Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes

While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for different traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo4j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo4j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities offered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.

The giant diploid faba genome unlocks variation in a global protein crop

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.

Abnormal amplitude and kinetics of digital postocclusive reactive hyperemia in systemic sclerosis

OBJECTIVES

Postocclusive reactive hyperemia is mediated by two major mediators: sensory nerves and endothelium-derived hyperpolarizing factors. We hypothesized that the skin microvascular response to 5 min ischemia would differ depending upon the hand location in patients with systemic sclerosis (SSc), primary Raynaud's phenomenon (PRP) and healthy controls.

METHODS

Fifteen patients with SSc, 15 sex- and age-matched patients with PRP and healthy controls were enrolled. Their right hands were subjected to 5 min ischemia followed by a postocclusive hyperemia test, with local microcirculation monitoring by laser speckle contrast imaging on the dorsal face of the hand.

RESULTS

Postocclusive reactive hyperemia was abnormal in terms of peak and area under the curve (AUC) on all fingers except the thumb in patients with SSc and PRP compared with controls. In contrast, the kinetics of the response was longer only in SSc patients, with mean (SD) time to peak on the index, middle and ring finger were respectively 72 (58), 73 (51) and 67 (47) s for SSc; 40 (20), 40 (20) and 36 (19) s for PRP; and 34 (30), 34 (30) and 29 (24) s for controls (P=0.009 for interaction).

CONCLUSIONS

We observed decreased distal digital microvascular perfusion following 5 min of ischemia in patients presenting with PRP or SSc, while the kinetics was prolonged only in SSc. A dynamic assessment of digital skin blood flow using laser speckle contrast imaging following 5 min ischemia could be used as a tool to assess microvascular abnormalities in patients with Raynaud's phenomenon secondary to SSc.

[Recurrent deep vein thrombosis and myeloproliferative syndrom: emergence of JAK2 mutation five years after the initial event]

JAK 2 mutation is the molecular event responsible for 95% of polycythemia cases and 50% of thrombocythemia vera and myelofibrosis cases. It can be used as a tool for the diagnosis of myeloproliferative disorders. We report a case illustrating the fact that a negative result does not definitively eliminate the diagnosis. A 40-year old woman, with a medical history of familial deep vein thrombosis, developed thrombosis of the inferior vena cava with extension to the suprahepatic veins and pulmonary embolism. No constitutional or acquired thrombophilia was diagnosed; search for JAK 2 mutation was negative. The patient was treated with fluindione. Five years later, she relapsed with popliteo-femoral and vena cava deep vein thrombosis. The etiological work-up included a PET scan which revealed diffuse uptake in bones and suspected neoplasic bone marrow invasion. Progenitor cell cultures were positive and JAK 2 mutation was confirmed. The bone marrow aspirate had the cytologic appearance of a myeloproliferative disorder. This case illustrates the fact that JAK 2 mutation can be identified several years after onset of a latent myeloproliferative disorder. Cases with a high clinical likelihood should lead to renewed search for this mutation. Secondary discovery of this mutation can be explained by a higher proportion of mutation expressing clones.

[Temporary vena caval filters: report on cohort of 72 patients in Grenoble, France]

Patients with a contra-indication for anticoagulation can benefit from temporary vena caval filters for protection against pulmonary embolism or recurrence. The filter can be removed secondarily, once the contra-indication is overcome, enabling better long-term outcome by reducing the risk of thrombotic and mechanic complications inherent in these devices. However, it has been shown in several studies that effective withdrawal rates were low and could be improved by the establishment of protocols and registries. We report a retrospective study of withdrawal in 72 patients in whom an ALN® vena caval filter was implanted at the Grenoble University Hospital over a period of three years with an intention for secondary retrieval. Seventy percent of the indications were related to the coexistence of thrombotic and hemorrhagic conditions. Fifty-five percent of filters were removed, the remaining 45% shared involved patients who died before retrieval (11%), those lost to follow-up (4%), technical failure of retrieval (6%), withdrawal technically unfeasible (3%), retrieval refused by patients (6%) and medical indications for continuing filtration (15%). Despite an effective follow-up of these patients and 91% success rate of withdrawal, nearly one out of two filters remains in place. A long-term follow-up of these patients is needed to learn more about the outcome of these filters.

Ischémie subaiguë d’un membre inférieur et toxicité artérielle périphérique de la cocaïne chez une patiente présentant une artériopathie juvénile

A 35-year-old woman was hospitalized for subacute ischemia of the left leg following an intermittent claudication for some weeks. She also presented paleness and coldness of both hands. The radial pulses could not be palpated. Smoking was the only cardiovascular risk factor. Duplex ultrasonography and angiography revealed a left popliteal thrombus combined with low diameter leg arteries and in the upper limbs stenosis of the left radial artery and thrombosis of the right radial artery. Search for a metabolic, embolic or thrombophilic etiology was negative. More minute history taking revealed use of cannabis and recent nasal administration of cocaine. Her condition improved with heparin therapy except for the upper limbs with ischemia of the hands and disabling Raynaud's phenomenon. This report highlights the combined arterial toxicity of drugs often used together by drug addicts. The association of cannabis use and tobacco smoking is not rare in patients with Buerger-like juvenile arteriopathy and cocaine may provoke peripheral vascular disease by embolism or in situ thrombosis. Interrogation of a patient presenting with Buerger-like peripheral arterial disease should insist on detecting use of drugs in association with tobacco smoking.

Thromboses aortiques « isolées » : analyse rétrospective de 10 observations

INTRODUCTION

Thrombi of the aorta are mostly linked to atheromatous plaques on the aortic wall of patients with classical risk factors for cardiovascular disease. The thrombus rarely appears on sound arteries and in this case is called "isolated".

METHODS

We present a retrospective study of ten patients with "isolated" thrombi of the aorta treated between 1995 and 2004 at the Hospital of Grenoble. The following parameters were considered in this analysis: age of the patient when the thrombosis appeared, gender, cardiovascular risk factors, revealing mode of the thrombus, its anatomic location, biological and morphological exploration results and the treatment performed. Patients with atheromatous plaques on the aortic wall were excluded.

RESULTS

In eight out of ten cases the clinical presentation of the aortic thrombus is an acute ischemia of a limb. In all of the cases the diagnosis was confirmed by an injected thoraco-abdominal scan apart from one case where the primary diagnosis was made using an arterial echo-Doppler. The search for the thrombophilia can be considered to have been exhaustive in seven cases. For the search of an anti-phospholipid antibody syndrome this has been achieved in eight cases. Two etiologic diagnoses could be placed. The first one revealed during the aortic thrombosis a neoplasia of adenocarcinomic type without any primary identified. The second case was an essential thrombocythemia diagnosed one year after the thrombosis. The eight other cases remained "isolated" after an average 2.5 years follow-up.

DISCUSSION

Less than one hundred cases of aortic thromboses could be identified in the literature. The cases developing on a sound artery are difficult to quantify and the word "isolated" thrombus may be sometimes used by default. The hypothesis of an isolated focal atheromatous plaque or of inflammatory pathologies inducing a thrombus can be an example. The biological and morphological explorations have to be exhaustive even if in most of the cases they are not sufficient for the diagnosis. Therapy calls for anti-coagulation but is not standardized. The clinical follow-up appears to be essential since pathological conditions can possibly develop after the event of the thrombosis. It also enables refinement of the actions to be taken especially regarding long-term use of anticoagulants.

Syndrome de Sneddon avec anticorps anti-mitochondries de type M5

INTRODUCTION

Antimitochondrial type M5 antibodies (AMA-M5) are among the immunological abnormalities associated with Sneddon syndrome.

CASE

A 45 year-old woman, hospitalized for diplopia and with a 20-year history of obstetrical accidents, internuclear ophthalmoplegia and livedo, was diagnosed with Sneddon syndrome associated with primary antiphospholipid syndrome (APS) aggravated by the presence of AMA-M5.

DISCUSSION

AMA-M5 are immunological markers of APS to the same extent as antiphospholipid antibodies. This case demonstrates the interest of screening for AMA-M5 in cases of strong clinical suspicion of APS when the anticoagulant lupus test is normal and no anti-cardiolipin, anti-b2 glycoprotein I or antiprothrombin antibodies are found.

Site and clinical outcome of deep vein thrombosis of the lower limbs: an epidemiological study

Clinical outcomes of patients diagnosed with venous thromboembolic disease (VTED) have rarely been assessed on large series of patients from single institutions. This was work based on our practice to routinely screen all suspected pulmonary embolism (PE) and deep venous thrombosis (DVT) patients with bilateral proximal and distal venous US was designed to evaluate survival, recurrence and cancer occurrence in patients diagnosed with symptomatic or asymptomatic DVT and to assess their relationship with the site of the DVT (proximal vs. distal, bilateral vs. unilateral). Our study is based on the cross-matching of the VTED register of the Grenoble University Hospital with the local Cancer Register and community mortality data. Survival analyses were performed with the Kaplan-Meier method; prognostic variables were tested using the log-rank test. A total of 1913 patients with a DVT of the lower limbs from 1993 to 1998 were included (57% women; mean age, 69 years). Of these, 1018 patients were diagnosed with proximal DVT (156 bilateral) and 895 distal DVT (112 bilateral). PE was associated in 760 patients. Patients with PE and no detected DVT were not included. At 2 years, adjusted survival rates were 80% in patients with unilateral-distal DVT, 67% in bilateral-distal, 72% in unilateral-proximal and 65% in bilateral-proximal DVT patients. The cumulated VTED recurrence rates were 7.7% in unilateral-distal DVT, 13.3% when DVT was bilateral-distal, 14% when unilateral-proximal and 13.2% when bilateral-proximal. The rate of new cancer was 6.4% in unilateral-distal DVT, 10.8% when it was bilateral-distal, 6.5% when unilateral-proximal and 6.1% when bilateral-proximal. Based on a large series of unselected patients, our results show that the site of the DVT and principally the bilaterality provides important prognostic information that may be used in the setting up of medical strategies.

Thromboses artérielles des membres inférieurs : responsabilité des anticorps antiphosphatidyléthanolamine ?

BACKGROUND

At the beginning the antiphospholipid antibodies syndrome was associated with systemic lupus erythematosus. But since 1988 it has become a sole entity. Its current definition is based on the criteria established in 1999 by Sapporo and consists of associating the clinical criteria of thrombosis of arteries or peripheral veins and of miscarriage of pregnancy with the biological criteria. Either anti-cardiolipin antibodies or lupus anticoagulant must be present. Anti-phosphatidylethanolamine antibodies are not included in the Sapporo criteria.

CASE REPORT

A non smoking, 43 year-old man showed a clinical manifestation of livedo on the thighs, and left knee and foot, associated with a rapidly extending cutaneous necrosis on the left toes. One year earlier his right leg was amputated up to half of the calf following distal gangrene. The gangrene was consecutive to a stent implantation after a significant stenosis of the right superficial femoral artery. The etiological investigations revealed neither thrombophily nor cholesterol embolism nor vasculitis. No sign of underlying neoplasia could be found. These clinical symptoms as well as the anamnesis were strongly suggestive of an antiphospholipid antibodies syndrome. The immunological dosages revealed isolated positive anti-phosphatidylethanolamine antibodies, persistent six weeks later.

DISCUSSION

Several cases of clinical manifestations of the antiphospholipid antibodies syndrome have been described, without any anti-cardiolipin antibodies or lupus anticoagulant, but with presence of anti-phosphatidylethanolamine antibodies. In cases of these strong evocative symptoms but no evidence of the classical biological Sapporo criteria, these antibodies should be systematically searched for.

Validation of a clinical guideline on prevention of venous thromboembolism in medical inpatients: a before-and-after study with systematic ultrasound examination

BACKGROUND

Clinical practice guidelines on prevention of venous thromboembolism in medical inpatients have been implemented in various settings, although few studies have assessed their impact on venous thromboembolism events.

OBJECTIVE

To determine whether the implementation of a locally developed guideline is followed by changes in the rate of deep vein thrombosis.

DESIGN

A before-and-after study consisting in two "1-day" cross-sectional studies.

SETTING

Thirteen adult medical wards in a teaching hospital in France.

SUBJECTS

All the patients hospitalized on the day of the cross-sectional study.

INTERVENTION

A clinical guideline integrating scientific evidence and data on target medical providers' practices was developed by a local expert panel and implemented through a multifaceted intervention.

MEASUREMENTS

Prevalence of deep vein thrombosis detected by systematic ultrasound examination.

RESULTS

The study included 338 patients in the preintervention sample and 340 in the postintervention sample. The prevalence of deep vein thrombosis decreased from 9.5% (95% CI, 6.6-13.1) in the preintervention sample to 3.2% (95% CI, 1.6-5.7) in the postintervention sample (P < 0.01). The decrease in the rate of thrombosis involved all deep veins of the lower limbs and remained significant after adjustment for risk factors (adjusted odds ratio = 0.47, 95% CI, 0.32-0.70). No additional cases of pulmonary embolism or deep vein thrombosis were reported either on the day of the study or in the following 2 days.

CONCLUSIONS

Active implementation of a clinical practice guideline directed at medical providers (doctors, nurses and physical therapists) can be followed by a significant decrease in prevalence of deep vein thrombosis.

Short-term corticosteroids then lamivudine and plasma exchanges to treat hepatitis B virus-related polyarteritis nodosa

OBJECTIVE

To assess the efficacy and safety of lamivudine, an antiviral agent that strongly inhibits hepatitis B virus (HBV) DNA replication, combined with plasma exchanges after short-term corticosteroids for HBV-related polyartertitis nodosa (PAN).

METHODS

Ten patients (8 men, 2 women, mean +/- SD age 50.4 +/- 14.4 years) with previously untreated HBV-related PAN were included in a multicenter, prospective, observational trial. Oral prednisone (1 mg/kg/day) was given for 1 week, then tapered and withdrawn within 1 week. Then, lamivudine (100 mg/day or less in the case of renal insufficiency) was started for a maximum of 6 months. Plasma exchanges were performed simultaneously and scheduled as follows: 3/week for 3 weeks, 2/week for 2 weeks, then 1/week until hepatitis B e antigen (HBeAg) to anti-HBe antibody (HBeAb) seroconversion was obtained or until 2-3 months of clinical recovery was sustained. The primary trial endpoint was clinical recovery from HBV-PAN at 6 months. The secondary endpoint was loss of detectable serum HBeAg and HBV DNA, and HBeAg to HBeAb seroconversion at 9 months.

RESULTS

One death, attributed to catheter-related septicemia, was recorded. At 6 months, all 9 survivors had achieved clinical recovery and by 9 months, 6 of 9 (66%) had seroconverted.

CONCLUSION

The strategy of short-term steroids followed by lamivudine and plasma exchanges effectively led to recovery from HBV-PAN. Because of its oral administration and good safety profile, lamivudine should henceforth be considered the antiviral agent of choice to treat HBV-related PAN.

Enhanced in vivo lipid peroxidation in scleroderma spectrum disorders

OBJECTIVE

A new family of prostaglandin F2 isomers called F2-isoprostanes, produced by free radical peroxidation of arachidonic acid, has recently been described in vivo. Its quantification has been suggested to be a reliable measure of oxidant injury in vivo. The purpose of this study was to investigate urinary F2-isoprostane formation as an index of lipid peroxidation in scleroderma spectrum disorders.

METHODS

Urine samples were obtained from 52 patients with systemic sclerosis (SSc; n = 37) or undifferentiated connective tissue diseases (UCTD; n = 15) and from 20 healthy volunteers. Urinary isoprostaglandin F2alpha type III (iPF2alpha-III) and 11-dehydro thromboxane B2 (11-dehydroTXB2) concentrations were determined using enzyme immunoassays.

RESULTS

The urinary concentration of iPF2alpha-III was approximately twice as high in patients (mean +/- SEM 229+/-16 pmoles/mmoles creatinine) as in controls (116+/-9 pmoles/mmoles creatinine) (P < 0.0001). However, the urinary concentration of iPF2alpha-III was not significantly different among patients with UCTD, limited SSc, and diffuse SSc (mean +/- SEM 221+/-27 versus 245+/-32 versus 220+/-25 pmoles/mmoles creatinine, respectively). No significant correlation was found between the urinary concentrations of iPF2alpha-III and 11-dehydroTXB2.

CONCLUSION

This study provides evidence of enhanced lipid peroxidation in both SSc and UCTD, and suggests a rationale for antioxidant treatment of SSc. Formation of F2-isoprostanes has to be investigated as a means for the evaluation of such therapy.

[Morphometric analysis of erythrocyte aggregates in vitro: pharmacological application with buflomedil]

Erythrocyte aggregation is usually evaluated through indirect measurements such as the sedimentation rate and rheometric measurements of aggregation and disaggregation thresholds. The aim of this study was a preliminary evaluation of a morphometric approach of aggregates in vitro. A sample of blood (on EDTA) was examined under the microscope, and a picture with magnification X 640 was obtained after stabilization of the cellular structure. The digital image was analyzed with a home made dedicated software that allows the measurement of the cellular density and the evaluation of several shape parameters. Ten samples obtained from different donors were analysed within one hour after blood withdrawal and 24 hours later (preservation temperature: 4 degrees C), with and without adjunction of Buflomedil (4 microg/ml). Results showed an important anti-aggregant effect of Buflomedil administrated in these conditions, both on fresh and preserved blood (p<10(-3)). These results illustrate the potential interest of a morphometric approach to erythrocyte aggregation. They show new pharmacological properties of Buflomedil administered in vitro, which have to be confirmed with a therapeutic administration of the compound.

[Adverse effects and medication errors: incidence and role of the organization of drug distribution]

The true incidence of adverse drug events is controversial and there are few data concerning the percentage of potentially preventable adverse drug events. Over 2 months, in two internal medicine units, we asked the staff to report adverse drug events. All incidents were evaluated: adverse drug events (preventable and non-preventable) and potential adverse drug events (non-intercepted potential adverse drug events and intercepted potential adverse drug events). The severity, the stage in the process at which the error occurred and the type of error were evaluated by a physician reviewer. Over the 240 admissions, the incidence of adverse drug events is 18 per 1000 patient-days. The system design caused 77 per cent of the incidents. The medication errors occurred at all stages from ordering to administration. Adverse drug events resulting in medication errors (n = 22) were more serious than non-preventable adverse drug events (n = 26) (p = 0.003). A prevention strategy by pharmacovigilance centres (Centres Régionaux de Pharmacovigilance) should target all stages of the drug delivery process.

[Neuropsychic side-effects of therapeutic doses of zipeprol]]

We report the two first cases of neuropsychic side-effects with zipeprol (non opiate antitussive) given at therapeutic doses. In both cases, the patients showed confusion, whereas, hallucinations occurred only in one case. The anticholinergic activity of zipeprol might explain these effects. These two cases are in agreement with zipeprol central nervous system action.