FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards.

The current rise of Open Science and Reproducibility in the Life Sciences requires the creation of rich, machine-actionable metadata in order to better share and reuse biological digital resources such as datasets, bioinformatics tools, training materials, etc. For this purpose, FAIR principles have been defined for both data and metadata and adopted by large communities, leading to the definition of specific metrics. However, automatic FAIRness assessment is still difficult because computational evaluations frequently require technical expertise and can be time-consuming.

RapGreen, an interactive software and web package to explore and analyze phylogenetic trees.

RapGreen is a modular software package targeted at scientists handling large datasets for phylogenetic analysis. Its primary function is the graphical visualization and exploration of large trees. In addition, RapGreen offers a tree pattern search function to seek evolutionary scenarios among large collections of phylogenetic trees.

Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis.

Background: Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. Several hundreds of different nsLTP sequences-and counting-have been characterized so far, but their biological functions remain unclear. It has been clear for years that they present a certain interest for agronomic and nutritional issues.

Accurate protein-peptide titration experiments by nuclear magnetic resonance using low-volume samples.

NMR spectroscopy allows measurements of very accurate values of equilibrium dissociation constants using chemical shift perturbation methods, provided that the concentrations of the binding partners are known with high precision and accuracy. The accuracy and precision of these experiments are improved if performed using individual capillary tubes, a method enabling full automation of the measurement. We provide here a protocol to set up and perform these experiments as well as a robust method to measure peptide concentrations using tryptophan as an internal standard.

Lipid transfer proteins in coffee: isolation of Coffea orthologs, Coffea arabica homeologs, expression during coffee fruit development and promoter analysis in transgenic tobacco plants.

The aim of the present study was to perform a genomic analysis of non-specific lipid-transfer proteins (nsLTPs) in coffee. Several nsLTPs-encoding cDNA and gene sequences were cloned from Coffea arabica and Coffea canephora species. In this work, their analyses revealed that coffee nsLTPs belong to Type II LTP characterized under their mature forms by a molecular weight of around 7.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

Background: In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses.

Characterization of a cassiicolin-encoding gene from Corynespora cassiicola, pathogen of rubber tree (Hevea brasiliensis).

Corynespora Leaf Fall (CLF) is a major disease of rubber tree (Hevea brasiliensis) caused by the Ascomycota Corynespora cassiicola. Here we describe the cloning and characterization of a gene encoding cassiicolin (Cas), a glycosylated cystein-rich small secreted protein (SSP) identified as a potential CLF disease effector in rubber tree. Three isolates with contrasted levels of aggressiveness were analyzed comparatively.

Alert management for home healthcare based on home automation analysis.

Rising healthcare for elder and disabled people can be controlled by offering people autonomy at home by means of information technology. In this paper, we present an original and sensorless alert management solution which performs multimedia and home automation service discrimination and extracts highly regular home activities as sensors for alert management. The results of simulation data, based on real context, allow us to evaluate our approach before application to real data.

Structural analysis of cassiicolin, a host-selective protein toxin from Corynespora cassiicola.

Cassiicolin is a host-selective toxin (HST) produced by the fungus Corynespora cassiicola (strain CCP). It is responsible for the Corynespora leaf fall (CLF) disease, which is among the main pathologies affecting rubber tree (Hevea brasiliensis). Working on purified cassiicolin and using electron microscopy, we have demonstrated that this 27-residue O-glycosylated protein is able to induce cellular damages identical to those induced by the fungus on rubber tree leaves and displays the same host selectivity.

Purification and characterization of cassiicolin, the toxin produced by Corynespora cassiicola, causal agent of the leaf fall disease of rubber tree.

Cassiicolin, a phytotoxin produced by the necrotrophic fungus Corynespora cassiicola, was purified to homogeneity from a rubber tree isolate. The optimized protocol involves reverse phase chromatography followed by size exclusion chromatography, with monitoring of the toxicity on detached rubber tree leaves. Cassiicolin appeared to be a peptide composed of 27 amino acids, glycosylated on the second residue, with a N-terminal pyroglutamic acid and 6 cysteines involved in disulfide bonds.

Biotinylation of glycan chains in beta2 glycoprotein I induces dimerization of the molecule and its detection by the human autoimmune anti-cardiolipin antibody EY2C9.

Binding of beta2GPI (beta2 glycoprotein I), a human plasma protein, to AnPLs (anionic phospholipids) plays a key role in the formation of antiphospholipid antibodies involved in autoimmune diseases like antiphospholipid syndrome or systemic lupus erythematosus. We recently showed that binding of beta2GPI to AnPLs was enhanced by biotinylation of its glycan chains with biotin-hydrazide. In the present study, we investigated why this chemical modification of beta2GPI increased both its affinity for AnPLs and its recognition by anti-cardiolipin antibodies.

Structure of a liganded type 2 non-specific lipid-transfer protein from wheat and the molecular basis of lipid binding.

In plants, a family of ubiquitous proteins named non-specific lipid-transfer proteins (ns-LTPs) facilitates the transfer of fatty acids, phospholipids and steroids between membranes. Recent data suggest that these secreted proteins play a key role in the formation of cuticular wax layers and in defence mechanisms against pathogens. In this study, X-ray crystallography has been used to examine the structural details of the interaction between a wheat type 2 ns-LTP and a lipid, L-alpha-palmitoyl-phosphatidyl glycerol.

Single step purification of a series of wheat recombinant proteins with expanded bed absorption chromatography.

Expanded bed absorption chromatography (EBA) was used to improve and simplify the purification of several wheat recombinant proteins. Binding and elution conditions were set to allow the purification of the over expressed protein in a single step. In comparison with our previous multi step protocol, same purity was obtained while EBA required less time (one day instead of five) and gave a higher yield (63% instead of 10%).

The thioredoxin h system: potential applications.

The thioredoxin h system has the specific capability to reduce intramolecular disulfide bonds of proteins, thereby modifying their tertiary structure. It is involved in many processes: in the activation or deactivation of enzymes and enzyme inhibitors and in the germination process. This system can be used to improve the breadmaking quality of wheat by strengthening the dough.

Refined solution structure of a liganded type 2 wheat nonspecific lipid transfer protein.

The refined structure of a wheat type 2 nonspecific lipid transfer protein (ns-LTP2) liganded with l-alpha-palmitoylphosphatidylglycerol has been determined by NMR. The (15)N-labeled protein was produced in Pichia pastoris. Physicochemical conditions and ligandation were intensively screened to obtain the best NMR spectra quality.

Adjuvant radiation therapy for recurrent PSA after radical prostatectomy in T1-T2 prostate cancer.

To evaluate retrospectively the efficacy of adjuvant radiation therapy (ART) in patients with T1-T2 prostate cancer (CaP) in whom extracapsular cancer (pT3) was detected after radical prostatectomy (RP), together with biochemical failure characterized by a recurrent level of serum prostate-specific antigen (PSA)>0.1 ng/mL. Twenty-two patients with T1-T2 CaP treated by RP who subsequently were found to have pT3 CaP with (13) or without (9) positive surgical margins and/or seminal vesicle invasion, exhibited biochemical failure characterized by a recurrent level of serum PSA, 2-40 (mean: 25) months after RP and were treated with ART (65 Gy).

NMR monitoring of accumulation and folding of 15N-labeled protein overexpressed in Pichia pastoris.

Postgenomic studies have led to an increasing demand for isotope-labeled proteins. We present a method for producing large quantities of truly native (15)N-labeled protein. Based on the secretion capabilities of the yeast Pichia pastoris, the recombinant protein is easily purified in a single step as it is secreted.

Glutathione reductase in wheat grain. 1. Isolation and characterization.

Durum wheat (Triticum durum, Desf.) endosperm of mature kernels contained a single form of glutathione reductase (GR); it appeared about the 18th day after anthesis while another isoform, present at the early stages of grain development, disappeared between the 20th and 30th days after flowering. The form that was present at grain maturity was isolated and characterized.

[Treatment of ureteral calculi: report of 152 calculi].

Objective: To define the therapeutic approach to ureteric stones.

Material And Methods: 137 patients with 152 ureteric stones were treated between January 1990 and January 1997. Sixty seven stones (44%) were situated in the lumbar ureter, 16 stones (10%) were in the iliac ureter, 69 stones (46%) were in the pelvic ureter.

[Urinary continence after retropubic radical prostatectomy: retrospective study with self-administered questionnaire].

Objectives: To precisely evaluate the incidence of urinary incontinence after radical prostatectomy and its impact on quality of life.

Material And Methods: A self-administered questionnaire was sent to 116 patients operated between 1987 and 1996. Preoperative and postoperative urinary continence, the time until urinary continence was achieved, the presence of urgent micturition, the degree of discomfort caused by urinary incontinence and associated voiding disorders were assessed.

Determinants of retinopathy progression in type 1 diabetes mellitus.

Purpose: To determine the risk factors for retinopathy progression in type 1 (insulin-dependent) diabetes mellitus in a prospective cohort study.

Subjects And Methods: Subjects were 485 participants in the Sorbinil Retinopathy Trial, a randomized trial of aldose reductase inhibition among patients aged 18 to 56 years with type 1 diabetes mellitus (duration of 1 to 15 years) and no or only mild retinopathy. Retinopathy progression, assessed by seven-field stereoscopic fundus photography, was defined as worsening by two or more levels on a standardized grading scale at the end of follow-up (median, 41 months).

Early versus delayed angiotensin-converting enzyme inhibition therapy in acute myocardial infarction. The healing and early afterload reducing therapy trial.

Background: Although ACE inhibitor therapy has been shown to reduce mortality in patients with acute myocardial infarction (MI), the optimal dose and the timing of its initiation have not been determined.

Methods And Results: In a double-blind trial of 352 patients with anterior MI, we compared the safety and effectiveness of early (day 1) versus delayed (day 14) initiation of the ACE inhibitor ramipril (10 mg) on echocardiographic measures of left ventricular (LV) area and ejection fraction (EF). An early, low-dose ramipril (0.

Lack of effect of long-term supplementation with beta carotene on the incidence of malignant neoplasms and cardiovascular disease.

Background: Observational studies suggest that people who consume more fruits and vegetables containing beta carotene have somewhat lower risks of cancer and cardiovascular disease, and earlier basic research suggested plausible mechanisms. Because large randomized trials of long duration were necessary to test this hypothesis directly, we conducted a trial of beta carotene supplementation.

Methods: In a randomized, double-blind, placebo-controlled trial of beta carotene (50 mg on alternate days), we enrolled 22,071 male physicians, 40 to 84 years of age, in the United States; 11 percent were current smokers and 39 percent were former smokers at the beginning of the study in 1982.

Self-reported breast implants and connective-tissue diseases in female health professionals. A retrospective cohort study.

Objective: To evaluate the association of breast implants with connective-tissue diseases.

Design And Participants: Retrospective cohort study of 395,543 female health professionals who completed mailed questionnaires for potential participation in the Women's Health Study. A total of 10,830 women reported breast implants and 11,805 reported connective-tissue diseases between 1962 and 1991.

A prospective evaluation of an angiotensin-converting-enzyme gene polymorphism and the risk of ischemic heart disease.

Background: In a previous study, men with a history of myocardial infarction were found to have an increased prevalence of homozygosity for the deletional allele (D) of the angiotensin-converting-enzyme (ACE) gene. The D allele is associated with higher levels of ACE, which may predispose a person to ischemic heart disease. We investigated the association between the ACE genotype and the incidence of myocardial infarction, as well as other manifestations of ischemic heart disease, in a large, prospective cohort of U.