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Studies on 3D-printed porous bone scaffolds mostly focus on materials or structural parameters, while the repair of large femoral defects needs to select appropriate structural parameters according to the needs of different parts. In this paper, a kind of stiffness gradient scaffold design idea is proposed. Different structures are selected according to the different functions of different parts of the scaffold. At the same time, an integrated fixation device is designed to fix the scaffold. Finite element method was used to analyze the stress and strain of homogeneous scaffolds and the stiffness gradient scaffolds, and the relative displacement and stress between stiffness gradient scaffolds and bone in the case of integrated fixation and steel plate fixation. The results showed that the stress distribution of the stiffness gradient scaffolds was more uniform, and the strain of host bone tissue was changed greatly, which was beneficial to the growth of bone tissue. The integrated fixation method is more stable, less stress and evenly distributed. Therefore, the integrated fixation device combined with the design of stiffness gradient can repair the large femoral bone defect well. [ABSTRACT FROM AUTHOR]

Background: A priori sample size calculation requires an a priori estimate of the size of the effect. An incorrect estimate may result in a sample size that is too low to detect effects or that is unnecessarily high. An alternative to a priori sample size calculation is Bayesian updating, a procedure that allows increasing sample size during the course of a study until sufficient support for a hypothesis is achieved. This procedure does not require and a priori estimate of the effect size. This paper introduces Bayesian updating to researchers in the biomedical field and presents a simulation study that gives insight in sample sizes that may be expected for two-group comparisons.Methods: Bayesian updating uses the Bayes factor, which quantifies the degree of support for a hypothesis versus another one given the data. It can be re-calculated each time new subjects are added, without the need to correct for multiple interim analyses. A simulation study was conducted to study what sample size may be expected and how large the error rate is, that is, how often the Bayes factor shows most support for the hypothesis that was not used to generate the data.Results: The results of the simulation study are presented in a Shiny app and summarized in this paper. Lower sample size is expected when the effect size is larger and the required degree of support is lower. However, larger error rates may be observed when a low degree of support is required and/or when the sample size at the start of the study is small. Furthermore, it may occur sufficient support for neither hypothesis is achieved when the sample size is bounded by a maximum.Conclusions: Bayesian updating is a useful alternative to a priori sample size calculation, especially so in studies where additional subjects can be recruited easily and data become available in a limited amount of time. The results of the simulation study show how large a sample size can be expected and how large the error rate is. [ABSTRACT FROM AUTHOR]

Background: Posterior wall acetabular fractures remain one of the most difficult fracture injuries to treat. Accurate assessment of fracture characteristics and appropriate preoperative surgical strategies are essential for excellent reduction. This paper evaluates the feasibility and effectiveness of a one-stop computerized virtual planning system for the surgical management of posterior wall acetabular fractures. Methods: 52 cases of posterior wall acetabular fractures treated surgically were selected in our department between January 2015 and December 2020 for retrospective analysis. 52 cases were classified into group A (25 patients) and group B (27 patients) according to whether computerized virtual planning procedures were performed preoperatively. In group A, virtual surgical simulation was conducted using a one-stop computerized planning system preoperatively. In group B, traditional surgery was employed. Reduction quality, surgical time, blood loss, hip function, complications, and instrumentation time were compared between the two groups. Results: The actual surgery for all patients in group A was essentially the same as the virtual surgery before the operation. Compared to group B, patients in group A had markedly shorter surgical time (−43 min), shorter instrumentation time (−20 min), and less intraoperative blood loss (−130 ml). However, no significant statistical difference was observed in reduction quality and hip function. The complication rate was slightly lower in group A (4/25) than in group B (7/27), without a significant difference. Conclusion: The one-stop computerized virtual planning system is a highly effective, user-friendly and educational tool for allowing the cost-efficient surgical simulation of posterior wall acetabular fractures and providing a more individualized therapeutic schedule. The one-stop computerized planning system is feasible to treat posterior wall acetabular fractures, which is an effective method than the conventional treatment of posterior wall acetabular fractures. Trial registration: retrospective registration. [ABSTRACT FROM AUTHOR]

Background: Current dose-finding designs for phase I clinical trials can correctly select the MTD in a range of 30-80% depending on various conditions based on a sample of 30 subjects. However, there is still an unmet need for efficiency and cost saving.Methods: We propose a novel dose-finding design based on Bayesian stochastic approximation. The design features utilization of dose level information through local adaptive modelling and free assumption of toxicity probabilities and hyper-parameters. It allows a flexible target toxicity rate and varying cohort size. And we extend it to accommodate historical information via prior effective sample size. We compare the proposed design to some commonly used methods in terms of accuracy and safety by simulation.Results: On average, our design can improve the percentage of correct selection to about 60% when the MTD resides at a early or middle position in the search domain and perform comparably to other competitive methods otherwise. A free online software package is provided to facilitate the application, where a simple decision tree for the design can be pre-printed beforehand.Conclusion: The paper proposes a novel dose-finding design for phase I clinical trials. Applying the design to future cancer trials can greatly improve the efficiency, consequently save cost and shorten the development period. [ABSTRACT FROM AUTHOR]

Background: The minimum variance (MV) beamformer can significantly improve the image resolution in ultrasound imaging, but it has limited performance in noise reduction. We recently proposed the covariance matrix-based statistical beamforming (CMSB) for medical ultrasound imaging to reduce sidelobes and incoherent clutter.Methods: In this paper, we aim to improve the imaging performance of the MV beamformer by introducing a new pixel-based adaptive weighting approach based on CMSB, which is named as covariance matrix-based adaptive weighting (CMSAW). The proposed CMSAW estimates the mean-to-standard-deviation ratio (MSR) of a modified covariance matrix reconstructed by adaptive spatial smoothing, rotary averaging, and diagonal reducing. Moreover, adaptive diagonal reducing based on the aperture coherence is introduced in CMSAW to enhance the performance in speckle preservation.Results: The proposed CMSAW-weighted MV (CMSAW-MV) was validated through simulation, phantom experiments, and in vivo studies. The phantom experimental results show that CMSAW-MV obtains resolution improvement of 21.3% and simultaneously achieves average improvements of 96.4% and 71.8% in average contrast and generalized contrast-to-noise ratio (gCNR) for anechoic cyst, respectively, compared with MV. in vivo studies indicate that CMSAW-MV improves the noise reduction performance of MV beamformer.Conclusion: Simulation, experimental, and in vivo results all show that CMSAW-MV can improve resolution and suppress sidelobes and incoherent clutter and noise. These results demonstrate the effectiveness of CMSAW in improving the imaging performance of MV beamformer. Moreover, the proposed CMSAW with a computational complexity of [Formula: see text] has the potential to be implemented in real time using the graphics processing unit. [ABSTRACT FROM AUTHOR]

Background: The overcrowded patients, which cause the long waiting time in public hospitals, become significant problems that affect patient satisfaction toward the hospital. Particularly, the bottleneck usually happens at front-end departments (e.g., the triage and medical record department) as every patient is firstly required to visit these departments. The problem is mainly caused by ineffective resource management. In order to support decision making in the resource management at front-end departments, this paper proposes a framework using simulation and multi-objective optimization techniques considering both operating cost and patient satisfaction.Methods: To develop the framework, first, the timestamp of patient arrival time at each station was collected at the triage and medical record department of Thammasat University Hospital in Thailand. A patient satisfaction assessment method was used to convert the time spend into a satisfaction score. Then, the simulation model was built from the current situation of the hospital and was applied scenario analyses for the model improvement. The models were verified and validated. The weighted max-min for fuzzy multi-objective optimization was done by minimizing the operating cost and maximizing the patient satisfaction score. The operating costs and patient satisfaction scores from various scenarios were statistically compared. Finally, a decision-making guideline was proposed to support suitable resource management at the front-end departments of the hospital.Result: The three scenarios of the simulation model were built (i.e., a real situation, a one-stop service, and partially shared resources) and ensured to be verified and valid. The optimized results were compared and grouped into three situations which are (1) remain the same satisfaction score but decrease the cost (cost decreased by 2.8%) (2) remain the same satisfaction score but increase the cost (cost increased up to 80%) and (3) decrease the satisfaction score and decrease the cost (satisfaction decreased up to 82% and cost decreased up to 59%). According to the guideline, the situations 1 and 3 were recommended to use in the improvement and the situation 2 was rejected.Conclusion: This research demonstrates the resource management framework for the front-end department of the hospital. The experimental results imply that the framework can be used to support the decision making in resource management and used to reduce the risk of applying a non-improvement model in a real situation. [ABSTRACT FROM AUTHOR]

Background: Traditional approaches to identify missing mechanisms are usually based on the hypothesis test and confronted with both theoretical and practical challenges. It has been proved that the Bayesian network is powerful in integrating, analyzing and visualizing information, and some previous researches have verified the promising features of Bayesian network to deal with the aforementioned challenges in missing mechanism identification. Based on the above reasons, this paper explores the application of Bayesian network to the identification of missing mechanisms for the first time, and proposes a new method, the Bayesian network-based missing mechanism identification (BN-MMI) method, to identify missing mechanism in medical research.Methods: The procedure of BN-MMI method consists three easy-to-implement steps: estimating the missing data structure by the Bayesian network; assessing the credibility of the estimated missing data structure; and identifying the missing mechanism from the estimated missing data structure. The BN-MMI method is verified by simulation research and empirical research.Results: The simulation study verified the validity, consistency and robustness of BN-MMI method, and indicated its outperformance in contrast to the traditional logistic regression method. In addition, the empirical study illustrated the applicability of BN-MMI method in the real world by an example of medical record data.Conclusions: It was confirmed that the BN-MMI method itself, together with human knowledge and expertise, could identify the missing mechanisms according to the probabilistic dependence/independence relations among variables of interest. At the same time, our research shed light upon the potential application of BN-MMI method to a broader range of missing data issues in medical studies. [ABSTRACT FROM AUTHOR]

Background: In many clinical applications, evolution of a longitudinal marker is censored by an event occurrence, and, symmetrically, event occurrence can be influenced by the longitudinal marker evolution. In such frameworks joint modeling is of high interest. The Joint Latent Class Model (JLCM) allows to stratify the population into groups (classes) of patients that are homogeneous both with respect to the evolution of a longitudinal marker and to the occurrence of an event; this model is widely employed in real-life applications. However, the finite sample-size properties of this model remain poorly explored.Methods: In the present paper, a simulation study is carried out to assess the impact of the number of individuals, of the censoring rate and of the degree of class separation on the finite sample size properties of the JLCM. A real-life application from the neurology domain is also presented. This study assesses the precision of class membership prediction and the impact of covariates omission on the model parameter estimates.Results: Simulation study reveals some departures from normality of the model for survival sub-model parameters. The censoring rate and the number of individuals impact the relative bias of parameters, especially when the classes are weakly distinguished. In real-data application the observed heterogeneity on individual profiles in terms of a longitudinal marker evolution and of the event occurrence remains after adjusting to clinically relevant and available covariates; CONCLUSION: The JLCM properties have been evaluated. We have illustrated the discovery in practice and highlights the usefulness of the joint models with latent classes in this kind of data even with pre-specified factors. We made some recommendations for the use of this model and for future research. [ABSTRACT FROM AUTHOR]

Background: The influenza surveillance has been received much attention in public health area. For the cases with excessive zeroes, the zero-inflated Poisson process is widely used. However, the traditional control charts based on zero-inflated Poisson model, ignore the association between influenza cases and risk factors, and thus may lead to unexpected mistakes when implementing monitoring charts.Method: In this paper, we proposed risk-adjusted zero-inflated Poisson cumulative sum control charts, in which the risk factors were put to adjust the risk of influenza and the adjustment was made by zero-inflated Poisson regression. We respectively proposed the control chart monitoring the parameters individually and simultaneously.Results: The performance of our proposed risk-adjusted zero-inflated Poisson cumulative sum control chart was evaluated and compared with the unadjusted standard cumulative sum control charts in simulation studies. The results show that for different distribution of impact factors and different coefficients, the risk-adjusted cumulative sum charts can generate much less false alarm than the standard ones. Finally, the influenza surveillance data from Hong Kong is used to illustrate the application of the proposed chart.Conclusions: Our results suggest that the adjusted cumulative sum control chart we proposed is more accurate and credible than the unadjusted standard control charts because of the lower false alarm rate of the adjusted ones. Even the unadjusted control charts may signal a little faster than the adjusted ones, the alarm they raise may have low credibility since they also raise alarm frequently even the processes are in control. Thus we suggest using the risk-adjusted cumulative sum control charts to monitor the influenza surveillance data to alert accurately, credibly and relatively quickly. [ABSTRACT FROM AUTHOR]

Background: This paper deals with the location of emergency medical stations where ambulances waiting to be dispatched are parked. The literature reports a lot of mathematical programming models used to optimize station locations. Most studies evaluate the models only analytically applying the same simplifying assumptions that were used in the modelling phase. In addition, they concentrate on systems operating one type of emergency units in homogeneous urban areas. The goal of our study is to identify which optimization criterion the emergency medical service (EMS) outcomes benefit from the most and which model should be used to design tiered systems in large urban–rural areas. Methods: A bi-criteria mathematical programming model is proposed. The criteria include the accessibility of high-priority patients within a short time limit and average response time to all patients. This model is being compared to the p-median model with a single response time objective and to a hierarchical pq-median model that considers two different vehicle types. A detailed computer simulation model is used to evaluate the solutions. The methodology is verified in the conditions of the Slovak Republic using real historical data on 149,474 ambulance trips performed in 2015. Results: All mathematical models improve EMS performance by relocating some stations compared to the current distribution. The best results are achieved by the hierarchical median-type model. The average response time is reduced by 58 s, the number of calls responded to within 15 min is increased by 5% and the number of high-priority calls responded to within 8 min by 6%. Conclusions: The EMS systems operating in heterogeneous areas should be designed to minimize response times, and not to maximize the number of calls served within a given time limit. [ABSTRACT FROM AUTHOR]

Background: Accurately counting maize tassels is important for monitoring the growth status of maize plants. This tedious task, however, is still mainly done by manual efforts. In the context of modern plant phenotyping, automating this task is required to meet the need of large-scale analysis of genotype and phenotype. In recent years, computer vision technologies have experienced a significant breakthrough due to the emergence of large-scale datasets and increased computational resources. Naturally image-based approaches have also received much attention in plantrelated studies. Yet a fact is that most image-based systems for plant phenotyping are deployed under controlled laboratory environment. When transferring the application scenario to unconstrained in-field conditions, intrinsic and extrinsic variations in the wild pose great challenges for accurate counting of maize tassels, which goes beyond the ability of conventional image processing techniques. This calls for further robust computer vision approaches to address in-field variations. Results: This paper studies the in-field counting problem of maize tassels. To our knowledge, this is the first time that a plant-related counting problem is considered using computer vision technologies under unconstrained field-based environment. With 361 field images collected in four experimental fields across China between 2010 and 2015 and corresponding manually-labelled dotted annotations, a novel Maize Tassels Counting (MTC) dataset is created and will be released with this paper. To alleviate the in-field challenges, a deep convolutional neural network-based approach termed TasselNet is proposed. TasselNet can achieve good adaptability to in-field variations via modelling the local visual characteristics of field images and regressing the local counts of maize tassels. Extensive results on the MTC dataset demonstrate that TasselNet outperforms other state-of-the-art approaches by large margins and achieves the overall best counting performance, with a mean absolute error of 6.6 and a mean squared error of 9.6 averaged over 8 test sequences. Conclusions: TasselNet can achieve robust in-field counting of maize tassels with a relatively high degree of accuracy. Our experimental evaluations also suggest several good practices for practitioners working on maize-tassel-like counting problems. It is worth noting that, though the counting errors have been greatly reduced by TasselNet, infield counting of maize tassels remains an open and unsolved problem. [ABSTRACT FROM AUTHOR]

Background: The characterization of protein-peptide interactions is a challenge for computational molecular docking. Protein-peptide docking tools face at least two major difficulties: (1) efficient sampling of large-scale conformational changes induced by binding and (2) selection of the best models from a large set of predicted structures. In this paper, we merge an efficient sampling technique with external information about side-chain contacts to sample and select the best possible models.Methods: In this paper we test a new protocol that uses information about side-chain contacts in CABS-dock protein-peptide docking. As shown in our recent studies, CABS-dock enables efficient modeling of large-scale conformational changes without knowledge about the binding site. However, the resulting set of binding sites and poses is in many cases highly diverse and difficult to score.Results: As we demonstrate here, information about a single side-chain contact can significantly improve the prediction accuracy. Importantly, the imposed constraints for side-chain contacts are quite soft. Therefore, the developed protocol does not require precise contact information and ensures large-scale peptide flexibility in the broad contact area.Conclusions: The demonstrated protocol provides the extension of the CABS-dock method that can be practically used in the structure prediction of protein-peptide complexes guided by the knowledge of the binding interface. [ABSTRACT FROM AUTHOR]

Background: With the invention of fitness trackers, it has been possible to continuously monitor a user's biometric data such as heart rates, number of footsteps taken, and amount of calories burned. This paper names the time series of these three types of biometric data, the user's "activeness", and investigates the feasibility in modeling and predicting the long-term activeness of the user.Methods: The dataset used in this study consisted of several months of biometric time-series data gathered by seven users independently. Four recurrent neural network (RNN) architectures-as well as a deep neural network and a simple regression model-were proposed to investigate the performance on predicting the activeness of the user under various length-related hyper-parameter settings. In addition, the learned model was tested to predict the time period when the user's activeness falls below a certain threshold.Results: A preliminary experimental result shows that each type of activeness data exhibited a short-term autocorrelation; and among the three types of data, the consumed calories and the number of footsteps were positively correlated, while the heart rate data showed almost no correlation with neither of them. It is probably due to this characteristic of the dataset that although the RNN models produced the best results on modeling the user's activeness, the difference was marginal; and other baseline models, especially the linear regression model, performed quite admirably as well. Further experimental results show that it is feasible to predict a user's future activeness with precision, for example, a trained RNN model could predict-with the precision of 84%-when the user would be less active within the next hour given the latest 15 min of his activeness data.Conclusions: This paper defines and investigates the notion of a user's "activeness", and shows that forecasting the long-term activeness of the user is indeed possible. Such information can be utilized by a health-related application to proactively recommend suitable events or services to the user. [ABSTRACT FROM AUTHOR]

Background: Gene networks in living cells can change depending on various conditions such as caused by different environments, tissue types, disease states, and development stages. Identifying the differential changes in gene networks is very important to understand molecular basis of various biological process. While existing algorithms can be used to infer two gene networks separately from gene expression data under two different conditions, and then to identify network changes, such an approach does not exploit the similarity between two gene networks, and it is thus suboptimal. A desirable approach would be clearly to infer two gene networks jointly, which can yield improved estimates of network changes. Results: In this paper, we developed a proximal gradient algorithm for differential network (ProGAdNet) inference, that jointly infers two gene networks under different conditions and then identifies changes in the network structure. Computer simulations demonstrated that our ProGAdNet outperformed existing algorithms in terms of inference accuracy, and was much faster than a similar approach for joint inference of gene networks. Gene expression data of breast tumors and normal tissues in the TCGA database were analyzed with our ProGAdNet, and revealed that 268 genes were involved in the changed network edges. Gene set enrichment analysis identified a significant number of gene sets related to breast cancer or other types of cancer that are enriched in this set of 268 genes. Network analysis of the kidney cancer data in the TCGA database with ProGAdNet also identified a set of genes involved in network changes, and the majority of the top genes identified have been reported in the literature to be implicated in kidney cancer. These results corroborated that the gene sets identified by ProGAdNet were very informative about the cancer disease status. A software package implementing the ProGAdNet, computer simulations, and real data analysis is available as Additional file 1. Conclusion: With its superior performance over existing algorithms, ProGAdNet provides a valuable tool for finding changes in gene networks, which may aid the discovery of gene-gene interactions changed under different conditions. [ABSTRACT FROM AUTHOR]

Background: Data from genome-wide association studies (GWASs) have been used to estimate the heritability of human complex traits in recent years. Existing methods are based on the linear mixed model, with the assumption that the genetic effects are random variables, which is opposite to the fixed effect assumption embedded in the framework of quantitative genetics theory. Moreover, heritability estimators provided by existing methods may have large standard errors, which calls for the development of reliable and accurate methods to estimate heritability. Results: In this paper, we first investigate the influences of the fixed and random effect assumption on heritability estimation, and prove that these two assumptions are equivalent under mild conditions in the theoretical aspect. Second, we propose a two-stage strategy by first performing sparse regularization via cross-validated elastic net, and then applying variance estimation methods to construct reliable heritability estimations. Results on both simulated data and real data show that our strategy achieves a considerable reduction in the standard error while reserving the accuracy. Conclusions: The proposed strategy allows for a reliable and accurate heritability estimation using GWAS data. It shows the promising future that reliable estimations can still be obtained with even a relatively restricted sample size, and should be especially useful for large-scale heritability analyses in the genomics era. [ABSTRACT FROM AUTHOR]

Background: For many practical hypothesis testing (H-T) applications, the data are correlated and/or with heterogeneous variance structure. The regression t-test for weighted linear mixed-effects regression (LMER) is a legitimate choice because it accounts for complex covariance structure; however, high computational costs and occasional convergence issues make it impractical for analyzing high-throughput data. In this paper, we propose computationally efficient parametric and semiparametric tests based on a set of specialized matrix techniques dubbed as the PB-transformation. The PB-transformation has two advantages: 1. The PB-transformed data will have a scalar variance-covariance matrix. 2. The original H-T problem will be reduced to an equivalent one-sample H-T problem. The transformed problem can then be approached by either the one-sample Student's t-test or Wilcoxon signed rank test. Results: In simulation studies, the proposed methods outperform commonly used alternative methods under both normal and double exponential distributions. In particular, the PB-transformed t-test produces notably better results than the weighted LMER test, especially in the high correlation case, using only a small fraction of computational cost (3 versus 933 s). We apply these two methods to a set of RNA-seq gene expression data collected in a breast cancer study. Pathway analyses show that the PB-transformed t-test reveals more biologically relevant findings in relation to breast cancer than the weighted LMER test. Conclusions: As fast and numerically stable replacements for the weighted LMER test, the PB-transformed tests are especially suitable for "messy" high-throughput data that include both independent and matched/repeated samples. By using our method, the practitioners no longer have to choose between using partial data (applying paired tests to only the matched samples) or ignoring the correlation in the data (applying two sample tests to data with some correlated samples). Our method is implemented as an R package 'PBtest' and is available at https://github.com/yunzhang813/PBtest-R-Package. [ABSTRACT FROM AUTHOR]

Background: Ultrasound computed tomography (USCT) is usually realized with a ring array. It can provide better imaging performance and more tissue information by emitting and receiving the ultrasound signal in different directions simultaneously. However, USCT imaging is usually applied with the synthetic aperture (SA) emission method, which leads to a long scanning time with a large number of elements on the ring array. The echo image can provide the structural information, and has a higher resolution than maps of other parameters in USCT. Hence, we proposed plane wave (PW) imaging for ring array to acquire the echo wave and reduce the scanning time considerably.Results: In this paper, an emitting and receiving process was proposed to realize plane wave imaging with a ring array. With the proposed scanning method, the number of emission events can be reduced greatly. A beamforming method based on the eigenspace-based minimum variance (ESBMV) was also combined with the scanning method. With ESBMV beamformer, the resolution and contrast ratio of reconstruction result can be maintained or even improved under a fewer-emissions condition. We validated the method using both computer simulations with Field II and phantom experiments with a ring array of 512 elements. The Verasonics® system was used to transmit and receive the ultrasound signal in the phantom experiments.Conclusions: According to the results of the experiments, the imaging results will have a better contrast ratio with a higher emitting energy. Additionally, the scanning time with the proposed method can be only one-tenth of that with the SA emission method, while the echo imaging performance still remains at a similar level or even better. [ABSTRACT FROM AUTHOR]

Background: Wolbachia invasion has been proved to be a promising alternative for controlling vector-borne diseases, particularly Dengue fever. Creating computer models that can provide insight into how vector population modification can be achieved under different conditions would be most valuable for assessing the efficacy of control strategies for this disease. Methods: In this paper, we present a computer model that simulates the behavior of native mosquito populations after the introduction of mosquitoes infected with the Wolbachia bacteria. We studied how different factors such as fecundity, fitness cost of infection, migration rates, number of populations, population size, and number of introduced infected mosquitoes affect the spread of the Wolbachia bacteria among native mosquito populations. Results: Two main scenarios of the island model are presented in this paper, with infected mosquitoes introduced into the largest source population and peripheral populations. Overall, the results are promising; Wolbachia infection spreads among native populations and the computer model is capable of reproducing the results obtained by mathematical models and field experiments. Conclusions: Computer models can be very useful for gaining insight into how Wolbachia invasion works and are a promising alternative for complementing experimental and mathematical approaches for vector-borne disease control. [ABSTRACT FROM AUTHOR]

Computational modeling techniques are playing increasingly important roles in advancing a systems-level mechanistic understanding of biological processes. Computer simulations guide and underpin experimental and clinical efforts. This study presents ENteric Immune Simulator (ENISI), a multiscale modeling tool for modeling the mucosal immune responses. ENISI's modeling environment can simulate in silico experiments from molecular signaling pathways to tissue level events such as tissue lesion formation. ENISI's architecture integrates multiple modeling technologies including ABM (agent-based modeling), ODE (ordinary differential equations), SDE (stochastic modeling equations), and PDE (partial differential equations). This paper focuses on the implementation and developmental challenges of ENISI. A multiscale model of mucosal immune responses during colonic inflammation, including CD4+ T cell differentiation and tissue level cell-cell interactions was developed to illustrate the capabilities, power and scope of ENISI MSM. Background: Computational techniques are becoming increasingly powerful and modeling tools for biological systems are of greater needs. Biological systems are inherently multiscale, from molecules to tissues and from nano-seconds to a lifespan of several years or decades. ENISI MSM integrates multiple modeling technologies to understand immunological processes from signaling pathways within cells to lesion formation at the tissue level. This paper examines and summarizes the technical details of ENISI, from its initial version to its latest cutting-edge implementation. Implementation: Object-oriented programming approach is adopted to develop a suite of tools based on ENISI. Multiple modeling technologies are integrated to visualize tissues, cells as well as proteins; furthermore, performance matching between the scales is addressed. Conclusion: We used ENISI MSM for developing predictive multiscale models of the mucosal immune system during gut inflammation. Our modeling predictions dissect the mechanisms by which effector CD4+ T cell responses contribute to tissue damage in the gut mucosa following immune dysregulation. [ABSTRACT FROM AUTHOR]

Background: Physical inactivity is widely recognized as one of the leading causes of mortality, and transport accounts for a large part of people's daily physical activity. This study develops a simulation approach to evaluate the impact of the Ile-de-France Urban Mobility Plan (2010-2020) on physical activity, under the hypothesis that the intended transport mode shifts are realized. Methods: Based on the Global Transport Survey (2010, n = 21,332) and on the RECORD GPS Study (2012-2013, n =229) from the French capital region of Paris (Ile-de-France), a simulation method was designed and tested. The simulation method used accelerometer data and random forest models to predict the impact of the transport mode shifts anticipated in the Mobility Plan on transport-related moderate-to-vigorous physical activity (T-MVPA). The transport mode shifts include less private motorized trips in favor of more public transport, walking, and biking trips. Results: The simulation model indicated a mean predicted increase of 2 min per day of T-MVPA, in case the intended transport mode shifts in the Ile-de-France Urban Mobility Plan were realized. The positive effect of the transport mode shifts on T-MVPA would, however, be larger for people with a higher level of education. This heterogeneity in the positive effect would further increase the existing inequality in transport-related physical activity by educational level. Conclusions: The method presented in this paper showed a significant increase in transport-related physical activity in case the intended mode shifts in the Ile-de-France Urban Mobility Plan were realized. This simulation method could be applied on other important health outcomes, such as exposure to noise or air pollution, making it a useful tool to anticipate the health impact of transport interventions or policies. [ABSTRACT FROM AUTHOR]

Background: Nowadays, sleep quality is one of the most important measures of healthy life, especially considering the huge number of sleep-related disorders. Identifying sleep stages using polysomnographic (PSG) signals is the traditional way of assessing sleep quality. However, the manual process of sleep stage classification is time-consuming, subjective and costly. Therefore, in order to improve the accuracy and efficiency of the sleep stage classification, researchers have been trying to develop automatic classification algorithms. Automatic sleep stage classification mainly consists of three steps: pre-processing, feature extraction and classification. Since classification accuracy is deeply affected by the extracted features, a poor feature vector will adversely affect the classifier and eventually lead to low classification accuracy. Therefore, special attention should be given to the feature extraction and selection process.Methods: In this paper the performance of seven feature selection methods, as well as two feature rank aggregation methods, were compared. Pz-Oz EEG, horizontal EOG and submental chin EMG recordings of 22 healthy males and females were used. A comprehensive feature set including 49 features was extracted from these recordings. The extracted features are among the most common and effective features used in sleep stage classification from temporal, spectral, entropy-based and nonlinear categories. The feature selection methods were evaluated and compared using three criteria: classification accuracy, stability, and similarity.Results: Simulation results show that MRMR-MID achieves the highest classification performance while Fisher method provides the most stable ranking. In our simulations, the performance of the aggregation methods was in the average level, although they are known to generate more stable results and better accuracy.Conclusions: The Borda and RRA rank aggregation methods could not outperform significantly the conventional feature ranking methods. Among conventional methods, some of them slightly performed better than others, although the choice of a suitable technique is dependent on the computational complexity and accuracy requirements of the user. [ABSTRACT FROM AUTHOR]

Background: The sample size required to power a study to a nominal level in a paired comparative diagnostic accuracy study, i.e. studies in which the diagnostic accuracy of two testing procedures is compared relative to a gold standard, depends on the conditional dependence between the two tests - the lower the dependence the greater the sample size required. A priori, we usually do not know the dependence between the two tests and thus cannot determine the exact sample size required. One option is to use the implied sample size for the maximal negative dependence, giving the largest possible sample size. However, this is potentially wasteful of resources and unnecessarily burdensome on study participants as the study is likely to be overpowered. A more accurate estimate of the sample size can be determined at a planned interim analysis point where the sample size is re-estimated.Methods: This paper discusses a sample size estimation and re-estimation method based on the maximum likelihood estimates, under an implied multinomial model, of the observed values of conditional dependence between the two tests and, if required, prevalence, at a planned interim. The method is illustrated by comparing the accuracy of two procedures for the detection of pancreatic cancer, one procedure using the standard battery of tests, and the other using the standard battery with the addition of a PET/CT scan all relative to the gold standard of a cell biopsy. Simulation of the proposed method illustrates its robustness under various conditions.Results: The results show that the type I error rate of the overall experiment is stable using our suggested method and that the type II error rate is close to or above nominal. Furthermore, the instances in which the type II error rate is above nominal are in the situations where the lowest sample size is required, meaning a lower impact on the actual number of participants recruited.Conclusion: We recommend multinomial model maximum likelihood estimation of the conditional dependence between paired diagnostic accuracy tests at an interim to reduce the number of participants required to power the study to at least the nominal level.Trial Registration: ISRCTN ISRCTN73852054 . Registered 9th of January 2015. Retrospectively registered. [ABSTRACT FROM AUTHOR]

Background: In photoacoustic tomography (PAT), total variation (TV) based iteration algorithm is reported to have a good performance in PAT image reconstruction. However, classical TV based algorithm fails to preserve the edges and texture details of the image because it is not sensitive to the direction of the image. Therefore, it is of great significance to develop a new PAT reconstruction algorithm to effectively solve the drawback of TV.Methods: In this paper, a directional total variation with adaptive directivity (DDTV) model-based PAT image reconstruction algorithm, which weightedly sums the image gradients based on the spatially varying directivity pattern of the image is proposed to overcome the shortcomings of TV. The orientation field of the image is adaptively estimated through a gradient-based approach. The image gradients are weighted at every pixel based on both its anisotropic direction and another parameter, which evaluates the estimated orientation field reliability. An efficient algorithm is derived to solve the iteration problem associated with DDTV and possessing directivity of the image adaptively updated for each iteration step.Results and Conclusion: Several texture images with various directivity patterns are chosen as the phantoms for the numerical simulations. The 180-, 90- and 30-view circular scans are conducted. Results obtained show that the DDTV-based PAT reconstructed algorithm outperforms the filtered back-projection method (FBP) and TV algorithms in the quality of reconstructed images with the peak signal-to-noise rations (PSNR) exceeding those of TV and FBP by about 10 and 18 dB, respectively, for all cases. The Shepp-Logan phantom is studied with further discussion of multimode scanning, convergence speed, robustness and universality aspects. In-vitro experiments are performed for both the sparse-view circular scanning and linear scanning. The results further prove the effectiveness of the DDTV, which shows better results than that of the TV with sharper image edges and clearer texture details. Both numerical simulation and in vitro experiments confirm that the DDTV provides a significant quality improvement of PAT reconstructed images for various directivity patterns. [ABSTRACT FROM AUTHOR]

Background: The number of people with dementia is increasing along with people's ageing trend worldwide. Therefore, there are various researches to improve a dementia diagnosis process in the field of computer-aided diagnosis (CAD) technology. The most significant issue is that the evaluation processes by physician which is based on medical information for patients and questionnaire from their guardians are time consuming, subjective and prone to error. This problem can be solved by an overall data mining modeling, which subsidizes an intuitive decision of clinicians.Methods: Therefore, in this paper we propose a quad-phased data mining modeling consisting of 4 modules. In Proposer Module, significant diagnostic criteria are selected that are effective for diagnostics. Then in Predictor Module, a model is constructed to predict and diagnose dementia based on a machine learning algorism. To help clinical physicians understand results of the predictive model better, in Descriptor Module, we interpret causes of diagnostics by profiling patient groups. Lastly, in Visualization Module, we provide visualization to effectively explore characteristics of patient groups.Results: The proposed model is applied for CREDOS study which contains clinical data collected from 37 university-affiliated hospitals in republic of Korea from year 2005 to 2013.Conclusions: This research is an intelligent system enabling intuitive collaboration between CAD system and physicians. And also, improved evaluation process is able to effectively reduce time and cost consuming for clinicians and patients. [ABSTRACT FROM AUTHOR]

Background: Relative survival analysis is a subfield of survival analysis where competing risks data are observed, but the causes of death are unknown. A first step in the analysis of such data is usually the estimation of a net survival curve, possibly followed by regression modelling. Recently, a log-rank type test for comparison of net survival curves has been introduced and the goal of this paper is to explore its properties and put this methodological advance into the context of the field.Methods: We build on the association between the log-rank test and the univariate or stratified Cox model and show the analogy in the relative survival setting. We study the properties of the methods using both the theoretical arguments as well as simulations. We provide an R function to enable practical usage of the log-rank type test.Results: Both the log-rank type test and its model alternatives perform satisfactory under the null, even if the correlation between their p-values is rather low, implying that both approaches cannot be used simultaneously. The stratified version has a higher power in case of non-homogeneous hazards, but also carries a different interpretation.Conclusions: The log-rank type test and its stratified version can be interpreted in the same way as the results of an analogous semi-parametric additive regression model despite the fact that no direct theoretical link can be established between the test statistics. [ABSTRACT FROM AUTHOR]

Background: Minimisation ensures excellent balance between groups for several prognostic factors, even in small samples. However, its use with unequal allocation ratios has been problematic. This paper describes a new minimisation scheme named sequence balance minimisation for unequal treatment allocations.Methods: Treatment- and factor-balancing properties were assessed in simulation studies for two- and three-arm trials with 1:2 and 1:2:3 allocation ratios. Sample sizes were set 30, 60 and 120. The number of prognostic factors on which to achieve balance was ranged from zero (treatment totals only) to ten with two levels occurring in equal probabilities. Random elements were set at 0.95, 0.9, 0.85, 0.80, 0.7, 0.6 and 0.5. Characteristics of the randomisation distributions and the impact of changing the block size while maintaining the allocation ratio were also examined.Results: Sequence balance minimisation has good treatment- and factor-balancing capabilities, and the randomisation distribution was centred at zero for all scenarios. The mean and median number of allocations achieved were the same as the number expected in most scenarios, and including additional factors (up to ten) in the minimisation scheme had little impact on treatment balance. Treatment balance tended to depart from the target as the random element was lowered. The variability in allocations achieved increased slightly as the number of factors increased, as the random element was decreased and as the sample size increased. The mean and median factor imbalance remained tightly around zero even when the chosen factor was not included in the minimisation scheme, though the variability was greater. The variability in factor imbalance increased slightly as the random element decreased, as well as when the number of prognostic factors and sample size increased. Increasing block size while maintaining the allocation ratio improved treatment balance notably with little impact on factor imbalance.Conclusions: Sequence balance minimisation has good treatment- and factor-balancing properties and is particularly useful for small trials seeking to achieve balance across several prognostic factors. [ABSTRACT FROM AUTHOR]

Background: When developing a prediction model for survival data it is essential to validate its performance in external validation settings using appropriate performance measures. Although a number of such measures have been proposed, there is only limited guidance regarding their use in the context of model validation. This paper reviewed and evaluated a wide range of performance measures to provide some guidelines for their use in practice.Methods: An extensive simulation study based on two clinical datasets was conducted to investigate the performance of the measures in external validation settings. Measures were selected from categories that assess the overall performance, discrimination and calibration of a survival prediction model. Some of these have been modified to allow their use with validation data, and a case study is provided to describe how these measures can be estimated in practice. The measures were evaluated with respect to their robustness to censoring and ease of interpretation. All measures are implemented, or are straightforward to implement, in statistical software.Results: Most of the performance measures were reasonably robust to moderate levels of censoring. One exception was Harrell's concordance measure which tended to increase as censoring increased.Conclusions: We recommend that Uno's concordance measure is used to quantify concordance when there are moderate levels of censoring. Alternatively, Gönen and Heller's measure could be considered, especially if censoring is very high, but we suggest that the prediction model is re-calibrated first. We also recommend that Royston's D is routinely reported to assess discrimination since it has an appealing interpretation. The calibration slope is useful for both internal and external validation settings and recommended to report routinely. Our recommendation would be to use any of the predictive accuracy measures and provide the corresponding predictive accuracy curves. In addition, we recommend to investigate the characteristics of the validation data such as the level of censoring and the distribution of the prognostic index derived in the validation setting before choosing the performance measures. [ABSTRACT FROM AUTHOR]

Background: Geographically weighted regression (GWR) is a modelling technique designed to deal with spatial non-stationarity, e.g., the mean values vary by locations. It has been widely used as a visualization tool to explore the patterns of spatial data. However, the GWR tends to produce unsmooth surfaces when the mean parameters have considerable variations, partly due to that all parameter estimates are derived from a fixed- range (bandwidth) of observations. In order to deal with the varying bandwidth problem, this paper proposes an alternative approach, namely Conditional geographically weighted regression (CGWR). Methods: The estimation of CGWR is based on an iterative procedure, analogy to the numerical optimization problem. Computer simulation, under realistic settings, is used to compare the performance between the traditional GWR, CGWR, and a local linear modification of GWR. Furthermore, this study also applies the CGWR to two empirical datasets for evaluating the model performance. The first dataset consists of disability status of Taiwan's elderly, along with some social-economic variables and the other is Ohio's crime dataset. Results: Under the positively correlated scenario, we found that the CGWR produces a better fit for the response surface. Both the computer simulation and empirical analysis support the proposed approach since it significantly reduces the bias and variance of data fitting. In addition, the response surface from the CGWR reviews local spatial characteristics according to the corresponded variables. Conclusions: As an explanatory tool for spatial data, producing accurate surface is essential in order to provide a first look at the data. Any distorted outcomes would likely mislead the following analysis. Since the CGWR can generate more accurate surface, it is more appropriate to use it exploring data that contain suspicious variables with varying characteristics. [ABSTRACT FROM AUTHOR]

Background: NGS technology represents a powerful alternative to the standard Sanger sequencing in the context of clinical setting. The proprietary software that are generally used for variant calling often depend on preset parameters that may not fit in a satisfactory manner for different genes. GATK, which is widely used in the academic world, is rich in parameters for variant calling. However the self-adjusting parameter calibration of GATK requires data from a large number of exomes. When these are not available, which is the standard condition of a diagnostic laboratory, the parameters must be set by the operator (hard filtering). The aim of the present paper was to set up a procedure to assess the best parameters to be used in the hard filtering of GATK. This was pursued by using classification trees on true and false variants from simulated sequences of a real dataset data. Results: We simulated two datasets, with different coverages, including all the sequence alterations identified in a real dataset according to their observed frequencies. Simulated sequences were aligned with standard protocols and then regression trees were built up to identify the most reliable parameters and cutoff values to discriminate true and false variant calls. Moreover, we analyzed flanking sequences of region presenting a high rate of false positive calls observing that such sequences present a low complexity make up. Conclusions: Our results showed that GATK hard filtering parameter values can be tailored through a simulation study based-on the DNA region of interest to ameliorate the accuracy of the variant calling. [ABSTRACT FROM AUTHOR]

Background: When developing risk models for binary data with small or sparse data sets, the standard maximum likelihood estimation (MLE) based logistic regression faces several problems including biased or infinite estimate of the regression coefficient and frequent convergence failure of the likelihood due to separation. The problem of separation occurs commonly even if sample size is large but there is sufficient number of strong predictors. In the presence of separation, even if one develops the model, it produces overfitted model with poor predictive performance. Firth-and logF-type penalized regression methods are popular alternative to MLE, particularly for solving separation-problem. Despite the attractive advantages, their use in risk prediction is very limited. This paper evaluated these methods in risk prediction in comparison with MLE and other commonly used penalized methods such as ridge.Methods: The predictive performance of the methods was evaluated through assessing calibration, discrimination and overall predictive performance using an extensive simulation study. Further an illustration of the methods were provided using a real data example with low prevalence of outcome.Results: The MLE showed poor performance in risk prediction in small or sparse data sets. All penalized methods offered some improvements in calibration, discrimination and overall predictive performance. Although the Firth-and logF-type methods showed almost equal amount of improvement, Firth-type penalization produces some bias in the average predicted probability, and the amount of bias is even larger than that produced by MLE. Of the logF(1,1) and logF(2,2) penalization, logF(2,2) provides slight bias in the estimate of regression coefficient of binary predictor and logF(1,1) performed better in all aspects. Similarly, ridge performed well in discrimination and overall predictive performance but it often produces underfitted model and has high rate of convergence failure (even the rate is higher than that for MLE), probably due to the separation problem.Conclusions: The logF-type penalized method, particularly logF(1,1) could be used in practice when developing risk model for small or sparse data sets. [ABSTRACT FROM AUTHOR]

Background: The Stochastic Process Model (SPM) represents a general framework for modeling the joint evolution of repeatedly measured variables and time-to-event outcomes observed in longitudinal studies, i.e., SPM relates the stochastic dynamics of variables (e.g., physiological or biological measures) with the probabilities of end points (e.g., death or system failure). SPM is applicable for analyses of longitudinal data in many research areas; however, there are no publicly available software tools that implement this methodology. Results: We developed an R package stpm for the SPM-methodology. The package estimates several versions of SPM currently available in the literature including discrete- and continuous-time multidimensional models and a one-dimensional model with time-dependent parameters. Also, the package provides tools for simulation and projection of individual trajectories and hazard functions. Conclusion: In this paper, we present the first software implementation of the SPM-methodology by providing an R package stpm, which was verified through extensive simulation and validation studies. Future work includes further improvements of the model. Clinical and academic researchers will benefit from using the presented model and software. The R package stpm is available as open source software from the following links: https://cran.r-project.org/package=stpm (stable version) or https://github.com/izhbannikov/spm (developer version). [ABSTRACT FROM AUTHOR]

Background: In Australia, screening for colorectal cancer (CRC) with colonoscopy is meant to be reserved for people at increased risk, however, currently there is a mismatch between individuals' risk of CRC and the type of CRC screening they receive. This paper describes the development and optimisation of a Colorectal cancer RISk Prediction tool ('CRISP') for use in primary care. The aim of the CRISP tool is to increase risk-appropriate CRC screening.Methods: CRISP development was informed by previous experience with developing risk tools for use in primary care and a systematic review of the evidence. A CRISP prototype was used in simulated consultations by general practitioners (GPs) with actors as patients. GPs were interviewed to explore their experience of using CRISP, and practice nurses (PNs) and practice managers (PMs) were interviewed after a demonstration of CRISP. Transcribed interviews and video footage of the 'consultations' were qualitatively analyzed. Themes arising from the data were mapped onto Normalization Process Theory (NPT).Results: Fourteen GPs, nine PNs and six PMs were recruited from 12 clinics. Results were described using the four constructs of NPT: 1) Coherence: Clinicians understood the rationale behind CRISP, particularly since they were familiar with using risk tools for other conditions; 2) Cognitive participation: GPs welcomed the opportunity CRISP provided to discuss healthy and unhealthy behaviors with their patients, but many GPs challenged the screening recommendation generated by CRISP; 3) Collective Action: CRISP disrupted clinician-patient flow if the GP was less comfortable with computers. GP consultation time was a major implementation barrier and overall consensus was that PNs have more capacity and time to use CRISP effectively; 4) Reflexive monitoring: Limited systematic monitoring of new interventions is a potential barrier to the sustainable embedding of CRISP.Conclusions: CRISP has the potential to improve risk-appropriate CRC screening in primary care but was considered more likely to be successfully implemented as a nurse-led intervention. [ABSTRACT FROM AUTHOR]

Background: Bivariate random-effects models represent a widely accepted and recommended approach for meta-analysis of test accuracy studies. Standard likelihood methods routinely used for inference are prone to several drawbacks. Small sample size can give rise to unreliable inferential conclusions and convergence issues make the approach unappealing. This paper suggests a different methodology to address such difficulties.Methods: A SIMEX methodology is proposed. The method is a simulation-based technique originally developed as a correction strategy within the measurement error literature. It suits the meta-analysis framework as the diagnostic accuracy measures provided by each study are prone to measurement error. SIMEX can be straightforwardly adapted to cover different measurement error structures and to deal with covariates. The effortless implementation with standard software is an interesting feature of the method.Results: Extensive simulation studies highlight the improvement provided by SIMEX over likelihood approach in terms of empirical coverage probabilities of confidence intervals under different scenarios, independently of the sample size and the values of the correlation between sensitivity and specificity. A remarkable amelioration is obtained in case of deviations from the normality assumption for the random-effects distribution. From a computational point of view, the application of SIMEX is shown to be neither involved nor subject to the convergence issues affecting likelihood-based alternatives. Application of the method to a diagnostic review of the performance of transesophageal echocardiography for assessing ascending aorta atherosclerosis enables overcoming limitations of the likelihood procedure.Conclusions: The SIMEX methodology represents an interesting alternative to likelihood-based procedures for inference in meta-analysis of diagnostic accuracy studies. The approach can provide more accurate inferential conclusions, while avoiding convergence failure and numerical instabilities. The application of the method in the R programming language is possible through the code which is made available and illustrated using the real data example. [ABSTRACT FROM AUTHOR]

Background: Average treatment effects on the treated (ATT) and the untreated (ATU) are useful when there is interest in: the evaluation of the effects of treatments or interventions on those who received them, the presence of treatment heterogeneity, or the projection of potential outcomes in a target (sub-) population. In this paper we illustrate the steps for estimating ATT and ATU using g-computation implemented via Monte Carlo simulation.Methods: To obtain marginal effect estimates for ATT and ATU we used a three-step approach: fitting a model for the outcome, generating potential outcome variables for ATT and ATU separately, and regressing each potential outcome variable on treatment intervention.Results: The estimates for ATT, ATU and average treatment effect (ATE) were of similar magnitude, with ATE being in between ATT and ATU as expected. In our illustrative example, the effect (risk difference [RD]) of a higher education on angina among the participants who indeed have at least a high school education (ATT) was -0.019 (95% CI: -0.040, -0.007) and that among those who have less than a high school education in India (ATU) was -0.012 (95% CI: -0.036, 0.010).Conclusions: The g-computation algorithm is a powerful way of estimating standardized estimates like the ATT and ATU. Its use should be encouraged in modern epidemiologic teaching and practice. [ABSTRACT FROM AUTHOR]

Background: Sequential and single grafting are two surgical procedures of coronary artery bypass grafting. However, it remains unclear if the sequential graft can be used between the right and left coronary artery system. The purpose of this paper is to clarify the possibility of right coronary artery system anastomosis to left coronary system.Methods: A patient-specific 3D model was first reconstructed based on coronary computed tomography angiography (CCTA) images. Two different grafts, the normal multi-graft (Model 1) and the novel multi-graft (Model 2), were then implemented on this patient-specific model using virtual surgery techniques. In Model 1, the single graft was anastomosed to right coronary artery (RCA) and the sequential graft was adopted to anastomose left anterior descending (LAD) and left circumflex artery (LCX). While in Model 2, the single graft was anastomosed to LAD and the sequential graft was adopted to anastomose RCA and LCX. A zero-dimensional/three-dimensional (0D/3D) coupling method was used to realize the multi-scale simulation of both the pre-operative and two post-operative models.Results: Flow rates in the coronary artery and grafts were obtained. The hemodynamic parameters were also showed, including wall shear stress (WSS) and oscillatory shear index (OSI). The area of low WSS and OSI in Model 1 was much less than that in Model 2.Conclusions: Model 1 shows optimistic hemodynamic modifications which may enhance the long-term patency of grafts. The anterior segments of sequential graft have better long-term patency than the posterior segments. With rational spatial position of the heart vessels, the last anastomosis of sequential graft should be connected to the main branch. [ABSTRACT FROM AUTHOR]

Background: Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. Results: From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. Conclusions: ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self-contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the published knowledge. The tools will be updated to support new requirements revealed in this case study. [ABSTRACT FROM AUTHOR]

Background: Microelectrode array (MEA) is a widely used technique to study for example the functional properties of neuronal networks derived from human embryonic stem cells (hESC-NN). With hESC-NN, we can investigate the earliest developmental stages of neuronal network formation in the human brain.Methods: In this paper, we propose an in silico model of maturating hESC-NNs based on a phenomenological model called INEX. We focus on simulations of the development of bursts in hESC-NNs, which are the main feature of neuronal activation patterns. The model was developed with data from developing hESC-NN recordings on MEAs which showed increase in the neuronal activity during the investigated six measurement time points in the experimental and simulated data.Results: Our simulations suggest that the maturation process of hESC-NN, resulting in the formation of bursts, can be explained by the development of synapses. Moreover, spike and burst rate both decreased at the last measurement time point suggesting a pruning of synapses as the weak ones are removed.Conclusions: To conclude, our model reflects the assumption that the interaction between excitatory and inhibitory neurons during the maturation of a neuronal network and the spontaneous emergence of bursts are due to increased connectivity caused by the forming of new synapses. [ABSTRACT FROM AUTHOR]

Background: Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at achieving either objective, but not both. Such limitations can be effectively tackled leveraging a Web service-based modeling and mining approach. Results: Inspired by molecular recognitions and drug discovery processes, we developed a Web service mining tool, named PathExplorer, to discover potentially interesting biological pathways linking service models of biological processes. The tool uses an innovative approach to identify useful pathways based on graph-based hints and service-based simulation verifying user's hypotheses. Conclusion: Web service modeling of biological processes allows the easy access and invocation of these processes on the Web. Web service mining techniques described in this paper enable the discovery of biological pathways linking these process service models. Algorithms presented in this paper for automatically highlighting interesting subgraph within an identified pathway network enable the user to formulate hypothesis, which can be tested out using our simulation algorithm that are also described in this paper. [ABSTRACT FROM AUTHOR]

Background: This exploratory paper outlines an epidemic simulator built on an agent-based, data-driven model of the spread of a disease within an urban environment. An intent of the model is to provide insight into how a disease may reach a tipping point, spreading to an epidemic of uncontrollable proportions. Methods: As a complement to analytical methods, simulation is arguably an effective means of gaining a better understanding of system-level disease dynamics within a population and offers greater utility in its modeling capabilities. Our investigation is based on this conjecture, supported by data-driven models that are reasonable, realistic and practical, in an attempt to demonstrate their efficacy in studying system-wide epidemic phenomena. An agent-based model (ABM) offers considerable flexibility in extending the study of the phenomena before, during and after an outbreak or catastrophe. Results: An agent-based model was developed based on a paradigm of a 'discrete-space scheduled walker' (DSSW), modeling a medium-sized North American City of 650,000 discrete agents, built upon a conceptual framework of statistical reasoning (law of large numbers, statistical mechanics) as well as a correct-by-construction bias. The model addresses where, who, when and what elements, corresponding to network topography and agent characteristics, behaviours, and interactions upon that topography. The DSSW-ABM has an interface and associated scripts that allow for a variety of what-if scenarios modeling disease spread throughout the population, and for data to be collected and displayed via a web browser. Conclusion: This exploratory paper also presents several research opportunities for exploiting data sources of a non-obvious and disparate nature for the purposes of epidemic modeling. There is an increasing amount and variety of data that will continue to contribute to the accuracy of agent-based models and improve their utility in modeling disease spread. The model developed here is well suited to diseases where there is not a predisposition for contraction within the population. One of the advantages of agent-based modeling is the ability to set up a rare event and develop policy as to how one may mitigate damages arising from it. [ABSTRACT FROM AUTHOR]

Background: The 2014 Ebola epidemic is the largest in history, affecting multiple countries in West Africa. Some isolated cases were also observed in other regions of the world. Method: In this paper, we introduce a deterministic SEIR type model with additional hospitalization, quarantine and vaccination components in order to understand the disease dynamics. Optimal control strategies, both in the case of hospitalization (with and without quarantine) and vaccination are used to predict the possible future outcome in terms of resource utilization for disease control and the effectiveness of vaccination on sick populations. Further, with the help of uncertainty and sensitivity analysis we also have identified the most sensitive parameters which effectively contribute to change the disease dynamics. We have performed mathematical analysis with numerical simulations and optimal control strategies on Ebola virus models. Results: We used dynamical system tools with numerical simulations and optimal control strategies on our Ebola virus models. The original model, which allowed transmission of Ebola virus via human contact, was extended to include imperfect vaccination and quarantine. After the qualitative analysis of all three forms of Ebola model, numerical techniques, using MATLAB as a platform, were formulated and analyzed in detail. Our simulation results support the claims made in the qualitative section. Conclusion: Our model incorporates an important component of individuals with high risk level with exposure to disease, such as front line health care workers, family members of EVD patients and Individuals involved in burial of deceased EVD patients, rather than the general population in the affected areas. Our analysis suggests that in order for R0 (i.e., the basic reproduction number) to be less than one, which is the basic requirement for the disease elimination, the transmission rate of isolated individuals should be less than one-fourth of that for non-isolated ones. Our analysis also predicts, we need high levels of medication and hospitalization at the beginning of an epidemic. Further, optimal control analysis of the model suggests the control strategies that may be adopted by public health authorities in order to reduce the impact of epidemics like Ebola. [ABSTRACT FROM AUTHOR]

Background: Recent developments in psychometric modeling and technology allow pooling well-validated items from existing instruments into larger item banks and their deployment through methods of computerized adaptive testing (CAT). Use of item response theory-based bifactor methods and integrative data analysis overcomes barriers in cross-instrument comparison. This paper presents the joint calibration of an item bank for researchers keen to investigate population variations in general psychological distress (GPD).Methods: Multidimensional item response theory was used on existing health survey data from the Scottish Health Education Population Survey (n = 766) to calibrate an item bank consisting of pooled items from the short common mental disorder screen (GHQ-12) and the Affectometer-2 (a measure of "general happiness"). Computer simulation was used to evaluate usefulness and efficacy of its adaptive administration.Results: A bifactor model capturing variation across a continuum of population distress (while controlling for artefacts due to item wording) was supported. The numbers of items for different required reliabilities in adaptive administration demonstrated promising efficacy of the proposed item bank.Conclusions: Psychometric modeling of the common dimension captured by more than one instrument offers the potential of adaptive testing for GPD using individually sequenced combinations of existing survey items. The potential for linking other item sets with alternative candidate measures of positive mental health is discussed since an optimal item bank may require even more items than these. [ABSTRACT FROM AUTHOR]

Background: Electroporation-based applications require multidisciplinary expertise and collaboration of experts with different professional backgrounds in engineering and science. Beginning in 2003, an international scientific workshop and postgraduate course electroporation based technologies and treatments (EBTT) has been organized at the University of Ljubljana to facilitate transfer of knowledge from leading experts to researches, students and newcomers in the field of electroporation. In this paper we present one of the integral parts of EBTT: an e-learning practical work we developed to complement delivery of knowledge via lectures and laboratory work, thus providing a blended learning approach on electrical phenomena involved in electroporation-based therapies and treatments.Methods: The learning effect was assessed via a pre- and post e-learning examination test composed of 10 multiple choice questions (i.e. items). The e-learning practical work session and both of the e-learning examination tests were carried out after the live EBTT lectures and other laboratory work. Statistical analysis was performed to compare and evaluate the learning effect measured in two groups of students: (1) electrical engineers and (2) natural scientists (i.e. medical doctors, biologists and chemists) undergoing the e-learning practical work in 2011-2014 academic years. Item analysis was performed to assess the difficulty of each item of the examination test.Results: The results of our study show that the total score on the post examination test significantly improved and the item difficulty in both experimental groups decreased. The natural scientists reached the same level of knowledge (no statistical difference in total post-examination test score) on the post-course test take, as do electrical engineers, although the engineers started with statistically higher total pre-test examination score, as expected.Conclusions: The main objective of this study was to investigate whether the educational content the e-learning practical work presented to the students with different professional backgrounds enhanced their knowledge acquired via lectures during EBTT. We compared the learning effect assessed in two experimental groups undergoing the e-learning practical work: electrical engineers and natural scientists. The same level of knowledge on the post-course examination was reached in both groups. The results indicate that our e-learning platform supported by blended learning approach provides an effective learning tool for populations with mixed professional backgrounds and thus plays an important role in bridging the gap between scientific domains involved in electroporation-based technologies and treatments. [ABSTRACT FROM AUTHOR]

Background: The main objective of this paper is to study the mechanical influence of the tympanic cavity (TC) in the auditory system (AS). It is done for a frequency range from 0.1 to 20 kHz and the pressure source was applied in the external ear canal (EEC) entrance.Methods: Numerical simulations were developed for seven different models by means of finite element model. On the basis of an EEC finite elements model, the additional elements are coupled and removed in order to evaluate the contribution of the TC. Tympanic membrane, ossicular chain, simplified cochlea and TC were modeled and simulated in four different combinations.Results: Pressure, velocity, and displacement measures were obtained in AS key points in order to be compared with experimental results. Umbo and stapes transfer functions have been represented.Conclusions: The main conclusion is that we find evidence that the presence of the TC in the AS introduces a second resonance in middle ear transfer functions at frequencies above 3 kHz. [ABSTRACT FROM AUTHOR]

Background: The UN Millennium Development Goals (MDGs) and Sustainable Development Goals (SDGs) have brought heightened global attention to the measurement of maternal mortality. It is imperative that new and novel approaches be used to measure maternal mortality and to better understand existing data. In this paper we present one approach: an epidemiologic framework for identifying the identification and quantification of systematic error (multiple-bias analysis), outline the necessary steps for investigators interested in conducting multiple-bias analyses in their own data, and suggest approaches for reporting such analyses in the literature. Methods: To conceptualize the systematic error present in studies of abortion-related deaths, we propose a bias framework. We posit that selection bias and misclassification are present in both verbal autopsy studies and facilitybased studies. The multiple-bias analysis framework provides a relatively simple, quantitative strategy for assessing systematic error and resulting bias in any epidemiologic study. Results: In our worked example of multiple-bias analysis on a study reporting 20.6 % of maternal deaths to be abortion related, after adjustment for selection bias, misclassification, and random error, the median increased, on average, to 0.308, approximately 20 % greater than the reported proportion of abortion-related deaths. Conclusions: Reporting results of multiple-bias analyses in estimates of abortion-related mortality, predictors of unsafe abortion, and other reproductive health questions that suffer from similar biases would not only improve reporting practices in the field, but might also provide a more accurate understanding of the range of potential impact of policies and programs that target the underlying causes of unsafe abortion and abortion-related mortality. [ABSTRACT FROM AUTHOR]

Background: Although some nonparametric methods have been proposed in the literature to test for the equality of median survival times for censored data in medical research, in general they have inflated type I error rates, which make their use limited in practice, especially when the sample sizes are small.Methods: In this paper, we propose a new nonparametric test with a simple test statistic to compare median survival times.Results: The results from our comprehensive simulation study show the new test controls type I error rate very well under all situations considered, even for small sample sizes. In addition, it has comparable detecting power compared to existing methods. Another advantage of the proposed test is its relatively simple formula that requires less computation.Conclusions: We propose a new statistical method for comparing survival curves based on their medians. The new method can be easily implemented and applied to censored event time data. [ABSTRACT FROM AUTHOR]

The benefit of hyperthermia as a potent modifier of radiotherapy has been well established and more recently also the combination with chemotherapy was shown beneficial. Also for head and neck cancer, the impact of hyperthermia has been clinically demonstrated by a number of clinical trials. Unfortunately, the technology applied in these studies provided only limited thermal dose control, and the devices used only allowed treatment of target regions close to the skin. Over the last decade, we developed the technology for deep and controlled hyperthermia that allows treatment of the entire head and neck region. Our strategy involves focused microwave heating combined with 3D patient-specific electromagnetic and thermal simulations for conformal, reproducible and adaptive hyperthermia application. Validation of our strategy has been performed by 3D thermal dose assessment based on invasively placed temperature sensors combined with the 3D patient specific simulations. In this paper, we review the phase III clinical evidence for hyperthermia in head and neck tumors, as well as the heating and dosimetry technology applied in these studies. Next, we describe the development, clinical implementation and validation of 3D guided deep hyperthermia with the HYPERcollar, and its second generation, i.e. the HYPERcollar3D. Lastly, we discuss early clinical results and provide an outlook for this technology. [ABSTRACT FROM AUTHOR]

Background: The assessment of treatment success in clinical trials when multiple (repeated) doses (courses) are involved is quite common, for example, in the case of infertility treatment with assisted reproductive technology (ART), and medical abortion using misoprostol alone or in combination with mifepristone. Under these or similar circumstances, most researchers assess success using binomial proportions after a certain number of consecutive doses, and some have used survival analysis. In this paper we discuss the main problems in using binomial proportions to summarize (the overall) efficacy after two or more consecutive doses of the relevant treatment, particularly for the case of misoprostol in medical abortion studies. We later discuss why the survival analysis is best suited under these circumstances, and illustrate this by using simulated data.Methods: The formulas required for the binomial proportion and survival analysis (without and with competing risks) approaches are summarized and analytically compared. Additionally, numerical results are computed and compared between the two approaches, for several theoretical scenarios.Results: The main conceptual limitations of the binomial proportion approach are identified and discussed, caused mainly by the presence of censoring and competing risks, and it is demonstrated how survival analysis can solve these problems. In general, the binomial proportion approach tends to underestimate the "real" success rate, and tends to overestimate the corresponding standard error.Conclusions: Depending on the rates of censored observations or competing events between repeated doses of the treatment, the bias of the binomial proportion approach as compared to the survival analysis approaches varies; however, the use of the binomial approach is unjustified as the survival analysis options are well known and available in multiple statistical packages. Our conclusions also apply to other situations where success is estimated after multiple (repeated) doses (courses) of the treatment. [ABSTRACT FROM AUTHOR]

Background: A ubiquitous issue in research is that of selecting a representative sample from the study population. While random sampling strategies are the gold standard, in practice, random sampling of participants is not always feasible nor necessarily the optimal choice. In our case, a selection must be made of 12 hospitals (out of 89 Dutch hospitals in total). With this selection of 12 hospitals, it should be possible to estimate blood use in the remaining hospitals as well. In this paper, we evaluate both random and purposive strategies for the case of estimating blood use in Dutch hospitals.Methods: Available population-wide data on hospital blood use and number of hospital beds are used to simulate five sampling strategies: (1) select only the largest hospitals, (2) select the largest and the smallest hospitals ('maximum variation'), (3) select hospitals randomly, (4) select hospitals from as many different geographic regions as possible, (5) select hospitals from only two regions. Simulations of each strategy result in different selections of hospitals, that are each used to estimate blood use in the remaining hospitals. The estimates are compared to the actual population values; the subsequent prediction errors are used to indicate the quality of the sampling strategy.Results: The strategy leading to the lowest prediction error in the case study was maximum variation sampling, followed by random, regional variation and two-region sampling, with sampling the largest hospitals resulting in the worst performance. Maximum variation sampling led to a hospital level prediction error of 15%, whereas random sampling led to a prediction error of 19% (95% CI 17%-26%). While lowering the sample size reduced the differences between maximum variation and the random strategies, increasing sample size to n = 18 did not change the ranking of the strategies and led to only slightly better predictions.Conclusions: The optimal strategy for estimating blood use was maximum variation sampling. When proxy data are available, it is possible to evaluate random and purposive sampling strategies using simulations before the start of the study. The results enable researchers to make a more educated choice of an appropriate sampling strategy. [ABSTRACT FROM AUTHOR]

The POpulation HEalth Model (POHEM) is a health microsimulation model that was developed at Statistics Canada in the early 1990s. POHEM draws together rich multivariate data from a wide range of sources to simulate the lifecycle of the Canadian population, specifically focusing on aspects of health. The model dynamically simulates individuals' disease states, risk factors, and health determinants, in order to describe and project health outcomes, including disease incidence, prevalence, life expectancy, health-adjusted life expectancy, quality of life, and healthcare costs. Additionally, POHEM was conceptualized and built with the ability to assess the impact of policy and program interventions, not limited to those taking place in the healthcare system, on the health status of Canadians. Internationally, POHEM and other microsimulation models have been used to inform clinical guidelines and health policies in relation to complex health and health system problems. This paper provides a high-level overview of the rationale, methodology, and applications of POHEM. Applications of POHEM to cardiovascular disease, physical activity, cancer, osteoarthritis, and neurological diseases are highlighted. [ABSTRACT FROM AUTHOR]

A systems approach offers a novel conceptualization to natural and social systems. In recent years, this has led to perceiving population health outcomes as an emergent property of a dynamic and open, complex adaptive system. The current paper explores these themes further and applies the principles of systems approach and complexity science (i.e. systems science) to conceptualize social determinants of health inequalities. The conceptualization can be done in two steps: viewing health inequalities from a systems approach and extending it to include complexity science. Systems approach views health inequalities as patterns within the larger rubric of other facets of the human condition, such as educational outcomes and economic development. This anlysis requires more sophisticated models such as systems dynamic models. An extension of the approach is to view systems as complex adaptive systems, i.e. systems that are 'open' and adapt to the environment. They consist of dynamic adapting subsystems that exhibit non-linear interactions, while being 'open' to a similarly dynamic environment of interconnected systems. They exhibit emergent properties that cannot be estimated with precision by using the known interactions among its components (such as economic development, political freedom, health system, culture etc.). Different combinations of the same bundle of factors or determinants give rise to similar patterns or outcomes (i.e. property of convergence), and minor variations in the initial condition could give rise to widely divergent outcomes. Novel approaches using computer simulation models (e.g. agent-based models) would shed light on possible mechanisms as to how factors or determinants interact and lead to emergent patterns of health inequalities of populations. [ABSTRACT FROM AUTHOR]