cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q2r87q9
title: Data from: Ecological opportunity shapes a large Arctic charr species radiation

description: Ecological opportunity is considered a crucial factor for adaptive
 radiation. Here, we combine genetic, morphological and ecological data to
 assess species and ecomorphological diversity of Artic charr in six lakes
 of a catchment in southernmost Greenland, harbouring only charr and
 stickleback. Because the diversity of habitats and resources increases
 with lake size, we predict a positive association between lake size and
 the extent of ecomorphological diversity. The largest lake of the
 catchment harbours the largest Arctic charr assemblage known today. It
 consists of six genetically differentiated species belonging to five
 ecomorphs (anadromous, littoral benthic, profundal dwarf, planktivorous,
 piscivorous), of which the latter comprises two ecomorphologically
 extremely similar species. Lakes of intermediate size contain two
 ecomorphologically and genetically distinct species. Small lakes harbour
 one genetically homogenous, yet sometimes ecomorphologically variable
 population. Supporting our prediction, lake size is positively correlated
 with the extent of ecomorphological specialization towards profundal,
 pelagic and piscivorous lifestyle. Furthermore, assemblage-wide
 morphospace increases sharply when more than one genetic cluster is
 present. Our data suggest that ecological opportunity and speciation
 jointly determine phenotypic expansion in this charr radiation.
description: Individual genetic,
 morphological and ecological data of Greenlandic charrIndividual data on charr
 diversity in Greelandic lakes. Net_trap_rod indicates the type of fishing:
 benthic nets are indicated with B, pelagic nets with P, stickleback traps
 with ST, scoop nets with SN, flyfishing with F, catching a fish with the
 hand with H. Depth_site indicates the depth of the lake at the site where
 the fish was caught, Catching_Depth the depth at which the fish was
 caught. Geno_max indicates the genetic assignment obtained in the
 hierarchical structure analysis for the full dataset. Cluster1-7 are
 individual genetic assignments to each of the 7 clusters from the
 structure analysis. Alleles of the 9 microsatellite markers are coded as
 retention time, missing data is indicated with -9. d13C, d13C_lipidcorr,
 d15N, CNratio are stable isotopic data. Linear morphometric distances
 (TL-BDA) were measured on the preserved fish using a digital caliper, are
 given in mm, and are described in Figure S1 in the supplementary material.
 Visual_ecomorph_assignment: CJD and AKK used cuvette and standard photos
 of freshly caught fish to assign each individual to one of five
 specialized ecomorphs or to generalist. Unassigned individuals were either
 juveniles, damaged, morphologically intermediate, or the two searchers
 could not agree on an assignment. Ecomorph descriptions are given in
 Appendix S2, and criteria used for assignment in Table
 S3.Greenland_Eqaluit_Charr_data.txt
DOI: 10.5061/dryad.3qk1303
title: Data from: CRISPR/cas9-mediated targeted mutagenesis for functional genomics research of Crassulacean acid metabolism plants

description: Crassulacean acid metabolism (CAM) is an important photosynthetic pathway
 in diverse lineages of plants featuring high water-use efficiency and
 drought tolerance. A big challenge facing the CAM research community is to
 understand the function of the annotated genes in CAM plant genomes.
 Recently, a new genome editing technology using CRISPR/Cas9 has become a
 more precise and powerful tool than traditional approaches for functional
 genomics research in C3 and C4 plants. In this study, we seek to realize
 the potential of CRISPR/Cas9 to characterize the function of CAM-related
 genes in the model CAM species Kalanchoë fedtschenkoi. We demonstrate that
 CRISPR/Cas9 is effective to create biallelic indel mutagenesis to reveal
 previously unknown roles of blue light receptor phototropin 2 (KfePHOT2)
 in the CAM pathway. Knocking-out of the KfePHOT2 reduced stomatal
 conductance and CO2 fixation in the late afternoon and increased stomatal
 conductance and CO2 fixation in the early evening, indicating that blue
 light signaling plays an important role in the CAM pathway. Lastly, we
 provide a genome-wide gRNA database targeting 45,183 protein-coding genes
 annotated in the K. fedtschenkoi genome.
description: Supplementary file
 1This
 file contains gRNA design for genome sequence of Kalanchoe fedtschenkoi
 v1.1 in Phytozome:
 https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_KfedtschenkoiSupplementary file 2Genome-wide off-target analysisSupplementary_file_2_Genome-wide off-target-analysis.txt
DOI: 10.5061/dryad.660d317
title: Data from: Adiposity is related to cerebrovascular and brain volumetry outcomes in the RUN DMC Study

description: Objective: Adiposity predictors, body mass index (BMI), waist
 circumference (WC), and blood leptin and total adiponectin levels were
 associated with components of cerebral small vessel disease (CSVD) and
 brain volumetry in 503 adults with CSVD age ≥50 years and enrolled in the
 Radboud University Nijmegen Diffusion tensor and Magnetic resonance
 imaging Cohort (RUN DMC). Methods: RUN DMC participants were followed for
 9 years (2006-2015). BMI, WC, brain imaging and dementia diagnoses were
 evaluated at baseline and follow-up. Adipokines were measured at baseline.
 Brain imaging outcomes included CSVD components, white matter
 hyperintensities, lacunes and microbleeds; and gray and white matter,
 hippocampal, total brain, and intracranial volumes. Results:
 Cross-sectionally among men at baseline, higher BMI, WC and leptin were
 associated with lower gray matter and total brain volumes, and higher BMI
 and WC were associated with lower hippocampal volume. At follow-up 9 years
 later, higher BMI was cross-sectionally associated with lower gray matter
 volume, and an obese WC (&gt;102cm) was protective for &gt;1
 lacune or &gt;1 microbleed in men. In women, increasing BMI and
 overweight or obesity (BMI &gt;25 kg/m2 or WC &gt;88 cm) were
 associated with &gt;1 lacune. Longitudinally, over 9 years, a baseline
 obese WC was associated with decreasing hippocampal volume particularly in
 men, and increasing WMH volume in women and men. Conclusions:
 Anthropometric and metabolic adiposity predictors were differentially
 associated with CSVD component and brain volumetry outcomes by sex. Higher
 adiposity is associated with a vascular-neurodegenerative spectrum among
 adults at-risk for vascular forms of cognitive impairment and dementias.
description: Supplementary
 TablesGiven the printed Table
 number limit, these are supplementary files to accompany the manuscript,
 at the request of the reviewers.NEUROLOGY2018937870_e-tables_20190315.docx
DOI: 10.5061/dryad.b9q0dg4
title: Data from: Automated CT perfusion imaging for acute ischemic stroke: pearls and pitfalls for real world use

description: Recent positive trials have thrust acute cerebral perfusion imaging into
 the routine evaluation of acute ischemic stroke. Updated guidelines state
 that in patients with anterior circulation large vessel occlusions
 presenting beyond 6 hours from time last known well, advanced imaging
 selection including perfusion based selection is necessary. Centers that
 receive acute stroke patients must now have the capability to perform and
 interpret CT or MR perfusion imaging, or provide rapid transfer to centers
 with the capability of selecting patients for a highly impactful
 endovascular therapy, particularly in delayed time windows. Many stroke
 centers are quickly incorporating the use of automated perfusion
 processing software to interpret perfusion raw data. As CT perfusion is
 being assimilated in real world clinical practice, it is essential to
 understand the basics of perfusion acquisition, quantification and
 interpretation. It is equally important to recognize the common technical
 and clinical diagnostic challenges of automated CTP including ischemic
 core and penumbral misclassifications that could result in underestimation
 or overestimation of the core and penumbra volumes. This review highlights
 the pitfalls of automated CT perfusion along with practical pearls to
 address the common challenges. This is particularly tailored to aid the
 acute stroke clinician who must interpret automated perfusion studies, in
 an emergency setting to make time-dependent treatment decisions for acute
 ischemic stroke patients.
DOI: 10.5061/dryad.8md722p
title: Stochastic fluctuations in apoptotic threshold of tumor cells can enhance apoptosis and combat fractional killing

description: Fractional killing, which is a significant impediment to successful
 chemotherapy, is observed even in a population of genetically identical
 cancer cells exposed to apoptosis-inducing agents. This phenomenon arises
 not from genetic mutation but from cell-to-cell variation in the
 activation timing and level of the proteins that regulate apoptosis. To
 understand the mechanism behind the phenomenon, we formulate complex
 fractional killing processes as a first-passage time (FPT) problem with a
 stochastically fluctuating boundary. Analytical calculations are performed
 for the FPT distribution in a toy model of stochastic p53 gene expression,
 where the cancer cell is killed only when the p53 expression level crosses
 an activity apoptotic threshold. Counterintuitively, we find that
 threshold fluctuations can effectively enhance cellular killing by
 significantly decreasing the mean time that the p53 protein reaches the
 threshold level for the first time. Moreover, faster fluctuations lead to
 the killing of more cells. These qualitative results imply that dynamic
 variability in threshold is an unneglectable stochastic source, and can be
 taken as a strategy for combating fractional killing of cancer cells.
description: Matlab code to generate
 figures as presented in papermaltabcodes.rar
DOI: 10.5061/dryad.6r5df1t
title: Data from: Sibling competition is stronger in blue tit homozygous broods

description: It is known that heterozygosity affects mate selection in various taxa.
 But also beyond mating, in species with parental care, heterozygosity can
 modulate interactions among family members and their fitness-related
 decisions. However, to date, this question remains little explored. Here,
 we studied whether nestling heterozygosity was related to parent-offspring
 interactions and sib-sib competition in the blue tit, Cyanistes caeruleus,
 while controlling for the degree of relatedness among nestlings. It has
 been argued that heterozygosity-fitness correlations are more easily
 detected under demanding environmental conditions. Thus, we also
 investigated whether the decision rules of family members according to
 offspring heterozygosity were affected by brood size, as a proxy of the
 strength of sibling conflict. First, we found that chick individual
 heterozygosity was positively although weakly associated with individual
 body mass. Mean brood heterozygosity did not predict fledging success, but
 broods that fledged more chicks showed a higher number of less common
 alleles. Interestingly, fathers, but not mothers, favored heterozygous
 broods with many nestlings, that is, heterozygous broods with higher
 potential for sibling conflict. Moreover, the lower the mean brood
 heterozygosity the stronger the begging intensity when parents were
 absent, regardless of brood size. Finally, the degree of relatedness among
 nestlings was not associated with any behavioral parameter, supporting a
 more prominent role for heterozygosity in shaping intra-family
 interactions. Importantly, our findings suggest sex-specific rules of
 parental care according to offspring heterozygosity and that genetic
 diversity is associated with lower sibling competition.
description: Nest average
 dataThis database includes
 average behavioural data per nest (prey size, feeding rates, begging
 intensity during feeding bouts and begging intensity when parents are
 absent).nest average
 data.csvChick individual
 dataThis database includes
 chick individual measurements (tarsus and body mass) as well as chick
 sex.chick
 data.csv
DOI: 10.5061/dryad.t8m55vv
title: Data from: Framing advance care planning in Parkinson disease: patient and care partner perspectives

description: Objective: Advance care planning (ACP) is a core quality measure in caring
 for individuals with Parkinson’s disease (PD) and there are no best
 practice standards for how to incorporate ACP into PD care. This study
 describes patient and care partner perspectives on ACP to inform a patient
 and care partner-centered framework for clinical care. Methods:
 Qualitative descriptive study of 30 patients and 30 care partners affected
 by PD within a multi-site, randomized clinical trial of neuropalliative
 care compared to standard care. Participants were individually interviewed
 about perspectives on ACP, including prior and current experiences,
 barriers to ACP, and suggestions for integration into care. Interviews
 were analyzed using theme analysis to identify key themes. Results: Four
 themes illustrate how patients and care partners perceive ACP as part of
 clinical care: 1) personal definitions of ACP vary in the context of PD;
 2) patient, relationship, and healthcare system barriers exist to engaging
 in ACP; 3) care partners play an active role in ACP; 4) a palliative care
 approach positively influences ACP. Taken together, the themes support
 clinician initiation of ACP discussions and interdisciplinary approaches
 to help patients and care partners overcome barriers to ACP. Conclusions:
 ACP in PD may be influenced by patient and care partner perceptions and
 misperceptions, symptoms of PD (e.g. apathy, cognitive dysfunction,
 disease severity), and models of clinical care. Optimal engagement of PD
 patients and care partners in ACP should proactively address
 misperceptions of ACP and utilize clinic teams and workflow routines to
 incorporate ACP into regular care.
description: Appendix
 3Themes and Illustrative
 QuotationsNEUROLOGY_2018_943506 appndx
 3.docx
DOI: 10.5061/dryad.2gb8f4j
title: Data from: Description of a new species of Hedruris Nitzsch, 1821 (Nematoda, Hedruridae) from freshwater turtles in Argentina, with information on its life cycle and a review of the genus’s host and geographic distribution

description: Hedruris dratini n. sp. (Nematoda, Hedruridae) is described from
 freshwater turtles in Argentina and information about its life cycle
 provided. The new species differs from the remaining species of the genus
 by possessing an excretory pore, and the nerve ring and deirids being
 positioned at equal distance from the anterior end. Additionally, H.
 dratini n. sp. has mammilated eggs and males possess nine pairs of caudal
 papillae. The first life cycle within the genus including an amphipod as
 intermediate host and a reptile as a definitive host is presented.
 Furthermore, the host and geographic distribution of species of the genus
 Hedruris Nitzsch, 1821 are analyzed. Although the genus has a cosmopolitan
 distribution and parasitizes a great diversity of hosts, the majority of
 its species follow a Gondwanian distribution and its preferred hosts are
 amphibians.
description: Video
 1The
 video shows several specimens of Hedruris dratini in a petri dish filmed
 from the eyepiece of a stereoscopic microscope. The individuals were
 removed from the stomach of a specimen of Hydromedusa tectifera hit on a
 road hours ago.
DOI: 10.5061/dryad.3t2v0f9
title: Data from: Perspective-taking Across Cultures: Shared biases in Taiwanese and British Adults

description: The influential hypothesis by Markus and Kitayama (1991) postulates that
 individuals from interdependent cultures place others above self in
 interpersonal contexts. This led to the prediction and finding that
 individuals from interdependent cultures are less egocentric than those
 from independent cultures (Wu et al., 2013; Wu & Keysar, 2007).
 However, variation in egocentrism can only provide indirect evidence for
 the Markus and Kitayama hypothesis. The current study sought direct
 evidence by giving British (independent) and Taiwanese (interdependent)
 participants two perspective-taking tasks on which an other-focused
 “altercentric” processing bias might be observed. One task assessed the
 calculation of simple perspectives, the other assessed the use of others’
 perspectives in communication. Sixty-two Taiwanese and British adults were
 tested in their native languages at their home institutions of study.
 Results revealed similar degrees of both altercentric and egocentric
 interference between the two cultural groups. This is the first evidence
 that listeners account for a speaker’s limited perspective at the cost of
 their own performance. Furthermore, the shared biases point towards
 similarities rather than differences in perspective-taking across
 cultures.
description: Culture
 dataTrial level data from
 the director task (s3data.csv) and the visual perspective-taking task
 (VPT.csv).Culture R
 codeR
 code used for data analysis
DOI: 10.25934/00002502
title: A Phase 3, Randomized, Placebo-Controlled, Blinded, Multicenter Study of the Induction and Maintenance of Clinical Response and Remission by Vedolizumab (MLN0002) in Patients With Moderate to Severe Crohn's Disease

description: The primary purpose of this study was to determine the effect of vedolizumab induction treatment on clinical response and remission at 6 weeks and to determine the effect of vedolizumab maintenance treatment on clinical remission at 52 weeks.
DOI: 10.25934/00006457
title: A Phase 3, Open-label Study to Determine the Long-term Safety and Efficacy of Vedolizumab (MLN0002) in Subjects With Ulcerative Colitis and Crohn's Disease

description: The purpose of this multicenter, open-label study is to collect data on the occurrence of important clinical safety events resulting from chronic vedolizumab (MLN0002) administration.
DOI: 10.25934/pr00007404
title: A Study to Assess the Correlation Between  Harvey Bradshaw Index and Patient Reported Outcome 2 in Crohn's Disease Patients Enrolled in Large Scale Randomized Controlled Trials

description: Crohn's disease (CD) is a chronic inflammatory condition of the gastrointestinal tract that is characterized by repeated episodes of abdominal pain, diarrhea, and weight loss.  This disease predominantly affects the young, resulting in poor quality of life and can lead to severe consequences including colorectal cancer.  

The Impact Report by Crohn’s and Colitis Canada in 2012 conservatively estimated the total annual direct and indirect costs of inflammatory bowel disease at $11,900/person. In 2012, 104,000 Canadians were living with CD, equating to a total national cost of over $1.5 billion annually; thus, effective strategies are needed for optimizing medical care for CD while reducing the risk of side effects and minimizing costs. The use of drug concentrations enables optimization of therapies.  

Several clinical indices are available for use when treating the disease, including the Harvey Bradshaw Index (HBI) and Patient Reported Outcome 2 (PRO2).  However it is not clear which index is best for use in clinical practice.  This study will assess how closely the two indices agree with each other and with other markers of disease activity to help guide tools in practice.  It will also help clinicians interpret data.  

The authors proposed to assess data from large trials that have been published to assess the correlation between the clinical indices and other markers of disease activity.  Since these data have been already been collected it will provide an answer relatively quickly.
DOI: 10.5061/dryad.18j31ch
title: Data from: Virus evolution in Wolbachia-infected Drosophila

description: Wolbachia, a common vertically transmitted symbiont, can protect insects
 against viral infection and prevent mosquitoes from transmitting viral
 pathogens. For this reason, Wolbachia-infected mosquitoes are being
 released to prevent the transmission of dengue and other arboviruses. An
 important question for the long-term success of these programs is whether
 viruses can evolve to escape the antiviral effects of Wolbachia. We have
 found that Wolbachia altered the outcome of competition between strains of
 the DCV virus in Drosophila. However, Wolbachia still effectively blocked
 the virus genotypes that were favoured in the presence of the symbiont. We
 conclude that Wolbachia did cause an evolutionary response in viruses but
 this has little or no impact on the effectiveness of virus-blocking.
description: Clustal alignment of
 Drosophila C Virus isolates genome sequencesalignment_DCV_isolates.fasAllele frequency analysis of evovled DCV populationsOutput file generated using PoPoolation2DCV_snps_rc.txtR script for reformatting and filtering DCV sequencing dataSequencing data reformatting and filtering.RR script for Principal Component and Discriminant AnalysisPCA and DAPC.RR script for running Mantel test on pairwise genetic distancesMantel test.RVirus titer data for isolates DCV-C -EB and -MVirus titer data - DCV isolates.txtR function to compute nls mcmc confidence intervalsnls mcmc confidence intervals.RR script for DCV titer time-course analysisDCV titer time-course analysis_DCV isolates.RDCV-C and non-DCV-C base calls per sequencing readBase calls matching DCV-C specific alleles were identified using custom script snps_by_read.R and the 150 bp paired-end sequencing data generated from the 24 DCV populations evolved with and without Wolbachia. Each row stands for a given sequencing read. Each column indicates for each DCV-C specific allele whether the base call matches the DCV-C enome (D) or not (ND). x and y respectively stand for forward and reverse sequencing read belonging to the same pair.readsummary_overlap_allsamples.csvR script for generating DCV-C and non DCV-C base calls by sequencing readsnps_by_read.RR script for estimating sequencing error rate and recombinationrecombination2.RDCV-C and non-DCV-C base calls per sequencing readBase calls matching DCV-C specific alleles were identified using custom script snps_by_read.R and the 250 bp paired-end sequencing data generated from the 24 DCV populations evolved with and without Wolbachia. Each row stands for a given sequencing read. Each column indicates for each DCV-C specific allele whether the base call matches the DCV-C genome (D) or not (ND). x and y respectively stand for forward and reverse sequencing read belonging to the same read pair.readsummary_overlap_allsamples_allinvariantreads.csvR script for generating DCV-C and non DCV-C base calls by sequencing readsnps_by_read.RR script for estimating sequencing error and recombination ratesrecombination2.R