cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hx3ffbggd
title: Data from: A millennium of climatic and floristic dynamics in the Eastern Cordillera of the Colombian Andes

description: The transition from the Medieval Climate Anomaly (MCA, 950-1250 CE) to the
 Little Ice Age (LIA, 1350 to 1800 CE) is the largest pre-industrial
 climate shift within the last two millennia, offering an opportunity to
 study how vegetation responds to rapid climate change. We analyzed a
 sedimentary record from the Colombian Andes to reconstruct regional
 vegetation dynamics during this time interval, identify the modern
 environmental distribution of taxa present in the fossil record, and
 provide a reference for modern regional temperature change. A sediment
 core was analyzed for organic geochemistry and pollen to reconstruct
 environmental and vegetation variability between 800 and 1800 CE. Modern
 occurrences of individuals of the genera found in the fossil record were
 used to model the distribution of taxa across gradients of mean annual
 temperature and precipitation. These models were used to reconstruct
 temperature and precipitation across time and evaluate the probability of
 occurrence of taxa from the fossil record across the contemporary
 landscape.  Reconstructed regional vegetation dynamics
 were highly coupled with global temperature patterns. Reconstructed
 climate showed that conditions were warm and dry during the MCA, and cold
 and relatively wet during the LIA, although quantitative estimations might
 have been amplified by human disturbances. Rates of temperature change
 during the MCA-LIA transition were substantially lower than those
 calculated for the last two decades. Vegetation turnover between 800 and
 1800 CE resembled those expressed through a transect extending ~30 km
 southeast from the lake. Around lake Tota, modern rates of temperature
 change have no precedent within the last two millennia. The modern
 environmental affinities of taxa involved in vegetation turnover during
 the MCA-LIA transition point to the importance of landscape diversity and
 connectivity for rapid vegetation response to climate change.
description: Twenty samples spread along a
 40-cm sediment core from Lake Tota, Esatern Cordillera of Colombia, were
 analyzed for palynological content. Samples were prepared according to
 standard protocols. Pollen counts were carried out under transmitted light
 microscope at x400 and x1000 magnifications, aiming at a pollen count of
 250 grains per sample.
description: Pollen taxa are in columns and samples in rows with sampled depth
 and estimated age in both Common Era (CE) and Before Present
 (BP).
DOI: 10.5061/dryad.7m0cfxpwk
title: Cluster investigation results from model-predicted mountain lion feeding sites and non-predicted sites in southwest Wyoming

description: Global positioning system (GPS) receivers allow researchers to collect
 location data that provide information about fine-scale animal movements.
 For large carnivores, these data are routinely processed to identify
 clusters of GPS locations which are investigated to validate feeding
 sites, estimate prey species composition, and model the likelihood of
 predation events based on characteristics of GPS location data within
 clusters. Although developing predation models entails a high level of
 field effort, researchers are apprehensive in applying system-specific
 models to other systems both spatially and temporally. Our objectives were
 to apply and compare multiple predation models to predict and identify
 feeding events outside of the geographic areas where models were
 developed. Using our multi-model approach, we identified feeding sites and
 estimated kill rates and prey composition of mountain lions (Puma
 concolor) in southwest Wyoming, USA from 2017 to 2019. Our approach
 increased our field efficiency by reducing potential field site
 investigations by 63%. We provide results of estimated diet composition in
 our study area where mountain lion prey included relatively high
 proportions of pronghorn (12.3%) and smaller mammals, particularly coyotes
 (7.6%). We also provide a comparison of the predation models developed
 across unique ecoregions of North America, and how they performed when
 applied to our area. We believe a similar approach could be adopted for
 other large carnivore populations where multiple models have been
 developed to characterize feeding events.
description: Data includes model-predicted predation sites that were
 investigated for feeding events, and non-predicted clusters used to
 validate multimodel performance.
DOI: 10.5061/dryad.3tx95x6hx
title: Supplementary material for: nQMaker: estimating time non-reversible amino acid substitution models

description: Amino acid substitution models are a key component in phylogenetic
 analyses of protein sequences. All commonly-used amino acid models
 available to date are time-reversible, an assumption designed for
 computational convenience but not for biological reality. Another
 significant downside to time-reversible models is that they do not allow
 inference of rooted trees without outgroups. In this paper, we introduce a
 maximum likelihood approach nQMaker, an extension of the recently
 published QMaker method, that allows the estimation of time non-reversible
 amino acid substitution models and rooted phylogenetic trees from a set of
 protein sequence alignments. We show that the non-reversible models
 estimated with nQMaker are a much better fit to empirical alignments than
 pre-existing reversible models, across a wide range of datasets including
 mammals, birds, plants, fungi, and other taxa, and that the improvements
 in model fit scale with the size of the dataset. Notably, for the recently
 published plant and bird trees, these non-reversible models correctly
 recovered the commonly estimated root placements with very high
 statistical support without the need to use an outgroup. We provide
 nQMaker as an easy-to-use feature in the IQ-TREE software
 (http://www.iqtree.org), allowing users to estimate non-reversible models
 and rooted phylogenies from their own protein datasets.
DOI: 10.5061/dryad.31zcrjdnj
title: Microhabitat use, daily activity pattern and diet of Liolaemus etheridgei in the Andean Polylepis forests of Arequipa, Peru

description: This study describes the microhabitat use, daily activity pattern and diet
 of Liolaemus etheridgei Laurent 1998
 in the El Simbral and
 Tuctumpaya Polylepis forests in Arequipa, Peru. El
 Simbral is a fragmented forest, whereas Tuctumpaya is
 unfragmented. Our results reveal that L.
 etheridgei shows no positive selection for any of the
 microhabitats we identified in Polylepis forests; on the
 contrary, it selects negatively against Polylepis trees
 and non-thorny bushes. The daily activity patterns indicate a bimodal
 pattern with peaks at 9:00-10:59 and 13:00-13:59 h. The diet
 of L. etheridgei consists mainly of plant material, and
 the most important animal prey category is Lygaeidae: Hemiptera, which is
 selected for positively. In particular, microhabitat
 selection varied for non-thorny bushes, which were
 selected negatively in the Tuctumpaya population but neither positively
 nor negatively in the El Simbral population. According to the proportions
 of plant material found, the L. etheridgei from El
 Simbral were found to be omnivorous, whereas the Tuctumpaya
 population washerbivorous. However, the percentage
 of plant material consumed in the El
 Simbral population was close to the critical value for
 herbivory-omnivory. We conclude that the three ecological
 aspects of L.
 etheridgei studied here are virtually
 identical in El Simbral and Tuctumpaya;
 therefore, this species is not affected significantly by
 the current fragmentation of forest.
DOI: 10.5061/dryad.j9kd51cfd
title: Data from: Identification and protection of puce unlined clothing with printed gold and color-painted lace

description: A large number of Southern Song Dynasty costumes were unearthed from
 Huangsheng Tomb in Fuzhou city, Fujian Province. The unlined clothing was
 among funeral objects, and was made of the most common leno fabric, which
 was light and transparent, and the clothing was in extremely poor
 condition. To protect the unlined clothing, scientific evaluation and
 protection were carried out. Three-dimensional microscopy was used to
 analyze the weave structure and X-ray fluorescence spectroscopy (XRF) and
 indirect enzyme-linked immunosorbent assay (iELISA) were used to
 scientifically analyze the printed gold and color paint components of the
 unlined clothing. The results showed that the structure of the unlined
 clothing was a two-warp twisted leno, the printed gold contained Au, Cu,
 Fe and other elements, the colored paint contained Pb and Hg elements, and
 the binding material component of the colored paint was type I collagen.
 Based on the results of the analysis, the silk fibroin consolidation
 method was used to improve resistance to the stress and strain caused by
 the needle-thread repair method, and the needle-thread repair method was
 then used to restore the original clothing shape. This study provides a
 new approach for the protection of fragile silk fabrics in the future.
DOI: 10.5061/dryad.qnk98sfjn
title: Prevalence, severity, and risk factors of disability among adults living with HIV accessing routine outpatient HIV care in London, United Kingdom (UK): A cross-sectional self-report study

description: Background The study objectives were to measure disability prevalence and
 severity, and examine disability risk factors, among adults living with
 HIV in London, United Kingdom (UK). Methods Self-reported questionnaires
 were administered: World Health Organization Disability Assessment
 Schedule 2.0 (WHODAS), HIV Disability Questionnaire (HDQ), Equality Act
 disability definition (EADD), and demographic questionnaire. We calculated
 proportion (95% Confidence Interval; CI) of “severe” and “moderate”
 disability measured using EADD and WHODAS scores ≥2 respectively. We
 measured disability severity with HDQ domain severity scores. We used
 demographic questionnaire responses to assess risk factors of “severe” and
 “moderate” disability using logistic regression analysis, and HDQ severity
 domain scores using linear regression analysis. Results Of 201
 participants, 176 (87.6%) identified as men, median age 47 years, and 194
 (96.5%) virologically suppressed. Severe disability prevalence was 39.5%
 (n=79/201), 95% CI [32.5%, 46.4%]. Moderate disability prevalence was
 70.5% (n=141/200), 95% CI [64.2%, 76.8%]. Uncertainty was the most severe
 HDQ disability domain. Late HIV diagnosis was a risk factor for severe
 disability [Odds Ratio (OR) 2.71; CI 1.25, 5.87]. Social determinants of
 health, economic inactivity [OR 2.79; CI 1.08, 7.21] and receiving
 benefits [OR 2.87; CI 1.05, 7.83], were risk factors for “severe”
 disability. Economic inactivity [OR 3.14; CI 1.00, 9.98] was a risk factor
 for “moderate” disability. Economic inactivity, receiving benefits, and
 having no fixed abode were risk factors (P≤0.05) across HDQ domains;
 physical, mental and emotional, difficulty with day-to-day activities, and
 challenges to social participation. Personal factors, identifying as a
 woman and being aged &lt;50 years, were risk factors (P≤0.05) for HDQ
 domains; mental and emotional, uncertainty, and challenges with social
 participation. Conclusions People living with well-controlled HIV in
 London UK experienced multi-dimensional and episodic disability. Results
 help to better understand the prevalence, severity, and risk factors of
 disability experienced by adults living with HIV, identify areas to target
 interventions, and optimise health and functioning.
DOI: 10.5061/dryad.95x69p8n1
title: Phylogenomics reveals deep relationships and diversification within phylactolaemate bryozoans

description: Bryozoans are mostly sessile colonial invertebrates that inhabit all kinds
 of aquatic ecosystems. Extant bryozoan species fall into two clades with
 one of them, Phylactolaemata, being the only exclusively freshwater clade.
 Phylogenetic relationships within the class Phylactolaemata have long been
 controversial owing to their limited distinguishable characteristics that
 reflect evolutionary relationships. Here, we present the first
 phylogenomic analysis of Phylactolaemata using transcriptomic data
 combined with dense taxon sampling of six families to better resolve the
 interrelationships and to estimate divergence time. Using maximum
 likelihood and Bayesian inference approaches, we recovered a robust
 phylogeny for Phylactolaemata in which the interfamilial relationships are
 fully resolved. We show Stephanellidae is the sister taxon of all other
 phylactolaemates and confirm that Lophopodidae represents the second
 offshoot within the phylactolaemate tree. Plumatella fruticosa clearly
 falls outside Plumatellidae as previous investigations have suggested, and
 instead clusters with Pectinatellidae and Cristatellidae as the sister
 taxon of Fredericellidae. Our results demonstrate that cryptic speciation
 is very likely in F. sultana and in two species of Plumatella (P. repens
 and P. casmiana). Divergence time estimates show that Phylactolaemata
 appeared at the end of the Ediacaran and started to diverge in the
 Silurian, although confidence intervals were large for most nodes. The
 radiation of most extant phylactolaemate families occurred mainly in the
 Paleogene and Neogene highlighting post-extinction diversification.
description: Please refer to READMe
 file.
DOI: 10.5061/dryad.pk0p2ngq7
title: Data from: Modeling spatiotemporal abundance and movement dynamics using an integrated spatial capture-recapture movement model

description: Animal movement is a fundamental ecological process affecting the survival
 and reproduction of individuals, the structure of populations, and the
 dynamics of communities. Methods to quantify animal movement and
 spatiotemporal abundances, however, are generally separate and thus omit
 linkages between individual-level and population-level processes. We
 describe an integrated spatial capture-recapture (SCR) movement model to
 jointly estimate (1) the number and distribution of individuals in a
 defined spatial region and (2) movement of those individuals through time.
 We applied our model to a study of polar bears (Ursus maritimus) in a
 28,125 km2 survey area of the eastern Chukchi Sea, USA in 2015 that
 incorporated capture-recapture and telemetry data. In simulation studies,
 the model provided unbiased estimates of movement, abundance, and
 detection parameters using a bivariate normal random walk and correlated
 random walk movement process. Our case study provided detailed evidence of
 directional movement persistence for both male and female bears, where
 individuals regularly traversed areas larger than the survey area during
 the 36-day study period. Scaling from individual- to population-level
 inferences, we found that densities varied from &lt; 0.75 bears/625
 km2 grid cell/day in nearshore cells to 1.6–2.5 bears/grid cell/day for
 cells surrounded by sea ice. Daily abundance estimates ranged from 53–69
 bears, with no trend across days. The cumulative number of unique bears
 that used the survey area increased through time due to movements into and
 out of the area, resulting in an estimated 171 individuals using the
 survey area during the study (95% credible interval 124–250). Abundance
 estimates were similar to a previous multi-year integrated population
 model using capture-recapture and telemetry data (2008–2016; Regehr et al.
 2018). Overall, the SCR-movement model successfully quantified both
 individual- and population-level space use, including the effects of
 landscape characteristics on movement, abundance, and detection, while
 linking the movement and abundance processes to directly estimate density
 within a prescribed spatial region and temporal period. Integrated
 SCR-movement models provide a generalizable approach to incorporate
 greater movement realism into population dynamics and link movement to
 emergent properties including spatiotemporal densities and abundances.
description: Data are formatted for analyses described in Hostetter et al.
 <em>Modeling spatiotemporal abundance and movement dynamics using an
 integrated spatial capture-recapture movement model</em>
description: Please contact the manuscript's first author (njhostet@ncsu.edu)
 for details regarding this dataset and associated R scripts.
DOI: 10.5281/zenodo.16092883
title: STOPUP. WP3. Technological pollution control and risk mitigation measures. Task3.1. Subtask 3.1.2 Development of the compact Retention Soil Filter (RSFcompact) technology

description: This data set includes the data that will be produced by RWTH in the framework of StopUP regarding the development of the compact RSF technology. Two types of data will be generated: experimental data, produced in the RWTH laboratories and at the case study site and performance indicators, calculated on the basis of the experimental data. Before performing tests at the RSF pilot plant, laboratory experiments will be conducted to assess already suitable biodegradable flocculants and appropriate operational conditions. Here, jar-tests and a subsequent filtration test set-up will be applied. The flocculation-filtration performance will be evaluated by monitoring the turbidity, pH, conductivity and pollutant concentration. The selection for suitable flocculant types will be based on pollutant retention, flocculant concentration and energy input (rpm). Resulting conclusions of the lab experiments will then be transferred to the pilot RSF plant. Performance indicators will be the retention of pollutants and infiltration capacity. Analytical parameters are expected to be: TSS, AFS63, and heavy metals. With regard to patents, protective or property rights, access rights may have to be handled individually.
DOI: 10.5281/zenodo.16961693
title: STOPUP. WP3. Technological pollution control and risk mitigation measures. Task3.1. Subtask 3.1.2 Development of the compact Retention Soil Filter (RSFcompact) technology

description: This data set includes the data that will be produced by RWTH in the framework of StopUP regarding the development of the compact RSF technology. Two types of data will be generated: experimental data, produced in the RWTH laboratories and at the case study site and performance indicators, calculated on the basis of the experimental data. Before performing tests at the RSF pilot plant, laboratory experiments will be conducted to assess already suitable biodegradable flocculants and appropriate operational conditions. Here, jar-tests and a subsequent filtration test set-up will be applied. The flocculation-filtration performance will be evaluated by monitoring the turbidity, pH, conductivity and pollutant concentration. The selection for suitable flocculant types will be based on pollutant retention, flocculant concentration and energy input (rpm). Resulting conclusions of the lab experiments will then be transferred to the pilot RSF plant. Performance indicators will be the retention of pollutants and infiltration capacity. Analytical parameters are expected to be: TSS, AFS63, and heavy metals. With regard to patents, protective or property rights, access rights may have to be handled individually.
DOI: 10.5061/dryad.bzkh189bp
title: Data from: Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago

description: This study aimed to reveal the evolutionary timescale and processes
 underlying the diversity of Rubus in the Japanese Archipelago. We
 conducted molecular phylogenetic analyses of most native species (35
 species), along with previously published data from 116 foreign species,
 based on nuclear ribosomal internal transcribed spacer (ITS) and
 chloroplast DNA sequences. Most of the northern species of Japan, that is,
 R. chamaemorus, R. pedatus, R. vernus, R. pseudojaponicus, and R.
 ikenoensis, were found to belong to anciently diverged lineages; in
 particular, R. ikenoensis formed a unique lineage distinct from other
 species. The other species diverged into two evolutionary groups. One
 included subg. Malachobatus, Chamaebatus, and sects. Pungentes, Idaeanthi,
 and Parvifolii (subg. Idaeobatus), which was further divided into two
 clades in the chloroplast phylogenies. Although the phylogenetic
 structures within this group were unresolved, R. sieboldii has been proven
 to be recently derived. The second group represented a well-supported
 clade, comprising sects. Microphylli, Corchorifolii, Peltati, and
 Rosifolii (subg. Idaeobatus), and suggested early Miocene diversification
 of this Asian lineage associated with character specialization in
 vegetative reproduction and leaf shape. This clade was further resolved
 into lower clades primarily representing the sectional classifications,
 although the placement of the earliest diverged species, R. sumatranus, R.
 peltatus, R. corchorifolius, and R. chingii, was incongruent among gene
 trees. At the lower taxonomic levels, R. illecebrosus, R. grayanus, and
 the thornless species of sect. Microphylli showed earlier divergence.
DOI: 10.5061/dryad.0zpc86709
title: Coupled stochastic modelling of hierarchical channel network dynamics and metapopulation persistency - Dataset

description: Dynamic changes in the active portion of stream networks represent a
 phenomenon common to diverse climates and geologic settings. However,
 the  ecological implications of river network
 expansions/retractions remain poorly understood owing to operational
 difficulties in mechanistically describing these processes at the relevant
 spatio-temporal scales. Here we present a novel Bayesian framework for the
 simulation of event-based channel network dynamics capitalizing on the
 concept of "hierarchical structuring of temporary streams" - a
 general principle to identify the activation/deactivation order of network
 nodes. The framework incorporates a dynamic version of a stochastic
 occupancy metapopulation model, and is used to analyze the impact of
 pulsing river networks on species persistence in different scenarios.
 Climate strongly controls temporal variations of the active length,
 influencing the preferential configuration of the active channels and the
 speed of network retraction during drying. We also identify a
 climate-dependent detrimental effect of network dynamics on species spread
 and persistence. This effect is enhanced by dry climates, where flashy
 expansions and retractions of the flowing channels induce metapopulation
 extinction. Survival probabilities are particularly reduced in settings
 where the spatial heterogeneity of network connectivity is pronounced. The
 proposed framework provides novel insight on the multi-faced ecological
 legacies of channel network dynamics.
description: The provided data were downloaded from the Veneto Region
 Geoportal. The dtm was processed with the Taudem toolbox for the
 calculation of the accumulated area and topographic wetness
 index.
description: The code should work as is, provided that it is run on Matlab
 2021a (or newer), with the mapping and symbolic math toolbox are
 installed. Additionally, the user may provide an
 alternative shapefile of the stream network and raster layer of
 contributing area / topographic wetness index, to run the code on a
 different study catchment.