cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z08kprrg8
title: DYRK1a inhibitor mediated rescue of Drosophila models of Alzheimer’s disease-Down Syndrome phenotypes

description: Alzheimer’s disease (AD) is the most common neurodegenerative disease
 which is becoming increasingly prevalent due to ageing populations
 resulting in huge social, economic, and health costs to the community.
 Despite the pathological processing of genes such as Amyloid Precursor
 Protein (APP) into Amyloid-b and Microtubule Associated Protein Tau (MAPT)
 gene, into hyperphosphorylated Tau tangles being known for decades, there
 remains no treatments to halt disease progression. One population with
 increased risk of AD are people with Down syndrome (DS), who have a 90%
 lifetime incidence of AD, due to trisomy of human chromosome 21 (HSA21)
 resulting in three copies of APP and other AD-associated genes, such as
 DYRK1A (Dual specificity tyrosine-phosphorylation-regulated kinase 1A)
 overexpression. This suggests that blocking DYRK1A might have therapeutic
 potential. However, it is still not clear to what extent DYRK1A
 overexpression by itself leads to AD-like phenotypes and how these compare
 to Tau and Amyloid-b mediated pathology. Likewise, it is still not known
 how effective a DYRK1A antagonist may be at preventing or improving any
 Tau, Amyloid-b and DYRK1a mediated phenotype. To address these outstanding
 questions, we characterised Drosophila models with targeted overexpression
 of human Tau, human Amyloid-b or the fly orthologue of DYRK1A, called
 minibrain (mnb). We found targeted overexpression of these AD-associated
 genes caused degeneration of photoreceptor neurons, shortened lifespan, as
 well as causing loss of locomotor performance, sleep, and memory.
 Treatment with the experimental DYRK1A inhibitor PST-001 decreased
 pathological phosphorylation of human Tau (at serine (S) 262). PST-001
 reduced degeneration caused by human Tau, Amyloid-b or mnb lengthening
 lifespan as well as improving locomotion, sleep and memory loss caused by
 expression of these AD and DS genes. This demonstrated PST-001
 effectiveness as a potential new therapeutic targeting AD and DS
 pathology.
description: MS Office app
DOI: 10.5281/zenodo.18401101
title: Newick file Breve phylogeny
DOI: 10.5281/zenodo.18401102
title: Newick file Breve phylogeny
DOI: 10.25338/b8c35t
title: Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models (GC-FID dataset infant brains)

description: Maternal obesity during pregnancy is associated with neurodevelopmental
 disorder (NDD) risk. We utilized integrative multi-omics to examine
 maternal obesity effects on offspring neurodevelopment in rhesus macaques
 by comparison to lean controls and two interventions. Differentially
 methylated regions (DMRs) from longitudinal maternal blood-derived
 cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from
 infant brain. The DMRs were enriched for neurodevelopmental functions,
 methylation-sensitive developmental transcription factor motifs, and human
 NDD DMRs identified from brain and placenta. Brain and cffDNA methylation
 levels from a large region overlapping mir-663 correlated with maternal
 obesity, metabolic and immune markers, and infant behavior. A DUX4
 hippocampal co-methylation network correlated with maternal obesity,
 infant behavior, infant hippocampal lipidomic and metabolomic profiles,
 and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and
 metabolites. Ultimately, maternal obesity altered infant brain and
 behavior, and these differences were detectable in pregnancy through
 integrative analyses of cffDNA methylation with immune and metabolic
 factors.
description: Samples were analyzed on a Perkin Elmer Clarus 500 GC-FID system
 (Perkin Elmer) equipped with a DB-FFAP polyethylene glycol fused capillary
 column (30 m × 0.25 mm inner diameter, 0.25 μm film thickness; Agilent
 Technologies; 1223232). The injector and detector temperatures were 285°C
 and 300°C, respectively. The initial oven temperature was 80°C. It was
 held at 80°C for 2 min, increased by 10°C/min to 185°C, raised to 249°C at
 6°C/min and lastly held at 240°C for 44 min. The total run time was 65
 min. Helium was used as the carrier gas with a maintained flow rate of 1.3
 mL/min. The injection volume was 1 µL per sample. The split ratio was
 10:1. A custom-made mix of 29 FAME standards was used to identify each
 fatty acid based on retention time. Fatty acid concentrations were
 determined by comparing GC peak areas to the internal standard area.
 Cholesterol concentration was calculated based on a five-point standard
 curve of cholesterol and 5α-Cholestane as surrogate. The linear dynamic
 range of the calibration curve for cholesterol was 0.125 mg/mL to 2 mg/mL.
 All chromatograms were analyzed on Totalchrom Navigator Software Version
 6.3.2 and converted to pdf formats.
description: Files are in pdf format. Adobe pdf reader is required. Excel is
 used for calculation. Please copy the report containing peak area and
 retention time from each pdf file and paste to excel for further
 calculation.
DOI: 10.5061/dryad.18931zd0p
title: New insights into the formation of biodiversity hotspots of the Kenyan flora

description: Aim: Kenya intersects with the biodiversity hotspots Eastern Afromontane,
 Coastal Forests of Eastern Africa, and Horn of Africa. This study aims to
 investigate the distribution pattern of plant diversity in the low
 latitude arid area influenced by climatic fluctuation and orogeny at long
 historical period, and explore the formation of beta diversity pattern in
 Kenya. Location: Kenya, East Africa. Taxon: Angiosperms. Methods: We
 quantified patterns of turnover and nestedness components of phylogenetic
 beta diversity among neighbouring sites for angiosperm species by using a
 well-resolved phylogenetic tree and extensive distribution records from
 public database and a set of books. We applied clustering methods to do
 biota delineation based on the pairwise similarities among multiple sites,
 and used a random assembly null model to assess the effects of species
 abundance distribution on phylogenetic beta diversity. Results:
 Phylogenetic turnover for the Kenyan flora showed a non-monotonic pattern
 along the latitudinal gradient, which is strongly structured in volcanic
 and coastal areas. Whereas other areas were mainly dominated by
 phylogenetic nestedness, even in the eastern part of equatorial region
 which is parallel with volcanic area. Phylogenetic diversity and
 phylogenetic structure analyses elaborate the mechanism under the
 phylogenetic turnover or nestedness patterns we observed. We identified
 five phytogeographical regions in Kenya: the Mandera, Turkana, Volcanic,
 Pan Coastal and West Highland Regions. Conclusions: The variation extent
 of turnover gradient and the coexistence situation are highly dependent on
 the regional biogeographical history, that is, the process of climatic
 fluctuations and long-lasting orogeny jointly shaped the biodiversity
 pattern. The nestedness component dominated climatically unstable regions
 are presumed to be caused by heavy local species extinction and
 recolonization from the Volcanic Region. The high turnover component in
 climatically stable regions may preserve old lineages and the prevalence
 of endemic species within narrow ranges.
description: We quantified patterns of turnover and nestedness components of
 phylogenetic β-diversity for angiosperm species among neighbouring sites
 using a well-resolved phylogenetic tree and extensive distribution records
 from public databases and other published sources. We applied clustering
 methods to delineate biota based on pairwise similarities among multiple
 sites and used a random assembly null model to assess the effects of
 species abundance distribution on phylogenetic β-diversity.
DOI: 10.5061/dryad.pg4f4qrsr
title: Data for: Movements and residency of fin whales (Balaenoptera physalus) in the California Current System

description: This dataset represents the sighting histories of 932 individual fin
 whales (Balaentoptera physalus) photographed along the west coast of the
 continental United States and northern Mexico, 1987–2018. Because the fin
 whale is an endangered species, the sighting locations have been
 generalized. The full resolution sighting location data files and the R
 code used to conduct the analyses for the associated manuscript may be
 requested from the authors.
description: The data collection and processing methods are provided in the
 associated manuscript.
DOI: 10.5061/dryad.9p8cz8wk7
title: Data from: genetic evidence of differential dispersal pattern in Asiatic wild dog: comparing populations with different pack size and tiger densities

description: Dispersal is a multi-causal, crucial life-history event in shaping the
 genetic and behavioral structure of mammals. We assessed the dispersal
 pattern of dholes aka Asiatic wild dog (Cuon alpinus), a social monogamous
 mammal at two tiger reserves of Maharashtra with different degrees of pack
 size and competition with tigers i.e. Tadoba-Andhari (TATR, smaller pack
 size, higher tiger density) and Nawegaon-Nagzira (NNTR, larger pack size,
 lower tiger density). We used the microsatellite data of 174 individual
 genotypes (98 males and 67 females) to assess the dispersal pattern of
 dholes from two populations with varying pack size, tiger density, and
 landscape connectivity using gene flow as a proxy.  We compared
 the population structure, pairwise F statistics, assignment index, and
 relatedness across a spatial scale. Overall, the results suggested a
 difference in sex-bias dispersal pattern for the two sub-populations,
 exhibiting significant results for female-biased dispersal in the TATR
 population with a smaller pack size and higher tiger density. Our study
 highlights the variability in sex-biased dispersal patterns in two
 different populations which could be the consequence of different
 variables such as pack size, tiger density, and geographical scale. The
 study warrants further quantitative investigation including several
 factors including individual behavior, pack composition, pack size, tiger
 density, etc. In the present Anthropocene era, determining the sex bias in
 dispersal patterns for a short-range, pack-living carnivore will help in
 devising an effective conservation management plan for their long-term
 survival.
description: # Genetic evidence of differential dispersal pattern in Asiatic wild dog:
 Comparing populations with different pack size and tiger densities --- The
 files contain genotyping microsatellite dataset for the male and female
 dholes of Tadoba-Andhari Tiger Reserve and Nawegaon-Nagzira Tiger Reserve.
 ## Description of the Data and file structure The data is separated in
 four different sheets as M_TATR, F_TATR, M_NNTR and F_NNTR
DOI: 10.5061/dryad.vx0k6djvh
title: Data from: Exotic fishes that are phylogenetically close but functionally distant to native fishes are more likely to establish

description: Since Darwin’s time, the ecological similarity between exotic and native
 species has been assumed to affect the establishment success or failure of
 exotic species. However, a direct test of the effect of exotic-native
 similarity on establishment of exotics is scarce because of the difficulty
 in recognizing failures of species to establish in the field. Here, using
 a database on the establishment success and failure of exotic fish species
 introduced into 673 freshwater lakes, we evaluate the effect of similarity
 on establishment of exotic fishes by combining the phylogenetic and
 functional information. We illustrate that exotic-native phylogenetic and
 functional similarities were the most important correlates of successful
 establishment relative to other biotic and abiotic factors.
 Those exotic species phylogenetically close to, but functionally
 distant from, native fishes were most likely to establish successfully.
 Our results suggest that, while phylogenetic relatedness allows exotic
 fish species to pre-adapt better to novel environments, they need to
 possess distinct functional traits to reduce competition with resident
 fish species.
DOI: 10.5061/dryad.sn02v6x72
title: Understory plant removal counteracts tree thinning effect on soil respiration in a temperate forest

description: Elucidating the response mechanism of soil respiration (Rs) to
 silvicultural practices is pivotal to evaluating the effects of management
 practices on soil carbon cycling in planted forest ecosystems. However, as
 common management practices, how thinning, understory plant removal, and
 their interactions affect Rs and its autotrophic and heterotrophic
 components (Ra and Rh) remains unclear. Therefore, we investigated Rs, Ra
 and Rh by the trenching method from 2011 to 2015 in a Pinus tabuliformis
 plantation in northern China, subjecting to four treatments [intact
 control plots (CK), thinning (T), understory removal (UR), and thinning
 with understory removal (TUR)]. Mean annual Rs was significantly increased
 by thinning (by 15.3%), whereas decreased by UR (by 17.4%), compared with
 CK. These variations in Rs were mainly attributed to changes in Ra. The
 increments of Ra were caused by the enhanced growth of fine root biomass
 after thinning. However, UR led to lower Ra compared with CK (P &lt;
 0.05), indicating that understory growth is inadequate to compensate for
 the decreased respiring root biomass induced by understory removal. Rs was
 unchanged between TUR and the intact control plot due to the opposite
 effects of thinning and UR on the Ra. Changes in Rh exhibited no
 significant differences among the treatments, partly because of the stable
 microbial biomass carbon (MBC) and forest floor mass (litter and fine
 woody debris). No interaction effect between thinning and understory
 removal was detected on Rs, Ra and Rh. The lowest temperature sensitivity
 (Q10) value of Ra was found in CK. This study highlights the necessity of
 incorporating understory plant effects on soil CO2 efflux in assessing
 forest management practices on soil carbon cycling.
DOI: 10.5061/dryad.fj6q573xz
title: SSR data of Plutella xylostella samples collected from Southern China and Southeast Asia

description: Genetic makeup of insect pest is informative for source-sink
 dynamics, spreading of resistant genes, and effective management. However,
 collecting samples from geographical populations without
 considering temporal resolution and calculating parameters
 related to historical gene flow may not
 capture contemporary genetic pattern
 and metapopulation dynamics of highly dispersive pests.
 Plutella xylostella (L.), the most widely distributed
 Lepidopteran pest that developed resistance to almost all current
 insecticides, migrates heterogeneously across space and time. To
 investigate its real-time genetic pattern and dynamics,
 we executed four samplings over two
 consecutive years across Southern China and Southeast Asia, and
 constructed population network based on contemporary gene flow. Across
 48 populations, genetic structure analysis identified
 two differentiated insect swarms, of which the one with higher genetic
 variation was replaced by the other over time. We further inferred gene
 flow by estimation of kinship relationship and constructed
 migration network in each sampling time. Interestingly,
 we found mean migration distance at around 1000 km. Such
 distance might have contributed to the formation of
 step-stone migration and migration circuit over large geographical
 scale. Probing network clustering across sampling times,
 we found a dynamic metapopulation of P. xylostella with
 more active migration in spring than in winter,
 and identified some regions are
 consistent sources (e.g., Yunnan in China, Myanmar and
 Vietnam) while several others are persistent sinks (e.g.,
 Guangdong and Fujian in China) in its
 overwintering regions. Rapid turnover of insect swarms and highly
 dynamic metapopulation highlight the importance of temporal sampling and
 network analysis in investigation of
 source-sink relationships and thus effective pest management.
DOI: 10.5061/dryad.hmgqnk9kr
title: Cereal legume intercropping studies in Malawi

description: Innovations in Technology, Institutional and Extension Approaches towards
 Sustainable Agriculture and enhanced Food and Nutritional Security in
 Africa (InnovAfrica), a European Commission funded project validated and
 upscaled cereal legume intercropping technology in Dedza and Mzimba
 districts of Malawi involving farmers in between year 2017 and 2020. The
 results from the intercropping experiment of three cereals (maize,
 sorghum, and finger millet) and various legume species (pigeonpea,
 soyabeans, Bambara nut, groundnut, cowpea, and common beans) are presented
 in this data set.
description: Three cereal crops; maize, sorghum, and finger millet and various
 legume species; including pigeonpea, soyabeans, Bambara nut, groundnut,
 cowpea, and common beans were tested using different farming practices in
 farmer’s fields of Dedza and Mzimba districts of Malawi. The performance
 data of different cereal-legume intercropping systems were recorded. Field
 data were collected on paper and latter entered into computer using
 Microsoft Excel and reviewed for accurateness.
description: Microsoft Excel. There is no restriction for this data use.
DOI: 10.5061/dryad.1g1jwsv0d
title: Haemosporidian parasites and incubation period influence plumage coloration in tanagers (Passeriformes: Thraupidae)

description: Birds are visually oriented and use their plumage coloration as an
 important signaling trait in social communication. Males and females may
 have different patterns of plumage coloration, a phenomenon known as
 sexual dichromatism. Because males tend to have more complex plumages,
 sexual dichromatism is usually attributed to female choice. However,
 plumage coloration is partly condition-dependent, therefore other
 selective pressures affecting individuals’ success may also drive the
 evolution of this trait. Here we used tanagers to study the relationships
 between dichromatism and plumage coloration complexity with parasitism by
 haemosporidians, investment in reproduction, and life-history traits. We
 screened blood samples from 2849 birds belonging to 52 tanager species for
 detecting haemosporidian parasites. We used publicly available data for
 plumage coloration, bird phylogeny, and life-history traits to run models
 with plumage dichromatism and complexity in males and females. We found
 that dichromatism was more pronounced in bird species with higher
 prevalence of haemosporidian parasites. Lastly, females with high plumage
 coloration complexity were associated with a longer incubation period. Our
 results indicate an association between haemosporidian parasites and
 plumage coloration suggesting that parasites impact mechanisms of both
 sexual selections, increasing differences between sexes, and social
 (non-sexual) selection, driving females to develop more complex
 colorations. 
description: We have screened 4234 individuals from 53 species (all belonging
 to the Thraupidae family) for the presence of hemosporidian parasites
 (Order Haemosporidae, genera <em>Plasmodium</em> and
 <em>Parahaemoproteus</em>). First, we performed PCR to
 identify the status of infection of each individual by amplyfing a barcode
 region of the cytochrome b. We then used BIOEDIT v.7.2.0 to alling
 sequences and compare them with the MalAvi database. Finally, we used the
 number of lineages and weighted it by the number of captures per species
 as our variable "lineage richness". The haemosporidian parasite
 prevalence (<em>Plasmodium</em> and
 <em>Parahaemoproteus</em>) was the number of infected
 individuals divided by the total capture individuals as well.
description: All analysis can be performed in the R software.
DOI: 10.5061/dryad.00000005x
title: Reproductive maturity in boreal trees, Northwest Territories, Canada

description: In boreal North America, much of the landscape is covered by fire-adapted
 forests dominated by serotinous conifers. For these forests, reductions in
 fire return interval could limit reproductive success, owing to
 insufficient time for stands to reach reproductive maturity i.e., to
 initiate cone production. Improved understanding of the drivers of
 reproductive maturity can provide important information about the capacity
 of these forests to self-replace following fire. Here, we assessed the
 drivers of reproductive maturity in two dominant and widespread conifers,
 semi-serotinous black spruce and serotinous jack pine. Presence or absence
 of female cones were recorded in approximately 15,000 individuals within
 old and recently burned stands in two distinct ecozones of the Northwest
 Territories (NWT), Canada. Our results show that reproductive maturity was
 triggered by a minimum tree size threshold rather than an age threshold,
 with trees reaching reproductive maturity at smaller sizes where
 environmental conditions were more stressful. The number of reproductive
 trees per plot increased with stem density, basal area, and at higher
 latitudes (colder locations). The harsh climatic conditions present at
 these higher latitudes, however, limited the recruitment of jack pine at
 the treeline ecotone. The number of reproductive black spruce trees
 increased with deeper soils, whereas the number of reproductive
 jack pine trees increased where soils were shallower. We examined the
 reproductive efficiency i.e., the number of seedlings recruited
 per reproductive tree, linking pre-fire reproductive maturity of recently
 burned stands and post-fire seedling recruitment (recorded up to 4 years
 after the fires) and found that a reproductive jack pine can
 recruit on average three times more seedlings than a reproductive black
 spruce. We suggest that the higher reproductive efficiency of jack pine
 can explain the greater resilience of this species to wildfire compared
 with black spruce. Overall, these results help link life history
 characteristics such as reproductive maturity to variation in post-fire
 recruitment of dominant serotinous conifers.
description: Methodology is available in : Alfaro-Sánchez
 R, Johnstone JF, Cumming SG, Day N, Mack MC, Walker XJ and Baltzer JL
 (2022) What Drives Reproductive Maturity and Efficiency in Serotinous
 Boreal Conifers? Front. Ecol. Evol. 10:869130. doi:
 10.3389/fevo.2022.869130
description: This dataset can be open in excel.