cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qz612jmfq
title: Ectomycorrhizal fungal community assembly on seedlings of a Neotropical monodominant tree

description: Ectomycorrhizal tree species may benefit from positive plant-soil
 feedbacks, where soil environments near adult trees enhance conspecific
 seedling growth and survival. In tropical monodominant forests seedling
 survival is particularly important, as seedling banks help maintain
 stand-level dominance over generations. Positive plant-soil feedbacks may
 be mediated by diverse ectomycorrhizal fungal communities, which improve
 nutrient acquisition of heavily shaded seedlings. Despite the potential
 importance of these fungi, little is known about ectomycorrhizal fungal
 community development on seedlings of tropical monodominant trees. In
 Guyana, we sequentially monitored percent colonization and species
 composition of ectomycorrhizal fungi on an even-age cohort of seedlings of
 the tropical monodominant tree Dicymbe corymbosa (Fabaceae subfamily
 Detarioideae). Ectomycorrhizal fungi found on D. corymbosa seedlings over
 a twelve-month period of early development were compared to those of
 conspecific adults and four other ectomycorrhizal tree species in the
 region. Species turnover was high (80%) between six- and twelve-month-old
 seedlings, though the /russula-lactarius, /clavulina, and
 /tomentella-thelephora lineages were species-rich on seedlings at all
 ages. The number of ectomycorrhizal morphotypes per seedling increased
 with age, but extent of fungal colonization did not. Seedling
 ectomycorrhizal fungi were shared with sympatric conspecific adults (55%)
 and, to a lesser extent, regional heterospecific adults (27%), but
 numerous species were previously unrecorded for Guyana. Over their
 development D. corymbosa seedlings did not rely strictly on adult trees
 for their mycobionts but appeared to foster unique assemblages of
 ectomycorrhizal fungi.
DOI: 10.5061/dryad.pvmcvdnm2
title: Interferon beta drives intestinal regeneration after radiation

description: The cGAS-STING cytosolic DNA sensing pathway is critical for host defense.
 Here, we report that cGAS-STING–dependent type 1 interferon (IFN) response
 drives intestinal regeneration and animal recovery from radiation injury.
 STING deficiency has no effect on radiation-induced DNA damage or crypt
 apoptosis but abrogates epithelial IFN beta production, local
 inflammation, innate transcriptional response, and subsequent crypt
 regeneration. cGAS KO, IFNAR1 KO, or CCR2 KO also abrogates
 radiation-induced acute crypt inflammation and regeneration. Impaired
 intestinal regeneration and survival in STING-deficient mice are fully
 rescued by a single IFN beta  treatment given 48 hours after
 irradiation but not by wild-type (WT) bone marrow. IFN treatment
 remarkably improves the survival of WT mice and Lgr5+ stem cell
 regeneration through elevated compensatory proliferation and more rapid
 DNA damage removal. Our findings support that inducible IFN production in
 the niche couples ISC injury and regeneration and its potential use to
 treat acute radiation injury.
description: Please refer to referenced publication.
 Leibowitz et.al  Science Advances (2021), Ms# abi5253
description: Please refer to ReadMe file.
DOI: 10.5061/dryad.cz8w9gj3x
title: Integrating demography and distribution modelling for the iconic Leontopodium alpinum Colm. in the Romanian Carpathians

description: Both climate change and human exploitation are major threats to plant life
 in mountain environments. One species that may be particularly sensitive
 to both of these stressors is the iconic alpine flower edelweiss
 (Leontopodium alpinum Colm.). Its populations have declined across Europe
 due to over-collection for its highly prized flowers. Edelweiss is still
 subject to harvesting across the Romanian Carpathians but no study has
 measured to what extent populations are vulnerable to anthropogenic
 change. Here we estimated the effects of climate and human disturbance on
 the fitness of edelweiss. We combined demographic measurements with
 predictions of future range distribution under climate change to assess
 the viability of populations across Romania. We found that per-capita and
 per-area seed number and seed mass were similarly promoted by both
 favourable environmental conditions, represented by rugged landscapes with
 relatively cold winters and wet summers, and reduced exposure to
 harvesting, represented by the distance of plants from hiking trails.
 Modelling these responses under future climate scenarios suggested a
 slight increase in per-area fitness. However, we found plant ranges
 contracted by between 14 to 35% by 2050, with plants pushed into high
 elevation sites.  Synthesis. Both total seed number and seed mass
 are expected to decline across Romania despite individual edelweiss
 fitness benefiting from a warmer and wetter climate. More generally, our
 approach of coupling species distribution models with demographic
 measurements may better inform conservation strategies of ways to protect
 alpine life in a changing world.
DOI: 10.5281/zenodo.18397207
title: Hamiltonian Worldlines Triangle

description: Worldlines theory expanded with Hamiltonian

 

This manuscript is current in Official Peer Review.

Not final version.Copyright©2026 Alex De Giuseppe.All rights reserved.

This work is protected by copyright. Any form of plagiarism, unauthorized reproduction, or misappropriation of ideas, mathematically results, or text without proper citation constitutes a violation of academic and intellectual property standards and common laws.

No commercial use, adaptation, or derivative works are permitted without explicit written permission from the author.

For correspondence, citations, collaboration inquiries, or feedback please contact:degiuseppealex@gmail.com

The hash files that determine ownership have been created
DOI: 10.5061/dryad.p8cz8w9qs
title: CPR dataset for: Testing Bergmann's Rule in Marine Copepods

description: This is the global dataset used for the Campbell et al. (2021) paper
 “Testing Bergmann’s Rule in marine copepods”. The dataset includes the
 mean length of copepods weighted by abundance found in 97,830 continuous
 plankton recorder (CPR) samples. Further, it contains satellite
 observations for sea surface temperature, chlorophyll-a, and dissolved
 oxygen (see paper for details). It was a massive collaborative effort to
 get this dataset assembled by the Global Alliance of CPR Surveys (GACS
 2011, Batten et al. 2019).
description: See details in "Testing Bergmann's Rule in marine
 copepods".
description: See the CopeData_description.Rmd
DOI: 10.5061/dryad.0p2ngf21r
title: Data for: Non-host species reduce parasite infection in a focal host species within experimental fish communities

description: The dilution effect describes the negative association between host
 biodiversity and the risk of infectious disease. Tests designed to
 understand the relative roles of host species richness, host species
 identity, and rates of exposure within experimental host communities would
 help resolve ongoing contention regarding the importance and generality of
 dilution effects. We exposed fathead minnows to infective larvae of the
 trematode, Ornithodiplostomum ptychocheilus in minnow-only containers and
 in mixed containers that held 1-3 other species of fish. Parasite
 infection was estimated as the numbers of encysted worms (i.e.,
 brainworms) present in minnows following exposure. The results of exposure
 trials showed that non-minnow fish species were incompatible with O.
 ptychocheilus larvae. There was no reduction in mean brainworm counts in
 minnows in mixed containers with brook sticklebacks or longnose dace. In
 contrast, brainworm counts in minnows declined by 51% and 27% in mesocosms
 and aquaria, respectively, when they co-occurred with emerald shiners.
 Dilution within minnow + shiner containers may arise from shiner-induced
 alterations in minnow or parasite behaviours that reduced encounter rates
 between minnows and parasite larvae. Alternatively, shiners may act as
 parasite sinks for parasite larvae. These results highlight the role of
 host-species identity in the dilution effect. Our results also emphasize
 the complex and idiosyncratic effects of host community composition on
 rates of parasite infection within contemporary host communities that
 contain combinations of introduced and native species.
DOI: 10.6078/d1p98m
title: Longitudinal assessment of thermal and perceived air quality acceptability in relation to temperature, humidity, and CO2 exposure in Singapore

description: Thermal acceptability (TA) and perceived air quality acceptability (PAQA)
 are typically analyzed in climate chambers or cross-sectional field
 studies. Individual factors, such as expectations and perceived
 environment history, may influence the acceptability response.
 Longitudinal studies with multi-day design are absent in the literature.
 Fifteen Singaporean subjects participated in a 7-day longitudinal
 experiment in which they carried a portable sensor that continuously
 recorded personal air temperature, relative humidity and carbon
 dioxide concentration at 1-min intervals. Instantaneous TA and
 PAQA were regularly sampled by survey for each subject. High acceptability
 was found at home, restaurants and workplaces, whereas low acceptability
 was found for outdoor and transport environments. The participants, from
 Singapore's modern tropical environment spent an average of 96% of
 their time indoors. Weak associations were reported between
 acceptabilities and measured physical parameters taken independently.
 Clustering data by location, subject's sleeping ventilation habit,
 air-conditioning operation status and the changes in physical parameters
 over a designated time period enhanced the understanding of the
 acceptability results. In general, acceptability was lower for those who
 slept in air-conditioned environments than for those who slept without
 air-conditioning. The carbon dioxide mixing ratio was critical for PAQA
 predictions but not for TA. The Gaussian process (GP) had a better
 predictive power than a multiple linear regression approach. Using GP, we
 found that a general predictive model had comparable simulation
 performance as for individual predictive models. The longitudinal
 experiment has demonstrated effectiveness for TA and PAQA analysis, which
 could be beneficial to future studies in personal comfort prediction.
description: Fifteen Singaporean subjects participated in a 7-day longitudinal
 experiment in which they carried a portable sensor that continuously
 recorded personal air temperature, relative humidity and carbon dioxide
 concentration at 1-min intervals. Instantaneous TA and PAQA were regularly
 sampled by survey for each subject.
DOI: 10.5061/dryad.kkwh70s4v
title: Fungal data of leafless epiphytic orchids

description: This dataset contains fungal phylogenetic and community data from the
 paper: “Qin, Jiao; Zhang, Wei; Feng, Jing‑Qiu; Zhang, Shi‑Bao (2021),
 Leafless epiphytic orchids share Ceratobasidiaceae mycorrhizal fungi.
 Mycorrhiza. https://doi.org/10.1007/s00572-021-01043-4”. One sequence
 matrix and the relevant phylogenetic tree were displayed to show the
 relationships among fungi of Ceratobasidiaceae. The sequence abundances of
 each mycorrhizal fungal OTU detected from different samples, together with
 the sampling information, were listed in the uploaded excel.
description: The fungal
 amplicons of orchid mycorrhizas were sequenced by using primer pairs
 ITS3/ITS4OF and ITS86/ITS4 on MiSeq PE-250 platforms. The obtained clean
 reads were clustered into operational taxonomic units (OTUs) at a 97%
 identity threshold using the UPARSE-OTU algorithm. The representative
 sequence of each OTU was annotated using UNITE database (Feb 2020).The OTU
 abundance tables were generated from all the merged sequences and OTUs,
 and were then filtered by excluding OTUs with a low sequence abundance and
 homogenized using rarefaction.py in Qiime 2 according to the lowest
 sequence abundance in all samples (22,044 reads). The OTU abundance data
 merged from sequencings of two different primer pairs was deposited in
 Dryad Data Repository. Phylogenetic analyses of three“rhizoctonia”fungal
 lineages (Ceratobadiaceae, Tulasnellaceae, and Sebacinales) and
 Psathyrellaceae were carried out using Maximum Likelihood (ML). The
 relevant sequence matrixes (aligned using Mafft) and the
 ML trees were also provided here. These data has
 been processed to produce a MS published in
 Mycorrhiza.
description: More detailed information
 of each fungal OTU can be found in the referenced manuscript and readme
 file.
DOI: 10.5061/dryad.rfj6q579w
title: Non-biodegradable objects may boost microbial growth in water bodies by harnessing bubbles

description: Given the ubiquity of bubbles and non-biodegradable wastes in aqueous
 environments, their transport through bubbles should be widely extant in
 water bodies.  In this study, we investigate the effect
 of bubble-induced waste transport on microbial
 growth by using yeasts as model microbes and a silicone
 rubber object as a model waste. Noteworthily, this object repeatedly rises
 and sinks in fluid through fluctuations
 in bubble acquired buoyant forces produced by cyclic
 nucleation, growth and release of bubbles from object’s surface. The
 rise-sink movement of object gives rise to a strong bulk
 mixing and an enhanced resuspension of cells from the floor. Such
 spatially dynamic contaminant inside a nutrient-rich
 medium also leads to an increment in the total
 microbe concentration in the
 fluid. The enhanced concentration is caused
 by strong nutrient mixing generated by the object’s
 movement which increases the nutrient supply to growing microbes and
 thereby, prolonging their growth phases. We
 confirm these findings through a theoretical model for
 cell concentration and nutrient distribution in fluid medium. The
 model is based on the continuum hypothesis and it uses the general
 conservation law which takes an
 advection-diffusion-growth form. We conclude the study
 with demonstration of bubble-induced digging of objects from model sand.
DOI: 10.5061/dryad.hx3ffbgdv
title: A tradeoff between robustness to environmental fluctuations and speed of evolution

description: The ability of a species to cope with both long-term and short-term
 environmental fluctuations might vary with the species' life history.
 While some life-history characteristics promote large and stable
 population sizes despite interannual environmental fluctuations, other
 life-history strategies might allow to evolve quickly in response to
 long-term gradual changes. In a theoretical study, we show that there is a
 tradeoff between both properties. Life-history characteristics that
 promote fast rates of evolution come at the expense of a poor response to
 short-term environmental fluctuations, and vice versa. We demonstrated the
 presence of this tradeoff by the use of a mathematical analysis and
 individual-based simulations.
description: The dataset contains the simulation source code, simulation
 configuration files, the simulation results, a Mathematica notebook, and R
 scripts of the manuscript "A tradeoff between robustness to
 environmental fluctuations and speed of evolution" that was published
 in the American Naturalist.
DOI: 10.5061/dryad.x69p8czjd
title: Genomic data from: Are you ready for the heat? Phenotypic plasticity vs adaptation of heat tolerance in three-spined stickleback

description: Heat waves constitute a challenge for aquatic ectotherms. However, the
 thermal tolerance of animals and their individual phenotypic plasticity to
 respond to heat waves may be influenced by thermal history. We tested
 these hypotheses by comparing the upper thermal tolerance and the
 individual capacities of three-spined sticklebacks from populations with
 different thermal histories to respond to heat waves. Two populations
 originated from thermally polluted nuclear power plant (NPP) habitats,
 while four locations represented geographically
 adjacent control areas. To disentangle the genetic
 adaptation from the phenotypic plastic response, we measured the
 individual upper thermal tolerance and the responses at molecular level in
 common garden conditions before and after a laboratory-mimicked heat wave.
 We found that the sticklebacks exhibit considerable phenotypic plasticity
 in thermal tolerance since the heat wave increased fish upper thermal
 tolerance significantly. The individual plasticity to respond to the heat
 wave was also negatively correlated to initial thermal tolerance. On the
 other hand, neither the thermal tolerance nor the plastic responses
 differed between NPP and control sites despite detection of significant
 but low genome-wide divergence in 10 out of 15 pairwise comparisons. Our
 results suggest that five decades of nuclear power plant activity with
 warmer water has not resulted in a detectable evolutionary change in
 either the upper thermal tolerance or its plasticity in three-spined
 sticklebacks potentially rendering them sensitive to frequent heat waves.
description: <b>1. fasta_files.tar.gz </b> Compressed directory with fastq files for each individual used in this study. <b>2. populations.snps.vcf</b> Genotype file in VCF format <b>3. populations_map.txt</b> Individuals and their corresponding population. <b>4. Readme.txt</b>
DOI: 10.5061/dryad.zs7h44j8v
title: Data from: Asexual freshwater snails make poor mate choice decisions

description: Once-useful traits that no longer contribute to fitness tend to decay over
 time. We address whether the expression of mating-related traits that
 increase the fitness of sexually reproducing individuals but are likely
 less useful or even costly to asexual counterparts seems to exhibit decay
 in the latter. Potamopyrgus antipodarum is a New Zealand freshwater snail
 characterized by repeated transitions from sexual to asexual reproduction.
 The frequent coexistence of sexual and asexual lineages makes P.
 antipodarum an excellent model for the study of mating-related trait loss.
 We used a mating choice assay including sexual and asexual P. antipodarum
 females and conspecific (presumed better choice) vs. heterospecific
 (presumed worse choice) males to evaluate the loss of behavioural traits
 related to sexual reproduction. We found that sexual females engaged in
 mating behaviours with conspecific mating partners more frequently and for
 a greater duration than with heterospecific mating partners, while asexual
 females seemed to lack the ability to make a choice. These results suggest
 that selection acting to maintain mate choice in asexual P. antipodarum is
 weak or ineffective relative to sexual females and that asexual
 reproduction likely contributes to the evolutionary decay of behavioural
 traits in this system.
DOI: 10.5061/dryad.1vhhmgqsz
title: Structural MRI signatures in genetic presentations of the FTD/MND spectrum

description: Objective: To assess cortical, subcortical and cerebellar grey
 matter (GM) atrophy using magnetic resonance imaging (MRI) in patients
 with disorders of the frontotemporal lobar degeneration (FTLD) spectrum
 with known genetic mutations. Methods: Sixty-six patients
 carrying FTLD-related mutations were enrolled, including 44 with pure
 motor neuron disease (MND) and 22 with frontotemporal dementia (FTD).
 Sixty-one patients with sporadic FTLD (sFTLD) matched for age, sex and
 disease severity with genetic FTLD (gFTLD) were also included, as well as
 52 healthy controls. A whole-brain voxel-based morphometry (VBM) analysis
 was performed. GM volumes of subcortical and cerebellar structures were
 obtained. Results: Compared with controls, GM atrophy on VBM was
 greater and more diffuse in genetic FTD, followed by sporadic FTD and
 genetic MND cases, whereas sporadic MND (sMND) patients showed focal motor
 cortical atrophy. Patients carrying C9orf72 and GRN mutations showed the
 most widespread cortical volume loss, in contrast with GM sparing in SOD1
 and TARDBP. Globally, gFTLD patients showed greater atrophy of parietal
 cortices and thalami compared with sFTLD. In volumetric analysis, gFTLD
 patients showed volume loss compared with sFTLD in the caudate nuclei and
 thalami, in particular comparing C9-MND with sMND cases. In the
 cerebellum, gFTLD patients showed greater atrophy of the right lobule VIIb
 than sFTLD. Thalamic volumes of gFTLD patients with a C9orf72 mutation
 showed an inverse correlation with Frontal Behavioral Inventory scores.
 Conclusions: Measures of deep GM and cerebellar structural
 involvement may be useful markers of gFTLD, particularly C9orf72-related
 disorders, regardless the clinical presentation within the FTLD spectrum.
DOI: 10.5061/dryad.xsj3tx9fq
title: Raw data for Urine DNA (uDNA) as a non-lethal method for endoparasite biomonitoring: development and validation

description: Changes in environmental conditions alter host-parasite interactions,
 raising the need for effective epidemiological surveillance. Developing
 operational, accurate, and cost-effective methods to assess individual
 infection status and potential for pathogen spread is a prerequisite to
 anticipate future disease outbreaks in wild populations. For
 endoparasites, effective detection of infections usually relies on
 host-lethal approaches, which are barely compatible with wildlife
 conservation objectives. Here, we used the brown trout (Salmo trutta) -
 Tetracapsuloides bryosalmonae host-parasite system to develop a non-lethal
 method for endoparasite infection detection, hereafter called “uDNA” for
 urine DNA. The uDNA diagnostic test is based on the amplification of
 endoparasite DNA from host urine. We sampled wild fish (N = 111) from
 eight sites, let them excrete in individual buckets filled with mineral
 water and performed parasite DNA amplification from water filtration. We
 compared the results of the uDNA diagnostic test for host infection status
 and parasite load to those from kidney samples (the current standard
 method). uDNA was sensitive in determining host infection status (even for
 infected hosts showing no sign of the disease), since up to 90% of fish
 individuals were correctly assigned to their infection status. The
 quantity of uDNA detected from the hosts depended on the sampling sites,
 suggesting a spatial variation in the parasite spread. uDNA was
 positively, but weakly correlated with parasite load in the kidney. This
 correlation depended on the severity of macroscopic lesions caused by the
 disease, and was negative in fish with severely damaged kidney, likely due
 to impaired urine excretion. The uDNA approach provides novel avenues to
 non-lethally infer infection parameters from wildlife populations at large
 spatial scales. By targeting parasite transmission stage, uDNA is also
 valuable to get insights on the parasite fitness and the ecological and
 evolutionary dynamics of this host-parasite interaction.
description: Sample: name of the sampled individual site:
 sampled site kDNA: number of copies of Tetracapsuloides
 bryosalmonae DNA detected in fish kidney divided by the number of copies
 of Salmo trutta DNA detected in the same sample
 uDNA_qPCR: Relative concentration of Tetracapsuloides
 bryosalmonae DNA found with the uDNA method and qPCR
 amplification uDNA_ddPCR: Concentraton of
 Tetracapsuloides bryosalmonae DNA found with the uDNA method and ddPCR
 amplification Time_in_bucket: the time spent by the
 fish in the bucket filled with mineral water (in minutes)
 Fish_size: Size of the fish (mm) Fish_mass:
 Mass of the fish (g) Gross_lesions_score: Score of
 proliferative kidney disease (PKD) gross lesions after macroscopic
 examination of the kidney, spleen and gills of the sampled fish. 0: no
 sign of PKD, 3: very high PKD suspicion