Find research datasets worth reusing

opencc-by-4.0Dec 2021View details →

Block Tectonics across Western Tibet and Multi-Millennial Recurrence of Great Earthquakes on the Karakax Fault

Table 1: Analytical results of 10Be and 26Al geochronology and surface-exposure ages at Taersa site along Karakax fault. LMC.las = UAV point cloud data of the offset shoreline along the Longmu Co fault KXF.txt = LiDAR x-y-z data of the Taersa site

opencc-by-4.0Aug 2021View details →

Data deposition of the article 'Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence'

Data deposition of the article 'Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence'

opencc-zeroSep 2021View details →

Phenotypic plasticity versus ecotypic differentiation under recurrent summer drought in two drought-tolerant pine species

1. Despite worldwide reports of high tree mortality, growing evidence indicates that many tree species are well adapted to survive repeated dry spells. The drought resilience of trees is related to their phenotypic plasticity and ecotypic differentiation. Whether these two mechanisms act at the same organisational level of a tree and involve similar plant traits is still unknown. 2. We assessed phenotypic plasticity and ecotypic differentiation across four populations of Pinus sylvestris and Pinus nigra seedlings grown for three years under a recurrent summer drought treatment or well-watered control conditions in a common garden. We measured the response to the summer drought treatment of a total of 26 traits including shoot and needle morphology, needle anatomy, and foliar macronutrients, and related the traits to the growing season water deficit (GSWD) at the location of the seed origin. 3. Foliar phenotypic plasticity in response to recurrent summer drought was surprisingly low, with the needle length and the fraction of mesophyll and phloem tissue adjusting to some extent. In comparison, shoot morphological traits were much more plastic in both species with predominant responses to the summer drought stress including shorter and less numerous apical and lateral shoots. These three traits were also correlated with GSWD at the seed origin, indicating local adaptation. In contrast, between-population variation of foliar morphological and anatomical traits, and macronutrients were mostly unrelated to the GSWD at the seed origin. 4. Consequently, phenotypic plasticity and ecotypic differentiation occurred at the same level of organisation and in the same plant traits, i.e. shoot morphology. This combination of plasticity and ecotypic differentiation allowed P. sylvestris and P. nigra seedlings to rapidly acclimate to recurrent and long-lasting dry-spells. 5. Synthesis: P. sylvestris and P. nigra seedlings showed considerable ecotypic differentiation and phenotypic plasticity of shoot morphological traits, and not foliar traits. Acclimation to recurrent severe summer drought was achieved by reducing shoot growth.

opencc-zeroOct 2021View details →

Fire recurrence and time since last fire interact to determine the supply of multiple ecosystem services by Mediterranean forests

Wildfires shape the composition and functioning of Mediterranean ecosystems, but we do not know how these ecosystems respond to both the higher fire recurrence and shorter recovery times expected for future climatic scenarios. We sampled 29 plots with different fire recurrences (from 0 to 4 fires over the past decades) and time since the last fire (up to 35 years; hereafter TSLF) in Southeast Spain, to assess the effect of fire recurrence and TSLF on 25 ecosystem attributes, five related ecosystem services (biodiversity conservation, carbon sequestration, disturbance regulation, food production, and supporting services), plus the synergies and trade-offs between them. High fire recurrence (number of fires) and TSLF interacted to determine ecosystem services but did not affect the synergies and trade-offs between them. Fire recurrence reduced many ecosystem functions and ecosystem multifunctionality. However, this effect dampened, and even became positive, for biodiversity conservation and food production services provided enough (> 20 years) time to recover. The combined effects of fire recurrence and TSLF, however, reduced carbon sequestration and had no overall effects on supporting services. Disturbance regulation, in turn, diminished drastically with the first fire, with no effect of further fires or their interaction with TSLF. Our results show which ecosystem services will suffer more from an increase in fire recurrence, and where restoration and management efforts should focus to maximize the provision of those services more demanded by stakeholders.

opencc-zeroFeb 2023View details →

Sweepstakes reproductive success via pervasive and recurrent selective sweeps

Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modeling no sweepstakes) and the Xi-Beta coalescent (modeling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.

opencc-by-4.0Feb 2022View details →

Recurrent, founder and hypomorphic variants contribute to shaping the genetic landscape of Joubert syndrome

Introduction: This database includes the raw data linked with the paper “Recurrent, founder and hypomorphic variants contribute to the genetic landscape of Joubert syndrome”. In this paper we reported eleven recurrent variants in seven distinct JS genes occurring in our large European JS cohort, including a previously unreported variant in KIAA0586 (c.1006C>T). Methods: We evaluated the frequencies of these variants in our cohort of >500 European JS patients and compared them with controls (from three large Italian non-JS cohorts and from the gnomAD database), and with an independent cohort of about 600 JS probands from the United States. Results: All variants were markedly enriched in the European JS cohort compared to all controls. When comparing allele frequencies in the two JS cohorts, the Ashkenazi Jewish founder variant (TMEM216 c.218G>T) was significantly enriched in American JS compared to European JS patients, while the MKS1 c.1476T>G variant was about ten times more frequent among European JS. Frequencies of all remaining variants were comparable in the two cohorts. Genotyping of several microsatellite markers across the gene loci in carriers of seven variants identified four novel founder haplotypes. Of note, MKS1 c.1476T>G was consistently detected in compound heterozygosity with deleterious variants in JS patients, while it was found in homozygosity in an unaffected parent. Functional studies on fibroblasts from this healthy carrier and her affected son showed a similarly reduced percentage of ciliated cells compared to unaffected controls, but much shorter cilia in the patient than in the unaffected homozygous parent, consistent with a hypomorphic effect.

opencc-by-4.0Dec 2022View details →

A physical perspective of recurrent water quality degradation: a case study in the Jiangsu coastal waters, China

This dataset is created for manuscript entitle of A physical perspective of recurrent water quality degradation: a case study in the Jiangsu coastal waters, China submitted to Journal of Geophysical Research: Oceans. This dataset should not be used without agreement from authors before the paper published.

opencc-by-4.0Feb 2023View details →

Recurrent Campylobacter jejuni infections with in vivo selection of resistance to macrolides and carbapenems – assembly dataset

Dataset This dataset comprises the genome assemblies of the first isolate collected from each clinical case (A1 and B1), together with the respective annotation. File “Cje_metadata.xlsx” contains the genome assembly statistics for each isolate, including the European Nucleotide Archive (ENA) accession numbers, genotyping and antibiotic resistance profiles. The directory “Assemblies/” contains the genome assembly (.fasta and .gbk formats) of each isolate presented in the metadata file.   Genome assembly and annotation Reads quality control and improvement, species confirmation (using the 8GB database available at https://ccb.jhu.edu/software/kraken/) and de novo assembly were performed using the INNUca v4.2.2 pipeline (https://github.com/B-UMMI/INNUca). Briefly, after reads’ quality analysis using FastQC v0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and cleaning with Trimmomatic v0.38 (http://www.usadellab.org/cms/?page=trimmomatic), genomes were de novo assembled with SPAdes 3.14.0 (http://bioinf.spbau.ru/spades) with a mean depth of coverage above 160x, and subsequently improved using Pilon v1.23. Multi-Locus Sequence Typing (MLST) was performed using mlst v2.18.1 software (https://github.com/tseemann/mlst). Genome annotation was performed with RAST server v2.0 (http://rast.nmpdr.org/). The raw sequence reads of each isolate were deposited at ENA under the study accession numbers PRJEB42628 and PRJNA505131.   Funding This work was supported by GenomePT (ref. POCI-01-0145-FEDER-022184) from Fundação para a Ciência e Tecnologia, Portugal.

opencc-by-4.0Jul 2023View details →

Search strategies for generic justification of 18F-PSMA PET/CT in the staging of primary prostate cancer and the restaging of recurrent and metastatic prostate cancer

The dataset includes the complete, reproducible search strategies for all literature databases searched during this project. The search strategies address the following research questions: RQ 1: In the primary staging of patients with high risk prostate cancer, what is the sensitivity, specificity and diagnostic accuracy of 18F-PSMA? RQ 2: In patients with biochemically recurrrent prostate cancer, what is the sensitivity, specificity and diagnostic accuracy of 18F-PSMA? RQ 3: What is the risk of adverse events (including dose) associated with receiving 18F-PSMA? RQ 4: Is 18F-PSMA uptake associated with response to treatments for metastatic prostate cancer?

opencc-by-4.0Jul 2023View details →

BriTROC-1 study: genomic landscape of recurrent ovarian high grade serous carcinoma - pre processed data

Dataset containing pre-processed data files required to replicate analysis performed in the publication "The genomic landscape of recurrent ovarian high grade serous carcinoma: the BriTROC-1 study" (<a href="https://doi.org/10.1038/s41467-023-39867-7">Smith & Bradley et al. 2023</a>).

opencc-zeroSep 2023View details →

Data from: Different effects of fire age and fire recurrence on grass and woody plant chemistry in Kafue National Park, Zambia

In savannas, fire and herbivores are important drivers of natural ecosystem processes. Fire is also used intensively for management purposes. However, reported fire effects differ between studies. Reasons for these differences are still poorly understood. Here, we investigated the effects of fire on leaf chemistry of grasses and woody plants in the savanna of the Busanga Flood Plain, Zambia, in relation to the time elapsed between plant sampling and the last fire (fire age) and the frequency of fires during the last 16 years (fire recurrence). We analyzed leaves for their nitrogen, carbon and fiber concentrations, and estimated their metabolizable energy content, reflecting feed quality for browsers and grazers. Grasses and woody plants differed in all chemical components and showed different responses to fire. Grass quality was higher at sites burnt in the year of sample collection than at sites burnt only in previous years, but did not change under different fire recurrences. Leaves of woody plants did not differ in relation to fire age but their quality increased with increasing fire recurrence. In woody plants, the carbon content responded to the interaction between fire age and fire recurrence, indicating changes in carbon allocation in response to fire. Thus, burning increased feed quality for grazers and browsers but on different temporal scales. The scale effects may contribute to the differences in resource allocation described by different studies. They merit more attention in management decisions as well as in future studies on fire effects in savanna systems.

opencc-by-4.0Sep 2023View details →

Phytoplankton metabolism in a stratified nearshore ecosystem with recurrent Harmful Algal Blooms (HABs)

Datasets from HAB monitoring program in Mallorca

Efficacy of Oral Vancomycin Prophylaxis for Prevention of Recurrent Clostridium Difficile Infection

ClinicalTrials.gov study NCT03462459. IPD Sharing: Not stated. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Re-irradiation With Fractionated Stereotactic Radiosurgery Plus Cetuximab in Patients With Recurrent Squamous Cell Carcinoma of the Head and Neck

ClinicalTrials.gov study NCT01104922. IPD Sharing: NO. Countries: 1. Publications: 1.

Rovalpituzumab Tesirine (SC16LD6.5) in Recurrent Small Cell Lung Cancer

ClinicalTrials.gov study NCT01901653. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Capecitabine and Docetaxel in Treating Patients With Recurrent or Progressive Metastatic Pancreatic Cancer

ClinicalTrials.gov study NCT00290693. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Doxorubicin and Gemcitabine in Treating Patients With Locally Recurrent or Metastatic Unresectable Renal Cell Carcinoma

ClinicalTrials.gov study NCT00068393. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Sargramostim, Vaccine Therapy, or Sargramostim and Vaccine Therapy in Preventing Disease Recurrence in Patients With Melanoma That Has Been Removed By Surgery

ClinicalTrials.gov study NCT01989572. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Irinotecan and Etoposide in Treating Patients With Recurrent, Locally Advanced, or Metastatic Breast Cancer

ClinicalTrials.gov study NCT00693719. IPD Sharing: Not stated. Countries: 1. Publications: 1.