cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25349/d9qw4j
title: Behavioral probabilities and sample videos for "Behavioral evidence for nested central pattern generator control of Drosophila grooming"

description: Central pattern generators (CPGs) are neurons or neural circuits that
 produce periodic output without requiring patterned input. More complex
 behaviors can be assembled from simpler subroutines, and nested CPGs have
 been proposed to coordinate their repetitive elements, organizing control
 over different time-scales. Here, we use behavioral experiments to
 establish that Drosophila grooming may be controlled by nested CPGs. On a
 short time-scale (5-7 Hz), flies execute periodic leg sweeps and rubs.
 More surprisingly, transitions between bouts of head cleaning and leg
 rubbing are also periodic on a longer time-scale (0.3 - 0.6 Hz). We
 examine grooming at a range of temperatures to show that the frequencies
 of both oscillations increase – a hallmark of CPG control – and also that
 the two time-scales increase at the same rate, indicating that the nested
 CPGs may be linked. This relationship also holds when sensory drive is
 held constant using optogenetic activation, but the rhythms can decouple
 in spontaneously grooming flies, showing that alternative control modes
 are possible. Loss of sensory feedback does not disrupt periodicity but
 slows the longer time-scale alternation. Nested CPGs simplify generation
 of complex but repetitive behaviors, and identifying them in Drosophila
 grooming presents an opportunity to map the neural circuits that
 constitute them.
description: The data folder contains two CSV files, sample videos, including,
 Dusted.avi, Ch2, and Unstim, corresponding to figures 2F, 4F, and 6F
 respectively.  It also includes a Jupyter Notebook document (IPYNB).
 Please refer to the README.txt file for more information.
DOI: 10.25349/d9m606
title: Stimulus-dependent representational drift in primary visual cortex

description: To produce consistent sensory perception, neurons must maintain stable
 representations of sensory input. However, neurons in many regions exhibit
 progressive drift across days. Longitudinal studies have found stable
 responses to artificial stimuli across sessions in visual areas, but it is
 unclear whether this stability extends to naturalistic stimuli. We
 performed chronic 2-photon imaging of mouse V1 populations to directly
 compare the representational stability of artificial versus naturalistic
 visual stimuli over weeks. Responses to gratings were highly stable across
 sessions. However, neural responses to naturalistic movies exhibited
 progressive representational drift across sessions. Differential drift was
 present across cortical layers, in inhibitory interneurons, and could not
 be explained by differential response strength or higher order stimulus
 statistics. However, representational drift was accompanied by similar
 differential changes in local population correlation structure. These
 results suggest representational stability in V1 is stimulus-dependent and
 may relate to differences in preexisting circuit architecture of co-tuned
 neurons.
description: See the methods section of the manuscript for details on data
 collection and processing.
description: All code used for data processing, analysis, and figure
 generation for the associated manuscript can be found on the Github page
 listed under related software, and the Goard Lab website: https://goard.mcdb.ucsb.edu/resources.
DOI: 10.7272/q6ft8j92
title: Single-cell glycomics analysis by CyTOF-Lec reveals glycan features defining cells differentially susceptible to HIV

description: High-parameter single-cell phenotyping has enabled in-depth classification
 and interrogation of immune cells, but to date has not allowed for glycan
 characterization. Here, we develop CyTOF-Lec as an approach to
 simultaneously characterize many protein and glycan features of human
 immune cells at the single-cell level. We implemented CyTOF-Lec to compare
 glycan features between different immune subsets from blood and multiple
 tissue compartments, and to characterize HIV-infected cell cultures. Using
 bioinformatics approaches to distinguish preferential infection of
 cellular subsets from viral-induced remodeling, we demonstrate that HIV
 upregulates the levels of cell surface fucose and sialic acid in a
 cell-intrinsic manner, and that memory CD4+ T cells co-expressing high
 levels of fucose and sialic acid are highly susceptible to HIV infection.
 Sialic acid levels were found to distinguish memory CD4+ T cell subsets
 expressing different amounts of viral entry receptors, pro-survival
 factors, homing receptors, and activation markers. The ability of sialic
 acid to distinguish memory CD4+ T cells with different susceptibilities to
 HIV infection was experimentally validated through sorting experiments.
 Together, these results suggest that HIV remodels not only cellular
 proteins but also glycans, and that glycan expression can differentiate
 memory CD4+ T cells with vastly different susceptibility to HV infection.
DOI: 10.6078/d1ct5v
title: Change and persistence of hunting & dietary practices among Kadazandusun-Murut (KDM) bearded pig hunters in Sabah, Malaysia

description: This dataset consists of 38 semi-structured interviews that we conducted
 with Kadazandusun-Murut (KDM) hunters in Sabah, Malaysian Borneo. The
 dataset is based on information shared during over 50 hours of time with
 the hunters. The data cover a variety of topics about the relationships
 between KDM hunters and bearded pigs, the favored game animal for this
 hunting group. We asked the hunters about their hunting and dietary
 practices, changes in hunting practices, and perceived changes in
 bearded pig behavior over time. These data were collected prior to the
 2020/2021 outbreak in Sabah of African Swine Fever, which caused
 the collapse of a number of bearded pig populations throughout
 the state. 
description: We interviewed Kadazandusun-Murut (KDM) bearded pig hunters in
 Sandakan District, Sabah, Malaysia. We carried out semi-structured
 interviews with them, asking them a combination of closed and open-ended
 questions about their hunting and dietary practices, changes in hunting
 practices, and perceived changes in bearded pig behavior over
 time. In this dataset, we share the de-identified raw
 data, which include a combination of notes, direct quotations, and
 responses to closed-ended questions. Potentially identifying information,
 such as location names, have been removed. The data are recorded in both
 English and Malay, with translations from Malay to English included in
 many places. 
description: See README file
 ('README_KDM_beardedpig_data_Kurz_et_al_2021.txt').
DOI: 10.5061/dryad.dncjsxm0b
title: Rates of expansion of invasive cane toads in New South Wales

description: Geographical variation in abiotic and biotic conditions can significantly
 affect the rate that an invasive species expands its range. The
 colonisation of Australia by cane toads (Rhinella marina) has attracted
 extensive research, but mostly in tropical regions rather than cooler
 climatic zones. We assembled multiple datasets to characterise the
 historical spread of toads at their southern (cool-climate) invasion front
 in north-eastern New South Wales (NSW). Perhaps because toads are
 relatively easy to find, visual and acoustic surveys appear to be as
 effective as eDNA-based surveys in detecting the species’ presence.
 Expansion of the toads’ range in NSW has occurred through the
 establishment of satellite populations as well as by growth of the
 range-core. Overall rates of spread have been more than tenfold lower than
 on the tropical front (means of &lt;5 km vs. &gt;50 km per year),
 and in some decades, the toads’ southern range has declined rather than
 expanded. Overall rates of spread since 1970 have accelerated to the south
 (through coastal habitats), but not to the west (into montane areas). The
 toads’ range has expanded most rapidly in decades with dry, warm weather
 conditions, but predicted future changes to climate are likely to have
 only minor effects on rates of toad spread. Understanding historical
 patterns of toad invasion in NSW can clarify probable future spread, and
 hence identify priority areas for control programs.
description: Data on the distribution of invasive cane toads in New South
 Wales was collated from all available sources, to quantify rates of
 expansion and to identify correlates of that rate of spread. We also
 conducted pilot studies to comapre alternative emthods of detecting
 invasion-front populations of toads in the field.
description: The Excel sheet provides data for 342 points that represent the
 edges of the toad invasion front across a series of decades for which data
 are available. The dataset also includes climatic and habitat attributes
 of each of those sites, as determined from relevant GIS layers, as well as
 estimates of interdecadal changes in the location of the toads'
 range-edge.
DOI: 10.5061/dryad.dz08kprxv
title: White stork tri-axial accelerometer data with behaviour labels

description: The tri-axial ACC demo dataset from white stork (Ciconia ciconia)
 (data accessible from the AcceleRater website:
 http://accapp.move-ecol-minerva.huji.ac.il/) was measured at 10.54 Hz.
 Forty tri-axial measurements, totalling 3.8 seconds, were used to form a
 behaviour segment. The dataset includes 1746 segments each forming a row
 in the dataset. Each row contains 121 columns. The first 120 columns are
 ACC measurements from three orthogonal axes, arranged as x, y, z, x, y, z,
 ...,x, y, z. The final column is of type character containing the
 corresponding behaviour. The dataset contains 5 different behaviours
 including "A_FLIGHT" - active flight (77 cases),
 "P_FLIGHT" - passive filght (96), "WALK" - walking
 (437), "STND" - standing (863), "SITTING" - sitting
 (273).
DOI: 10.5061/dryad.v9s4mw6wp
title: Data from: Open notes sounds great, but will a provider’s documentation change?

description: Background: The effects of shared clinical notes on patients, care
 partners, and clinicians (“open notes”) were first studied as a
 demonstration project in 2010. Since then, multiple studies have shown
 clinicians agree shared progress notes are beneficial to patients, and
 patients and care partners report benefits from reading notes. To
 determine if implementing open notes at a hematology/oncology practice
 changed providers’ documentation style, we assessed the length and
 readability of clinicians’ notes before and after open notes
 implementation at an academic medical center in Boston, MA. Methods: We
 analyzed 143,888 notes from 60 hematology/oncology clinicians before and
 after the open notes debut at Beth Israel Deaconess Medical Center, from
 January 1, 2012, to September 1, 2016. We measured the providers’ (medical
 doctor/nurse practitioner) documentation styles by analyzing character
 length, the number of addenda, note entry mode (dictated vs. typed) and
 note readability. Measurements used five different readability formulas
 and were assessed on notes written before and after the introduction of
 open notes on November 25, 2013. Results: After the introduction of open
 notes, the mean length of progress notes increased from 6,174 characters
 to 6,648 characters (P&lt;0.001), and the mean character length of the
 “assessment and plan” (A&P) increased from 1,435 characters to
 1,597 characters (P&lt;0.001). The Average Grade Level Readability of
 progress notes decreased from 11.50 to 11.33, and overall readability
 improved by 0.17 (P=0.01). There were no statistically significant changes
 in the length or readability of “Initial Notes” or Letters, inter-doctor
 communication, nor in the modality of the recording of any kind of note.
 Conclusions: After the implementation of open notes, progress notes and
 A&P sections became both longer and easier to read. This suggests
 clinician documenters may be responding to the perceived pressures of a
 transparent medical records environment.
description: We conducted analyses to evaluate how
 providers' documentation styles changed after the initiation of open
 notes. Outcome measures included note length, length of the Assessment and
 Plan section of the note, number of addenda, whether the note was dictated
 (as opposed to typed), and a variety of measures of note
 readability.
DOI: 10.15468/dl.x5hkea
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is bc092ff0-02e4-11dc-991f-b8a03c50a862",
 "TaxonKey is Neanthes micromma"
 ]
}

 The dataset includes 74 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002887-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n02v6wwxm
title: Alarm cues and alarmed conspecifics: Neural activity during social learning from different cues in Trinidadian guppies

description: Learning to respond appropriately to novel dangers is often essential to
 survival and success, but carries risks. Learning about novel threats from
 others (social learning) can reduce these risks. Many species, including
 the Trinidadian guppy (Poecilia reticulata), respond defensively to both
 conspecific chemical alarm cues and conspecifix anti-predator behaviours,
 and in other fish such social information can lead to a learned aversion
 to novel threats. However, relatively little is known about the neural
 substrates underlying social learning and the degree to which different
 forms of learning share similar neural mechanisms. Here, we explored the
 neural substrates mediating social learning of novel threats from two
 different conspecific cues (i.e. social cue-based threat learning). We
 first demonstrated that guppies rapidly learn about threats paired with
 either alarm cues or with conspecific threat responses (demonstration).
 Then, focusing on acquisition rather than recall, we discovered that
 phospho-S6 expression, a marker of neural activity, was elevated in
 guppies during learning from alarm cues in the putative homologue of the
 mammalian lateral septum and the preoptic area. Surprisingly, these
 changes in neural activity were not observed in fish learning from
 conspecific demonstration. Together, these results implicate forebrain
 areas in social learning about threat but raise the possibility that
 circuits contribute to such learning in a stimulus-specific manner.
DOI: 10.5061/dryad.ghx3ffbp7
title: VTC proteins of arbuscular mycorrhizal fungi

description: Polyphosphate polymerizing and depolymerizing reactions of VTC4 protein in
 an arbuscular mycorrhizal fungus Arbuscular mycorrhizal (AM) fungi form
 symbiotic associations with land plants and supply soil minerals including
 phosphorus to their hosts. AM fungi accumulate polyphosphate (polyP), a
 linear phosphate polymer, in their mycelia, which functions in phosphorus
 storage and translocation. In the budding yeast Saccharomyces cerevisiae,
 it has been demonstrated that the vacuolar transporter chaperone 4 (VTC4)
 protein, a subunit of the VTC complex, is responsible for polyP synthesis.
 Here, we conducted a comprehensive survey of VTC proteins in AM fungal
 genomes. The genomes of eight AM fungal species encode VTC1, VTC2, and
 VTC4.
description: Amino acid sequences of AM
 fungal VTCs were obtained by blastp searches using protein queries from
 <em>S. cerevisiae</em> (https://www.yeastgenome.org) against AM fungal genome databases. Amino acid sequences were aligned using ClustalW with some manual adjustment. Maximum-likelihood tree inference and bootstrapping with 100 replicates was performed with RAxML-NG version 1.0.1 (Kozlov <em>et al</em>., 2019) using the LG+I+G amino acid substitution model. The best-fitted evolutionary model was identified using ModelTest-NG version 0.1.3 (Darriba <em>et al.</em>, 2020). A tree was visualized and annotated with the iTOL platform version 5.7 (Letunic & Bork, 2019).
description: <strong>C-terminal region of VTC proteins -
 alignment</strong><br>Alignment of amino acid sequences of
 C-terminal sequences containing Duf202 domain of VTC1, VTC2, and VTC4 in
 eight AM fungal species and the budding yeast Saccharomyces
 cerevisiae.<br>C-terminal_region_alignment.fas
 <strong>C-terminal region of VTC proteins - ML
 tree</strong><br>Maximum likelihood tree of C-terminal
 sequences containing Duf202 domain of VTC1, VTC2, and VTC4 in eight AM
 fungal species and the budding yeast Saccharomyces
 cerevisiae. <br>C-terminal_region_ML.tre 
 <strong>Whole region of VTC proteins -
 alignment</strong><br>Alignment of amino acid sequences of
 whole sequences of VTC2 and VTC4 in eight AM fungal species and the
 budding yeast Saccharomyces
 cerevisiae.<br>whole_region_alignment.fas
 <strong>Whole region of VTC proteins - ML
 tree</strong><br>Maximum likelihood tree of whole sequences of
 VTC2 and VTC4 in eight AM fungal species and the budding yeast
 Saccharomyces cerevisiae.<br>whole_region_ML.tre
DOI: 10.5061/dryad.2bvq83bqk
title: Pollination and plant reproductive success of two ploidy levels in red clover (Trifolium pratense L.)

description: This dataset includes hand pollination, honey bee pollination and pollen
 germination experiments described in the article "Pollination and
 plant reproductive success of two ploidy levels in red clover (Trifolium
 pratense L.)", published in Frontiers in Plant Science (DOI:
 10.3389/fpls.2021.720069).  In a series of hand pollination
 experiments, the influence of visitation rate (10, 20, 40, 80
 pollinated florets per flower head) on the seed number per pollinated
 floret and seed number per flower head were investigated, respectively.
 The influence of flowering stage (early, middle, and full flowering) on
 the seed number per pollinated floret was also investigated.
 Self-incompatibility was studied by comparing the seed number per flower
 head under self-pollination and interploidy pollination treatments. In
 order to study the autonomous pollination, we compared the seed
 number per flower head between self-pollination and control treatment. In
 the honey bee pollination experiments, we investigated the overall seed
 number per floret and compare the number of one-seeded and two-seeded
 florets in the studied red clover cultivars. Further, we investigated the
 pollen germination rate of each red clover cultivar.  The main
 findings of this article include:  (1) In hand pollination,
 increasing the visitation rates increased the seed number per flower head,
 but reduced the seed number per pollinated floret; (2) In hand
 pollination, different flowering stages did not influence the seed number
 per pollinated floret significantly; (3) In honey bee pollination, diploid
 red clover cultivars had more two-seeded florets compared to tetraploids.
DOI: 10.5061/dryad.76hdr7sx1
title: Kangaroo fathers modulate maternal control of offspring sex but not post-partum maternal expenditure

description: When sons and daughters have different fitness costs and benefits,
 selection may favor deviations from an even offspring sex ratio. Most
 theories on sex ratio manipulation focus on maternal strategies and
 sex-biased maternal allocation. Recent studies report paternal influences
 on both offspring sex ratio and post-partum sex-biased maternal
 allocation. We used long-term data on marked kangaroos to investigate if
 and how paternal mass and skeletal size, both determinants of male
 reproductive success, influenced (a) offspring sex in interaction with
 maternal mass, and (b) post-partum sex-biased maternal allocation. When
 mothers were light, the probability of having a son increased with
 paternal mass. Heavy mothers showed the opposite trend. A similar result
 emerged when considering paternal size instead of mass. Post-partum
 maternal sex-specific allocation was independent of paternal mass or size.
 Studies of offspring sex manipulation or maternal allocation would benefit
 from an explicit consideration of paternal traits, as paternal and
 maternal effects can modulated each other.
description: Data collection and processing is described in the paper.
description: Notes on data files and R scripts can be found in the file
 README.txt
DOI: 10.5061/dryad.dfn2z3526
title: Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies

description: Introgressive hybridization plays a key role in adaptive evolution and
 species diversification in many groups of species. However,
 frequent hybridization and gene flow between species make estimation of
 the species phylogeny and key population parameters
 challenging. Here, we show that by accounting for phasing and
 using full-likelihood methods, introgression histories and population
 parameters can be estimated reliably from whole-genome sequence
 data. We employ the multispecies coalescent (MSC) model with and
 without gene flow to infer the species phylogeny and cross-species
 introgression events using genomic data from six members of the erato-sara
 clade of Heliconius butterflies. The methods naturally accommodate random
 fluctuations in genealogical history across the genome due to deep
 coalescence. To avoid heterozygote phasing errors in haploid sequences
 commonly produced by genome assembly methods, we process and compile
 unphased diploid sequence alignments and use analytical methods to average
 over uncertainties in heterozygote phase resolution. There is
 robust evidence for introgression across the genome, both among distantly
 related species deep in the phylogeny and between sister species in
 shallow parts of the tree. We obtain chromosome-specific
 estimates of key population parameters such as introgression directions,
 times and probabilities, as well as species divergence times and
 population sizes for modern and ancestral species. We confirm
 ancestral gene flow between the sara clade and an ancestral population of
 H. telesiphe, a likely hybrid speciation origin for H. hecalesia, and gene
 flow between the sister species H. erato and H. himera. Inferred
 introgression among ancestral species also explains the history of two
 chromosomal inversions deep in the phylogeny of the group. This study
 illustrates how a full-likelihood approach based on the multispecies
 coalescent makes it possible to extract rich historical information of
 species divergence and gene flow from genomic data.