BK DNA viral load in plasma: evidence for an association with hemorrhagic cystitis in allogeneic hematopoietic cell transplant recipients.

We performed a case-control study to determine the association of BK plasma viremia with hemorrhagic cystitis (HC) in hematopoietic cell transplant (HCT) recipients. Thirty cases of HC (14 of which occurred after platelet engraftment with documented BK viruria [BK-HC]) were compared with matched controls. Weekly plasma samples were tested for BK virus DNA by polymerase chain reaction (PCR). BK viremia detected before or during the disease was independently associated with HC (adjusted odds ratio = 30, P < .001); BK viremia was even important before clinical symptoms of HC occurred (odds ratio = 11, P < .001). Cases of HC and BK-HC had a significantly higher peak of BK plasma viral load than controls. BK virus was detected by in situ hybridization in bladder biopsies of 2 cases with severe HC and long-lasting BK viremia. BK virus seems to play a role in the development of HC and quantitative detection of BK DNA in plasma appears to be a marker of BK virus disease in HCT recipients.

Front-crawl instantaneous velocity estimation using a wearable inertial measurement unit.

Monitoring the performance is a crucial task for elite sports during both training and competition. Velocity is the key parameter of performance in swimming, but swimming performance evaluation remains immature due to the complexities of measurements in water. The purpose of this study is to use a single inertial measurement unit (IMU) to estimate front crawl velocity. Thirty swimmers, equipped with an IMU on the sacrum, each performed four different velocity trials of 25 m in ascending order. A tethered speedometer was used as the velocity measurement reference. Deployment of biomechanical constraints of front crawl locomotion and change detection framework on acceleration signal paved the way for a drift-free integration of forward acceleration using IMU to estimate the swimmers velocity. A difference of 0.6 ± 5.4 cm · s(-1) on mean cycle velocity and an RMS difference of 11.3 cm · s(-1) in instantaneous velocity estimation were observed between IMU and the reference. The most important contribution of the study is a new practical tool for objective evaluation of swimming performance. A single body-worn IMU provides timely feedback for coaches and sport scientists without any complicated setup or restraining the swimmer's natural technique.

Meadow Saffron Used as a Spice

Introduction: Intoxications with colchicine usually occur by ingestion of meadow saffron leaves (Colchicum autumnale) which are mistakenly collected for alimentary purposes instead of the leaves of crow garlic (Allium ursinum). Colchicine, the main alkaloid of Colchicum autumnale, is present in all parts of the plant. We report a rarer source of mistake, i.e. between the flowers of Colchicum autumnale and Crocus sativus. The similarity in this case is limited to the appearance of the flowers, but Colchicum autumnale, which is also flowering in autumn, lacks the crimson stigma from which the saffron spice is derived from Crocus sativus. Case report: A 47-year-old woman collected the stamens of a flower resembling Crocus sativus for use as saffron. Her knowledge about Crocus sativus was limited to having seen this plant previously at a museum of saffron (Mund, Switzerland). She prepared a meal with rice using three pinches of ''saffron'' for ten tablespoons of rice. She and her 8-year-old child, both ate the usual amount of rice (6 and 2 tablespoons, respectively). The 2 brothers (4- and 9-years-old) only ate 3 teaspoons of rice each. A slightly bitter taste and the absence of a yellow colouration were peculiar. Three to four hours after the meal, the mother developed nausea and contacted the Swiss Toxicological Information Centre, suspecting a plant misidentification. All family members were referred to the regional university hospital for administration of oral activated charcoal. No other symptoms were reported, notably no symptoms in the 8-year-old boy and his brothers. Colchicine serum concentration (blood sample obtained 15 hours after ingestion) measured by HPLC-mass spectrometry was 0.36 mg/L for the mother, and 0.13 mg/L for the 8-year-old child, respectively (therapeutic levels: 0.30-2.5 mg/L). Conclusion: This report demonstrates that a significant amount of colchicine may be absorbed even after ingestion of very small quantities of Colchicum autumnale, which in this case was confused with Crocus sativus. Serum colchicine concentrations in the sub-/therapeutic range can be quantified by HPLC-mass spectrometry, which allows a very sensitive and specific detection of this alkaloid in blood and urine.

Targeting intratumoral B cells with rituximab in addition to CHOP in angioimmunoblastic T-cell lymphoma. A clinicobiological study of the GELA.

Background In angioimmunoblastic T-cell lymphoma, symptoms linked to B-lymphocyte activation are common, and variable numbers of CD20(+) large B-blasts, often infected by Epstein-Barr virus, are found in tumor tissues. We postulated that the disruption of putative B-T interactions and/or depletion of the Epstein-Barr virus reservoir by an anti-CD20 monoclonal antibody (rituximab) could improve the clinical outcome produced by conventional chemotherapy. DESIGN AND METHODS: Twenty-five newly diagnosed patients were treated, in a phase II study, with eight cycles of rituximab + chemotherapy (R-CHOP21). Tumor infiltration, B-blasts and Epstein-Barr virus status in tumor tissue and peripheral blood were fully characterized at diagnosis and were correlated with clinical outcome. RESULTS: A complete response rate of 44% (95% CI, 24% to 65%) was observed. With a median follow-up of 24 months, the 2-year progression-free survival rate was 42% (95% CI, 22% to 61%) and overall survival rate was 62% (95% CI, 40% to 78%). The presence of Epstein-Barr virus DNA in peripheral blood mononuclear cells (14/21 patients) correlated with Epstein-Barr virus score in lymph nodes (P<0.004) and the detection of circulating tumor cells (P=0.0019). Despite peripheral Epstein-Barr virus clearance after treatment, the viral load at diagnosis (>100 copy/μg DNA) was associated with shorter progression-free survival (P=0.06). Conclusions We report here the results of the first clinical trial targeting both the neoplastic T cells and the microenvironment-associated CD20(+) B lymphocytes in angioimmunoblastic T-cell lymphoma, showing no clear benefit of adding rituximab to conventional chemotherapy. A strong relationship, not previously described, between circulating Epstein-Barr virus and circulating tumor cells is highlighted.

A steroidomic approach for biomarkers discovery in doping control.

Anti-doping authorities have high expectations of the athlete steroidal passport (ASP) for anabolic-androgenic steroids misuse detection. However, it is still limited to the monitoring of known well-established compounds and might greatly benefit from the discovery of new relevant biomarkers candidates. In this context, steroidomics opens the way to the untargeted simultaneous evaluation of a high number of compounds. Analytical platforms associating the performance of ultra-high pressure liquid chromatography (UHPLC) and the high mass-resolving power of quadrupole time-of-flight (QTOF) mass spectrometers are particularly adapted for such purpose. An untargeted steroidomic approach was proposed to analyse urine samples from a clinical trial for the discovery of relevant biomarkers of testosterone undecanoate oral intake. Automatic peak detection was performed and a filter of reference steroid metabolites mass-to-charge ratio (m/z) values was applied to the raw data to ensure the selection of a subset of steroid-related features. Chemometric tools were applied for the filtering and the analysis of UHPLC-QTOF-MS(E) data. Time kinetics could be assessed with N-way projections to latent structures discriminant analysis (N-PLS-DA) and a detection window was confirmed. Orthogonal projections to latent structures discriminant analysis (O-PLS-DA) classification models were evaluated in a second step to assess the predictive power of both known metabolites and unknown compounds. A shared and unique structure plot (SUS-plot) analysis was performed to select the most promising unknown candidates and receiver operating characteristic (ROC) curves were computed to assess specificity criteria applied in routine doping control. This approach underlined the pertinence to monitor both glucuronide and sulphate steroid conjugates and include them in the athletes passport, while promising biomarkers were also highlighted.

Going the distance: human population genetics in a clinal world.

Global human genetic variation is greatly influenced by geography, with genetic differentiation between populations increasing with geographic distance and within-population diversity decreasing with distance from Africa. In fact, these 'clines' can explain most of the variation in human populations. Despite this, population genetics inferences often rely on models that do not take geography into account, which could result in misleading conclusions when working at global geographic scales. Geographically explicit approaches have great potential for the study of human population genetics. Here, we discuss the most promising avenues of research in the context of human settlement history and the detection of genomic elements under natural selection. We also review recent technical advances and address the challenges of integrating geography and genetics.

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

PURPOSE: Mutations in IDH3B, an enzyme participating in the Krebs cycle, have recently been found to cause autosomal recessive retinitis pigmentosa (arRP). The MDH1 gene maps within the RP28 arRP linkage interval and encodes cytoplasmic malate dehydrogenase, an enzyme functionally related to IDH3B. As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28. METHODS: With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). PCR products were then sequenced by short-read UHTs with no further processing. Computer-based mapping of the reads and mutation detection were performed by three independent software packages. RESULTS: Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. The two patients were homozygous for all DNA variants identified in the region, which confirms previous linkage and homozygosity mapping results, but had different haplotypes, indicating genetic or allelic heterogeneity. None of the DNA changes detected could be associated with the disease. CONCLUSIONS: The MDH1 gene is not the cause of RP28-linked arRP. Our experimental strategy shows that long-range genomic PCR followed by UHTs provides an excellent system to perform a thorough screening of candidate genes for hereditary retinal degeneration.

New biomarkers in T-cell lymphomas.

Peripheral T-cell lymphomas (PTCLs) are heterogeneous and uncommon malignancies characterized by an aggressive clinical course and a mostly poor outcome with current treatment strategies. The recent genome-wide molecular characterization of several entities has provided novel insights into their pathobiology and led to the identification of new biomarkers with diagnostic, prognostic or therapeutic implications for PTCL patients. Cell lineage and differentiation antigens (markers of γδ or NK lineage, of cytotoxicity, of follicular helper T cells) reflect the tumour's biological behaviour, and their detection in tissue samples may refine the diagnostic and prognostic stratification of the patients. Previously unrecognized gene rearrangements are being discovered (ITK-SYK translocation, IRF4/MUM1 and DUSP22 rearrangements), and may serve as diagnostic genetic markers. Deregulated molecules within oncogenic pathways (NF-κB, Syk, PDGFRα) and immunoreactive cell-surface antigens (CD30, CD52) have been brought to the fore as potential targets for guiding the development of novel therapies.

Kernel-based Mapping of Meteorological Fields in Complex Orography

Due to the advances in sensor networks and remote sensing technologies, the acquisition and storage rates of meteorological and climatological data increases every day and ask for novel and efficient processing algorithms. A fundamental problem of data analysis and modeling is the spatial prediction of meteorological variables in complex orography, which serves among others to extended climatological analyses, for the assimilation of data into numerical weather prediction models, for preparing inputs to hydrological models and for real time monitoring and short-term forecasting of weather.In this thesis, a new framework for spatial estimation is proposed by taking advantage of a class of algorithms emerging from the statistical learning theory. Nonparametric kernel-based methods for nonlinear data classification, regression and target detection, known as support vector machines (SVM), are adapted for mapping of meteorological variables in complex orography.With the advent of high resolution digital elevation models, the field of spatial prediction met new horizons. In fact, by exploiting image processing tools along with physical heuristics, an incredible number of terrain features which account for the topographic conditions at multiple spatial scales can be extracted. Such features are highly relevant for the mapping of meteorological variables because they control a considerable part of the spatial variability of meteorological fields in the complex Alpine orography. For instance, patterns of orographic rainfall, wind speed and cold air pools are known to be correlated with particular terrain forms, e.g. convex/concave surfaces and upwind sides of mountain slopes.Kernel-based methods are employed to learn the nonlinear statistical dependence which links the multidimensional space of geographical and topographic explanatory variables to the variable of interest, that is the wind speed as measured at the weather stations or the occurrence of orographic rainfall patterns as extracted from sequences of radar images. Compared to low dimensional models integrating only the geographical coordinates, the proposed framework opens a way to regionalize meteorological variables which are multidimensional in nature and rarely show spatial auto-correlation in the original space making the use of classical geostatistics tangled.The challenges which are explored during the thesis are manifolds. First, the complexity of models is optimized to impose appropriate smoothness properties and reduce the impact of noisy measurements. Secondly, a multiple kernel extension of SVM is considered to select the multiscale features which explain most of the spatial variability of wind speed. Then, SVM target detection methods are implemented to describe the orographic conditions which cause persistent and stationary rainfall patterns. Finally, the optimal splitting of the data is studied to estimate realistic performances and confidence intervals characterizing the uncertainty of predictions.The resulting maps of average wind speeds find applications within renewable resources assessment and opens a route to decrease the temporal scale of analysis to meet hydrological requirements. Furthermore, the maps depicting the susceptibility to orographic rainfall enhancement can be used to improve current radar-based quantitative precipitation estimation and forecasting systems and to generate stochastic ensembles of precipitation fields conditioned upon the orography.

A Behavioral Account of the Labor Market: The Role of Fairness Concerns

In this paper, we argue that important labor market phenomena can be better understood if one takes (a) the inherent incompleteness and relational nature of most employment contracts and (b) the existence of reference-dependent fairness concerns among a substantial share of the population into account. Theory shows and experiments confirm that, even if fairness concerns were to exert only weak effects in one-shot interactions, repeated interactions greatly magnify the relevance of such concerns on economic outcomes. We also review evidence from laboratory and field experiments examining the role of wages and fairness on effort, derive predictions from our approach for entry-level wages and incumbent workers' wages, confront these predictions with the evidence, and show that reference-dependent fairness concerns may have important consequences for the effects of economic policies such as minimum wage laws.

Mise au point concernantl'utilisation du dosagede l'antigène carcino-embryonnaire (CEA)en clinique

The carcinoembryonic antigen (CEA) is a tumor marker defined by specific heterologous antisera. Elevated levels of circulating CEA have been detected by radioimmunoassay in 20-90 per cent of cases of colorectal carcinomas depending on the degree of tumor spread. The fact that elevation of CEA level can also be observed in other types of carcinomas and in several non malignant conditions greatly limit the value of the CEA test for the early diagnosis of colorectal carcinoma. Thus, the CEA assay should not be used as a screening test for cancer. Repeatecl CEA mesurements, however, appear to be of importance for the evaluation of tumor resection and the detection of tumor recurrence. The only localized tumors known to produce elevation of CEA above the levels observed in non malignant diseases are carcinomas of the large bowel and the pancreas. In carcinomas derived from other organs a marked increase of CEA level is always associated with the presence of distant metastasis. Therefore at the present time the clinical applications of the CEA radioimmunoassay should be limited to the differentiai diagnosis of patients with suspicion of primary colorectal or pancreatic carcinoma, to the detection of distant metastasis in other types of carcinomas and to the post operative follow up of patients who had elevated levels of CEA before surgery. Well-controlled studies are still needed to determine if therapeutic decisions based on CEA results can lead to improved survival.

Comparaison objective de systèmes d'imagerie conventionnelle et numérique en mammographie

L'objectif de ce travail est le développement d'une méthode de caractérisation objective de la qualité d'image s'appliquant à des systèmes de mammographie analogique, utilisant un couple écran-film comme détecteur, et numérique, basé sur une technologie semi-conductrice, ceci en vue de la comparaison de leurs performances. La méthode développée tient compte de la gamme dynamique du détecteur, de la détectabilité de structures de haut contraste, simulant des microcalcifications, et de structures de bas contraste, simulant des opacités (nodules tumoraux). La méthode prend également en considération le processus de visualisation de l'image, ainsi que la réponse de l'observateur. Pour réaliser ceci, un objet-test ayant des propriétés proches de celles d'un sein comprimé, composé de différents matériaux équivalents aux tissus, allant du glandulaire à l'adipeux, et comprenant des zones permettant la simulation de structures de haut et bas contraste, ainsi que la mesure de la résolution et celle du bruit, a été développé et testé. L'intégration du processus de visualisation a été réalisée en utilisant une caméra CCD mesurant directement les paramètres de qualité d'image, à partir de l'image de l'objet-test, dans une grandeur physique commune au système numérique et analogique, à savoir la luminance arrivant sur l'oeil de l'observateur. L'utilisation d'une grandeur synthétique intégrant dans un même temps, le contraste, le bruit et la résolution rend possible une comparaison objective entre les deux systèmes de mammographie. Un modèle mathématique, simulant la réponse d'un observateur et intégrant les paramètres de base de qualité d'image, a été utilisé pour calculer la détectabilité de structures de haut et bas contraste en fonction du type de tissu sur lequel celles-ci se trouvent. Les résultats obtenus montrent qu'à dose égale la détectabilité des structures est significativement plus élevée avec le système de mammographie numérique qu'avec le système analogique. Ceci est principalement lié au fait que le bruit du système numérique est plus faible que celui du système analogique. Les résultats montrent également que la méthodologie, visant à comparer des systèmes d'imagerie numérique et analogique en utilisant un objet-test à large gamme dynamique ainsi qu'une caméra, peut être appliquée à d'autres modalités radiologiques, ainsi qu'à une démarche d'optimisation des conditions de lecture des images.<br/><br/>The goal of this work was to develop a method to objectively compare the performance of a digital and a screen-film mammography system in terms of image quality and patient dose. We propose a method that takes into account the dynamic range of the image detector and the detection of high contrast (for microcalcifications) and low contrast (for masses or tumoral nodules) structures. The method also addresses the problems of image visualization and the observer response. A test object, designed to represent a compressed breast, was constructed from various tissue equivalent materials ranging from purely adipose to purely glandular composition. Different areas within the test object permitted the evaluation of low and high contrast detection, spatial resolution, and image noise. All the images (digital and conventional) were captured using a CCD camera to include the visualization process in the image quality assessment. In this way the luminance reaching the viewer?s eyes can be controlled for both kinds of images. A global quantity describing image contrast, spatial resolution and noise, and expressed in terms of luminance at the camera, can then be used to compare the two technologies objectively. The quantity used was a mathematical model observer that calculates the detectability of high and low contrast structures as a function of the background tissue. Our results show that for a given patient dose, the detection of high and low contrast structures is significantly better for the digital system than for the conventional screen-film system studied. This is mainly because the image noise is lower for the digital system than for the screen-film detector. The method of using a test object with a large dynamic range combined with a camera to compare conventional and digital imaging modalities can be applied to other radiological imaging techniques. In particular it could be used to optimize the process of radiographic film reading.

Quantitative performance of a quadrupole-orbitrap-MS in targeted LC-MS determinations of small molecules.

High-resolution mass spectrometry (HRMS) has been associated with qualitative and research analysis and QQQ-MS with quantitative and routine analysis. This view is now challenged and for this reason, we have evaluated the quantitative LC-MS performance of a new high-resolution mass spectrometer (HRMS), a Q-orbitrap-MS, and compared the results obtained with a recent triple-quadrupole MS (QQQ-MS). High-resolution full-scan (HR-FS) and MS/MS acquisitions have been tested with real plasma extracts or pure standards. Limits of detection, dynamic range, mass accuracy and false positive or false negative detections have been determined or investigated with protease inhibitors, tyrosine kinase inhibitors, steroids and metanephrines. Our quantitative results show that today's available HRMS are reliable and sensitive quantitative instruments and comparable to QQQ-MS quantitative performance. Taking into account their versatility, user-friendliness and robustness, we believe that HRMS should be seen more and more as key instruments in quantitative LC-MS analyses. In this scenario, most targeted LC-HRMS analyses should be performed by HR-FS recording virtually "all" ions. In addition to absolute quantifications, HR-FS will allow the relative quantifications of hundreds of metabolites in plasma revealing individual's metabolome and exposome. This phenotyping of known metabolites should promote HRMS in clinical environment. A few other LC-HRMS analyses should be performed in single-ion-monitoring or MS/MS mode when increased sensitivity and/or detection selectivity will be necessary.