cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xsj3tx9j8
title: Comparison of mosquitoes and fly derived DNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany

description: The use of invertebrate-derived DNA (iDNA) is a promising non-invasive
 tool to monitor wildlife. While most studies have been carried out in
 dense tropical and sub-tropical forests and have focused on the use of a
 single category of invertebrates, this study compares the use of flies-
 and mosquito-derived DNA to assess vertebrate diversity in semi-urban
 environments. We conducted our sampling in four different forest plots in
 Berlin, Germany. Pools of flies and non-bloodfed mosquitoes were
 metabarcoded using 108 bp vertebrate-specific 12S rRNA (12S-V5) and 94 bp
 mammal-specific 16S rRNA (16Smam) mitochondrial markers, and individual
 bloodfed mosquitoes were sequenced using the 340 bp vertebrate-specific
 12S rRNA fragment (Mam-12S-340). From the fly pools, we detected 10 mammal
 species using 16Smam, while 12S-V5 detected four bird, two amphibian and
 six mammal species. From the non-bloodfed mosquito pools, we only
 amplified putative contaminant DNA, indicating that mosquito females
 without visual signs of a blood meal carry no traces of vertebrate DNA.
 Finally, in the bloodfed mosquitoes, we identified four mammal and one
 bird species. Focusing on mammal species, we did not find significant
 differences in the proportion of species detected regarding the total
 available number of species between sampling localities. Fly samples were
 easier to obtain and more abundant over the sampled localities compared to
 mosquito samples. We conclude that, while there are a few advantages in
 using mosquito blood meals, the use of flies in the detection of wildlife
 in a suburban environment is more effective in terms of collection of
 samples and detection of vertebrates, although this technique is limited
 to few mammal species in the urban environment.
DOI: 10.22008/promice/data/ice_discharge/d/v02/aokpis
title: GIS_err.csv

description: Greenland error. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/fb22hg
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/klnbrm
title: README.txt

description: README. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/ckntar
title: region_D.csv

description: Regional discharge. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/yclo5c
title: region_coverage.csv

description: Regional coverage. Git hash: d194a5c
DOI: 10.5061/dryad.8w9ghx3q2
title: Data from: Public opinion in Japanese newspaper readers’ posts under the prolonged COVID-19 infection spread 2019-2021: Contents analysis using Latent Dirichlet Allocation

description: These data are based on free description from readers’ posts on Japanese
 hardcopy newspaper articles in the public domain. Upon searching
 for “coronavirus,” we found 412 reader submissions during the April 7,
 2020 to May 25, 2020, 521 during January 8, 2021 to March 21, 2021, 458
 during the April 25, 2021 to June 6, 2021, and 519 during July 12, 2021 to
 September 30, 2021. Topics of content were extracted by Latent
 Dirichlet Allocation, and then calculating the ratio of topic occurrence
 in each description.
description: We conducted document analysis
 on reader’s posts about newspaper articles in the public domain. Many
 Japanese newspapers have a section where readers can submit their opinions
 on any topic. Submissions can be made by mail, fax, or e-mail, and readers
 are asked to disclose their name, occupation, age, address, and contact
 information. All or part of these disclosed details are often published in
 the paper.
DOI: 10.22008/promice/data/ice_discharge/d/v02/ascqfq
title: region_err.csv

description: Regional error. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/tdyzrs
title: sector_coverage.csv

description: Sector coverage. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/yilybn
title: region.nc

description: Regional discharge, coverage, and error. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/djnwle
title: sector_D.csv

description: Sector discharge. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/jwcgeu
title: sector_err.csv

description: Sector error. Git hash: d194a5c
DOI: 10.5061/dryad.573n5tb9n
title: Behavior of riparian Iguana iguana: Cano Palma boat traffic study

description: Although frequently studied in captivity, less is known about
 wild Iguana iguana. Herein behavior of riparian I.
 iguana was collected alongside climate, vigilance, and boat
 traffic data. Observations showed boat tourism potentially
 affects I. iguana negatively. We recommend minor changes
 by the ecotourism industry to alleviate visitor pressure on I.
 iguana.
description: Field observations of I. iguana took place from a viewing gallery
 dock tower that acted as a hide for observers above the Caño Palma. Data
 was collected during December 2004 (the breeding season for I. iguana
 regionally in northeast Costa Rica). Behavior observation was collected
 using scan sampling with frequency of behavior scored. Behaviors recorded
 included; thermoregulation (in sun / shade), vigilance, head bobbing,
 movement, foraging, displaying, retreating, feeding, dewlap displays
 (males) and time activity in sun / shade. Observations were recorded by
 two observers (one spotter and one recorder) that were kept consistent for
 the daily observations. Observation were recorded in two hour intervals;
 0600–0800 h, 0800–1000 h, 1000–1200 h, 1100–1300 h, 1200–1400 h, 1300–1500
 h, 1400–1600 h and 1500–1700 h. Abiotic data was collected to account for
 climatic influence and included; temperature, humidity, precipitation,
 cloud cover, canal height/state of water level measured from centre depth
 of canal in cm (flooding). The presence and number of boats was recorded
 during observation sessions and linked with predictors in the behavior
 model.
description: Microsoft Excel (TM).
DOI: 10.22008/promice/data/ice_discharge/d/v02/kqdwte
title: gate_coverage.csv

description: Gate coverage. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/wuk05j
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/aao5tz
title: gate_D.csv

description: Gate discharge. Git hash: cc3a372
DOI: 10.5061/dryad.gqnk98sr3
title: Pearson correlation tests for environmental variables, Student t-test for range shift and comparisons for habitat loss in 2070

description: Habitat loss and shifts associated with climate change threaten global
 biodiversity, with impacts likely to be most pronounced at high latitudes.
 With the disappearance of the tundra breeding habitats, migratory
 shorebirds that breed at these high latitudes are likely to be even more
 vulnerable to climate change than those in temperate regions. We examined
 this idea using new distributional information on two subspecies of
 Black-tailed Godwits Limosa limosa in Asia: the northerly, bog-breeding L.
 l. bohaii and the more southerly, steppe-breeding L. l. melanuroides.
 Based on breeding locations of tagged and molecularly assayed birds, we
 modelled the current breeding distributions of the two subspecies with
 species distribution models, tested those models for robustness, and then
 used them to predict climatically suitable breeding ranges in 2070
 according to bioclimatic variables and different climate change scenarios.
 Our models were robust and showed that climate change is expected to push
 bohaii into the northern rim of the Eurasian continent. Melanuroides is
 also expected to shift northward, stopping in the Yablonovyy and Stanovoy
 Ranges, and breeding elevation is expected to increase. Climatically
 suitable breeding habitat ranges would shrink to 16% and 11% of the
 currently estimated ranges of bohaii and melanuroides, respectively.
 Overall, this study provides the first predictions for the future
 distributions of two little-known Black-tailed Godwit subspecies and
 highlights the importance of factoring in shifts in bird distribution when
 designing climate-proof conservation strategies.
description: <strong>1. Pearson correlation tests for environmental
 variables</strong> All variables for species
 distribution modelling were loaded to Qgis 3.8. We extracted the values of
 each variable from 101 occurrence locations (60
 <em>bohaii</em> and 41 <em>melanuroides</em>)
 using the "raster values to points" function in Qgis 3.8. The
 outcome was saved as a .csv file. Next, the Pearson correlation
 coefficient was calculated using "tidyverse" package in
 R.  <strong>2. Student t-test for range
 shift</strong> see methods of the paper
 <strong>3. Comparisons for habitat loss in
 2070  </strong> see methods of the
 paper
DOI: 10.22008/promice/data/ice_discharge/d/v02/b39o3a
title: GIS_coverage.csv

description: Greenland coverage. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/ds1ic3
title: gate_err.csv

description: Gate errors. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/7ejwms
title: GIS_D.csv

description: Greenland discharge. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/ucsujc
title: GIS_err.csv

description: Greenland error. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/nsm7uw
title: README.txt

description: README. Git hash: cc3a372
DOI: 10.5061/dryad.fttdz08w3
title: Data from: In both directions: Expansions of European land snails to the north and south from glacial refugia

description: Aim: The location of glacial refugia and the timing of postglacial
 colonisations remain of interest because together they inform about the
 ability of species to track shifting climates. In the associated paper, we
 tested a hypothesis that a central European forest land snail species
 survived in a northern refugium, which was proposed based on fossil finds
 indirectly dated to the Last Glacial Maximum and Late Glacial. We assessed
 the credibility of our results by comparing them to those obtained from
 three other, broadly sympatric land snail species. Location: Central
 Europe and the Balkans. Taxon: Pulmonate land snails: Monachoides
 incarnatus (Hygromiidae) and Helix pomatia, Helix thessalica, and
 Caucasotachea vindobonensis (Helicidae). Methods: We used continuous
 phylogeographic analysis of mitochondrial data to trace the origin of
 postglacially expanding lineages and direct radiocarbon dating to verify
 the presumed glacial presence of M. incarnatus on the territories of
 Czechia and Slovakia. Geolocated concatenated sequences of
 partial 16S rRNA and cytochrome c oxidase subunit I were analysed using
 BEAST 1.10.4. and conclusions were drawn from the reconstructed geographic
 positions of internal nodes in the resulting phylogenetic trees. Data:
 Input files for the phylogeograpic analyses, containing the sequence
 alignments and analysis settings, and the trees summarizing the results of
 the analyses.
DOI: 10.22008/promice/data/ice_discharge/d/v02/tzguci
title: region_coverage.csv

description: Regional coverage. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/ytx5pd
title: region_D.csv

description: Regional discharge. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/bgsqbb
title: region_err.csv

description: Regional error. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/zbxlw2
title: sector_coverage.csv

description: Sector coverage. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/ey10pa
title: sector_D.csv

description: Sector discharge. Git hash: cc3a372
DOI: 10.5061/dryad.sxksn0363
title: A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella

description: Dissemination of antimicrobial resistance (AMR) genes by horizontal gene
 transfer (HGT) mediated through plasmids is a major global concern.
 Genomic epidemiology studies have shown varying success of different AMR
 plasmids during outbreaks, but the underlying reasons for these
 differences are unclear. Here, we investigated two Shigella plasmids
 (pKSR100 and pAPR100) that circulated in the same transmission network but
 had starkly contrasting epidemiological outcomes to identify plasmid
 features that may have contributed to the differences. We used plasmid
 comparative genomics to reveal divergence between the two plasmids in
 genes encoding AMR, SOS response alleviation, and conjugation.
 Experimental analyses revealed that these genomic differences corresponded
 with reduced conjugation efficiencies for the epidemiologically successful
 pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS
 response in the presence of antimicrobials, compared with the less
 successful pAPR100. The discrepant phenotypes between the two plasmids are
 consistent with the hypothesis that plasmid associated phenotypes
 contribute to determining the epidemiological outcome of AMR HGT and
 suggest that phenotypes relevant in responding to antimicrobial pressure
 and fitness impact may be more important than those around conjugation in
 this setting. Plasmid phenotypes could thus be valuable tools in
 conjunction with genomic epidemiology for predicting AMR dissemination.
description: Microsoft Excel /OpenOffice Calc R
DOI: 10.22008/promice/data/ice_discharge/d/v02/bhjenz
title: region.nc

description: Regional discharge, coverage, and error. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/uujhm9
title: sector_err.csv

description: Sector error. Git hash: cc3a372
DOI: 10.22008/promice/data/ice_discharge/d/v02/fs55zu
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/zdmam0
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: d194a5c
DOI: 10.22008/promice/data/ice_discharge/d/v02/t7ufv9
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: d194a5c
DOI: 10.5061/dryad.70rxwdc18
title: The occurrence data of wild apple in the Mountains of Central Asia Biodiversity Hotspot

description: To obtain high-quality occurrence records for wild apple across its whole
 distribution range, we compiled data from field surveys, herbariums and
 the literature. The field surveys were conducted in all of the countries
 with wild apple distribution in Central Asia. Precisely, we had several
 exhaustive investigations of wild apple populations in Xinjiang, China
 from 2008 to 2021, including distribution range and abundance of wild
 apple across its whole elevational ranges in six counties. For herbarium
 data, we combined the records from Global Biodiversity Information
 Facility and Chinese Virtual Herbarium. Finally, we obtained 8344
 occurrence records for wild apple. 
description: We compiled data from field surveys, herbariums and the
 literature.
DOI: 10.22008/promice/data/ice_discharge/d/v02/3vg9ms
title: gate_coverage.csv

description: Gate coverage. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/onukyd
title: gate_D.csv

description: Gate discharge. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/38sd15
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/yrdhbr
title: GIS_coverage.csv

description: Greenland coverage. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/jfvk9f
title: GIS_D.csv

description: Greenland discharge. Git hash: b67fd57
DOI: 10.5061/dryad.rfj6q57d9
title: Social evolution of shared biofilm matrix components

description: Biofilm formation is an important and ubiquitous mode of growth among
 bacteria. Central to the evolutionary advantage of biofilm formation is
 cell-cell and cell-surface adhesion achieved by a variety of factors, some
 of which are diffusible compounds that may operate as classical public
 goods – factors that are costly to produce but may benefit other cells. An
 outstanding question is how diffusible matrix production, in general, can
 be stable over evolutionary timescales. In this work, using Vibrio
 cholerae as a model, we show that shared diffusible biofilm matrix
 proteins are indeed susceptible to cheater exploitation, and that the
 evolutionary stability of producing these matrix components fundamentally
 depends on biofilm spatial structure, intrinsic sharing mechanisms of
 these components, and flow conditions in the environment. We further show
 that exploitation of diffusible adhesion proteins is localized within a
 well-defined spatial range around cell clusters that produce them. Based
 on this exploitation range and the spatial distribution of cell clusters,
 we construct a model of costly diffusible matrix production and relate
 these length scales to the relatedness coefficient in social evolution
 theory. Our results show that production of diffusible biofilm matrix
 components is evolutionarily stable under conditions consistent with
 natural biofilm habitats and host environments. We expect the mechanisms
 revealed in this study to be relevant to other secreted factors that
 operate as cooperative public goods in bacterial communities, and the
 concept of exploitation range and the associated analysis tools to be
 generally applicable.
description: The detail of the collection method is specified in the
 supplementary materials of the paper. 
description: Files are can opened with Microsoft Excel.
DOI: 10.22008/promice/data/ice_discharge/d/v02/59wybu
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/k21cwk
title: README.txt

description: README. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/mevb7m
title: region_D.csv

description: Regional discharge. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/vbns1e
title: region_coverage.csv

description: Regional coverage. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/9htrac
title: region.nc

description: Regional discharge, coverage, and error. Git hash: b67fd57
DOI: 10.5061/dryad.zpc866tbg
title: Wisenden zebrafish embryo early hatching

description: Plasticity in hatching time allows embryos to maximize fitness by
 balancing benefits and costs of remaining bound within the chorion against
 the benefits and costs of emerging as a free-swimming larva. In our first
 experiment, we exposed zebrafish (Danio rerio) embryos to either chemical
 cues from crushed embryos (simulating egg predation) or to blank water
 control. Embryos exposed to alarm cues hatched sooner with shorter body
 lengths and underdeveloped fins relative to larvae from the water
 treatment. Burst swimming speed was significantly slower for larvae that
 hatched from the alarm cue treatment. In a second 2 x 2 experiment, we
 exposed zebrafish embryos to either chemical alarm cues from conspecific
 embryos, mechanical disturbance (magnetic stir bar) to simulate a predator
 probing the substrate for developing embryos, both chemical and mechanical
 indicators of risk, or neither (control). We found similar effects in
 terms of earlier time to hatch at an earlier stage of development and
 poorer swimming performance of hatchling larvae. In the second experiment
 these effects occurred in response to mechanical disturbance with or
 without the presence of chemical alarm cues. Alarm cues alone produced no
 effects in the second experiment. Taken together, these data indicate that
 zebrafish embryos demonstrate a facultative tradeoff between risk of
 predation acting on two stages of their life history.
description: The data set is in two parts. The first tab is for a test of
 chemical alarm cues only (versus water control). The second tab is for a
 test of the independent and combined effects of chemical and mechanical
 forms of disturbance.
DOI: 10.22008/promice/data/ice_discharge/d/v02/exvu3r
title: sector_D.csv

description: Sector discharge. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/twypcs
title: sector_coverage.csv

description: Sector coverage. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/74gno9
title: gate_coverage.csv

description: Gate coverage. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/vneod5
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: b67fd57
DOI: 10.22008/promice/data/ice_discharge/d/v02/ghqp1b
title: gate_D.csv

description: Gate discharge. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/vdayxh
title: gate_err.csv

description: Gate errors. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/ywjfeg
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/olhwzv
title: GIS_D.csv

description: Greenland discharge. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/wd7els
title: GIS_coverage.csv

description: Greenland coverage. Git hash: a158097
DOI: 10.5061/dryad.xsj3tx9j9
title: A mechanism for red coloration in vertebrates

description: Red coloration is a salient feature of the natural world. Many vertebrates
 produce red color by converting dietary yellow carotenoids into red
 ketocarotenoids via an unknown mechanism. Here, we show that two enzymes,
 cytochrome P450 2J19 (CYP2J19) and 3-hydroxybutyrate dehydrogenase 1-like
 (BDH1L), are sufficient to catalyze this conversion. In birds, both
 enzymes are expressed at sites of ketocarotenoid biosynthesis (feather
 follicles and red cone photoreceptors), and genetic evidence implicates
 these enzymes in yellow/red color variation in feathers. In fish, homologs
 of CYP2J19 and BDH1L are required for ketocarotenoid production, and we
 show that these enzymes are sufficient to produce ketocarotenoids in cell
 culture and when ectopically expressed in fish skin. Finally, we
 demonstrate that the red-cone-enriched tetratricopeptide repeat protein
 39B (TTC39B) enhances ketocarotenoid production when co-expressed with
 CYP2J19 and BDH1L. The discovery of this mechanism of ketocarotenoid
 biosynthesis has major implications for understanding the evolution of
 color diversity in vertebrates.
description: Chromatograms and spectra were collected by reverse-phase
 high-performance liquid chromatography (HPLC) with UV-Vis DAD detection.
 Tissue carotenoid content was measured by HPLC. Tissue lipid content was
 measured with a Miura 200 analyzer with reagent kits (I.S.E. S.r.l.;
 Guidonia, Italy; A-R0100000901, A-R0200001301, and
 A-R0200001401).
description: No specialized software is required to open files.
DOI: 10.22008/promice/data/ice_discharge/d/v02/uscknw
title: GIS_err.csv

description: Greenland error. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/com4yl
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/wjige8
title: README.txt

description: README. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/dl0d3h
title: region_coverage.csv

description: Regional coverage. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/fqlqee
title: region_D.csv

description: Regional discharge. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/h83env
title: region.nc

description: Regional discharge, coverage, and error. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/ijcjej
title: region_err.csv

description: Regional error. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/ld3pbr
title: sector_coverage.csv

description: Sector coverage. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/2zpgqg
title: sector_D.csv

description: Sector discharge. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/yddgca
title: sector_err.csv

description: Sector error. Git hash: a158097
DOI: 10.22008/promice/data/ice_discharge/d/v02/3jftxn
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: a158097