cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zpc866t78
title: Redox controls RecA protein activity via reversible oxidation of its methionine residues

description: Reactive oxygen species (ROS) cause damage to DNA and proteins. The RecA
 protein plays a central role in the bacterial response to DNA damage. Here
 we report that RecA itself is also targeted by ROS. In vivo consequences
 of RecA oxidation include defects in SOS induction, DNA repair efficiency,
 and P1 transduction. In vitro, oxidized RecA fails to display ATPase
 activity, DNA strand exchange capacity and formation of nucleofilaments.
 Consistently, mass spectrometry analysis of oxidized RecA revealed that
 four out of 9 Met residues have been converted to methionine sulfoxide
 (Met-O). Specifically, mimicking the oxidation of Met35 by changing it for
 Gln caused complete loss of function whereas mimicking oxidation of Met164
 resulted in constitutive SOS activation and loss of recombination
 activity. The harmful effects of oxidation of RecA were mitigated by
 repairing activities of methionine sulfoxide reductases MsrA and MsrB,
 which suppressed all ROS-induced modifications of RecA activity. This work
 identifies RecA as a substrate of the anti-ROS activity of the MsrA/B
 enzymes. These findings indicate that under oxidative stress, MsrA/B
 maintains a level of reduced functional RecA necessary to carry out both
 efficient recombination and SOS regulation. The implication of this work
 is that ROS might inflict damages to DNA both directly and indirectly via
 hampering RecA repair activity.
DOI: 10.5061/dryad.79cnp5ht3
title: Knowledge and attitudes on infant feeding among Namibian medical students

description: Understanding the level of knowledge and attitudes of medical students on
 breastfeeding provides an avenue for interventions that aim at providing
 them with adequate training on breastfeeding to future health
 professionals. We aimed to determine the attitudes on infant feeding and
 knowledge of breastfeeding among themedical students at the University of
 Namibia, Namibia. We conducted a cross-sectional survey of the medical
 students at the University of Namibia, Hage Geingob Campus, Namibia. Study
 participants who consented and from any year of study were included in the
 study by stratified random sampling based on the year of study. Interviews
 were administered through a pretested anonymous online questionnaire
 powered by google forms over 1 month. The questionnaire used contained
 information on student demographics, an adapted Iowa Infant Feeding
 Attitude scale to assess attitudes on infant feeding, and items to assess
 their knowledge on breastfeeding.
DOI: 10.5061/dryad.zgmsbcc8z
title: Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer

description: Small cell lung cancer (SCLC) is classified as a high-grade neuroendocrine
 (NE) tumor, but a subset of SCLC has been termed “variant” due to the loss
 of NE characteristics. In this study, we computed NE scores for
 patient-derived SCLC cell lines and xenografts, as well as human tumors.
 We aligned NE properties with transcription factor-defined molecular
 subtypes. Then we investigated the different immune phenotypes associated
 with high and low NE scores. We found repression of immune response genes
 as a shared feature between classic SCLC and pulmonary neuroendocrine
 cells of the healthy lung. With loss of NE fate, variant SCLC tumors
 regain cell-autonomous immune gene expression and exhibit higher
 tumor-immune interactions. Pan-cancer analysis revealed this NE
 lineage-specific immune phenotype in other cancers. Additionally, we
 observed MHC I re-expression in SCLC upon development of chemoresistance.
 These findings provide a new framework to guide design of treatment
 regimens in SCLC.
DOI: 10.5061/dryad.rr4xgxd72
title: Tropical riparian forests in danger from large savanna wildfires

description: 1. Tropical savannas are known for the fire-prone ecosystems, yet,
 riparian evergreen forests are another important landscape feature. These
 forests usually remain safe from wildfires in the wet riparian zones. With
 global changes, large wildfires are now more frequent in savanna
 landscapes, exposing riparian forests to unprecedented impact. 2. In 2017,
 a large wildfire spread across the Chapada dos Veadeiros National Park, an
 iconic UNESCO site in central Brazil, raising concerns about its impact on
 the fire-sensitive ecosystems. By combining remote sensing analysis of
 Google Earth images (2003-2019) with detailed field information from 36
 sites, we assessed wildfire impacts on riparian forests. For this, we
 measured the structure of trees, saplings and herbaceous plants, as well
 as topsoil variables. 3. Since 2003, all riparian forests had canopy cover
 above 90 %, but after 2017, canopy cover dropped to 20 % in some forests,
 indicating large variation in wildfire damage. A closer look in the field
 revealed that, on average, the wildfire killed 52 % of adult trees and 87
 % of tree saplings in flooded forests. In non-flooded forests, impacts on
 adult trees were negligible, but fire killed 75 % of tree saplings.
 Opportunistic vines and the invasive grass Melinis minutiflora were
 already present in severely disturbed flooded forests. In all forests,
 impacts on many ecosystem variables were related to canopy damage, a
 variable measurable from satellite. Overall, seasonally flooded riparian
 forests were the most severely impacted, possibly due to the relatively
 thinner barks of their trees. 4. Synthesis and applications. Our findings
 reveal how riparian forests embedded in tropical savanna landscapes are in
 danger from large wildfires. The destruction of some forests has opened
 space for new plant species that may propel a shift to an alternative
 ecosystem state. Riparian forests are habitat of large savanna animals and
 their loss could affect entire trophic networks. Managing wildfires and
 invasive grasses locally is probably the best strategy to maintain
 riparian forests resilient. As wildfire regimes intensify in tropical
 savanna landscapes, our findings stress the need for an integrated
 management that considers riparian forests as a vulnerable element of the
 system.
DOI: 10.7280/d19987
title: The tale of two ice shelves: Zachariae Isstrøm and Nioghalvfjerdsfjorden, Northeast Greenland

description: Oceanography and gravity data of Northeastern Greenland reveal ocean
 temperature and bathymetry in front of Zachariae Isstrøm (ZI) and
 Nioghalvfjerdsfjorden (79N), which hold a 1.1-m sea-level rise ice volume
 equivalent but underwent different evolutions. Sub-surface, warm, salty
 water of Atlantic origin has easier access to ZI than to 79N because of
 bathymetric barriers. We reconstruct ice removal by the ocean at the
 grounding line and floatation retreat from thinning to explain the
 observed grounding line retreat since 1979. The agreement between observed
 and calculated retreat demonstrates that ocean thermal forcing is a major
 control on the glacier evolution and undercutting of grounded ice must be
 included in numerical ice sheet models to reproduce the high rates of
 retreat.
description: This dataset includes all the data files we used and produced for
 this manuscript: 1. Ocean flux gates of 79N and
 ZI. 2. Bathymetry inferred from gravity of 79N and
 ZI. 3. Grounding line positions from year 1979 to 2019
 of 79N and ZI. 4. All CTDs used to construct thermal
 forcing in Norske Trough.(Lat, Lon, Depth, Salinity,
 Temperature). 5. Greenland basins shapefile.
 6. ICESat-2 data in Northeast area we used to calculate the
 groundling line in 2019.
DOI: 10.5061/dryad.9p8cz8wf3
title: The names don’t matter but the numbers do: searching for stability in Carboniferous brachiopod paleocommunities from the North American Midcontinent

description: A key question in paleoecology and macroevolution is whether assemblages
 of species (paleocommunities) are persistent entities that endure over
 millions of years. Whilst community turnover in the face of abiotic change
 is the presumed norm, paleocommunities have been shown to persist for long
 time periods and regardless of environmental disruption. It remains an
 open question however, as to what processes allow for this. We investigate
 these questions by analyzing the Carboniferous brachiopod paleocommunities
 from the Midcontinent of North America. These diverse communities were
 subjected to repeated and geologically rapid changes in sea level. Using a
 suite of statistical techniques, we characterize the nature and scope of
 changes in these paleocommunities over time. We find that, at the
 paleocommunity scale, there is no evidence for obdurate ecological stasis,
 with fluctuations in both taxonomic composition and the associated
 abundance of taxa. However, at a higher ecological scale, stability is
 manifest, as diversity patterns remain stable across time, with a
 consistent number of species that can exist in any given paleocommunity.
 This suggests ecological rules such as taxon packing are in effect,
 resulting in a form of ecological stability even in the face of constant
 disequilibrium, and parallels ecological patterns of disruption and
 recovery previously observed for invertebrate communities from modern
 marine systems. Based on these results, we advocate for consideration of
 different hierarchical entities and scales when interpreting the
 ecological dynamics of fossil assemblages, as focusing exclusively on
 changes in taxon identity/abundance or diversity levels can lead to very
 different results.
DOI: 10.5061/dryad.95x69p8jc
title: Data from: Minimum size limits and the reproductive value of numerous, young, mature female fish

description: Fisheries management relies on various catch and effort controls to
 preserve spawning stock biomass and maximise sustainable yields while
 limiting fishery impacts on marine ecosystems. These include
 species-specific minimum or maximum size limits to protect either small
 non-reproductive sub-adults, a portion of reproductively mature adults, or
 large highly fecund individuals. Protecting size classes of mature fish is
 expected to yield a viable source of larvae for replenishing populations
 and reduce the risk of recruitment overfishing, yet size-specific
 recruitment contributions have rarely been assessed empirically. Here we
 apply genetic parentage analysis to measure the reproductive success of a
 size-structured population of a commercially important species of coral
 grouper (Plectropomus maculatus - Serranidae) in no-take marine reserves
 in the Great Barrier Reef Marine Park, Australia. Although the per-capita
 reproductive success of individual fish increases rapidly with
 body-length, the numerous young mature female fish (NYMFFs), below the
 minimum size limit (38 cm total length), were responsible for generating
 disproportionately large contributions (36%) towards larval replenishment
 of both fished and reserve reefs. Our findings indicate that minimum size
 limits are an effective harvest control measure to safeguard a portion of
 the spawning stock biomass for coral grouper and supplement recruitment
 subsidies assured from no-take marine reserves.
description: Methods and results appear in manuscript
description: Required data of sampled adults and offspring-assigned adults
 from genetic parentage analysis, as well as abundance data of the target
 species are provided as .csv files. See attached R file
 ‘fit.distribution.gamma.R’ in order to execute Gamma distribution fit. The
 script for all analyses and results is included in the R Markdown
 file.
DOI: 10.5061/dryad.nk98sf7s3
title: Photo-activatable Ub-PCNA probes reveal new structural features of the S. cerevisiae Polη/PCNA complex

description: The Y-family DNA polymerase η (Polη) is critical for the synthesis past
 damaged DNA nucleotides in yeast through translesion DNA synthesis (TLS).
 TLS is initiated by monoubiquitination of proliferating cell nuclear
 antigen (PCNA) and the subsequent recruitment of TLS polymerases. Although
 individual structures of the Polη catalytic core and PCNA have been
 solved, a high-resolution structure of the complex of Polη/PCNA or
 Polη/monoubiquitinated PCNA (Ub-PCNA) still remains elusive, partly due to
 the disordered Polη C-terminal region and the flexibility of ubiquitin on
 PCNA. To circumvent these obstacles and obtain structural insights into
 this important TLS polymerase complex, we developed photo-activatable PCNA
 and Ub-PCNA probes containing a p-benzoyl-L-phenylalanine (pBpa)
 crosslinker at selected positions on PCNA. By photo-crosslinking the
 probes with full-length Polη, specific crosslinking sites were identified
 following tryptic digestion and tandem mass spectrometry analysis. We
 discovered direct interactions of the Polη catalytic core and its
 C-terminal region with both sides of the PCNA ring. Model
 building using the crosslinking site information as a
 restraint revealed multiple conformations of Polη in the
 polymerase complex. Availability of the photo-activatable PCNA and Ub-PCNA
 probes will also facilitate investigations into other PCNA-containing
 complexes important for DNA replication, repair and damage
 tolerance. 
description: Dataset was collected by Q-exative Orbitrap. In-gel digestion was carried out for crosslinking products. Samples were reduced by DTT, alkylated by iodoacetamide, trypsin digested and desalted by C18 ZipTip before Q-exative Orbitrap analysis. Mgf files are spectrum files used for MeroX analysis. Zhrm files are result from MeroX analysis. Protein docking models are saved as cif files.
description: The following data contains the mass spectrometry file in the
 .raw, .mgf and . zhrm file. The .raw file can be opened by the Thermo
 Fisher Xcalibur software. The .mgf fils is generated by the Thermo Fisher
 Proteome Disocoverer 1.4 for the analysis of the crosslinking peptides by
 the MeroX Software. The .zhrm file is the result file of the identified
 crosslinking peptides and can be opened by the MeroX software. The .cif
 file is the docking result from HADDOCK which can be opened by the PyMOL
 software.  Detailed explanataion of each file is in the readme
 file.
DOI: 10.5061/dryad.zkh18938m
title: Survey of Core Facilities Raw Data

description: Recently, it has become evident that academic research faces issues with
 the reproducibility of research data. As Core Facilities (CFs) have a
 central position in the research infrastructure they are able to promote
 and disseminate good research standards through their users. To identify
 the most important factors for research quality, we polled 253 CFs across
 Europe about their practices and analysed in detail the interaction
 process between CFs and their users, from the first contact to the
 publication of the results. Although the survey showed that CFs aim to
 train and advise their users, it highlighted the following areas, the
 improvement of which would directly increase research quality: 1)
 motivating users to follow the advice and procedures for best research
 practice, 2) providing clear guidance on data management practices, 3)
 improving communication along the whole research process and 4) clearly
 defining the responsibilities of each party.
description: We developed a 68-question online survey asking various questions
 about research quality in core facilities (CFs) using Limesurvey software.
 We sent the survey individually to 1000 CFs’ leaders by email. In
 addition, our survey was publicized in the CTLS newsletter (Core
 Technologies for Life Sciences) and several facilities we contacted by
 initial email further forwarded the survey link to their colleagues. The
 survey was open from December 2019 to July 2020. All survey participants
 were anonymous. We received 276 total forms (28% participation rate), 253
 of which were complete. The survey contained yes/no,
 multiple-choice and open-field text questions. The survey data was
 analysed using Microsoft Office 365 Excel. We had 28 free text fields to
 allow the respondents express themselves freely, to eliminate potential
 bias stemming from suggested answers. Open-field answers were evaluated by
 reading each of them personally and defining categories manually based on
 the replies so that they correspond to the opinions of the participants as
 faithfully as possible (see the last sheet “explanations” of the excel
 file). Keywords were then chosen to allow automatic counting in
 Excel. We analysed the data using standard Excel tools
 in three different ways: 1) all facilities together, 2) facilities grouped
 by their type/specialization (genomics, microscopy, etc) and 3) grouped by
 their operating mode (full-, hybrid-, self-service).
DOI: 10.5061/dryad.w9ghx3fn7
title: Characteristics of households that were interviewed in a study that investigated factors driving tree species in cocoa farms in Cote d'Ivoire

description: 1. Intensive cocoa production in Côte d’Ivoire, the World’s leading cocoa
 producer, has grown at the expense of forest cover. To reverse this trend,
 the country has adopted a ‘zero deforestation’ agricultural policy and
 committed to rehabilitate its forest cover through the planting of
 high-value tree species in cocoa landscapes using a participatory
 approach. However, less is known on the factors influencing farmers’
 introduction of high-value tree species in cocoa landscapes. 2. We tested
 the hypothesis that ten factors previously reported to influence
 agroforestry systems adoption predict the number and choice of tree
 species that farmers introduce in cocoa farms. We interviewed 683
 households in the cocoa-producing zone of Côte d’Ivoire and counted tree
 species in their cocoa farms. 3. On average two tree species were recorded
 per surveyed farm. Generalized Poisson regression models revealed that
 cocoa production area, experience in tree planting and expected benefits
 influence tree species introduction through planting or ‘retention’ when
 clearing land for cocoa establishment. Age of farmer also influenced (P =
 0.017) farmers’ tree species planting in cocoa farms. Few tree species
 were introduced in current intensive cocoa-production areas than in ‘old
 cocoa-loop’ and forested areas. The number of tree species introduced in
 cocoa farms increased with expected benefits and experience in tree
 planting. The number of planted tree species also increased with farmers’
 age. Tree species were mostly selected for provision of shade to cocoa,
 production of useful tree products (38%) and income from the sale of these
 products (7%). Fruit tree species were the most planted while timber tree
 species were mostly spared when clearing land for cocoa production.
 Synthesis and applications. Agroforestry is gaining momentum in Côte
 d’Ivoire, as public and private institutions including the World
 Agroforestry Centre are developing and deploying multi-strata cocoa-based
 agroforestry systems. The results of the present study can guide the
 design and implementation of biodiverse cocoa-based agroforestry in the
 cocoa-producing zones of the country
description: A questionnaire was used to interviewed 683 cocoa households in
 the cocoa-producing zone of Cote d'Ivoire. Households were sampled
 using systematic sampling as described by Zinger (1963). The number of
 tree species were also counted in the cocoa farms of interviewees and
 recorded.
DOI: 10.5061/dryad.dz08kprw9
title: Trait-fitness associations do not predict within-species phenotypic evolution over 2 million years

description: Long-term patterns of phenotypic change are the cumulative results of tens
 of thousands to millions of years of evolution. Yet, empirical and
 theoretical studies of phenotypic selection are largely based on
 contemporary populations. The challenges in studying phenotypic evolution,
 in particular trait-fitness associations in the deep past, are barriers to
 linking micro- and macroevolution. Here, we capitalize on the unique
 opportunity offered by a marine colonial organism commonly preserved in
 the fossil record to investigate trait-fitness associations over 2 million
 years. We use the density of female polymorphs in colonies of Antartothoa
 tongima as a proxy for fecundity, a fitness component, and investigate
 multivariate signals of trait-fitness associations in six time intervals
 on the backdrop of Pleistocene climatic shifts. We detect negative
 trait-fitness associations for feeding polymorph (autozooid) sizes,
 positive associations for autozooid shape but no particular relationship
 between fitness and brood chamber size. In addition, we demonstrate that
 long-term trait patterns are explained by palaeoclimate and to a lesser
 extent by ecological interactions. Our analyses show that
 macroevolutionary outcomes of trait evolution are not a simple scaling-up
 from the trait-fitness associations.
DOI: 10.5061/dryad.tb2rbnzzh
title: Fast and accurate estimation of species-specific diversification rates using data augmentation

description: Diversification rates vary across species as a response to various
 factors, including environmental conditions and species-specific features.
 Phylogenetic models that allow accounting for and quantifying this
 heterogeneity in diversification rates have proven particularly useful for
 understanding clades diversification. Recently, we introduced the
 cladogenetic diversification rate shift model (ClaDS), which allows
 inferring subtle rate variations across lineages. Here we present a new
 inference technique for this model that considerably reduces computation
 time through the use of data augmentation and provide an implementation of
 this method in Julia. In addition to drastically reducing computation
 time, this new inference approach provides a posterior distribution of the
 augmented data, that is the tree with extinct and unsampled lineages as
 well as associated diversification rates. In particular, this allows
 extracting the distribution through time of both the mean rate and the
 number of lineages. We assess the statistical performances of our approach
 using simulations and illustrate its application on the entire bird
 radiation.
description: These additionnal data contains supplementary figures supporting
 the paper, as well as a tutorial for the use of the Julia
 package. The .jld2 file is the result of the run of
 ClaDS on the complete bird phylogeny computed with molecular data from Jetz
 (2012) with the
 Hackett
 backbone, containing 6670 species. We use TreeAnnotator
 from the
 software Beast with the Common Ancestor option for node height (Bouckaert
 2019) to obtain
 a Maximum Clade
 Credibility (MCC) tree computed from a sample of
 1000  trees from
 the posterior distribution. We fix the sampling fractions for each of the
 subtrees of the
 tree from Jetz (2012) as the ratio between the number of
 species in the molecular phylogeny over that in the phylogeny including
 all bird species. We attach the results of this analysis as a
 supplementary material to this paper.
   Bouckaert, R., T. G. Vaughan, J.
 Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina,<br> J.
 Heled, G. Jones, D. Kühnert, N. De Maio, et al. 2019. Beast 2.5: An
 advanced software<br> platform for bayesian evolutionary analysis.
 PLoS computational biology 15:e1006650. Jetz, W., G.
 Thomas, J. Joy, K. Hartmann, and A. Mooers. 2012. The global diversity of
 birds in<br> space and time. Nature 491:444.