cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bzkh1895z
title: Data from: Clinical spectrum of CANVAS

description: Objective: To elucidate the clinical significance of an intronic biallelic
 pentanucleotide repeat expansion in the gene encoding Replication Factor C
 subunit 1 (RFC1) in patients with late-onset Cerebellar Ataxia, Neuropathy
 and Vestibular Areflexia Syndrome (CANVAS), other ataxias and in healthy
 controls by comprehensive genetic analyses. Methods: In this case-control
 study, we included 457 individuals comprising 26 patients with complete or
 incomplete CANVAS, 70 patients with late-onset cerebellar ataxia, 208
 healthy controls and 153 individuals from 39 multigenerational non-ataxia
 families to determine repeat stability. All 96 patients were screened for
 the repeat expansion by duplex PCR. To further characterize the repeat
 type and lengths, we used fragment length analysis, repeat-primed PCR,
 Sanger sequencing, and Southern blotting. Expression of RFC1 and the
 neighboring gene WDR19 were determined by quantitative PCR. Results:
 Massive biallelic pentanucleotide expansions were found in 15/17 complete
 CANVAS patients (88%), in 2/9 (22%) with incomplete CANVAS, in 4/70 (6%)
 patients with unspecified, late-onset cerebellar ataxia, but not in
 controls. In patients, the expansion comprised 800-1,000 mostly AAGGG
 repeats. Non-massively expanded repeat numbers were in the range of 7 to
 137 repeats and relatively stable during transmission. Expression of RFC1
 and WDR19 were unchanged and RFC1 intron retention was not found.
 Conclusions: A biallelic pentanucleotide repeat expansion is a frequent
 cause of CANVAS and found in a considerable number of patients with an
 incomplete clinical presentation or other forms of cerebellar ataxia. The
 mechanism by which the repeat expansions are causing disease remains
 unclear and warrants further investigations.
DOI: 10.5061/dryad.t4b8gthzr
title: Data from: Ecological regime shift preserved in the Anthropocene stratigraphic record

description: Paleoecological data are unique historical archives that extend back far
 beyond the last several decades of ecological observations. However, the
 fossil record of continental shelves has been perceived as too coarse and
 incomplete to detect processes occurring at decadal scales relevant to
 ecology and conservation. Here we show that the youngest (Anthropocene)
 fossil record on a continental shelf of the Adriatic Sea provides
 decadal-scale temporal resolution that is adequate for documenting an
 abrupt ecological shift affecting benthic communities during the 20th
 century. The magnitude and the duration of the 20th century shift in body
 size of a dominant bivalve species (Corbula gibba) is unprecedented given
 that this species was consistently small throughout the Holocene in the
 whole northern Adriatic Sea. The size shift coincided with compositional
 change of the benthic community, with the median per-assemblage abundance
 of C. gibba increasing from ~25% to ~70% in the late 20th century, and
 occurred at sites that experienced at least one hypoxic event per decade
 in the 20th century. This regime shift, which coincided with mass
 mortality of competitors and predators associated with higher frequency of
 seasonal hypoxic events, may reflect ecological release. The observed body
 size shift is coupled with a decline in the depth and rate of
 bioturbational mixing. This decline in burrowing benthic organisms
 resulted in the improved stratigraphic resolution of fossil assemblages,
 making it possible to detect sub-centennial ecological changes in the
 stratigraphic record on continental shelves.
description: Body size (length) of bivalve Corbula gibba from sediment cores
 in the northern Adriatic in the ESM 2 and the compilation of genus-level
 molluscan abundance data in death and living assemblages on the basis of
 published data in the ESM 6. See the ESM 1 for details. ESM 3-5 are R
 language scripts where body-size data  (ESM 3) are analyzed and the
 effects of time averaging on the detection of regime shift is simulated
 (ESM 5). The function for analogue matching is in the ESM 4.
  
description: See the ESM 1 for details
DOI: 10.5061/dryad.bnzs7h47f
title: Multi year social stability and social information use in reef sharks with diel fission-fusion dynamics: Raw acoustic detection

description: Animals across vertebrate taxa form social communities and often exist as
 fission-fusion societies. Central place foragers (CPF) may form social
 groups, from which they will predictably disperse to forage, either
 individually or in smaller groups, before returning to fuse with the
 larger group. However, the function and stability of social associations
 in predatory fish acting as CPFs is unknown, as individuals do not need to
 return to a shelter, yet show fidelity to core areas. Using dynamic social
 networks generated from acoustic tracking data, we document spatially
 structured sociality in CPF grey reef sharks at a Pacific Ocean atoll. We
 show that sharks form stable, social groups over multi-year periods, with
 some dyadic associations consistent for up to four years. Groups primarily
 formed during the day, increasing in group size before sharks dispersed
 from the reef to forage at night. Our simulations suggest that multiple
 individuals sharing a central place and using social information while
 foraging (i.e. local enhancement), will outperform non-CPF social
 foragers. We show multiyear social stability in sharks and suggest that
 social foraging with information transfer could provide a generalisable
 mechanism for the emergence of sociality with group central place
 foraging.
description: Acoustic listening stations (VR2W) were placed on the reef and
 listening continuously for sharks that have been tagged with long life
 acoustic transmitters. Every time a shark swam within range of a listening
 station, the time and date of detection was recorded along with the unique
 transmitter ID number. Raw data is provided
description: The was data shows all detections when tagged animals were
 detected at specific receivers. Data includes transmitter numbers (unique
 to each tagged sharks) and the acoustic listening station (VR2W) number
 which describes the specific listening station. The listening station has
 a specific geographic location where it was located on the reef. Date and
 times of detections are also provided.
DOI: 10.5061/dryad.51c59zw5g
title: Data from: Cortical microstructure in the amyotrophic lateral sclerosis-frontotemporal dementia continuum

description: Objective: We aimed to characterize cortical macro- and
 micro-structure of behavioral and cognitive changes along the amyotrophic
 lateral sclerosis (ALS) – frontotemporal dementia (FTD) continuum.
 Methods: We prospectively recruited 88 participants with
 a three-Tesla MRI structural and diffusion-weighted imaging sequences: 31
 ALS, 20 bvFTD, and 37 cognitively normal controls. ALS participants
 underwent a comprehensive cognitive and behavioral assessment and were
 dichotomized in ALS without cognitive or behavioral impairment (ALSno-cbi,
 n=12) and ALS with cognitive or behavioral impairment (ALScbi, n=19). We
 computed cortical thickness and cortical mean diffusivity using a
 surface-based approach and explored the cortical correlates of cognitive
 impairment with the Edinburgh Cognitive and Behavioral Amyotrophic lateral
 sclerosis Screen (ECAS).  Results: ALSno-cbi and ALScbi
 groups showed different patterns of reduced cortical thickness and
 increased cortical mean diffusivity. In the ALSno-cbi group, cortical
 thinning was mainly restricted to the dorsal motor cortex. In contrast, in
 the ALScbi group, cortical thinning was observed primarily on
 fronto-insular and temporal regions bilaterally. There were progressive
 cortical mean diffusivity changes along the ALSno-cbi, ALScbi, and bvFTD
 clinical continuum.  Importantly, ALS participants with
 either cognitive or behavioral impairment showed increased cortical mean
 diffusivity in the prefrontal cortex in the absence of cortical
 thickness.  Conclusions: Cortical mean diffusivity might
 be a useful biomarker for the study of extra motor cortical
 neurodegeneration in the ALS-FTD clinical spectrum.
DOI: 10.5061/dryad.msbcc2fvm
title: Data from: ClinicNet: machine learning for personalized order set recommendations

description: Objective This study assesses whether neural networks trained on
 electronic health record (EHR) data can anticipate what individual
 clinical orders and existing institutional order set templates clinicians
 will use more accurately than existing decision support tools. Materials
 and Methods We process 57,624 patients-worth of clinical event EHR data
 from 2008-2014. We train a feed-forward neural network (ClinicNet) and
 logistic regression applied to the traditional problem structure of
 predicting individual clinical items  as well as our proposed
 workflow of predicting existing institutional order set template usage.
 Results ClinicNet predicts individual clinical orders (precision=0.32,
 recall=0.47) better than existing institutional order sets
 (precision=0.15, recall=0.46). The ClinicNet model predicts clinician
 usage of existing institutional order sets (avg. precision=0.31) with
 higher average precision than  a baseline of order set usage
 frequencies (avg. precision=0.20) or a logistic regression model (avg.
 precision=0.12). Discussion Machine learning methods can predict clinical
 decision-making patterns with greater accuracy and less manual effort than
 existing static order set templates. This can streamline existing clinical
 workflows, but may not fit if historical clinical ordering practices are
 incorrect. For this reason, manually authored content such as order set
 templates remain valuable for purposeful design of care pathways.
 ClinicNet’s capability of predicting such personalized order set templates
 illustrates the potential of combining both top-down and bottom-up
 approaches to delivering clinical decision support content. Conclusion
 ClinicNet illustrates the capability for machine learning methods applied
 to the EHR to anticipate both individual clinical orders and existing
 order set templates, which has the potential to improve upon current
 standards of practice in clinical order entry.
description: See manuscript Methods section.
description: See README file   Files
 that end in .pkl are pickle files, they can be loaded using Python's
 pickle module (see pickle module documentation). Files
 that end in .h5 are hdf5 files, they can be loaded using Python's
 h5py module (see h5py module documentation).   Example
 for loading .h5 files: h5f = h5py.File(filename,
 'r') data =
 h5f['key'].value<br> h5f.close()
DOI: 10.5061/dryad.9w0vt4bc3
title: Fluorescence‐based detection of field targets using an autonomous unmanned aerial vehicle system

description: This dataset comprises of the IDL code referenced in the 'Open
 Research' section of the Kaye and Pittman (2020) study
 'Fluorescence‐based detection of field targets using an autonomous
 unmanned aerial vehicle system' published in Methods in Ecology and
 Evolution (https://doi.org/10.1111/2041-210X.13402). This
 study describes a proof‐of‐concept autonomous unmanned aerial
 vehicle (UAV) system that utilizes the fluorescence characteristics unique
 to different materials to scan and acquire targets in the field e.g.
 fossils, rocks and minerals, organisms and archaeological artefacts. This
 is possible because these targets are often highly fluorescent against
 lower fluorescence backgrounds and may exhibit different colours.
 Fluorescence is stimulated by a near‐UV laser that is projected
 across the ground as a horizontal line directly below the UAV. The IDL
 code is for laser line and colour extractions in the laser scan strip. The
 raw .jpeg data for the IDL code is not provided here as
 this depends on what target is being scanned. All image data are
 made available in the paper. Additional contextual information is
 provided in the '2 MATERIALS AND METHODS' section of the paper,
 especially in Figure 3.
description: Computer code running under IDL.
 <em>readalljpgs.pro</em> extracts laser lines from jpeg
 images. <em>extractcolor.pro</em> extracts a predefined color
 in a laser scan strip. The raw .jpeg data for the IDL code is not provided
 here as this depends on what target is being scanned. All image data are
 made available in the paper (Kaye and Pittman, 2020: Fluorescence‐based
 detection of field targets using an autonomous unmanned aerial vehicle
 system in <em>Methods in Ecology and Evolution</em> [https://doi.org/10.1111/2041-210X.13402]). Additional contextual information is provided in the '2 MATERIALS AND METHODS' section of the paper, especially in Figure 3.
DOI: 10.5061/dryad.mw6m905tk
title: Simulation models from: Can CRISPR-mediated gene drive work in pest and beneficial haplodiploid species?

description: Gene drives based on CRISPR/Cas9 have the potential to reduce the enormous
 harm inflicted by crop pests and insect vectors of human disease, as well
 as to bolster valued species. In contrast with extensive empirical and
 theoretical studies in diploid organisms, little is known about CRISPR
 gene drive in haplodiploids, despite their immense global impacts as
 pollinators, pests, natural enemies of pests, and invasive species in
 native habitats. Here we analyze mathematical models demonstrating that,
 in principle, CRISPR homing gene drive can work in haplodiploids, as well
 as at sex-linked loci in diploids. However, relative to diploids,
 conditions favoring the spread of alleles deleterious to haplodiploid
 pests by CRISPR gene drive are narrower, the spread is slower, and
 resistance to the drive evolves faster. By contrast, the spread of alleles
 that impose little fitness cost or boost fitness was not greatly hindered
 in haplodiploids relative to diploids. Therefore, altering traits to
 minimize damage caused by harmful haplodiploids, such as interfering with
 transmission of plant pathogens, may be more likely to succeed than
 control efforts based on introducing traits that reduce pest fitness.
 Enhancing fitness of beneficial haplodiploids with CRISPR gene drive is
 also promising.
description: Jun Li created these six simulation models to compare
 evolutionary trajectories with CRISPR homing gene drive in haplodiploid
 versus diploid organisms.
description: The computer code is in R.
DOI: 10.5061/dryad.3j9kd51fb
title: Data from: Phylogenetic and functional distinctiveness explain alien plant population responses to competition

description: Several invasion hypotheses predict a positive association between
 phylogenetic and functional distinctiveness of aliens and their
 performance, leading to the idea that distinct aliens compete less with
 their resident communities. However, synthetic pattern relationships
 between distinctiveness and alien performance and direct tests of
 competition as the driving mechanism have not been forthcoming. This is
 likely because different patterns are observed at different spatial
 grains, because functional trait and phylogenetic information are often
 incomplete, and due to the need for competition experiments that measure
 demographic responses across a variety of alien species that vary in their
 distinctiveness. We conduct a competitor removal experiment and
 parameterize matrix population and integral projection models for 14 alien
 plant species. More novel aliens compete less strongly with co-occurring
 species in their community, but these results dissipate at a larger
 spatial grain of investigation. Further, we find that functional traits
 used in conjunction with phylogeny improve our ability to explain
 competitive responses. Our investigation shows that competition is an
 important mechanism underlying the differential success of alien species.
DOI: 10.7272/q6h993dv
title: ZipSeq : barcoding for real-time mapping of single cell transcriptomes

description: Spatial transcriptomics seeks to integrate single-cell transcriptomic data
 within the 3-dimensional space of multicellular biology. Current methods
 use glass substrates pre-seeded with matrices of barcodes or fluorescence
 hybridization of a limited number of probes. We developed an alternative
 approach, called ‘ZipSeq’, that uses patterned illumination and photocaged
 oligonucleotides to serially print barcodes (Zipcodes) onto live cells
 within intact tissues, in real-time and with on-the-fly selection of
 patterns. Using ZipSeq, we mapped gene expression in three settings:
 in-vitro wound healing, live lymph node sections and in a live tumor
 microenvironment (TME). In all cases, we discovered new gene expression
 patterns associated with histological structures. In the TME, this
 demonstrated a trajectory of myeloid and T cell differentiation, from
 periphery inward. A combinatorial variation of ZipSeq efficiently scales
 in number of regions defined, providing a pathway for complete mapping of
 live tissues, subsequent to real-time imaging or perturbation.
description: Raw stitched images supporting main and supplementary figures
 from manuscript. Samples were prepared as detailed in the methods
 section.
description: Please refer to the metadata file.
DOI: 10.5061/dryad.x0k6djhgc
title: Data from: Diverse nucleosome site-selectivity among histone deacetylase complexes

description: Histone acetylation regulates chromatin structure and gene expression and
 is removed by histone deacetylases (HDACs). HDACs are commonly found in
 various protein complexes to confer distinct cellular functions, but how
 the multi-subunit complexes influence deacetylase activities and
 site-selectivities in chromatin is poorly understood. Recent studies on
 the HDAC1 containing CoREST complex and acetylated nucleosome substrates
 revealed a notable preference for deacetylation of histone H3 acetyl-Lys9
 vs. acetyl-Lys14 (M. Wu et al, 2018). Here we analyze the enzymatic
 properties of five class I HDAC complexes: CoREST, NuRD, Sin3B, MiDAC and
 SMRT with site-specific acetylated nucleosome substrates. Our results
 demonstrate that these HDAC complexes show a wide variety of deacetylase
 rates in a site-selective manner. A Gly13 in the histone H3 tail is
 responsible for a sharp reduction in deacetylase activity of the CoREST
 complex for H3K14ac. These studies provide a framework for connecting
 enzymatic and biological functions of specific HDAC complexes.
DOI: 10.5061/dryad.xsj3tx9bz
title: Data from: Chromosome-level assembly of Southern catfish (Silurus meridionalis) provides insights into visual adaptation to the nocturnal and benthic lifestyles

description: Southern catfish (Silurus meridionalis) is a nocturnal and benthic
 freshwater fish endemic to the Yangtze River and its
 tributaries with an important economic value but a drastically
 declining wild population. In this study, we constructed a
 chromosome-level draft genome of S. meridionalis using 69.7 Gb
 Nanopore long reads and 49.5 Gb Illumina short
 reads. The genome assembly was 741.2 Mb in size with a contig N50
 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data
 were applied to assemble contigs into scaffolds and further into
 29 chromosomes, resulting in a 738.9 Mb genome with a
 scaffold N50 of 28.04 Mb. A total of 22,965
 protein-coding genes were predicted from the genome with 22,519
 (98.06%) genes functionally annotated. Comparative genomic and
 transcriptomic analyses revealed that
 catfish possess a rod-dominated visual
 system which is responsible for scotopic
 vision. The absence of cone opsins SWS1 and
 SWS2 resulted in the lack of UV and violet sensitivity. Mutations
 at key amino acid sites of RH1.1, RH1.2 and RH2 resulted
 in spectral tuning good for dim light vision
 and narrow color vision. A higher expression
 level of rod phototransduction genes than that of cone genes and
 higher rod-to-cone ratio leaded to higher optical sensitivity
 under dim light conditions. In addition, analysis of
 the genes involved in eye morphogenesis and
 development revealed the loss of conserved
 noncoding elements (CNEs), which might be associated
 with the small eyes in catfish. Taken together, our
 study provided important clues for the adaptation of the
 catfish visual system to a benthic lifestyle. The draft genome of
 S. meridionalis represents a valuable resource for
 elucidation of molecular mechanism of ecological adaptation, as
 well as genetic breeding in aquaculture.
DOI: 10.5061/dryad.cjsxksn39
title: Captive-bred populations of a partially migratory salmonid fish are unlikely to maintain migratory polymorphism in natural habitats

description: Supplementation of wild populations with captive-bred individuals is often
 ineffective for boosting long-term productivity of wild populations. On
 the other hand, it remains unknown whether supplementation can act to
 maintain life-history variation in natural habitats, which is also
 important for the long-term persistence of populations and species.
 Partial migration, in which both migratory and resident individuals are
 maintained in a population, is commonly found across animal taxa. However,
 human-induced habitat fragmentation continues to cause rapid decline in a
 migratory phenotype among many natural populations. By using field and
 hatchery experiments, we here demonstrated that while migrants and
 residents could be maintained in captive environments, few fish became
 migrants in natural streams in red-spotted masu salmon Oncorhynchus masou
 ishikawae. Released captive-bred fish rarely reached the threshold body
 size necessary to become migrants in natural streams, presumably due to
 lower growth condition in natural than in captive environments. The
 decision to migrate is often considered a threshold trait in salmonids and
 other animal taxa. Our findings highlight the need for supplementation
 programs to acknowledge environmentally induced changes in life-history
 decisions for partially migratory species.
description: Experimental stocking was conducted in 10 sections of seven
 streams in an upper drainage of the Arida River system in southwest
 Honshu, Japan. Data S1 and S2 sheets in the excel file were obtained in
 the experiment. Captive-bred fish from the
 two hatcheries were reared in outdoor mesocosms. Data S3 sheet in the
 excel file was obtained in the mecosocm experiment.