IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.

MOTIVATION: Microarray results accumulated in public repositories are widely reused in meta-analytical studies and secondary databases. The quality of the data obtained with this technology varies from experiment to experiment, and an efficient method for quality assessment is necessary to ensure their reliability. RESULTS: The lack of a good benchmark has hampered evaluation of existing methods for quality control. In this study, we propose a new independent quality metric that is based on evolutionary conservation of expression profiles. We show, using 11 large organ-specific datasets, that IQRray, a new quality metrics developed by us, exhibits the highest correlation with this reference metric, among 14 metrics tested. IQRray outperforms other methods in identification of poor quality arrays in datasets composed of arrays from many independent experiments. In contrast, the performance of methods designed for detecting outliers in a single experiment like Normalized Unscaled Standard Error and Relative Log Expression was low because of the inability of these methods to detect datasets containing only low-quality arrays and because the scores cannot be directly compared between experiments. AVAILABILITY AND IMPLEMENTATION: The R implementation of IQRray is available at: ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R. CONTACT: Marta.Rosikiewicz@unil.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Reproducibility and feasibility of a 22 joints ultrasound score in rheumatoid arthritis: a study among rheumatologists with diverse expertise in musculoskeletal ultrasound

Objective: To assess reproducibility and feasibility of amusculoskeletal ultrasound (US) score for rheumatoid arthritis amongrheumatologist with diverse expertise in US, working in private orhospital practice.Methods: The Swiss Sonography in Arthritis and Rheumatism(SONAR) group has developed a semi-quantitative score for RA usingOMERACT criteria for synovitis and erosion. The score was taught torheumatologists trained in US through two workshops. Subsequently,they were encouraged to practice in their office. For the study, we used6 US machines of different quality, each with a different patient.19 readers randomly selected among rheumatologists who haveattended both workshops, were asked to score anonymously at leastone patient. To assess whether some factors influence the score, weasked each reader to answer questionnaire describing his experiencewith US.Results: 19 rheumatologists have performed 29 scans, each patienthaving been evaluated by 4 to 6 readers. Median time for examcompletion was 20 minutes (range 15 to 60 mn). 53% ofrheumatologists work in private practice. Graph 1 show the global greyscale score for each patient. Weighted kappa was calculated for eachpair of reader using stata11. Almost all kappa of poor agreement wereobtained with a low quality device or by an assessor who havepreviously performed less than 5 scores himself.Conclusions: This is the first study to show an US score for RAfeasible by rheumatologists with diverse expertise in US both in privateand hospital practice. Reproducibility seemed to be influenced by thequality of device and previous experience with the score.

Pédiatrie. 4. La calprotectine fécale en pédiatrie: utilisation et interprétation [Pediatrics. Fecal calprotectin in children: use and interpretation].

Fecal calprotectin is a small protein released mainly by neutrophils. It is recognized as a reliable, easy and non-invasive biomarker of gastro-intestinal inflammation. Normal values vary with age, with higher cut-off values during the first year of life (<350 microg/g) than in children (<275 microg/g) or adults (<50 microg/g). Fecal calprotectin can be a useful tool in initial evaluation of recurrent abdominal pain, helping to distinguish between functional gastro-intestinal disorders, where it is normal, and inflammatory bowel disease (IBD). It is not a specific marker of IBD but is increased in other situations of gastro-intestinal inflammation. In patients with IBD, fecal calprotectin is used to monitor treatment response.

Validation of a score for predicting fatal bleeding in patients receiving anticoagulation for venous thromboembolism.

BACKGROUND: The only available score to assess the risk for fatal bleeding in patients with venous thromboembolism (VTE) has not been validated yet. METHODS: We used the RIETE database to validate the risk-score for fatal bleeding within the first 3 months of anticoagulation in a new cohort of patients recruited after the end of the former study. Accuracy was measured using the ROC curve analysis. RESULTS: As of December 2011, 39,284 patients were recruited in RIETE. Of these, 15,206 had not been included in the former study, and were considered to validate the score. Within the first 3 months of anticoagulation, 52 patients (0.34%; 95% CI: 0.27-0.45) died of bleeding. Patients with a risk score of <1.5 points (64.1% of the cohort) had a 0.10% rate of fatal bleeding, those with a score of 1.5-4.0 (33.6%) a rate of 0.72%, and those with a score of >4 points had a rate of 1.44%. The c-statistic for fatal bleeding was 0.775 (95% CI 0.720-0.830). The score performed better for predicting gastrointestinal (c-statistic, 0.869; 95% CI: 0.810-0.928) than intracranial (c-statistic, 0.687; 95% CI: 0.568-0.806) fatal bleeding. The score value with highest combined sensitivity and specificity was 1.75. The risk for fatal bleeding was significantly increased (odds ratio: 7.6; 95% CI 3.7-16.2) above this cut-off value. CONCLUSIONS: The accuracy of the score in this validation cohort was similar to the accuracy found in the index study. Interestingly, it performed better for predicting gastrointestinal than intracranial fatal bleeding.

Can the trabecular bone score be considered as a major clinical risk factor of osteoporotic fractures? A meta-like analysis.

To have an added value over BMD, a CRF of osteoporotic fracture must be predictable of the fracture, independent of BMD, reversible and quantifiable. Many major recognized CRF exist. Out of these factors many of them are indirect factor of bone quality. TBS predicts fracture independently of BMD as demonstrated from previous studies. The aim of the study is to verify if TBS can be considered as a major CRF of osteoporotic fracture. Existing validated datasets of Caucasian women were analyzed. These datasets stem from different studies performed by the authors of this report or provided to our group. However, the level of evidence of these studies will vary. Thus, the different datasets were weighted differently according to their design. This meta-like analysis involves more than 32000 women (≥50years) with 2000 osteoporotic fractures from two prospective studies (OFELY&MANITOBA) and 7 cross-sectional studies. Weighted relative risk (RR) for TBS was expressed for each decrease of one standard deviation as well as per tertile difference (TBS=1.300 and 1.200) and compared with those obtained for the major CRF included in FRAX®. Overall TBS RR obtained (adjusted for age) was 1.79 [95%CI-1.37-2.37]. For all women combined, RR for fracture for the lowest compared with the middle TBS tertile was 1.55[1.46-1.68] and for the lowest compared with the highest TBS tertile was 2.8[2.70-3.00]. TBS is comparable to most of the major CRF and thus could be used as one of them. Further studies have to be conducted to confirm these first findings.

Trabecular Bone Score Helps Classifying Women At Riskof Fracture Prospectively In The Ofely Study

Objectives: Trabecular Bone Score (TBS, Med-Imaps, France) is an index of bone microarchitecture calculated from antero-posterior spine DXA scan and reported to be associated with fracture in prior case-control studies and in a large prospective study with the Prodigy DXA device. Our aim was to assess the ability of TBS to predict incident fracture and improve the classification of fracture prospectively in the OFELY study.Materials/Methods: TBS was assessed in 564 postmenopausal women (66±8 years old) from the OFELY cohort, who had a spine DXA scan (QDR 4500A, Hologic, USA) between year 2000 and 2001. During a mean follow up of 7.8±1.3 years, 94 women sustained a fragility fracture.Results: At the time of baseline DXA scan, women with incident fracture were significantly older (70±9 vs. 65± 8 years), had a lower spine BMD (T-score: −1.9±1.2 vs. −1.3±1.3, p<0.001) and spine TBS (−3.1%, p<0.001) than women without incident fracture. After adjustment for age, BMI and the presence of prevalent fracture, the magnitude of fracture prediction was similar for spine BMD (OR=1.42 [1.11;1.82] per SD decrease [95% CI]) and TBS (OR=1.34 [1.04;1.74]) but the combination of TBS and spine BMD did not improve fracture prediction. Spine BMD and TBS were both correlated with age (respectively r=−0.17 and −0.49, p<0.001) and correlated together with 39% of TBS explained by spine BMD (r=0.63, p<0.001). When using the WHO classification, 38% of the fractures occurred in osteoporotic (fracture rate=29%), 47% in osteopenic (fracture rate=16%) and 15% in women with T-score >−1 (fracture rate=9%). By classifying our population in tertiles of TBS, we found that 47% of the fractures occurred in the lowest tertile of TBS (fracture rate=23%) and 39% of the fracture that occurred in osteopenic women were in the lowest tertile of TBS.Conclusions: Spine BMD and TBS predicted fractures equally well. The addition of TBS to spine BMD added only limited information on fracture risk prediction in our cohort when considering the all range of BMD. Nevertheless combining the osteopenic T-score and the lowest TBS helped defining a subset of osteopenic women at higher risk of fracture.Disclosure of Interest: None declared.

Facteurs Influençant la Progression du Score EDSS dans la Sclérose en Plaques Récurrente-Rémittente

Introduction : la Sclérose en plaques (SEP) est le prototype de désordre auto-immun du système nerveux central. Avec environ 110 malades par 100'000 habitants, la Suisse est considérée un pays à haute prévalence. Chez environ 80% des patients, la maladie débute par la forme récurrente- rémittente (RR), où des poussées aiguës s'intercalent avec des périodes de rémission. Cette phase se conclut dans son évolution naturelle généralement en une phase secondairement progressive, pendant laquelle le déficit progresse en l'absence de poussée. Sur le plan physiopathologique, deux phénomènes interagissent : l'atteinte inflammatoire démyélinisante et l'atteinte neurodégénerative. La première est { l'origine des poussées aiguës, la deuxième se manifeste cliniquement par la progression irréversible du déficit neurologique. En Suisse les immunomodulateurs ont été utilisés comme thérapies de fond pour la SEP à partir des années 1995. Leur effet sur le taux de poussées a été largement démontré, tandis que leur efficacité sur l'évolution de la maladie à long terme reste ouverte. Le moyen le plus répandu pour quantifier le niveau du handicap neurologique est la Kurtzke Expanded Disability Status Scale (EDSS). Cette échelle évalue les troubles neurologiques en les classifiant de 0 (examen normal) à 10 (décès) avec des marches de demi-points. Notre recherche à voulu identifier des facteurs cliniques précoces { valeur prédictif sur l'évolution du déficit neurologique permanent, ainsi qu'analyser le moment d'introduction du traitement pour extraire des informations utiles { la décision thérapeutique. Méthodes : Exploitation de la base de données iMed-CHUV comptant 1150 patients SEP (dont 622 SEP RR) pour analyser rétrospectivement, dans la SEP RR, l'influence de différentes variables cliniques précoces (taux de poussées pendant les premières deux années de maladie, intervalle entre les deux premières poussées, sévérité et site anatomique de la première poussée, déficit résiduel après la première poussée) et de deux caractéristiques liées { l'instauration du traitement immunosuppresseur de fond (âge et délai d'introduction) sur l'évolution du déficit neurologique vers un score EDSS ≥4.0. Les variables ont été testées avec la méthode d'estimation de taux de survie Kaplan-Meier. Résultats: 349 patients avec SEP RR possédaient les critères nécessaires pour faire partie de l'analyse, le suivi moyen étant de 8.26 ans (SD 4.77). Un taux de poussées élevé pendant les premiers 2 ans (>1 vs ≤1) et un long intervalle entre les 2 premiers épisodes (>36 vs >12-36 vs ≤12) étaient significativement associés au risque de progression du déficit neurologique vers un score EDSS de 4.0 ou plus (log Rank P=0.016 et P=0.008 respectivement). Par contre ni le site anatomique de la première poussée ni l'âge d'introduction du traitement immunomodulateur n'avaient d'influence significative sur la progression du déficit neurologique (log rank P=0.370 et P=0.945 respectivement). Etonnamment une introduction rapide du traitement était associée à une plus forte progression du déficit neurologique (log rank P=0.032), montrant qu'une partie des patients a une évolution bénigne même en l'absence de traitement. Conclusions : L'activité inflammatoire précoce, dont le niveau peut être estimé par indices précoces comme le taux de poussées et l'intervalle entre les deux premières poussées, mais non le site de primo-manifestation prédit la progression ultérieure du déficit neurologique. Ces indices doivent être utilisés en combinaison avec les informations fournies par l'IRM pour l'individuation et le traitement précoce des patients à risque, indépendamment de leur âge. En raison des effets indésirables et des coûts élevés, les thérapies doivent cibler de façon spécifique les classes à risque, et épargner les patients avec évolution lente.

Symptomatic intracranial hemorrhage after stroke thrombolysis: the SEDAN score.

OBJECTIVE: A study was undertaken to develop a score for assessing risk for symptomatic intracranial hemorrhage (sICH) in ischemic stroke patients treated with intravenous (IV) thrombolysis. METHODS: The derivation cohort comprised 974 ischemic stroke patients treated (1995-2008) with IV thrombolysis at the Helsinki University Central Hospital. The predictive value of parameters associated with sICH (European Cooperative Acute Stroke Study II) was evaluated, and we developed our score according to the magnitude of logistic regression coefficients. We calculated absolute risks and likelihood ratios of sICH per increasing score points. The score was validated in 828 patients from 3 Swiss cohorts (Lausanne, Basel, and Geneva). Performance of the score was tested with area under a receiver operating characteristic curve (AUC-ROC). RESULTS: Our SEDAN score (0 to 6 points) comprises baseline blood Sugar (glucose; 8.1-12.0 mmol/l [145-216 mg/dl] = 1; >12.0 mmol/l [>216 mg/dl] = 2), Early infarct signs (yes = 1) and (hyper)Dense cerebral artery sign (yes = 1) on admission computed tomography scan, Age (>75 years = 1), and NIH Stroke Scale on admission (≥10 = 1). Absolute risk for sICH in the derivation cohort was: 1.4%, 2.9%, 8.5%, 12.2%, 21.7%, and 33.3% for 0, 1, 2, 3, 4, and 5 score points, respectively. In the validation cohort, absolute risks were similar (1.0%, 3.5%, 5.1%, 9.2%, 16.9%, and 27.8%, respectively). AUC-ROC was 0.77 (0.71-0.83; p < 0.001). INTERPRETATION: Our SEDAN score reliably assessed risk for sICH in IV thrombolysis-treated patients with anterior- and posterior circulation ischemic stroke, and it can support clinical decision making in high-risk patients. External validation of the score supports its generalization.

Extent of Hypoattenuation On CT Angiography Source Images In Basilar Artery Occlusion: Prognostic Accuracy Of Posterior Circulation ASPECTS And The Pons-midbrain Score In The Basilar Artery International Cooperation Study

Background: The posterior circulation Acute Stroke Prognosis Early CT Score (pc-ASPECTS) and the combined Pons-midbrain score quantify the extent of early ischemic changes in the posterior circulation. We compared the prognostic accuracy of both scores if applied to CT angiography (CTA) source images (CTA-SI) of patients in the Basilar Artery International Cooperation Study (BASICS).Methods: BASICS was a prospective, observational, multi-centre, registry of consecutive patients who presented with acute symptomatic basilar artery occlusion (BAO). Functional outcome was assessed at 1 month. We applied pc-ASPECTS and the combined Pons-midbrain score to CTA-SI by 3-reader-consensus. Readers were blinded to clinical data. We performed multivariable logistic regression analysis, adjusting for thrombolysis, baseline NIHSS score and age, and used the output to derive ROC curves to compare the ability of both scores to discriminate patients with favourable (modified Rankin Scale [mRS] scores 0-3) from patients with unfavourable (mRS scores 4-6) functional outcome.Results: We reviewed CTAs of 158 patients (64% men, mean age 65 _ 15 years, median NIHSS score 25 [0-38], median GCS score 7 [3-15], median onset-to-CTA time 234 minutes [11-7380]). At 1 month, 40 (25%) patients had a favourable outcome, 49 (31%) had an unfavourable outcome (mRS score 4-5) and 69 (44%) were deceased. Both techniques of assessing CTA-SI hypoattenuation in the posterior circulation showed equally good discriminative value in predicting final outcome (C-statistics; area under ROC curve 0.74 versus 0.75, respectively; p_0.37). Pc-ASPECTS dichotomized at _6 versus _6 was an independent predictor of favourable functional outcome (RR _ 2.2; CI95 1.1-4.7; p _ 0.034).Conclusion: Compared to the combined Pons-midbrain score, the pc-ASPECTS score has similar prognostic accuracy to identify patients with a favourable functional outcome in BASICS. Dichotomized pc-ASPECTS (_6 versus _6) is an independent predictor of favourable functional outcome in this population. Author Disclosures: V. Puetz: None. A. Khomenko: None. M.D. Hill: None. I. Dzialowski: None. P. Michel: None. C. Weimar: None. C.A.C. Wijman: None. H. Mattle: None. K. Muir: None. T. Pfefferkorn: None. D. Tanne: None. S. Engelter: None. K. Szabo: None. A. Algra: None. A.M. Demchuk: None. W.J. Schonewille: None.

Scores de mesure fonctionnelle articulaire pour le praticien [Joint functional outcome score for the clinician].

The sports clinician faces multiple treatment options when dealing with overload injuries, and it is important to evaluate their outcomes. Multiple scores exist, some clincian rated (CRO), others patient rated (PRO), the latter being currently favoured. This review presents some of these scores and we selected the ones we feel are the most appropriate for a sports clinician. We considered these common problems: tennis elbow, rotator cuff issues, groin pain, patellofemoral pain syndrome, achilles tendinopathy and ankle instability. In addition, an activity level score is useful to weigh the result in the context of return to performance. These scores help to create a common language between therapists and to evaluate treatments objectively.

Ruling out coronary heart disease in primary care patients with chest pain : a clinical prediction score

ABSTRACT: BACKGROUND: Chest pain raises concern for the possibility of coronary heart disease. Scoring methods have been developed to identify coronary heart disease in emergency settings, but not in primary care. METHODS: Data were collected from a multicenter Swiss clinical cohort study including 672 consecutive patients with chest pain, who had visited one of 59 family practitioners' offices. Using delayed diagnosis we derived a prediction rule to rule out coronary heart disease by means of a logistic regression model. Known cardiovascular risk factors, pain characteristics, and physical signs associated with coronary heart disease were explored to develop a clinical score. Patients diagnosed with angina or acute myocardial infarction within the year following their initial visit comprised the coronary heart disease group. RESULTS: The coronary heart disease score was derived from eight variables: age, gender, duration of chest pain from 1 to 60 minutes, substernal chest pain location, pain increases with exertion, absence of tenderness point at palpation, cardiovascular risks factors, and personal history of cardiovascular disease. Area under the receiver operating characteristics curve was of 0.95 with a 95% confidence interval of 0.92; 0.97. From this score, 413 patients were considered as low risk for values of percentile 5 of the coronary heart disease patients. Internal validity was confirmed by bootstrapping. External validation using data from a German cohort (Marburg, n = 774) revealed a receiver operating characteristics curve of 0.75 (95% confidence interval, 0.72; 0.81) with a sensitivity of 85.6% and a specificity of 47.2%. CONCLUSIONS: This score, based only on history and physical examination, is a complementary tool for ruling out coronary heart disease in primary care patients complaining of chest pain.

Trabecular Bone Score: A Noninvasive Analytical Method Based Upon the DXA Image.

The trabecular bone score (TBS) is a gray-level textural metric that can be extracted from the two-dimensional lumbar spine dual-energy X-ray absorptiometry (DXA) image. TBS is related to bone microarchitecture and provides skeletal information that is not captured from the standard bone mineral density (BMD) measurement. Based on experimental variograms of the projected DXA image, TBS has the potential to discern differences between DXA scans that show similar BMD measurements. An elevated TBS value correlates with better skeletal microstructure; a low TBS value correlates with weaker skeletal microstructure. Lumbar spine TBS has been evaluated in cross-sectional and longitudinal studies. The following conclusions are based upon publications reviewed in this article: 1) TBS gives lower values in postmenopausal women and in men with previous fragility fractures than their nonfractured counterparts; 2) TBS is complementary to data available by lumbar spine DXA measurements; 3) TBS results are lower in women who have sustained a fragility fracture but in whom DXA does not indicate osteoporosis or even osteopenia; 4) TBS predicts fracture risk as well as lumbar spine BMD measurements in postmenopausal women; 5) efficacious therapies for osteoporosis differ in the extent to which they influence the TBS; 6) TBS is associated with fracture risk in individuals with conditions related to reduced bone mass or bone quality. Based on these data, lumbar spine TBS holds promise as an emerging technology that could well become a valuable clinical tool in the diagnosis of osteoporosis and in fracture risk assessment. © 2014 American Society for Bone and Mineral Research.

The prediction of cardiovascular events is improved by combination of Framingham risk score and subclinical atherosclerosis imaging

Purpose: In primary prevention of cardiovascular disease (CVD), it is accepted that the intensity of risk factor treatment should be guided by the magnitude of absolute risk. Risk factors tools like Framingham risk score (FHS) or noninvasive atherosclerosis imaging tests are available to detect high risk subjects. However, these methods are imperfect and may misclassify a large number of individuals. The purpose of this prospective study was to evaluate whether the prediction of future cardiovascular events (CVE) can be improved when subclinical imaging atherosclerosis (SCATS) is combined with the FRS in asymptomatic subjects. Methods: Overall, 1038 asymptomatic subjects (413 women, 625 men, mean age 49.1±12.8 years) were assessed for their cardiovascular risk using the FRS. B-mode ultrasonography on carotid and femoral arteries was performed by two investigators to detect atherosclerotic plaques (focal thickening of intima-media > 1.2 mm) and to measure carotid intima-media thickness (C-IMT). The severity of SCATS was expressed by an ATS-burden Score (ABS) reflecting the number of the arterial sites with >1 plaques (range 0-4). CVE were defined as fatal or non fatal acute coronary syndrome, stroke, or angioplasty for peripheral artery disease. Results: during a mean follow-up of 4.9±3.1 years, 61 CVE were recorded. Event rates the rate of CVE increased significantly from 2.7% to 39.1% according to the ABS (p<0.001) and from 4% to 24.6% according to the quartiles of C-IMT. Similarly, FRS predicted CVE (p<0.001). When computing the angiographic markers of SCATS in addition of FRS, we observed an improvement of net reclassification rate of 16.6% (p< 0.04) for ABS as compared to 5.5% (p = 0.26) for C-IMT. Conclusion: these results indicate that the detection of subjects requiring more attention to prevent CVE can be significantly improved when using both FRS and SCATS imaging.

Trabecular bone score improves fracture risk prediction in non-osteoporotic women: the OFELY study.

The use of areal bone mineral density (aBMD) for fracture prediction may be enhanced by considering bone microarchitectural deterioration. Trabecular bone score (TBS) helped in redefining a significant subset of non-osteoporotic women as a higher risk group. INTRODUCTION: TBS is an index of bone microarchitecture. Our goal was to assess the ability of TBS to predict incident fracture. METHODS: TBS was assessed in 560 postmenopausal women from the Os des Femmes de Lyon cohort, who had a lumbar spine (LS) DXA scan (QDR 4500A, Hologic) between years 2000 and 2001. During a mean follow-up of 7.8 ± 1.3 years, 94 women sustained 112 fragility fractures. RESULTS: At the time of baseline DXA scan, women with incident fracture were significantly older (70 ± 9 vs. 65 ± 8 years) and had a lower LS_aBMD and LS_TBS (both -0.4SD, p < 0.001) than women without fracture. The magnitude of fracture prediction was similar for LS_aBMD and LS_TBS (odds ratio [95 % confidence interval] = 1.4 [1.2;1.7] and 1.6 [1.2;2.0]). After adjustment for age and prevalent fracture, LS_TBS remained predictive of an increased risk of fracture. Yet, its addition to age, prevalent fracture, and LS_aBMD did not reach the level of significance to improve the fracture prediction. When using the WHO classification, 39 % of fractures occurred in osteoporotic women, 46 % in osteopenic women, and 15 % in women with T-score > -1. Thirty-seven percent of fractures occurred in the lowest quartile of LS_TBS, regardless of BMD. Moreover, 35 % of fractures that occurred in osteopenic women were classified below this LS_TBS threshold. CONCLUSION: In conclusion, LS_aBMD and LS_TBS predicted fractures equally well. In our cohort, the addition of LS_TBS to age and LS_aBMD added only limited information on fracture risk prediction. However, using the lowest quartile of LS_TBS helped in redefining a significant subset of non-osteoporotic women as a higher risk group which is important for patient management.