How reliable is Ki-67 immunohistochemistry in grade 2 breast carcinomas? A QA study of the Swiss Working Group of Breast- and Gynecopathologists

Adjuvant chemotherapy decisions in breast cancer are increasingly based on the pathologist's assessment of tumor proliferation. The Swiss Working Group of Gyneco- and Breast Pathologists has surveyed inter- and intraobserver consistency of Ki-67-based proliferative fraction in breast carcinomas. Methods Five pathologists evaluated MIB-1-labeling index (LI) in ten breast carcinomas (G1, G2, G3) by counting and eyeballing. In the same way, 15 pathologists all over Switzerland then assessed MIB-1-LI on three G2 carcinomas, in self-selected or pre-defined areas of the tumors, comparing centrally immunostained slides with slides immunostained in the different laboratoires. To study intra-observer variability, the same tumors were re-examined 4 months later. Results The Kappa values for the first series of ten carcinomas of various degrees of differentiation showed good to very good agreement for MIB-1-LI (Kappa 0.56–0.72). However, we found very high inter-observer variabilities (Kappa 0.04–0.14) in the read-outs of the G2 carcinomas. It was not possible to explain the inconsistencies exclusively by any of the following factors: (i) pathologists' divergent definitions of what counts as a positive nucleus (ii) the mode of assessment (counting vs. eyeballing), (iii) immunostaining technique, and (iv) the selection of the tumor area in which to count. Despite intensive confrontation of all participating pathologists with the problem, inter-observer agreement did not improve when the same slides were re-examined 4 months later (Kappa 0.01–0.04) and intra-observer agreement was likewise poor (Kappa 0.00–0.35). Conclusion Assessment of mid-range Ki-67-LI suffers from high inter- and intra-observer variability. Oncologists should be aware of this caveat when using Ki-67-LI as a basis for treatment decisions in moderately differentiated breast carcinomas.

Utilization of Probabilistic Models in Short Read Assembly from Second-Generation Sequencing

With the advent of cheaper and faster DNA sequencing technologies, assembly methods have greatly changed. Instead of outputting reads that are thousands of base pairs long, new sequencers parallelize the task by producing read lengths between 35 and 400 base pairs. Reconstructing an organism’s genome from these millions of reads is a computationally expensive task. Our algorithm solves this problem by organizing and indexing the reads using n-grams, which are short, fixed-length DNA sequences of length n. These n-grams are used to efficiently locate putative read joins, thereby eliminating the need to perform an exhaustive search over all possible read pairs. Our goal was develop a novel n-gram method for the assembly of genomes from next-generation sequencers. Specifically, a probabilistic, iterative approach was utilized to determine the most likely reads to join through development of a new metric that models the probability of any two arbitrary reads being joined together. Tests were run using simulated short read data based on randomly created genomes ranging in lengths from 10,000 to 100,000 nucleotides with 16 to 20x coverage. We were able to successfully re-assemble entire genomes up to 100,000 nucleotides in length.

The Influence of the Social and Cultural Environment on a Child's Playing in the First Three Years of Life

The research focused on children's behaviour in playing with objects both independently and in interaction with adults. It was based on studies of 40 Slovene children in 4 age groups (6,12,18 and 24 months) and of 23 Croatian children in 2 age groups (18 and 24 months). All the children were sampled proportionally by their gender and the educational level of their parents (middle and higher). Several coding check lists with satisfactory internal consistency were constructed during the study and used to analyse the video-recorded playing sessions with each child. The basic conclusion reached was that even in early childhood playing behaviour differs significantly between the infants from the two Central European countries. The difference lies not so much in the structure or the content of the playing actions, but in the way in which the infants deal playfully with the objects. This difference appears regardless of the type of object the infants are playing with and even regardless of the playing condition. It can best be described as the difference between the first significant discriminant function activity versus passivity. The Slovene infants were found to be on the active pole and the Croatians on the passive one. Social and gender differences were much less significant than cultural ones in determining the structure, the content and the way of playing. Significant age differences appeared in all three aspects, which was consistent with general trends in infants' psychological development. The group define the Slovene interactive playing style as object oriented, while the Croatian one was largely communicated oriented. Within the experimenter-infant dyads, children of both cultures played at a developmentally more advanced level than they did with their mothers, showing that the mothers were not as successful at reaching the ZPD as were the trained experimenters. In addition, the children of mothers who attributed more cognitive benefit to play played on a more advanced level than those whose mothers attributed more emotional benefit to play. The quality of the object the children were playing with was also significantly related to the structure, content and partly the way of dealing with the objects. Highly-structured objects stimulated complex play and low-structured ones stimulated simple play, regardless of playing conditions. The group concluded that both culture and the quality of the available object have an important impact on young children's play. Through the playing interaction, the infants internalise culturally specific patterns of behaviour and culturally specific meanings. These internalisations become apparent very early in their lives, even in non-social situations. On the other hand, the objects themselves have an impact on the level of infants' play. When they do not provide sufficient perceptive and functional support for a representational action, the infants' play will lag behind their actual developmental capacities.

Effects of probiotic bacteria in dogs with food responsive diarrhoea treated with an elimination diet

We evaluated whether a probiotic supplementation in dogs with food responsive diarrhoea (FRD) has beneficial effects on intestinal cytokine patterns and on microbiota. Twenty-one client-owned dogs with FRD were presented for clinically needed duodeno- and colonoscopy and were enrolled in a prospective placebo (PL)-controlled probiotic trial. Intestinal tissue samples and faeces were collected during endoscopy. Intestinal mRNA abundance of interleukin (IL)-5, -10, -12p40 and -13, tumour necrosis factor-alpha, transforming growth factor-beta1 and interferon (IFN)-gamma were analysed and numbers of Lactobacillus spp., Bifidobacterium spp., Enterococcus spp. and Enterobacteriaceae and supplemented probiotic bacteria were determined in faeces. The Canine Inflammatory Bowel Disease Activity Index, a scoring system comprising general attitude, appetite, faecal consistency, defecation frequency, and vomitus, decreased in all dogs (p < 0.0001). Duodenal IL-10 mRNA levels decreased (p = 0.1) and colonic IFN-gamma mRNA levels increased (p = 0.08) after probiotic treatment. Numbers of Enterobacteriaceae decreased in FRD dogs receiving probiotic cocktail (FRD(PC)) and FRD dogs fed PL (FRD(PL)) during treatment (p < 0.05), numbers of Lactobacillus spp. increased in FRD(PC after) when compared with FRD(PC before) (p < 0.1). One strain of PC was detected in five of eight FRD(PC) dogs after probiotic supplementation. In conclusion, all dogs clinically improved after treatment, but cytokine patterns were not associated with the clinical features irrespective of the dietary supplementation.

Efficacy of psychological therapy in schizophrenia: conclusions from meta-analyses

Over the past years, evidence for the efficacy of psychological therapies in schizophrenia has been summarized in a series of meta-analyses. The present contribution aims to provide a descriptive survey of the evidence for the efficacy of psychological therapies as derived from these meta-analyses and to supplement them by selected findings from an own recent meta-analysis. Relevant meta-analyses and randomized controlled trials were identified by searching several electronic databases and by hand searching of reference lists. In order to compare the findings of the existing meta-analyses, the reported effect sizes were extracted and transformed into a uniform effect size measure where possible. For the own meta-analysis, weighted mean effect size differences between comparison groups regarding various types of outcomes were estimated. Their significance was tested by confidence intervals, and heterogeneity tests were applied to examine the consistency of the effects. From the available meta-analyses, social skills training, cognitive remediation, psychoeducational coping-oriented interventions with families and relatives, as well as cognitive behavioral therapy of persistent positive symptoms emerge as effective adjuncts to pharmacotherapy. Social skills training consistently effectuates the acquisition of social skills, cognitive remediation leads to short-term improvements in cognitive functioning, family interventions decrease relapse and hospitalization rates, and cognitive behavioral therapy results in a reduction of positive symptoms. These benefits seem to be accompanied by slight improvements in social functioning. However, open questions remain as to the specific therapeutic ingredients, to the synergistic effects, to the indication, as well as to the generalizability of the findings to routine care.

Efficiency of the Sieved-NPMLE in CAR-Missing Data Models

We consider nonparametric missing data models for which the censoring mechanism satisfies coarsening at random and which allow complete observations on the variable X of interest. W show that beyond some empirical process conditions the only essential condition for efficiency of an NPMLE of the distribution of X is that the regions associated with incomplete observations on X contain enough complete observations. This is heuristically explained by describing the EM-algorithm. We provide identifiably of the self-consistency equation and efficiency of the NPMLE in order to make this statement rigorous. The usual kind of differentiability conditions in the proof are avoided by using an identity which holds for the NPMLE of linear parameters in convex models. We provide a bivariate censoring application in which the condition and hence the NPMLE fails, but where other estimators, not based on the NPMLE principle, are highly inefficient. It is shown how to slightly reduce the data so that the conditions hold for the reduced data. The conditions are verified for the univariate censoring, double censored, and Ibragimov-Has'minski models.

[Intraoral lipoma in the region of the mental nerve--report of a case and review of the literature]

The intraoral lipoma is a benign, slowly growing, painless soft tissue neoplasia, which can cause esthetic or functional problems for the patient, depending on its size. All parts of the body can be affected, whereas the oral cavity is rarely involved. Clinically, the tumour often exhibits an exophytic growth pattern, a soft consistency, a broad base connected to the underlying tissue, and frequently has a reddish-yellowish colour. Instead of a superficial mucosal involvement, a deep localization in the soft tissues is also possible. Depending on the localization of the tumour, the diagnosis and the resulting therapy can turn out to be a challenge for the clinician. A clear differentiation to malign neoplasias of the fat tissues and other soft tissue expansions is essential. The following case report presents a female patient who is affected by a lipoma in the proximity of the mental nerve. The diagnostic work-up and resulting therapy including a review of the current literature are presented and discussed.

Accuracy and consistency of the visual diagnosis of exposed dentine on worn occlusal/incisal surfaces

Most indices for the assessment of wear of various aetiologies include the distinction between 'enamel still present' and 'dentine exposed' for grading. Since the visual diagnosis of exposed dentine has not yet been validated, the present study is a first attempt to investigate its accuracy and consistency. Sixty-one examiners (23 scientists, 18 university dentists and 20 dental students) were asked to diagnose 49 tooth areas with different grades of wear and to decide whether dentine was exposed (positive test) or not (negative test). Afterwards, the teeth were histologically evaluated. In 44 areas, dentine (also in all cases with minor wear) was exposed, and in 5 areas enamel was present. Overall sensitivity was 0.65, specificity 0.88 and the proportion of correct diagnoses was 0.67. The diagnosis 'dentine is exposed' was about 5 times as likely and the diagnosis 'dentine is not exposed' half as likely to come from an area with exposed dentine than from an enamel-covered area. The closeness of the visual diagnosis to the histological findings was only fair (kappa=0.27), no significant impact of professional experience was found. For inter- and intra-examiner agreement, kappa was 0.28 and 0.55, respectively. It was concluded that the diagnosis of exposed dentine is difficult.

Are beta-blockers needed in patients receiving spironolactone for severe chronic heart failure? An analysis of the COPERNICUS study

BACKGROUND: The beneficial effects of beta-blockers and aldosterone receptor antagonists are now well established in patients with severe systolic chronic heart failure (CHF). However, it is unclear whether beta-blockers are able to provide additional benefit in patients already receiving aldosterone antagonists. We therefore examined this question in the COPERNICUS study of 2289 patients with severe CHF receiving the beta1-beta2/alpha1 blocker carvedilol compared with placebo. METHODS: Patients were divided post hoc into subgroups according to whether they were receiving spironolactone (n = 445) or not (n = 1844) at baseline. Consistency of the effect of carvedilol versus placebo was examined for these subgroups with respect to the predefined end points of all-cause mortality, death or CHF-related hospitalizations, death or cardiovascular hospitalizations, and death or all-cause hospitalizations. RESULTS: The beneficial effect of carvedilol was similar among patients who were or were not receiving spironolactone for each of the 4 efficacy measures. For all-cause mortality, the Cox model hazard ratio for carvedilol compared with placebo was 0.65 (95% CI 0.36-1.15) in patients receiving spironolactone and 0.65 (0.51-0.83) in patients not receiving spironolactone. Hazard ratios for death or all-cause hospitalization were 0.76 (0.55-1.05) versus 0.76 (0.66-0.88); for death or cardiovascular hospitalization, 0.61 (0.42-0.89) versus 0.75 (0.64-0.88); and for death or CHF hospitalization, 0.63 (0.43-0.94) versus 0.70 (0.59-0.84), in patients receiving and not receiving spironolactone, respectively. The safety and tolerability of treatment with carvedilol were also similar, regardless of background spironolactone. CONCLUSION: Carvedilol remained clinically efficacious in the COPERNICUS study of patients with severe CHF when added to background spironolactone in patients who were practically all receiving angiotensin-converting enzyme inhibitor (or angiotensin II antagonist) therapy. Therefore, the use of spironolactone in patients with severe CHF does not obviate the necessity of additional treatment that interferes with the adverse effects of sympathetic activation, specifically beta-blockade.

Family satisfaction in the intensive care unit: cross-cultural adaptation of a questionnaire

PURPOSE: Family needs and expectations are often unmet in the intensive care unit (ICU), leading to dissatisfaction. This study assesses cross-cultural adaptability of an instrument evaluating family satisfaction in the ICU. MATERIALS AND METHODS: A Canadian instrument on family satisfaction was adapted for German language and central European culture and then validated for feasibility, validity, internal consistency, reliability, and sensitivity. RESULTS: Content validity of a preliminary translated version was assessed by staff, patients, and next of kin. After adaptation, content and comprehensibility were considered good. The adapted translation was then distributed to 160 family members. The return rate was 71.8%, and 94.4% of questions in returned forms were clearly answered. In comparison with a Visual Analogue Scale, construct validity was good for overall satisfaction with care (Spearman rho = 0.60) and overall satisfaction with decision making (rho = 0.65). Cronbach alpha was .95 for satisfaction with care and .87 for decision-making. Only minor differences on repeated measurements were found for interrater and intrarater reliability. There was no floor or ceiling effect. CONCLUSIONS: A cross-cultural adaptation of a questionnaire on family satisfaction in the ICU can be feasible, valid, internally consistent, reliable, and sensitive.

Tenofovir use is associated with a reduction in calculated glomerular filtration rates in the Swiss HIV Cohort Study

BACKGROUND: A growing number of case reports have described tenofovir (TDF)-related proximal renal tubulopathy and impaired calculated glomerular filtration rates (cGFR). We assessed TDF-associated changes in cGFR in a large observational HIV cohort. METHODS: We compared treatment-naive patients or patients with treatment interruptions > or = 12 months starting either a TDF-based combination antiretroviral therapy (cART) (n = 363) or a TDF-sparing regime (n = 715). The predefined primary endpoint was the time to a 10 ml/min reduction in cGFR, based on the Cockcroft-Gault equation, confirmed by a follow-up measurement at least 1 month later. In sensitivity analyses, secondary endpoints including calculations based on the modified diet in renal disease (MDRD) formula were considered. Endpoints were modelled using pre-specified covariates in a multiple Cox proportional hazards model. RESULTS: Two-year event-free probabilities were 0.65 (95% confidence interval [CI] 0.58-0.72) and 0.80 (95% CI 0.76-0.83) for patients starting TDF-containing or TDF-sparing cART, respectively. In the multiple Cox model, diabetes mellitus (hazard ratio [HR] = 2.34 [95% CI 1.24-4.42]), higher baseline cGFR (HR = 1.03 [95% CI 1.02-1.04] by 10 ml/min), TDF use (HR = 1.84 [95% CI 1.35-2.51]) and boosted protease inhibitor use (HR = 1.71 [95% CI 1.30-2.24]) significantly increased the risk for reaching the primary endpoint. Sensitivity analyses showed high consistency. CONCLUSION: There is consistent evidence for a significant reduction in cGFR associated with TDF use in HIV-infected patients. Our findings call for a strict monitoring of renal function in long-term TDF users with tests that distinguish between glomerular dysfunction and proximal renal tubulopathy, a known adverse effect of TDF.

Clinical end points in coronary stent trials: a case for standardized definitions

BACKGROUND: Although most clinical trials of coronary stents have measured nominally identical safety and effectiveness end points, differences in definitions and timing of assessment have created confusion in interpretation. METHODS AND RESULTS: The Academic Research Consortium is an informal collaboration between academic research organizations in the United States and Europe. Two meetings, in Washington, DC, in January 2006 and in Dublin, Ireland, in June 2006, sponsored by the Academic Research Consortium and including representatives of the US Food and Drug Administration and all device manufacturers who were working with the Food and Drug Administration on drug-eluting stent clinical trial programs, were focused on consensus end point definitions for drug-eluting stent evaluations. The effort was pursued with the objective to establish consistency among end point definitions and provide consensus recommendations. On the basis of considerations from historical legacy to key pathophysiological mechanisms and relevance to clinical interpretability, criteria for assessment of death, myocardial infarction, repeat revascularization, and stent thrombosis were developed. The broadly based consensus end point definitions in this document may be usefully applied or recognized for regulatory and clinical trial purposes. CONCLUSION: Although consensus criteria will inevitably include certain arbitrary features, consensus criteria for clinical end points provide consistency across studies that can facilitate the evaluation of safety and effectiveness of these devices.

Clinical endpoints in peripheral endovascular revascularization trials: a case for standardized definitions

BACKGROUND: Endovascular therapy is a rapidly expanding option for the treatment of patients with peripheral arterial disease (PAD), leading to a myriad of published studies reporting on various revascularization strategies. However, these reports are often difficult to interpret and compare because they do not utilize uniform clinical endpoint definitions. Moreover, few of these studies describe clinical outcomes from a patients' perspective. METHODS AND RESULTS: The DEFINE Group is a collaborative effort of an ad-hoc multidisciplinary team from various specialties involved in peripheral arterial disease therapy in Europe and the United States. DEFINE's goal was to arrive at a broad based consensus for baseline and endpoint definitions in peripheral endovascular revascularization trials for chronic lower limb ischemia. In this project, which started in 2006, the individual team members reviewed the existing pertinent literature. Following this, a series of telephone conferences and face-to-face meetings were held to agree upon definitions. Input was also obtained from regulatory (United States Food and Drug Administration) and industry (device manufacturers with an interest in peripheral endovascular revascularization) stakeholders, respectively. The efforts resulted in the current document containing proposed baseline and endpoint definitions in chronic lower limb PAD. Although the consensus has inevitably included certain arbitrary choices and compromises, adherence to these proposed standard definitions would provide consistency across future trials, thereby facilitating evaluation of clinical effectiveness and safety of various endovascular revascularization techniques. CONCLUSION: This current document is based on a broad based consensus involving relevant stakeholders from the medical community, industry and regulatory bodies. It is proposed that the consensus document may have value for study design of future clinical trials in chronic lower limb ischemia as well as for regulatory purposes.