cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m63xsj43b
title: Supplementary information for: A biased fossil record can preserve reliable phylogenetic signal

description: Abstract.­­––The fossil record is notoriously imperfect and biased in
 representation, hindering our ability to place fossil specimens into an
 evolutionary context. For groups with fossil records mostly
 consisting of disarticulated parts (e.g., vertebrates, echinoderms,
 plants), the limited morphological information preserved sparks concerns
 about whether fossils retain reliable evidence of phylogenetic
 relationships, and lends uncertainty to analyses of diversification,
 paleobiogeography, and biostratigraphy in Earth history. To
 address whether a fragmentary past can be trusted, we need to assess
 whether incompleteness affects the quality of phylogenetic information
 contained in fossil data. Herein, we characterize skeletal incompleteness
 bias in a large dataset (6,585 specimens; 14,417 skeletal
 elements) of fossil squamates (lizards, snakes, amphisbaenians,
 and mosasaurs). We show that jaws + palatal bones, vertebrae, and ribs
 appear more frequently in the fossil record than other parts of the
 skeleton. This incomplete anatomical representation in the fossil record
 is biased against regions of the skeleton that contain the majority of
 morphological phylogenetic characters used to assess squamate evolutionary
 relationships. Despite this bias, parsimony- and model-based comparative
 analyses indicate that the most frequently-occurring parts of the skeleton
 in the fossil record retain similar levels of phylogenetic signal as parts
 of the skeleton that are rarer. These results demonstrate that the biased
 squamate fossil record contains reliable phylogenetic information, and
 support our ability to place incomplete fossils in the Tree of
 Life.
DOI: 10.5061/dryad.3j9kd51k9
title: Cross-correlated ambient data recorded on a distributed acoustic sensing array

description: Distributed acoustic sensing (DAS) is a relatively new technology used in
 many geophysical applications. The versatility and high temporal-spatial
 resolution make DAS ideal for rapid deployment surveys such as
 earthquake-aftershock monitoring and hazard assessment. However, these
 applications often rely on trenched cable installations that are time
 consuming and cost prohibitive, or on existing telecom fibers that are
 limited in spatial coverage. We deploy a DAS array composed of six
 parallel linear subsections directly on ground surfaces with different
 conditions. We apply ambient interferometry and adopt a simplified
 spectral-analysis-of-surface waves (SASW) method to determine the average
 shear-wave velocity of the top 30 m (VS30). Our methodology results in
 robust VS30 estimates for each surface deployment subsection that are
 consistent with collocated 1 m-depth trenched cables. The implications of
 these findings support DAS as a viable method for non-invasive rapid
 deployment surface surveys for earthquake hazard assessment.
description: Approximately 1.0 hour of DAS data were recorded at the Colorado
 School of Mines campus on December 2nd, 2020 at a 4467 Hz sampling rate
 with a channel spacing of approximately 2.45 m. A gauge length of 4.0
 times the channel spacing was used. We recorded hammer-shot data at 47
 locations at the surface, as well as ambient waveforms from a nearby road.
 The attached data files are virtual shot gathers produced by applying
 seismic-noise interferometry to the raw DAS data. See manuscript for
 detailed description of methodology.
description: The attached Jupyter Notebook and data files can be used to
 reproduce the results corresponding to the submitted manuscript
 "Rapid-surface deployment of a DAS system for earthquake hazard
 assessment".
DOI: 10.5061/dryad.tb2rbp027
title: Data for: Specificity of California mouse pup vocalizations in response to olfactory stimuli

description: To investigate flexibility in vocal signaling by rodent pups, we examined
 whether olfactory stimuli influence characteristics of pup calls and how
 these calls may be affected by sex and litter size in California mice
 (Peromyscus californicus). Pups were isolated and recorded during a
 3-minute baseline period followed by a 5-minute exposure to bedding
 containing scent from their home cage, scent from the home cage of an
 unfamiliar family, coyote urine, or no scent (control). Latency to call,
 call rate, and call characteristics (duration, frequency, and amplitude)
 were compared between the baseline and scent-exposure periods and among
 olfactory conditions. Compared to the control condition, pups from 2-pup
 litters called more quietly when exposed to odor from a predator, while
 pups from 3-pup litters called more loudly. Additionally, pups showed
 non-significant tendencies to reduce call rates in response to odors from
 their home cage and to increase call rates when exposed to predator urine.
 Lastly, males produced higher-frequency calls and more ultrasonic
 vocalizations than females. These results indicate that pup calling
 behavior in this species can be influenced by acute olfactory stimuli as
 well as litter size and sex. The flexibility of pup calling in response to
 these three variables potentially increases the communication value of pup
 calls and help shape the parents’ responses.
DOI: 10.5061/dryad.qrfj6q5hh
title: High resolution dynamic mapping of the C. elegans intestinal brush border

description: The intestinal brush border is made of an array of microvilli that
 increases the membrane surface area for nutrient processing, absorption,
 and host defense. Studies on mammalian cultured epithelial cells uncovered
 some of the molecular players and physical constrains required to
 establish this apical specialized membrane. However, the building and
 maintenance of a brush border in vivo has not been investigated in detail
 yet. Here, we combined super-resolution imaging, transmission electron
 microscopy and genome editing in the developing nematode C. elegans to
 build a high-resolution and dynamic localization map of known and new
 brush border markers. Notably, we show that microvilli components are
 dynamically enriched at the apical membrane during microvilli outgrowth
 and maturation but become highly stable once microvilli are built. This
 new toolbox will be instrumental to understand the molecular processes of
 microvilli growth and maintenance in vivo as well as the effect of genetic
 perturbations, notably in the context of disorders affecting brush border
 integrity.
description: Sanger sequencing of C. elegans genomic DNA in strains modified
 by CRISRP/Cas9 to add fluorophores to genetic loci.
DOI: 10.5061/dryad.tqjq2bw15
title: DNA methylation of the natriuretic peptides system genes and ischemic stroke: gene-based and gene-set analyses

description: Background The natriuretic peptides (NP) system has been considered an
 important regulator for ischemic stroke (IS) with a limited clinical
 implication. A better understanding of the underlying molecular mechanisms
 is urgent. Here, we aimed to examine the role of NP system genes
 methylation in IS. Methods and Results DNA methylation at promoter regions
 of four core NP system genes, e.g., CORIN, FURIN, NPPA, and NPPB, was
 measured by targeted bisulfite sequencing in 853 IS patients and 918
 healthy controls. We first examined the association between DNA
 methylation at each single CpG and IS, followed by gene-based and gene-set
 analyses to examine the joint associations of DNA methylation at multiple
 CpGs in a gene or all four genes as a pathway with IS. After control of
 covariates and multiple testing, DNA methylation at 19 of the 36 assayed
 CpGs were individually associated with IS at q&lt;0.05. The average
 methylation levels at the targeted regions of CORIN (OR=0.64, 95%CI:
 0.56-0.73), FURIN (OR=0.78, 95%CI: 0.69-0.88), and NPPA (OR=0.78, 95%CI:
 0.69-0.88) were inversely associated with IS (all q&lt;0.05). The
 truncated product method revealed the same gene-based associations (all
 q&lt;0.05) and found that DNA methylation at all four NP system genes
 together was jointly associated with IS (P=0.0001). Conclusions DNA
 methylation at NP system genes was downregulated in IS patients. Our
 results may unravel a molecular mechanism underlying the regulating effect
 of the NP system on IS, and highlight the relevance of testing the joint
 effect of multiple CpGs in the epigenetic analysis.
DOI: 10.5061/dryad.c59zw3r8n
title: Input data for estimating dimensionless number (Reynolds, Swimming and Strouhal number) of swimming penguin

description: Propulsion performance of swimming and flying animals is often evaluated
 by using dimensionless numbers, such as the Strouhal and Reynolds numbers.
 They have been shown to allow better understanding of locomotion
 efficiency, using relatively simple approaches and avoiding overly complex
 computational models. Specifically, it has been reported that efficient
 propulsion is more likely to occur when Strouhal number values – estimated
 from propulsive frequencies and amplitudes – are within a relatively
 narrow range, depending on the corresponding Reynolds number, broadly
 expressing the fluid resistance to the animal motion. We have estimated
 both Strouhal and Reynolds numbers for seven species of penguins after
 analysing relevant kinematic data taken from the literature. The obtained
 values neatly indicate that, as expected, penguins employ efficient
 propulsion mechanisms. Additionally, by comparing these values with those
 for alcids – seabirds that can also fly – we have found that penguins swim
 at least as efficiently as alcids. However, we have also found that the
 swimming number – proportional to the product of Strouhal and Reynolds
 numbers – neatly correlates to the diving abilities of the considered
 species and apparently indicates, in a straightforward hierarchical
 manner, the gains in diving due to the loss of flying abilities. Within
 the penguin species, a clear correlation is also observed between diving
 performance and drag coefficient values.
description: The data was collected from different literature and no
 preprocessing was performed.
DOI: 10.5061/dryad.9s4mw6mhz
title: Immunohistochemistry localises myosin-7a to cochlear efferent boutons

description: Myosin 7a is often used to visualise sensory hair cells due to its
 well-characterised and localised expression profile. We thus conducted
 myosin-7a immunostaining across all 3 turns of the adult rat organ of
 Corti to visualise hair cells. As expected, we observed myosin 7a staining
 in both inner and outer hair cells. Unexpectedly, we also observed strong
 myosin 7a staining in the medial olivocochlear efferent synaptic boutons
 contacting the outer hair cells. Efferent bouton myosin-7a staining was
 present across all 3 turns of the cochlea. We verified this localisation
 by co-staining with a known efferent bouton marker, the vesicular
 acetylcholine transporter. 
description: A Leica SP5 upright confocal microscope with two-photon imaging
 capabilities was used to image the exposed and stained organs of Corti.
 Cochleas were superglued to the lids of 55-mm diameter cell culture Petri
 dishes prior to imaging to ensure the organ of Corti would be in an
 appropriate orientation and immersed in PBS. The Argon 488, Diode 543,
 Diode 594 and Diode 633 were used for single-photon excitation of the
 Alexa dyes conjugated to the secondary antibodies and the Mai Tai eHP
 DeepSee 5332 laser set to a wavelength of 800 nm was used for two-photon
 excitation of the phalloidin conjugated Alexa 405. A 25x/0.95NA water
 immersion objective (HCX IRAPO L25x/0.95 W) was used. Images were recorded
 in 12 bits at a resolution of 1024 x 1024 and further appropriate Look Up
 Table colors and processed in ImageJ (https://imagej.nih.gov/ij/). Methods
 are described in detail in the publication "Immunohistochemistry
 localises myosin-7a to cochlear efferent boutons" which has been
 conditionally accepted for publication in the journal Welcome Open
 Research. Article DOI will be linked to dataset once published. 
description: Data is in the tiff file format, which can be opened using ImageJ
 (https://imagej.nih.gov/ij/) or any other program with similar
 capabilities. Data has been zipped up for easier download and organised in
 the zip file according to which figure it is associated within the
 manuscript. Labelling of individual files reflects the stainings, turn of
 the rat cochlea from which it has been acquired (base, mid, apex), rat
 from which it was acquired and/or cochlea of the rat, if
 relevant.
DOI: 10.5061/dryad.0k6djhb1q
title: Working memory capacity of crows and monkeys arises from similar neuronal computations

description: Complex cognition relies on flexible working memory, which is severely
 limited in its capacity. The neuronal computations underlying these
 capacity limits have been extensively studied in humans and in monkeys,
 resulting in competing theoretical models. We probed the working memory
 capacity of crows (Corvus corone) in a change detection task, developed
 for monkeys (Macaca mulatta), while we performed extracellular recordings
 of the prefrontal-like area nidopallium caudolaterale. We found that
 neuronal encoding and maintenance of information were affected by item
 load, in a way that is virtually identical to results obtained from monkey
 prefrontal cortex. Contemporary neurophysiological models of working
 memory employ divisive normalization as an important mechanism that may
 result in the capacity limitation. As these models are usually
 conceptualized and tested in an exclusively mammalian context, it remains
 unclear if they fully capture a general concept of working memory or if
 they are restricted to the mammalian neocortex. Here we report that
 carrion crows and macaque monkeys share divisive normalization as a
 neuronal computation that is in line with mammalian models. This indicates
 that computational models of working memory developed in the mammalian
 cortex can also apply to non-cortical associative brain regions of birds.
description: Data was collected from two carrion crows. Behavioral data was
 collected by Matlab. Electrophysiological data was collected by
 extracellular single neuron recordings using multi-channel microelectrodes
 and Intan RHD2000 headstages and USB-Interface board. Recordings were
 performed at a sampling rate of 30 kHz with a band-pass filter (0.5 kHz -
 7.5 kHz). Spike sorting was performed using Klusta-suite software and
 spike times were imported into Matlab. Data were further processed and
 organized using custom Matlab code.
description: Data and code have been compressed into a .zip folder each.
 Unpack the contents of the folders to use the dataset. The dataset is
 split into two main folders and one Matlab file:
 'code'<br> contains all analysis code to produce
 all figures and reported statistics of the manuscript (refer to
 the<br>  MATLAB live script 'exeResultsLiveScript.m' to
 run the analysis, please adjust the path information of where the data is
 stored on your computer)
 'ResultsStatistics.mat'<br> contains all reported
 statistical values (generated by
 'exeResultsLiveScript.m')
 'sourceData'<br> contains all required source
 data files (i.e. pre-processed data) required to run the analyses stored
 in<br> 'code'
DOI: 10.5061/dryad.sj3tx9664
title: Current nest box designs may not be optimal for the larger forest dormice; pre-hibernation increase in body mass might lead to sampling bias in ecological data

description: Biologists commonly use nest boxes to study small arboreal mammals,
 including forest dormouse (Dryomys nitedula). Hibernating dormouse species
 often experience pronounced seasonal variations in body mass, which might
 lead to sampling biases if it is not taken into account when designing
 nest boxes. In our study of forest dormouse, we noticed that the entrance
 hole of nest boxes had been gnawed on. We hypothesized that this behavior
 was exhibited by individual dormice who had higher body mass and,
 therefore, were unable to pass through the entrance holes. To test our
 hypothesis, we categorized individual dormice present inside nest boxes
 based on their body mass; then compared the seasonal body mass dynamics
 with the timing of the gnawing behavior. We also compared nest box
 occupancy by forest dormouse before and after the gnawing behavior.
 Interestingly, we found that the gnawing behavior was displayed
 exclusively when part of the dormouse population increased considerably in
 body mass, which supports our hypothesis. Additionally, nest box occupancy
 decreased significantly from 20% before to 4.6% after the gnawing
 behavior. We suggest that researchers use nest boxes with entrance holes
 larger than 4 cm in future studies of forest dormouse to prevent the
 possible exclusion of the conspecifics that have higher body mass before
 hibernation. This type of sampling bias can probably happen in studies of
 other species, such as fat dormouse, that similarly show pronounced
 seasonal variations in body mass. We recommend that biologists consider
 the seasonal body mass dynamics of the target species when designing nest
 boxes to minimize bias in ecological data and improve management actions.
description: I surveyed 65 nest boxes for dormice in North-western Iran in
 late-September and early-November 2019. I considered a nest box occupied
 only if one or more dormice were present in the nest box at the time of
 visit. 0=occupied, and 1=unoccupied.
DOI: 10.5061/dryad.m63xsj43f
title: Tipping the balance: the role of seed density, abiotic filters, and priority effects in seed-based wetland restoration

description: Sowing native seeds is a common approach to reintroduce native plants to
 degraded systems. However, this method is often overlooked in wetland
 restoration despite the immense global loss of diverse native wetland
 vegetation. Developing guiding principles for seed-based wetland
 restoration is critical to maximize native plant recovery, particularly in
 previously invaded wetlands. Doing so requires a comprehensive
 understanding of how restoration manipulations, and their interactions,
 influence wetland plant community assembly. With a focus on the invader
 Phragmites australis, we established a series of mesocosm experiments to
 assess how native sowing density, invader propagule pressure, abiotic
 filters (water and nutrients), and native sowing timing (i.e., priority
 effects) interact to influence plant community cover and biomass in
 wetland habitats. Increasing the density of native seeds yielded higher
 native cover and biomass, but P. australis suppression with increasing
 sowing densities was minimal. Rather, community outcomes were largely
 driven by invader propagule pressure—Phragmites australis densities of ≤
 500 seeds/m2 maintained high native cover and biomass. Low-water
 conditions increased the susceptibility of P. australis to native
 competition. Early sowing of native seeds showed a large and significant
 benefit to native cover and biomass, regardless of native sowing density,
 suggesting that priority effects can be an effective restoration
 manipulation to enhance native plant establishment. Given the urgent
 wetland restoration need combined with the limited studies on seed-based
 wetland restoration, these findings provide guidance on restoration
 manipulations that are grounded in ecological theory to improve seed-based
 wetland restoration outcomes.
DOI: 10.5061/dryad.63xsj3v3q
title: Immunosenescence in the wild? A longitudinal study in a long‐lived seabird

description: 1. Longitudinal studies of various vertebrate populations have
 demonstrated senescent declines in reproductive performance and survival
 probability to be almost ubiquitous. Longitudinal studies of potential
 underlying proximate mechanisms, however, are still scarce.  2.
 Due to its critical function in the maintenance of health and viability,
 the immune system is among the potential (mediators of) proximate
 mechanisms that could underlie senescence.  3. Here, we studied
 three innate immune parameters - hemagglutination titre, haemolysis titre
 and haptoglobin concentration - in a population of common terns (Sterna
 hirundo) known to undergo actuarial senescence. We repeatedly sampled
 birds of known sex and age across 11 years and used random regression
 models to (i) quantify how immune parameters vary among individuals, and
 (ii) describe within-individual age-specific changes in, and potential
 trade-offs between, immune parameters. 4. Our models revealed no
 differences between males and females in hemagglutination titre and
 haptoglobin concentration, and very low among-individual variation in
 these parameters in general. Within individuals, hemagglutination titre
 increased with age, while haptoglobin concentration did not change. We
 found no indication for selective (dis)appearance in relation to
 hemagglutination titre or haptoglobin concentration, nor for the existence
 of a trade-off between them. Haemolysis was absent in the majority (76%)
 of samples. 5. Common terns do not exhibit clear senescence in
 hemagglutination titre and haptoglobin concentration and show very little
 among-individual variation in these parameters in general. This may be
 explained by canalisation of the immune parameters or by the colonial
 breeding behaviour of our study species, but more longitudinal studies are
 needed to facilitate investigation of links between species’
 characteristics and immunosenescence in wild animals.