cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7h44j0zsg
title: Lee and Daunizeau choice data from: Trading mental effort for confidence in the metacognitive control of value-based decision-making

description: Why do we carefully ponder some decisions, but not others? In this work,
 we derive a computational model of the metacognitive control of decisions
 or MCD. In brief, we assume that fast and automatic processes first
 provide an initial (and largely uncertain) representation of options'
 values, yielding prior estimates of decision difficulty. This uncertain
 value representation is then refined by deploying cognitive (e.g.,
 attentional, mnesic) resources, the allocation of which is controlled by
 an effort-confidence tradeoff. Importantly, the anticipated benefit of
 allocating resources varies in a decision-by-decision manner according to
 the prior estimate of decision difficulty. The ensuing MCD model predicts
 choices, response time, subjective feeling of effort, choice confidence,
 and choice-induced preference change. We test these predictions in a
 systematic manner, using a dedicated behavioral paradigm. Our results
 provide a quantitative link between mental effort, choice confidence, and
 preference reversals, which could inform interpretations of related
 neuroimaging findings.
description: participants provided subjective value estimate ratings for
 individual snack foods, along with subjective certainty about each
 rating participants chose between pairs of items, along
 with confidence in each choice participants again
 provided subjective value estimate ratings for individual snack foods,
 along with subjective certainty about each rating
DOI: 10.5061/dryad.9cnp5hqgc
title: Genetic diversity of Bubalus bubalis in Germany and global relations of its genetic background

description: This is the first study aimed to explore the genetic diversity and
 population structure of domestic water buffalo (Bubalus bubalis) in
 Germany and their potential relations to herds in other parts of Europe or
 worldwide. To this end, ear tissue samples of 285 animals from four
 different herds, including Brandenburg (n=27), Mecklenburg-Western
 Pomerania (n=28), Lower Saxony (n=26), and Saxony (n=28), together with
 animals from herds in Bulgaria (n=58), Romania (n=63), and Hungary (n=55)
 were collected and genotyped using the Axiom Buffalo Single Nucleotide
 Polymorphism (SNP) Array (90K). This dataset was then merged with 220
 genotypes from Brazil, Colombia, Egypt, Turkey, India, Pakistan, Iran, and
 Italy obtained from public repositories. The multidimensional scaling
 based on identity by state matrix distances followed by a model-based
 estimation of population structure revealed a mixed genetic make-up of
 German buffalos with contribution from Bulgaria (Murrah breed), Romania,
 and Italy. This analysis was confirmed with a phylogenetic tree based on
 the fixation index (FST) between populations. Moreover, we performed an
 analysis for run of homozygosity (ROH) distribution in the genome with our
 own data. By using ROH, we calculated the inbreeding coefficient (FROH)
 and identified genomic regions that are potentially under historical
 selection pressure for German populations. A high degree of genetic
 diversity and a low inbreeding level was identified in German buffalos,
 suggesting familiar relations to buffalos in Italy, Romania, and Bulgaria.
 We further demonstrate that European buffalos stand out from other buffalo
 populations worldwide, supporting the idea that buffalos not completely
 disappeared from the European continent during the late Pleistocene. In
 addition, a novel genotype was identified in Hungarian buffalos, also
 clearly separate from other buffalo populations included in this study.
 The high genetic diversity in European buffalos seems to be an excellent
 prerequisite for the establishment of local breeds characterized by unique
 traits and features. This study may also be considered as an initial step
 on the way to genome characterization for the sustainable development of
 the buffalo economy in Germany and other parts of Europe in the future.
description: Genomic DNA, Axiom Buffalo Single Nucleotide Polymorphism (SNP)
 Array (90K),
description: Plink files, raw data. ReadMe file uploaded
DOI: 10.5061/dryad.9p8cz8wdp
title: Data matrices for: Phylogenomics of peacock spiders and their kin (Salticidae, Maratus), with implications for the evolution of male courtship displays

description: Understanding diversity has been a pursuit in evolutionary biology since
 its inception. A challenge arises when sexual selection has played a role
 in diversification. Questions of what constitutes a “species”, homoplasy
 versus synapomorphy, and whether sexually-selected traits show
 phylogenetic signal have hampered work on many systems. Peacock spiders
 are famous for sexually selected male courtship dances and peacock-like
 abdominal ornamentation. This lineage of jumping spiders currently
 includes over 90 species classified into two genera, Maratus and Saratus.
 Most Maratus species have been placed into groups based on secondary
 sexual characters, but evolutionary relationships remain unresolved. Here
 we assess relationships in peacock spiders using phylogenomic data (UCEs
 and RAD-seq). Analyses reveal that Maratus and the related genus Saitis,
 are paraphyletic. Many, but not all, groups within a “core Maratus” clade
 are recovered as genetic clades but we find evidence for undocumented
 speciation. Based on original observations of male courtship, our
 comparative analyses suggest that courtship behavior and peacock-like
 abdominal ornamentation has evolved sequentially with some traits
 inherited from ancestors with others evolving repeatedly and independently
 from “simple” forms. Our results have important implications for the
 taxonomy of these spiders, and provide a much-needed evolutionary
 framework for comparative studies of sexual signal character evolution.
DOI: 10.5061/dryad.zgmsbcc8q
title: Functional and genetic diversity changes through time in a cloud forest ant assemblage

description: Climate change in the Neotropics is causing upslope range shifts. We used
 arrays of ant species collected in a cloud forest at 1,500 m in Área de
 Conservación Guanacaste (ACG), northwestern Costa Rica, collected in two
 time periods (1998-2000 and 2008-2011) to measure changes in species
 richness and diversity over a decade. Using metrics of community
 structure, we found that the species assemblage in the collections from
 the 1990s were significantly phylogenetically clustered and functionally
 less diverse as compared to collections from the early 2000’s. At both
 time points, the assemblages were significantly phylogenetically clustered
 and while the difference in functional diversity between the time points
 was not significant, the ant assemblage has become lighter in color (on
 average) over time. When individual species are considered the overall
 pattern of replacement is consistent with the cloud forest ant assemblage
 being colonized by arrivals from lower-elevation forests.  The
 invertebrate communities on cloud forested mountain tops are especially
 vulnerable to a changing climate as there are two factors working
 together; no higher terrain to which they can move and the invasion of
 more and more taxa from lower downslope.  This vulnerability is
 already measurable.
description: BITR-19-251 - community matrix.csv - community matrix of ants
 across the Cacao elevational gradient (Smith et al 2014) as well as
 categories for the two time periods analysed here. Used in phylogenetic
 and NMDS evaluations of community structure.  
 BITR-19-251 - community metadata.csv - matrix of environmental
 conditions measured and derived for the sites in the community matrix
 (here) and measured in Smith et al (2014). 
 BITR-19-251.nwk - ML phylogeny used in calculating measurements
 of phylogenetic diversity.  BITR-19-251 Supplemental
 Appendix - 201106.xlsx - collection information for ants from both time
 periods as well as morphological measurments for each ant.
DOI: 10.5061/dryad.b2rbnzscn
title: Phylogeny of the ingoid clade (Caesalpinioideae, Fabaceae), based on nuclear and plastid data

description: We investigated generic relationships in the ingoid clade (Fabaceae)
 (sensu Koenen & al. 2020a), with main focus on genera with a
 taxonomic history in Calliandra s.l. of the tribe Ingeae
 (i.e. Afrocalliandra, Calliandra s.s., Sanjappa,Thailentadopsis, Viguieranthus, Zapoteca), and three genera of the tribe Acacieae (i.e., Acacia, Acaciella, Senegalia). The nuclear ribosomal ETS and ITS, and the plastid matK, trnL-trnF and ycf1 DNA-regions were analysed for 246 representatives from 36 genera using maximum likelihood as implemented in IQ-tree. The results show an Ingeae–Acacia clade within the ingoid clade, resolved in three major clades. Clade 1 (Calliandra s.s. and Afrocalliandra) is sister to clades 2 and 3. Clade 2 comprises Faidherbia, Sanjappa, Thailentadopsis, Viguieranthus and Zapoteca. Clade 3 comprises the remaining genera of the Ingeae, plus Acacia. The ingoid genus Senegalia is excluded from the Ingeae–Acacia clade. Acaciella is sister to the remaining ingoid clade when nuclear ribosomal data is included in the analyses, but included in the Ingeae–Acacia clade based on plastid data. Acacia and perhaps also Acaciella are thus nested within Ingeae. Species traditionally referred to Calliandra (Calliandra s.l.) are resolved in two clades, and the “Calliandra-pod” has apparently evolved independently several times.
description: Alignment files of the DNA sequences ETS, ITS,
 <em>trnL</em>-<em>trnF</em>,
 <em>matK</em> and <em>ycf1</em>. Sequences
 amplified using sanger sequencing and DNA extracted from herbarium
 material or silica dried leaf material. Additional sequences downloaded
 from Genbank, information in appendix 1. The consensus trees from the
 separate analyses of the nuclear (Suppl. Fig. 1) and plastid datasets
 (Suppl. Fig. 2) are also provided, as well as the results from the
 combined (nuclear and plastid) analysis excluding nuclear sequences for
 <em>Acaciella</em> (Suppl. Fig. 3). All phylogenetic trees are
 provided with support values, approximate Bayes support values (aBS) and
 maximum likelihood Bootstrap support values (BS), on nodes, presented
 aBS/BS.
description: Nuclear dataset: ETS 1-844; ITS 845-2049
 Plastid dataset:
 <em>trnL</em>-<em>trnF</em> 1-1562;
 <em>matK</em> 1563-5000; <em>ycf1</em>
 5001-12107 Datasets with excluded bases shown, as used
 for analysis.
DOI: 10.5061/dryad.ffbg79csg
title: Assisted colonization of a regionally native predator impacts benthic invertebrates in fishless mountain lakes

description: The intentional introduction of native cold-water trout into
 high-elevation fishless lakes has been considered a tool to build
 resilience to climate change (i.e. assisted colonization); however,
 ecological impacts on recipient communities are understudied. The purpose
 of this study was to inform native cold-water trout recovery managers by
 assessing potential consequences of translocating a regionally native
 trout (westslope cutthroat trout; Oncorhynchus clarkii) into
 fishless mountain lakes. This study compared littoral benthic invertebrate
 richness, diversity, community structure, and density between three groups
 of lakes (fishless, native trout, nonnative trout) in the Canadian Rocky
 Mountains. While richness and diversity were preserved across all
 lake groups, other lines of evidence suggested that the introduction of
 native westslope cutthroat trout into fishless lakes can alter littoral
 benthic invertebrate communities in similar ways as nonnative brook trout
 (Salvelinus fontinalis). The community structure of cutthroat
 trout lakes resembled brook trout lakes compared to that of fishless
 lakes. For example, both trout-lake groups contained a lower
 density of free-swimming ameletid mayflies and a higher density
 of certain burrowing taxa. Risk assessments for trout-recovery actions
 should consider the potential for collateral damage to recipient
 invertebrate communities. Future research should identify possible
 cascading trophic effects on species subsidized by invertebrate prey.
description: For a full description of methodology, please refer
 to "<i>Assisted colonization of a regionally native predator
 impacts benthic invertebrates in fishless mountain
 lakes</i>", published in Conservation Science and
 Practice. 
description: The data package includes:
 <strong>1)</strong> raw count data collected from 202
 sample sites at 36 alpine and sub-alpine lakes (including
 zooplankton) <strong>(RAW_taxa_2015_2016.xlsx)</strong>; <strong>2)</strong> density values (individuals·m2) for 26 common (present in &gt;10 % of lakes) littoral invertebrate (rare taxa and zooplankton excluded), categorized by lake group (fishless, nonnative, native) <strong>(taxa.csv)</strong>;  <strong>3)</strong> density values (individuals·m2) for 50 littoral invertebrate families (rare taxa included, zooplankton excluded), categorized by lake group (fishless, nonnative, native) <strong>(taxa_diversitymeasures.csv),</strong> and;  <strong>4)</strong> environmental predictor variables for each lake, categorized by lake group (fishless, nonnative, native) <strong>(env.csv)</strong>. All anlayses performed in the publication are combined into one R script (<strong>R_Script_Banting_etal.R</strong>).   All data comes from Kootenay National Park, B.C., and Banff National Park, Alberta.  Date of data collection: June & July of 2015 & 2016
DOI: 10.5061/dryad.2bvq83bnv
title: Comparison of health literacy profile of patients with end stage kidney disease on dialysis versus non-dialysis chronic kidney disease and the influencing factors: a cross-sectional study

description: Objectives: Lower health literacy (HL) is associated with poor outcomes in
 patients with kidney disease. Since HL matches the patient’s competencies
 with the complexities of the care package, the level of HL sufficient in
 earlier stages of chronic kidney disease (CKD) may be inadequate for
 end-stage kidney disease (ESKD) patients on dialysis. We aimed to analyse
 the HL profile of ESKD and non-dialysis CKD patients and examine if there
 were significant associations with covariates which could be targeted to
 address HL deficits, thereby improving patient outcomes. Design and
 setting: Cross-sectional study of CKD and ESKD patients from a single
 Australian health district. Methods: We assessed the HL profile of 114 CKD
 and 109 ESKD patients using a 44-item multi-domain HL Questionnaire (HLQ)
 and examined its association with demographic factors (age, gender, race),
 smoking, income, education, comorbidities, carer status, cognitive
 function and depression. Using multi-variable logistic regression models,
 HL profiles of CKD and ESKD patients were evaluated after adjusting for
 covariates. Results: Patients with ESKD had similar demographics and
 educational levels compared to CKD patients. ESKD had significantly higher
 frequency of vascular disease, cognitive impairment and depression. ESKD
 patients had better HL scores for the social support domain (37.1% vs
 19.5% in higher HLQ4 tertile, p=0.004), whereas all other HL domains
 including engagement with healthcare providers were comparable to CKD.
 Depression was independently associated with nearly all of the HL domains
 (HLQ1: OR 2.6, p=0.030, HLQ2: OR 7.9, p=&lt;0.001, HLQ3: OR 7.6,
 p&lt;0.001, HLQ4: OR 3.5, p=0.010, HLQ5: OR 8.9, p=0.001, HLQ6: OR
 3.9, p=0.002, HLQ7: OR 4.8, p=0.001, HLQ8: OR 5.3, p=0.001) and education
 with HL domains relevant to processing health related information (HLQ8:
 OR 2.6, p=0.008, HLQ9: OR 2.5, p=0.006). Conclusions: Despite very
 frequent interactions with health systems, ESKD patients on dialysis did
 not have higher HL in engagement with health providers and most other HL
 domains, compared to CKD patients. Strategies promoting patient-provider
 engagement and managing depression which strongly associates with lower HL
 may address the impact of HL deficits and favourably modify clinical
 outcomes in renal patients. 
description: Data was collected by research assistants by patient interviews
 and administering validated test instruments. Data was
 entered into an excel spreadsheet by research assistants.
 The data was analyzed using Stata 16.0.
description: A readme file has been added to give description of the variables
 and label values.  Any reasonable requests for
 additional data will be provided on contacting the author at
 karumathil.murali@health.nsw.gov.au 90 days after publication of the
 manuscript in BMJ Open. Missing data was managed in
 analysis by list-wise deletion.
DOI: 10.5061/dryad.f1vhhmgv6
title: The scale and dynamics of COVID-19 epidemics across Europe

description: The number of COVID-19 deaths reported from European countries has varied
 more than 100-fold. In terms of coronavirus transmission, the relatively
 low death rates in some countries could be due to low intrinsic (e.g. low
 population density) or imposed contact rates (e.g. non-pharmaceutical
 interventions) among individuals, or because fewer people were exposed or
 susceptible to infection (e.g. smaller populations). Here we develop a
 flexible empirical model (skew-logistic) to distinguish among these
 possibilities. We find that countries reporting fewer deaths did not
 generally have intrinsically lower rates of transmission and epidemic
 growth, and flatter epidemic curves. Rather, countries with fewer deaths
 locked down earlier, had shorter epidemics that peaked sooner, and smaller
 populations. Consequently, as lockdowns are eased we expect, and are
 starting to see, a resurgence of COVID-19 across Europe.
description: File "SEIRModel Germany Fig 1.xlsm" is a SEIR model,
 described in the Supplementary Materials and implemnted in Excel.
 Instructions for entering the data are on sheet "Data".
 Insrructions for running the model are on sheets "SEIRModel
 (eqs)" and "Fit". Visual Basic Macros are visible in
 "Developer".  Two main public data sources,
 used as described in the Supplementary Materials (included with the
 manuscript): Figs 2 & 3 were drawn from public
 data provided by European Centre for Disease Prevention and Control,
 COVID-19. 2020, which can be downloaded from:
 https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide (data in "Data skew-logistic Figs 2&3") Fig 4 was drawn from public data provided by T. Hale, S. Webster, A. Petherick, T. Phillips, B. Kira. (Blavatnik School of Government, Oxford, 2020), which can be downloaded from: https://www.bsg.ox.ac.uk/research/research-projects/coronavirus-government-response-tracker (data in "Containment index Fig 4"). Fitting of the skew-logistic model is carried out in "Skew Logistic fit template Fig 2.xlsm" as described on sheet "Instructions". Visual Basic Macros are visible in "Developer". 
description: The data used for analysis are provided in the Excel files, in
 which cells contain formulae for carrying out basic computations. Graphics
 in the paper are also presented in the Excel files, which point to the
 source data in each file. Click "don't update" when opening
 Excel files. Although the SEIR and skew-logistic models cna be run from
 the Excel files provided, readers can also construct these models from the
 information given in the Supplementary Materials (included with the
 manuscript).
DOI: 10.5061/dryad.xksn02vdn
title: The effect of methylene blue on white matter injury after MCAO in rats and mice

description: Objectives: Methylene blue, the FDA-grandfathered drug was proved to be
 neuroprotective in ischemic stroke in rat. However, the mechanism of the
 protective effect was unknown. In this study, we used different animal
 models to investigate the effect of MB administration given within and
 beyond the therapeutic time window on behavioral deficits and infarct
 volume and related mechanism about the white matter protection. Methods:
 Middle cerebral artery occlusion and reperfusion (MCAO) and
 photothrombotic middle cerebral artery occlusion (PT-MCAO) models were
 used. Behavioral deficits and infarct volume were measured by foot fault
 test, Garcia neurological score and TTC staining. Black gold staining and
 western blot were used to evaluate the brain white matter injury. Results:
 We found that intraperitoneal administration of MB immediately or 24h
 after the MCAO or PT-MCAO surgery reduced infarct volume, improved the
 neurological deficits, reduced the white matter injury via myelin Basic
 Protein (BMP) protection. Conclusion: These findings suggested that MB
 relieved white matter injury besides neuronal protection and has potential
 therapeutic effects on ischemic stroke.
description: All data were obtained from randomized, double-blind, and
 vehicle-controlled design.
DOI: 10.5061/dryad.nk98sf7rq
title: Data from: Vitamin D status and COVID-19 clinical outcomes in hospitalized patients

description: Context: Populations severely affected by COVID-19 are also at
 risk for vitamin D deficiency. Common risk factors include older age,
 chronic illness, obesity, and non-Caucasian race. Vitamin D deficiency has
 been associated with risk for respiratory infections and failure,
 susceptibility and response to therapy for enveloped virus infection, and
 immune-mediated inflammatory reaction. Objective: To test the
 hypothesis that 25-hydroxyvitamin D[25(OH)D] deficiency is a risk factor
 for severity of COVID-19 respiratory and inflammatory complications.
 Design: We examined the relationship between retrospectively
 obtained prehospitalization 25(OH)D levels and COVID-19 clinical outcomes
 in 700 COVID-19 positive hospitalized patients. Primary
 Outcomes: Discharge status, mortality, length of stay, intubation
 status, renal replacement Secondary Outcomes: Inflammatory
 markers Results: 25(OH)D levels were available in 93 patients
 [25(OH)D:25(IQR:17–33)ng/mL]. Compared to those without 25(OH)D levels,
 those with measurements did not differ in age, BMI or distribution of sex
 and race, but were more likely to have comorbidities. Those with
 25(OH)D&lt;20ng/mL (n=35) did not differ from those with
 25(OH)D³20ng/mL in terms of age, sex, race, BMI, or comorbidities. Low
 25(OH)D tended to be associated with younger age and lower frequency of
 preexisting pulmonary disease. There were no significant between-group
 differences in any outcome. Results were similar in
 those ³50years, in male/female-only cohorts, and when differing
 25(OH)D thresholds were used (&lt;15ng/ml and &lt;30ng/ml). There
 was no relationship between 25(OH)D as a continuous variable and any
 outcome, even after controlling for age and pulmonary disease. 
 Conclusions: These preliminary data do not support a relationship
 between vitamin D status and COVID-19 clinical outcomes.