Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS.

GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems.

Seasonality of sodium and potassium consumption in Switzerland. Data from three cross-sectional, population-based studies.

BACKGROUND AND AIM: Blood pressure displays a seasonal pattern. Whether this pattern is related to high sodium and/or low potassium intakes has not been investigated. We assessed if sodium and potassium consumption present a seasonal pattern. We also simulated the impact of seasonality of sodium consumption on systolic blood pressure levels. METHODS AND RESULTS: Data from three Swiss population-based studies (n = 2845). Sodium and potassium consumption were assessed by urinary excretion using 24 h urine collection. Seasonality was assessed using the cosinor model and was adjusted for study, gender, age, body mass index, antihypertensive drug treatment, urinary creatinine and atmospheric relative humidity. The effect of sodium variation on blood pressure levels was estimated using data from a recent meta-analysis. Both sodium and potassium excretions showed a seasonal pattern. For sodium, the nadir occurred between August and October, and the peak between February and April, with a multivariate-adjusted seasonal variation (difference between peak and nadir) of 9.2 mmol. For potassium, the nadir occurred in October and the peak in April, with a multivariate-adjusted seasonal variation of 4.0 mmol. Excluding participants on antihypertensive drug treatment or stratifying the analysis by gender cancelled the seasonality of sodium consumption. The maximum impact of the seasonal variation in sodium consumption on systolic blood pressure ranged from 0.4 to 1.1 mm Hg, depending on the model considered. CONCLUSION: Sodium and potassium consumptions present specific seasonal variations. These variations do not explain the seasonal variations in blood pressure levels.

Mining Plant Genomic and Genetic Data Using the GnpIS Information System.

GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.

Towards an open grapevine information system.

Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.

Raman spectroscopic and visible absorption investigation of LiCrSi2O6 pyroxene under pressure.

The first observation of the vibrational spectrum of the synthetic pyroxene Li-kosmochlor (LiCrSi2O6) is reported herein. The Raman and visible spectra are reported as a function of pressure. Though the pyroxene retains its P21/c symmetry, changes in the Raman spectra are observed between 6.8 and 7.7 GPa, possibly due to the formation of an additional bond between Li and O3 or some other transition that retains the mineral's P21/c space group. Splitting of the peak appearing at approximately 700 cm(-1), used to characterize the P21/c phase in other studies, is not observed. Comparison is made with the Raman spectra of LiAlSi2O6 and LiFeSi2O6 in the P21/c phase and the visible spectra of NaCrSi2O6 at high pressures.

NIR chemical imaging to guide/support BMS-561389 tablet formulation development.

The objective of this study was to determine whether the particle size of extra-granular tartaric acid affects the uniformity of its distribution within BMS-561389 tablets. A near-infrared imaging technique was used to assess the distribution of tartaric acid near the surface of tablet tops and bottoms. Three batches of BMS-561389 tablets were manufactured using three lots of granular tartaric acid having different particle size distributions. Near-Infrared chemical images were acquired on the tops and bottoms of 15 tablets from each lot. Spectra were collected from 1350 to 1600 nm in 10 nm increments and 16 co-added scans at each wavelength. Data were analyzed using ISys 3.1 (Spectral Dimensions, Inc.) Chemical Imaging Software. Data analysis consisted of preprocessing, principal component analysis, and image analysis of the principal component scores image. It was feasible to map tartaric acid particles near the surface of BMS-561389 tablets using near infrared chemical imaging. The tartaric acid particle size statistics based on image analysis results correlated well with pre-compaction measurements using a laser-light scattering method. The image analysis results indicate that segregation of tartaric acid between tablet tops and bottoms was apparent in tablets lots containing both the largest and intermediate-size tartaric acid particles. For tablets made with the smallest tartaric acid particles, differences between tablet tops and bottoms in either the number of tartaric acid particles or the percent tablet surface area covered by tartaric acid were not statistically different at the 95% confidence level.

[Amniotic fluid embolism: successful evolution course after uterine arteries embolization]. / Embolie de liquide amniotique: évolution favorable après embolisation thérapeutique des artères utérines.

A 28-year-old woman, G3P3, who was otherwise healthy and had taken no medication and had no known allergy, was admitted to our hospital for delivery after a normal pregnancy. An epidural catheter was inserted for analgesia and labour was induced with oxytocin. Two hours later, she suffered a sudden cardiac arrest. She was immediately treated and, since a normal cardiac rhythm and a blood pressure of 90 mmHg has been obtained 30 minutes later, a 3750 g child was delivered by caesarean section. Soon after delivery, a life-threatening uterine haemorrhage appeared, due to DIC. Evolution was favourable, after bilateral uterine arteries embolization had been performed. The diagnosis of amniotic fluid embolism was established by the clinical course, the absence of local cause and the presence of a large number of amniotic cells in the mother's peripheral blood. Tryptase blood concentration was normal in the mother's blood.

[Hemoperitoneum and pregnancy in a patient with von Willebrand's disease type 3]. / Hémopéritoine et grossesse chez une patiente atteinte de la maladie de von Willebrand de type 3.

A 24-year-old woman with type 3 (characterised by a blood level of von Willebrand factor less than 1%) was admitted to the surgical intensive care unit with an haemorrhagic shock. She was pregnant (Beta HCG = 115 Ul.L-1), the echography of the abdomen, soon after admission, revealed a haemoperitoeum. She underwent abdominal surgery after substitution treatment. The surgeon found an ovarian haemorrhagic cyst. Later the course of pregnancy was normal and she was delivered by caesarean section. We describe the therapeutic strategy of that care.

[Percutaneous tracheostomy]. / Trachéotomie percutanée.

OBJECTIVES: The aim of this study was to evaluate the different techniques of percutaneous tracheostomies, their advantages, drawbacks, complications and to compare them to standard surgical tracheostomies. This study will consider only elective (non emergency) bedside procedures in intensive care units. DATA SOURCES: Extraction from Medline database of english and french articles on percutaneous tracheostomies and searching along with major review articles. STUDY SELECTION: The collected articles were selected according to their qualities regarding to their evidence level. In addition to several important or historic references, the literature of the five past years was studied. DATA EXTRACTION: The articles were reviewed according to their contribution for techniques, perioperative and postoperative complications, recent advances, advantages and drawbacks of all procedures. Publications addressing recent comparisons between surgical and percutaneous tracheostomies were specially studied. DATA SYNTHESIS: Four techniques of bedside percutaneous tracheostomies are available and marketed, in France: Ciaglia's dilation technique (with multiple or unique dilator), Griggs's technique (using a special designed forceps), and Fantoni's technique (Trans Laryngeal Tracheostomy). The most spred but also first described technique is the Ciaglia's (1985). The most recent articles comparing surgical and percutaneous tracheostomies techniques are not able to demonstrate a superiority of one of them in terms of feasibility or safety. In other words, there should be a slight advantage for the percutaneous tracheostomy regarding to the late post-operative complications, as there should be a slight advantage for the surgical techniques regarding to the perioperative complications. The literature analysis point out firstly the learning curve for percutaneous dilational tracheostomy, with a significant decrease of complication incidence with the operator's experience and secondly the continuous endoscopic guidance seems to increase the safety of the percutaneous procedure. CONCLUSION: Since there has been a great deal of percutaneous tracheostomy in the intensive care units, the incidence of tracheostomy have increased in those services. There is a trend to replace the surgical procedure by the percutaneous one. However, according to the potentially jeopardizing complications, percutaneous tracheostomy should be done by an experienced operator with the help of a continuous endoscopic guidance.

[Tracheal gas insufflation associated with mechanical ventilation for CO2 removal]. / Insufflation trachéale de gaz associée à la ventilation mécanique pour l'épuration du CO2.

OBJECTIVE: Tracheal gas insufflation (TGI) either continuously, or at inspiration, or at expiration, is a technique associated with mechanical ventilation aimed to enhance CO2 elimination in favouring washout of anatomical dead space. This article analyses the mechanism of action, the techniques and the effects of TGI in presence of hypercapnia, especially in the fame of ARDS in adults. DATA SOURCES: In addition to some historical or major references, the articles on TGI published over the past five years have been searched in the Medline data base. STUDY SELECTION: Articles with data on TGI associated with mechanical ventilation were selected. DATA EXTRACTION: Data on mechanisms of action, technical and practical aspects of TGI were extracted. DATA SYNTHESIS: CO2 elimination is increased when the TGI catheter tip is close to the carina, when the gas jet is directed towards the latter, by a continuous gas jet, by a high washing gas volume. The effect on oxygenation is minor. The work of breathing is decreased. An increased intracranial pressure is decreased. Circulatory effects are minor. The major risk is dynamic pulmonary over distension. Local complications include dessiccation and lesion of bronchial mucosa by the gas jet. CONCLUSION: In mechanically ventilated patients, additional TGI is a valuable technique for decreasing anatomical dead space. TGI decreases hypercapnia during mechanical ventilation with limited tidal volumes in permissive hypercapnia. Further clinical studies with large series of patients are required to assess the benefits and the effect of TGI on outcome.

[Treatment of pain in children burns]. / Traitement de la douleur de l'enfant brûlé.

Burn injury is considered by children as one of the most painful traumas (just after bone factures). Burn pain in children can and must be controlled as well as for adult patients, with almost identical techniques. Continuous pain from injury and intermittent pain caused by therapeutic procedures must be evaluated and treated separately. Due to very high levels of nociception, satisfactory management of procedural pain requires the use of opioid therapy. Non pharmacological methods are meaningless if pharmacological treatment is not optimal.

[Surgery for epidermolysis bullosa in children: value of the association of inhalation anesthesia and locoregional anesthesia]. / Chirurgie de l'épidermolyse bulleuse grave chez l'enfant: intérêt de l'association anesthésie générale par inhalation-anesthésie locorégionale.

Due to the cutaneous and mucosal fragility associated with epidermolysis bullosa, this disease is a source of various practical problems for the anaesthesiologist concerning the surgical posture, the monitoring of vital functions, the airways control and the vascular access, as all these procedures may worsen, sometimes dramatically, the lesions in these young patients, still in a precarious health state. Basing on published studies and their own experience, the authors have used in these patients a combined locoregional and general anaesthesia. The latter was obtained with isoflurane, administered in the non intubated and spontaneously breathing patient through a closed surgical isolation container (Vi-Drape), including the patient's head and ventilated with a ventilator generating a PEEP for long procedures. The results obtained during 9 procedures in 3 children are reported and discussed. For several shorter procedures (for example wound dressing), intramuscular ketamine was used.

Oxygen uptake and mixed venous oxygen saturation during aortic surgery and the first three postoperative hours.

This study was designed to determine the significance of changes in mixed venous oxygen saturation (SVO2) associated with aortic surgery. In 12 patients undergoing aortic aneurysm repair, SVO2 was monitored using a fiberoptic pulmonary arterial catheter, and oxygen uptake (VO2) was measured at 2-min intervals by a mass-spectrometer system. Excluding the phase of aortic clamping, VO2, hemoglobin, and arterial oxygen saturation were moderately stable during anesthesia, and changes in SVO2 were correlated with changes in cardiac output (CO). SVO2 remained stable during infrarenal aortic clamping, but increased during supraceliac aortic clamping. During the first three postoperative hours, changes in SVO2 were opposite to changes in VO2 and CO. They were especially marked in the patients whose preoperative left ventricular ejection fraction was less than 50%. We conclude that SVO2 changes are an indicator of same-direction changes in CO during general anesthesia except during periods of aortic clamping. The interpretation of SVO2 changes is more complex during aortic clamping and during the immediate postoperative period, two critical periods during which simultaneous changes in VO2 and CO occur.

[Aneurysm of iliac arteries. Is it anatomo-clinical entity? Report of 18 cases]. / L'anévrisme des artères iliaques. Une entité anatomo-clinique? A propos de 18 cas.

338 patients with aorto iliac aneurysms were operated in the Department of vascular surgery (Hosp. E.-Herriot-University A.-Carrel Lyon). Retrospective evaluation found 20 solitary iliac artery aneurysms (AAIS) in 18 patients (2 bilateral AAIS). 77% of aneurysms were on the common iliac artery, 17% on the internal iliac artery, and one case of mycotic aneurysm on the external iliac artery. 8 patients (44.4%) were asymptomatic, 5 (27.8%) had non specific complaints. Rupture or acute ischemia occurred in 5 cases (27.8%). The incidence of non atherosclerotic cause (dysplasia 33.3%, infection 16.7%) in this series shows a real difference with AAA (atherosclerotic dominant etiologic factor). The value of C.T. scanning and sonographic evaluation and their extensive use in vascular and non vascular diagnostic problems are an obvious explanation for increasing AAIS reports. The risk of rupture is probably higher than in AAA because of the incidence of arterial dysplasias (1/3 in this study) and mycotic origin. This occurrence suggests an aggressive surgical management. Aneurysmorrhaphy with graft interposition by intraperitoneal approach is the routine technique for most of surgeons. An alternative procedure (retroperitoneal approach) was performed on ten of our patients (55.5%). No perioperative mortality and low morbidity rate (one case of phlebitis) in our cases support this surgical management. The survival rate based on actuarial method is estimated 64% at five years (all grafts patent).