cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9k0v2nn
title: Data from: Combining micro-volume isotope analysis and numerical simulation to reproduce fish migration history

description: 1. Tracking the movement of migratory fish is of great importance for
 efficient conservation, although this has been technically difficult to
 achieve in small fish to which artificial tags cannot be attached. 2. We
 show that migration history can be reproduced by combining high-resolution
 otolith stable oxygen isotope ratio (δ18O) analysis and numerical
 simulation. 3. High-precision micro-milling and micro-volume carbonate
 analysing systems had the remarkable capability of extracting the otolith
 δ18O profiles with 10–30 days resolution. Furthermore, reasonable
 movements were reproduced by searching the routes consistent with the
 otolith δ18O profile, using an individual-based model with random swimming
 behaviour. 4. This method will be a valuable alternative to tagging and
 electronic loggers for revealing migration routes in early life stages,
 thereby providing crucial information to understand population structures
 and the environmental cause of recruitment variabilities, and to validate
 and improve fish movement models.
description: Otolith
 d18OThis file contains
 hatched date, capture date, captured location and otolith δ18O profile of
 the six Japanese sardine individuals that have used in the modelling
 study.Seawater
 d18OThis file contains the
 surface seawater δ18O in the Kuroshio-Oyashio system together with
 sampling date, location and CTD measured salinity at 5 or 10m
 depth.
DOI: 10.5061/dryad.10n4r3g
title: Data from: Effect of aerobic exercise on cognition in younger adults: a randomized clinical trial

description: Objective: To determine efficacy of aerobic exercise for cognitive
 function in younger healthy adults. Methods: In a randomized,
 parallel-group, observer-masked, community-based clinical trial, 132
 cognitively normal individuals aged 20-67 with below median aerobic
 capacity were randomly assigned to one of two 6-month, four-times-weekly
 conditions: aerobic exercise and stretching/toning. Efficacy measures
 included: aerobic capacity; cognitive function in six domains (executive
 function, episodic memory, processing speed, language, and attention),
 everyday function, BMI and cortical thickness. Results: Aerobic capacity
 increased significantly (β=2.718; p=0.003), and BMI decreased
 significantly (β=-0.596; p=0.013) in the aerobic exercise but not in the
 stretching/toning condition. Executive function improved significantly in
 the aerobic exercise condition; this effect was moderated by age (β=0.018
 s.d. per year; p=0.028). At age 40 the executive function measure
 increased by 0.228 s.d. (95% CI: 0.007 - 0.448), and by 0.596 s.d. (95%
 CI: 0.219 - 0.973) at age 60. Cortical thickness increased significantly
 in the aerobic exercise group in a left frontal region and did not
 interact with age. Controlling for age and baseline performance,
 individuals with at least one APOE ε4 allele showed less improvement in
 executive function with aerobic exercise (β=0.5129, 95%CI 0.0381 to 0.988;
 p=0.0346). Conclusions: This randomized clinical trial demonstrates the
 efficacy of aerobic exercise for cognition in adults age 20 – 67. The
 effect of aerobic exercise on executive function was more pronounced as
 age increased, suggesting that it may mitigate age-related declines.
 Increased cortical thickness suggests that aerobic exercise contributes to
 brain health in individuals as young as age 20. Clinicaltrials.gov
 Identifier: NCT01179958 Classification of evidence: This study provides
 Class II evidence that for adults age 20-67 with below median aerobic
 capacity, aerobic exercise significantly improves executive function but
 not other measures of cognitive function.
description: Supplementary Tables and
 FigureSupplementaery Tables
 and Figure
DOI: 10.5061/dryad.73b9h
title: Data from: Genetic diversity, sexual condition, and microhabitat preference determine mating patterns in Sphagnum (Sphagnaceae) peat-mosses.

description: In bryophytes, the possibility of intragametophytic selfing creates
 complex mating patterns that are not possible in seed plants, although
 relatively little is known about patterns of inbreeding in natural
 populations. In the peat-moss genus Sphagnum, taxa are generally bisexual
 (gametophytes produce both sperm and egg) or unisexual (gametes produced
 by separate male and female plants). We sampled populations of 14 species,
 aiming to assess inbreeding variation and inbreeding depression in
 sporophytes, and to evaluate correlations between sexual expression,
 mating systems, and microhabitat preferences. We sampled maternal
 gametophytes and their attached sporophytes at 12–19 microsatellite loci.
 Bisexual species exhibited higher levels of inbreeding than unisexual
 species but did generally engage in some outcrossing. Inbreeding
 depression did not appear to be common in either unisexual or bisexual
 species. Genetic diversity was higher in populations of unisexual species
 compared to populations of bisexual species. We found a significant
 association between species microhabitat preference and population genetic
 diversity: species preferring hummocks (high above water table) had
 populations with lower diversity than species inhabiting hollows (at the
 water table). We also found a significant interaction between sexual
 condition, microhabitat preference, and inbreeding coefficients,
 suggesting a vital role for species ecology in determining mating patterns
 in Sphagnum populations.
description: Population Allele Tables
 and Sporophyte SizesMicrosatellite allele
 tables for all sporophytes used in the mating systems study, one text file
 per population. The size (in micrometers) of each sporophyte is listed, as
 well as the identity of the maternal and paternal clone via the paternity
 script (see text). More information about each population (such as
 lat/long coordinates) can be found in the Appendix to the main
 text.Allele_Tables.zip
DOI: 10.5061/dryad.670
title: Data from: Repeated Evolution of Dioecy from Monoecy in Siparunaceae (Laurales)

description: Siparunaceae comprise Glossocalyx with one species in West Africa and
 Siparuna with 65 species in the neotropics; all have unisexual flowers,
 and 15 species are monoecious, 50 dioecious. Parsimony and maximum
 likelihood analyses of combined nuclear ribosomal ITS and chloroplast
 trnL-trnF intergenic spacer sequences yielded almost identical topologies,
 which were used to trace the evolution of the two sexual systems. The
 African species, which is dioecious, was sister to all neotropical
 species, and the monoecious species formed a grade basal to a large
 dioecious Andean clade. Dioecy evolved a second time within the monoecious
 grade. Geographical mapping of 6,496 herbarium collections from all
 species sorted by sexual system showed that monoecy is confined to
 low-lying areas (altitude &lt; 700 m) in the Amazon basin and southern
 Central America. The only morphological trait with a strong phylogenetic
 signal is leaf margin shape (entire or toothed), although this character
 also correlates with altitude, probably reflecting selection on leaf
 shapes by temperature and rainfall regimes. The data do not reject the
 molecular clock, and branch lengths suggest that the shift to dioecy in
 the lowlands occurred many million years after the shift to dioecy in the
 ancestor of the Andean clade.
description: Renner and Won Data
 SetRenner.nexus
DOI: 10.5061/dryad.5hb0fb8
title: Data from: Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers

description: Quantitative information regarding reproduction is essential for
 conserving endangered animals; however, some conventional quantitative
 methods can be damaging to the target population and their habitats. In
 the present study, the reproductive migration of a threatened endemic
 fish, three-lips (Opsariichthys uncirostris uncirostris), was
 non-invasively monitored by quantitative PCR of species-specific
 environmental DNA (eDNA), the usefulness of which has been under-studied.
 Water sampling and from-shore visual inspection were performed weekly
 along a tributary of Lake Biwa (Japan), where adult fish seasonally
 migrate upstream to reproduce as well as at lake sites near the river
 mouth. Species-specific eDNA was collected at all locations at times when
 the fish were visually observed and at certain sites where the fish were
 not observed. Log-transformed individual counts from visual inspection
 were positively correlated with log-transformed eDNA concentration in the
 river sites, indicating that eDNA analysis can be a reliable quantitative
 tool for fish abundance in rivers. Furthermore, distance from the lake did
 not influence eDNA concentration, suggesting that eDNA transport by river
 flow had a negligible effect on eDNA quantification. eDNA concentration
 and individual counts both gradually increased from May–July, then both
 decreased in August. Importantly, eDNA analysis showed that the fish
 occupied more habitats in the peak reproductive season and stayed for
 longer time at any given site. An additional underwater survey confirmed
 unexpected eDNA detections as true positives. eDNA analysis has great
 potential to quantitatively monitor reproductive fish migrations under
 certain conditions.
description: eDNA conc. and field
 data for each eDNA samplingeDNA concentrations and
 visual inspection results together with other field data including pH,
 temperature, depth, velocity etc. for each threelips eDNA sampling along
 Chinai River, central JapanqPCReDNA_ChinaiThreelips.csv
DOI: 10.6084/m9.figshare.31111802
title: A review of e-cigarettes and their effects on DNA methylation in human studies

description: The effects of conventional cigarette (c-cig) use on DNA methylation are well established, but the impact of electronic cigarettes (e-cigs) remains unclear. Objective: This scoping review aimed to map and synthesize available evidence regarding the effects of e-cig use on DNA methylation profiles in human studies. Methods: PubMed, Lilacs, Scopus, Web of Science and Cochrane were searched using terms related to e-cigs and DNA methylation up to April 2025. Seven studies were included, analyzing samples from saliva, peripheral blood, and bronchial epithelial tissue. The findings indicate that e-cig use is associated with changes in DNA methylation profiles compared to nonsmokers, with alterations observed in global methylation, specific sites, and epigenetic aging markers (GrimAge). Some methylation changes were shared with c-cig users, while others appeared unique to e-cig exposure. The heterogeneity of study designs, exposure duration, and biological samples precludes definitive conclusions regarding the magnitude and clinical relevance of these changes. E-cig use is associated with distinct alterations in DNA methylation in multiple human tissues, some of which are unique compared to conventional cigarettes. Further research is needed to clarify the long-term implications and potential health risks of these epigenetic changes. An electronic cigarette is a device that heats a liquid containing nicotine, flavorings, and other substances to produce an inhaled aerosol rather than smoke. Use of electronic cigarettes has increased significantly in recent years, particularly among young people. Electronic cigarettes emerged as an alternative for traditional cigarette smokers to reduce their intake of toxic substances. However, studies show that electronic cigarettes also contain toxic substances and can be addictive. Their use has become a major public health issue, as many users have experienced heart, mouth, lung, and brain problems. These health issues may result from the ability of electronic cigarette substances to cause changes in molecules within our cells, such as DNA (our genetic material). Alterations in these molecules can disrupt the functioning of our body’s cells, leading to disease. This study showed that e-cigarette users do exhibit changes in their DNA molecules compared to nonsmokers. Notably, some of these changes found in electronic cigarette users are also present in conventional cigarette users. This finding demonstrates that electronic cigarettes are not harmless and their use can lead to diseases in the mouth and throughout the body.
DOI: 10.6084/m9.figshare.31111802.v1
title: A review of e-cigarettes and their effects on DNA methylation in human studies

description: The effects of conventional cigarette (c-cig) use on DNA methylation are well established, but the impact of electronic cigarettes (e-cigs) remains unclear. Objective: This scoping review aimed to map and synthesize available evidence regarding the effects of e-cig use on DNA methylation profiles in human studies. Methods: PubMed, Lilacs, Scopus, Web of Science and Cochrane were searched using terms related to e-cigs and DNA methylation up to April 2025. Seven studies were included, analyzing samples from saliva, peripheral blood, and bronchial epithelial tissue. The findings indicate that e-cig use is associated with changes in DNA methylation profiles compared to nonsmokers, with alterations observed in global methylation, specific sites, and epigenetic aging markers (GrimAge). Some methylation changes were shared with c-cig users, while others appeared unique to e-cig exposure. The heterogeneity of study designs, exposure duration, and biological samples precludes definitive conclusions regarding the magnitude and clinical relevance of these changes. E-cig use is associated with distinct alterations in DNA methylation in multiple human tissues, some of which are unique compared to conventional cigarettes. Further research is needed to clarify the long-term implications and potential health risks of these epigenetic changes. An electronic cigarette is a device that heats a liquid containing nicotine, flavorings, and other substances to produce an inhaled aerosol rather than smoke. Use of electronic cigarettes has increased significantly in recent years, particularly among young people. Electronic cigarettes emerged as an alternative for traditional cigarette smokers to reduce their intake of toxic substances. However, studies show that electronic cigarettes also contain toxic substances and can be addictive. Their use has become a major public health issue, as many users have experienced heart, mouth, lung, and brain problems. These health issues may result from the ability of electronic cigarette substances to cause changes in molecules within our cells, such as DNA (our genetic material). Alterations in these molecules can disrupt the functioning of our body’s cells, leading to disease. This study showed that e-cigarette users do exhibit changes in their DNA molecules compared to nonsmokers. Notably, some of these changes found in electronic cigarette users are also present in conventional cigarette users. This finding demonstrates that electronic cigarettes are not harmless and their use can lead to diseases in the mouth and throughout the body.
DOI: 10.6084/m9.figshare.30902699
title: Emerging roles of RNA modifications in normal development and congenital craniofacial malformations

description: RNA modifications represent a pivotal epitranscriptomic layer modulating gene expression beyond the classic central dogma. Increasing studies have revealed their essential roles in orchestrating mammalian development and contributing to congenital disorders. In this review, we focus on seven well-characterized RNA modifications, including N<sup>6</sup>-methyladenosine(m<sup>6</sup>A), N<sup>1</sup>-methyladenosine(m<sup>1</sup>A), 5-methylcytosine (m<sup>5</sup>C), N<sup>4</sup>-acetylcytosine (ac<sup>4</sup>C), N<sup>7</sup>-methylguanosine (m<sup>7</sup>G), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I) editing, and briefly introduce emerging marks like N<sup>1</sup>-methylguanosine at position 9 (m<sup>1</sup>G9) and N<sup>2</sup>-methylguanosine (m<sup>2</sup>G). We first summarize their distribution patterns and regulatory mechanisms. Then, we examine their stage-specific functions during early embryogenesis, from fertilization to post-implantation. Further, we integrate current evidence linking RNA modifications to craniofacial development, categorized into system-associated and localized craniofacial malformations. Special attention is given to their crosstalk with chromatin dynamics and neural crest cell plasticity. Finally, we discuss their potential as environmental sensors and therapeutic targets, emphasizing the need to decode their roles in craniofacial morphogenesis. Understanding the mechanistic roles of RNA modifications in craniofacial morphogenesis opens new avenues for uncovering disease etiology, discovering diagnostic biomarkers, and designing targeted therapies. A structured literature review using PubMed and Web of Science was performed, using keywords like RNA modifications, craniofacial malformations and epitranscriptomics.
DOI: 10.6084/m9.figshare.30902699.v1
title: Emerging roles of RNA modifications in normal development and congenital craniofacial malformations

description: RNA modifications represent a pivotal epitranscriptomic layer modulating gene expression beyond the classic central dogma. Increasing studies have revealed their essential roles in orchestrating mammalian development and contributing to congenital disorders. In this review, we focus on seven well-characterized RNA modifications, including N<sup>6</sup>-methyladenosine(m<sup>6</sup>A), N<sup>1</sup>-methyladenosine(m<sup>1</sup>A), 5-methylcytosine (m<sup>5</sup>C), N<sup>4</sup>-acetylcytosine (ac<sup>4</sup>C), N<sup>7</sup>-methylguanosine (m<sup>7</sup>G), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I) editing, and briefly introduce emerging marks like N<sup>1</sup>-methylguanosine at position 9 (m<sup>1</sup>G9) and N<sup>2</sup>-methylguanosine (m<sup>2</sup>G). We first summarize their distribution patterns and regulatory mechanisms. Then, we examine their stage-specific functions during early embryogenesis, from fertilization to post-implantation. Further, we integrate current evidence linking RNA modifications to craniofacial development, categorized into system-associated and localized craniofacial malformations. Special attention is given to their crosstalk with chromatin dynamics and neural crest cell plasticity. Finally, we discuss their potential as environmental sensors and therapeutic targets, emphasizing the need to decode their roles in craniofacial morphogenesis. Understanding the mechanistic roles of RNA modifications in craniofacial morphogenesis opens new avenues for uncovering disease etiology, discovering diagnostic biomarkers, and designing targeted therapies. A structured literature review using PubMed and Web of Science was performed, using keywords like RNA modifications, craniofacial malformations and epitranscriptomics.
DOI: 10.6084/m9.figshare.30997902
title: Circulating histones as potential biomarkers of MASLD-MASH-HCC progression

description: Reliable biomarkers are warranted to identify patients with metabolic dysfunction-associated steatotic liver disease (MASLD), including metabolic dysfunction-associated steatohepatitis (MASH), at risk for developing hepatocellular carcinoma (HCC). We evaluated whether circulating histones can predict this risk. Plasma histones were measured using imaging flow cytometry in patients with MASLD (n = 25), MASH (n = 25), HCC (n = 40), and 30 healthy controls. We detected (<i>p</i> &lt; 0.05), compared to controls: 1) elevated levels of H2A, H3, H2A/H2B/H3/H4, macroH2A1.1, macroH2A1.2 in MASLD/MASH and HCC; 2) decreased levels of macroH2A1.2/H2B/H3/H4 in MASLD/MASH and increased in HCC; 3) reduced H4 levels discriminating between MASH and non-MASH. Machine-learning analysis showed that being diabetic/dyslipidemic, having decreased H2A (<i>p</i> = 0.002) and H4 (<i>p</i> = 0.0156) levels favor MASH. Our data indicate plasma histones H2A and H4 as new biomarkers of liver disease progression. The identification of histone-based biomarkers using imaging flow cytometry could provide a rapid approach to discriminate between non-MASH and MASH, and to predict the risk of HCC development. Patients with fatty liver disease linked to metabolism (MASLD or its more severe inflammatory form MASH) need better ways to spot who might later develop liver cancer (HCC). In this study, we measured different types of histones (proteins that bind our DNA and then float in the blood if cells die) using a special imaging technique in 25 people with MASLD, 25 with MASH, 40 with HCC, and 30 healthy people. We found clear differences: several histones and histone complexes were higher in all patient groups than in healthy controls. Some histone levels were lower in MASLD/MASH but rose again in HCC, while histone H4 was particularly low in MASH and helped tell MASH apart from milder disease. Using machine learning, the strongest signals for having MASH (rather than a simpler fatty liver) were diabetes or high blood fats combined with lower circulating histones H2A and H4. Overall, blood levels of histones H2A and H4 look like promising new markers to track how serious the liver disease is, distinguish MASH from less severe forms, and possibly predict who will go on to develop liver cancer. This histone test is fast and could be useful in everyday practice.
DOI: 10.6084/m9.figshare.30997902.v1
title: Circulating histones as potential biomarkers of MASLD-MASH-HCC progression

description: Reliable biomarkers are warranted to identify patients with metabolic dysfunction-associated steatotic liver disease (MASLD), including metabolic dysfunction-associated steatohepatitis (MASH), at risk for developing hepatocellular carcinoma (HCC). We evaluated whether circulating histones can predict this risk. Plasma histones were measured using imaging flow cytometry in patients with MASLD (n = 25), MASH (n = 25), HCC (n = 40), and 30 healthy controls. We detected (<i>p</i> &lt; 0.05), compared to controls: 1) elevated levels of H2A, H3, H2A/H2B/H3/H4, macroH2A1.1, macroH2A1.2 in MASLD/MASH and HCC; 2) decreased levels of macroH2A1.2/H2B/H3/H4 in MASLD/MASH and increased in HCC; 3) reduced H4 levels discriminating between MASH and non-MASH. Machine-learning analysis showed that being diabetic/dyslipidemic, having decreased H2A (<i>p</i> = 0.002) and H4 (<i>p</i> = 0.0156) levels favor MASH. Our data indicate plasma histones H2A and H4 as new biomarkers of liver disease progression. The identification of histone-based biomarkers using imaging flow cytometry could provide a rapid approach to discriminate between non-MASH and MASH, and to predict the risk of HCC development. Patients with fatty liver disease linked to metabolism (MASLD or its more severe inflammatory form MASH) need better ways to spot who might later develop liver cancer (HCC). In this study, we measured different types of histones (proteins that bind our DNA and then float in the blood if cells die) using a special imaging technique in 25 people with MASLD, 25 with MASH, 40 with HCC, and 30 healthy people. We found clear differences: several histones and histone complexes were higher in all patient groups than in healthy controls. Some histone levels were lower in MASLD/MASH but rose again in HCC, while histone H4 was particularly low in MASH and helped tell MASH apart from milder disease. Using machine learning, the strongest signals for having MASH (rather than a simpler fatty liver) were diabetes or high blood fats combined with lower circulating histones H2A and H4. Overall, blood levels of histones H2A and H4 look like promising new markers to track how serious the liver disease is, distinguish MASH from less severe forms, and possibly predict who will go on to develop liver cancer. This histone test is fast and could be useful in everyday practice.