed family-level convergence in these
 habitats reflects a reproducible metabolic organization, where the ratio
 of the dominant metabolic groups can be explained from a simple
 resource-partitioning model. In turn, taxonomic divergence among replicate
 communities arises from multistability in population dynamics.
 Multistability can also lead to alternative functional states in closed
 ecosystems, but not in metacommunities. Our findings empirically
 illustrate how the evolutionary conservation of quantitative metabolic
 traits, multistability, and the inherent stochasticity of population
 dynamics, may all conspire to generate the patterns of reproducibility and
 variability at different levels of organization that are commonplace in
 microbial community assembly.
description: This dataset contains the taxonomy and relative abundance of each
 ESV in each community. The community composition was determined using 16S
 rRNA amplicon sequencing. DADA2 (version 1.6.0) was used to infer exact
 sequence variants (ESVs) from each sample, and the taxonomy was assigned
 using the SILVA reference database.
DOI: 10.5061/dryad.cvdncjt53
title: Sequential and efficient neural-population coding of complex task information

description: Condensed neural and behavioral data, included secondary results from
 model fits and analyses. This dataset contains all information required to
 recreate figures from the paper.
description: Transgenic mice expressing the calcium-sensitive fluorescent
 indicator GCamp6f were trained in the Accumulating Towers task and
 two-photon calcium imaging was performed of functionally identified
 primary and secondary visual cortical areas, as well as retrosplenial
 cortex. Regions of interest representing putative single neurons were
 extracted using a semi-customized demixing and deconvolution procedure.
 Behavioral data were separately collected by a computer that ran a virtual
 reality control engine, and synchronized with imaging data via a
 synchronization timestamp sent to the imaging computer at every graphics
 refresh cycle.
DOI: 10.5061/dryad.hhmgqnkhj
title: Chicken and junglefowl cerebellar anatomy data

description: Domestication is the process by which wild organisms become adapted for
 human use. Many phenotypic changes are associated with animal
 domestication, including decreases in brain and brain region sizes. In
 contrast to this pattern, the chicken has a larger cerebellum compared
 with the wild red junglefowl, but what neuroanatomical changes are
 responsible for this difference have yet to be investigated. Here, we
 quantified cell layer volumes, neuron numbers and neuron sizes in the
 cerebella of chickens and junglefowl. Chickens have larger, more folded
 cerebella with more and larger granule cells than junglefowl, but neuron
 numbers and cerebellar folding were proportional to cerebellum size.
 However, chickens do have relatively larger granule cell layer volumes and
 relatively larger granule cells than junglefowl. Thus, the chicken
 cerebellum can be considered a scaled-up version of the junglefowl
 cerebellum, but with enlarged granule cells. The combination of scaling
 neuron number and disproportionate enlargement of cell bodies partially
 supports a recent theory that domestication does not affect neuronal
 density within brain regions. Whether the neuroanatomical changes we
 observed are typical of domestication or not requires similar quantitative
 analyses in other domesticated species and across multiple brain regions.
description: All of the data was collected from histological sections using
 unbiased stereology as outlined in the accompanying manuscript.
DOI: 10.5061/dryad.79cnp5hwc
title: Dataset for: No evidence for short-term evolutionary response to a warming environment in Drosophila

description: Adaptive evolution is key in mediating responses to global warming and may
 sometimes be the only solution for species to survive. Such evolution will
 expectedly lead to changes in the populations’ thermal reaction norm and
 improve their ability to cope with stressful conditions. Conversely,
 evolutionary constraints might limit the adaptive response. Here, we test
 these expectations by performing a real-time evolution experiment in
 historically differentiated Drosophila subobscura populations. We address
 the phenotypic change after nine generations of evolution in a daily
 fluctuating environment with average constant temperature, or in a warming
 environment with increasing average and amplitude temperature across
 generations. Our results showed that (1) evolution under a global warming
 scenario did not lead to a noticeable change in the thermal response; (2)
 historical background appears to be affecting responses under the warming
 environment, particularly at higher temperatures; (3) thermal reaction
 norms are trait-dependent: while lifelong exposure to low temperature
 decreases fecundity and productivity but not viability, high temperature
 causes negative transgenerational effects on productivity and viability,
 even with high fecundity. These findings in such an emblematic organism
 for thermal adaptation studies raise concerns about the short-term
 efficiency of adaptive responses to the current rising temperatures.
description: Data corresponds to a phenotypic assay performed on experimental
 populations after 9 generations of evolution in different thermal
 selection regimes. Assay included populations from 3 thermal selection
 regimes (each three fold replicated) tested in 5 temperature treatments.
  Raw data is the mean value for each replicate population and temperature
 treatment (e.g., the mean of PT1 for the 14-14 treatment is one of the
 three data values for PT in this treatment).
DOI: 10.5061/dryad.gxd2547n3
title: Data for: Exocytosis of the silicified cell wall of diatoms involves extensive membrane disintegration

description: Diatoms are unicellular algae, characterized by silica cell walls. The
 silica elements are formed intracellularly in a membrane-bound silica
 deposition vesicle (SDV), and are exocytosed after completion. How diatoms
 maintain membrane homeostasis during the exocytosis of these large and
 rigid silica elements is a long-standing enigma. We studied membrane
 dynamics during cell wall formation and exocytosis in two model diatom
 species, using live-cell confocal microscopy, transmission electron
 microscopy and cryo-electron tomography. Our results show that during the
 formation of the mineral phase it is in tight association with the SDV
 membranes, which are forming a precise mold of the delicate geometrical
 patterns. During exocytosis, the distal SDV membrane and the plasma
 membrane gradually detach from the mineral and disintegrate in the
 extracellular space, without any noticeable endocytic retrieval or
 extracellular repurposing. Within the cell, there is no evidence for the
 formation of a new plasma membrane, thus the proximal SDV membrane becomes
 the new barrier between the cell and its environment, and assumes the role
 of a new plasma membrane. These results provide direct structural
 observations of diatom silica exocytosis, and point to an extraordinary
 mechanism in which membrane homeostasis is maintained by discarding,
 rather than recycling, significant membrane patches.
description: Raw microscopy files.
DOI: 10.5061/dryad.hdr7sqvjk
title: Biological experimental raw data from: The Incubascope : A simple, compact and large ﬁeld of view microscope for long-term

description: Optical imaging has rapidly evolved in the last decades. Sophisticated
 microscopes allowing optical sectioning for 3D imaging or sub-diffraction
 resolution are available. Due to price and maintenance issues, these
 microscopes are often shared between users in facilities. Consequently,
 long term access is often prohibited and does not allow to monitor slowly
 evolving biological systems or to validate new models like organoids.
 Preliminary coarse long-term data that do not require do acquisition of
 terabytes of high-resolution images are important as a first step. By
 contrast with expansive all-in-one commercialized stations standard
 microscopes equipped with incubator stages offer a more cost-effective
 solution despite imperfect long run atmosphere and temperature control.
 Here, we present the Incubascope, a custom-made compact microscope that
 fits into a table-top incubator. It is cheap and simple to implement
 user-friendly and yet provides high imaging performances. The system has a
 field of view of 5.5×8 mm2, a 3 µm resolution, a 10 frames/second
 acquisition rate, and is controlled with a Python-based graphical
 interface. We exemplify the capabilities of the Incubascope on biological
 applications such as the hatching of Artemia salina eggs, the growth of
 the slime mold Physarum polycephalum and of encapsulated spheroids of
 mammalian cells.
description: The dataset was collected with the microscope developped in this
 work : The Incubascope. <br>The dataset contains both fluorescence
 and bright field images.<br>No image processing was applied on the
 dataset
description: All the raw data provided in this dataset are tiff files and can
 be opened easily with software such as ImageJ.
DOI: 10.5061/dryad.8cz8w9gr1
title: Data for the detection of the boreal chorus frog (Pseudacris maculata) using environmental DNA and call surveys at 180 ponds sampled in 2017-2018 in southeastern Québec, Canada

description: The boreal chorus frog (Pseudacris maculata) is at risk of extinction in
 parts of its range in Canada. Our objectives were to quantify the
 influence of local and landscape characteristics on the occurrence of the
 species in wetlands in southern Québec. We hypothesized that site
 occupancy depends on local characteristics and landscape characteristics
 contributing to site connectivity. We developed an environmental DNA
 (eDNA) method to detect the species and compared the detection probability
 of this method to traditional call surveys. We collected water samples at
 a total of 180 sites (90 in 2017, 110 in 2018), whereas we surveyed a
 subset of 63 sites using both eDNA and call surveys in 2018. Site
 occupancy varied across years, but was higher in sites where the species
 had been previously detected during the last 12 years by other studies.
 Site occupancy did not vary with other local and landscape
 characteristics, in part due to an apparent decrease in the number of
 sites occupied by the species since the last 12 years. Detection
 probability via eDNA (0.81; 95% CI: [0.31; 0.98]) did not differ from that
 of call surveys (0.62; 95% CI: [0.25; 0.89]). To identify the optimal
 sampling period for the boreal chorus frog, future studies should estimate
 the detection probability of eDNA during the breeding season and the
 larval development period of the species.
description: The data presented in the files include the detection data of the
 boreal chorus frog (<em>Pseudacris maculata</em>) using
 environmental DNA (eDNA) and call surveys in southeastern Québec, Canada.
 A total of 180 ponds were sampled during the breeding season in 2017 and
 2018 with eDNA, whereas a subset of these ponds were also sampled with
 call surveys.
description: The values presented in the data set are the original variables.
 Note that numeric explanatory variables (except PCA scores) were
 standardized to mean 0 and unit variance before being entered in the
 analyses.
DOI: 10.6086/d10q22
title: Pollen diet mediates how pesticide exposure impacts brain gene expression in nest-founding bumble bee queens

description: A primary goal in biology is to understand the effects of multiple,
 interacting environmental stressors on organisms. Wild and domesticated
 bees are exposed to a wide variety of interacting biotic and abiotic
 stressors, with widespread declines in floral resources and agrochemical
 exposure being two of the most important. In this study, we used
 examinations of brain gene expression to explore the sublethal
 consequences of neonicotinoid pesticide exposure and pollen diet
 composition in nest-founding bumble bee queens. We demonstrate for the
 first time that pollen diet composition can influence the strength of
 bumble bee queen responses to pesticide exposure at the molecular level.
 Specifically, one pollen mixture in our study appeared to buffer bumble
 bee queens entirely against the effects of pesticide exposure, with
 respect to brain gene expression. Additionally, we detected unique effects
 of pollen diet and sustained (versus more temporary) pesticide exposure on
 queen gene expression. Our findings support the hypothesis that
 nutritional status can help buffer animals against the harmful effects of
 other stressors, including pesticides, and highlight the importance of
 using molecular approaches to explore sublethal consequences of stressors.
description: Brain gene expression - RNAseq 
 Read counts table was generated using featureCount v1.5.0-p3
 (Liao et al. 2014), wherein it determines the number of reads uniquely
 mapping to exons and summed at the gene level using gene features
 annotated in the B. impatiens OGSv1.0. 
 Pollen diet - Metabolomic data
 Pollen samples were examined through untargeted liquid
 chromatography-mass spectrometry (LC-MS) metabolomics.
description: The complete data file contains raw data for all analyses on
 Costa et al. in prep. Raw sequence reads are deposited in the SRA
 (Accession ID: PRJNA763214). All analyses and pipelines can be found on
 the first author’s GitHub
 (https://github.com/claudinpcosta/2022-PesticideQueens-Bimpatiens).