cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5qj120q
title: Data from: DNA barcoding fishes from the Congo and the Lower Guinean provinces: assembling a reference library for poorly inventoried fauna

description: The Congolese and Lower Guinean ichthyological provinces are understudied
 hotspots of the global fish diversity. Here, we barcoded 741 specimens
 from the Lower and Middle Congo River and from three major drainage basins
 of the Lower Guinean ichthyological province, Kouilou-Niari, Nyanga and
 Ogowe. We identified 195 morphospecies belonging to 82 genera and 25
 families. Most morphospecies (92.8%) corresponded to distinct clusters of
 DNA barcodes. Of the four morphospecies present in both neighbouring
 ichthyological provinces, only one showed DNA barcode divergence
 &lt;2.5%. A small fraction of the fishes barcoded here (12.9% of the
 morphospecies and 16.1% of the barcode clusters representing putative
 species) were also barcoded in a previous large-scale DNA analysis of
 freshwater fishes of the Lower Congo published in 2011 (191 specimens, 102
 morphospecies). We compared species assignments before and after taxonomic
 updates and across studies performed by independent research teams and
 observed that most cases of inconsistent species assignments were due to
 unknown diversity (undescribed species and unknown intraspecific
 variation). Our results report more than 17 putative new species and show
 that DNA barcode data provide a measure of genetic variability that
 facilitates the inventory of underexplored ichthyofaunae. However,
 taxonomic scrutiny, associated with revisions and new species
 descriptions, is indispensable to delimit species and build a coherent
 reference library.
description: Alignment of COI
 sequences of data set AAlignment of 741 DNA
 sequences of the 5'-end of the cytochrome c oxidase subunit I gene
 (COI, 652 bp) obtained in this study (data set A). Labels indicate the
 sequence ID, the (morpho)species identification, the voucher unique ID and
 the molecular operational taxonomic unit (MOTU) identifier obtained using
 four methods (ABGD, RESL, GMYC and bPTP).Sonet-et-al_MolEcolRes_COIAlignment-DatasetA.fasAlignment of COI sequences of data set A+BAlignment of 932 DNA sequences of the 5'-end of the cytochrome c oxidase subunit I gene (COI, 652 bp) obtained in this study (741 sequences) and retrieved from public repositories (191 sequences which were collected in the same part of the Congolese drainage system) (data set A+B). Labels indicate the sequence ID, the (morpho)species identification, the voucher unique ID and the molecular operational taxonomic unit (MOTU) identifier obtained using three methods (ABGD, GMYC and bPTP).Sonet-et-al_MolEcolRes_COIAlignment-DatasetA+B.fas
DOI: 10.15468/dl.fs7cys
title: Occurrence Download

description: A dataset containing 737 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Biofokus",
 "Issue is Country coordinate mismatch",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 737 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001557-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17761787
title: INRIM_Brand1_60F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 60F SC sample 3 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.17761788
title: INRIM_Brand1_60F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 60F SC sample 3 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.30010gs
title: Data from: Small RNAs in rat sperm are a predictive and sensitive biomarker of exposure to the testicular toxicant ethylene glycol monomethyl ether.

description: Testicular histology and semen parameters are considered the gold
 standards when determining male reproductive toxicity. Ethylene glycol
 monomethyl ether (EGME) is a testicular toxicant with well-described
 effects on histopathology and sperm parameters. To compare the
 predictivity and sensitivity of molecular biomarkers of testicular
 toxicity to the traditional endpoints, small RNAs in the sperm were
 analyzed by next generation RNA-sequencing (RNA-seq). Adult rats were
 exposed to 0, 50, 60, or 75 mg/kg EGME by oral gavage for 5 consecutive
 days. Testis histology, epididymal sperm motility and sperm small RNAs,
 including microRNAs (miRNAs), mRNA fragments, piwi-associated RNAs
 (piRNAs), and tRNA fragments (tRFs), were analyzed 5 weeks after cessation
 of exposure. Testicular histology showed a significant dose-dependent
 increase in retained spermatid heads (RSH), while sperm motility declined
 with increasing dose. RNA-seq of sperm small RNAs was used to identify
 significant dose-dependent changes in percent mRNA fragments (of total
 reads), percent miRNAs (of total reads), average tRF length, average piRNA
 length, and piRNA and tRF length-distributions. Discriminant analysis
 showed relatively low predictivity of treatment based on RSH or motility
 compared to the average read length of all aligned RNAs. Benchmark dose
 (BMD) modeling resulted in a BMD of 62 mg/kg using RSH, whereas average
 read length of all aligned RNAs resulted in a BMD of 47 mg/kg. These
 results showed that sperm small RNAs are sensitive and predictive
 biomarkers of EGME-induced male reproductive toxicity.
description: Supplemental Figures for
 Stermer et al.Supplemental Figures
 include a photomicrograph from a sperm motility video of sperm collected
 from a 100 mg/kg treated rat in a preliminary EGME dose-response
 experiement, and the best-fit BMD curves of the z-transformed data for
 normally distributed endpoints measured after EGME
 exposure.Stermer_et_al_Supplemental_Figures.pdfSupplemental Tables for Stermer et al.Supplemental Tables include BMD modeling summary for the z-transformed data of normally distributed endpoints after EGME exposure, and a summary of the coeffecient of variance for each of these endpoints.Stermer_et_al_Supplemental_Tables.xlsx
DOI: 10.5061/dryad.r58d342
title: Data from: INTREPAD: a randomized trial of naproxen to slow progress of presymptomatic Alzheimer disease

description: Objective: Evaluate the safety and efficacy of low-dose naproxen for
 prevention of progression in pre-symptomatic AD among cognitively intact
 persons at-risk. Methods: INTREPAD, a two-year double-masked
 pharmaco-prevention trial, enrolled 195 AD family history-positive elderly
 (mean age 63 years) screened carefully to exclude cognitive disorder.
 These were randomized 1:1 to naproxen sodium 220mg twice-daily or placebo.
 Multimodal imaging, neurosensory, cognitive and (in ~50%) CSF biomarker
 evaluations were performed at Baseline, 3, 12, and 24 months. A modified
 intent-to-treat analysis considered 160 participants who remained
 on-treatment through their first follow-up examination. The primary
 outcome was rate of change in a multimodal composite pre-symptomatic
 Alzheimer Progression Score (APS). Results: Safety: Naproxen-treated
 individuals showed a clear excess of adverse events. Efficacy: Among
 treatment groups combined, the APS increased by 0.101 points/year (S.E =
 0.014; P &lt; 10-5), but rate of change showed little difference by
 treatment assignment (0.017 points/year). The treatment-related slope
 ratio of 1.10 (95% Confidence Interval 0.588–2.04) suggested that naproxen
 does not reduce the rate of APS progression by more than 41%. Secondary
 analyses revealed no notable treatment effects on individual CSF,
 cognitive, or neurosensory biomarker indicators of progressive
 pre-symptomatic AD. Conclusions: In cognitively intact individuals
 at-risk, sustained treatment with naproxen sodium 220 mg twice-daily
 increases frequency of adverse health effects but does not reduce apparent
 progression of pre-symptomatic AD. Classification of Evidence: This study
 provides Class I evidence that, for people who are cognitively intact,
 low-dose naproxen does not significantly reduce progression of a composite
 indicator of pre-symptomatic AD.
description: Supplementary_RevisedeMethods, eTables (Table e1, Table e2, Table e3, Table e4), eFigures (Figure e1, Figure e2), eReferences (1)
DOI: 10.5061/dryad.n829mt4
title: Data from: Predator-induced changes in dissolved organic carbon dynamics

description: The fate of dissolved organic carbon (DOC) is partly determined by its
 availability to microbial degradation. Organisms at upper trophic levels
 could influence the bioavailability of DOC via cascading effects on
 primary producers and bacteria. Here we experimentally tested whether the
 presence of fish in aquatic food webs can indirectly affect the
 composition of the DOC pool. We found that fish had strong positive
 effects on phytoplankton biomass that affected the dynamics of DOC
 composition. Specifically, fish increased protein-like, algae-derived DOC
 mid-experiment, concurrent with the strongest fish-induced increase in
 phytoplankton biomass. Fish also increased bacterial abundance, altered
 the community composition and diversity of bacteria, and temporarily
 increased DOC compounds with fluorescence properties indicative of
 microbially-reprocessed organic matter. Overall, our experiment revealed
 that fish can positively influence the substrate (algae-produced DOC) and
 the key players (bacteria) of the microbial carbon pump. Consequently,
 fish could contribute to carbon sequestration by stimulating both the
 production of bioavailable DOC and the microbial degradation of
 bioavailable to persistent DOC. We propose this as a novel mechanism
 whereby the loss of predators from global ecosystems could alter carbon
 cycling.
description: Time series data of
 biotic and DOC parameterstime_series_data.csvAbundance and diversity of bacteria, phyto- and zooplanktoncommunity_data.csv
DOI: 10.5061/dryad.34j84c0
title: Data from: Kin selection and allocare in sperm whales

description: Cooperative care and defense of young are hypothesized to be foundational
 to the societies of several species, including the sperm whale (Physeter
 macrocephalus). However, the extent of allocare among sperm whales and the
 mechanisms driving it have not been well-characterized. Sperm whale social
 units are matrilineally-based, making kin selection a likely key driver of
 allocare, but the relationship between kinship and calf care is
 essentially unknown. We investigate calf care in the context of kinship,
 by combining association and interaction data with genetic profiles for 16
 calves from 7 eastern Caribbean social units. Mothers were the primary
 associate for 62.5% of calves, and the primary nurse for 87.5%, so
 behavioral observations are not always sufficient for assigning maternity.
 Babysitting and allonursing were frequent in some cases, particularly for
 calves less than a year old. Within social units, babysitting rates were
 correlated with relatedness (rs = 0.4, p &lt; 0.05), and allonurses
 were, on average, closer maternal relatives of the calves they nursed than
 were available females who were not allonurses (Δr = 0.14, p = 0.054).
 Exceptions to the overall positive relationship between allocare and
 kinship suggest that additional factors influencing allocare among sperm
 whales may include reciprocity, group augmentation and gaining maternal
 experience.
description: Konrad_Sperm_Whale_PhotoID_Dominica_2005_2016Identifiation data for sperm whales off Dominica 2005-2016
DOI: 10.17044/scilifelab.31150372
title: Data from: Seasonal variation in heteromorphic sperm size in <i>Littorina</i> snails on the Swedish West Coast

description: <b>Abstract of the journal article "</b><b>Seasonal variation in heteromorphic sperm size in </b><b><i>Littorina</i></b><b> snails on the Swedish West Coast":</b>Sperm are among the most morphologically diverse cells in the animal kingdom, with many species producing distinct sperm morphs-a phenomenon known as sperm heteromorphism. Typically, fertilizing eusperm are accompanied by non-fertilizing parasperm, which in some taxa play roles related to sperm competition. In <i>Littorina</i> snails, a genus of marine gastropods, the function of parasperm remains unresolved, but it appears to represent a substantial reproductive investment and thus may change through the breeding season. Here, we investigated seasonal changes in parasperm volume and eusperm length in four <i>Littorina</i> species, including two with distinct ecotypes. Measurements were taken across their breeding seasons to assess temporal shifts in sperm size and variation in size. Both parasperm and eusperm exhibited pronounced seasonal dynamics, with larger sizes typically occurring early in the breeding season and smaller sizes toward the end. Seasonal fluctuations in parasperm volume may reflect changes in reproductive investment or sperm competition intensity, whereas increasing variation in eusperm length toward the end of the season may indicate reduced control of spermatogenesis and lower selective pressure for optimal sperm lengths. We suggest that hormonal fluctuations or temperatures might cause the observed differences. Our findings provide the first evidence of seasonal size variation in heteromorphic sperm in a marine invertebrate, paralleling patterns observed in avian systems. These results suggest that seasonal environmental and reproductive factors shape sperm traits in <i>Littorina</i>, highlighting the plasticity of sperm form and function in response to ecological pressures.<br><b>Description of the data:</b># R-CodeAnalysis.rThis is the R-Code that was used for all analyses and plotting.<br># csv filesAnalysis.csvThis is the data that was acquired during our study, it contains parasperm and eusperm sizes as well as sampling information.<br># word documentsHow to automatically analyze my parasperm images in Fiji.docxThis is a manual how to measure parasperm cells automatically in Fiji (ImageJ).<br>ImageJ.docxThis is the Macro that was used to measure parasperm cells automatically in Fiji/ImageJ (threshold here is set to 100-145, needs to be applied according to the images)<br>Note that data from eusperm measurements from March 2023 were also used in the dataset: https://doi.org/10.17044/scilifelab.28590188.v2. <br><br>
DOI: 10.5061/dryad.dv3vg56
title: Data from: Pollen limitation as a main driver of fruiting dynamics in oak populations

description: In many perennial wind-pollinated plants, the dynamics of seed production
 is commonly known to be highly fluctuating from year to year and
 synchronized among individuals within populations. The proximate causes of
 such seeding dynamics, called masting, are still poorly understood in oak
 species that are widespread in the northern hemisphere, and whose fruiting
 dynamics dramatically impacts forest regeneration and biodiversity.
 Combining long-term surveys of oak airborne pollen amount and acorn
 production over large-scale field networks in temperate areas, and a
 mechanistic modeling approach, we found that the pollen dynamics is the
 key driver of oak masting. Mechanisms at play involved both internal
 resource allocation to pollen production synchronized among trees and
 spring weather conditions affecting the amount of airborne pollen
 available for reproduction. The sensitivity of airborne pollen to weather
 conditions might make oak masting and its ecological consequences highly
 sensitive to climate change.
description: data_Schermer_et_al
DOI: 10.17044/scilifelab.31150372.v1
title: Data from: Seasonal variation in heteromorphic sperm size in <i>Littorina</i> snails on the Swedish West Coast

description: <b>Abstract of the journal article "</b><b>Seasonal variation in heteromorphic sperm size in </b><b><i>Littorina</i></b><b> snails on the Swedish West Coast":</b>Sperm are among the most morphologically diverse cells in the animal kingdom, with many species producing distinct sperm morphs-a phenomenon known as sperm heteromorphism. Typically, fertilizing eusperm are accompanied by non-fertilizing parasperm, which in some taxa play roles related to sperm competition. In <i>Littorina</i> snails, a genus of marine gastropods, the function of parasperm remains unresolved, but it appears to represent a substantial reproductive investment and thus may change through the breeding season. Here, we investigated seasonal changes in parasperm volume and eusperm length in four <i>Littorina</i> species, including two with distinct ecotypes. Measurements were taken across their breeding seasons to assess temporal shifts in sperm size and variation in size. Both parasperm and eusperm exhibited pronounced seasonal dynamics, with larger sizes typically occurring early in the breeding season and smaller sizes toward the end. Seasonal fluctuations in parasperm volume may reflect changes in reproductive investment or sperm competition intensity, whereas increasing variation in eusperm length toward the end of the season may indicate reduced control of spermatogenesis and lower selective pressure for optimal sperm lengths. We suggest that hormonal fluctuations or temperatures might cause the observed differences. Our findings provide the first evidence of seasonal size variation in heteromorphic sperm in a marine invertebrate, paralleling patterns observed in avian systems. These results suggest that seasonal environmental and reproductive factors shape sperm traits in <i>Littorina</i>, highlighting the plasticity of sperm form and function in response to ecological pressures.<br><b>Description of the data:</b># R-CodeAnalysis.rThis is the R-Code that was used for all analyses and plotting.<br># csv filesAnalysis.csvThis is the data that was acquired during our study, it contains parasperm and eusperm sizes as well as sampling information.<br># word documentsHow to automatically analyze my parasperm images in Fiji.docxThis is a manual how to measure parasperm cells automatically in Fiji (ImageJ).<br>ImageJ.docxThis is the Macro that was used to measure parasperm cells automatically in Fiji/ImageJ (threshold here is set to 100-145, needs to be applied according to the images)<br>Note that data from eusperm measurements from March 2023 were also used in the dataset: https://doi.org/10.17044/scilifelab.28590188.v2. <br><br>
DOI: 10.5061/dryad.3fg5r56
title: Data from: Optimal foraging or surplus killing: selective consumption and discarding of salmon by brown bears

description: Selective consumption of prey by predators, observed in many animals, is
 often attributed to optimal foraging. Consistent with this idea, brown
 bears (Ursus arctos) often exhibit partial consumption, feeding
 exclusively on lipid-rich tissues of Pacific salmon (Oncorhynchus spp.),
 and discarding remains. However, bears also kill and abandon salmon
 without consuming any tissue. These discarded fish may be consistent with
 optimal foraging choices if they are of poor quality and if bears have
 easy access to better prey, or may reveal non-adaptive surplus killing
 behavior if fish are killed and discarded at random or solely based on
 prey abundance. Using 21 consecutive years of data from sockeye salmon (O.
 nerka) carcass surveys in Alaska, we found that foraging to maximize
 energy intake best explained prey discarding behavior. Specifically,
 discarding was more common under high prey abundance, late in the salmon
 run, and with low quality prey. Patterns of tissue consumption were
 consistent with these findings; bears were less likely to consume belly,
 body, and brain tissue when prey condition decreased. Other factors not
 quantified here (e.g., bear demography, alternative food resources) almost
 certainly influence prey discard and partial consumption, though the
 salmon-related factors explored here strongly influenced bear foraging
 decisions that were consistent with optimal foraging theory. We did not
 find clear evidence of surplus killing behavior in brown bears foraging on
 salmon, but prey selectivity manifested itself through both discarding and
 partial consumption, which contributes to our ability to predict transport
 of salmon nutrients by bears across ecosystem boundaries.
description: Lincoln Quinn bear
 consumption data 9-19-18This file consists of
 data associated with the manuscript “Optimal foraging or surplus killing:
 selective consumption and discarding of salmon by brown bears.” Each row
 represents a bear-killed sockeye salmon, and contains an individual ID,
 the year and date of the observation, the fish sex and length (measured
 mid-eye to hypural plate), a binary code for bear consumption of
 body/hump/belly/brain/skin tissue, habitat type (1=stream, 2=pond), and a
 binary code for consumption or discard (1=consumption, 0=discard).
 Additionally, the Julian date of fish death, the daily local fish
 availability, annual local fish availability, neighborhood fish
 availability, and the in-stream lifespan are provided.
DOI: 10.5061/dryad.t62h737
title: Data from: Symmetry breaking and inter-clonal behavioural variability in slime molds

description: Cells are dynamic systems capable of switching from an isotropic growth to
 a polarized growth even in the absence of any pre-existing external
 asymmetry. Here, we study this process of symmetry breaking in the
 acellular slime mold Physarum polycephalum. In the experiments slime molds
 could grow on two identical opposed sources of calcium. We highlighted a
 positive correlation between growth dynamic, level of symmetry breaking
 and calcium concentration. We identified three populations of slime molds
 within our clonal lineage with similar symmetry breaking behaviours but
 different motility characteristics. These behavioural differences between
 slime molds emerged in absence of any environmental differences. Such
 behavioural plasticity could generate cellular diversity, which might be
 critical for survival.
description: Raw
 DataRaw data of the size of
 the slime molds at each time step on each branches for each
 replicateTabGDUpload.txt