cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4qrfj6q62
title: Reappraising plastid markers of the red algae for phylogenetic community ecology in the gnomic era

description: Selection of appropriate genetic markers to quantify phylogenetic
 diversity is crucial for phylogenetic community ecology studies. Yet,
 systematic evaluation of marker genes for this purpose is scarcely done.
 Recently, the combined effort of the phycological community has produced a
 rich plastid genome resource with taxonomic representation spanning all of
 the major lineages of the red algae (Rhodophyta). As a proof-of-concept
 study, we leverage this resource to develop and apply a phylogenomic
 strategy to seek candidate plastid markers that best capture the identity
 of component species in an eDNA metabarcoding study. We ranked the core
 plastid genes of 107 published plastid genomes based on various
 sequence-derived properties and their tree distance to plastid genome
 phylogenies and found that the most widely used marker, rbcL, is not
 necessarily the optimal marker, while more informative markers might have
 been overlooked. We designed and tested PCR primers for several candidate
 marker genes, and successfully amplified one of these, rpoC1, for a
 taxonomically broad set of red algal specimens. We suggest that our
 general marker identification methodology and the rpoC1 primers will be
 useful to the phycological community for eDNA metabarcoding of the red
 algae.
DOI: 10.5061/dryad.zw3r2284m
title: Data and R code from: Modelling the evolution of cognitive styles

description: Background Individuals consistently differ in behaviour, exhibiting
 so-called personalities. In many species, individuals differ also in their
 cognitive abilities. When personalities and cognitive abilities occur in
 distinct combinations, they can be described as ‘cognitive styles’. Both
 empirical and theoretical investigations produced contradicting or mixed
 results regarding the complex interplay between cognitive styles and
 environmental conditions. Results Here we use individual-based simulations
 to show that, under just slightly different environmental conditions,
 different cognitive styles exist and under a variety of conditions, can
 also co-exist. Co-existences are based on individual specialization on
 different resources, or, more generally speaking, on individuals adopting
 different niches or microhabitats. Conclusions The results presented here
 suggest that in many species, individuals of the same population may adopt
 different cognitive styles. Thereby the present study may help to explain
 the variety of styles described in previous studies and why different,
 sometimes contradicting, results have been found under similar conditions.
description: The data presented here are organized in two dataframes per
 simulation run. One DF "dfLE_x"gives the mean values for each
 generation for the focus traits E = "exploration tendency" and L
 = "learning speed". The number e.g. "dfLE_200"
 specifies the SL= seasonlength. The other DF "pop_200" gives the
 individuals results of the last generation.  The R code
 is also provided with the main function "season". Within the
 code a description is provided.
DOI: 10.5061/dryad.3xsj3txb8
title: Data from: Impact of a pre-feeding oral stimulation program on first feed attempt in preterm infants: Double-blind controlled clinical trial

description: Objective: To evaluate the effect of an oral stimulation program
 in preterm on the performance in the first oral feeding, oral feeding
 skills and transition time from tube to total oral intake. Study
 Designer: Double-blind randomized clinical trial including very
 preterm newborns. Congenital malformations, intracranial hemorrhage grade
 III or IV, bronchopulmonary dysplasia, and necrotizing enterocolitis were
 excluded. Intervention group (GI) received an oral stimulation program of
 tactile extra-, peri-, and intraoral tactile manipulation once a day for
 15 minutes, during a 10-day period. Control group (GII) received sham
 procedure with same duration of time. Feeding ability was assessed by a
 speech-language pathologist blinded to group assignment. The
 classification of infants’ oral performance was determined by Oral Feeding
 Skills (OFS). Neonates were monitored until hospital discharge.
 Results: Seventy-four (37 in each group) were randomized. Mean
 gestational ages and birth weights were 30±1.4 and 30±1.5 weeks, and
 1,452±330g and 1,457±353g for intervention and control groups,
 respectively. Mean proficiency (PRO), transfer rate (RT), and overall
 transfer (OT) were 41.5%±18.3 and 19.9%±11.6 (p&lt;0.001), 2.3 mL/min
 and 1.1 mL/min (p&lt;0.001), 57.2%±19.7 and 35.0%±15.7
 (p&lt;0.001) in intervention and control groups, respectively. Median
 transition time from tube to oral feeding was 4 (3-11) and 8 
 days in intervention and control groups, respectively (p=0.003). Intake of
 breast milk was found to reduce transition time from tube feeds to
 exclusive oral feeding (p&lt;0.001, HR 1.01, 95%CI 1.005-1.019), but
 the impact of the study intervention remained significant (p=0.007, HR
 1.97, 95%CI 1.2-3.2). Conclusion: Infants who were breast-fed and
 an oral stimulation program proved beneficial in reducing transition time
 from tube feeding to oral feeding. ClinicalTrials.gov number NCT03025815
DOI: 10.5061/dryad.jm63xsj6b
title: Data from: Overcoming the detectability costs of symmetrical colouration

description: For camouflaged prey, enhanced conspicuousness due to bilaterally
 symmetrical colouration increases predation risk. The ubiquity of
 symmetrical body patterns in nature is therefore paradoxical, perhaps
 explicable through tight developmental constraints. Placing patterns that
 would be salient when symmetrical (e.g. high contrast markings) away from
 the axis of symmetry is one possible strategy to reduce the predation cost
 of symmetrical colouration. Artificial camouflaged prey with symmetrical
 patterns placed at different distances from the axis were used in both
 visual search tasks with humans and survival experiments with wild avian
 predators. Targets were less conspicuous when symmetrical patterning was
 placed outside a ‘critical zone’ near the midline. To assess whether real
 animals have evolved as predicted from these experiments, the saliency of
 features at different distances from the midline was measured in the
 cryptically coloured forewings of 36 Lepidopteran species. Salience, both
 in absolute terms and relative to wing area, was greatest away from the
 axis of symmetry. Our work therefore demonstrates that prey morphologies
 may have evolved to exploit a loophole in the ability of mammalian and
 avian visual systems to spot symmetrical patterns.
DOI: 10.5061/dryad.hx3ffbg9n
title: Genetic control of collective behavior in zebrafish

description: Many animals, including humans, have evolved to live and move in
 groups. In humans, disrupted social interactions are a
 fundamental feature of many psychiatric disorders.  However, we
 know little about how genes regulate social behavior.  Zebrafish
 may serve as a powerful model to explore this question.  By
 comparing the behavior of wild-type fish to 90 genetic lines, we show that
 mutations of genes associated with human psychiatric disorders can alter
 the collective behavior of adult zebrafish.  We identify three
 categories of behavioral variation across mutants: "scattered",
 in which fish show reduced cohesion; "coordinated", in which
 fish swim more in aligned schools; and "huddled", in which fish
 form dense but disordered groups. Changes in individual interaction rules
 can explain these differences.  This work demonstrates how
 emergent patterns in animal groups can be altered by genetic changes in
 individuals, and establishes a framework for understanding the
 fundamentals of social information processing.
DOI: 10.25934/pr00012474.0
title: Available datapackage for study 'Community Network-driven COVID-19 Testing and Vaccination of Vulnerable Populations in the Central US (C3)'

description: This C3 project, Community network-driven COVID-19 testing of vulnerable populations in the Central US, will implement and evaluate a COVID-19 testing and vaccination approach that combines an evidence-based Social Network Testing Strategy (SNS) with community developed COVID-19 public health messages (SNS+). C3 will engage two disenfranchised populations across rural and urban sites in states across the Central US (Texas (TX), Louisiana (LA), Arkansas (AR), Indiana (IN), Illinois (IL)). C3 leverages NIDA's Justice Community Opioid Innovation Network (JCOIN), the PIs' extensive community located COVID-19 testing programs, and a network of established community partnerships. The collaborative community-academic partnerships, research and engagement infrastructure, and team's leadership across JCOIN will ensure that C3 can rapidly recruit, enroll and test most disenfranchised community members, (n=2400) and through this process, accelerate any forthcoming COVID-19 public health prevention interventions. C3 focuses on two communities most impacted by COVID-19: 1) Criminal justice involved (CJI) - non-incarcerated people with previous history of arrest/jail/prison, probation/parole, drug-court attendance, witnessed or experienced a negative interaction with police or law enforcement; and 2) Low-income Latinx - community members at 250% or below Federal Poverty Level. Both of these diverse populations, and the overlap between them, have some of the highest rates of COVID-19 infection and death in the United States. Messaging that affirms individual agency and corrects misinformation, combined with accessible and acceptable testing, is required to accelerate COVID-19 prevention for these populations.Using a two-arm randomized controlled trial design, participants will be enrolled into the Social Network testing Strategy (SNS) arm (involves social networking referrals only) or the Social Network testing Strategy with COVID-19 prevention messages (SNS+) messaging arm. The latter includes affirmation/misinformation correction messaging (discussion tools and coaching). SNS and SNS+messaging arms will both include an initial group of index study participants who will refer their network members into the study and the process will repeat itself one more time for a total of 3 waves. Indexes will refer network members (1st degree) and then those network members will refer one more round (2nd degree).
DOI: 10.5061/dryad.70rxwdbt3
title: Data from: Decoupling transcription factor expression and activity enables dimmer switch gene regulation

description: Gene-regulatory networks achieve complex mappings of inputs to outputs
 through mechanisms that are poorly understood. We found that in the
 galactose-responsive pathway in Saccharomyces cerevisiae, the decision to
 activate the transcription of genes encoding pathway components is
 controlled independently from the expression level, resulting in behavior
 resembling that of a mechanical dimmer switch. This was not a direct
 result of chromatin regulation or combinatorial control at
 galactose-responsive promoters; rather, this behavior was achieved by
 hierarchical regulation of the expression and activity of a single
 transcription factor. Hierarchical regulation is ubiquitous, and thus
 dimmer switch regulation is likely a key feature of many biological
 systems. Dimmer switch gene regulation may allow cells to fine-tune their
 responses to multi-input environments on both physiological and
 evolutionary time scales.
description: Data is organized in .zip folders corresponding to Figures /
 Supplemental Figures from the associated publication, each containing a
 README.txt file and the relevant code in MATLAB (version R2019b), Python
 (version 3), or shell script necessary to reproduce the analysis and plots
 in those figures. With two exceptions noted below ([1] and [2]), each
 folder directly contains the relevant raw data files. 
 "Fig1_S1_S2.zip" - Figure 1, Figure S1, Figure
 S2 "Fig2a_FigS4dehijk" - Figure 2 panel A;
 Figure S4 panels D,E,H,I,J,K
 "Fig2BC_S5CDEFG" - Figure 2 panels B,C; Figure S5
 panels C,D,E,F,G "Fig2d_S6ab" - Figure 2
 panel D; Figure S6 panels A,B "Fig2e" -
 Figure 2 panel E "Fig4_S7" - Figure 4,
 Figure S7 "FigS3" - Figure S3
 "FigS5_JKLMNO" - Figure S5 panels
 J,K,L,M,N,O "FigS6_CDEFGH" - Figure S6
 panels C,D,E,F,G,H [1]:
 microscopy raw images associated with folder "Figure2d_S6ab.zip"
 are located in the parent Dryad directory in the following .zip
 folders: "20201006
 microscopy.zip" - microscopy dataset 1, 8hr timepoint
 "20201007 microscopy.zip" - microscopy dataset 2, 8hr
 timepoint "20201021 microscopy 8h.zip" -
 microscopy dataset 3, 8hr timepoint "20201021
 microscopy 24h 32h.zip" - microscopy dataset 3, 24hr and 32hr
 timepoints [2]: raw sequencing read data
 files associated with folder "Fig2a_FigS4dehijk.zip" are located
 in the parent Dryad directory as .fastq.gz files:  
 Sequencing run 1 (L93) files are named with the prefix
 "A_S###" where sample number ### is clarified by
 "L93_IDglobal.csv" and "Key.xlsx" in
 "Fig2a_FigS4dehijk.zip". "R1" and "R2" in
 file names designate paired end reads 1 and 2.
 Sequencing run 2 (L108) files are named with the prefix
 "S###" where sample number ### is clarified by
 "L108_IDglobal.csv" and "Key.xlsx" in
 "Fig2a_FigS4dehijk.zip". "R1" and "R2" in
 file names designate paired end reads 1 and 2.
DOI: 10.5061/dryad.1ns1rn8q8
title: Predicting hydrologic responses to climate changes in highly glacierized and mountainous region Upper Indus Basin

description: The Upper Indus Basin (UIB) is a major source of supplying water to
 different areas because of snow and glaciers melt and is also enduring the
 regional impacts of global climate change. The expected changes in
 temperature, precipitation, and snowmelt could be reasons for further
 escalation of the problem. Therefore, estimation of hydrological processes
 is critical for UIB. The objectives of this paper were to estimate the
 impacts of climate change on water resources and future projection for
 surface water under different climatic scenarios using Soil and Water
 Assessment Tool (SWAT). The methodology includes: (i) development of SWAT
 model using land cover, soil and meteorological data; (ii) calibration of
 the model using daily flow data from 1978-1993; (iii) model validation for
 the time 1994-2003; (iv) bias correction of Regional Climate Model (v)
 utilization of bias corrected RCM for future assessment under RCP4.5 and
 RCP8.5 for mid (2041-2070) and late century (2071-2100). The results of
 the study revealed a strong correlation between simulated and observed
 flow with R2 and NSE equals 0.85 each for daily flow. For validation, R2
 and NSE were found to be 0.84 and 0.80 respectively. Compared to baseline
 period (1976-2005), the result of RCM showed an increase in temperature
 ranging from 2.36°C to 3.50°C and 2.92°C to 5.23°C for RCP4.5 and RCP8.5
 respectively, till the end of 21st century. Likewise, the increase in
 annual average precipitation is 2.4% to 2.5% and 6.0% to 4.6% (mid to late
 century) under RCP 4.5 and 8.5 respectively. The model simulation results
 for RCP4.5 showed increase in flow by 19.24% and 16.78% for mid and late
 century respectively. For RCP8.5, the increase in flow is 20.13% and
 15.86% during mid and late century respectively. The model was more
 sensitive towards available moisture and snowmelt parameters. Thus, SWAT
 model could be used as effective tool for climate change valuation and for
 sustainable management of water resources in future.
DOI: 10.5061/dryad.12jm63xt6
title: Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides

description: Despite the growing resources and tools for high-throughput
 characterization and analysis of genomic information, the discovery of the
 genetic elements that regulate complex traits remains a challenge. Systems
 genetics is an emerging field that aims to understand the flow of
 biological information that underlies complex traits from genotype to
 phenotype. In this study, we used a systems genetics approach to identify
 and evaluate regulators of the lignin biosynthesis pathway in Populus
 deltoides by combining genome, transcriptome and phenotypic data from a
 population of unrelated individuals of P. deltoides. The discovery of
 lignin regulators began with the quantitative genetic analysis of the
 xylem transcriptome and resulted in the detection of 6,706 and 4,628
 significant local- and distant-eQTL associations, respectively. Among the
 locally-regulated genes, we identified the R2-R3-MYB transcription factor
 MYB125 as a putative trans-regulator of the majority of genes in the
 lignin biosynthesis pathway. The gene expression of MYB125 in a diverse
 population positively correlated with lignin content. Furthermore,
 overexpression of MYB125 in transgenic poplar resulted in increased lignin
 content, as well as altered gene expression of structural genes in the
 lignin biosynthesis pathway. Altogether, our findings indicate that MYB125
 is involved in the control of a transcriptional co-expression network of
 lignin biosynthesis genes during secondary cell wall formation in P.
 deltoides.
DOI: 10.5061/dryad.18931zcs4
title: Biotic predictors with phenological information improve range estimates for migrating monarch butterflies in Mexico

description: Although long-standing theory suggests that biotic variables are only
 relevant at local scales for explaining the patterns of species’
 distributions, recent studies have demonstrated improvements to species
 distribution models (SDMs) by incorporating predictor variables informed
 by biotic interactions. However, some key methodological questions remain,
 such as which kinds of interactions are permitted to include in these
 models, how to incorporate the effects of multiple interacting species,
 and how to account for interactions that may have a temporal dependence.
 We addressed these questions in an effort to model the distribution of the
 monarch butterfly (Danaus plexippus L. 1758) during its fall migration
 (September – November) through Mexico, a region with new monitoring data
 and uncertain range limits even for this well-studied insect. We estimated
 species richness of selected nectar plants (Asclepias spp.) and roosting
 trees (various highland species) for use as biotic variables in our
 models. To account for flowering phenology, we additionally estimated
 nectar plant richness of flowering species per month. We evaluated three
 types of models: climatic variables only (abiotic), plant richness
 estimates only (biotic), and combined (abiotic and biotic). We selected
 models with AICc and additionally determined if they performed better than
 random on spatially withheld data. We found that the combined models
 accounting for phenology performed best for all three months, and better
 than random for discriminatory ability but not omission rate. These
 combined models also produced the most ecologically realistic spatial
 patterns, but the modeled response for nectar plant richness matched
 ecological predictions for November only. These results represent the
 first model-based monarch distributional estimates for the Mexican
 migration route and should provide foundations for future conservation
 work. More generally, the study demonstrates the potential benefits of
 using SDM-derived richness estimates and phenological information for
 biotic factors affecting species distributions.
description: Please find below the DOI for the GBIF occurrence data for
 species of <em>Asclepias</em> and trees downloaded on June 04,
 2014 for use in the analyses in this paper.
 https://doi.org/10.15468/dl.fdzhj0 The monarch
 butterfly occurrence data used for analyses in this paper is from two
 sources. One is the citizen science database Journey North
 (https://journeynorth.org/), accessed in March 2018, which is an open data
 source. Please find the details of the time periods of this dataset used
 for analysis in the paper. The other is from the Mexican federal agency
 Comisión Nacional de Áreas Naturales Protegidas (CONANP) and represents
 field data for the fall season in 2015 (the only processed data available
 at the time of the study)--this data is currently proprietary.
DOI: 10.15468/dl.bfrvev
title: Occurrence Download

description: A dataset containing 136453 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is BRA.14.90_2",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 136453 records from 220 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002012-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c866t1g3b
title: Behavioural synchronization in a multilevel society of feral horses

description: Behavioural synchrony among individuals is essential for group-living
 organisms to maintain their cohesiveness necessary to get information and
 against predation. It is still largely unknown how synchronization
 functions in a multilevel society, a nested assemblage of multiple social
 levels between many individuals. Our aim was to build a model to explain
 the synchronization of activity in a multilevel society of feral horses.
 We used multi-agent based models based on four hypotheses: A) independent
 model: horses do not synchronize, B) anonymous model: horses synchronize
 with any individual in any unit, C) unit-level social model: horses
 synchronize only within units and D) herd-level social model: horses
 synchronize across and within units, but internal synchronization is
 stronger. We simulated each model 100 times and compared simulations to
 the empirical data obtained from drone observations. The hypothesis D best
 supported empirical data. This result suggests that synchronization
 occurred at an intra- and inter-unit level.