cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4mw6m9094
title: The shellome of the crocus clam Tridacna crocea emphasizes essential components of mollusc shell biomineralization

description: Molluscan shells are among the most fascinating research objects because
 of their diverse morphologies and textures. The formation of these
 delicate biomineralized structures is a matrix-mediated process. A
 question that arises is what are the essential components required to
 build these exoskeletons. In order to understand the molecular mechanisms
 of molluscan shell formation, it is crucial to identify organic
 macromolecules in different shells from diverse taxa. In the case of
 bivalves, however, taxon sampling in previous shell proteomics studies are
 biased and focus exclusively on representatives of the class Pteriomorphia
 such as pearl oysters, edible oysters and mussels. In this study, we have
 characterized the shell organic matrix from the crocus clam, Tridacna
 crocea, (Heterodonta) using various biochemical techniques, including
 SDS-PAGE, FT-IR, monosaccharide analysis, and enzyme-linked lectin assay
 (ELLA). Furthermore, we have identified a number of shell matrix proteins
 (SMPs) using a comprehensive proteomics approach combined to RNA-seq. The
 biochemical studies confirmed the presence of proteins, polysaccharides,
 and sulphates in the T. crocea shell organic matrix. Proteomics analysis
 revealed that the majority of the T. crocea SMPs are novel and dissimilar
 to known SMPs identified from the other bivalve species. Meanwhile, the
 SMP repertoire of the crocus clam also includes proteins with conserved
 functional domains such as chitin-binding domain, VWA domain, and protease
 inhibitor domain. We also identified BMSP (Blue Mussel Shell Protein,
 originally reported from Mytilus), which is widely distributed among
 molluscan shell matrix proteins. Tridacna SMPs also include low-complexity
 regions or LCRs that are absent in the other molluscan genomes, indicating
 that these genes may have evolved in specific lineage. These results
 highlight the diversity of the organic molecules - in particular proteins
 - that are essential for molluscan shell formation.
DOI: 10.5061/dryad.fxpnvx0rm
title: Mammals, wildlife trade, and the next global pandemic

description: Most new infectious diseases emerge when pathogens transfer from animals
 to humans1,2. The suspected origin of the COVID pandemic in wildlife wet
 market has resurfaced debates on the role of wildlife trade as a potential
 source of emerging zoonotic diseases3,4,5. Yet, there are no studies
 quantitatively assessing zoonotic disease risk associated with wildlife
 trade. Combining data of mammal species hosting zoonotic viruses and data
 on mammals known to be in current and future wildlife trade6, we find that
 one-quarter (26.5%) of the mammals in wildlife trade harbor 75% of known
 zoonotic viruses, at levels much higher than domesticated and non-traded
 mammals. The traded mammals also harbor distinct composition of zoonotic
 viruses and different host reservoirs than non-traded and domesticated
 mammals. Furthermore, we highlight that species of primates, ungulates,
 carnivores, and bats represent significant zoonotic diseases risk as they
 host a 132 (58%) of 226 known zoonotic viruses in present wildlife trade.
 Whereas species of bats, rodents, and marsupials represent significant
 zoonotic diseases risk in future wildlife trade. Thus, the risk of
 carrying zoonotic diseases is not equal for all mammal species in wildlife
 trade. Overall, our findings strengthen the evidence that wildlife trade
 and zoonotic disease risks are strongly associated and that mitigation
 measures should prioritize species with the highest risk of carrying
 zoonotic viruses.  Curbing the sales of wildlife products and
 developing principles that support the sustainable and healthy trade of
 wildlife could be a cost-effective investment given the potential risk and
 consequences of zoonotic outbreaks.
description: Dataset was collected through literature survey
DOI: 10.5061/dryad.4tmpg4f99
title: Structural modulation of π-conjugated linkers in D-π-A dyes based on Triphenylamine dicyanovinylene framework to explore the NLO properties

description: A donor-π-acceptor type series of Triphenylamine-dicyanovinylene based
 chromophores (DPMN1-DPMN11) was designed theoretically by the structural
 tailoring of π-linkers to exploit changes in the optical properties and
 their NLO behaviour. Density functional theory (DFT) computations were
 employed to understand the electronic structures, absorption spectra,
 charge transfer phenomena and the influence of these structural
 modifications on NLO properties. Interestingly, all investigated
 chromophores exhibited lower band gap (2.22-2.60 eV) with broad absorption
 spectra in the visible region, reflecting the remarkable NLO response.
 Furthermore, natural Bond Orbital (NBO) findings revealed a strong
 push-pull mechanism in DPMN1-DPMN11 as donor and π-conjugates exhibited
 positive, while all acceptors showed negative values. Examination of
 electronic transitions from donor to acceptor moieties via π-conjugated
 linkers revealed greater linear (&lt;α&gt;=526.536-641.756 a.u)
 and non-linear (βtot =51313.8-314412.661 a.u) response. It was noted that
 the chromophores containing imidazole in 2nd p-linker expressed greater
 hyperpolarizability when compared with the ones containing pyrrole. This
 study reveals that by controlling the type of π-spacers, interesting
 metal-free NLO materials can be designed, which can be valuable for the
 hi-tech NLO applications.
DOI: 10.5061/dryad.5qfttdz4q
title: Invasive spread in meta-food-webs depends on landscape structure, fertilization and species characteristics

description: Land use change and biological invasions collectively threaten
 biodiversity. Yet, few studies have addressed how altering the landscape
 structure and nutrient supply can promote biological invasions and
 particularly invasive spread (the spread of an invader from the place of
 introduction), or asked whether and how these factors interact with biotic
 interactions and invader properties. We here bridge this knowledge gap by
 providing a holistic network-based approach. Our approach combines a
 trophic network model with a spatial network model allowing us to test
 which combinations of abiotic and biotic factors can facilitate invasions
 and in particular invasive spread in food webs. We numerically simulated
 6300 single-species invasions in clustered and random landscapes at
 different levels of nutrient supply. In total, our simulation experiment
 yielded 69\% successful invasions---71% in clustered landscapes and 66% in
 random landscapes, with the proportion of successful invasions increasing
 with nutrient supply. However, invasive spread was generally higher in
 random than in clustered landscapes. The latter can facilitate invasive
 spread within a habitat cluster, but prevent invasive spread between
 clusters. Low nutrient levels generally prevented the establishment of
 invasive species and their subsequent spread. However, successful invaders
 could have more severe impacts as they contribute more to total biomass
 density and species richness under such conditions. Good dispersal
 abilities drive the broad-scale spread of invasive species in fragmented
 landscapes. Our approach makes an important contribution towards a better
 understanding of what combination of landscape and invader properties can
 facilitate or prevent invasive spread in natural ecosystems. This should
 allow ecologists to more effectively predict and manage biological
 invasions.
description: This data
 package includes the files needed to reproduce the data and analyses of
 the following paper: Invasive spread in meta-food-webs depends on
 landscape structure, fertilization and species characteristics. DOI:
 10.1111/oik.07503   Detailed information on
 the code and data structure and on how to run invasion simulations are
 provided in the README.md
DOI: 10.5061/dryad.x69p8czhv
title: eNOS/NO and their role in modifying the vascular barrier in retinopathy - Source data

description: Background: Hypoxia and consequent production of vascular endothelial
 growth factor A (VEGFA) promote blood vessel leakiness and edema in ocular
 diseases. Anti-VEGFA therapeutics may aggravate hypoxia; therefore,
 therapy development is needed. Methods: Oxygen-induced retinopathy was
 used as a model to test the role of nitric oxide (NO) in pathological
 neovascularization and vessel permeability. Suppression of NO formation
 was achieved chemically using L-NMMA, or genetically, in endothelial NO
 synthase (eNOS) serine to alanine (S1176A) mutant mice. Results:
 Suppression of NO formation resulted in reduced retinal neoangiogenesis.
 Remaining vascular tufts exhibited reduced vascular leakage through
 stabilized endothelial adherens junctions, indicated by reduced
 phosphorylation of vascular endothelial (VE)-cadherin Y685 in a
 c-Src-dependent manner. Treatment with a single dose of L-NMMA in
 established retinopathy restored the vascular barrier and prevented
 leakage. Conclusion: We conclude that NO destabilizes adherens junctions,
 resulting in vascular hyperpermeability, by converging with the
 VEGFA/VEGFR2/c-Src/VE-cadherin pathway. Funding: This study was supported
 by the Swedish Cancer foundation (19 0119 Pj 01 H), the Swedish Research
 Council (2020-01349), the Knut and Alice Wallenberg foundation (KAW
 2020.0057) and a Fondation Leducq Transatlantic Network of Excellence
 Grant in Neurovascular Disease (17 CVD 03). KAW also supported LCW with a
 Wallenberg Scholar grant (2015.0275). WCS was supported by Grants R35
 HL139945, P01 HL1070205, AHA MERIT Award.  
description: The data uploaded here contains excel work sheets.
 Figure (1-5)_Ninchoji et al_ 16-11-2020-RA-eLife-64944_source
 data.xlsx - Each figure and it accompanying supplemental figure are on a
 individual spread sheets (labelled with the figure number). The data for
 each specific figure is labelled on said sheets. The data contained within
 is raw data obtained from various experiments/methods and reflects what is
 shown in the figures. Supplementary file 1A-C.xlsx -
 The tables contained in this spread sheet contain the weights of each
 mouse used in each experiment. Each table corresponds with the label in
 the article text.
DOI: 10.5061/dryad.bg79cnpb3
title: Noctuid and geometrid moth assemblages show divergent elevational gradients in body size and color lightness

description: Previous macroecological studies have suggested that larger and darker
 insects are favored in cold environments and that the importance of body
 size and color for the absorption of solar radiation is not limited to
 diurnal insects. However, whether these effects hold true for local
 communities and are consistent across taxonomic groups and sampling years
 remains unexplored. This study examined the variations in body size and
 color lightness of the two major families of nocturnal moths, Geometridae
 and Noctuidae, along an elevational gradient of 700 m in Southern Germany.
 An assemblage-based analysis was performed using community-weighted means
 and a fourth-corner analysis to test for variations in color and body size
 within communities as a function of elevation. This was followed by a
 species-level analysis to test whether species occurrence and abundance
 along an elevation gradient were related to these traits, after
 controlling for host plant availability. In both 2007 and 2016,
 noctuid moth assemblages became larger and darker with increasing
 elevation, whereas geometrids showed an opposite trend in terms of color
 lightness and no clear trend in body size. In single species models, the
 abundance of geometrids, but not of noctuids was driven by habitat
 availability. In turn, the abundance of dark-colored noctuids, but not
 geometrids increased with elevation. While body size and color lightness
 affect insect physiology and the ability to cope with harsh conditions,
 divergent trait-environment relationships between both families underline
 that observations from coarse scales are not necessarily transferable to
 finer scales. Local abundance and occurrence of noctuids are shaped by
 morphological traits, whereas that of geometrids are rather shaped by
 local habitat availability, which can modify their
 trait-environment-relationship. We discuss potential explanations such as
 taxon-specific flight characteristics and the effect of microclimatic
 conditions.
description: For a description of the methods see the related manuscript
 https://doi.org/10.1111/ecog.05558
DOI: 10.5061/dryad.qfttdz0gs
title: Data from: Molecular signatures of reticulate evolution within the complex of European pine taxa

description: Speciation mechanisms, including the role of interspecific gene flow and
 introgression in emergence of new species, are the major focus of
 evolutionary studies. Inference of taxonomic relationship between closely
 related species maybe challenged by past hybridization events, but at the
 same time it may provide new knowledge about mechanisms responsible for
 the maintenance of species integrity despite interspecific gene flow.
 Here, using nucleotide sequence variation and utilizing a coalescent
 modelling framework, we tested the role of hybridization and introgression
 in the evolutionary history of closely related pine taxa from Pinus mugo
 complex and P. sylvestris. We compared the patterns of polymorphism and
 divergence between taxa and found great overlap of neutral variation
 within P. mugo complex. Our phylogeny reconstruction indicated multiple
 instances of reticulation events in the past, suggesting an important role
 of interspecific gene flow in the species divergence. The best fitting
 model revealed P. mugo and P. uncinata as sister species with basal P.
 uliginosa and asymmetric migration between all investigated species after
 their divergence. The magnitude of interspecies gene flow differed
 greatly, and it was consistently stronger from representatives of P. mugo
 complex to P. sylvestris than in the opposite direction. The results
 indicate the prominent role of reticulation evolution in those forest
 trees and provide genetic framework to study species integrity maintained
 by selection and local adaptation.
description: INIDIVIDUAL & CONCATENATED FASTA FILES
 Individual and concatenated fasta files for 48 nuclear genes for
 6 pine species: <em>P. uliginosa</em>, <em>P.
 mugo,</em> <em>P. uncinata</em>, <em>P.
 sylvestris</em>, <em>P. pinaster</em> and <em>P.
 nigra</em>. Note, that <em>P. nigra</em> was not used in
 the Manuscript.
 Łabiszak_&_Wachowiak_2021_Forests.zip
DOI: 10.5061/dryad.pnvx0k6mk
title: Water demand, price and temperature from 2014 to 2018 in Hadano City, Kanagawa Prefecture, Japan

description: In this study, the price elasticity of water demand was estimated using
 disaggregated data of approximately 30,000 households recorded over five
 years: two years before and three years after a tariff revision. From the
 results of the latent class analysis, the mean price elasticity was −
 -0.1. The households were divided into three groups: 35%–55% of the
 households did not respond to the tariff revision, and households with
 high water demand prior to the revision had higher elasticity. In
 addition, no statistically significant difference was observed in
 elasticity between the first and third years after revision. This dataset
 includes household water demand, price, and average temperature
 by month in Hadano City, Kanagawa, Japan. 
description: Provided by Hadano City.
description: ID: household ID Year: year
 Month: month Water: water demand (cubic
 meter) tanka1: price definition 1 (merginal
 cost) tanka2: price definition 2 (average
 cost) tenper: average temperature (Celsius
 degree)
DOI: 10.5061/dryad.4mw6m9095
title: Supplementary 1: Underwater photogrammetry for close-range 3D imaging of dry-sensitive objects: The case study of cephalopod beaks

description: Technical advances in 3D imaging have contributed to quantifying and
 understanding biological variability and complexity. However, small,
 dry-sensitive objects are not easy to reconstruct using common and easily
 available techniques such as photogrammetry, surface scanning, or micro-CT
 scanning. Here we use cephalopod beaks as an example as their size,
 thickness, transparency, and dry-sensitive nature make them particularly
 challenging. We developed a new, underwater, photogrammetry protocol in
 order to add these types of biological structures to the panel of
 photogrammetric possibilities. We used a camera with a macro-photography
 mode in a waterproof housing fixed in a tank with clear water. The beak
 was painted and fixed on a colored rotating support. Three angles of view,
 two acquisitions, and around 300 pictures per specimen were taken in order
 to reconstruct a full 3D-model. These models were compared to others
 obtained with micro-CT scanning to verify their accuracy. The models can
 be obtained quickly and cheaply compared to micro-CT scanning, and have
 sufficient precision for quantitative inter-specific morphological
 analyses. Our work shows that underwater photogrammetry is a fast,
 non-invasive, efficient, and accurate way to reconstruct 3D models of
 dry-sensitive objects while conserving their shape. While the
 reconstruction of the shape is accurate, some internal parts cannot be
 reconstructed with photogrammetry as they are not visible. In contrast,
 these structures are visible using reconstructions based on micro-CT
 scanning. The mean difference between both methods is very small
 (10-5 to 10-4 mm) and is significantly lower than differences
 between meshes of different individuals. This photogrammetry protocol is
 portable, easy-to-use, fast, and reproducible. Micro-CT scanning, in
 contrast, is time-consuming, expensive and non-portable. This protocol can
 be applied to reconstruct the 3D shape of many other dry-sensitive objects
 such as shells of shellfish, cartilage, plants and other chitinous
 materials.
DOI: 10.5061/dryad.h9w0vt4hk
title: Microclimate sensor data from 3 locations

description: Three datasets of microclimate temperature. Dataset 1, obtained between
 7th April and 10th July 2020 over several short intervals in Cornwall, UK
 (50.1739°N, 5.1042°W), was used to quantify errors yielded by different
 logger types close to the ground in an open grassland. Dataset 2,
 obtained between 1st May and 10th July 2020 in Leuven, Belgium
 (50.8217°N, 4.7336°E), was used to quantify errors
 different logger and shield types over several months, in both open
 grassland and closed-canopy mixed forest and at different heights above
 ground. Dataset 3, obtained between 22nd December 2017 and 2nd August 2020
 in Gontrode, Belgium (50.9803°N, 3.8160°E) was used to determine whether
 consumer-grade sensors and radiation shields can be used in place of a
 weather station. 
description: <strong>Dataset 1:</strong> Measurements obtained using a
 research-grade ultrafine-wire thermocouple were
 compared with those obtained using consumer-grade ultrafine-wire
 thermocouples, standard unshielded Lascar thermocouples and iButton
 thermochrons. We deployed unshielded iButtons, and iButtons shielded with
 (i) aluminium foil, (ii) 25.1 mm diameter PVC tubing and (iii) translucent
 open-ended film canisters. Also, both unshielded and shielded (using the
 shield provided by the manufacturer) TMS4 dataloggers were also compared.
 Measurements are of air temperatures 10 cm above
 a short grass lawn in Cornwall, UK (50.1739°N,
 5.1042°W). <strong>Dataset
 2:</strong> Measurements obtained using consumer-grade
 ultrafine-wire thermocouples were compared to those obtained using TMS4
 dataloggers (with and without shields) and iButton thermochrons: (i) no
 treatment, (ii) shielded with 10 cm diameter x 15 cm long horizontal white
 PVC tube and (iii) coated  in transparent liquid rubber). Measurements are
 of air temperatures at 0, 15 and 150 cm above ground in a forest and
 nearby grassland in Leuven, Belgium (50.8217°N, 4.7336°E).
 <strong>Dataset
 3:</strong> Measurements obtained using Lascar loggers with internal
 thermometers with two types of shield. The first shield type was a 10 cm
 diameter x 15 cm long horizontal white PVC tube. The second, a cone-like,
 home-made shield consisting of two white funnels on top of each other. The
 bottom funnel had holes to stimulate passive air displacement.
 Measurements are of air temperature 2 m above ground from a mixed forest
 and nearby (&lt; 1km away) open area in Gontrode, Belgium (50.9803°N,
 3.8160°E).
description: Data provided as csv files. Time stamp is local time. Some
 missing data reported as NA (logger mulfunction). Full details of methods
 provided in manuscript associated with this dataset.
DOI: 10.5061/dryad.rxwdbrv83
title: Characterizing the clinical features and atrophy patterns of MAPT-related frontotemporal dementia with disease progression modelling (Supplementary Data)

description: Background and Objective: Mutations in
 the MAPT gene cause frontotemporal dementia (FTD). Most
 previous studies investigating the neuroanatomical signature
 of MAPT mutations have grouped all different mutations
 together and shown an association with focal atrophy of the temporal lobe.
 However, the variability in atrophy patterns between each
 particular MAPT mutation is less well
 characterised. We aimed to investigate whether there were
 distinct groups of MAPT mutation carriers based on their
 neuroanatomical signature. Methods: We applied Subtype and Stage
 Inference (SuStaIn), an unsupervised machine learning technique that
 identifies groups of individuals with distinct progression patterns, to
 characterise patterns of regional atrophy in MAPT-associated FTD
 within the Genetic FTD Initiative (GENFI) cohort study. 
 Results: 82 MAPT mutation carriers were
 analysed, the majority of whom had P301L, IVS10+16 or R406W mutations,
 along with 48 healthy non-carriers. SuStaIn identified two groups
 of MAPT mutation carriers with distinct atrophy
 patterns: a ‘temporal’ subtype in which atrophy was most prominent in the
 hippocampus, amygdala, temporal cortex and insula, and a ‘frontotemporal’
 subtype in which atrophy was more localised to the lateral temporal lobe
 and anterior insula, as well as the orbitofrontal and ventromedial
 prefrontal cortex and anterior cingulate. There was a one-to-one mapping
 between IVS10+16 and R406W mutations and the temporal subtype, and a near
 one-to-one mapping between P301L mutations and the frontotemporal subtype.
 There were differences in clinical symptoms and neuropsychological test
 scores between subtypes: the temporal subtype was associated with amnestic
 symptoms, whereas the frontotemporal subtype was associated with executive
 dysfunction.  Discussion: Our results demonstrate that
 different MAPT mutations give rise to distinct atrophy
 patterns and clinical phenotype, providing insights into the underlying
 disease biology, and potential utility for patient stratification in
 therapeutic trials.