cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57707/fmi-b2share.5tw3g-gvv95
title: Data and code for the manuscript "Future snow scenarios for Northern Europe  based on Coupled Model Intercomparison Project Phase 6 data" by Petri Räisänen et al.

description: This dataset contains analyses of changes in snow conditions in Northern Europe (land areas between 4-40 E, 50-72N) simulated by the latest CMIP6 generation of global climate models. Also provided are fortran programs and GrADS and R scripts employed to generate the results in the manuscript (Räisänen et al. 2024, submitted to International Journal of Climatology).

REFERENCE TO THE MANUSCRIPT (please refer to the final accepted version if/when the paper will be accepted):

Räisänen, P., Luomaranta, A., and Jylhä, K. (2024): Future snow scenarios for Northern Europe based on Coupled Model Intercomparison Project phase 6 data. International Journal of Climatology, submitted.
description: The starting point for the analysis was daily snow water equivalent (SWE) data for CMIP6 models for years 1951-2100, where historical experiments extending to year 2014 were combined with Shared Socieconomic Pathways scenarios SSP126, SSP245, SSP370 and SSP585 for years 2015-2100. A single ensemble member (i.e., model run) was analyzed for 15-17 CMIP6 models, depending on the scenario. In addition, large single-model ensembles (40-50 parallel runs) were analyzed for three CMIP6 models (ACCESS-ESM1-5, CanESM5 and MIROC6) for the SSP245 scenario. Based on these data, several snow season metrics were first computed for each "snow year" (from 1 Sep of the previous year to 31 Aug) in the period 1951-2100. These metrics included (but are not limited to) the maximum SWE in winter and the length, start date and end date of the longest continuous snow period. Based on these yearly metrics, trends over the periods 1951-2023 and 2023-2100 and 20-year running-mean changes compared to the reference period 1981-2010 were further computed and analyzed. Similar analysis was also performed for ERA5-Land reanalysis data (years 1951-2023).
description: The contents of the data files are described in the file "README_data.txt". The contents of the file containing code ("code_and_scripts.zip") are described in "README_code.txt" as well as in README files included in the zip file. The terms of use for the data and the code are given in the files "License_data.txt" and "License_code.txt", respectively.
DOI: 10.5061/dryad.jq2bvq8bv
title: Evolution of a mosquito’s hatching behavior to match its human-provided habitat

description: A subspecies of the yellow fever mosquito, Aedes aegypti, has recently
 evolved to specialize in biting and living alongside humans. It prefers
 human odor and breeds in human-provided artificial containers rather than
 the forest tree holes of its ancestors. Here, we report one way this human
 specialist has adapted to the distinct ecology of human environments.
 While eggs of the ancestral subspecies rarely hatch in pure water, those
 of the derived human-specialist do so readily. We trace this novel
 behavior to a shift in how eggs respond to dissolved oxygen, low levels of
 which may signal food abundance. Moreover, we show that while tree holes
 are consistently low in dissolved oxygen, artificial containers often have
 much higher levels. There is thus a concordance between the hatching
 behavior of each subspecies and the aquatic habitat it uses in the wild.
 We find this behavioral variation is heritable, with both maternal and
 zygotic effects. The zygotic effect depends on dissolved oxygen
 concentration (i.e., GxE), pointing to potential changes in
 oxygen-sensitive circuits. Together, our results suggest that a shift in
 hatching response contributed to the pernicious success of this
 human-specialist mosquito and illustrate how animals may rapidly adapt to
 human-driven changes in the environment.
DOI: 10.5281/zenodo.18385285
title: Bulk RNA-seq of treatment-naïve advanced gastric cancer tumors prior to chemotherapy or chemo-immunotherapy

description: This project aimed to identify transcriptional programs and candidate genes associated with primary resistance to chemotherapy or combined chemo-immunotherapy in patients with advanced gastric cancer. To this end, bulk RNA sequencing was performed on treatment-naïve primary tumor samples collected at diagnosis, prior to any systemic therapy. By using pre-treatment tumor gene expression profiles, the study sought to uncover intrinsic molecular features that may predispose tumors to therapeutic resistance.The generated data provide a resource for the discovery of predictive biomarkers, the stratification of patients according to treatment response, and the investigation of mechanisms underlying resistance to cytotoxic and immunomodulatory therapies in advanced gastric cancer.

This dataset contains bulk RNA sequencing (RNA-seq) gene expression profiles from 23 primary tumor samples obtained from patients diagnosed with advanced gastric cancer. All samples were collected prior to any systemic treatment (treatment-naïve). After tumor sampling, patients subsequently received either standard chemotherapy or chemotherapy combined with immunotherapy, allowing this dataset to serve as a baseline transcriptional reference for future comparative and outcome-associated studies
DOI: 10.5061/dryad.zkh1893ch
title: Developmental temperature alters the thermal sensitivity of courtship activity and signal-preference relationships, but not mating rates

description: Mating behaviours are susceptible to novel or stressful thermal
 conditions, particularly for ectothermic organisms. One way to deal with
 changes in thermal conditions is to exhibit developmental plasticity,
 whereby the thermal sensitivity of mating behaviours depend on
 developmental conditions. We test how developmental temperature affects
 the thermal sensitivity of courtship behaviour and mating rates, as well
 as mating signal and preference coupling. We rear treehoppers under two
 temperature regimes and then test how a range of ambient temperature
 affects behaviours involved in the coordination of mating. We also test
 for sex-specific thermal sensitivity and developmental plasticity. We find
 developmental plasticity in the thermal sensitivity of courtship behaviour
 and mating signals for males. However, we found no developmental
 plasticity in females, and no change in the thermal sensitivity of mating
 rates. We discuss the implications of signal-preference decoupling for
 sexual selection, how reversible acclimation may drive sex-specific
 results, and the potential for mismatches between developmental and mating
 thermal environments under future climate change predictions.
DOI: 10.5281/zenodo.18385284
title: Bulk RNA-seq of treatment-naïve advanced gastric cancer tumors prior to chemotherapy or chemo-immunotherapy

description: This project aimed to identify transcriptional programs and candidate genes associated with primary resistance to chemotherapy or combined chemo-immunotherapy in patients with advanced gastric cancer. To this end, bulk RNA sequencing was performed on treatment-naïve primary tumor samples collected at diagnosis, prior to any systemic therapy. By using pre-treatment tumor gene expression profiles, the study sought to uncover intrinsic molecular features that may predispose tumors to therapeutic resistance.The generated data provide a resource for the discovery of predictive biomarkers, the stratification of patients according to treatment response, and the investigation of mechanisms underlying resistance to cytotoxic and immunomodulatory therapies in advanced gastric cancer.

This dataset contains bulk RNA sequencing (RNA-seq) gene expression profiles from 23 primary tumor samples obtained from patients diagnosed with advanced gastric cancer. All samples were collected prior to any systemic treatment (treatment-naïve). After tumor sampling, patients subsequently received either standard chemotherapy or chemotherapy combined with immunotherapy, allowing this dataset to serve as a baseline transcriptional reference for future comparative and outcome-associated studies
DOI: 10.5061/dryad.fj6q573xj
title: Code and data for: Interpolant-based demosaicing routines for dual-mode visible/near-infrared imaging systems

description: Dual-mode visible/near-infrared imaging systems, including a bioinspired
 six-channel design and more conventional four-channel implementations,
 have transitioned from a niche in surveillance to general use in machine
 vision. However, the demosaicing routines that transform the raw images
 from these sensors into processed images that can be consumed by humans or
 computers rely on assumptions that may not be appropriate when the two
 portions of the spectrum contribute different information about a scene. A
 solution can be found in a family of demosaicing routines that utilize
 interpolating polynomials and splines of different dimensionalities and
 orders to process images with minimal assumptions.
description: The steps used to collect and process the data in this dataset
 have been documented in the associated manuscript.
description: The information needed to use the data in this dataset has been
 provided in the associated README files.
DOI: 10.5061/dryad.5qfttdz81
title: A longitudinal study of DNA and RNA viruses plasma detection in allogeneic hematopoietic stem cell transplant recipients

description: Background: Viral infections are among the most common complications after
 allogeneic hematopoietic stem cell transplantation (allo-HSCT) and can be
 associated with transient or sustained viremia. Besides viruses that are
 common causes of infection, metagenomics revealed the presence of several
 novel viruses and variants that are overlooked in clinical routine and
 represent potential sources of unrecognized systemic infections. Our aim
 was to describe the prevalence and the dynamics of 17 DNA and 3 RNA viral
 infections using (r(RT-)PCR) assays on plasma samples of adult allo-HSCT
 recipients over a one-year period after HSCT. Methods: 109 adult patients
 that received a first allo-HSCT from 1st March 2017 to 31st January 2019
 we included in this longitudinal observational monocentric cohort study.
 17 DNA and 3 RNA viral species were screened with qualitative and/or
 quantitative r(RT)-PCR assays performed on plasma samples collected at
 five time-points (day 0 and 30 days, 3 months, 6 months and one year after
 HSCT). Results: TTV was the most prevalent with an increasing prevalence
 to 96% of patients at 3 months. HPgV-1 prevalence ranged from 26 to 36% of
 patients. TTV and HPgV-1 plasma viral load peaked at month 3 (TTV: median
 3.29E5 copies/ml [range, 3.37E2 to 4.06E9 copies/ml]; HPgV-1: median
 1.18E6 copies/ml [range, 2.61E3 to 4.49E7 copies/ml]). Among
 Polyomaviridae, BKPyV, JCPyV, MCPyV, HPyV6 and 7 were detected in ≥10% of
 patients at ≥1 time-point. HPyV6 and HPyV7 prevalence reached 27% and 12%
 of patients at month 3. Among those, 41% and 63% had quantifiable viral
 loads, with median viral loads above 1E3copies/ml and results may suggest
 HPyV6 sustained viremia. Co-detections were frequent, in particular at 3
 months with ≥2 viruses detected in 72% of patients. Conclusion: Our study
 confirms that TTV and HPgV-1 infections are highly prevalent and that
 infection may be sustained up to one year after allo-HSCT. Our systematic
 and large strategy of screening also revealed diverse and numerous
 co-detections, and that several novel Polyomaviridae (MCPyV, HPyV6/7) that
 are overlooked in clinical routine are as or more frequently detected
 compared to classical culprits. Our results underscores the need for
 further studies investigating the clinical impact of classical culprits
 together with other viruses in particular novel Polyomaviridae and HPgV-1.
DOI: 10.5061/dryad.2bvq83bsm
title: Restoring faith in conservation action: maintaining wild genetic diversity through the Tasmanian devil insurance program

description: Conservation breeding programs aim to maintain 90% wild genetic diversity,
 but rarely assess functional diversity. Here, we compare both genome-wide
 and functional diversity (in over 500 genes) of Tasmanian devils
 (Sarcophilus harrisii) within the insurance metapopulation and across the
 species’ range (64,519 km2). Populations have declined by 80% since 1996
 due to a contagious cancer, devil facial tumour disease (DFTD). However,
 predicted local extinctions have not occurred. Recent suggestions of
 selection for “resistance” alleles in the wild precipitated concerns that
 insurance population devils may be unsuitable for translocations. Using
 830 wild samples collected at 31 locations between 2012-2021, and 553
 insurance metapopulation devils, we show that the insurance metapopulation
 is representative of current wild genetic diversity. Allele frequencies at
 DFTD-associated loci were not substantially different between captive and
 wild devils. Methods presented here are valuable for others investigating
 evolutionary potential in threatened species, particularly ones under
 significant selective pressures.
description: There are three datasets included here: 1. A
 set of SNPs generated using DArTseq, a form of reduced representation
 sequencing. The raw files were cleaned, aligned to the Tasmanian devil
 reference genone, and a catalogue of consitent SNPs were called using
 STACKS. The SNP set was further filtered in R using the following
 parameters of 2.5x read depth, 80% call rate, 90% reproducibility based on
 technical replicates, 0.001 minor allele frequency and a maximum
 heterozygosity of 70%. 2. A set of SNPs generated using
 a custom target capture approach to assess functional diversity in the
 Tasmanian devil. The custom probe set was deisgned to capture three
 categories of sequence targes: 1) immune genes, 2) reproductive genes, and
 3) DFTD-associated loci. Raw reads were aligned to the Tasmanian devil
 reference genome using BWA and variant calling and filtering was performed
 in GATK. Linked SNPs were pruned using SNPRelate R package.
 3. The same SNP set generated in step 2 but without the linkage
 pruning.
DOI: 10.5061/dryad.4qrfj6qcr
title: Interactions between soil microbes and native species drive a diversity-invasibility relationship

description: Soil microbes can affect both the invasiveness of exotic plants and the
 invasibility of native plant communities, but it still remains unclear
 whether soil microbes can influence the relationship between native plant
 species diversity and community invasibility. We constructed native plant
 communities with three levels of species richness (one, three, or six
 species) in un-sterilized or sterilized soil (i.e., with or without soil
 microbes) and let them not be invaded by exotic plant species or invaded
 by one of three exotic species (Solidago canadensis, Erigeron canadensis
 or Symphyotrichum subulatum) highly invasive in China. The soils
 conditioned by the native plant communities not invaded by the exotic
 species were used as soil microbe inocula to test whether richness-induced
 differences in soil microbes affect the growth of each of the three
 invasive species. Compared with the presence of soil microbes, the absence
 of soil microbes weakened the negative species richness-invasibility
 relationship, indicating that soil microbes can contribute to the higher
 invasion resistance of more diverse native plant communities. In the
 presence of soil microbes, the higher invasion resistance of more diverse
 communities was mainly ascribed to the complementarity effect. However,
 soil microbes from communities with a higher species richness did not have
 a stronger negative effect on the growth of any of the three invasive
 species. We conclude that soil microbes can alter the
 diversity-invasibility relationship through promoting the complementarity
 effect on the community invasion resistance. Our results highlight the
 importance to integrate the role of soil microbes in testing the
 diversity-invasibility hypothesis.
description: Exp1: Colume D-M for plot with invasive species Solidago
 canadensis(SC)           Colume N-W for plot with
 invasive species Erigeron canadensis(EC)          
 Colume X-G for plot with invasive species Symphyotrichum
 subulatum(SS) Exp2: Colume AH-AO
DOI: 10.5061/dryad.vx0k6djv3
title: Novel code for: Synchrony in adult survival is remarkably strong among common temperate songbirds across France

description: Synchronous variation in demographic parameters across species
 destabilizes populations, metapopulations and metacommunities and
 increases extinction risks. Revealing the processes that synchronize
 population dynamics across species allows us to identify trans-specific
 demographic processes that are subject to environmental forcing of
 overarching importance. Using a Bayesian, hierarchical multi-site,
 multi-species mark-recapture model, we investigated temporal interspecific
 synchrony in annual adult local survival across 16 common songbird species
 across France for the period 2001–2016. Adult annual survival was largely
 synchronous among species (73% [47–94] of the variation among years was
 common to all species), despite species differing in ecological niche and
 life-histories. This result was robust to differences in migratory
 strategy among species, uneven species sample sizes, and time de-trending.
 Shared synchrony across migratory strategy suggests that environmental
 forcing during the 4-month temperate breeding season has large-scale,
 cross-specific, impacts among songbirds. At a scale ~1000 km, a likely
 proximate mechanism of synchronization is forcing by weather-driven
 variation in resources, which, in particular, determines the cost of
 reproduction. However, the strong interspecific synchrony was not easily
 explained by a set of a priori defined candidate weather variables, with
 spring weather variables explaining only 1.4% [0.01–5.5] of synchrony,
 while the contribution of large-scale winter weather indices may be
 stronger, but uncertain (12% [0.3–37]). Future research may up-scale these
 results to community dynamics, to understand compensatory intra- and
 inter-specific demographic processes that preserve meta-communities from
 synchronization.
DOI: 10.5061/dryad.8931zcrsz
title: Mesocosm experiments reveal the loss of migratory tendencies in a recently isolated population of three-spined sticklebacks

description: In the 1970s, water management in the Netherlands resulted in numerous
 isolated populations of three-spined sticklebacks, which can no longer
 migrate from freshwater to the sea. We tested whether ~50 years of
 isolation resulted in reduced migratory tendencies in these resident
 sticklebacks. Lab-based individual testing showed behavioural divergence
 between residents and migrants, but also produced counter-intuitive
 results, especially with regards to movement tendencies. To detect
 differences in migration tendencies, we set up a semi-natural mesocosm,
 consisting of connected ponds, where movements of numerous individuals
 could continually be tracked at larger spatial scales. We found that
 wild-caught residents and migrants exhibited no differences in movement
 tendencies within ponds, but residents moved significantly less between
 ponds than migrants. Between-pond movements were consistent and the
 observed differences were robust across contexts (changes in water flow
 and group size). Our study reveals that larger-scale movement tendencies
 can diverge over short time scales in response to human-induced isolation,
 and highlights the importance of observing behaviour in ecologically
 relevant setups that bridge the gap between lab and field studies.
description: Data are collected from the Radio-frequency identification
 decoders, which recorded the date, time stamp, attenna of detection and
 the unique RFID of individual fish that is detected at the antenna. From
 this data, we used a self-written R script to calculate the number of
 crosses each individual fish made between antennas (for within-pond
 movement) and number of crosses fish made between ponds, through the
 corridor (between-pond movement). All analyses are done on these
 crosses.
DOI: 10.5061/dryad.kwh70rz68
title: Using by-catch camera trapping data for estimating the population size of spotted hyena (Crocuta crocuta)

description: Spotted hyenas (Crocuta crocuta) are an important carnivore species whose
 dual role of scavenger and predator is vital to trophic energy flows of
 systems in which they are found. Where populations of spotted hyenas are
 small, the environment has few cleaners and carcasses can remain
 unprocessed. Despite being largely characterized as scavengers, spotted
 hyenas actively hunt and take down live prey and at high densities can
 have depressing effects on fragile or choice ungulate populations. In
 addition, they can alter the structure and composition dynamics of the
 carnivore guild through direct conflict or indirectly through competition
 for food and space. Despite their importance to ecosystem function and
 balance, reliable estimates of spotted hyena densities are rare. This is
 because unlike lions and leopards, spotted hyenas are generally not
 regarded as a charismatic species and, as such, survey resources, which
 are costly, are seldom solely allocated towards surveying them.
 Nonetheless, being able to confidently estimate spotted hyena numbers is
 important for the effective management of carnivore and herbivore
 populations whose dynamics they influence.
description: Photographic data were collected using baited camera traps and
 analysed using the capture-recapture software DENSITY.
DOI: 10.5061/dryad.44j0zpcgv
title: Global analysis of floral longevity reveals latitudinal gradients and biotic and abiotic correlates

description: The length of time a flower remains open and functional – floral longevity
 – governs important reproductive processes influencing pollination and
 mating and varies considerably among angiosperm species. However, little
 is known about large-scale biogeographic patterns and the correlates of
 floral longevity. Using published data on floral longevity from 818
 angiosperm species in 134 families and 472 locations worldwide, we present
 the first global quantification of the latitudinal pattern of floral
 longevity and the relationships between floral longevity and a range of
 biotic and abiotic factors. Floral longevity exhibited a significant
 phylogenetic signal, and was longer at higher latitudes in both northern
 and southern hemispheres, even after accounting for elevation. This
 latitudinal variation was associated with several biotic and abiotic
 variables. The mean temperature of the flowering season had the highest
 predictive power for floral longevity, followed by pollen number per
 flower. Surprisingly, compatibility status, flower size, pollination mode,
 and growth form had no significant effects on flower longevity. Our
 results suggest that physiological processes associated with floral
 maintenance play a key role in explaining latitudinal variation in floral
 longevity across global ecosystems, with potential implications for floral
 longevity under global climate change and species distributions.