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Open Access publication trends in the Coimbra research community – evolution and impact assessment
No full textWeb of Science bibliometric dataset used in a study aimed at evaluating how Open Access publication practices evolved over the years in the scientific community based in Coimbra (city of Portugal). To a fair approximation, this community represents the sphere of action of the University of Coimbra. It covers all research domains and spans all publications years when using All Databases of WoS and years 1980 to March 2022 for the InCites analysis using WoS core collection. Untreated data
Gonadal transcriptome assembly, functional annotation and open reading frames of the edible sea urchin, Paracentrotus lividus. Support dataset of the article https://doi.org/10.1016/j.aqrep.2021.100936
No full textGonadal transcriptome assembly, functional annotation and open reading frames of the edible sea urchin, Paracentrotus lividus - Support dataset of the article.
1 - Data Description:
Compressed transcriptome assemblies (versions 0 and 1) of Paracentrotus lividus (RNA sequence
;EDAM:data_3495 ; FASTA;EDAM:format_1929 ; GZIP format
;EDAM:format_3989).
P.lividus_Transcriptome_V0.fasta.gz
P.lividus_Transcriptome_V1.fasta.gz
Compressed functional annotation reports of versions 0 and 1 of transcriptome assembly of Paracentrotus lividus (xlsx;EDAM:format_3620 ; GZIP format;EDAM:format_3989).
P.lividus_Transcriptome_V0_Annotation_Report.xlsx.gz
P.lividus_Transcriptome_V1_Annotation_Report.xlsx.gz
Compressed open reading frames predicted in version 0 transcriptome assembly of Paracentrotus lividus (Protein sequence;EDAM:data_2976 ; FASTA;EDAM:format_1929 ; GZIP format
;EDAM:format_3989).
P.lividus_Transcriptome_V0_Transdecoder_orfs.fasta.gz
2 - Data Processing:
Transcriptome assemblies of Paracentrotus lividus.
Version 0 - The initial version of the Paracentrotus lividus gonadal transcriptome assembly (V0) was performed using the raw RNASeq reads of 6 specimens (3 males, 3 females ; BioProject:PRJNA625933) and the Trinity (RRID:SCR_013048) (version 2.8.4) assembler, with the specific parameter (SS_lib_type RF). The detailed process can be consulted in the Material and methods - Section 2.3 of the original publication.
Version 1 - The V1 version of the Paracentrotus lividus gonadal transcriptome assembly was obtained by the filtering and redundancy removal of V0 version, based on three criteria, codifying status, functional annotation, and read coverage of the transcripts. The detailed process can be consulted in the Material and methods - Section 2.5 of the original publication.
Functional annotation report of versions 0 and 1 of the transcriptome assembly of Paracentrotus lividus.
The annotation report of the Paracentrotus lividus gonadal transcriptome assembly (V0) was performed using the Trinotate (RRID:SCR_018930) pipeline (version 3.0.2). The V1 annotation report corresponds to a sub-dataset of V0 transcriptome assembly version. The detailed process can be consulted in the Material and methods - Section 2.4 of the original publication.
Open reading frames predicted in version 0 transcriptome assembly of Paracentrotus lividus.
The open reading frames of Paracentrotus lividus gonadal transcriptome assembly (V0) were predicted using the TransDecoder (RRID:SCR_017647) pipeline (version 5.3.0). The detailed process can be consulted in the Material and methods - Section 2.4 of the original publication.
3 - Data ontology and nomenclature :
Data type:
Species : Paracentrotus lividus;NCBI:txid7656
Tissue: gonad;UBERON:0000991
Experiment Type: RNA-seq assay;OBI:0001271
Developmental stage: adult organism;UBERON:0007023
Raw Data: Sequence Read Archive BioProject:PRJNA625933
Custom nucleotide sequence headers follow the nomenclature:
>Name.OfSpecies_TrinityCode (e.g. >P.lividus_DN0_c10_g1_i2)
Custom protein sequence headers follow the nomenclature:
>Name.OfSpecies_TrinityCode.NumberofOrfDetected (e.g.>P.lividus_DN0_c10_g1_i2.p1) </p
Danio rerio confocal images of a 72 hours post-amputation longitudinal fin cryosection immunostained for Yap, pSmad1/5/8 and DAPI. Support dataset to the article: https://doi.org/10.1242/jcs.231993
No full textWild-type AB Danio Rerio (Zebrafish) confocal images of a 72 hours post-amputation longitudinal fin cryosection immunostained for Yap, pSmad1/5/8, and DAPI. All Images contain multiple z-stacks covering the whole 12 micrometer cryosection and contain 4 channels: DAPI (nuclei), Transmitted light, AlexaFluor488 (YAP), AlexaFluor561(pSmad1/5/8). Images were acquired using a 40x 1.2NA water immersion objective in a Zeiss LSM 710 confocal microscope
Klebsiella pneumoniae genomes
No full textThe dataset includes assembled whole genome sequences from Klebsiella pneumoniae multidrug resistant clinical strain
Evaluation of P. pinaster response to pine wood nematode artificial inoculation in a 510-panel from five half-sib progenies
No full textdoi:10.34636/DMPortal/14N7WMThis dataset includes phenotypic data from an artificial pine wood nematode inoculation assay using a panel of 510 plants from five Pinus pinaster half-sib progenies (family 17, 77, 152, 440, and 465). The plants were maintained in 2,5 L pots in a greenhouse, placed according to a completely randomised experimental design organised in nine blocks. Symptoms after PWN inoculation were assessed weekly from the 14th dpi until the 447th dpi and were classified according to a visual scale: level 1 – 0 % of brown/wilting needles; level 2 – 1-25 % of brown/wilting needles; level 3 – 26-50 % of brown/wilting needles; level 4 – 51-75 % of brown/wilting needles; and level 5 – 76-100 % of brown/wilting needles. Symptom scores were combined into a single value for each plant, to quantitatively summarise the pine wilt disease progression over time and encompass a greater range of phenotypic variance compared to relying only on a single time-point measurement
Development and evaluation of gluten-free rice biscuits: impact on glycaemic index and bioactive compounds
No full textWithin the scope of the TRACE-RICE project, this study performed at INIAV research institute (Portugal) aims to characterize different rice bran biscuits formulations with 2 different rice varieties (Type III and Ariete)
CADPAth.AI colorectal 1000
No full textThe CRC dataset contains 1132 colorectal biopsy and polypectomy WSIs (svs. files), retrieved from the data archive of IMP Diagnostics laboratory, Portugal, digitised at 40X by 2 Leica GT450 WSI scanners.
All cases are classified within one of the three categories:
- Non-neoplastic (label 0)
- Low-grade lesions (label 1) - conventional adenomas with low-grade dysplasia
- High-grade lesions (label 2) - conventional adenomas with high-grade dysplasia, intra-mucosal carcinomas and invasive adenocarcinomas
Soil dehydrogenase activity under long-term HDPE mulch application in a Vaccinium virgatum plantation
No full textMeasurements of soil dehydrogenase activity from a long-term field experiment conducted in southern Portugal. Blueberry plants (Vaccinium virgatum cv. ‘Centra Blue’) were cultivated for 10 years under green high-density polyethylene (HDPE) mulch in sandy loam soil. Soil samples were collected at 0-20 cm depth and analyzed for dehydrogenase activity using the triphenyl tetrazolium chloride (TTC) reduction method. The dataset includes three biological replicates per treatment (mulched vs. bare soil control), providing insight into the long-term effects of plastic mulch on soil microbial activit
Physiological response of Vaccinium corymbosum exposed to soil microplastics under controlled conditions
No full textEvaluation of physiological response of Vaccinium corymbosum (cv. Ozarkblue) to two concentrations of polypropylene microplastics applied to the soil under controlled greenhouse conditions. Photosynthetic parameters and leaf gas exchange were measured before and over a two-month period following microplastic application