cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pzgmsbckd
title: Dopa-responsive dystonia patient response before and after levodopa treatment

description: Dopa-responsive dystonia (DRD), also known as Segawa syndrome, is a
 phenotypically and genetically heterogeneous group of neurological
 disorders that typically presents as early-onset lower limb dystonia with
 diurnal fluctuation and exhibits a marked, persistent response to
 levodopa. Heterozygous loss-of-function mutations in the guanosine
 triphosphate cyclohydrolase 1 (GCH1) are the most common cause of DRD. In
 addition to the classic form of the disease, there have been a number of
 studies addressing atypical clinical features of GCH1related-DRD with
 variable age of onset. This report describes a mid-30-year-old Japanese
 male patient with a 10-year history of focal upper limb dystonia that
 initially emerged as task-specific, guitarist’s cramp. The dystonic
 symptoms responded very well to levodopa treatment, and genetic analysis
 identified a novel heterozygous mutation in the C-terminal catalytic
 domain of GCH1. Insufficient recognition of this treatable condition often
 leads to misdiagnosis, which causes delays in the patient receiving
 adequate dopamine replenishing therapy. A diagnostic trial with levodopa
 should be considered in all patients with relatively young-onset dystonia,
 whether they have classic features of DRD or not.
DOI: 10.5061/dryad.kh1893257
title: Data from: Bacteria, protists and fungi may hold clues of seamount impact on diversity and connectivity of deep-sea pelagic communities

description: The interacting features of topography and hydrography around deep
 seamounts have strong influence on plankton biogeography. In addition, the
 intrinsic properties of various biological taxa inherently shape their
 distribution. Therefore, bacterial, protist and fungal diversity was
 investigated across the water column above and below the summit of a
 flat-topped seamount in the Western Pacific Ocean. We determined the
 distribution and connectivity patterns of bacteria, protists and fungi
 around the seamount, and explored the processes driving the observed
 distribution patterns. We found that the seamount enhanced the
 vertical connectivity of bacterial and protist communities, but
 significantly reduced the protist community connectivity along the
 horizontal dimension. Such effects provide ecological opportunities for
 eukaryotic adaption and diversification, resulting in a greater diversity
 on seamounts than in surrounding deep seas.
description: Thirty-eight water samples from five sampling stations were
 collected at the Kocebu Guyot in the Magellan Seamount chain located in
 the oligotrophic tropical Western Pacific Ocean. A total of 20 L seawater
 was collected from each water layer at all sampling stations with Niskin
 Bottles attached to a rosette equipped with a Seabird CTD probe. Samples
 were pre-filtered first through a 200 µm sieve, and subsequently filtered
 through a 0.22 µm polycarbonate filter. Filters were then flash frozen in
 liquid nitrogen and stored at −80°C until further processing. 
 Environmental DNA was extracted from seawater samples using the
 All Prep DNA/RNA Mini Kit (Qiagen, Germany) following the manufacturer’s
 instructions. Specific primers and PCR protocols were utilized to amplify
 different target sequences. In order to amplify 16S gene sequences in
 bacteria, forward primer U341F  and reverse primer R685  were set. The
 hypervariable V4 region of protist 18S rRNA was amplified using a set of
 eukaryote-specific primers Reuk454FWD1 and TAReukREV3 . For the detection
 of fungi, the ITS2 (Internal transcribed spacer 2) gene was amplified
 using specific primers ITS3 and ITS4 . Each sample was analyzed in three
 PCR replicates for each primer pair to minimize PCR bias.
description: Magellan.zip
 DNA clean sequence
 data. 
 Environmental_data.xlsx
 Contains coordinate, depth,
 salinity, temperature and nutrients values of samples (except A2-3000,
 A8-3000, B8-3000, B8-4000). 
 OTUtable.xlsx
 OTU table normalized with minimum
 sample size. 
 Magellan_Rcode.zip
 R
 code for barplot, co-occurrence, RCbary, βNTI and dbRDA
 analysis. 
 Magellan_Readme.txt
 Readme file for the
 dataset.
DOI: 10.15468/dl.ryr332
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dialium kunstleri",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 28 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002819-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cjsxksn5g
title: High blood parasite infection rate and low fitness suggest ecological traps for pied flycatchers breeding near forest water-bodies

description: Blood parasites are considered to have strong negative effects on host
 fitness. There is some evidence that suggests that negative fitness
 consequences may be associated with the proximity to the areas where blood
 parasite vectors reproduce. This study tested for relationships between
 haemosporidian infection prevalence and parasitemia of breeding pied
 flycatchers (Ficedula hypoleuca) and their fitness parameters at different
 distances from forest water bodies. Prevalence and parasitemias (the
 intensity of infection) of haemosporidians generally decreased with
 increasing distance from forest lakes, streams, and bogs. Fledgling
 numbers were lower, and their condition was worse in the vicinity of water
 bodies, compared to one kilometer away from lakes and streams. This study
 suggests that forest areas around water bodies represent ecological traps.
 Installing nest boxes in the vicinity of forest water-bodies creates
 unintended ecological traps that may have conservation implications.
DOI: 10.5061/dryad.66t1g1k1r
title: Decline and Fall: the causes of group failure in cooperatively breeding meerkats

description: In many social vertebrates, variation in group persistence exerts an
 important effect on individual fitness and population demography. However,
 few studies have been able to investigate the failure of groups or the
 causes of the variation in their longevity. We use data from a long-term
 study of cooperatively breeding meerkats, Suricata suricatta, to
 investigate the different causes of group failure and the factors that
 drive these processes. Many newly formed groups failed within a year of
 formation and smaller groups were more likely to fail due to collapse.
 Groups that breed successfully and increase their size, could persist for
 several years, even decades. For long lived groups, the principal cause of
 failure for was infection with tuberculosis, Mycobacterium suricattae, a
 fatal disease that commonly spread throughout the group and killing group
 members. Infection risk was higher in groups with mobile individuals, that
 were small or experienced immigration.
DOI: 10.5061/dryad.stqjq2c32
title: Distinctive mitogenomic lineages within populations of white-tailed eagles (Haliaeetus albicilla)

description: Using whole mitochondrial DNA sequences from 89 white-tailed eagles
 (Haliaeetus albicilla) sampled from Iceland, Greenland, Norway, Denmark
 and Estonia between 1990-2018, we investigate the mitogenomic variation
 within and between countries. We show that there is a substantial
 population differentiation between the countries, reflecting similar major
 phylogeographic patterns obtained previously for the control region of the
 mitochondria, which suggested two main refugia during the last glacial
 period of Ice Age. Distinct mitogenomic lineages are observed within
 countries which divergence times exceeds the time since last glacial
 period of Ice Age ended. The lineages appear to have been maintained by
 natural selection. An excess of segregating amino acids in comparison with
 number of fixations, as revealed by the neutrality index suggests a load
 of deleterious mutations. The maintenance of mtDNA lineages within
 countries inflates our estimates of effective national population sizes
 and the times of their divergence.
description: Quality of
 the 89 individual fastq files was checked with FastQC, and then run
 through AdapterRemoval v2 to remove potential adapters when appropriate,
 using standard setting with the following customizing arguments:
 --collapse and --trimns. Individuals were mapped to the white-tailed eagle
 mitochondrial genome of a Korean specimen (NCBI: NC_040858.1) with bwa mem
 and converted to bam files using samtools view and sort. Bam files were
 transformed to vcf and fasta files using samtools mpileup with quality
 filters -q 30 and -Q 20, and bcftools call. The Korean reference sequence
 includes a NUMT in the 12s rRNA from position 492-538 (both included)
 which was removed from the alignment, resulting in total sequence length
 of 17,461 bp. Quality, depth, ratio of the common allele and binomial
 probabilities for all segregating sites were evaluated from the vcf file.
 A recently published mitochondrial genome of a German specimen (NCBI:
 MN356434.1) was retrieved from genebank and compared to our
 sequences.
DOI: 10.5061/dryad.f1vhhmgw8
title: Cognitive maps in the wild: Revealing the use of metric information in black howler monkeys' route navigation

description: When navigating, wild animals rely on internal representations of the
 external world to take movement decisions – called “cognitive maps”. As a
 rule, flexible navigation is hypothesized to be supported by sophisticated
 spatial skills (i.e., Euclidean cognitive maps); however, constrained
 movements along habitual routes is the most commonly reported navigation
 strategy. Even though incorporating metric information (i.e., distances
 and angles between locations) in route-based cognitive maps would likely
 enhance an animal’s navigation efficiency, there has been no evidence of
 this strategy reported for non-human animals to date. Here, we examine the
 properties of the cognitive map used by a wild population of primates by
 testing a series of cognitive hypotheses against spatially-explicit
 movement simulations. We collected 3104 hours of ranging and behavioural
 data on five groups of black howler monkeys (Alouatta pigra) at Palenque
 National Park, Mexico, from September 2016 through August 2017. We
 simulated correlated-random walks mimicking the ranging behaviour of the
 study subjects and tested for differences between observed and simulated
 movement patterns. Our results indicated that black howler monkeys engaged
 in constrained movement patterns characterized by a high path recursion
 tendency, which limited their capacity to travel in straight lines and
 approach feeding trees from multiple directions. In addition, we found
 that the structure of observed route networks was more complex and
 efficient than simulated route networks, suggesting that black howler
 monkeys incorporate metric information into their cognitive map. Our
 findings not only expand the use of metric information during route
 navigation to non-human animals but also highlight the importance of
 considering efficient route-based navigation as a cognitively demanding
 mechanism.
DOI: 10.5061/dryad.qjq2bvqfs
title: High-speed videos of siphonophore tentilla and nematocyst discharge

description: Siphonophores are free-living predatory colonial hydrozoan cnidarians
 found in every ocean of the world. Siphonophore tentilla (tentacle side
 branches) are unique biological structures for prey capture, composed of a
 complex arrangement of cnidocytes (stinging cells) bearing different types
 of nematocysts (stinging capsules) and auxiliary structures. Tentilla
 present an extensive morphological and functional diversity across
 species. Tentilla have a precisely coordinated high-speed strike mechanism
 of synchronous unwinding and nematocysts discharge. Here we characterize
 the kinematic diversity of this prey capture reaction using high-speed
 video and find relationships with morphological characters.
description: Offshore live siphonophore tentilla and nematocyst discharge
 videos. Phantom Miro 320S High-Speed camera C-mounted on a stereoscopic
 microscope. Kinematic measurements taken from the original .cine files
 using PCC software and a static photograph of a ruler at the same
 magnification for scale. Cine files can be reconstituted from the mp4 and
 chd files.
description: Install Phantom PCC software on a Windows PC. Batch convert
 MP4+chd files to CINE files. Open the scalebar image to set scale. Open
 the .cine file to measure accelerations, distances, and speeds.
DOI: 10.5061/dryad.dv41ns1xn
title: Impatiens glandulifera SNP and SilicoDArT genotyping data

description: We conducted genomic characterization based on SNP and SilicoDArT markers
 on the invasive Himalayan balsam (Impatiens glandulifera) plants
 originating from the native and non-native regions of their distribution.
 When genetic relationships were explored by PCoA based on SNP and
 SilicoDArT marker data, the first, second and third principal coordinates
 explained altogether 37.4% and 31.0% of the variability, respectively.
 Samples from the UK, Canada and Pakistan grouped together, while Indian
 plants were clearly distinct based on SNP markers but relatively close to
 the UK-Canada-Pakistan group based on SilicoDArT markers. Constructed
 trees differentiated the individuals into clusters resembling the patterns
 observed by PCoA. The Bayesian BAPS analysis revealed that the individuals
 were distributed in seven clusters, representing samples from each of the
 four Finnish populations, India, Pakistan and the combination of the UK
 and Canada. Similar clustering was visible in the constructed UPGMA tree.
 The Indian cluster did not display any ancestral gene flow with the
 others, while the Pakistani cluster showed ancestral gene flow only with
 the combined UK and Canada cluster. Furthermore, the latter cluster
 displayed ancestral gene flow with the Finnish populations varying from 0%
 to 3.1%. The AMOVA analysis showed that 45% and 26% of genetic variation
 was present among the I. glandulifera groups/populations and the rest
 within them based on SNP and SilicoDArT markers, respectively. Overall,
 the Bayesian BAPS analysis and the following gene flow network were the
 most informative tools for resolving relationships among native and
 introduced plants.
DOI: 10.5061/dryad.hx3ffbgdf
title: Data from: TRANSCENDS: a career development program for underrepresented in medicine scholars in academic neurology

description: Background: The Training in Research for Academic Neurologists to Sustain
 Careers and Enhance the Numbers of Diverse Scholars (TRANSCENDS) program
 is a career advancement opportunity for individuals underrepresented in
 biomedical research, funded by the National Institute and Neurological
 Disorders and Stroke; and American Academy of Neurology (AAN). Objective:
 To report on qualitative and quantitative outcomes in TRANSCENDS. Design:
 Early career individuals (neurology fellows and junior faculty) from
 groups underrepresented in medicine were competitively selected from a
 national pool of applicants (2016-2019). TRANSCENDS activities comprised
 an online Clinical Research degree program, monthly webinars, AAN meeting
 activities, and mentoring. Participants were surveyed during and after
 completion of TRANSCENDS to evaluate program components. Outcomes: Of 23
 accepted scholars (comprising four successive cohorts), 56% were women;
 61% Hispanic/Latinx, 30% Black/African American, 30% assistant professors.
 To date, 48% have graduated the TRANSCENDS program and participants have
 published 180 peer-reviewed articles.   Mentees'
 feedback noted that professional skills development (i.e., manuscript and
 grant writing), networking opportunities, and mentoring were the most
 beneficial elements of the program. Stated opportunities for improvement
 included: incorporating a mentor-the-mentor workshop, providing more
 transitional support for mentees in the next stage of their careers, and
 requiring mentees to provide quarterly reports. Conclusions: TRANSCENDS is
 a feasible program for supporting underrepresented in medicine
 neurologists towards careers in research and faculty academic appointments
 attained thus far have been sustained. While longer term outcomes and
 process enhancements are warranted, programs like this may help increase
 the numbers of diverse academic neurologists, and further drive
 neurological innovation.
description: The dataset includes 3 supplemental figures and 1 supplemental
 table. Figure 1. TRANSCENDS Orientation Session with
 scholars and mentors at the American Academy of Neurology Annual Meeting
 in 2018 in Los Angeles, CA. Figure 2. National
 Institutes of Health - TRANSCENDS Showcase Session Presenters at the 2018
 Academy of Neurology Annual Meeting in Los Angeles, CA comprising
 TRANSCENDS Program Directors and Scholars, as well as National Institute
 for Neurological Disorders and Stroke (NINDS) leaders. Dr. Walter
 Koroshetz NINDS Director (first on the left of front row) and Dr. Michelle
 Jones-London NINDS Chief, Office of Programs to Enhance Neuroscience
 Workforce Diversity (last on the right of the back row).
 Figure 3. AAN President, Dr. Ralph Sacco with TRANSCENDS scholars
 and faculty at the Academy of Neurology Annual Meeting in 2017 in Boston,
 Massachusetts. Table 5. List of TRANSCENDS Mentors
 (2017-2022)
DOI: 10.7272/q6z036dr
title: Fluorescent in situ hybridization of Mycobacterium tuberculosis rRNA species for analysis of ribosomal synthesis as a marker of bacterial growth of individual bacilli in distinct lesional microenvironments of lung granulomas from C3HeB/FeJ mice

description: There is urgent need for new drug regimens that more rapidly cure
 tuberculosis (TB). Existing TB drugs and regimens vary in
 treatment-shortening activity, but the molecular basis of these
 differences is unclear, and no existing assay directly quantifies the
 ability of a drug or regimen to shorten treatment. Drugs historically
 classified as sterilizing and non-sterilizing have distinct impacts on a
 fundamental aspect of Mycobacterium tuberculosis physiology: ribosomal RNA
 (rRNA) synthesis. In culture, in mice, and in human studies, measurement
 of precursor rRNA reveals that sterilizing drugs and highly effective drug
 regimens profoundly suppress M. tuberculosis rRNA synthesis, whereas
 non-sterilizing drugs and weaker regimens do not. The rRNA synthesis ratio
 provides a readout of drug effect that is orthogonal to traditional
 measures of bacterial burden. Here, we show that M. tuberculosis
 have markedly different levels of ongoing rRNA synthesis in
 varying key histologic microenvironments. 
description: Raw images and datasets of
 single-bacillary quantitative image analysis of multiplexed <i>in
 situ</i> hybridization (ISH) of rRNA species
 in <em>Mycobacterium
 tuberculosis</em> (<em>Mtb</em>) in lung granulomas from C3HeB/FeJ mice. Granulomas were stained by fluorescent ISH for <i>Mtb</i> 23S rRNA and pre-rRNA, and counterstained with DAPI. Datasets are available as *csv and original images used for analysis are available as *tif or *czi. Observations from analysis of these data have been submitted for review to Nature Communications as figures 2b, 2e and extended figure 2, 3b and 3c from the manuscript entitled "<i>Mycobacterium tuberculosis precursor rRNA indicates treatment-shortening activity of drugs and regimens</i>".
DOI: 10.5061/dryad.sj3tx964d
title: Introduced populations of ragweed show as much evolutionary potential as native populations

description: Invasive species are a global economic and ecological problem. They also
 offer an opportunity to understand evolutionary processes in a colonizing
 context. The impacts of evolutionary factors, such as genetic variation,
 on the invasion process are increasingly appreciated, but there remain
 gaps in the empirical literature. The adaptive potential of populations
 can be quantified using genetic variance–covariance matrices (G),
 which encapsulate the heritable genetic variance in a population. Here, we
 use a multivariate Bayesian approach to assess the adaptive potential of
 invasive populations of ragweed (Ambrosia artemisiifolia), a serious
 allergen and agricultural weed. We compared several aspects of genetic
 architecture and the structure of G matrices between
 three native and three introduced populations, based on phenotypic data
 collected in a field common garden experiment. We found moderate
 differences in the quantitative genetic architecture among populations,
 but we did not find that introduced populations suffer from a limited
 adaptive potential or increased genetic constraint compared with native
 populations. Ragweed has an annual life history, is an obligate
 outcrosser, and produces very large numbers of seeds and pollen grains.
 These characteristics, combined with the significant additive genetic
 variance documented here, suggest ragweed will be able to respond quickly
 to selection pressures in both its native and introduced ranges.
description: See paper.
description: See read me file.
DOI: 10.5061/dryad.4f4qrfjbm
title: Timing the SARS-CoV-2 index case in Hubei Province

description: Understanding when SARS-CoV-2 emerged is critical to evaluating our
 current approach to monitoring novel zoonotic pathogens and understanding
 the failure of early containment and mitigation efforts for COVID-19. We
 employed a coalescent framework to combine retrospective molecular clock
 inference with forward epidemiological simulations to determine how long
 SARS-CoV-2 could have circulated prior to the time of the most recent
 common ancestor. Our results define the period between mid-October and
 mid-November 2019 as the plausible interval when the first case of
 SARS-CoV-2 emerged in Hubei province. By characterizing the likely
 dynamics of the virus before it was discovered, we show that over
 two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying
 out without igniting a pandemic. Our findings highlight the shortcomings
 of zoonosis surveillance approaches for detecting highly contagious
 pathogens with moderate mortality rates.
description: The dataset was collected by using BEAST and FAVITES to generate
 phylogenetic analyses and epidemic simulations, respectively. Both were
 manually processed to determine the tMRCA and stable coalescence,
 respectively. Refer to the manuscript for further details. 
description: BEAST data is available for use, along with the aggregated
 FAVITES results. The input files for the final results in the manuscript
 are available and they can be used with the python script provided. Please
 see the README.txt file and manuscript for further details.