Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation.

BACKGROUND: With the large amount of biological data that is currently publicly available, many investigators combine multiple data sets to increase the sample size and potentially also the power of their analyses. However, technical differences ("batch effects") as well as differences in sample composition between the data sets may significantly affect the ability to draw generalizable conclusions from such studies. FOCUS: The current study focuses on the construction of classifiers, and the use of cross-validation to estimate their performance. In particular, we investigate the impact of batch effects and differences in sample composition between batches on the accuracy of the classification performance estimate obtained via cross-validation. The focus on estimation bias is a main difference compared to previous studies, which have mostly focused on the predictive performance and how it relates to the presence of batch effects. DATA: We work on simulated data sets. To have realistic intensity distributions, we use real gene expression data as the basis for our simulation. Random samples from this expression matrix are selected and assigned to group 1 (e.g., 'control') or group 2 (e.g., 'treated'). We introduce batch effects and select some features to be differentially expressed between the two groups. We consider several scenarios for our study, most importantly different levels of confounding between groups and batch effects. METHODS: We focus on well-known classifiers: logistic regression, Support Vector Machines (SVM), k-nearest neighbors (kNN) and Random Forests (RF). Feature selection is performed with the Wilcoxon test or the lasso. Parameter tuning and feature selection, as well as the estimation of the prediction performance of each classifier, is performed within a nested cross-validation scheme. The estimated classification performance is then compared to what is obtained when applying the classifier to independent data.

The weaker points of fish acute toxicity tests and how tests on embryos can solve some issues.

Fish acute toxicity tests play an important role in environmental risk assessment and hazard classification because they allow for first estimates of the relative toxicity of various chemicals in various species. However, such tests need to be carefully interpreted. Here we shortly summarize the main issues which are linked to the genetics and the condition of the test animals, the standardized test situations, the uncertainty about whether a given test species can be seen as representative to a given fish fauna, the often missing knowledge about possible interaction effects, especially with micropathogens, and statistical problems like small sample sizes and, in some cases, pseudoreplication. We suggest that multi-factorial embryo tests on ecologically relevant species solve many of these issues, and we shortly explain how such tests could be done to avoid the weaker points of fish acute toxicity tests.

The association between inflammatory biomarkers and metabolically healthy obesity depends of the definition used.

BACKGROUND/OBJECTIVES: To assess the distribution of interleukin (IL)-1β, IL-6, tumour necrosis factor (TNF)-α and C-reactive protein (CRP) according to the different definitions of metabolically healthy obesity (MHO). SUBJECTS/METHODS: A total of 881 obese (body mass index (BMI) > or =30 kg/m2) subjects derived from the population-based CoLaus Study participated in this study. MHO was defined using six sets of criteria including different combinations of waist, blood pressure, total high-density lipoprotein cholesterol or low-density lipoprotein -cholesterol, triglycerides, fasting glucose, homeostasis model, high-sensitivity CRP, and personal history of cardiovascular, respiratory or metabolic diseases. IL-1β, IL-6 and TNF-α were assessed by multiplexed flow cytometric assay. CRP was assessed by immunoassay. RESULTS: On bivariate analysis some, but not all, definitions of MHO led to significantly lower levels of IL-6, TNF-α and CRP compared with non-MH obese subjects. Most of these differences became nonsignificant after multivariate analysis. An posteriori analysis showed a statistical power between 9 and 79%, depending on the inflammatory biomarker and MHO definition considered. Further increasing sample size to overweight+obese individuals (BMI > or =25 kg/m2, n=2917) showed metabolically healthy status to be significantly associated with lower levels of CRP, while no association was found for IL-1β. Significantly lower IL-6 and TNF-α levels were also found with some but not all MHO definitions, the differences in IL-6 becoming nonsignificant after adjusting for abdominal obesity or percent body fat. CONCLUSIONS: MHO individuals present with decreased levels of CRP and, depending on MHO definition, also with decreased levels in IL-6 and TNF-α. Conversely, no association with IL-1β levels was found.

Uso de la estadística en la oncología y la hematología

En este artículo abordamos el uso y la importancia de las herramientas estadísticas que se utilizan principalmente en los estudios médicos del ámbito de la oncología y la hematología, pero aplicables a muchos otros campos tanto médicos como experimentales o industriales. El objetivo del presente trabajo es presentar de una manera clara y precisa la metodología estadística necesaria para analizar los datos obtenidos en los estudios rigurosa y concisamente en cuanto a las hipótesis de trabajo planteadas por los investigadores. La medida de la respuesta al tratamiento elegidas en al tipo de estudio elegido determinarán los métodos estadísticos que se utilizarán durante el análisis de los datos del estudio y también el tamaño de muestra. Mediante la correcta aplicación del análisis estadístico y de una adecuada planificación se puede determinar si la relación encontrada entre la exposición a un tratamiento y un resultado es casual o por el contrario, está sujeto a una relación no aleatoria que podría establecer una relación de causalidad. Hemos estudiado los principales tipos de diseño de los estudios médicos más utilizados, tales como ensayos clínicos y estudios observacionales (cohortes, casos y controles, estudios de prevalencia y estudios ecológicos). También se presenta una sección sobre el cálculo del tamaño muestral de los estudios y cómo calcularlo, ¿Qué prueba estadística debe utilizarse?, los aspectos sobre fuerza del efecto ¿odds ratio¿ (OR) y riesgo relativo (RR), el análisis de supervivencia. Se presentan ejemplos en la mayoría de secciones del artículo y bibliografía más relevante.

Wasps (Insecta: Vespida=Hymenoptera) from the Early Cretaceous of Spain.

Wasps and their relatives from the Lower Cretaceous lithographic limestones of Spain have been studied. Thirty specimens representing 30 species (4 of them with undetermined placement), at least 21 genera and 11 families are recorded. We erect 1 new family - Andrenelidae-, 6 new genera and 11 new species: Meiaghilarella cretacica n.gen., n.sp. (Sepulcidae Ghilarellinae), Eosyntexis catalonicus n.sp., Cretosyntexis montsecensis n.gen., n.sp. (Anaxyelidae Syntexinae), Montsecephialtites zherikhini n.gen., n.sp. (Ephialtitidae Ephialtitinae), Karataus hispanicus n.sp. (Ephialtitidae Symphytopterinae), Manlaya ansorge i n.sp. (Gasteruptiidae Baissinae), Andrenelia pennata n.gen., n.sp. (Andrenelidae n. fam.), Cretoserphus gomezi n.gen., n.sp. (Mesoserphidae), Montsecosphex jarzembow skii n.gen., n.sp., Angarosphex penyalveri n.sp., Pompilopterus (?) noguerensis n.sp. (Sphecidae Angarosphecinae), Cretoscolia conquensis n.sp. (Scoliidae Archaeoscoliinae). The Mesozoic family Ephialtitidae is revisited based on the restudy of the type-species. We compare these Spanish Cretaceous assemblages with other ones from various parts of the world: Central and Eastern Asia, England, Australia, and Brazil. The number of genera and families identified in the Spanish fossil-sites is almost the same as in the English Purbeck and Wealden. The absence of some hymenopteran groups as Xyelidae, is consistent with the warm climate know to exist in Spain during the Early Cretaceous. We conclude that both La Cabrúa and La Pedrera assemblages - the two sites that have yielded the greatest number of species- correspond to the Lower Cretaceous"Baissin type" (sensu Rasnitsyn et al., 1998), but including some Jurassic"survivors". La Pedrera assemblage fits equally well in the"angarosphecine subtype", while La Cabrúa roughly corresponds to the"proctotrupid" one, although shows a comparative ly high proportion of angarosphecins. This fact may suggest: a) possibly asynchrony between these two fossilsites, b) environmental differences not reflected in the lithological record, c) different taphonomic processes and/or, d) insufficient sample size - to reflect the reality of the source populations-. La Pedrera assemblage is very similar to those from Weald Clay (England), Bon Tsagan (Mongolia) and Santana (Brazil). La Cabrúa approaches to a some extent, though not quite agrees with the Purbeck (UK), Koonwarra (Australia), and most Lower Cretaceous Asian assemblages.

Host genetic determinants of spontaneous hepatitis C clearance

Acute infection with the hepatitis C virus (HCV) induces a wide range of innate and adaptive immune responses. A total of 20-50% of acutely HCV-infected individuals permanently control the virus, referred to as 'spontaneous hepatitis C clearance', while the infection progresses to chronic hepatitis C in the majority of cases. Numerous studies have examined host genetic determinants of hepatitis C infection outcome and revealed the influence of genetic polymorphisms of human leukocyte antigens, killer immunoglobulin-like receptors, chemokines, interleukins and interferon-stimulated genes on spontaneous hepatitis C clearance. However, most genetic associations were not confirmed in independent cohorts, revealed opposing results in diverse populations or were limited by varying definitions of hepatitis C outcomes or small sample size. Coordinated efforts are needed in the search for key genetic determinants of spontaneous hepatitis C clearance that include well-conducted candidate genetic and genome-wide association studies, direct sequencing and follow-up functional studies.

Event-related potentials and changes of brain rhythm oscillations during working memory activation in patients with first-episode psychosis.

Background: Earlier contributions have documented significant changes in sensory, attention-related endogenous event-related potential (ERP) components and θ band oscillatory responses during working memory activation in patients with schizophrenia. In patients with first-episode psychosis, such studies are still scarce and mostly focused on auditory sensory processing. The present study aimed to explore whether subtle deficits of cortical activation are present in these patients before the decline of working memory performance. Methods: We assessed exogenous and endogenous ERPs and frontal θ event-related synchronization (ERS) in patients with first-episode psychosis and healthy controls who successfully performed an adapted 2-back working memory task, including 2 visual n-backworking memory tasks as well as oddball detection and passive fixation tasks. Results: We included 15 patients with first-episode psychosis and 18 controls in this study. Compared with controls, patients with first-episode psychosis displayed increased latencies of early visual ERPs and phasic θ ERS culmination peak in all conditions. However, they also showed a rapid recruitment of working memory-related neural generators, even in pure attention tasks, as indicated by the decreased N200 latency and increased amplitude of sustained θ ERS in detection compared with controls. Limitations: Owing to the limited sample size, no distinction was made between patients with first-episode psychosis with positive and negative symptoms. Although we controlled for the global load of neuroleptics, medication effect cannot be totally ruled out. Conclusion: The present findings support the concept of a blunted electroencephalographic response in patients with first-episode psychosis who recruit the maximum neural generators in simple attention conditions without being able to modulate their brain activation with increased complexity of working memory tasks.

Observer-rated Coping Associated with Borderline Personality Disorder: An Exploratory Study.

BACKGROUND: Little is known about coping specificities, as operationalization of the concept of affect regulation, in borderline personality disorder (BPD). It is most important to take into account methodological criticisms addressed to the self-report questionnaire approach and to compare BPD coping specificities to the ones of neighbouring diagnostic categories, such as bipolar disorder (BD). SAMPLING AND METHODS: The present exploratory study compared the coping profiles of N = 25 patients presenting BPD to those of N = 25 patients presenting BD and to those of N = 25 healthy controls. All participants underwent a clinical interview that was transcribed and rated using the Coping Patterns observer-rater system. RESULTS: Results partially confirmed study hypotheses and showed differences between BPD patients and healthy controls in all coping domains (competence, resources and autonomy), whereas the only coping domain presenting a BPD-specific lack of skills, compared with the BD patients, was autonomy, a set of coping strategies facing stress appraised as challenge. These coping processes were linked to general and BPD symptomatology. CONCLUSIONS: These results extend conclusions of earlier studies on affect regulation processes in BPD and bear important clinical implications, in the context of dialectical behavior therapy and other therapeutic approaches. Limitations of this exploratory study, such as the small sample size, are acknowledged. Copyright © 2012 John Wiley & Sons, Ltd. KEY PRACTITIONER MESSAGE: Coping can be reliably assessed in the narrative process in an non-structured interview frame. Patients with borderline personality disorder present with a specific lack of skills in affect regulation related to autonomy issues, compared to patients with bipolar disorder and healthy controls. Lack of skills in accommodation to distressing emotions in borderline personality disorder is related to symptom gravity and may be treated using radical acceptance strategies.

Pediatric morphea (localized scleroderma): review of 136 patients.

BACKGROUND: Morphea is an autoimmune inflammatory sclerosing disorder that may cause permanent functional disability and disfigurement. OBJECTIVES: We sought to determine the clinical features of morphea in a large pediatric cohort. METHODS: We conducted a retrospective chart review of 136 pediatric patients with morphea from one center, 1989 to 2006. RESULTS: Most children showed linear morphea, with a disproportionately high number of Caucasian and female patients. Two patients with rapidly progressing generalized or extensive linear morphea and arthralgias developed restrictive pulmonary disease. Initial oral corticosteroid treatment and long-term methotrexate administration stabilized and/or led to disease improvement in most patients with aggressive disease. LIMITATIONS: Retrospective analysis, relatively small sample size, and risk of a selected referral population to the single site are limitations. CONCLUSIONS: These data suggest an increased prevalence of morphea in Caucasian girls, and support methotrexate as treatment for problematic forms. Visceral manifestations rarely occur; the presence of progressive problematic cutaneous disease and arthralgias should trigger closer patient monitoring.

The efficiency of different estimation methods of hydro-physical limits

The soil water available to crops is defined by specific values of water potential limits. Underlying the estimation of hydro-physical limits, identified as permanent wilting point (PWP) and field capacity (FC), is the selection of a suitable method based on a multi-criteria analysis that is not always clear and defined. In this kind of analysis, the time required for measurements must be taken into consideration as well as other external measurement factors, e.g., the reliability and suitability of the study area, measurement uncertainty, cost, effort and labour invested. In this paper, the efficiency of different methods for determining hydro-physical limits is evaluated by using indices that allow for the calculation of efficiency in terms of effort and cost. The analysis evaluates both direct determination methods (pressure plate - PP and water activity meter - WAM) and indirect estimation methods (pedotransfer functions - PTFs). The PTFs must be validated for the area of interest before use, but the time and cost associated with this validation are not included in the cost of analysis. Compared to the other methods, the combined use of PP and WAM to determine hydro-physical limits differs significantly in time and cost required and quality of information. For direct methods, increasing sample size significantly reduces cost and time. This paper assesses the effectiveness of combining a general analysis based on efficiency indices and more specific analyses based on the different influencing factors, which were considered separately so as not to mask potential benefits or drawbacks that are not evidenced in efficiency estimation.

Cycle length of spermatogenesis in shrews (mammalia: soricidae) with high and low metabolic rates and different mating systems.

The aim of the present study was to establish and compare the durations of the seminiferous epithelium cycles of the common shrew Sorex araneus, which is characterized by a high metabolic rate and multiple paternity, and the greater white-toothed shrew Crocidura russula, which is characterized by a low metabolic rate and a monogamous mating system. Twelve S. araneus males and fifteen C. russula males were injected intraperitoneally with 5-bromodeoxyuridine, and the testes were collected. For cycle length determinations, we applied the classical method of estimation and linear regression as a new method. With regard to variance, and even with a relatively small sample size, the new method seems to be more precise. In addition, the regression method allows the inference of information for every animal tested, enabling comparisons of different factors with cycle lengths. Our results show that not only increased testis size leads to increased sperm production, but it also reduces the duration of spermatogenesis. The calculated cycle lengths were 8.35 days for S. araneus and 12.12 days for C. russula. The data obtained in the present study provide the basis for future investigations into the effects of metabolic rate and mating systems on the speed of spermatogenesis.

Blood pressure and LDL-cholesterol targets for prevention of recurrent strokes and cognitive decline in the hypertensive patient: design of the European Society of Hypertension-Chinese Hypertension League Stroke in Hypertension Optimal Treatment randomized trial.

BACKGROUND AND OBJECTIVES: The SBP values to be achieved by antihypertensive therapy in order to maximize reduction of cardiovascular outcomes are unknown; neither is it clear whether in patients with a previous cardiovascular event, the optimal values are lower than in the low-to-moderate risk hypertensive patients, or a more cautious blood pressure (BP) reduction should be obtained. Because of the uncertainty whether 'the lower the better' or the 'J-curve' hypothesis is correct, the European Society of Hypertension and the Chinese Hypertension League have promoted a randomized trial comparing antihypertensive treatment strategies aiming at three different SBP targets in hypertensive patients with a recent stroke or transient ischaemic attack. As the optimal level of low-density lipoprotein cholesterol (LDL-C) level is also unknown in these patients, LDL-C-lowering has been included in the design. PROTOCOL DESIGN: The European Society of Hypertension-Chinese Hypertension League Stroke in Hypertension Optimal Treatment trial is a prospective multinational, randomized trial with a 3 × 2 factorial design comparing: three different SBP targets (1, <145-135; 2, <135-125; 3, <125 mmHg); two different LDL-C targets (target A, 2.8-1.8; target B, <1.8 mmol/l). The trial is to be conducted on 7500 patients aged at least 65 years (2500 in Europe, 5000 in China) with hypertension and a stroke or transient ischaemic attack 1-6 months before randomization. Antihypertensive and statin treatments will be initiated or modified using suitable registered agents chosen by the investigators, in order to maintain patients within the randomized SBP and LDL-C windows. All patients will be followed up every 3 months for BP and every 6 months for LDL-C. Ambulatory BP will be measured yearly. OUTCOMES: Primary outcome is time to stroke (fatal and non-fatal). Important secondary outcomes are: time to first major cardiovascular event; cognitive decline (Montreal Cognitive Assessment) and dementia. All major outcomes will be adjudicated by committees blind to randomized allocation. A Data and Safety Monitoring Board has open access to data and can recommend trial interruption for safety. SAMPLE SIZE CALCULATION: It has been calculated that 925 patients would reach the primary outcome after a mean 4-year follow-up, and this should provide at least 80% power to detect a 25% stroke difference between SBP targets and a 20% difference between LDL-C targets.

Role of hepatitis C virus genotype 3 in liver fibrosis progression: a systematic review and meta-analysis.

The progression of liver fibrosis in chronic hepatitis C has long been considered to be independent from viral genotypes. However, recent studies suggest an association between Hepatitis C virus (HCV) genotype 3 and accelerated liver disease progression. We completed a systematic review and meta-analysis of studies evaluating the association between HCV genotypes and fibrosis progression. PubMed, Embase and ISI Web of Knowledge databases were searched for cohort, cross-sectional and case-control studies on treatment-naïve HCV-infected adults in which liver fibrosis progression rate (FPR) was assessed by the ratio of fibrosis stage in one single biopsy to the duration of infection (single-biopsy studies) or from the change in fibrosis stage between two biopsies (paired biopsies studies). A random effect model was used to derive FPR among different HCV genotypes. Eight single-biopsy studies (3182 patients, mean/median duration of infection ranging from 9 to 21 years) and eight paired biopsies studies (mean interval between biopsies 2-12 years) met the selection criteria. The odds ratio for the association of genotype 3 with accelerated fibrosis progression was 1.52 (95% CI 1.12-2.07, P = 0.007) in single-biopsy studies and 1.37 (95% CI 0.87-2.17, P = 0.17) in paired biopsy studies. In conclusion, viral genotype 3 was associated with faster fibrosis progression in single-biopsy studies. This observation may have important consequences on the clinical management of genotype 3-infected patients. The association was not significant in paired biopsies studies, although the latter may be limited by important indication bias, short observation time and small sample size.

SA2RAGE: a new sequence for fast B1+ -mapping.

At high magnetic field strengths (≥ 3T), the radiofrequency wavelength used in MRI is of the same order of magnitude of (or smaller than) the typical sample size, making transmit magnetic field (B1+) inhomogeneities more prominent. Methods such as radiofrequency-shimming and transmit SENSE have been proposed to mitigate these undesirable effects. A prerequisite for such approaches is an accurate and rapid characterization of the B1+ field in the organ of interest. In this work, a new phase-sensitive three-dimensional B1+-mapping technique is introduced that allows the acquisition of a 64 × 64 × 8 B1+-map in ≈ 20 s, yielding an accurate mapping of the relative B1+ with a 10-fold dynamic range (0.2-2 times the nominal B1+). Moreover, the predominant use of low flip angle excitations in the presented sequence minimizes specific absorption rate, which is an important asset for in vivo B1+-shimming procedures at high magnetic fields. The proposed methodology was validated in phantom experiments and demonstrated good results in phantom and human B1+-shimming using an 8-channel transmit-receive array.

A systematic review of longitudinal population-based studies on the predictors of smoking cessation in adolescent and young adult smokers.

OBJECTIVE: To describe the determinants of self-initiated smoking cessation of duration of at least 6 months as identified in longitudinal population-based studies of adolescent and young adult smokers. METHODS: A systematic search of the PubMed and EMBASE databases using smoking, tobacco, cessation, quit and stop as keywords was performed. Limits included articles related to humans, in English, published between January 1984 and August 2010, and study population aged 10-29 years. A total of 4502 titles and 871 abstracts were reviewed independently by 2 and 3 reviewers, respectively. Nine articles were retained for data abstraction. Data on study location, timeframe, duration of follow-up, number of data collection points, sample size, age/grade of participants, number of quitters, smoking status at baseline, definition of cessation, covariates and analytic method were abstracted from each article. The number of studies that reported a statistically significant association between each determinant investigated and cessation were tabulated, from among all studies that assessed the determinant. RESULTS: Despite heterogeneity in methods across studies, five factors robustly predicted quitting across studies in which the factor was investigated: not having friends who smoke, not having intentions to smoke in the future, resisting peer pressure to smoke, being older at first use of cigarette and having negative beliefs about smoking. CONCLUSIONS: The literature on longitudinal predictors of cessation in adolescent and young adult smokers is not well developed. Cessation interventions for this population will remain less than optimally effective until there is a solid evidence base on which to develop interventions.