cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pzgmsbcj5
title: Stress in the city: meta-analysis indicates no overall evidence for stress in urban vertebrates

description: As cities continue to grow it is increasingly important to understand the
 long-term responses of wildlife to urban environments. There have been
 increased efforts to determine whether urbanization imposes chronic stress
 on wild animals, but empirical evidence is mixed. Here we conduct a
 meta-analysis to test whether there is, on average, a detrimental effect
 of urbanisation based on baseline and stress-induced glucocorticoid levels
 of wild vertebrates. We found no effect of urbanisation on glucocorticoid
 levels, and neither sex, season, life stage, taxon, size of the city nor
 methodology accounted for variation in the observed effect sizes. At face
 value our results suggest that urban areas are no more stressful for
 wildlife than rural or non-urban areas, but we offer a few reasons why
 this conclusion could be premature. We propose that refining methods of
 data collection will improve our understanding of how urbanization affects
 the health and survival of wildlife.
DOI: 10.5061/dryad.vx0k6djpp
title: Synaptic connectivity and neuronal network activity changes after extracellular matrix depletion

description: Maintaining the balance between excitation and inhibition is essential for
 the appropriate control of neuronal network activity. Sustained
 excitation-inhibition (E-I) balance relies on the orchestrated adjustment
 of synaptic strength, neuronal activity and network circuitry. While
 growing evidence indicates that extracellular matrix (ECM) of the brain is
 a crucial regulator of neuronal excitability and synaptic plasticity, it
 remains unclear whether and how ECM contributes to neuronal circuit
 stability. Here we demonstrate that the integrity of ECM supports the
 maintenance of E-I balance by retaining inhibitory connectivity. Depletion
 of ECM in mature neuronal networks preferentially decreases the density of
 inhibitory synapses and the size of individual inhibitory postsynaptic
 scaffolds. After ECM depletion, inhibitory synapse strength
 homeostatically increases via the reduction of presynaptic GABAB
 receptors. However, the inhibitory connectivity reduces to an extent that
 inhibitory synapse scaling is no longer efficient in controlling neuronal
 network activity. Our results indicate that the brain ECM preserves the
 balanced network state by stabilizing inhibitory synapses.
description: We performed multi-electrode array (MEA) recordings, synapse
 density quantifications, patch-clamp electrophysiology, STED microscopy
 and in silico neuronal network activity simulations. The data was
 processed with in-house scripts for ImageJ and MatLab, and with standard
 programs bundled with the equipment
description: All notes and nesessary explanations are provided within the
 uploaded file folders
DOI: 10.15468/dl.fd2zc2
title: Occurrence Download

description: A dataset containing 13411 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pylodictis olivaris",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13411 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002534-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.44j0zpcc3
title: Possibility of bridge inspection through drive-by vehicles

description: Based on virtual simulations of vehicle-bridge interactions, the
 possibility of detecting stiffness reduction damages in bridges through
 vehicle responses has been tested in two dimensional (2D) and three
 dimensional (3D) settings. Short Time Fourier Transformation (STFT) has
 been used to process the acceleration data of vehicles. The energy band
 variation was found strongly related to damage parameters. More important,
 initial entering conditions of vehicles are critical in obtaining vehicle
 responses through the vehicle bridge interaction models. Through different
 levels of road profile roughness, the offset distance needed before
 executing the vehicle-bridge interaction (VBI) modeling is obtained.
description: Series of ABAQUS models are simulated and data extracted through
 the bridge-vehicle interactions. From the vehicel acceleration data, FFT
 and short time fourier transformation have been conducted to extract the
 features of the data.
description: CAE files are the ABAQUS model files. .xls
 files are the vehicle acceleration data extracted. FFT
 and STFT are the matlab codes for the fourier transform and the short time
 fourier transform, respectively.
DOI: 10.5061/dryad.59zw3r25h
title: Interaction between cytochrome c and DNA: conformation, peroxidase activity and molecular dynamics simulation

description: A mixed system of cytochrome c (Cyt c, a typical hemoprotein) and DNA was
 constructed and the interaction between Cyt c and DNA were analyzed by
 experiment and molecular dynamics (MD) simulation methods, respectively.
 On the one hand, the experimental results showed: 1. The peroxidase
 activity of the mixed system was significantly enhanced relative to the
 Cyt c in 50 mM phosphate buffer solution at 25ºC. 2. UV-Vis spectra study
 found that, compared with the Cyt c solution, the absorbance of the Cyt
 c-DNA mixed system increased significantly at 280 nm, while the absorbance
 decreased at 405 nm, indicating that the overall structure of Cyt c in the
 mixed system became loose, and the structure around heme group became more
 compact. 3. Circular Dichroism (CD) studies showed that there was a weak
 interaction between DNA and Cyt c in the mixed system, which had little
 effects on the secondary structures of Cyt c. On the other hand, MD
 simulation results showed: 1. DNA and Cyt c were combined by hydrogen
 bonding and non-bonding interactions in the mixed system. 2. During the
 simulation process, N-Terminal α-Helix changed, and Lys13-Cys17 opened,
 exposing the active center (heme structure) of Cyt c, which may increase
 the binding of the mixed system to the substrate. 3. The bond length of
 Fe-N (N in His18 and Fe in heme group) became slightly shorter after
 equilibrium in the presence of DNA. 4. The Cyt c became loose after
 binding with DNA. 5. The total binding free energy between Cyt c and DNA
 was calculated to be -141.9 kJ/mol. The Cyt c-DNA system was in a
 relatively stable state from energy perspective. The results of the
 research on the structure and function of the Cyt c-DNA mixed system using
 experimental method and MD simulation method were consistent. The
 combination of experimental method and simulation method may provide
 useful research ideas and effective research methods for further studying
 the interaction mechanism between hemeprotein and DNA.
description: Horse heart Cyt c,
 2,2’-Azino-bis(3-Ethylbenzthiazoline-6-Sulfonic Acid) (ABTS), herring
 sperm DNA (DNA, &lt;50 bp), sodium dihydrogen phosphate and disodium
 hydrogen phosphate were purchased from Sigma (St. Louis, MO,
 USA). PDB file of
 crystal structure of Cyt c (PDB ID:1HRC) was achieved from the Protein
 Data Bank (http://www.rcsb.org). All Softwares used in this paper were from free sources: Ambertools: http://ambermd.org/ Gromacs: http://www.gromacs.org/ Pymol:  https://pymol.org/#opensource Vmd https://www.ks.uiuc.edu/Research/vmd/ APBS http://www.poissonboltzmann.org/ LigPlot https://www.ebi.ac.uk/thornton-srv/software/LigPlus/
DOI: 10.5061/dryad.05qfttf18
title: Functional investigation of monoterpenes for improved understanding of the relationship between hosts and bark beetle

description: Spruce bark beetle (Ips typographus L.) is the most destructive insect
 pest of spruce forest in Eurasia. However, contact toxicity, in vivo
 metabolism, and ecological functions of host monoterpenes are poorly
 understood at the spruce–bark beetle–predator tritrophic level. Spruce
 monoterpenes including S-(–)-α-pinene, R-(+)-α-pinene, and myrcene showed
 contact toxicity to spruce bark beetle, with LD50 values ranging from
 24–36 μg/mg. When topically treated with S-(–)-α-pinene or R-(+)-α-pinene,
 the amount of volatile metabolites [S-(–)-cis-verbenol,
 4S-(+)-/4R-(–)-trans-verbenol, and R-(+)-/S-(–)-verbenone] in the hindgut
 extract of spruce bark beetle varied significantly between sexes, and
 their quality varied significantly depending on the chirality of α-pinene.
 More importantly, S-(–)-α-pinene induced male adults to produce large
 amounts of S-(–)-cis-verbenol and S-(–)-verbenone. When topically treated
 with myrcene, the expected semiochemicals such as E-myrcenol, ipsenol, and
 ipsdienol were not detected in beetle hindgut, indicating that the
 pheromone biosynthetic system of spruce bark beetle does not participate
 in the metabolism of host myrcene. In the field trapping tests,
 S-(–)-α-pinene and R-(+)-α-pinene increased the trap catches of spruce
 bark beetle and Thanasimus substriatus (predator) compared with the
 pheromone source, whereas myrcene exhibited a strong repellent effect on
 bark beetle but not on its predator. Our results of contact toxicity, in
 vivo metabolism, and behavioural activity analyses indicate that spruce
 bark beetle adopts different ecological strategies to adapt to and
 tolerate different host monoterpenes; for example, avoidance mechanism for
 myrcene, and preference mechanism for α-pinene. Signalling interactions
 among the three monoterpenes at the tritrophic level help us understand
 their roles in manipulating the arms race between host plants and bark
 beetles, which indicate the plasticity and multifunctionality of host
 monoterpenes in the ecological context. Our results can be applied to the
 management of spruce bark beetle via the push-pull strategy using
 semiochemicals.
description: Data set collected by count mortality of Ips typographus
 after monoterpenes
 topically treated, and the volatiles in hindguts were
 identification and analysis by GC and GC-MS.
DOI: 10.5061/dryad.9cnp5hqg4
title: Pupal brain transcriptome for Bicyclus anynana

description: Seasonal plasticity in male courtship in Bicyclus anynana butterflies is
 due to variation in levels of the steroid hormone 20E (20-hydroxyecdysone)
 during pupation. Wet season (WS) males have high levels of 20E and become
 active courters. Dry season (DS) males, have lower levels of 20E and
 reduced courtship rates, although WS courtship rates can be achieved if DS
 male pupae are injected with 20E at 30% of pupation. Here, we investigated
 the genes involved in male courtship plasticity and examine whether 20E
 plays an organizational role in the pupal brain that later influences the
 sexual behaviour of adults. We show that DS pupal brains have a 7-fold
 upregulation of the yellow gene relative to the WS and that knocking out
 yellow leads to increased male courtship. We find that injecting 20E into
 DS pupa reduced yellow expression although not significantly. Our results
 show that yellow is a repressor of the neural circuity for male courtship
 behaviour in B. anynana. 20E levels experienced during pupation could play
 an organizational role during pupal brain development by regulating yellow
 expression, however, other factors might also be involved. Our findings
 are in striking contrast to Drosophila where yellow is required for male
 courtship.
description: This dataset represents the assembled transcriptome from
 the pupal brain of the butterfly, Bicyclus anynana. 
 This Transcriptome Shotgun Assembly project has been deposited at
 DDBJ/EMBL/GenBank under the accession
 GHRJ00000000/ GHRJ01000000. Raw reads of the RNA-seq
 libraries were uploaded to the SRA database with the SRA accession number
 PRJNA544388. The transcriptome was assembled from a
 total of 12 RNA-Seq libraries using Trinity 2.4.0
 Transcripts smaller than 200 bp were screened and removed from
 the assembly. Transcriptome was annotated by blasting
 to the Bicyclus anynana genome v1.2 on Lepbase.
DOI: 10.5061/dryad.n2z34tmv2
title: Camera trap survey of jaguars from Cockscomb Basin Wildlife Sanctuary in Belize

description: These data are from a camera trap survey of jaguars
 in Cockscomb Basin Wildlife Sanctuary in Belize that ran for a 6
 month period from August 2013 until February 2014. The associated
 manuscript contains analyses of these data using continuous-time spatial
 capture-recapture models, and demonstrates how one can make
 inference about animal activity patterns. The data include 287 detections
 of 19 individual male jaguars, and 44 detections of 8 individual female
 jaguars.
description: Twenty paired camera stations (Pantheracam v3) were deployed
 along the trail network within the eastern basin of Cockscomb Basin
 Wildlife Sanctuary in Belize. Neighbouring stations had an average spacing
 of 2.0 km (1.1 to 3.1 km) and digital photographic data were downloaded
 every two weeks. The data were collected by R. Foster and B.
 Harmsen.
description: The dataset contains captures for both males and female jaguars
 and includes three individuals with sex not determined that were excluded
 from analyses. A file with details of the camera trap stations as well as
 when the stations were operating is included, as well as an .Rdata object
 that contains masks of the survey area with several different spatial
 covariates.
DOI: 10.5061/dryad.cnp5hqc2v
title: Shift from short-term competition to facilitation with drought stress is due to a decrease in long-term facilitation

description: Disentangling short- and long-term neighbour effects, using both removal
 and observational methods within a single experiment, has strongly
 improved our understanding of the driving mechanisms of plant-plant
 interactions. However, there has been no attempt to assess two important
 underlying processes of their changes along gradients,
 environmental-severity (changes in target performance without neighbours)
 and neighbour-traits (changes in performance with neighbours) effects, the
 former previously shown in alpine communities to be involved in
 competition and the latter in facilitation. We addressed this goal in an
 experiment conducted in continental saline depressions (sebkhas) from the
 Mediterranean arid climate of central Tunisia. We quantified short- and
 long-term effects of dominant shrubs, transplanting three target grass
 species in open, nurse and removed-nurse microhabitats of two habitats of
 different salinity levels in height sebkhas. The design extended
 geographically from central Tunisia to the Libyan border, 500km
 southeastward. We used the Relative Interaction Index to calculate short-
 and long-term effects of neighbours on target species before and after the
 dry summer seasons and to disentangle environmental-severity from
 neighbour-trait effects. Short-term effects were slightly negative and
 long-term effects strongly positive before the dry summer season in the
 two habitats. Short-term effects switched to positive with increasing
 drought stress, due to increasing environmental severity (decrease in the
 response without neighbours), whereas long-term effects decreased due to
 decreasing environmental mitigation (decrease in the response with
 neighbours). Soil moisture measurements showed that both changes were due
 to vanishing shrub soil engineering-effects during the summer drought. We
 conclude that an increase in short-term facilitation with increasing
 drought stress through time, apparently supporting the
 Stress-Gradient-Hypothesis, might be due to a decrease in long-term
 facilitation. Our study highlights that assessing the effects of
 neighbours with both the removal and observational methods is crucial for
 understanding the driving processes of plant-plant interactions in arid
 systems.
DOI: 10.5061/dryad.4tmpg4f7j
title: Jumping the green wall: the use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research

description: As microbiome research moves away from model organisms to wildlife, new
 challenges for microbiome high throughput sequencing arise caused by the
 variety of wildlife diets. High levels of contamination are commonly
 observed emanating from the host (mitochondria) or diet (chloroplast).
 Such high contamination levels affect the overall sequencing depth of
 wildlife samples thus decreasing statistical power and leading to poor
 performance in downstream analysis. We developed an amplification protocol
 utilizing PNA-DNA clamps to maximize the use of resources and to increase
 the sampling depth of true microbiome sequences in samples with high
 levels of plastid contamination. We chose two study organisms, a bat
 (Leptonyteris yerbabuenae) and a bird (Mimus parvulus), both relying on
 heavy plant-based diets that sometimes lead to traces of plant-based
 faecal material producing high contamination signals from chloroplasts and
 mitochondria. On average, our protocol yielded a 13-fold increase in
 bacterial sequence amplification compared with the standard protocol
 (Earth Microbiome Protocol) used in wildlife research. For both focal
 species, we were able significantly to increase the percentage of
 sequences available for downstream analyses after the filtering of
 plastids and mitochondria. Our study presents the first results obtained
 by using PNA-DNA clamps to block the PCR amplification of chloroplast and
 mitochondrial DNA from the diet in the gut microbiome of wildlife. The
 method involves a cost-effective molecular technique instead of the
 filtering out of unwanted sequencing reads. As 33% and 26% of birds and
 bats, respectively, have a plant-based diet, the tool that we present here
 will optimize the sequencing and analysis of wild microbiomes.
description: Samples were colelcted in the field directly from the animals and
 stored in DNA shield at -20 Celsius. Total DNA was extracted and
 amplifications (V4 region of 16S rRNA. primers 515F/806R) with and without
 the PNA-DNA clamps (mPNA and cpPNA, PNA BIO Inc)  were used according to
 the sample treatment. Sequencing was conducted using Illumina MiSeq (2*250
 cycles) and post sequence processing was done using QIIME 2 and
 Phyloseq. Consult the paper for more on the methods and the clamp
 sequences.
description: Scripts are available at https://github.com/luisvqz/V4_pna_clamps_4_wildlife
DOI: 10.5061/dryad.tb2rbnzz5
title: Table e-1 and e-references for: Neurogenic dysphagia: a systematic review and proposal of a classification system

description: Objective: Introduction of a phenotypic classification of dysphagia with
 differential diagnostic implications and its validation in different
 disease groups using videos of flexible endoscopic evaluation of
 swallowing (FEES). Methods: A systematic literature review was performed
 to summarize disease-typical FEES-findings. In an interdisciplinary team,
 a FEES-based classification of neurogenic dysphagia was developed which
 distinguishes different dysphagia phenotypes. The classification was
 validated using 1012 randomly selected FEES videos of patients with
 various neurological disorders. Chi-square tests were applied to
 investigate the relationship between the disease groups and each dysphagia
 phenotype. Results: Seven dysphagia phenotypes were defined and all
 phenotypes were significantly  associated with specific
 neurological disease groups: (1) “Premature bolus spillage” and (2)
 “delayed swallowing reflex” occurred mainly in stroke patients, (3)
 “predominance of residue in the valleculae” was most common in
 Parkinson's disease, (4) “predominance of residue in the piriform
 sinus” occurred only in myositis, motoneuron disease and brainstem stroke
 patients, (5) “pharyngolaryngeal movement disorder” was found in atypical
 Parkinsonian syndromes and stroke patients, (6) “fatigable swallowing
 weakness” was common in patients with myasthenia gravis, and (7) “complex
 disorder” with a heterogeneous dysphagia pattern was the leading mechanism
 in amyotrophic later sclerosis. The interrater reliability showed a strong
 agreement (kappa = 0.84). Conclusion: Neurogenic dysphagia is not a mere
 symptom, but a multi-etiological syndrome with different phenotypic
 patterns depending on the underlying disease. Dysphagia phenotypes can
 facilitate differential diagnosis in patients with dysphagia of unclear
 etiology.
DOI: 10.5061/dryad.51c59zw65
title: Domestication phenotype linked to vocal behavior in marmoset monkeys

description: The domestication syndrome refers to a set of traits that are the
 incidental by-products of artificial selection for increased tolerance
 towards humans. One hypothesis is that some species like humans and
 bonobos “self domesticated”, that they have been under selection for that
 same suite of domesticated phenotypes. However, the evidence for this has
 been largely circumstantial. Here, we provide evidence that in marmoset
 monkeys, the size of a domestication phenotype—a white facial fur patch—is
 linked to their degree of affiliative vocal responses. During development,
 the amount of parental vocal feedback experienced by influences the rate
 of growth of this facial white patch and this suggests a mechanistic link
 between the two phenotypes, possibly neural crest cells. Our study
 provides evidence for links between vocal behavior and the development of
 morphological phenotypes associated with domestication in a nonhuman
 primate.
description: The zipped folder contains all the data, and analysis/figures
 codes. It contains also a read me file explaining the content. The codes
 are commented to help understand what is going on.  Our figures 1 and 3
 and related analyses are completely reproducible with these
 contents.
DOI: 10.5061/dryad.jdfn2z38m
title: The whole protein sequences of the nuclear genome of Chrysosplenium sinicum

description: We used PacBio and Illumina sequencing to de novo assemble the nuclear
 genome of Chrysosplenium sinicum, and further annotated the whole protein
  sequences of the nuclear genome of Chrysosplenium sinicum.
DOI: 10.15468/dl.6xzv2y
title: Occurrence Download

description: A dataset containing 427 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Canavalia papuana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 427 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002536-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.