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Glioma detection and segmentation is a challenging task for radiologists and clinicians. The research reported in this paper seeks to develop a better clinical decision support algorithm for clinicians diagnosis. This paper presents a probabilistic method for detection and segmentation between abnormal tissue regions and brain tumour (tumour core and edema) portions from Magnetic Resonance Imaging (MRI). A framework is constructed to learn structure of undirected graphical models that can represent the spatial relationships among variables and apply it to glioma segmentation. Compared with the pixel of image, the superpixel is more consistent with human visual cognition and contains less redundancy, thus, the superpixels are considered as the basic unit of structure learning and glioma segmentation scheme. ℓ1-regularization techniques are applied to learn the appropriate structure for modeling graphical models. Conditional Random Fields (CRF) are used to model the spatial interactions among image superpixel regions and their measurements. A number of features including statistics features, the combined features from the local binary pattern as well as gray level run length, curve features, and fractal features were extracted from each superpixel. The features are then passed by ℓ1-regularization to ensure a robust classification. The proposed method is compared with support vector machine and Fuzzy c-means to classify each superpixel into normal and abnormal tissue. The proposed system is tested for the presence of low grade as well as high grade glioma tumors on images collected from BRATS2013, BRATS2015 data set and Henan Provincial People’s Hospital (HNPPH) data set. The experiments performed provides similarity between segmented and truth image up to 91.5% by correlation method. [ABSTRACT FROM AUTHOR]

The ensemble method random forests has become a popular classification tool in bioinformatics and related fields. The out-of-bag error is an error estimation technique often used to evaluate the accuracy of a random forest and to select appropriate values for tuning parameters, such as the number of candidate predictors that are randomly drawn for a split, referred to as mtry. However, for binary classification problems with metric predictors it has been shown that the out-of-bag error can overestimate the true prediction error depending on the choices of random forests parameters. Based on simulated and real data this paper aims to identify settings for which this overestimation is likely. It is, moreover, questionable whether the out-of-bag error can be used in classification tasks for selecting tuning parameters like mtry, because the overestimation is seen to depend on the parameter mtry. The simulation-based and real-data based studies with metric predictor variables performed in this paper show that the overestimation is largest in balanced settings and in settings with few observations, a large number of predictor variables, small correlations between predictors and weak effects. There was hardly any impact of the overestimation on tuning parameter selection. However, although the prediction performance of random forests was not substantially affected when using the out-of-bag error for tuning parameter selection in the present studies, one cannot be sure that this applies to all future data. For settings with metric predictor variables it is therefore strongly recommended to use stratified subsampling with sampling fractions that are proportional to the class sizes for both tuning parameter selection and error estimation in random forests. This yielded less biased estimates of the true prediction error. In unbalanced settings, in which there is a strong interest in predicting observations from the smaller classes well, sampling the same number of observations from each class is a promising alternative. [ABSTRACT FROM AUTHOR]

Background: The aim of the present systematic review was to evaluate the hypothesis of an association between periodontitis and the development of cancer. Methods: Two reviewers independently screened electronic and manual sources for pertinent articles. Primary outcome measures were the occurrence of neoplasm diagnosis in exposed and non-exposed groups, reported to evaluate association between cancer and periodontitis. Results: Of the 490 initially retrieved papers 10 were included in the qualitative synthesis and eight in the quantitative synthesis; the eight papers covered six studies. Considering hazard ratios, a statistically significant association was found for all cancers studied (1.14; CI 95%: 1.04, 1.24), digestive tract cancer (1.34; CI 95%: 1.05, 1.72), pancreatic cancer (1.74; CI 95%: 1.21, 2.52), prostate cancer (1.25; CI 95%: 1.04, 1.51), breast cancer (1.11; CI 95%: 1.00, 1.23), corpus uteri cancer (2.20; CI 95%: 1.16, 4.18), lung cancer (1.24; CI 95%: 1.06, 1.45), hematological cancer (1.30; CI 95%: 1.11, 1.53), esophagus / oropharyngeal cancer pooled together (2.25; CI 95%: 1.30, 3.90) and Non-Hodgkin lymphoma (1.30; CI 95%: 1.11, 1.52). Conclusions: Despite the sparse scientific evidence and considering the low statistical power of the results, this systematic review revealed a substantial lack of studies with standardized and comparable methods to speculate about the association between periodontitis and cancer; more studies are need in order to explore further the scientific evidence of such correlation. [ABSTRACT FROM AUTHOR]

Objective: This study aimed to elucidate the effects of cholecystectomy on the risk of colorectal cancer (CRC) by conducting a meta-analysis of 10 cohort studies. Methods: The eligible cohort studies were selected by searching the PubMed and EMBASE databases from their origination to June 30, 2016, as well as by consulting the reference lists of the selected articles. Two authors individually collected the data from the 10 papers. When the data showed marked heterogeneity, we used a random-effects model to estimate the overall pooled risk; otherwise, a fixed effects model was employed. Results: The final analysis included ten cohort studies. According to the Newcastle-Ottawa Scale (NOS), nine papers were considered high quality. After the data of these 9 studies were combined, an increased risk of CRC was found among the individuals who had undergone cholecystectomy (risk ratio (RR) 1.22; 95% confidence interval (CI) 1.08–1.38). In addition, we also found a promising increased risk for colon cancer (CC) (RR 1.30, 95% CI 1.07–1.58), but no relationship between cholecystectomy and rectum cancer (RC) (RR 1.09; 95% CI 0.89–1.34) was observed. Additionally, in the sub-group analysis of the tumor location in the colon, a positive risk for ascending colon cancer (ACC) was found (RR 1.18, 95% CI 1.11–1.26). After combining the ACC, transverse colon cancer (TCC), sigmoid colon cancer (SCC) and descending colon cancer (DCC) patients, we found a positive relationship with cholecystectomy (RR 1.18, 95% CI 1.11–1.26). Furthermore, after combining the ACC and DCC patients, we also found a positive relationship with cholecystectomy (RR 1.28; 95% CI 1.11–1.26) in the sub-group analysis. In an additional sub-group analysis of patients from Western countries, there was a positive relationship between cholecystectomy and the risk of CRC (RR 1.20; 95% CI 1.05–1.36). Furthermore, a positive relationship between female gender and CRC was also found (RR 1.17; 95% CI 1.03–1.34). However, there was no relationship between gender and CC or RC. Furthermore, no publication bias was observed, and the sensitivity analysis indicated stable results. Conclusions: This meta-analysis of 10 cohort studies revealed that cholecystectomy is associated with an increased risk for CRC, CC and ACC, particularly in Western countries. No relationship between cholecystectomy and RC was observed. There was no relationship between gender and either CC or RC, but a positive relationship between female gender and CRC was observed. [ABSTRACT FROM AUTHOR]

Distinguishing certain and uncertain information is of crucial importance both in the scientific field in the strict sense and in the popular scientific domain. In this paper, by adopting an epistemic stance perspective on certainty and uncertainty, and a mixed procedure of analysis, which combines a bottom-up and a top-down approach, we perform a comparative study (both qualitative and quantitative) of the uncertainty linguistic markers (verbs, non-verbs, modal verbs, conditional clauses, uncertain questions, epistemic future) and their scope in three different corpora: a historical corpus of 80 biomedical articles from the British Medical Journal (BMJ) 1840–2007; a corpus of 12 biomedical articles from BMJ 2013, and a contemporary corpus of 12 scientific popular articles from Discover 2013. The variables under observation are time, structure (IMRaD vs no-IMRaD) and genre (scientific vs popular articles). We apply the Generalized Linear Models analysis in order to test whether there are statistically significant differences (1) in the amount of uncertainty among the different corpora, and (2) in the categories of uncertainty markers used by writers. The results of our analysis reveal that (1) in all corpora, the percentages of uncertainty are always much lower than that of certainty; (2) uncertainty progressively diminishes over time in biomedical articles (in conjunction with their structural changes–IMRaD–and to the increase of the BMJ Impact Factor); and (3) uncertainty is slightly higher in scientific popular articles (Discover 2013) as compared to the contemporary corpus of scientific articles (BMJ 2013). Nevertheless, in all corpora, modal verbs are the most used uncertainty markers. These results suggest that not only do scientific writers prefer to communicate their uncertainty with markers of possibility rather than those of subjectivity but also that science journalists prefer using a third-person subject followed by modal verbs rather than a first-person subject followed by mental verbs such as think or believe. [ABSTRACT FROM AUTHOR]

The process of Nuclei detection in high-grade breast cancer images is quite challenging in the case of image processing techniques due to certain heterogeneous characteristics of cancer nuclei such as enlarged and irregularly shaped nuclei, highly coarse chromatin marginalized to the nuclei periphery and visible nucleoli. Recent reviews state that existing techniques show appreciable segmentation accuracy on breast histopathology images whose nuclei are dispersed and regular in texture and shape; however, typical cancer nuclei are often clustered and have irregular texture and shape properties. This paper proposes a novel segmentation algorithm for detecting individual nuclei from Hematoxylin and Eosin (H&E) stained breast histopathology images. This detection framework estimates a nuclei saliency map using tensor voting followed by boundary extraction of the nuclei on the saliency map using a Loopy Back Propagation (LBP) algorithm on a Markov Random Field (MRF). The method was tested on both whole-slide images and frames of breast cancer histopathology images. Experimental results demonstrate high segmentation performance with efficient precision, recall and dice-coefficient rates, upon testing high-grade breast cancer images containing several thousand nuclei. In addition to the optimal performance on the highly complex images presented in this paper, this method also gave appreciable results in comparison with two recently published methods—Wienert et al. (2012) and Veta et al. (2013), which were tested using their own datasets. [ABSTRACT FROM AUTHOR]

Motivation: Disease progression originates from the concept that an individual disease may go through different changes as it evolves, and such changes can cause new diseases. It is important to find a progression between diseases since knowing the prior-posterior relationship beforehand can prevent further complications or evolutions to other diseases. Furthermore, the series of progressions can be represented in the form of a chain, which enables us to readily infer successive influences from one disease to another after many passages through other diseases. Methods: In this paper, we propose a systematic approach for finding a disease progression chain from a source disease to a target one via exploring a disease network. The network is constructed based on various sets of biomedical data. To find the most influential progression chains, the k-shortest path search algorithm is employed. The most representative algorithms such as A*, Dijkstra, and Yen’s are incorporated into the proposed method. Results: A disease network consisting of 3,302 diseases was constructed based on four sources of biomedical data: disease-protein relations, biological pathways, clinical history, and biomedical literature information. The last three sets of data contain prior-posterior information, and they endow directionality on the edges of the network. The results were interesting and informative: for example, when colitis and respiratory insufficiency were set as a source disease and a target one, respectively, five progression chains were found within several seconds (when k = 5). Each chain was provided with a progression score, which indicates the strength of plausibility relative to others. Similarly, the proposed method can be expanded to any pair of source-target diseases in the network. This can be utilized as a preliminary tool for inferring complications or progressions between diseases. [ABSTRACT FROM AUTHOR]

Feature screening has become a real prerequisite for the analysis of high-dimensional genomic data, as it is effective in reducing dimensionality and removing redundant features. However, existing methods for feature screening have been mostly relying on the assumptions of linear effects and independence (or weak dependence) between features, which might be inappropriate in real practice. In this paper, we consider the problem of selecting continuous features for a categorical outcome from high-dimensional data. We propose a powerful statistical procedure that consists of two steps, a nonparametric significance test based on edge count and a multiple testing procedure with dependence adjustment for false discovery rate control. The new method presents two novelties. First, the edge-count test directly targets distributional difference between groups, therefore it is sensitive to nonlinear effects. Second, we relax the independence assumption and adapt Efron’s procedure to adjust for the dependence between features. The performance of the proposed procedure, in terms of statistical power and false discovery rate, is illustrated by simulated data. We apply the new method to three genomic datasets to identify genes associated with colon, cervical and prostate cancers. [ABSTRACT FROM AUTHOR]

High dimensional biomedical data contain tens of thousands of features, accurate and effective identification of the core features in these data can be used to assist diagnose related diseases. However, there are often a large number of irrelevant or redundant features in biomedical data, which seriously affect subsequent classification accuracy and machine learning efficiency. To solve this problem, a novel filter feature selection algorithm based on redundant removal (FSBRR) is proposed to classify high dimensional biomedical data in this paper. First of all, two redundant criteria are determined by vertical relevance (the relationship between feature and class attribute) and horizontal relevance (the relationship between feature and feature). Secondly, to quantify redundant criteria, an approximate redundancy feature framework based on mutual information (MI) is defined to remove redundant and irrelevant features. To evaluate the effectiveness of our proposed algorithm, controlled trials based on typical feature selection algorithm are conducted using three different classifiers, and the experimental results indicate that the FSBRR algorithm can effectively reduce the feature dimension and improve the classification accuracy. In addition, an experiment of small sample dataset is designed and conducted in the section of discussion and analysis to clarify the specific implementation process of FSBRR algorithm more clearly. [ABSTRACT FROM AUTHOR]

Emerging evidence has shown microRNAs (miRNAs) play an important role in human disease research. Identifying potential association among them is significant for the development of pathology, diagnose and therapy. However, only a tiny portion of all miRNA-disease pairs in the current datasets are experimentally validated. This prompts the development of high-precision computational methods to predict real interaction pairs. In this paper, we propose a new model of Logistic Model Tree for predicting miRNA-Disease Association (LMTRDA) by fusing multi-source information including miRNA sequences, miRNA functional similarity, disease semantic similarity, and known miRNA-disease associations. In particular, we introduce miRNA sequence information and extract its features using natural language processing technique for the first time in the miRNA-disease prediction model. In the cross-validation experiment, LMTRDA obtained 90.51% prediction accuracy with 92.55% sensitivity at the AUC of 90.54% on the HMDD V3.0 dataset. To further evaluate the performance of LMTRDA, we compared it with different classifier and feature descriptor models. In addition, we also validate the predictive ability of LMTRDA in human diseases including Breast Neoplasms, Breast Neoplasms and Lymphoma. As a result, 28, 27 and 26 out of the top 30 miRNAs associated with these diseases were verified by experiments in different kinds of case studies. These experimental results demonstrate that LMTRDA is a reliable model for predicting the association among miRNAs and diseases. [ABSTRACT FROM AUTHOR]

Computer-aided polyp detection in gastric gastroscopy has been the subject of research over the past few decades. However, despite significant advances, automatic polyp detection in real time is still an unsolved problem. In this paper, we report on a convolutional neural network (CNN) for polyp detection that is constructed based on Single Shot MultiBox Detector (SSD) architecture and which we call SSD for Gastric Polyps (SSD-GPNet). To take full advantages of feature maps’ information from the feature pyramid and to acquire higher accuracy, we re-use information that is abandoned by Max-Pooling layers. In other words, we reuse the lost data from the pooling layers and concatenate that data as extra feature maps to contribute to classification and detection. Meanwhile, in the feature pyramid, we concatenate feature maps of the lower layers and feature maps that are deconvolved from upper layers to make explicit relationships between layers and to effectively increase the number of channels. The results show that our enhanced SSD for gastric polyp detection can realize real-time polyp detection with 50 frames per second (FPS) and can improve the mean average precision (mAP) from 88.5% to 90.4%, with only a little loss in time-performance. And the further experiment shows that SSD-GPNet has excellent performance in improving polyp detection recalls over 10% (p = 0.00053), especially in small polyp detection. This can help endoscopic physicians more easily find missed polyps and decrease the gastric polyp miss rate. It may be applicable in daily clinical practice to reduce the burden on physicians. [ABSTRACT FROM AUTHOR]

For studying cancer and genetic diseases, the issue of identifying high correlation genes from high-dimensional data is an important problem. It is a great challenge to select relevant biomarkers from gene expression data that contains some important correlation structures, and some of the genes can be divided into different groups with a common biological function, chromosomal location or regulation. In this paper, we propose a penalized accelerated failure time model CHR-DE using a non-convex regularization (local search) with differential evolution (global search) in a wrapper-embedded memetic framework. The complex harmonic regularization (CHR) can approximate to the combination and ℓq (1 ≤ q < 2) for selecting biomarkers in group. And differential evolution (DE) is utilized to globally optimize the CHR’s hyperparameters, which make CHR-DE achieve strong capability of selecting groups of genes in high-dimensional biological data. We also developed an efficient path seeking algorithm to optimize this penalized model. The proposed method is evaluated on synthetic and three gene expression datasets: breast cancer, hepatocellular carcinoma and colorectal cancer. The experimental results demonstrate that CHR-DE is a more effective tool for feature selection and learning prediction. [ABSTRACT FROM AUTHOR]

Robustly predicting outcome for cancer patients from gene expression is an important challenge on the road to better personalized treatment. Network-based outcome predictors (NOPs), which considers the cellular wiring diagram in the classification, hold much promise to improve performance, stability and interpretability of identified marker genes. Problematically, reports on the efficacy of NOPs are conflicting and for instance suggest that utilizing random networks performs on par to networks that describe biologically relevant interactions. In this paper we turn the prediction problem around: instead of using a given biological network in the NOP, we aim to identify the network of genes that truly improves outcome prediction. To this end, we propose SyNet, a gene network constructed ab initio from synergistic gene pairs derived from survival-labelled gene expression data. To obtain SyNet, we evaluate synergy for all 69 million pairwise combinations of genes resulting in a network that is specific to the dataset and phenotype under study and can be used to in a NOP model. We evaluated SyNet and 11 other networks on a compendium dataset of >4000 survival-labelled breast cancer samples. For this purpose, we used cross-study validation which more closely emulates real world application of these outcome predictors. We find that SyNet is the only network that truly improves performance, stability and interpretability in several existing NOPs. We show that SyNet overlaps significantly with existing gene networks, and can be confidently predicted (~85% AUC) from graph-topological descriptions of these networks, in particular the breast tissue-specific network. Due to its data-driven nature, SyNet is not biased to well-studied genes and thus facilitates post-hoc interpretation. We find that SyNet is highly enriched for known breast cancer genes and genes related to e.g. histological grade and tamoxifen resistance, suggestive of a role in determining breast cancer outcome. [ABSTRACT FROM AUTHOR]

Anxiety and depression can be heightened among individuals living with chronic diseases. Identifying these individuals is necessary for ensuring they are provided with adequate support. Traditional tools such as clinical interviews or symptom checklists are not always feasible to implement in practice. Robust single-item questions may be a useful alternative. This study aimed to measure agreement, sensitivity, specificity, positive predictive value and negative predictive value of a single-item question about anxiety and depression compared to the widely used Hospital Anxiety and Depression Scale (HADS). A cross-sectional survey of 2,811 people with cancer attending 19 treatment centres in Australia. Patients were approached in the waiting room prior to an outpatient clinic appointment and invited to complete a pen and paper survey. Participants completed the HADS as well as 2 single-items asking if they have felt anxious or depressed in the last week. The single-items for anxiety and depression each demonstrated moderate levels of sensitivity (0.78 for anxiety; 0.63 for depression) and specificity (0.75 for anxiety; 0.84 for depression) against the relevant HADS subscale. Positive predictive values were moderate (0.53 for anxiety and 0.52 for depression) while negative predictive values were high for both single-item questions (0.90 for anxiety and 0.89 for depression). The single-item measures of anxiety and depression may be useful to rule out individuals who do not require further psychological assessment or intervention for anxiety and depression. Further research is needed to explore whether these findings generalise to other chronic diseases. [ABSTRACT FROM AUTHOR]

Effective symptom management is a critical component of cancer treatment. Computational tools that predict the course and severity of these symptoms have the potential to assist oncology clinicians to personalize the patient’s treatment regimen more efficiently and provide more aggressive and timely interventions. Three common and inter-related symptoms in cancer patients are depression, anxiety, and sleep disturbance. In this paper, we elaborate on the efficiency of Support Vector Regression (SVR) and Non-linear Canonical Correlation Analysis by Neural Networks (n-CCA) to predict the severity of the aforementioned symptoms between two different time points during a cycle of chemotherapy (CTX). Our results demonstrate that these two methods produced equivalent results for all three symptoms. These types of predictive models can be used to identify high risk patients, educate patients about their symptom experience, and improve the timing of pre-emptive and personalized symptom management interventions. [ABSTRACT FROM AUTHOR]

Background: Preclinical evidence suggests statins may have anti-tumor properties. Large observational studies are also consistent with improved survival and cancer-specific outcomes among cancer patients on statins. We sought to evaluate the randomized controlled trials of statins in addition to usual anti-cancer therapy. Methods: A systematic search of MEDLINE, Embase, CINAHL, Cochrane Library, Web of Science, Papers First and Clinicaltrials.gov was performed from inception through to July 4, 2017 to identify randomized clinical trials that investigated statin therapy in cancer patients. Our primary outcome was overall survival and our secondary outcome was progression-free survival. We calculated summary hazard ratio’s (HR) and 95% confidence intervals (CI) based on random-effects models using aggregate data. PROSPERO (CRD42017065503). Results: Ten studies with 1,881 individuals were included with 1,572 deaths and a median follow-up of 23 months. All trials included patients with advanced (stage 3 or higher) disease. There was minimal between-study statistical heterogeneity (I2 = 1.8%, for OS; I2 = 0%, for PFS). The pooled HR for overall survival in patients randomized to statins plus standard anti-cancer therapy versus standard therapy alone was 0.94 (95% CI, 0.85 to 1.04). In the 9 studies that reported progression-free survival (1,798 participants), the pooled HR for statin plus standard therapy versus standard therapy alone was 0.97 (95% CI, 0.87 to 1.07). Conclusions: In patients with advanced cancer and a prognosis <2 years, the addition of statins to standard anti-cancer therapy does not appear to improve overall survival or progression-free survival. Future research should assess if cancer patients with better prognosis benefit from longer-term statin therapy. [ABSTRACT FROM AUTHOR]

Plasma cell segmentation is the first stage of a computer assisted automated diagnostic tool for multiple myeloma (MM). Owing to large variability in biological cell types, a method for one cell type cannot be applied directly on the other cell types. In this paper, we present PCSeg Tool for plasma cell segmentation from microscopic medical images. These images were captured from bone marrow aspirate slides of patients with MM. PCSeg has a robust pipeline consisting of a pre-processing step, the proposed modified multiphase level set method followed by post-processing steps including the watershed and circular Hough transform to segment clusters of cells of interest and to remove unwanted cells. Our modified level set method utilizes prior information about the probability densities of regions of interest (ROIs) in the color spaces and provides a solution to the minimal-partition problem to segment ROIs in one of the level sets of a two-phase level set formulation. PCSeg tool is tested on a number of microscopic images and provides good segmentation results on single cells as well as efficient segmentation of plasma cell clusters. [ABSTRACT FROM AUTHOR]

The paper presents the application of Grade Correspondence Analysis (GCA) and Grade Correspondence Cluster Analysis (GCCA) for ordering and grouping -omics datasets, using transcriptomic data as an example. Based on gene expression data describing 256 patients with Multiple Myeloma it was shown that the GCA method could be used to find regularities in the analyzed collections and to create characteristic gene expression profiles for individual groups of patients. GCA iteratively permutes rows and columns to maximize the tau-Kendall or rho-Spearman coefficients, which makes it possible to arrange rows and columns in such a way that the most similar ones remain in each other’s neighbourhood. In this way, the GCA algorithm highlights regularities in the data matrix. The ranked data can then be grouped using the GCCA method, and after that aggregated in clusters, providing a representation that is easier to analyze–especially in the case of large sets of gene expression profiles. Regularization of transcriptomic data, which is presented in this manuscript, has enabled division of the data set into column clusters (representing genes) and row clusters (representing patients). Subsequently, rows were aggregated (based on medians) to visualise the gene expression profiles for patients with Multiple Myeloma in each collection. The presented analysis became the starting point for characterisation of differentiated genes and biochemical processes in which they are involved. GCA analysis may provide an alternative analytical method to support differentiation and analysis of gene expression profiles characterising individual groups of patients. [ABSTRACT FROM AUTHOR]

Accurate estimation of motion field in respiration-correlated 4DCT images, is a precondition for the analysis of patient-specific breathing dynamics and subsequent image-supported treatment planning. However, the lung motion estimation often suffers from the sliding motion. In this paper, a novel lung motion method based on the non-rigid registration of point clouds is proposed, and the tangent-plane distance is used to represent the distance term, which describes the difference between two point clouds. Local affine transformation model is used to express the non-rigid deformation of the lung motion. The final objective function is expressed in the Frobenius norm formation, and matrix optimization scheme is carried out to find out the optimal transformation parameters that minimize the objective function. A key advantage of our proposed method is that it alleviates the requirement that the source point cloud and the reference point cloud should be in one-to-one corresponding relationship, and the requirement is difficult to be satisfied in practical application. Furthermore, the proposed method takes the sliding motion of the lung into consideration and improves the registration accuracy by reducing the constraint of the motion along the tangent direction. Non-rigid registration experiments are carried out to validate the performance of the proposed method using popi-model data. The results demonstrate that the proposed method outperforms the traditional method with about 20% accuracy increase. [ABSTRACT FROM AUTHOR]

Background: Recent advances in targeted therapies have raised expectations that the clinical application of biomarkers would improve patient’s health outcomes and potentially save costs. However, the cost-effectiveness of biomarkers remains unclear irrespective of the cost-effectiveness of corresponding therapies. It is thus important to determine whether biomarkers for targeted therapies provide good value for money. This study systematically reviews economic evaluations of biomarkers for targeted therapies in metastatic colorectal cancer (mCRC) and assesses the cost-effectiveness of predictive biomarkers in mCRC. Methods: A literature search was performed using Medline, Embase, EconLit, NHSEED. Papers published from 2000 until June 2018 were searched. All economic evaluations assessing biomarker-guided therapies with companion diagnostics in mCRC were searched. To make studies more comparable, cost-effectiveness results were synthesized as per biomarker tests and corresponding therapies. Methodological quality was assessed using the Quality of Health Economic Studies (QHES) instrument. Results: Forty-six studies were included in this review. Of these, 17 studies evaluated the intrinsic value of cancer biomarkers, whereas the remaining studies focused on assessing the cost-effectiveness of corresponding drugs. Most studies indicated favourable cost-effectiveness of biomarkers for targeted therapies in mCRC. Some studies reported that biomarkers were cost-effective, while their corresponding therapies were not cost-effective. A considerable number of economic evaluations were conducted in pre-defined genetic populations and thus, often failed to fully capture the biomarker’s clinical and economic values. The average QHES score was 73.6. Conclusion: Cancer biomarkers for targeted therapies in mCRC were mostly found to be cost-effective; otherwise, they at least improved the cost-effectiveness of targeted therapies by saving some costs. However, this did not necessarily make their corresponding therapies cost-effective. While companion biomarkers reduced therapy costs, the savings were not sufficient to make the corresponding agents cost-effective. Evaluation of biomarkers was often restricted to the cost of tests and did not consider their clinical values or biomarker prevalence. [ABSTRACT FROM AUTHOR]

Background: Evidence is growing that low-dose aspirin used as an adjuvant treatment of cancer is associated with an increased survival and a reduction in metastatic spread. We therefore extended up to August 2017 an earlier systematic search and meta-analyses of published studies of low-dose aspirin taken by patients with a diagnosis of cancer. Methods: Searches were completed in Medline and Embase to August 2017 using a pre-defined search strategy to identify reports of relevant studies. References in all the selected papers were scanned. Two reviewers independently applied pre-determined eligibility criteria and extracted data on cause-specific cancer deaths, overall mortality and the occurrence of metastatic spread. Meta-analyses were then conducted for different cancers and heterogeneity and publication bias assessed. Sensitivity analyses and attempts to reduce heterogeneity were conducted. Results: Analyses of 29 studies reported since an earlier review up to April 2015 are presented in this report, and these are then pooled with the 42 studies in our earlier publication. Overall meta-analyses of the 71 studies are presented, based on a total of over 120 thousand patients taking aspirin. Ten of the studies also give evidence on the incidence of metastatic cancer spread. There are now twenty-nine observational studies describing colorectal cancer (CRC) and post-diagnostic aspirin. Pooling the estimates of reduction by aspirin which are reported as hazard ratios (HR), gives an overall HR for aspirin and CRC mortality 0.72 (95% CI 0.64–0.80). Fourteen observational studies have reported on aspirin and breast cancer mortality and pooling those that report the association with aspirin as a hazard ratio gives HR 0.69 (0.53–0.90). Sixteen studies report on aspirin and prostate cancer mortality and a pooled estimate yields an HR of 0.87 (95% CI 0.73–1.05). Data from 12 reports relating to other cancers are also listed. Ten studies give evidence of a reduction in metastatic spread; four give a pooled HR 0.31 (95% CI 0.18, 0.54) and five studies which reported odds ratio of metastatic spread give OR 0.79 (0.66 to 0.95). Conclusion: Being almost entirely from observational studies, the evidence of benefit from aspirin is limited. There is heterogeneity between studies and the results are subject to important biases, only some of which can be identified. Nevertheless, the evidence would seem to merit wide discussion regarding whether or not it is adequate to justify the recommendation of low-dose therapeutic aspirin, and if it is, for which cancers? [ABSTRACT FROM AUTHOR]

Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiple chromosomes. The measured probes are by themselves less interesting scientifically; instead scientists seek to discover biologically interpretable genomic regions comprised of contiguous groups of probes which may act as biomarkers of disease or serve as a dimension-reducing pre-processing step for downstream analyses. In this paper, we introduce an unsupervised feature learning technique which maps technological units (probes) to biological units (genomic regions) that are common across all subjects. We use ideas from fusion penalties and convex clustering to introduce a method for Spatial Convex Clustering, or SpaCC. Our method is specifically tailored to detecting multi-subject regions of methylation, but we also test our approach on the well-studied problem of detecting segments of copy number variation. We formulate our method as a convex optimization problem, develop a massively parallelizable algorithm to find its solution, and introduce automated approaches for handling missing values and determining tuning parameters. Through simulation studies based on real methylation and copy number variation data, we show that SpaCC exhibits significant performance gains relative to existing methods. Finally, we illustrate SpaCC’s advantages as a pre-processing technique that reduces large-scale genomics data into a smaller number of genomic regions through several cancer epigenetics case studies on subtype discovery, network estimation, and epigenetic-wide association. [ABSTRACT FROM AUTHOR]

Feature selection and classification are the main topics in microarray data analysis. Although many feature selection methods have been proposed and developed in this field, SVM-RFE (Support Vector Machine based on Recursive Feature Elimination) is proved as one of the best feature selection methods, which ranks the features (genes) by training support vector machine classification model and selects key genes combining with recursive feature elimination strategy. The principal drawback of SVM-RFE is the huge time consumption. To overcome this limitation, we introduce a more efficient implementation of linear support vector machines and improve the recursive feature elimination strategy and then combine them together to select informative genes. Besides, we propose a simple resampling method to preprocess the datasets, which makes the information distribution of different kinds of samples balanced and the classification results more credible. Moreover, the applicability of four common classifiers is also studied in this paper. Extensive experiments are conducted on six most frequently used microarray datasets in this field, and the results show that the proposed methods have not only reduced the time consumption greatly but also obtained comparable classification performance. [ABSTRACT FROM AUTHOR]

Background: Low-dose aspirin has been shown to reduce the incidence of cancer, but its role in the treatment of cancer is uncertain. Objectives: We conducted a systematic search of the scientific literature on aspirin taken by patients following a diagnosis of cancer, together with appropriate meta-analyses. Methods: Searches were completed in Medline and Embase in December 2015 using a pre-defined search strategy. References and abstracts of all the selected papers were scanned and expert colleagues were contacted for additional studies. Two reviewers applied pre-determined eligibility criteria (cross-sectional, cohort and controlled studies, and aspirin taken after a diagnosis of cancer), assessed study quality and extracted data on cancer cause-specific deaths, overall mortality and incidence of metastases. Random effects meta-analyses and planned sub-group analyses were completed separately for observational and experimental studies. Heterogeneity and publication bias were assessed in sensitivity analyses and appropriate omissions made. Papers were examined for any reference to bleeding and authors of the papers were contacted and questioned. Results: Five reports of randomised trials were identified, together with forty two observational studies: sixteen on colorectal cancer, ten on breast and ten on prostate cancer mortality. Pooling of eleven observational reports of the effect of aspirin on cause-specific mortality from colon cancer, after the omission of one report identified on the basis of sensitivity analyses, gave a hazard ratio (HR) of 0.76 (95% CI 0.66, 0.88) with reduced heterogeneity (P = 0.04). The cause specific mortality in five reports of patients with breast cancer showed significant heterogeneity (P<0.0005) but the omission of one outlying study reduced heterogeneity (P = 0.19) and led to an HR = 0.87 (95% CI 0.69, 1.09). Heterogeneity between nine studies of prostate cancer was significant, but again, the omission of one study led to acceptable homogeneity (P = 0.26) and an overall HR = 0.89 (95% CI 0.79–0.99). Six single studies of other cancers suggested reductions in cause specific mortality by aspirin, and in five the effect is statistically significant. There were no significant differences between the pooled HRs for the three main cancers and after the omission of three reports already identified in sensitivity analyses heterogeneity was removed and revealed an overall HR of 0.83 (95% CI 0.76–0.90). A mutation of PIK3CA was present in about 20% of patients, and appeared to explain most of the reduction in colon cancer mortality by aspirin. Data were not adequate to examine the importance of this or any other marker in the effect of aspirin in the other cancers. On bleeding attributable to aspirin two reports stated that there had been no side effect or bleeding attributable to aspirin. Authors on the other reports were written to and 21 replied stating that no data on bleeding were available. Conclusions and Implications: The study highlights the need for randomised trials of aspirin treatment in a variety of cancers. While these are awaited there is an urgent need for evidence from observational studies of aspirin and the less common cancers, and for more evidence of the relevance of possible bio-markers of the aspirin effect on a wide variety of cancers. In the meantime it is urged that patients in whom a cancer is diagnosed should be given details of this research, together with its limitations, to enable each to make an informed decision as to whether or not to take low-dose aspirin. Systematic Review Protocol Number: CRD42015014145 [ABSTRACT FROM AUTHOR]

Background: Our systematic review summarizes the evidence concerning the accuracy of serum diagnostic and prognostic tests for colorectal cancer (CRC). Methods: The databases MEDLINE and EMBASE were searched iteratively to identify the relevant literature for serum markers of CRC published from 1950 to August 2012. The articles that provided adequate information to meet the requirements of the meta-analysis of diagnostic and prognostic markers were included. A 2-by-2 table of each diagnostic marker and its hazard ratio (HR) and the confidence interval (CI) of each prognostic marker was directly or indirectly extracted from the included papers, and the pooled sensitivity and specificity of the diagnostic marker and the pooled HR and the CI of the prognostic marker were subsequently calculated using the extracted data. Results: In total, 104 papers related to the diagnostic markers and 49 papers related to the prognostic serum markers of CRC were collected, and only 19 of 92 diagnostic markers were investigated in more than two studies, whereas 21 out of 44 prognostic markers were included in two or more studies. All of the pooled sensitivities of the diagnostic markers with > = 3 repetitions were less than 50%, and the meta-analyses of the prognostic markers with more than 3 studies were performed, VEGF with highest (2.245, CI: 1.347–3.744) and MMP-7 with lowest (1.099, CI: 1.018–1.187)) pooled HRs are presented. Conclusions: The quality of studies addressing the diagnostic and prognostic accuracy of the tests was poor, and the results were highly heterogeneous. The poor characteristics indicate that these tests are of little value for clinical practice. [ABSTRACT FROM AUTHOR]

How can we predict the occurrence of acute kidney injury (AKI) in cancer patients based on machine learning with serum creatinine data? Given irregular and heterogeneous clinical data, how can we make the most of it for accurate AKI prediction? AKI is a common and significant complication in cancer patients, and correlates with substantial morbidity and mortality. Since no effective treatment for AKI still exists, it is important to take timely preventive measures. While several approaches have been proposed for predicting AKI, their scope and applicability are limited as they either assume regular data measured over a short hospital stay, or do not fully utilize heterogeneous data. In this paper, we provide an AKI prediction model with a greater applicability, which relaxes the constraints of existing approaches, and fully utilizes irregular and heterogeneous data for learning the model. In a cohort of 21,022 cancer patients who were registered into Korea Central Cancer Registry (KCCR) in Seoul National University Hospital between January 1, 2004 and December 31, 2013, our method achieves 0.7892 precision, 0.7506 recall, and 0.7576 F-measure in predicting whether a patient will develop AKI during the next 14 days. [ABSTRACT FROM AUTHOR]

As an important way to help express the preference relation between alternatives, distributed preference relation (DPR) can represent the preferred, non-preferred, indifferent, and uncertain degrees of one alternative over another simultaneously. DPR, however, is unavailable in some situations where a decision maker cannot provide the precise degrees of one alternative over another due to lack of knowledge, experience, and data. In this paper, to address this issue, we propose interval-valued DPR (IDPR) and present its properties of validity and normalization. Through constructing two optimization models, an IDPR matrix is transformed into a score matrix to facilitate the comparison between any two alternatives. The properties of the score matrix are analyzed. To guarantee the rationality of the comparisons between alternatives derived from the score matrix, the additive consistency of the score matrix is developed. In terms of these, IDPR is applied to model and solve multiple criteria group decision making (MCGDM) problem. Particularly, the relationship between the parameters for the consistency of the score matrix associated with each decision maker and those for the consistency of the score matrix associated with the group of decision makers is analyzed. A manager selection problem is investigated to demonstrate the application of IDPRs to MCGDM problems. [ABSTRACT FROM AUTHOR]

High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to run-to-run variation in reagents, equipment, protocols, or personnel. Currently, batch correction methods are not commonly applied to microbiome sequencing datasets. In this paper, we compare different batch-correction methods applied to microbiome case-control studies. We introduce a model-free normalization procedure where features (i.e. bacterial taxa) in case samples are converted to percentiles of the equivalent features in control samples within a study prior to pooling data across studies. We look at how this percentile-normalization method compares to traditional meta-analysis methods for combining independent p-values and to limma and ComBat, widely used batch-correction models developed for RNA microarray data. Overall, we show that percentile-normalization is a simple, non-parametric approach for correcting batch effects and improving sensitivity in case-control meta-analyses. [ABSTRACT FROM AUTHOR]

This paper presents a novel two-stage image segmentation method using an edge scaled energy functional based on local and global information for intensity inhomogeneous image segmentation. In the first stage, we integrate global intensity term with a geodesic edge term, which produces a preliminary rough segmentation result. Thereafter, by taking final contour of the first stage as initial contour, we begin second stage segmentation process by integrating local intensity term with geodesic edge term to get final segmentation result. Due to the suitable initialization from the first stage, the second stage precisely achieves desirable segmentation result for inhomogeneous image segmentation. Two stage segmentation technique not only increases the accuracy but also eliminates the problem of initial contour existed in traditional local segmentation methods. The energy function of the proposed method uses both global and local terms incorporated with compacted geodesic edge term in an additive fashion which uses image gradient information to delineate obscured boundaries of objects inside an image. A Gaussian kernel is adapted for the regularization of the level set function and to avoid an expensive re-initialization. The experiments were carried out on synthetic and real images. Quantitative validations were performed on Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) 2015 and PH2 skin lesion database. The visual and quantitative comparisons will demonstrate the efficiency of the proposed method. [ABSTRACT FROM AUTHOR]

Microarray technology is important to simultaneously express multiple genes over a number of time points. Multiple classifier models, such as sparse representation (SR)-based method, have been developed to classify microarray gene expression data. These methods allocate the gene data points to different clusters. In this paper, we propose a novel collaborative representation (CR)-based classification with regularized least square to classify gene data. First, the CR codes a testing sample as a sparse linear combination of all training samples and then classifies the testing sample by evaluating which class leads to the minimum representation error. This CR-based classification approach is remarkably less complex than traditional classification methods but leads to very competitive classification results. In addition, compressive sensing approach is adopted to project the high-dimensional gene expression dataset to a lower-dimensional space which nearly contains the whole information. This compression without loss is beneficial to reduce the computational load. Experiments to detect subtypes of diseases, such as leukemia and autism spectrum disorders, are performed by analyzing the gene expression. The results show that the proposed CR-based algorithm exhibits significantly higher stability and accuracy than the traditional classifiers, such as support vector machine algorithm. [ABSTRACT FROM AUTHOR]

A closer association has been found between the microRNA-146a rs2910164 polymorphism and the risk of head and neck carcinoma in some molecular epidemiological studies. Recently two meta-analyses were performed to explore the relationship between miRNA-146a polymorphisms and the susceptibility of squamous cell carcinoma of the head and neck (SCCHN); however, they yielded conflicting results in susceptibility regarding ethnic variations. Hence, the present study was performed to explain the relationship between the miRNA-146a rs2910164 polymorphism and the risk of SCCHN development of Chinese patients. We retrieved databases and screened eligible papers up to March 10, 2017 and then we extracted the essential data. The subgroup analyses were also performed based on the tumor site, region, and genotyping means. Crude odds ratios (OR) at 95% confidence intervals (CI) were chosen to describe the strength of the association. As a result, 6 publications were included in our study which involved 8 independent case-control studies. A significant association was found between miR-146a rs2910164 polymorphisms and the risk of SCCHN in Chinese patients according to the overall data [CC+CG vs. GG: OR = 1.13; 95%CI = 1.00–1.29; CC vs. GG: OR = 1.19; 95%CI = 1.03–1.38]. According to the subgroup analysis based on tumor site, the risk of cancer was significantly increased among laryngeal cancer (dominant model: OR = 1.76, 95%CI = 1.26~2.46, P = 0.001; homozygote model: OR = 1.83, 95%CI = 1.25~2.67, P = 0.002) and nasopharyngeal carcinoma (homozygote model: OR = 1.41, 95%CI = 1.05~1.90, P = 0.022). In summary, variant alleles of miR-146a rs2910164 alleles may have an association with the increased risk of SCCHN in Chinese patients, and these associations differed based on tumor site. Further studies including a larger sample size will be necessary to clarify these results. [ABSTRACT FROM AUTHOR]

Integrative clustering is used to identify groups of samples by jointly analysing multiple datasets describing the same set of biological samples, such as gene expression, copy number, methylation etc. Most existing algorithms for integrative clustering assume that there is a shared consistent set of clusters across all datasets, and most of the data samples follow this structure. However in practice, the structure across heterogeneous datasets can be more varied, with clusters being joined in some datasets and separated in others. In this paper, we present a probabilistic clustering method to identify groups across datasets that do not share the same cluster structure. The proposed algorithm, Clusternomics, identifies groups of samples that share their global behaviour across heterogeneous datasets. The algorithm models clusters on the level of individual datasets, while also extracting global structure that arises from the local cluster assignments. Clusters on both the local and the global level are modelled using a hierarchical Dirichlet mixture model to identify structure on both levels. We evaluated the model both on simulated and on real-world datasets. The simulated data exemplifies datasets with varying degrees of common structure. In such a setting Clusternomics outperforms existing algorithms for integrative and consensus clustering. In a real-world application, we used the algorithm for cancer subtyping, identifying subtypes of cancer from heterogeneous datasets. We applied the algorithm to TCGA breast cancer dataset, integrating gene expression, miRNA expression, DNA methylation and proteomics. The algorithm extracted clinically meaningful clusters with significantly different survival probabilities. We also evaluated the algorithm on lung and kidney cancer TCGA datasets with high dimensionality, again showing clinically significant results and scalability of the algorithm. [ABSTRACT FROM AUTHOR]

Background: Published data on the relationship between matrix metalloproteinases (MMPs) polymorphisms and ovarian cancer risk have implicated inconclusive results. To evaluate the role of MMPs polymorphisms in ovarian cancer risk, a meta-analysis and systematic review were performed. Methods: MMPs polymorphisms which could be quantitatively synthesized were involved in meta-analysis. Five comparison models (homozygote model, heterozygote model, dominant model, recessive model, additive model) were carried out, a subgroup analysis was performed to clarify heterogeneity source. The remaining polymorphisms which could not be quantitatively synthesized were involved in systematic review. Results: 10 articles with 20 studies were included in this paper. Among those studies, 8 studies involving MMP1 rs1799750 and MMP3 rs34093618 could be meta-analyzed and 12 studies involving 12 polymorphisms could not. Meta-analysis showed that no associations were found between MMP1 rs1799750 (homozygote model: OR = 0.93, 95%CI = 0.70–1.23, POR = 0.60; heterozygote model: OR = 1.09, 95%CI = 0.78–1.54, POR = 0.61; dominant model: OR = 1.02, 95%CI = 0.83–1.25, POR = 0.84; recessive model: OR = 0.95, 95%CI = 0.75–1.21, POR = 0.67; additive model: OR = 1.00, 95%CI = 0.85–1.17, POR = 0.99), MMP3 rs34093618 (homozygote model: OR = 1.25, 95%CI = 0.70–2.24, POR = 0.46; heterozygote model: OR = 1.08, 95%CI = 0.51–2.31, POR = 0.84; dominant model: OR = 0.97, 95%CI = 0.68–1.38, POR = 0.85; recessive model: OR = 1.12, 95%CI = 0.69–1.80, POR = 0.65; additive model: OR = 1.01, 95%CI = 0.79–1.31, POR = 0.91) and ovarian cancer. Furthermore, similar results were detected in subgroup analysis. The systematic review on 12 polymorphisms suggested that MMP2 C-735T, MMP7 A-181G, MMP8 rs11225395, MMP9 rs6094237, MMP12 rs2276109, MMP20 rs2292730, MMP20 rs12278250, MMP20 rs9787933 might have a potential effect on ovarian cancer risk. Conclusions: In summary, polymorphisms of MMPs might not be associated with ovarian cancer risk. However, it is necessary to conduct more larger-scale, multicenter, and high-quality studies in the future. [ABSTRACT FROM AUTHOR]

Background: The association between height and lung cancer risk has been investigated by epidemiological studies but the results are inconsistent. This meta-analysis was to evaluate whether the height is associated with lung cancer. Methods: We identified relevant articles by searching the MEDLINE and EMBASE databases, and reviewed the reference lists of selected papers. A random effect model was used to calculate summary odds ratios (OR) and relative risk (RR) with 95% confidence intervals (95% CI). Publication bias was estimated using Egger’s regression asymmetry test. Results: We included a total 16 studies (15 prospective studies and one case–control study) on adult height and lung cancer risk in the meta-analysis. Overall, per 10-cm height increases were associated with increased risk of lung cancer (RR 1.06; 95% CI 1.03–1.09, I2 = 43.6%). Conclusions: In this meta-analysis, high adult height is related to increased lung cancer risk. Well-designed, large prospective studies are required to obtain a better indication of the relationship. [ABSTRACT FROM AUTHOR]

Renal cell carcinoma (RCC) comprises a heterogenous group of tumors. Traditionally, papillary RCC (pRCC) is associated with a favorable outcome compared to clear cell RCC (ccRCC), while other series report equivalent or worse prognosis. In this paper we comparatively evaluate outcome of pRCC versus ccRCC in two large multi-institutional databases (cohort study), including distribution of pRCC subtypes 1 and 2. Retrospective data of 1,943 surgically treated pRCC patients from 17 European/ North American centers between 1984–2015 were compared to 5,600 ccRCC patients from a database comprising 11 European/ North American centers (1984–2011). Median follow-up was 64.6 months. Differences between pRCC, subtypes, and ccRCC were compared with t-tests, Chi^2-tests, and exact Fisher tests. Cancer-specific mortality was analyzed with cumulative incidence curves and Cox cause-specific hazard models. The robustness of our results was examined with sensitivity analyses. We present that cancer-specific mortality rates and variables as stage, lymph node, and distant metastasis differ significantly between groups. Furthermore, we demonstrate that patients with non-metastatic pRCC had a significantly better cancer-specific mortality (HR 0.76, p = 0.007), when compared to ccRCC. Additionally, pRCC type 2 versus ccRCC exhibited no difference in cancer-specific mortality (HR 0.9, p = 0.722), whereas pRCC type 1 versus ccRCC displayed a risk of death reduced by 69% (p = 0.044). Taken together, outcome of pRCC versus ccRCC varies significantly in non-metastatic disease. Furthermore, pRCC type 2 exhibited no difference in cancer-specific mortality, whereas pRCC type 1 displayed a significantly reduced risk of death. Consequently, there is urgent need to respect histopathological entities and their subtypes, when assigning follow-up or targeted therapy to RCC patients. [ABSTRACT FROM AUTHOR]

In this paper we address the problem of automated grading of invasive breast carcinoma through the encoding of histological images as VLAD (Vector of Locally Aggregated Descriptors) representations on the Grassmann manifold. The proposed method considers each image as a set of multidimensional spatially-evolving signals that can be efficiently modeled through a higher-order linear dynamical systems analysis. Subsequently, each H&E (Hematoxylin and Eosin) stained breast cancer histological image is represented as a cloud of points on the Grassmann manifold, while a vector representation approach is applied aiming to aggregate the Grassmannian points based on a locality criterion on the manifold. To evaluate the efficiency of the proposed methodology, two datasets with different characteristics were used. More specifically, we created a new medium-sized dataset consisting of 300 annotated images (collected from 21 patients) of grades 1, 2 and 3, while we also provide experimental results using a large dataset, namely BreaKHis, containing 7,909 breast cancer histological images, collected from 82 patients, of both benign and malignant cases. Experimental results have shown that the proposed method outperforms a number of state of the art approaches providing average classification rates of 95.8% and 91.38% with our dataset and the BreaKHis dataset, respectively. [ABSTRACT FROM AUTHOR]

In the scientific literature, spin refers to reporting practices that distort the interpretation of results and mislead readers so that results are viewed in a more favourable light. The presence of spin in biomedical research can negatively impact the development of further studies, clinical practice, and health policies. This systematic review aims to explore the nature and prevalence of spin in the biomedical literature. We searched MEDLINE, PreMEDLINE, Embase, Scopus, and hand searched reference lists for all reports that included the measurement of spin in the biomedical literature for at least 1 outcome. Two independent coders extracted data on the characteristics of reports and their included studies and all spin-related outcomes. Results were grouped inductively into themes by spin-related outcome and are presented as a narrative synthesis. We used meta-analyses to analyse the association of spin with industry sponsorship of research. We included 35 reports, which investigated spin in clinical trials, observational studies, diagnostic accuracy studies, systematic reviews, and meta-analyses. The nature of spin varied according to study design. The highest (but also greatest) variability in the prevalence of spin was present in trials. Some of the common practices used to spin results included detracting from statistically nonsignificant results and inappropriately using causal language. Source of funding was hypothesised by a few authors to be a factor associated with spin; however, results were inconclusive, possibly due to the heterogeneity of the included papers. Further research is needed to assess the impact of spin on readers’ decision-making. Editors and peer reviewers should be familiar with the prevalence and manifestations of spin in their area of research in order to ensure accurate interpretation and dissemination of research. [ABSTRACT FROM AUTHOR]

The expression of Programmed cell Death Ligand 1 (PD-L1) is observed in many malignant tumors and is associated with poor prognosis including Gastric Cancer (GC). The relationship between PD-L1 expression and prognosis, however, is controversial in GC. This paper purports to use a meta-analysis to investigate the relationship between PD-L1 expression and prognosis in GC. For this study, the following databases were searched for articles published from June 2003 until February 2017: PubMed, EBSCO, Web of Science and Cochrane Library. The baseline information extracted were: authors, year of publication, country where the study was performed, study design, sample size, follow-up time, baseline characteristics of the study population, pathologic data, overall survival (OS). A total of 15 eligible studies covering 3291 patients were selected for a meta-analysis based on specified inclusion and exclusion criteria. The analysis showed that the expression level of PD-L1 was associated with the overall survival in GC (Hazard Ratio, HR = 1.46, 95%CI = 1.08–1.98, P = 0.01, random-effect). In addition to the above, subgroup analysis showed that GC patients with deeper tumor infiltration, positive lymph-node metastasis, positive venous invasion, Epstein-Barr virus infection positive (EBV+), Microsatellite Instability (MSI) are more likely to expression PD-L1. The results of this meta-analysis suggest that GC patients, specifically EBV+ and MSI, may be prime candidates for PD-1 directed therapy. These findings support anti-PD-L1/PD-1 antibodies as a kind of immunotherapy which is promising for GC. [ABSTRACT FROM AUTHOR]

With the recent technological developments a vast amount of high-throughput data has been profiled to understand the mechanism of complex diseases. The current bioinformatics challenge is to interpret the data and underlying biology, where efficient algorithms for analyzing heterogeneous high-throughput data using biological networks are becoming increasingly valuable. In this paper, we propose a software package based on the Prize-collecting Steiner Forest graph optimization approach. The PCSF package performs fast and user-friendly network analysis of high-throughput data by mapping the data onto a biological networks such as protein-protein interaction, gene-gene interaction or any other correlation or coexpression based networks. Using the interaction networks as a template, it determines high-confidence subnetworks relevant to the data, which potentially leads to predictions of functional units. It also interactively visualizes the resulting subnetwork with functional enrichment analysis. [ABSTRACT FROM AUTHOR]

Lung 4D computed tomography (4D-CT) plays an important role in high-precision radiotherapy because it characterizes respiratory motion, which is crucial for accurate target definition. However, the manual segmentation of a lung tumor is a heavy workload for doctors because of the large number of lung 4D-CT data slices. Meanwhile, tumor segmentation is still a notoriously challenging problem in computer-aided diagnosis. In this paper, we propose a new method based on an improved graph cut algorithm with context information constraint to find a convenient and robust approach of lung 4D-CT tumor segmentation. We combine all phases of the lung 4D-CT into a global graph, and construct a global energy function accordingly. The sub-graph is first constructed for each phase. A context cost term is enforced to achieve segmentation results in every phase by adding a context constraint between neighboring phases. A global energy function is finally constructed by combining all cost terms. The optimization is achieved by solving a max-flow/min-cut problem, which leads to simultaneous and robust segmentation of the tumor in all the lung 4D-CT phases. The effectiveness of our approach is validated through experiments on 10 different lung 4D-CT cases. The comparison with the graph cut without context constraint, the level set method and the graph cut with star shape prior demonstrates that the proposed method obtains more accurate and robust segmentation results. [ABSTRACT FROM AUTHOR]

Genetic risk prediction is an important goal in human genetics research and precision medicine. Accurate prediction models will have great impacts on both disease prevention and early treatment strategies. Despite the identification of thousands of disease-associated genetic variants through genome wide association studies (GWAS), genetic risk prediction accuracy remains moderate for most diseases, which is largely due to the challenges in both identifying all the functionally relevant variants and accurately estimating their effect sizes in the presence of linkage disequilibrium. In this paper, we introduce AnnoPred, a principled framework that leverages diverse types of genomic and epigenomic functional annotations in genetic risk prediction for complex diseases. AnnoPred is trained using GWAS summary statistics in a Bayesian framework in which we explicitly model various functional annotations and allow for linkage disequilibrium estimated from reference genotype data. Compared with state-of-the-art risk prediction methods, AnnoPred achieves consistently improved prediction accuracy in both extensive simulations and real data. [ABSTRACT FROM AUTHOR]

Background: LncRNA CCAT1 is significantly overexpressed in various types of cancers, suggesting that it might be associated with prognosis and clinicopathological features in patients with cancer. Methods: A comprehensive search was performed in Pubmed, Web of Science, OVID and CNKI databases. We also retrieved articles from other sources, such as retrieving from the reference lists of relevant articles. Eligible studies were included based on defined exclusion and inclusion criteria to perform a meta-analysis. STATA 14.0 was used to estimate pooled hazard ratios (HRs) with 95% confidence interval (95% CI), the heterogeneity among studies and publication bias to judge the prognostic value. Results: A total of 1587 patients from 11 eligible studies were included in the meta-analysis. The results showed that high expression level of CCAT1 was significantly associated with shorter overall survival in cancer patients (HR 2.335, 95% CI:1.551–3.517); in the subgroup analysis, region (China or UK), sample size (more or less than 100), type of cancer (digestive or non-digestive disease) and paper quality (score more or less than 7) did not alter the association between CCAT1 expression and cancer prognosis but preoperative treatment did. And CCAT1 expression was an independent prognostic marker for overall survival in patients with cancer (pooled HR 2.195, 95%CI:1.316–3.664) using Cox multivariate analyses. The clinicopathological parameters analysis further showed that increased expression level of CCAT1 was correlated with tumor size, lymph node metastasis, TNM stage, distant metastasis, microvascular invasion and capsular formation in relevant cancers. Conclusions: The meta-analysis results from present study suggested that increased expression level of CCAT1 was associated with poor prognosis and can serve as an independent biomarker. And the expression level of CCAT1 was associated with clinicopathological features in relevant cancers. [ABSTRACT FROM AUTHOR]

Blood oxygenation mapping by the means of optical oximetry is of significant importance in clinical trials. This paper uses hyperspectral imaging technology to obtain in vivo images for blood oxygenation detection. The experiment involves dorsal skin fold window chamber preparation which was built on adult (8–10 weeks of age) female BALB/c nu/nu mice and in vivo image acquisition which was performed by hyperspectral imaging system. To get the accurate spatial and spectral information of targets, an automatic registration scheme is proposed. An adaptive feature detection method which combines the local threshold method and the level-set filter is presented to extract target vessels. A reliable feature matching algorithm with the correlative information inherent in hyperspectral images is used to kick out the outliers. Then, the registration images are used for blood oxygenation mapping. Registration evaluation results show that most of the false matches are removed and the smooth and concentrated spectra are obtained. This intensity invariant feature detection with outliers-removing feature matching proves to be effective in hyperspectral vessel image registration. Therefore, in vivo hyperspectral imaging system by the assistance of the proposed registration scheme provides a technique for blood oxygenation research. [ABSTRACT FROM AUTHOR]

Background: Hepatocellular carcinoma (HCC) with bile duct tumor thrombus (BDTT) in the clinic is rare, and surgical treatment is currently considered the most effective treatment. However, the influence of BDTT on the prognosis of HCC patients who underwent surgery remains controversial in previous studies. Therefore, this paper uses meta-analysis method to elucidate this controversy. Methods: In this study, we conducted a literature search on databases PubMed, Embase and Web of Science from inception until September 2016. Each study was evaluated with Newcastle-Ottawa Scale (NOS). The pooled effect was calculated, and the association between BDTT and overall survival (OS) or disease-free survival (DFS) was reevaluated using meta-analysis for hazard ratio (HR) and 95% confidence interval (CI). Results: A total of 11 studies was included containing 5295 patients. The (HR) for OS and DFS was 3.21 and 1.81, 95%CI was 2.34–4.39 and 1.17–2.78 respectively. Conclusions: The results showed that HCC patients with BDTT had a worse prognosis than those without BDTT after hepatic resection or liver transplantation (LT). [ABSTRACT FROM AUTHOR]

Background: Previous studies have noted significant gender difference in the risk of liver cancer among hepatitis B chronic infection patients. Some indicated that it might be due to lifestyle-related differences. This paper tests whether or not such a gender discrepancy among the chronic hepatitis B population is confounded by lifestyle and environment related exposures. Methods: We retrieved a sample of 1863 participants from a prospective cohort in Haimen City, China in 2003. Liver disease severity was categorized as “normal”, “mild”, “moderate”, and “severe” based on a clinical diagnosis. Lifestyle and environmental exposures were measured by questionnaires. We used factor analysis and individual variables to represent lifestyle and environmental exposures. We applied the cumulative logit models to estimate the effect of gender on liver disease severity and how it was impacted by lifestyle and environmental exposures. Results: Gender and HBeAg positivity were independent risk factors for more severe liver disease. Compared to females, males were 2.08 times as likely to develop more severe liver disease (95% CI: 1.66–2.61). Participants who were HBeAg positivite were 2.19 times (95% CI: 1.61–2.96) as likely to develop more severe liver disease compared to those who were negative. Controlling for lifestyle and environmental exposures did not change these estimations. Conclusions: Males in the HBV infected population have an increased risk of severe liver disease. This gender effect is independent of the lifestyle and environmental exposures addressed in this study. Our findings support the hypothesis that gender discrepancies in HCC risk are attributable to intrinsic differences between males and females. [ABSTRACT FROM AUTHOR]

Fuzzy co-clustering extends co-clustering by assigning membership functions to both the objects and the features, and is helpful to improve clustering accurarcy of biomedical data. In this paper, we introduce a new fuzzy co-clustering algorithm based on information bottleneck named ibFCC. The ibFCC formulates an objective function which includes a distance function that employs information bottleneck theory to measure the distance between feature data point and the feature cluster centroid. Many experiments were conducted on five biomedical datasets, and the ibFCC was compared with such prominent fuzzy (co-)clustering algorithms as FCM, FCCM, RFCC and FCCI. Experimental results showed that ibFCC could yield high quality clusters and was better than all these methods in terms of accuracy. [ABSTRACT FROM AUTHOR]

One of the most accepted findings across psychology is that people are unrealistically optimistic in their judgments of comparative risk concerning future life events—they judge negative events as less likely to happen to themselves than to the average person. Harris and Hahn (2011), however, demonstrated how unbiased (non-optimistic) responses can result in data patterns commonly interpreted as indicative of optimism due to statistical artifacts. In the current paper, we report the results of 5 studies that control for these statistical confounds and observe no evidence for residual unrealistic optimism, even observing a ‘severity effect’ whereby severe outcomes were overestimated relative to neutral ones (Studies 3 & 4). We conclude that there is no evidence supporting an optimism interpretation of previous results using the prevalent comparison method. [ABSTRACT FROM AUTHOR]

Gene expression data analysis has paramount implications for gene treatments, cancer diagnosis and other domains. Clustering is an important and promising tool to analyze gene expression data. Gene expression data is often characterized by a large amount of genes but with limited samples, thus various projective clustering techniques and ensemble techniques have been suggested to combat with these challenges. However, it is rather challenging to synergy these two kinds of techniques together to avoid the curse of dimensionality problem and to boost the performance of gene expression data clustering. In this paper, we employ a projective clustering ensemble (PCE) to integrate the advantages of projective clustering and ensemble clustering, and to avoid the dilemma of combining multiple projective clusterings. Our experimental results on publicly available cancer gene expression data show PCE can improve the quality of clustering gene expression data by at least 4.5% (on average) than other related techniques, including dimensionality reduction based single clustering and ensemble approaches. The empirical study demonstrates that, to further boost the performance of clustering cancer gene expression data, it is necessary and promising to synergy projective clustering with ensemble clustering. PCE can serve as an effective alternative technique for clustering gene expression data. [ABSTRACT FROM AUTHOR]

Spatial scan statistics with circular or elliptic scanning windows are commonly used for cluster detection in various applications, such as the identification of geographical disease clusters from epidemiological data. It has been pointed out that the method may have difficulty in correctly identifying non-compact, arbitrarily shaped clusters. In this paper, we evaluated the Gini coefficient for detecting irregularly shaped clusters through a simulation study. The Gini coefficient, the use of which in spatial scan statistics was recently proposed, is a criterion measure for optimizing the maximum reported cluster size. Our simulation study results showed that using the Gini coefficient works better than the original spatial scan statistic for identifying irregularly shaped clusters, by reporting an optimized and refined collection of clusters rather than a single larger cluster. We have provided a real data example that seems to support the simulation results. We think that using the Gini coefficient in spatial scan statistics can be helpful for the detection of irregularly shaped clusters. [ABSTRACT FROM AUTHOR]

Stain colour estimation is a prominent factor of the analysis pipeline in most of histology image processing algorithms. Providing a reliable and efficient stain colour deconvolution approach is fundamental for robust algorithm. In this paper, we propose a novel method for stain colour deconvolution of histology images. This approach statistically analyses the multi-resolutional representation of the image to separate the independent observations out of the correlated ones. We then estimate the stain mixing matrix using filtered uncorrelated data. We conducted an extensive set of experiments to compare the proposed method to the recent state of the art methods and demonstrate the robustness of this approach using three different datasets of scanned slides, prepared in different labs using different scanners. [ABSTRACT FROM AUTHOR]