cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.69p8cz925
title: Seasonality affects specialisation of a temperate forest herbivore community

description: Understanding spatiotemporal trends on insect-plant interaction networks
 is essential to unveil the ecological and evolutionary processes driving
 herbivore specialisation. However, community studies accounting for
 temporal dynamics in host-plant specialisation of herbivorous insects are
 surprisingly scarce. Here, we provide the background data which were used
 to investigate how seasonality affects specialisation of a temperate
 forest herbivore community.  This dataset results from a
 comprehensive sampling of more than 4,700 folivorous caterpillars
 associated with 16 deciduous tree species in eastern North America.
 Specifically, we provide three abundance-based plant-caterpillar
 interaction matrices. Each interaction matrix represents a six-week period
 of the growing season. These time periods are defined as follow: early
 season, midseason, and late season. We observed a significantly less
 specialised herbivore fauna in the early season than in the two subsequent
 summer seasons. We further found that the seasonal increase in
 specialisation was driven by a remarkable turnover in species composition
 rather than by shifts in guild structure or intraspecific changes in diet
 breadth of the herbivores.
description: Location: Toms Brook (Virginia, USA; 38°55’ N, 78°25’ W; 220 m
 a.sl.) Folivorous caterpillars (miners excluded) were
 collected from all deciduous tree individuals ( ≥ 5 cm DBH) within two 0.1
 ha plots. Total: 184 tree indiviuals in 16 species;
 4710 caterpillars in 243 species. The sampling was
 carried out in two consecutive years - between April, 2016 and August,
 2017. Seasons: early season (26 Apr.-6 June), midseason
 (7 June-18 July), late season (19 July-29 Aug.) Species
 identification was based on caterpillar morphology, aided by comprehensive
 DNA barcoding
description: <em>Quercus rubra</em> agg. comprises tree
 individuals of <em>Quercus rubra </em>L., <em>Quercus
 velutina</em> Lam., as well as their hybrids.
DOI: 10.5061/dryad.51c59zw87
title: Public parks and the pandemic: how park usage has been affected by COVID-19 policies

description: Public parks serve an important societal function as recreational spaces
 for diverse communities of people, with well documented physical and
 mental health benefits. As such, parks may be crucial for how people have
 handled effects of the COVID-19 pandemic, particularly the increasingly
 limited recreational opportunities, widespread financial uncertainty, and
 consequent heightened anxiety. Despite the documented benefits of parks,
 however, many states have instituted park shutdown orders due to fears
 that public parks could facilitate SARS-CoV-2 transmission. Here we use
 geotagged social media data from state, county, and local parks throughout
 New Jersey to examine whether park visitation increased when the COVID-19
 pandemic began and whether park shutdown orders were effective at
 deterring park usage. We compare park usage during four discrete stages of
 spring 2020: (1) before the pandemic began, (2) during the beginning of
 the pandemic, (3) during the New Jersey governor’s state-wide park
 shutdown order, and (4) following the lifting of the shutdown. We find
 that park visitation increased by 63.4% with the onset of the pandemic.
 The subsequent park shutdown order caused visitation in closed parks to
 decline by 76.1% while parks that remained open continued to experience
 elevated visitation levels. Visitation then returned to elevated
 pre-shutdown levels when closed parks were allowed to reopen. Altogether,
 our results indicate that parks continue to provide crucial services to
 society, particularly in stressful times when opportunities for recreation
 are limited. Furthermore, our results suggest that policies targeting
 human behavior can be effective and are largely reversible. As such, we
 should continue to invest in public parks and to explore the role of parks
 in managing public health and psychological well-being.
description: We assessed park visitation at our selection of candidate parks
 using publicly available, geotagged social media data from Instagram. To
 gather data on park usage, we wrote a Python script to collect data from
 publicly accessible Instagram photos. We first matched candidate parks to
 their corresponding Instagram location tags, of which there were often
 several for a park, and visually verified that all location tags
 corresponded to the correct parks using Google maps. After we had created
 this list of accurate location tags for the parks that we identified in
 the NJ OSPRI dataset, we ran our Python script to collect the metadata of
 all photos associated with each tag; we collected the user handle, date,
 location tag, photo caption, and hashtags for each photo.
DOI: 10.6084/m9.figshare.31165561
title: Additional file 2 of Molecular architecture of mesoderm cells across early to middle stage of human embryo development at single-cell resolution

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.31165561.v1
title: Additional file 2 of Molecular architecture of mesoderm cells across early to middle stage of human embryo development at single-cell resolution

description: Supplementary Material 2
DOI: 10.5061/dryad.4tmpg4f9j
title: Reduced habitat suitability and landscape connectivity in a songbird migratory divide

description: Aim Seasonal migration is a common phenomenon in animals and connects
 geographically distant ecosystems. Considerable variation has been
 documented in this behaviour and migratory divides (contact zones between
 populations that use different routes to navigate around ecological
 barriers) are an example of this. Migratory divides could have important
 implications for ecological speciation as hybrids in divides take
 intermediate routes and it has been predicted that these routes will be
 ecologically inferior as they bring hybrids over barriers that parental
 forms avoid. We provide the first test of this prediction here using a
 well-characterized divide between coastal and inland subspecies of
 Swainson’s thrushes. Location North, Central and South America Time period
 2006-2013 Major taxa studied Birds Methods We used ecological niche models
 and analyses of landscape connectivity to predict suitable habitat for
 coastal and inland thrushes on migration and identify optimal migratory
 routes. We compared estimates of habitat suitability and landscape
 connectivity along the actual migratory routes of birds tracked with
 light-level geolocators. Results Consistent with predictions for migratory
 divides, niche models estimated lower habitat suitability in the
 intermediate range between the migratory ranges of parental forms.
 Furthermore, our models of landscape connectivity predicted optimal routes
 that circumvent this intermediate area. Birds taking intermediate routes
 used stopover sites of lower predicted habitat suitability than birds
 migrating on either side of the divide and overlapped less with optimal
 paths. Main conclusions Our results support the prediction that
 intermediate routes of hybrids in migratory divides are ecologically
 inferior to those of parental forms. This finding suggests ecological
 differences are helping to maintain divides and could have broad
 implications, with divides shaping the distribution and maintenance of
 species boundaries globally and across many taxonomic groups.
description: The readme file contains explanations for variables and
 abbreviations used in the datasets and information on where the data was
 downloaded from.
DOI: 10.5061/dryad.hmgqnk9gs
title: A Hopf Adaptive Oscillator Analog Circuit as a musical instrument

description: The utilization of a Hopf adaptive frequency oscillator as a musical
 instrument is explored. The analog circuit design of this nonlinear
 oscillator are presented, and the procedure to use it as a musical
 instrument is described. Although similar to other analog electronics
 instruments such as the theremin, the authors believe this is the first
 time that an adaptive oscillator has been implemented as a musical
 instrument. Ave Maria, D. 839-Bradley Chapman
 (https://musopen.org/music/1673-ave-ma...​), is used here as an
 example. The dataset contains four parts. 1) vocalAveMaria.mat is
 the time series data that was input to the adaptive frequency oscillator.
 2) afoAveMaria.mat is the response of the y state of the adaptive
 frequency oscillator. 3) pianoAveMaria.mat is the time series
 data of the piano accompaniment. 4) Exp_remix_by_y.wav is the
 sound file of the adaptive oscillator "singing" the vocal track,
 and it is overlaid on top of the piano accompaniment.
description: The time series, the vocals of Ave Maria plus pedal points
 (vocalAveMaria.mat), was sent to the circuit using a National Instrument
 (NI) cDAQ-9174 controlled by MATLAB, which was also used to record the x,
 y, and omega states of the circuit. No post-processing was performed on
 the data. The y state from the circuit (afoAveMaria.mat) was then added
 back to the piano accompaniment (pianoAveMaria.mat). The final sound file
 is Exp_remix_by_y.wav.
description: The time series data of the vocals (vocalAveMaria.mat) could be
 used as input to other types of circuits. The output of other circuits
 could then be added to the piano accompaniment (pianoAveMaria.mat) to
 create new versions of the piece of music. The produced sound file could
 then be compared to Exp_remix_by_y.wav.
DOI: 10.5061/dryad.9w0vt4bfn
title: Predominant spastic paraparesis associated with the D178N mutation in PRNP

description: Here we report on a 70-year-old female presenting with an unusual
 progressive syndrome with fatal outcome. The predominant features in this
 case were spastic paraparesis, cognitive decline and respiratory failure.
 Relatives affected with a similar syndrome were previously diagnosed with
 lipofuscinosis. However, whole-genome sequencing (WGS) in our case did not
 reveal any pathogenic variants in genes associated with lipofuscinosis,
 but instead detected the known D178 variant in PRNP. The course
 of disease was rapid despite the presence of methione at codon 129 in the
 mutated and valine in the healthy allele of PRNP. Typical
 neuropathological abnormalities for familial fatal insomnia (FFI) were
 found, Western blot analysis suggested a type 2B prion protein isoform.
 The serendipitous diagnosis obtained with WGS illustrates a role for the
 method in elusive cases.
DOI: 10.6084/m9.figshare.31165571
title: Additional file 3 of A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate

description: Supplementary Material 3. Table S1: Colony forming units.
DOI: 10.6084/m9.figshare.31165571.v1
title: Additional file 3 of A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate

description: Supplementary Material 3. Table S1: Colony forming units.
DOI: 10.6084/m9.figshare.31165577
title: Additional file 4 of A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate

description: Supplementary Material 4. Table S2: List of media.
DOI: 10.6084/m9.figshare.31165577.v1
title: Additional file 4 of A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate

description: Supplementary Material 4. Table S2: List of media.
DOI: 10.6084/m9.figshare.31165580
title: Additional file 5 of A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate

description: Supplementary Material 5. Table S3: Non-redundant isolates_extended.
DOI: 10.6084/m9.figshare.31165580.v1
title: Additional file 5 of A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate

description: Supplementary Material 5. Table S3: Non-redundant isolates_extended.
DOI: 10.6084/m9.figshare.31165583
title: Additional file 6 of A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate

description: Supplementary Material 6. Table S4: Data of Fig. 5.
DOI: 10.6084/m9.figshare.31165583.v1
title: Additional file 6 of A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate

description: Supplementary Material 6. Table S4: Data of Fig. 5.
DOI: 10.5061/dryad.2z34tmpmj
title: Data from: Restoration of forest resilience to fire from old trees is possible across a large Colorado dry-forest landscape by 2060, but only under the Paris 1.5 deg. C goal

description: Fire-prone dry forests often face increasing fires from climate change
 with low resistance and resilience due to logging of large, old
 fire-resistant trees. Their restoration across large landscapes is
 constrained by limited mature trees, physical settings, and protection.
 Active restoration has been costly and shown limited effectiveness, but
 lower cost passive restoration is less studied. I used GIS and machine
 learning to see if passive restoration of old trees could overcome
 constraints in time, by 2060, across 667,000 ha of montane forests in the
 San Juan Mountains, Colorado, where temperatures are increasing faster
 than the global average. Random Forest models of physical locations of
 reconstructed historical old growth (OG) and relatively frequent fire
 (RFF) show historical OG with RFF was favored between 6.1-7.9̊C annual
 mean temperatures. Random Forest models projected similar
 temperature-suitable locations were moved into the current middle montane
 ca 2015, and would be extended to just below the upper limit of the
 montane if the Paris 1.5̊C goal is reached, but beyond if not. US Forest
 Service Common Stand Exam data, which covered ∼15% of the study area and
 included 26,149 tree ages, show the highest potential for restoring
 resistance and resilience from old trees is a ≥120 year age class. This
 class could become a ≥160 year age class, which meets old-growth age
 criteria, over 81% of the area by ca 2060, nearly fully restoring
 historical old-growth levels. Half this age class is already protected,
 and much of the remainder could be retained using evidence-based diameter
 caps. Datasets thus are sufficient to show that passive restoration of
 old-tree resistance and resilience to fire is feasible by ca 2060 across a
 large montane landscape, although contingent on global success in
 achieving the Paris 1.5̊C goal. Passive restoration may be viable
 elsewhere.
description: Derived using GIS and Random Forest models from historical and
 modern datasets.
description: See pdf that explains the datasets.
DOI: 10.6084/m9.figshare.31165588
title: Additional file 2 of Ancient DNA study provides clues to leprosy susceptibility in medieval Europe

description: Additional file 2. Tables S1-S14.
DOI: 10.6084/m9.figshare.31165588.v1
title: Additional file 2 of Ancient DNA study provides clues to leprosy susceptibility in medieval Europe

description: Additional file 2. Tables S1-S14.
DOI: 10.5061/dryad.0gb5mkm1c
title: Effect of changes in MS diagnostic criteria over 25 years on time to treatment and prognosis in patients with clinically isolated syndrome

description: Objectives: To explore whether time to diagnosis, time to treatment
 initiation and age to reach disability milestones has changed in patients
 with clinically isolated syndrome (CIS) according to different multiple
 sclerosis (MS)-diagnostic criteria periods. Methods: Retrospective study
 based on data prospective collected from the Barcelona-CIS cohort between
 1994 and 2020. Patients were classified into five periods according to
 different MS criteria, and the time to MS diagnosis and treatment
 initiation were evaluated. The age at which MS patients reached an EDSS
 ≥3.0 was assessed by Cox regression analysis according to diagnostic
 criteria periods. Results: 1174 patients were included. The median time
 from CIS to MS diagnosis, and from CIS to treatment initiation showed a
 77% and 82 reduction from the Poser to the McDonald 2017 diagnostic
 criteria periods, respectively. Patients diagnosed in more recent
 diagnostic criteria periods had a lower risk of reaching age at EDSS ≥3.0
 compared to Poser period: Adjusted hazard ratio (aHR) 0.47 (95% confidence
 interval 0.24-0.90) for McDonald 2001, aHR 0.25 (0.12-0.54) for McDonald
 2005, aHR 0.30 (0.12-0.75) for McDonald 2010 and aHR 0.07 (0.01-0.45) for
 McDonald 2017. Early-treatment patients displayed an aHR of 0.53
 (0.33-0.85) of reaching age at EDSS ≥3.0 compared to late-treatment.
 Changes in prognosis together with early-treatment effect were maintained
 after excluding possible bias derived from the use of different diagnostic
 criteria over time (so called, “Will Rogers” phenomenon) Conclusion: A
 continuous decrease in the time to MS diagnosis and treatment initiation
 were observed across diagnostic criteria periods. Overall, patients
 diagnosed in more recent diagnostic criteria periods displayed a lower
 risk of reaching disability. Importantly, the prognostic improvement is
 maintained after discarding the “Will Rogers” phenomenon, and early
 treatment appears to be the most likely contributing factor.
DOI: 10.6084/m9.figshare.31165595
title: Additional file 1 of Phylograd: fast column-specific calculation of substitution model gradients

description: Supplementary file 1 (zip 4800 KB)
DOI: 10.6084/m9.figshare.31165595.v1
title: Additional file 1 of Phylograd: fast column-specific calculation of substitution model gradients

description: Supplementary file 1 (zip 4800 KB)
DOI: 10.6084/m9.figshare.31165598
title: Additional file 1 of Rat models for arterial calcification associated with chronic kidney disease: a systematic review and meta-analysis

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.31165598.v1
title: Additional file 1 of Rat models for arterial calcification associated with chronic kidney disease: a systematic review and meta-analysis

description: Supplementary Material 1.
DOI: 10.5061/dryad.fn2z34ttg
title: Data from: Genotype-environment mismatch of kelp forests under climate change

description: Climate change is increasingly impacting ecosystems globally.
 Understanding adaptive genetic diversity and whether it will keep pace
 with projected climatic change is necessary to assess species’
 vulnerability and design efficient mitigation strategies such as assisted
 adaptation. Kelp forests are the foundations of temperate reefs globally
 but are declining in many regions due to climate stress. A lack of
 knowledge of kelps’ adaptive genetic diversity hinders assessment of
 vulnerability under extant and future climates. Using 4245 single
 nucleotide polymorphisms (SNPs), we characterise patterns of neutral and
 putative adaptive genetic diversity for the dominant kelp in the southern
 hemisphere (Ecklonia radiata) from ~1000 km coastline off Western
 Australia. Strong population structure and isolation-by-distance was
 underpinned by significant signatures of selection related to temperature
 and light. Gradient forest analysis of temperature-linked SNPs under
 selection revealed a strong association with mean annual temperature range
 suggesting adaptation to local thermal environments. Critically, modelling
 revealed that predicted climate-mediated temperature changes will likely
 result in high genomic vulnerability via a mismatch between current and
 future predicted genotype-environment relationships such that kelp forests
 off Western Australia will need to significantly adapt to keep pace with
 projected climate change. Proactive management techniques such as assisted
 adaptation to boost resilience may be required to secure the future of
 these kelp forests and the immense ecological and economic values they
 support.
description: Population & Environmental data: latgrad_pop_env.csv Sample ID, site ID and Environmental data for variables used in lfmm and RDA analysis id = sample ID site = site ID LT_meantemp = long term annual mean temperature, calculated from https://coastwatch.pfeg.noaa.gov/erddap/griddap/jplMURSST41.html LT_rangetemp = Long term annual mean temperature range, calculated from https://coastwatch.pfeg.noaa.gov/erddap/griddap/jplMURSST41.html BO_damean = mean diffuse attenuation, downloaded from Bio-ORACLE v2.0 (Assis et al., 2018) BO2_curvelmean_bdmax = mean seawater velocity at depth, downloaded from Bio-ORACLE v2.0 (Assis et al., 2018) SNP datafile: latgrad_bayescan_nodup Bayescan input file SNP datafile: latgrad_geno Snmf input file in geno format, missing values are coded as 9 SNP datafile: latgrad_imputed SNP input file, imputed with snmf and used for lfmm, RDA and GF analysis
DOI: 10.6084/m9.figshare.31165603
title: Additional file 1 of Melanoma antigen genes A1 and A3 as predictors of treatment response and survival in HCV-associated hepatocellular carcinoma: a prospective study

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.31165603.v1
title: Additional file 1 of Melanoma antigen genes A1 and A3 as predictors of treatment response and survival in HCV-associated hepatocellular carcinoma: a prospective study

description: Supplementary Material 1
DOI: 10.5061/dryad.v6wwpzgw0
title: Canine 230K Consortium chip data originated from the drug detection dogs

description: Drug detection dogs play integral roles in society. However, the interplay
 between their behaviors and genetic characteristics underlying their
 performance remains uninvestigated. Herein, more than 120,000 genetic
 variants were evaluated in 326 German Shepherd or Labrador Retriever dogs
 to profile the genetic traits associated with various behavioral traits
 related to the successful training of drug detection dogs.
description: German shepherd and Labradore Retrivers were genotyped by using
 Infinium HD CanineHDPIs  Array (Illumina Inc.).
description: # **Illumina's Canine 230K Consortium BeadChip data for 124 German
 Shepherd and 229 Labrador Retriever** # Data sets for German Shepherd
 GSD_fs.bed : PLINK bed file GSD_fs.bim : PLINK ped file GSD_fs.fam : PLINK
 ped file GSD_fs_pheno.txt : phenotype files for 9 traits # Data sets for
 229 Labrador Retriever LR_fs.bed: : PLINK bed file LR_fs.bim : PLINK bim
 file LR_fs.fam : PLINK fam file LR_fs_pheno.txt: phenotype files for 9
 traits
DOI: 10.5061/dryad.rfj6q579q
title: Veloporphyrellus latisporus, a new and noteworthy species from moist temperate forests of Pakistan

description: Veloporphyrellus latisporus is proposed as a new species based on
 morphological characters and supporting molecular data from ITS and LSU
 regions of the nuclear DNA. The new species is characterized by its red to
 reddish brown granulose pileus and comparatively broader basidiospores. A
 key to the species of Veloporphyrellus is provided. This is the first
 report of any Veloporphyrellus species from Pakistan.