Exact change point detection with improved power in small-sample binomial sequences.

To detect a change in the probability of a sequence of independent binomial random variables, a variety of asymptotic and exact testing procedures have been proposed. Whenever the sample size or the event rate is small, asymptotic approximations of maximally selected test statistics have been shown to be inaccurate. Although exact methods control the type I error rate, they can be overly conservative due to the discreteness of the test statistics in these situations. We extend approaches by Worsley and Halpern to develop a test that is less discrete to increase the power. Building on ideas from binary segmentation, the proposed test utilizes unused information in the binomial sequences to add a new ordering to test statistics that are of equal value. The exact distributions are derived under side conditions that arise in hypothetical segmentation steps and do not depend on the type of test statistic used (e.g., log likelihood ratio, cumulative sum, or Fisher's exact test). Using the proposed exact segmentation procedure, we construct a change point test and prove that it controls the type-I-error rate at any given nominal level. Furthermore, we prove that the new test is uniformly at least as powerful as Worsley's exact test. In a Monte Carlo simulation study, the gain in power can be remarkable, especially in scenarios with small sample size. Giving a clinical database example about pin site infections and an example assessing publication bias in neuropsychiatric drug research, we demonstrate the wide-ranging applicability of the test.

Modified Pilates as an adjunct to standard physiotherapy care for urinary incontinence: a mixed methods pilot for a randomised controlled trial.

BACKGROUND: Urinary incontinence (UI) is a distressing condition affecting at least 5 million women in England and Wales. Traditionally, physiotherapy for UI comprises pelvic floor muscle training, but although evidence suggests this can be effective it is also recognised that benefits are often compromised by patient motivation and commitment. In addition, there is increasing recognition that physical symptoms alone are poor indicators of the impact of incontinence on individuals' lives. Consequently, more holistic approaches to the treatment of UI, such as Modified Pilates (MP) have been recommended. This study aimed to provide preliminary findings about the effectiveness of a 6-week course of MP classes as an adjunct to standard physiotherapy care for UI, and to test the feasibility of a randomised controlled trial (RCT) design. METHODS: The study design was a single centre pilot RCT, plus qualitative interviews. 73 women referred to Women's Health Physiotherapy Services for UI at Colchester Hospital University NHS Foundation Trust were randomly assigned to two groups: a 6-week course of MP classes in addition to standard physiotherapy care (intervention) or standard physiotherapy care only (control). Main outcome measures were self-reported UI, quality of life and self-esteem at baseline (T1), completion of treatment (T2), and 5 months after randomisation (T3). Qualitative interviews were conducted with a subgroup at T2 and T3. Due to the nature of the intervention blinding of participants, physiotherapists and researchers was not feasible. RESULTS: Post-intervention data revealed a range of benefits for women who attended MP classes and who had lower symptom severity at baseline: improved self-esteem (p = 0.032), decreased social embarrassment (p = 0.026) and lower impact on normal daily activities (p = 0.025). In contrast, women with higher symptom severity showed improvement in their personal relationships (p = 0.017). Qualitative analysis supported these findings and also indicated that MP classes could positively influence attitudes to exercise, diet and wellbeing. CONCLUSIONS: A definitive RCT is feasible but will require a large sample size to inform clinical practice. TRIAL REGISTRATION: ISRCTN74075972 Registered 12/12/12 (Retrospectively registered).

Skeletal maturation, fundamental motor skills and motor coordination in children 7-10 years.

Relationships between skeletal maturation and fundamental motor skills and gross motor coordination were evaluated in 429 children (213 boys and 216 girls) 7-10 years. Skeletal age was assessed (Tanner-Whitehouse 2 method), and stature, body mass, motor coordination (Körperkoordinations Test für Kinder, KTK) and fundamental motor skills (Test of Gross Motor Development, TGMD-2) were measured. Relationships among chronological age, skeletal age (expressed as the standardised residual of skeletal age on chronological age) and body size and fundamental motor skills and motor coordination were analysed with hierarchical multiple regression. Standardised residual of skeletal age on chronological age interacting with stature and body mass explained a maximum of 7.0% of the variance in fundamental motor skills and motor coordination over that attributed to body size per se. Standardised residual of skeletal age on chronological age alone accounted for a maximum of 9.0% of variance in fundamental motor skills, and motor coordination over that attributed to body size per se and interactions between standardised residual of skeletal age on chronological age and body size. In conclusion, skeletal age alone or interacting with body size has a negligible influence on fundamental motor skills and motor coordination in children 7-10 years.

A feature selection method for classification within functional genomics experiments based on the proportional overlapping score.

BACKGROUND: Microarray technology, as well as other functional genomics experiments, allow simultaneous measurements of thousands of genes within each sample. Both the prediction accuracy and interpretability of a classifier could be enhanced by performing the classification based only on selected discriminative genes. We propose a statistical method for selecting genes based on overlapping analysis of expression data across classes. This method results in a novel measure, called proportional overlapping score (POS), of a feature's relevance to a classification task. RESULTS: We apply POS, along-with four widely used gene selection methods, to several benchmark gene expression datasets. The experimental results of classification error rates computed using the Random Forest, k Nearest Neighbor and Support Vector Machine classifiers show that POS achieves a better performance. CONCLUSIONS: A novel gene selection method, POS, is proposed. POS analyzes the expressions overlap across classes taking into account the proportions of overlapping samples. It robustly defines a mask for each gene that allows it to minimize the effect of expression outliers. The constructed masks along-with a novel gene score are exploited to produce the selected subset of genes.

Quantitative proteome profiling of lymph node-positive vs. -negative colorectal carcinomas pinpoints MX1 as a marker for lymph node metastasis.

We used high-resolution mass spectrometry to measure the abundance of more than 9,000 proteins in 19 individually dissected colorectal tumors representing lymph node metastatic (n = 10) and nonmetastatic (n = 9) phenotypes. Statistical analysis identified MX1 and several other proteins as overexpressed in lymph node-positive tumors. MX1, IGF1-R and IRF2BP1 showed significantly different expression in immunohistochemical validation (Wilcoxon test p = 0.007 for IGF1-R, p = 0.04 for IRF2BP1 and p = 0.02 for MX1 at the invasion front) in the validation cohort. Knockout of MX1 by siRNA in cell cultures and wound healing assays provided additional evidence for the involvement of this protein in tumor invasion. The collection of identified and quantified proteins to our knowledge is the largest tumor proteome dataset available at the present. The identified proteins can give insights into the mechanisms of lymphatic metastasis in colorectal carcinoma and may act as prognostic markers and therapeutic targets after further prospective validation.

Short-term secular change in height, body mass and Tanner-Whitehouse 3 skeletal maturity of Madeira youth, Portugal.

BACKGROUND: Secular trends in height and weight are reasonably well documented in Europe. Corresponding observations for skeletal maturation are lacking. AIM: To assess secular trends in height, body mass and skeletal maturity of Portuguese children and adolescents and to provide updated reference values for skeletal maturity scores (SMSs). SUBJECTS AND METHODS: Data for 2856 children and adolescents of 4-17 years, 1412 boys and 1444 girls, from The 'Madeira Growth Study' (MGS; 1996-1998) and from the'Healthy Growth of Madeira Children Study' (CRES; 2006) were used. Height and body mass were measured. Skeletal maturity was assessed with the Tanner-Whitehouse 2 and 3 methods. RESULTS: Children from CRES were taller and heavier than peers from MGS. Differences in height reached 5.8 cm in boys and 5.5 cm in girls. RUS SMSs did not differ consistently between surveys boys, while higher RUS scores were observed in CRES girls. Adult RUS SMSs for MGS and CRES combined were attained at 15.8 years in boys and 14.8 years in girls. Corresponding ages for adult Carpal SMSs were 14.4 and 14.0, respectively. CONCLUSION: The short-term trends for height and mass were not entirely consistent with the trends in RUS and Carpal SMSs and SAs.

Informed citizen and empowered citizen in health: results from an European survey.

BACKGROUND: The knowledge about the relationship between health-related activities on the Internet (i.e. informed citizens) and individuals' control over their own experiences of health or illness (i.e. empowered citizens) is valuable but scarce. In this paper, we investigate the correlation between four ways of using the Internet for information on health or illness and citizens attitudes and behaviours toward health professionals and health systems and establish the profile of empowered eHealth citizens in Europe. METHODS: Data was collected during April and May 2007 (N = 7022), through computer-assisted telephone interviews (CATI). Respondents from Denmark, Germany, Greece, Latvia, Norway, Poland and Portugal participated in the survey. The profiles were generated using logistic regressions and are based on: a) socio-demographic and health information, b) the level of use of health-related online services, c) the level of use of the Internet to get health information to decide whether to consult a health professional, prepare for a medical appointment and assess its outcome, and d) the impact of online health information on citizens' attitudes and behavior towards health professionals and health systems. RESULTS: Citizens using the Internet to decide whether to consult a health professional or to get a second opinion are likely to be frequent visitors of health sites, active participants of online health forums and recurrent buyers of medicines and other health related products online, while only infrequent epatients, visiting doctors they have never met face-to-face. Participation in online health communities seems to be related with more inquisitive and autonomous patients. CONCLUSIONS: The profiles of empowered eHealth citizens in Europe are situational and country dependent. The number of Europeans using the Internet to get health information to help them deal with a consultation is raising and having access to online health information seems to be associated with growing number of inquisitive and self-reliant patients. Doctors are increasingly likely to experience consultations with knowledgeable and empowered patients, who will challenge them in various ways.

A systems biology approach to identify the combination effects of human herpesvirus 8 genes on NF-kappaB activation.

Human herpesvirus 8 (HHV-8) is the etiologic agent of Kaposi's sarcoma and primary effusion lymphoma. Activation of the cellular transcription factor nuclear factor-kappa B (NF-kappaB) is essential for latent persistence of HHV-8, survival of HHV-8-infected cells, and disease progression. We used reverse-transfected cell microarrays (RTCM) as an unbiased systems biology approach to systematically analyze the effects of HHV-8 genes on the NF-kappaB signaling pathway. All HHV-8 genes individually (n = 86) and, additionally, all K and latent genes in pairwise combinations (n = 231) were investigated. Statistical analyses of more than 14,000 transfections identified ORF75 as a novel and confirmed K13 as a known HHV-8 activator of NF-kappaB. K13 and ORF75 showed cooperative NF-kappaB activation. Small interfering RNA-mediated knockdown of ORF75 expression demonstrated that this gene contributes significantly to NF-kappaB activation in HHV-8-infected cells. Furthermore, our approach confirmed K10.5 as an NF-kappaB inhibitor and newly identified K1 as an inhibitor of both K13- and ORF75-mediated NF-kappaB activation. All results obtained with RTCM were confirmed with classical transfection experiments. Our work describes the first successful application of RTCM for the systematic analysis of pathofunctions of genes of an infectious agent. With this approach, ORF75 and K1 were identified as novel HHV-8 regulatory molecules on the NF-kappaB signal transduction pathway. The genes identified may be involved in fine-tuning of the balance between latency and lytic replication, since this depends critically on the state of NF-kappaB activity.

Sexual dysfunction after rectal surgery: a retrospective study of men without disease recurrence.

INTRODUCTION: Sexual dysfunction is a frequent complication of visceral surgery after rectal resections as a result of carcinoma of the rectum. AIM: The purpose of our study is to assess the incidence and form of sexual dysfunction in our own population of patients. METHODS: The study comprised all patients who had undergone surgery for carcinoma of the rectum at the Erlangen Surgery University Hospital, Germany, in the period 2000-04. All male patients were retrospectively surveyed and asked to complete standardized (International Index of Erectile Function 15) questionnaires regarding their pre- and postsurgical sexual function. One hundred and forty-five questionnaires could be analyzed. The statistical evaluation was conducted with aid of the SPSS statistics program. The univariate analysis was carried out with the chi-square test and the U-test (Mann-Whitney Test). MAIN OUTCOME MEASURES: Erectile dysfunction, libido, and ability to have and sustain ejaculation and orgasm (both before and after surgery in each case) were among the dependent variables when compiling the data. The impact various surgical procedures and radiochemotherapy had on the severity of the sexual dysfunctions was analyzed. The scope of the postoperative urological care given was also assessed. RESULTS: Erectile dysfunction was confirmed in N=112 patients (77.3%) after surgery (P-value<0.001). Other parameters such as orgasm capacity (4.1% vs. 16.5%), ejaculation ability (1.4% vs. 12.4%) and libido (3.4% vs. 22%) also showed a marked deterioration postoperatively. Postoperative erectile dysfunction was present in 77% of the patients with a colostomy and in 88.5% of the patients who had received neoadjuvant radiation. CONCLUSIONS: Male erectile dysfunction is a frequent complication after rectal resection as a result of carcinoma of the rectum. The high incidence of sexual dysfunctions results from the radical nature of the procedure and from additional radiation or colostomy therapy. These patients need accompanying urological care for treatment of their sexual dysfunction.

Online communication between doctors and patients in Europe: status and perspectives.

BACKGROUND: Use of the Internet for health purposes is steadily increasing in Europe, while the eHealth market is still a niche. Online communication between doctor and patient is one aspect of eHealth with potentially great impact on the use of health systems, patient-doctor roles and relations and individuals' health. Monitoring and understanding practices, trends, and expectations in this area is important, as it may bring invaluable knowledge to all stakeholders, in the Health 2.0 era. OBJECTIVE: Our two main goals were: (1) to investigate use of the Internet and changes in expectations about future use for particular aspects of communication with a known doctor (obtaining a prescription, scheduling an appointment, or asking a particular health question), and (2) to investigate how important the provision of email and Web services to communicate with the physician is when choosing a new doctor for a first time face-to-face appointment. The data come from the second survey of the eHealth Trends study, which addressed trends and perspectives of health-related Internet use in Europe. This study builds on previous work that established levels of generic use of the Internet for self-help activities, ordering medicine or other health products, interacting with a Web doctor/unknown health professional, and communicating with a family doctor or other known health professional. METHODS: A representative sample of citizens from seven European countries was surveyed (n = 7022) in April and May of 2007 through computer-assisted telephone interviews (CATI). Respondents were questioned about their use of the Internet to obtain a prescription, schedule an appointment, or ask a health professional about a particular health question. They were also asked what their expectations were regarding future use of the Internet for health-related matters. In a more pragmatic approach to the subject, they were asked about the perceived importance when choosing a new doctor of the possibility of using email and the Web to communicate with that physician. Logistic regression analysis was used to draw the profiles of users of related eHealth services in Europe among the population in general and in the subgroup of those who use the Internet for health-related matters. Changes from 2005 to 2007 were computed using data from the first eHealth Trends survey (October and November 2005, n = 7934). RESULTS: In 2007, an estimated 1.8% (95% confidence interval [CI], 1.5 - 2.1) of the population in these countries had used the Internet to request or renew a prescription; 3.2% (95% CI 2.8 - 3.6) had used the Internet to schedule an appointment; and 2.5% (95% CI 2.2 - 2.9) had used the Internet to ask a particular health question. This represents estimated increases of 0.9% (95% CI 0.5 - 1.3), 1.7% (95% CI 1.2 - 2.2), and 1.4% (95% CI 0.9 - 1.8). An estimated 18.0% (95% CI 17.1 - 18.9) of the populations of these countries expected that in the near future they would have consultations with health professionals online, and 25.4% (95% CI 24.4 - 26.3) expected that in the near future they would be able to schedule an appointment online. Among those using the Internet for health-related purposes, on average more than 4 in 10 people considered the provision of these eHealth services to be important when choosing a new doctor. CONCLUSIONS: Use of the Internet to communicate with a known health professional is still rare in Europe. Legal context, health policy issues, and technical conditions prevailing in different countries might be playing a major role in the situation. Interest in associated eHealth services is high among citizens and likely to increase.

Comparability of microarray data between amplified and non amplified RNA in colorectal carcinoma.

Microarray analysis reaches increasing popularity during the investigation of prognostic gene clusters in oncology. The standardisation of technical procedures will be essential to compare various datasets produced by different research groups. In several projects the amount of available tissue is limited. In such cases the preamplification of RNA might be necessary prior to microarray hybridisation. To evaluate the comparability of microarray results generated either by amplified or non amplified RNA we isolated RNA from colorectal cancer samples (stage UICC IV) following tumour tissue enrichment by macroscopic manual dissection (CMD). One part of the RNA was directly labelled and hybridised to GeneChips (HG-U133A, Affymetrix), the other part of the RNA was amplified according to the "Eberwine" protocol and was then hybridised to the microarrays. During unsupervised hierarchical clustering the samples were divided in groups regarding the RNA pre-treatment and 5.726 differentially expressed genes were identified. Using independent microarray data of 31 amplified vs. 24 non amplified RNA samples from colon carcinomas (stage UICC III) in a set of 50 predictive genes we validated the amplification bias. In conclusion microarray data resulting from different pre-processing regarding RNA pre-amplification can not be compared within one analysis.

Electrophysiological deficits in the retina of the DBA/2J mouse.

The DBA/2J (D2J) is a genetic mouse model for glaucomatous neurodegeneration because the animals develop anatomical and functional retinal deficits that partially can be correlated with elevated intraocular pressure (IOP). The IOP starts to increase at an age of about 6 months as a result of morphological changes within the anterior eye segment, e.g., pigment dispersion and iris synechiae. The purpose of the present study was to investigate how ERG responses change in individuals at different ages in D2J mice and to compare these changes with normal aging effects in pigmented C57/B6 (B6) mice. IOP was measured in awake, non-sedated D2J and B6 mice with a rebound tonometer. At ages between 2-3 and 10 months, scotopic flash ERGs were measured five times with about 2 months' intervals. In addition, light adapted flicker ERGs were recorded. Our data show that the D2J shows lower flicker ERG responses than the B6 mice already at an age of 2-3 months. Dark adapted flash ERG responses are not decreased at this age. In both mouse strains the ERG responses decrease as a function of age, but there is a stronger decrease in the D2J mice. The data of flicker ERGs suggest the presence of early functional deficits in the D2J retina that possibly have a post-receptoral origin. The scotopic flash ERG reveals a functional deficit that occurs at a later stage and that possibly is IOP dependent. But, the deficits appear at an age at which the IOP is still lower than in the B6 mouse, indicating that other factors play an additional role.

Molecular signature for lymphatic metastasis in colorectal carcinomas.

PURPOSE: TNM-staging of colorectal carcinomas (CRC) relies on the histopathologic workup of the surgically removed specimen. If valid preoperative staging methods existed, patients could be selected for adequate individual therapy before surgery. Microarray techniques provide a promising tool to identify stage-specific molecular signatures on primary tumor biopsies. MATERIAL AND METHODS: Forty tumor samples of stage UICC I, II CRC, 40 samples of stage III CRC, and 25 biopsies of healthy mucosa (MC) were shock frozen in liquid nitrogen and underwent cryotomy after manual dissection for tumor tissue or MC enrichment. Isolated RNA was hybridized to GeneChips (HG-U133A, Affymetrix). Preprocessing of the microarray results was done by the robust multichip average method, and differentially expressed genes were selected by the maximum Wilcoxon statistic over 22,215 probe sets. The results were validated at an independent clinical study. RESULTS: Fifty differently expressed genes between stage UICC I, II versus III CRC were identified respecting the selection criteria by allowing for multiple testing. The data validation by the independent clinical study confirmed our results. In comparison to MC, the genes were over- or underexpressed. They belong to various functional groups such as cellular adhesion, transporters, signaling, metabolism, protein synthesis, gene control, and immune system. CONCLUSION: Our large patient cohort and the data validation on an independent study identified 50 differentially expressed genes between CRC of different histopathologic stages. These findings indicate that molecular staging of CRC may be possible, which could help to guide individual CRC treatment before surgery.

eHealth trends in Europe 2005-2007: a population-based survey.

BACKGROUND: In the last decade, the number of Internet users worldwide has dramatically increased. People are using the Internet for various health-related purposes. It is important to monitor such use as it may have an impact on the individual's health and behavior, patient-practitioner roles, and on general health care provision. OBJECTIVES: This study investigates trends and patterns of European health-related Internet use over a period of 18 months. The main study objective was to estimate the change in the proportion of the population using the Internet for health purposes, and the importance of the Internet as a source of health information compared to more traditional sources. METHODS: The survey data were collected through computer-assisted telephone interviews. A representative sample (N = 14,956) from seven European countries has been used: Denmark, Germany, Greece, Latvia, Norway, Poland, and Portugal. The European eHealth Consumer Trends Survey was first conducted in October-November 2005 and repeated in April-May 2007. In addition to providing background information, respondents were asked to rate the importance of various sources of health information. They were also queried as to the frequency of different online activities related to health and illness and the effects of such use on their disposition. RESULTS: The percentage of the population that has used the Internet for health purposes increased from an estimated 42.3% (95% CI [Confidence Interval] 41.3 - 43.3) in 2005 to an estimated 52.2% (95% CI 51.3 - 53.2) in 2007. Significant growth in the use of the Internet for health purposes was found in all the seven countries. Young women are the most active Internet health users. The importance of the Internet as a source of health information has increased. In 2007, the Internet was perceived as an important source of health information by an estimated 46.8% (95% CI 45.7 - 47.9) of the population, a significant increase of 6.5 % (95% CI 4.9 - 8.1) from 2005. The importance of all the traditional health information channels has either decreased or remained the same. An estimated 22.7% (95% CI 21.7 - 23.6) are using it for more interactive services than just reading health information. CONCLUSION: The Internet is increasingly being used as a source of health information by the European population, and its perceived importance is rising. Use of the Internet for health purposes is growing in all age groups and for both men and women, with especially strong growth among young women. We see that experienced Internet health users are also using the Internet as an active communication channel, both for reaching health professionals and for communicating with peers.

Renal cell carcinoma under 35 years of age: comparison of survival rates for symptomatic and asymptomatic patients.

INTRODUCTION: Recent studies suggest that RCC detected in young adults is likely to be more symptomatic and potentially aggressive, since young patients are less likely to undergo radiologic examinations unless they have symptoms. The aim of this study is to identify the clinical, biological and histological entities of RCC in young patients, and to compare survival rates for symptomatic and asymptomatic patients. PATIENTS AND METHODS: A review of 2,510 records of patients with RCC from 1965 to 2007 was conducted. Thirty-four patients under 35 years old were identified. The Kaplan-Meier system was used to calculate the cumulative survival rate at five and ten years post-surgery as well as the survival prognoses for patients who presented with symptoms and for patients for whom RCC was incidentally diagnosed. RESULTS: The differences in cumulative survival rates at five and ten years between patients who presented with symptoms and patients whom RCC was incidentally diagnosed were not significant (P = 0.06). The Kaplan-Meier system used to calculate the cumulative survival rate at five and ten years postsurgery yielded survival rates of 79.4% at five years and 73.5% at ten years, respectively. DISCUSSION: The biological and histological entities as well as the survival prognosis for RCC in young patients are similar to those for patients who present with RCC in the sixth and seventh decades of life. Additionally, young adults are likely to be more symptomatic, but the difference in survival between patients with symptoms and those without symptoms is not statistically significant.

Ensemble of a subset of kNN classifiers.

Combining multiple classifiers, known as ensemble methods, can give substantial improvement in prediction performance of learning algorithms especially in the presence of non-informative features in the data sets. We propose an ensemble of subset of kNN classifiers, ESkNN, for classification task in two steps. Firstly, we choose classifiers based upon their individual performance using the out-of-sample accuracy. The selected classifiers are then combined sequentially starting from the best model and assessed for collective performance on a validation data set. We use bench mark data sets with their original and some added non-informative features for the evaluation of our method. The results are compared with usual kNN, bagged kNN, random kNN, multiple feature subset method, random forest and support vector machines. Our experimental comparisons on benchmark classification problems and simulated data sets reveal that the proposed ensemble gives better classification performance than the usual kNN and its ensembles, and performs comparable to random forest and support vector machines.

Glaucoma detection with frequency doubling perimetry and short-wavelength perimetry.

PURPOSE: The aim of this analysis was to evaluate the diagnostic usefulness of frequency doubling technology (FDT) perimetry and short-wavelength perimetry (SWAP). Moreover, to study a combination of both methods using the machine-learning technique double-bagging, which was recently established in glaucoma research. METHODS: Forty-three patients with "preperimetric" open-angle glaucoma (glaucomatous optic disc atrophy and no visual field defect in standard perimetry), 26 patients with "perimetric" open angle glaucoma (glaucomatous optic disc atrophy and visual field defect in standard perimetry), and 40 control subjects had FDT screening (protocol: C-20-5) and SWAP (Octopus 101, G2). Criteria for exclusion were color vision abnormalities, media opacities, and an age below 31 years or above 63 years. Data of 1 eye of each patient and control subject entered the statistical evaluation. A point wise evaluation of the diagnostic power of SWAP values was performed to derive spatial patterns of visual field loss. A double-bagging machine-learning algorithm was used to train classification rules on the basis of a combination of FDT scores and nerve fiber related visual field losses in SWAP. The diagnostic power of the classifiers was compared regarding their misclassification error rates and area under the receiver-operating characteristic curve. RESULTS: The combination of FDT perimetry and SWAP yielded better diagnostic results compared with FDT or SWAP separately. The overall estimated misclassification error rate of the combined classifier was 24% compared with 28% for both SWAP and FDT perimetry. Regarding the estimated performance of classifier at high specificities (>80%) in control eyes as measured by the partial area under the receiver-operating characteristic curve, the combination of both instruments is also superior to the individual instruments. CONCLUSIONS: A combination of SWAP and FDT perimetry, each targeting different neuronal pathways, may improve early glaucoma detection.

Improving glaucoma diagnosis by the combination of perimetry and HRT measurements.

PURPOSE: The aim of this study was to determine, whether the combination of morphologic data of the optic nerve head and visual field (VF) data would improve diagnosis of glaucoma, on the basis of the measurements alone. PATIENTS AND METHODS: Eighty-eight perimetric glaucomatous and 88 normal optic discs from the Erlangen Glaucoma Registry were matched for age. All normals and patients were examined in a standardized manner (Slitlamp biomicroscopy, gonioscopy, 24 h-applanation tonometry, automated VF testing, 15-degree optic disc stereographs, and Heidelberg Retina Tomograph (HRT)-scanning of the optic disc). The HRT variables were calculated in 4 optic disc sectors. All variables were calculated with the software's standard reference plane. To gain the same allocation of sectors as provided by the HRT software, the VF responses were averaged within 4 sectors. Classification results of these VF responses were compared with the summarized results within 4 sectors. Six different combinations of morphologic and VF data were used to assess their suitability to diagnose the disease. HRT measurements, and the standard output of the Octopus (HRT/PERI1), HRT measurements and the summarized sectors and their standard deviations (HRT/PERI2), HRT measurements, standard output of the octopus and the summarized sectors and their standard deviations (HRT/PERI1/PERI2), standard output of the Octopus (PERI1), summarized sectors of the Octopus and their standard deviations (PERI2) and HRT measurements. To assess the diagnostic value of the different data sets machine learning classifiers, stabilized linear discriminant analysis, classification trees, bagging, and double-bagging were applied. RESULTS: Combination of morphologic and VF data improved the automated classification rules. The accuracy to diagnose glaucoma just by VF and HRT indices was maximized for double-bagging using both diagnostic tools. An estimated misclassification probability of less than 0.07 could be achieved for the primary open angle glaucoma patients combining HRT and VF sectors by double bagging. So highest sensitivity was 95% and specificity 91%, achieved by double-bagging and combination of HRT, PERI1, and PERI2. CONCLUSIONS: The combination of optic disc measurements and VF data could not only improve glaucoma diagnosis in future, but could also help to find an objective way to diagnose glaucomatous optic atrophy. The limitation of the topographic relationship between structure and function is the individual variability of the optic disc morphology and the subjective variability of VF testing.

Decreased Usage of Specific Scrib Exons Defines a More Malignant Phenotype of Breast Cancer With Worsened Survival.

SCRIB is a polarity regulator known to be abnormally expressed in cancer at the protein level. Here we report that, in breast cancer, an additional and hidden dimension of deregulations exists: an unexpected SCRIB exon usage pattern appears to mark a more malignant tumor phenotype and significantly correlates with survival. Conserved exons encoding the leucine-rich repeats tend to be overexpressed while others are underused. Mechanistic studies revealed that the underused exons encode part of the protein necessary for interaction with Vimentin and Numa1, a protein which is required for proper positioning of the mitotic spindle. Thus, the inclusion/exclusion of specific SCRIB exons is a mechanistic hallmark of breast cancer, which could potentially be exploited to develop more efficient diagnostics and therapies.

Ensemble Pruning for Glaucoma Detection in an Unbalanced Data Set.

BACKGROUND: Random forests are successful classifier ensemble methods consisting of typically 100 to 1000 classification trees. Ensemble pruning techniques reduce the computational cost, especially the memory demand, of random forests by reducing the number of trees without relevant loss of performance or even with increased performance of the sub-ensemble. The application to the problem of an early detection of glaucoma, a severe eye disease with low prevalence, based on topographical measurements of the eye background faces specific challenges. OBJECTIVES: We examine the performance of ensemble pruning strategies for glaucoma detection in an unbalanced data situation. METHODS: The data set consists of 102 topographical features of the eye background of 254 healthy controls and 55 glaucoma patients. We compare the area under the receiver operating characteristic curve (AUC), and the Brier score on the total data set, in the majority class, and in the minority class of pruned random forest ensembles obtained with strategies based on the prediction accuracy of greedily grown sub-ensembles, the uncertainty weighted accuracy, and the similarity between single trees. To validate the findings and to examine the influence of the prevalence of glaucoma in the data set, we additionally perform a simulation study with lower prevalences of glaucoma. RESULTS: In glaucoma classification all three pruning strategies lead to improved AUC and smaller Brier scores on the total data set with sub-ensembles as small as 30 to 80 trees compared to the classification results obtained with the full ensemble consisting of 1000 trees. In the simulation study, we were able to show that the prevalence of glaucoma is a critical factor and lower prevalence decreases the performance of our pruning strategies. CONCLUSIONS: The memory demand for glaucoma classification in an unbalanced data situation based on random forests could effectively be reduced by the application of pruning strategies without loss of performance in a population with increased risk of glaucoma.