cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.98sf7m0hh
title: Colistin kills bacteria by targeting lipopolysaccharide in the cytoplasmic membrane - primary data for all experiments described in the manuscript

description: Colistin is an antibiotic of last resort, but has poor efficacy and
 resistance is a growing problem. Whilst it is well established that
 colistin disrupts the bacterial outer membrane by selectively targeting
 lipopolysaccharide (LPS), it was unclear how this led to bacterial
 killing. We discovered that MCR-1 mediated colistin resistance in
 Escherichia coli is due to modified LPS at the cytoplasmic rather than
 outer membrane. In doing so, we also demonstrated that colistin exerts
 bactericidal activity by targeting LPS in the cytoplasmic membrane. We
 then exploited this information to devise a new therapeutic approach.
 Using the LPS transport inhibitor murepavadin, we were able to cause LPS
 accumulation in the cytoplasmic membrane of Pseudomonas aeruginosa, which
 resulted in increased susceptibility to colistin in
 vitro and improved treatment efficacy in vivo. These
 findings reveal new insight into the mechanism by which colistin kills
 bacteria, providing the foundations for novel approaches to enhance
 therapeutic outcomes.
description: Detailed in the preprint and manuscript.
description: Data files can be viewed in the software Prism - GraphPad
DOI: 10.5061/dryad.b5mkkwhc7
title: Genome wide IStraw90 SNP array probes

description: The University of Florida strawberry (Fragaria ×ananassa) breeding program
 has implemented genomic  prediction (GP) as a tool for choosing
 outstanding parents for crosses over the last five seasons. This has
 allowed the use of some parents one year earlier than with traditional
 methods, thus reducing the duration of the breeding cycle. However, as the
 number of breeding cycles increases over time, greater knowledge is needed
 on how multiple cycles can be used in the practical implementation of GP
 in strawberry breeding. Advanced selections and cultivars totaling 1,558
 unique individuals were tested in field trials for yield and fruit quality
 traits over five consecutive years and genotyped for 9,908 SNP markers.
 Prediction of breeding values was carried out using Bayes B models.
 Independent validation was carried out using separate trials/years as
 training (TRN) and testing (TST) populations. Single-trial predictive
 abilities for five polygenic traits averaged 0.35, which was reduced to
 0.24 when individuals common across trials were excluded, emphasizing the
 importance of relatedness among training and testing populations. Training
 populations including up to four previous breeding cycles increased
 predictive abilities, likely due to increases in both training population
 size and relatedness. Predictive ability was also strongly influenced by
 heritability, but less so by changes in linkage disequilibrium and
 effective population size. Genotype by year interactions were minimal. A
 strategy for practical implementation of GP in strawberry breeding is
 outlined that uses multiple cycles to predict parental performance and
 accounts for traits not included in GP models when constructing crosses.
 Given the importance of relatedness to the success of GP in strawberry,
 future work could focus on the optimization of relatedness in the design
 of TRN and TST populations to increase predictive ability in the
 short-term without compromising long-term genetic gains.
description: DNA samples were sent to Affymetrix for genome scan using
 IStraw90 adn IStraw35 SNP arrays.
description: There are missing values in the dataset represented as
 "NaN".
DOI: 10.5061/dryad.hx3ffbgd1
title: Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers

description: Under the selfish centromere model, costs associated with female meiotic
 drive by centromeres select on interacting kinetochore proteins to restore
 Mendelian inheritance. We directly test this model in yellow monkeyflowers
 (Mimulus guttatus), which are polymorphic for a costly driving centromere
 (D). We show that the D haplotype is structurally and genetically distinct
 and swept to a high stable frequency within the past 1500 years.
 Quantitative genetic analyses reveal that variation in the strength of
 drive primarily depends on the identity of the non- D centromere, but also
 identified an unlinked modifier coincident with kinetochore protein
 Centromere-specific Histone 3 A (CenH3A). CenH3A has also experienced a
 recent (&lt;1000 years) selective sweep in our focal population,
 consistent with ongoing interactions with D shaping its evolution.
 Together, our results demonstrate an active co-evolutionary arms race
 between the DNA and protein components of the meiotic machinery, with
 important consequences for individual fitness and molecular
 divergence. 
description: These are F<sub>2</sub> genotype-phenotype data used
 for mapping of loci contributing to differences in the strength of
 heterospecific vs. conspecific centromere-associated drive by the driving
 <em>D</em> haplotype at MDL11 in <em>Mimulus nasutus x
 M. guttatus </em>hybrids. The %D<sub>fem</sub> phenotype
 is the inferred female transmission of <em>D</em> allele (vs.
 nondriving <em>d</em> from <em>M. nasutus</em> or
 <em>D<sup>-</sup></em> from <em>M.
 guttatus</em>) to selfed F<sub>3</sub> progeny, assuming
 Mendelian transmission through male function. Only
 F<sub>2</sub>s with at least 12
 F<sub>3</sub> progeny genotyped were included in our analyses,
 but all genotyped individuals were used for estimation of
 <em>D</em> transmission to F<sub>2</sub>s and are
 included for completeness. The CenH3A genotype (NN, GG, NG<sub>767
 </sub>and NG<sub>160 </sub>for the two classes of
 interspecific heterozygotes) are from an exon-primed intron-spanning PCR
 marker that could distinguish all 3 parental alleles. The genome-wide
 mapped genotypes (coded as N, G, H) were derived from
 multiplex-shotgun-genotyping, window-calling, and mapping protocols
 described in Flagel et al. 2018 (PLOS Computational Biology). Sheet 1 has
 the genotype-phenotype matrix, sheet 2 the marker positions on the genetic
 linkage map and the v1 contigs of <em>M. guttatus,</em> and v1
 windows can be matched to v2 and newer genome assemblies (with gene
 annotations) via the information in sheet 3.
description: The genotype-phenotype values provided are those analyzed,
 including missing data (as empty cells) as well as data excluded from the
 phenotypic analyses (individuals with &gt;12  F3 progeny). Further
 useful details of the genotyping and phenotyping protocols are given in
 the paper.
DOI: 10.5061/dryad.prr4xgxkk
title: Risky decision and happiness task: The Great Brain Experiment smartphone app

description: This resource consists of data from a risky decision and happiness task
 that was part of The Great Brain Experiment (GBE) smartphone app. Data
 were collected from 47,067 participants aged 18+ between March 8, 2013
 and October 5, 2015. These anonymous unpaid participants
 completed the task a total of 91,058 times making approximately 2.7
 million choices and 1.1 million happiness ratings in total. This resource
 represents at least 6,000 hours of task data. A subset of 1,858
 participants also completed a depression questionnaire and answered five
 questions about their depression history.
description: Data are stored in Matlab structure arrays. The Matlab script
 Rutledge_GBE_risk_data_code.m generates key results from published
 studies. Please read the associated README file.
DOI: 10.5061/dryad.31zcrjdjw
title: Georeferenced phylogenetic analysis of a global collection of wild and cultivated Citrullus species

description: The geographical origin of watermelon (Citrullus lanatus) remains debated.
 While a first hypothesis suggests the center of origin to be west Africa,
 where a sister endemic species C. mucosospermus thrives, a second
 hypothesis suggests north-eastern Africa where the white-fleshed Sudanese
 Kordophan melon is cultivated. In this study, we infer biogeographical and
 haplotype genealogy for C. lanatus, C. mucosospermus, C. amarus, and C.
 colocynthis using non-coding cpDNA sequences (trnT-trnL and ndhF-rpl32
 regions) from a global collection of 135 accessions. In total, we
 identified 38 haplotypes in C. lanatus, C. mucosospermus, C. amarus, and
 C. colocynthis; of these, 21 were found in Africa and 17 appear endemic to
 the continent. The least diverse species was C. mucosospermus (5
 haplotypes) and the most diverse was C. colocynthis (16 haplotypes). Some
 haplotypes of C. mucosospermus were nearly exclusive to West-Africa, and
 C. lanatus and C. mucosospermus shared haplotypes that were distinct from
 those of both C. amarus and C. colocynthis. The results support previous
 findings C. mucosospermus to be the closest relative to C. lanatus
 (including subsp. cordophanus). West Africa, as a center of endemism of C.
 mucosospermus, is an area of interest in the search of the origin of C.
 lanatus. This calls for further historical and phylogeographical
 investigations and wider collection of samples in West and North-East
 Africa.
description: We used 135 accessions of fCitrullus spp. to generate sequence
 data based on chloroplast regions. Two regions of the chloroplast genome
 were amplified using the following primer pairs: 1)
 <i>ndh</i>F (5'-GAAAGGTATKATCAAYGMATATT-3') and
 <i>rpl</i>32-R (5'-CCAATATCCCTTYYTTTTCCAA-3'); and
 2) <i>trn</i>L<sup>(UAG)</sup>
 (5'-CTGCTTCCTAAGAGCAGCCT-3') and
 <i>trn</i>T<sup>(GGU)</sup>
 (5'-CCCTTTTAACTCAGTGGTAG-3'). Parsimony networks were
 constructed to infer phylogeographical relationships among haplotypes
 using TCS v1.21 (Clément et al., 2000).
description: Data can be added to other sources of information to build a meta
 analysis or combined with other chloroplast regions to infer
 phylogeny.
DOI: 10.5061/dryad.tdz08kpzh
title: Type 1 diabetes adolescent transition study

description: Objectives: Adolescents with type 1 diabetes experience dramatic
 excursions in blood sugars as they transition to adult care. Trials on
 single interventions have struggled to demonstrate lasting improvements in
 clinical outcomes. Thus, the purpose of this study was to evaluate the
 effect of a multi-component intervention on glycemic control, clinic
 attendance, and diabetes distress amongst adolescents with type 1 diabetes
 transitioning to adult health services. Design: Prospective controlled
 quasi-experimental study. Setting: Adolescents with type 1 diabetes from
 an urban academic pediatric hospital (control group) and a community
 regional hospital (intervention group) were recruited and followed for 1
 year after their last pediatric diabetes visit. Participants: 101
 adolescents with type 1 diabetes transitioning to adult care, including 68
 from the control group and 33 from the intervention group. Interventions:
 The intervention group had access to (1) a diabetes nurse transition
 coordinator, (2) joint pediatric-adult diabetes clinic visits, and (3)
 pediatric and adult clinics being in the same building. Those in the
 control group were referred to an adult diabetes provider at their last
 pediatric diabetes visit without any formal transition program or
 additional supports. Primary and secondary outcome measures: The primary
 outcome was longitudinal change in A1C. The secondary outcomes were number
 of A1C tests obtained, number of adult diabetes visits attended, time gap
 between pediatric and adult visits, and diabetes distress. Results: There
 was a difference in A1C trajectory between the control and intervention
 groups (base model p=0.004, adjusted model p=0.003). A1C continued to rise
 in the control group after the transition to adult care, whereas A1C
 decreased in the intervention group. However, there were no statistically
 significant differences in the secondary outcomes between the two groups.
 Conclusion: A multi-component intervention can mitigate the glycemic
 excursions experienced by adolescents with type 1 diabetes transitioning
 to adult care.
DOI: 10.5061/dryad.8pk0p2nmb
title: Neutrophil extracellular traps are present in the airways of ENaC-overexpressing mice with cystic fibrosis-like lung disease

description: Background: Neutrophils are key components of the exacerbated inflammation
 and tissue damage in cystic fibrosis (CF) airways. Neutrophil
 extracellular traps (NETs) trap and kill extracellular pathogens. While
 NETs are abundant in the airways of CF patients and have been hypothesized
 to contribute to lung damage in CF, the in vivo role of NETs remains
 controversial, partially due to lack of appropriate animal models. The
 goal of this study was to detect NETs and to further characterize
 neutrophilmediated inflammation in the airways of mice overexpressing the
 epithelial sodium channel (βENaC-Tg mice on C57BL/6 background) in their
 lung with CF-like airway disease, in the absence of any apparent bacterial
 infections. Methods: Histology scoring of lung tissues, flow cytometry,
 multiplex ELISA, immunohistochemistry and immunofluorescence were used to
 characterize NETs and the airway environment in uninfected, βENaC-Tg mice
 at 6 and 8 weeks of age, the most chronic time points so far studied in
 this model. Results: Excessive neutrophilic infiltration characterized the
 lungs of uninfected, βENaC-Tg mice at 6 and 8 weeks of age. The
 bronchoalveolar lavage fluid (BALF) of βENaC-Tg mice contains increased
 levels of CF-associated cytokines and chemokines: KC, MIP-1α/β, MCP-1,
 G-CSF, IL-5, and IL-6. The BALF of βENaC-Tg mice contain MPO-DNA
 complexes, indicative of the presence of NETs. Immunofluorescence and flow
 cytometry of BALF neutrophils and lung tissues demonstrated increased
 histone citrullination, a NET-specific marker, in βENaC-Tg mice.
 Conclusions: NETs are detected in the airways of βENaC-Tg mice, in the
 absence of bacterial infections. These data demonstrate the usefulness of
 the βENaC-Tg mouse to serve as a model for studying the role of NETs in
 chronic CF airway inflammation. Keywords Cystic fibrosis; neutrophil
 extracellular traps; NET; ENaC, neutrophil.
description: Some of the results have been collected by flow cytometry and
 some of them by ELISA assays. Data were collected in the attached excel
 file and processed to calculate mean values and standard deviations or
 standard errors of means, as described in the manuscript in
 detail.
description: These datasets compare different readouts between wild-type and
 betaENaC-overexpressing mice that serve as a model for cystic fibrosis
 airway disease. Most of the datasets presents the comparisons between
 these two murine genotypes. What the results mean is indicated at each
 sheet of the excel file and refer only to data presented in that sheet,
 not others. There are no missing values.
DOI: 10.5061/dryad.9w0vt4bdp
title: Specialized terminology limits the citability of scientific papers

description: Words are the building blocks of communicating science. As our
 understanding of the world progresses, scientific disciplines naturally
 enrich their specialized vocabulary (jargon). However, in the era of
 interdisciplinarity, the use of jargon may hinder effective communication
 amongst scientists that do not share a common scientific background. The
 question of how jargon limits the transmission of scientific knowledge has
 long been debated but rarely addressed quantitatively. We explored the
 relationship between the use of jargon and citations, using 21,486
 articles focusing on cave research, a multidisciplinary field particularly
 prone to terminological specialization, and where linguistic disagreement
 among peers is frequent. We demonstrate a significant negative
 relationship between the proportion of jargon words in the title and
 abstract and the number of citations a paper receives. Given that these
 elements are the hook to readers, we urge scientists to restrict jargon to
 sections of the paper where its use is unavoidable
DOI: 10.5061/dryad.8w9ghx3kw
title: Lactate receptor HCAR1 regulates neurogenesis and microglia activation after neonatal hypoxia-ischemia

description: Neonatal cerebral hypoxia-ischemia (HI) is the leading cause of death and
 disability in newborns with the only current treatment being hypothermia.
 An increased understanding of the pathways that facilitate tissue repair
 after HI may aid the development of better treatments. Here, we study the
 role of lactate receptor HCAR1 in tissue repair after neonatal HI in mice.
 We show that HCAR1 knockout mice have reduced tissue regeneration compared
 with wildtype mice. Furthermore, proliferation of neural progenitor cells
 and glial cells, as well as microglial activation was impaired.
 Transcriptome analysis showed a strong transcriptional response to HI in
 the subventricular zone of wildtype mice involving about 7300 genes. In
 contrast, the HCAR1 knockout mice showed a modest response, involving
 about 750 genes. Notably, fundamental processes in tissue repair such as
 cell cycle and innate immunity were dysregulated in HCAR1 knockout. Our
 data suggest that HCAR1 is a key transcriptional regulator of pathways
 that promote tissue regeneration after HI.
description: Tissue samples from the subventricular zone and hippocampus in
 the ipsilateral (damaged) and contralateral (undamaged) hemispheres of
 mice were dissected 3 days after HI. The samples were snap-frozen in
 liquid N<sub>2</sub> and stored at −80°C before RNA isolation.
 RNA isolation was performed using QIAGEN allprep kit, and final RNA was
 dissolved in MQ H<sub>2</sub>O and stored at −80°C. Paired-end
 sequencing was performed with the Illumina platform by BGI Tech Solutions
 (Hong Kong).
description: Each file name describes genotype, mouse number, tissue type,
 hemisphere and forward/reverse RNAseq. Abbreviations
 and explanations: HCAR = HCAR1 knockout (-/-)
 WT = wildtype (HCAR1 +/+) SVZ = subventricular
 zone HC = hippocampus IPSI =
 ipsilateral hemisphere (damaged from hypoxia-ischemia)
 CONTRA = contralateral hemisphere (undamaged, used as
 control) 1 at the end of the file name =
 forward 2 at the end of the file name =
 reverse
DOI: 10.5061/dryad.rbnzs7h9t
title: Parkinson’s disease-related brain metabolic patterns and neurodegeneration in isolated REM sleep behavior disorder

description: Objective: To elucidate the role of Parkinson’s disease (PD)-related brain
 metabolic patterns as a biomarker in isolated rapid-eye-movement sleep
 behavior disorder (iRBD) for future disease conversion. Method: This is a
 prospective cohort study consisting of 30 iRBD patients, 25 de novo PD
 patients with a premorbid history of RBD, 21 long-standing PD patients on
 stable treatment and 24 healthy controls. iRBD group was longitudinally
 followed up. All participants underwent 18F-Fluorodeoxyglucose (FDG) PET
 and were evaluated with olfaction, cognition, and the Movement disorders
 society-Unified PD Rating Scale (MDS-UPDRS) at baseline. From FDG-PET
 scans, we derived metabolic patterns from the long-standing PD group
 (PD-RP) and de novo PD group with RBD (dnPDRBD-RP). Subsequently, we
 calculated the PD-RP and dnPDRBD-RP scores in iRBD patients. We validated
 the metabolic patterns in each PD group and separate iRBD cohort (n=14).
 Result: The two patterns significantly correlated with each other and were
 spatially overlapping yet distinct. The MDS-UPDRS motor scores
 significantly correlated with PD-RP (p = 0.013) but not with dnPDRBD-RP (p
 = 0.076). In contrast, dnPDRBD-RP correlated with olfaction in butanol
 threshold test (p = 0.018) in iRBD subjects, but PD-RP did not (p = 0.21).
 High dnPDRBD-RP in iRBD patients predicted future phenoconversion with all
 cut-off ranges from 1.5 to 3 standard deviations of the control value,
 whereas predictability of PD-RP was only significant in a partial range of
 cut-off. Conclusion: The dnPDRBD-RP is an efficient neuroimaging biomarker
 that reflects prodromal features of PD and predicts phenoconversion in
 iRBD that can be applied individually.
DOI: 10.5061/dryad.2547d7wpq
title: Data from: COVID-19 prevalence and predictors in United States adults during peak stay-at-home orders

description: This was a cross-sectional nationwide survey of adults in the US conducted
 between April 24 and May 13, 2020. The survey targeted a
 representative sample of approximately 5,000 respondents. The rate of
 COVID-19 cases and testing, most frequently reported symptoms, symptom
 severity, treatment received, impact of COVID-19 on mental and physical
 health, and factors predictive of testing positive were assessed.
description: Data was collected through
 an on-line cross-sectional survey of adults (18 years or older) in the US.
 The survey was conducted in accordance with Acumen Health Research
 Institute's (AHRI) established SOPs. A random stratified sampling
 framework ensured a community-based sample with a demographic composition
 representative of the US adult population by region, gender, age, and
 race, according to the US Census (US Census American Community Survey
 5-year estimate, 2011-2015). To participate in the study, respondents were
 required to be 18 years old or older, reside in the United States, and
 confirm their voluntarily agreement to participate (participants were
 informed they could leave the survey at any time). The survey was open to
 the general population and not restricted to patients hospitalized with
 COVID-19. Participants were recruited through AHRI’s online research
 panels. Analysis was carried out with SPSS v27.0.1.0.
description: See ReadMe file (code book).
DOI: 10.5061/dryad.b8gtht7bp
title: The impact of the program for medical male circumcision on HIV in South Africa: analysis using three epidemiological models

description: Background: South Africa began offering medical male circumcision (MMC) in
 2010. We evaluated the current and future impact of this program to see if
 it is effective in preventing new HIV infections. Methods: The Thembisa,
 Goals and EMOD HIV transmission models were calibrated to South Africa’s
 HIV epidemic, fitting to household survey data on HIV prevalence, risk
 behaviors, and proportions of men circumcised, and to programmatic data on
 intervention roll-out including program-reported MMCs over 2009-2017. We
 compared the actual program accomplishments through 2017 and program
 targets through 2021 with a counterfactual scenario of no MMC program.
 Results: The MMC program averted 71,000-83,000 new HIV infections from
 2010 to 2017. The future benefit of the circumcision already conducted
 will grow to 496,000-518,000 infections (6-7% of all new infections) by
 2030. If program targets are met by 2021 the benefits will increase to
 723,000-760,000 infections averted by 2030. The cost would be $1,070-1,220
 per infection averted relative to no MMC. The savings from averted
 treatment needs would become larger than the costs of the MMC program
 around 2034-2039. In the Thembisa model, when modelling South Africa’s 9
 provinces individually, the 9-provinces-aggregate results were similar to
 those of the single national model. Across provinces, projected long-term
 impacts were largest in Free State, KwaZulu-Natal and Mpumalanga (23-27%
 reduction over 2017-2030), reflecting these provinces’ greater MMC
 scale-up. Conclusions: MMC has already had a modest impact on HIV
 incidence in South Africa and can substantially impact South Africa’s HIV
 epidemic in the coming years.
description: The data files show the results from three different HIV
 simulation models used to project the expected effects of medical male
 circumcison on the HIV epidemic in South Africa. The data are organized in
 worksheets by indicator: new HIV infections, HIV prevalence, population
 size, people living with HIV (PLHIV), the number circumcised (VMMC) and
 the number receiving antiretroviral therapy (ART).
description: The data are internally documented.