cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.63xsj3v4d
title: Dataset for dopamine manipulated daphnia

description: The neurotransmitter dopamine has been shown to play an important role in
 modulating behavioural, morphological and life-history responses to food
 abundance. However, costs of expressing high dopamine levels remain poorly
 studied and are essential for understanding the evolution of the dopamine
 system. Negative maternal effects on offspring size from enhanced maternal
 dopamine levels have previously been documented in Daphnia. Here, we
 tested whether this translates into fitness costs in terms of lower
 starvation resistance in offspring. We exposed Daphnia
 magna mothers to aqueous dopamine (2.3 mg/L or 0 mg/L for the
 control) at two food levels (ad libitum versus 30% ad
 libitum) and recorded a range of maternal life history traits. The
 longevity of their offspring was then quantified in the absence of food.
 In both control and dopamine treatments, mothers that experienced
 restricted food ration had lower somatic growth rates and higher age at
 maturation. Maternal food restriction also resulted in production of
 larger offspring that had a superior starvation resistance, compared
 to ad libitum groups. However, although dopamine exposed mothers
 produced smaller offspring than controls at restricted food ration, these
 smaller offspring survived longer under starvation. Hence, maternal
 dopamine exposure provided an improved offspring starvation resistance.
description: See the file README.docx for description of data files.
DOI: 10.7489/1607-1
title: Girnock and Baddoch: Adult Return Rates - Previous Version

description: The Girnock and Baddoch catchments are long-term monitoring sites where the population dynamics of spring salmon have been assessed since 1966 and 1988 respectively. These long-term monitoring sites consist of a pair of fixed traps designed to catch emigrating juvenile salmon and returning adults. Trap protocols were similar, although not identical, over the monitoring period.
description: Adult return rates are expressed as a ratio of returning adult female salmon to live juvenile emigrants released at the trap site (smolts and parr). The numbers, sex and ages of returning adult Atlantic salmon were recorded at the Girnock and Baddoch traps since 1966 and 1988 respectively. Juvenile salmon are caught in the descending emigrant traps at the Girnock and Baddoch Burns in autumn and spring. Adults were lagged to their respective year of emigration based on scale read sea ages, and counts of autumn emigrants were positively lagged by one year to reflect entry to seawater and the start of adult growth. Both adult and juvenile data were the focus of a detailed validation and correction procedure carried out between 2013 and 2014. The adult and smolt data at the Girnock and Baddoch are considered to be robust and have been collected in a similar way, with a similar level of effort over the monitoring period. Counts of autumn emigrants were affected by low trap effort at the Girnock in a few years in the 1980s. Counts from some of these years have been corrected for effort (see Bacon et al. for details), other years were affected by such low effort that they are considered unusable and adult return rates for these years have been removed from the dataset. Return rates are shown for emigrant years where all adults in the expected age range of 1 to 3SW could have returned. For full details of the data and the correction process, see Bacon PJ, Malcolm IA, Fryer RJ, Glover RS, Millar CP, and Youngson AF. (in press). Can conservation stocking enhance juvenile emigrant production in wild Atlantic Salmon (Salmo salar)? Transactions of the American Fisheries Society.
DOI: 10.25349/d9031z
title: Extracellular Recordings from Human Brain Organoids Using High-density CMOS Arrays

description: Human brain organoids replicate much of the cellular diversity and
 developmental anatomy of the human brain. However, the physiological
 behavior of neuronal circuits within organoids remains relatively
 under-explored. With high-density CMOS microelectrode arrays (26,400
 electrodes) and shank electrodes (960 electrodes), we probed broadband and
 three-dimensional extracellular field recordings generated by spontaneous
 activity of human brain organoids. These recordings simultaneously
 captured local field potentials (LFPs) and single-unit activity extracted
 through spike sorting. From spiking activity, we estimated a directed
 functional connectivity graph of synchronous neural network activity,
 which showed a large number of weak functional connections enmeshed within
 a network skeleton of significantly fewer strong connections. Treatment of
 the organoid with a benzodiazepine induced a reproducible signature
 response that shortened the inter-burst intervals, increased the
 uniformity of the firing pattern within each burst and decreased the
 population of weakly connected edges. Simultaneously examining the
 spontaneous LFPs and their phase alignment to spiking showed that spike
 bursts were coherent with theta oscillations in the LFPs. Our results
 demonstrate that human brain organoids have self-organized neuronal
 assemblies of sufficient size, cellular orientation, and functional
 connectivity to co-activate and generate field potentials from their
 collective transmembrane currents that phase-lock to spiking activity.
 These results point to the potential of brain organoids for the study of
 neuropsychiatric diseases, drug mechanisms, and the effects of external
 stimuli upon neuronal networks.
description: Full experimental details are described in the associated
 manuscript.
description: Data sets consist of extracellular field recordings acquired from
 human brain organoids. Recodings from 500 um thick
 organoid slices were obtained using CMOS-based microelectrode arrays
 (MaxOne, Maxwell Biosystems, https://www.mxwbio.com/) 
 Recordings from whole organoids were acquired using Neuropixels
 probes (https://www.neuropixels.org). The data folder contains Hierarchical Data Format Version 5 (HDF5)  Comma-separated values (CSV) and MatLab (MAT) files, as well as a ReadMe to support reuse.
DOI: 10.5061/dryad.xsj3tx9hj
title: Morphometric, gametic and parasitological data of clam Ameghynomia antiqua and DNAmt sequences of parasite

description: The clam Ameghynomia antiqua is a highly important resource for
 fisheries due to its high catches volume. It is the bivalve mollusk with
 the highest fisheries landings from natural beds on the Pacific coast of
 southern South America; however, studies of the reproductive conditions of
 this species are scarce and date back many years. The object of the
 present work was to evaluate the reproductive characteristics of the
 species, analysing its gametogenic and gonadal cycle, and reproductive
 indices, in fishery locations that present the natural beds with the
 highest fisheries catches, as well as parasite loads in the species. The
 gonads of the individuals were sampled monthly over a year and classified
 into one of three states called: “in development”, “ripe” and
 “spawned”. Synchrony between the sexes was observed in the
 indicators of the Gonadosomatic Index and Condition Index in each of the
 locations, although no synchrony was observed between locations. In the
 gametogenic cycle, the "ripe" state was observed in females in
 spring-summer, followed by rapid recovery to new development of the
 gonads; in males the "ripe" state was observed throughout the
 year. It was observed that males entered the “spawned” state one month
 ahead of females. The presence of digenean parasites in the state of
 metacercariae was detected in the gonads and mantle. No significant
 differences were found in the prevalence or intensity of infection when
 analysed by sex and month. The metacercariae were identified, by
 sequencing of three DNA regions, as belonging to the clade shared by
 species of the genus Parvatrema and close to
 the Gymnophalloides; both these genera belong to the family
 Gymnophallidae of the superclass Digenea. Infection was observed to reduce
 the gonadal tissue, in some cases causing castration. This is the first
 record of the presence of these parasites of A. antiqua, with
 genetic identification at genus level. These results are relevant for act
 proper management of this resource, which is important for fishing.
DOI: 10.5061/dryad.6t1g1jx1n
title: Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus

description: Rapid speciation is an important aspect of adaptive radiations, but can
 obfuscate phylogenetic relationships among taxa. For recent radiations,
 there are challenges to reconstructing the relationships among the species
 due to often shorter branch lengths. Resolution of these relationships is
 further confounded when studies only use a few genetic markers. Double
 digest restriction-site associated DNA sequencing (ddRADseq) is a method
 of next generation sequencing that identifies many single nucleotide
 polymorphisms (SNPs) throughout the genome. This increases statistical
 power to resolve close phylogenetic relationships like those found within
 an adaptive radiation. We used this approach to understand the
 evolutionary history of the rockfishes of the genus Sebastes, which
 experienced an adaptive radiation between 3 to 5 mya. Here, we
 reconstructed the phylogenetic relationships among six species of rockfish
 within the subgenus Sebastosomus using over 11,600 SNPs. This
 reconstruction includes the two recently diverged species, Sebastes
 mystinus and S. diaconus, that were first described genetically in 2008
 using mtDNA control region sequence data and six microsatellite loci. We
 confirmed the relationship of these cryptic species as sister-taxa and
 found evidence that S. melanops and S. flavidus were also sister-taxa. The
 latter contradicts prior studies but is supported by our reconstruction
 using nuclear DNA and measures of genetic differentiation tests and a
 discriminant analysis of principal components. The relationships between
 the species of Sebastosomus are further supported by morphological,
 biological, and ecological justifications.
description: We have included the raw plink file using the <em>de
 novo</em> pipeline and <em>population</em> pipeline
 parameters highlighted in the manuscript. Note that one individual listed
 above was removed due to missingness. We have also included the RAW
 post-process radtag data files and a population map.
DOI: 10.5061/dryad.8pk0p2nq8
title: Telerobotic neurovascular interventions with magnetic manipulation

description: Advances in robotic technology have been adopted in various subspecialties
 of both open and minimally invasive surgery, offering benefits such as
 enhanced surgical precision and accuracy with reduced fatigue of the
 surgeon. Despite the advantages, robotic applications to endovascular
 neurosurgery have remained largely unexplored because of technical
 challenges such as the miniaturization of robotic devices that can reach
 the complex and tortuous vasculature of the brain. Although some
 commercial systems enable robotic manipulation of conventional guidewires
 for coronary and peripheral vascular interventions, they remain unsuited
 for neurovascular applications because of the considerably smaller and
 more tortuous anatomy of cerebral arteries. Here, we present a
 teleoperated robotic neurointerventional platform based on magnetic
 manipulation. Our system consists of a magnetically controlled guidewire,
 a robot arm with an actuating magnet to steer the guidewire, a set of
 motorized linear drives to advance or retract the guidewire and a
 microcatheter, and a remote-control console to operate the system under
 real-time fluoroscopy. We demonstrate our system’s capability to navigate
 narrow and winding pathways both in vitro with realistic neurovascular
 phantoms representing the human anatomy and in vivo in the porcine
 brachial artery with accentuated tortuosity for preclinical evaluation. We
 further demonstrate telerobotically assisted therapeutic procedures
 including coil embolization and clot retrieval thrombectomy for treating
 cerebral aneurysms and ischemic stroke, respectively. Our system could
 enable safer and quicker access to hard-to-reach lesions while minimizing
 the radiation exposure to physicians and open the possibility of remote
 procedural services to address challenges in current stroke systems of
 care.
DOI: 10.5061/dryad.3xsj3txjd
title: Can immune gene silencing via dsRNA feeding promote pathogenic viruses to control the globally invasive Argentine ant?

description: Pest control methods that can target pest species with limited
 environmental impacts are a conservation and economic priority.
 Species-specific pest control using RNA interference is a challenging but
 promising avenue in developing the next generation of pest management. We
 investigate the feasibility of manipulating a biological invader’s immune
 system using double-stranded RNA (dsRNA) in order to increase
 susceptibility to naturally occurring pathogens. We used the invasive
 Argentine ant as a model, targeting the immunity-associated genes Spaetzle
 and Dicer-1 with dsRNA. We show that feeding of Spaetzle dsRNA can result
 in partial target gene silencing for up to 28 days in the laboratory and
 five days in the field. Dicer-1 dsRNA only resulted in partial gene
 knockdown after two days in the laboratory. Double-stranded RNA treatments
 were associated with significant gene expression disruptions across immune
 pathways in the laboratory and to a lower extent in the field. We observed
 occasional changes in viral loads in dsRNA-treated groups. However, immune
 pathways disruption did not result in consistent increase in microbial
 infections, nor did they alter ant abundance in the field. Our study
 explores the feasibility of lowering a pest’s immunity as a control tool.
 We demonstate that it is possible to alter immune gene expression of pest
 species and pathogen loads, though in our system the affected pathogens
 did not appear to influence pest abundance. We provide advice on future
 directions for dsRNA-mediated immune disruption in pest species, including
 potential avenues to improve dsRNA delivery as well as the importance of
 the biology of the pest system and its pathogens.
description: TaqMan qPCR assays of Argentine ant immune genes and pathogen
 loads.
DOI: 10.5061/dryad.c866t1g8s
title: Data from: Morphological and molecular characterization of variation in common bean (Phaseolus vulgaris L.) germplasm from Azad Jammu and Kashmir, Pakistan

description: Phaseolus vulgaris, an essential food and source of protein, is cultivated
 across the world. This study was carried out to investigate the diversity
 and population structure of 34 P. vulgaris landrace accessions collected
 from the Azad Jammu and Kashmir (AJ&K) regions of Pakistan. The
 samples were analyzed both morphologically and using genetic variation
 identified through RNA sequencing. Our results indicated that most genetic
 variation occurs among local accessions, with little genetic variation
 occurring between geographical regions. In addition, the accessions fell
 into two major genetic groups. Morphological analysis revealed that these
 two genetic groups differ in a number of quantitative traits, including
 seed length, seed width, and seed weight. One accession, DUD-11, appears
 to be a mixture of the two major groups genetically as well as
 morphologically. Among the other accessions, DUD-8, RWK-2, and NGD-1
 depicted particularly high seed weight along with higher seed length, seed
 width, and seed yield per plant. We suggest focusing on these accessions
 in future breeding programs. More generally, our results provide baseline
 data that will be useful for crop improvement and effective cultivation
 practices in Pakistan.
description: Morphological traits were measured on plants grown in a field
 site in Muzaffarabad (latitude: 34˚22'10" N, longitude:
 73˚31'30" E, altitude 1,731 m) over two seasons (2018 and 2019)
 in a randomized complete block design with three replicates.
 RNA-seq libraries were prepared from leaf tissue from plants
 grown in a common greenhouse. Please see the associated
 publication for details. 
description: The raw sequencing data can be found on the SRA:
 PRJNA757521.
DOI: 10.5061/dryad.v9s4mw6z2
title: Molecular dynamics simulations of intrinsically disordered proteins p53TAD and Pup

description: Intrinsically disordered proteins (IDPs) are highly dynamic systems that
 play an important role in cell signaling processes and their misfunction
 often causes human disease. Proper understanding of IDP function not only
 requires the realistic characterization of their three-dimensional
 conformational ensembles at atomic-level resolution but also of the time
 scales of interconversion between their conformational substates. Large
 sets of experimental data are often used in combination with molecular
 modeling to restrain or bias models to improve agreement with experiment.
 It is shown here for the N-terminal transactivation domain of p53 (p53TAD)
 and Pup how the latest advancements in molecular dynamics (MD) simulations
 methodology produces native conformational ensembles by combining replica
 exchange with series of microsecond MD simulations. They closely reproduce
 experimental data at the global conformational ensemble level, in terms of
 the distribution properties of the radius of gyration tensor, and at the
 local level, in terms of NMR properties including 15N spin relaxation,
 without the need for reweighting. The IDP ensembles were analyzed by graph
 theory to identify dominant inter-residue contact clusters and
 characteristic amino-acid contact propensities. These findings indicate
 that modern MD force fields with residue-specific backbone potentials can
 produce highly realistic IDP ensembles sampling a hierarchy of nano- and
 picosecond time scales providing new insights into their biological
 function.
DOI: 10.5061/dryad.hx3ffbggk
title: Data from: Human impacts on mammals in and around a protected area before, during, and after COVID‐19 lockdowns

description: The dual-mandate for many protected areas (PAs) to simultaneously promote
 recreation and conserve biodiversity may be hampered by negative effects
 of recreation on wildlife. However, reports of these effects are not
 consistent, presenting a knowledge gap that hinders evidence-based
 decision-making. We used camera traps to monitor human activity and
 terrestrial mammals in Golden Ears Provincial Park and the adjacent
 Malcolm Knapp Research Forest near Vancouver, Canada, with the objective
 of discerning relative effects of various forms of recreation on cougars
 (Puma concolor), black bears (Ursus americanus), black-tailed deer
 (Odocoileus hemionus), snowshoe hares (Lepus americanus), coyotes (Canis
 latrans), and bobcats (Lynx rufus). Additionally, public closures of the
 study area associated with the COVD-19 pandemic offered an unprecedented
 period of human-exclusion through which to explore these effects. Using
 Bayesian generalized mixed-effects models, we detected negative effects of
 hikers (mean posterior estimate = -0.58, 95% credible interval (CI) -1.09
 to -0.12) on weekly bobcat habitat use and negative effects of motorized
 vehicles (estimate = -0.28, 95% CI -0.61 to -0.05) on weekly black bear
 habitat use. We also found increased cougar detection rates in the PA
 during the COVID-19 closure (estimate = 0.007, 95% CI 0.005 to 0.009), but
 decreased cougar detection rates (estimate = -0.006, 95% CI -0.009 to
 -0.003) and increased black-tailed deer detection rates (estimate = 0.014,
 95% CI 0.002 to 0.026) upon reopening of the PA. Our results emphasize
 that effects of human activity on wildlife habitat use and movement may be
 species- and/or activity-dependent, and that camera traps can be an
 invaluable tool for monitoring both wildlife and human activity,
 collecting data even when public access is barred. Further, we encourage
 PA managers seeking to promote both biodiversity conservation and
 recreation to assess trade-offs between these two goals in their PAs.
DOI: 10.5061/dryad.pk0p2ngqf
title: Data for: Long duration advertisement calls of nesting male plainfin midshipman fish are honest indicators of size and condition

description: The plainfin midshipman fish (Porichthys notatus) has long served as a
 model organism for neuroethology research on acoustic communication and
 related social behaviors. Type I or ‘singing’ males produce highly
 stereotyped, periodic advertisement calls that are the longest known
 uninterrupted vertebrate vocalizations. Despite the extensive literature
 on the acoustic behaviour of this species, it remains unclear whether
 reproductive males signal their quality via their highly energetic,
 multiharmonic advertisement calls. Here, we recorded the advertisement
 calls of 22 reproductive type I males at night in a controlled laboratory
 setting in which males were housed in aquaria maintained at a constant
 temperature (13.9±0.3°C). The duration of the advertisement calls from
 type I males was observed to increase from the first call of the night to
 the middle call after which call duration remained steady until the early
 morning hours and first light. A strong positive correlation was observed
 between loudness (sound pressure level and maximum sound pressure level)
 of the advertisement call and body size (mass and standard length;
 rs&gt;0.8). In addition, an asymptotic relationship was observed
 between the harmonic frequencies (f0–f10) of the advertisement calls and
 male body condition, with harmonic frequencies initially increasing with
 body condition indices, but then plateauing when body condition measures
 were high. Taken together, our results suggest that type I male
 advertisement calls provide reliable honest information about male quality
 regarding size and body condition. Such condition-dependent information of
 calling males could potentially be used by receptive females to help
 facilitate mate choice decisions.
description: Contains the data used in the manuscript titled, "Long
 duration advertisement calls of nesting male plainfin midshipman fish are
 honest indicators of size and condition" published in the journal of
 experimental biology. https://doi.org/10.1242/jeb.243889 In brief, this dataset contains overnight acoustic recordings from hydrophones placed on top of a type I male's nest, one minute call segments used to compute spectral features of the advertisement calls, spreadsheets containing data on the dates of acoustic recording and morphometric measures for each type I male, and codes used for data analysis. Please read the methods section on the manuscript for a detailed protocol on how the data was collected and processed.