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.

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.

The Cause of Acute Respiratory Failure Predicts the Outcome of Noninvasive Ventilation in Immunocompromised Children.

BACKGROUND: Noninvasive ventilation (NIV) may be superior to conventional therapy in immunocompromised children with respiratory failure. METHODS: Mortality, success rate, prognostic factors and side effects of NIV for acute respiratory failure (ARF) were investigated retrospectively in 41 in children with primary immunodeficiency, after stem cell transplantation or chemotherapy for oncologic disease. RESULTS: In 11/41 (27%) children invasive ventilation was avoided and patients were discharged from ICU. In children with NIV failure ICU-mortality was 19/30 (63%). 8/11 (72%) children with NIV success had recurrence of ARF after 27 days. Only 4/11 (36%) children with first episode NIV success and 8/30 (27%) with NIV failure survived to hospital discharge. Lower FiO2, SpO2/FiO2 and blood culture positive bacterial sepsis were predictive for NIV success, while fungal sepsis or culture negative ARF were predictive for NIV failure. We observed catecholamine treatment in 14/41 (34%), pneumothorax in 2/41 (5%), mediastinal emphysema in 3/41 (7%), a life threatening nasopharyngeal hemorrhage and need for resuscitation during intubation in 5/41 (12%) NIV-episodes. CONCLUSIONS: The prognosis of ARF in immunocompromised children remains guarded independent of initial success or failure of NIV due to a high rate of recurrent ARF. Reversible causes like bacterial sepsis had a higher NIV response rate. Relevant side effects of NIV were observed.

Favorable outcome in infants with AML after intensive first- and second-line treatment: an AML-BFM study group report.

Infants <1 year of age have a high prevalence of prognostically unfavorable leukemias and a presumed susceptibility to treatment-related toxicities. A total of 125 infants with acute myeloid leukemia (AML) were treated in studies AML-BFM-98 (n = 59) and -2004 (n = 66). Treatment regimens of both studies were comparable, consisting of intensive induction followed by four courses (mainly high-dose cytarabine and anthracyclines). Allogeneic-hematopoietic stem-cell-transplantation (allo-HSCT) in 1st remission was optional for high-risk (HR) patients. Most infants (120/125=96%) were HR patients according to morphological, cytogenetic/molecular genetic and response criteria. Five-year overall survival was 66 ± 4%, and improved from 61 ± 6% in study-98 to 75 ± 6% in study-2004 (P(logrank) 0.14) and event-free survival rates were 44 ± 6% and 51 ± 6% (P(logrank) 0.66), respectively. Results in HR infants were similar to those of older HR children (1-<2- or 2-<10-year olds, P(logrank) 0.90 for survival). Survival rates of HSCT in 1st remission, initial partial response and after relapse were high (13/14, 2/8 and 20/30 patients, respectively). The latter contributes to excellent 5-year survival after relapse (50±8%). Despite more severe infections and pulmonary toxicities in infants, treatment-related death rate was identical to that of older children (3%). Our data indicate that intensive frontline and relapse AML treatment is feasible in infants, toxicities are manageable, and outcome is favorable.

Standardization of WT1 mRNA quantitation for minimal residual disease monitoring in childhood AML and implications of WT1 gene mutations: a European multicenter study.

A standardized, sensitive and universal method for minimal residual disease (MRD) detection in acute myeloid leukemia (AML) is still pending. Although hyperexpression of Wilms' tumor (WT1) gene transcript has been frequently proposed as an MRD marker in AML, wide comparability of the various methods used for evaluating WT1 expression has not been given. We established and standardized a multicenter approach for quantifying WT1 expression by quantitative reverse transcriptase PCR (qRT-PCR), on the basis of a primer/probe set combination at exons 6 and 7. In a series of quality-control rounds, we analyzed 69 childhood AML samples and 47 normal bone marrow (BM) samples from 4 participating centers. Differences in the individual WT1 expressions levels ranged within <0.5 log of the mean in 82% of the cases. In AML samples, the median WT1/1E+04 Abelson (ABL) expression was 3.5E+03 compared with that of 2.3E+01 in healthy BM samples. As 11.5% of childhood AML samples in this cohort harbored WT1 mutations in exon 7, the effect of mutations on WT1 expression has been investigated, showing that mutated cases expressed significantly higher WT1 levels than wild-type cases. Hence, our approach showed high reproducibility and applicability, even in patients with WT1 mutations; therefore, it can be widely used for the quantitation of WT1 expression in future clinical trials.

[Experimental studies of long-term effect of a detergent disinfecting for surface on a strain of Escherichia coli]. / Etudes expérimentales de l'effet rémanent d'un détergent désinfectant pour surfaces sur une souche d'Escherichia coli.

We offer three complementary, original methods and reproducibles to study the antibacterial and long-term effect of a detergent disinfecting for surfaces commercialized lately in France. Long-term activity noticed-effect is compared with that of other products. We first study the curves of growth of a strain of Escherichia coli put in presence with the surface of the wells of a microplate beforehand and for several days (from D-10 to D0), coated with disinfecting detergents. Another method consisted on surfaces firstly treated from D-10 to D0 by the one or the other product to be tested, which are artificially contaminated in a standardized manner by a velvet footprint with a suspension of E. coli. The surviving microbes are counted after transfer on a Rodac plate. Finally, doorhandles are cleaned and disinfected with the product. The natural bacterial recolonization doorhandles is studied by daily Rodac plate within a week. These studies allow to prove that Bacoban introduces a bactericidal activity on E. coli with an long-term effect for at least 10 days. The most competitive products have a bacteriostatic effect during nine to 10 days, but bactericidal effect only during two days. This bactericidal long-term effect may be particularly interesting in hospital hygiene for the biocleaning of the most manipulated surfaces and should restrict the role of bacterial reservoir of certain surfaces participating in care or near of the patients.

Prenatal origin of childhood acute lymphoblastic leukemia, association with birth weight and hyperdiploidy.

Recent studies with very small numbers of patients showed that in some cases of childhood acute lymphoblastic leukemia (ALL), preleukemic cells are detectable on Guthrie cards that were used for newborn screening. We present here the largest series of ALL patients (n=32) in whom Guthrie cards were analyzed for the presence of preleukemic cells. Rearranged immunoglobulin heavy-chain genes were used as a marker for leukemic clones. We combined our set of patients with 17 previously published cases. Preleukemic cells were detected in 31 of all 49 patients (63%). Positive screening cards were not associated with patient's age at diagnosis but were almost always found in patients with hyperdiploidy (10/11; 91%; P=0.04). High birth weight is an established risk factor for childhood ALL. Positive screening cards were strongly associated with low birth weight (P=0.01). In conclusion, the majority of childhood B-precursor ALL arise prior to birth. In the search for causes of childhood leukemia we should concentrate on prenatal factors as well as postnatal factors. Our results suggest that autologous cord bloods could be a poor choice as the source of stem cells for transplantation in leukemia, which may contain preleukemic cells. Pending the development of suitable methods, childhood leukemia is a potentially screenable disease.

ABC transporters and drug resistance in leukemia: was P-gp nothing but the first head of the Hydra?

More than 30 years ago it was discovered that permeability glycoprotein (P-gp) can cause drug resistance. Over the following decades numerous studies showed that high expression of P-gp is associated with poor prognosis in acute myeloid leukemia in adults and that it causes multidrug resistance via ATP-dependent drug efflux. It was hoped that an inhibition of P-gp could sensitize resistant leukemic cells to chemotherapy and thus improve treatment results. Today we know that the family of ATP-binding cassette transporters (ABC transporters) comprises 48 different proteins. Some of them seem to be able to cause drug resistance as well as P-gp. This review focuses on emerging data on the clinical relevance of other ABC transporters, such as BCRP, MRP3, and ABCA3. When Heracles fought the ancient Hydra, he had to fight all the heads at ones but only one head was vital for the beast. Can we block all the relevant ABC transporters at once? Is there one transporter that is more important than the others?

[Bacteriological sampling of surfaces: importance of the step of enrichment and the choice of the culture media]. / Prélèvements bactériologiques des surfaces: importance de l'étape d'enrichissement et du choix des milieux de culture.

This study tested the efficiency of four different procedures for isolating bacteria found on hospital surfaces. The techniques studied use both rich and poor media with or without enrichment in nutritive broth. The sampling of surfaces in hospital care departments was carried out using a dampened sterile flue brush. Bacteria samples were then placed on TCSA agar plates (method 1) and blood agar plates (GS) (method 2) before immersion in a nutritive broth for enrichment. The following day, the broth was used to produce two new media: TCSA (method 3) and GS (method 4). For each sample, we established the global amount of different bacterial species isolated by all 4 methods combined. These values were then used as a reference to evaluate the efficiency of each technique. 360 smears were carried out, and a total of 718 bacterial strains were isolated. Methods 1 and 2 (without enrichment) permitted the isolation of 10.86 and 13.37% respectively of the total number of strains. Methods 3 and 4, with preliminary enrichment, made it possible to isolate 69.08% of bacterial strains on TCSA medium and 90.53% on GS medium. The combination of the enrichment stage and an enriched culture medium lead to an excellent output that highlights and identifies bacteria isolated from samples taken from hospital surfaces.

[Triploidy: prompt diagnosis based on typical clinical signs in a live-born extremely low birth-weight infant]. / Triploidie: Rasche Diagnosestellung anhand der typischen klinisch erhobenen Stigmata eines lebend geborenen extrem kleinen Frühgeborenen.

A child with complete triploidy is rarely born alive. However, owing to the advances in perinatal medicine even extremely immature preterm infants receive full support in the delivery room and are admitted to the neonatal ICU. Consequently, the clinician may also have to consider the diagnosis of triploidy when faced with a dysmorphic extremely preterm infant. We report here the smallest described live born girl of 25 + 5 weeks of gestational age with typical clinical findings of complete triploidy phenotype II. The aim of the case report is to make the neonatologist aware of this syndrome using photographs of this case as well as discussing the literature available. Prompt clinical diagnosis confirmed by chromosome analysis helps doctors and parents with the decision whether to continue promising or to limit futile life support measures.

[Parvovirus B 19 associated hemophagocytic syndrome in a patient with hereditary sperocytosis]. / Parvovirus-B-19-assoziiertes hämophagozytisches Syndrom bei einer Patientin mit hereditärer Sphärozytose.

Infections with parvovirus B 19 can cause aplastic crises with a rapid decline of hemoglobin levels in patients with hereditary spherocytosis. Usually, the symptoms and signs of the actual infection are mild. We here report on an eight year old girl with hereditary spherocytosis who was admitted to hospital with high temperature, headache, impaired consciousness and a profound anemia (Hb 2.9 mmol/l). Since she also developed low leukocyte and platelet counts a hematological malignancy was suspected. The bone marrow aspirate showed only 1 % erythroblasts and macrophages with active hemophagocytosis. The serum ferritin was 1381,4 ng/ml. Both, serology and PCR revealed an active infection with parvovirus B 19. Coagulation analysis suggested a low degree of disseminated intravasal coagulation (low fibrinogen, high D-dimers). We diagnosed a parvovirus B 19 associated hemophagocytic syndrome. With only symptomatic treatment the patient's condition and laboratory findings improved during the course of a few days. In accordance with other reported cases, the prognosis of parvovirus B 19 associated hemophagocytic syndrome seems to be better than in hemophagocytic syndrome of other origin.

BCRP gene expression is associated with a poor response to remission induction therapy in childhood acute myeloid leukemia.

Breast cancer resistance protein (BCRP), also known as mitoxantrone resistance protein (MRX) or placenta ABC protein (ABC-P), is the second member of the ABCG subfamily of ABC transport proteins (gene symbol ABCG2). Transfection and enforced expression of BCRP in drug-sensitive cells confers resistance to mitoxantrone, doxorubicin, daunorubicin and topotecan. In this study the expression of BCRP gene was measured using TaqMan real-time PCR in 59 children with newly diagnosed AML. Nine patients were also analyzed in relapse. The median of BCRP gene expression was more than 10 times higher in patients who did not achieve remission after the first phase of chemotherapy (n = 24) as compared to patients who did achieve remission at this stage (n = 21; P = 0.012). In first relapse the expression of the BCRP gene was higher than at diagnosis (P = 0.038). Although high levels of BCRP gene expression were more frequent in subtypes of AML with a favorable prognosis, we found that within both risk groups (high and low risk), patients who expressed high levels of BCRP had a worse prognosis (P = 0.023). Our results strongly suggest that the expression of the BCRP gene reduces the response to chemotherapy in AML and that BCRP expression is higher at the time of relapse.

[Improved results in the treatment of acute myeloid leukemia - Results of study AML-BFM-93 in East Germany with comparisons to the preceding studies AML-I-82 and AML-II-87]. / Verbesserte Ergebnisse in der Therapie der akuten myeloischen Leukämie - Ergebnisse der Therapiestudie AML-BFM-93 in den neuen Bundesländern im Vergleich mit den Vorgängerstudien AML-I/82 und AML-II/87 der DDR.

BACKGROUND: Three multicenter studies were conducted in East Germany on the treatment of acute myeloid leukaemia in children. The latest of the three studies (AML-BFM-93-OST) was part of the common German study AML-BFM-93. PATIENTS AND METHODS: The total number of registered patients was 262. The number and dosage of administered chemotherapeutic agents was elevated with each new study. RESULTS: Both the remission rate (85 %) and the likelihood of an event free survival (52 % after 5 years) could be improved significantly in study AML-BFM-93-OST. The results of the common German study AML-BFM-93 were identical to those of the East German part AML-BFM-93-OST. Compared with international studies it was one of the most successful treatment strategies in children with AML. Patients who showed toxic side effects to heart, liver, kidneys, skin or nervous system during the chemotherapy had a significantly lower risk of relapse, once they overcame the intensive therapy. During the five years of study AML-BFM-93-OST, treatment results could be improved despite an unchanged therapy strategy. This may partly be due to the modernisations and restorations that were carried out in many East German hospitals in this time. CONCLUSIONS: The therapy regimen of study AML-BFM-93 allowed a substantial improvement in the treatment of children with AML. Further intensification of chemotherapy should only be undertaken in accordance to the individual sensitivity of each patient.

Risk group definition in children with acute myeloid leukemia by calculating individual risk factors on the basis of a multivariate stepwise Cox regression analysis.

To define risk groups in children with acute myeloid leukaemia (AML), we conducted a multivariate stepwise Cox regression analysis of three consecutive multicentre studies in East Germany. The total number of patients was 240, but cytogenetics and remission status on day 15 were routinely investigated only in the most recent study, AML-III/93 (78 patients). We derived an equation to calculate individual risk factors, determined those risk factors for all patients of study AML-III/93 and divided them into three groups with 26 patients in each. The variables in the equation were: WBC, FAB-type, auer rods, cytogenetics and response status on day 15. The event-free survival was 80% in the low risk, 55% in the intermediate risk and 15% in the high risk group. Our results strongly suggest that calculating individual risk factors on the basis of a multivariate stepwise Cox regression analysis is a useful tool in defining risk groups.

Blocking of central nervous mineralocorticoid receptors counteracts inhibition of pituitary-adrenal activity in human sleep.

Pituitary-adrenal activity has been found to be inhibited during early nocturnal sleep in humans. This inhibition was supposed to reflect a regulatory influence of hippocampal cells characterized by the expression of mineralocorticoid receptors (MR). Pituitary adrenal responsiveness to bolus injections of CRH (50 micrograms) was examined in each of nine healthy men on four occasions: CRH was injected either during early nocturnal sleep or at the same time of night while the subject was kept awake. Both of these conditions were run after pretreatment with the selective MR antagonist, canrenoate (2 x 200 mg, 0800 and 1700 h, preceding the experimental night) and after placebo administration. After placebo, sleep reduced ACTH and cortisol secretory responses to CRH to about 65% of the size observed during wakefulness (P < 0.05). After canrenoate, ACTH and cortisol secretory responses during sleep and wakefulness did not differ and were comparable with those obtained in placebo-treated subjects during wakefulness. Compared with placebo, canrenoate also distinctly reduced the time spent in slow-wave sleep (P < 0.005). The findings confirm an inhibition of pituitary-adrenal responsiveness during early sleep. The inhibition disappearance after blockage of MR suggests that sleep exerts this influence via central nervous MR-expressing cells. These cells seem to be simultaneously involved in the generation of slow-wave sleep.