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Research paper recommenders emerged over the last decade to ease finding publications relating to researchers’ area of interest. The challenge was not just to provide researchers with very rich publications at any time, any place and in any form but to also offer the right publication to the right researcher in the right way. Several approaches exist in handling paper recommender systems. However, these approaches assumed the availability of the whole contents of the recommending papers to be freely accessible, which is not always true due to factors such as copyright restrictions. This paper presents a collaborative approach for research paper recommender system. By leveraging the advantages of collaborative filtering approach, we utilize the publicly available contextual metadata to infer the hidden associations that exist between research papers in order to personalize recommendations. The novelty of our proposed approach is that it provides personalized recommendations regardless of the research field and regardless of the user’s expertise. Using a publicly available dataset, our proposed approach has recorded a significant improvement over other baseline methods in measuring both the overall performance and the ability to return relevant and useful publications at the top of the recommendation list. [ABSTRACT FROM AUTHOR]

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary tree-child networks is one of the most studied ones. However, very little is known about the combinatorial structure of these networks. In this paper we address the problem of generating all possible binary tree-child (BTC) networks with a given number of leaves in an efficient way via reduction/augmentation operations that extend and generalize analogous operations for phylogenetic trees, and are biologically relevant. Since our solution is recursive, this also provides us with a recurrence relation giving an upper bound on the number of such networks. We also show how the operations introduced in this paper can be employed to extend the evolutive history of a set of sequences, represented by a BTC network, to include a new sequence. An implementation in python of the algorithms described in this paper, along with some computational experiments, can be downloaded from . [ABSTRACT FROM AUTHOR]

Open source software has been widely used in various industries due to its openness and flexibility, but it also brings potential security problems. Therefore, security analysis is required before using open source software. The current mainstream open source software vulnerability analysis technology is based on source code, and there are problems such as false positives, false negatives and restatements. In order to solve the problems, based on the further study of behavior feature extraction and vulnerability detection technology, a method of using dynamic behavior features to detect open source software vulnerabilities is proposed. Firstly, the relationship between open source software vulnerability and API call sequence is studied. Then, the behavioral risk vulnerability database of open source software is proposed as a support for vulnerability detection. In addition, the CNN-IndRNN classification model is constructed by improving the Independently Recurrent Neural Net-work (IndRNN) algorithm and applies to open source software security vulnerability detection. The experimental results verify the effectiveness of the proposed open source software security vulnerability detection method based on dynamic behavior features. [ABSTRACT FROM AUTHOR]

Since 1997 a considerable effort has been spent on the study of the swap (switch) Markov chains on graphic degree sequences. All of these results assume some kind of regularity in the corresponding degree sequences. Recently, Greenhill and Sfragara published a breakthrough paper about irregular normal and directed degree sequences for which rapid mixing of the swap Markov chain is proved. In this paper we present two groups of results. An example from the first group is the following theorem: let be a directed degree sequence on n vertices. Denote by Δ the maximum value among all in- and out-degrees and denote by the number of edges in the realization. Assume furthermore that . Then the swap Markov chain on the realizations of is rapidly mixing. This result is a slight improvement on one of the results of Greenhill and Sfragara. An example from the second group is the following: let d be a bipartite degree sequence on the vertex set U ⊎ V, and let 0 < c1 ≤ c2 < |U| and 0 < d1 ≤ d2 < |V| be integers, where c1 ≤ d(v) ≤ c2: ∀v ∈ V and d1 ≤ d(u) ≤ d2: ∀u ∈ U. Furthermore assume that (c2 − c1 − 1)(d2 − d1 − 1) < max{c1(|V| − d2), d1(|U| − c2)}. Then the swap Markov chain on the realizations of d is rapidly mixing. A straightforward application of this latter result shows that when a random bipartite or directed graph is generated under the Erdős—Rényi G(n, p) model with mild assumptions on n and p then the degree sequence of the generated graph has, with high probability, a rapidly mixing swap Markov chain on its realizations. [ABSTRACT FROM AUTHOR]

With the convergence of various broadcasting systems, the amount of content available in mobile terminals including IPTV has significantly increased. In this paper, we propose a system that enables users to schedule programs considering both section video clips and full video clips based on the user detection method with similar preference. And, since the system constituting the contents can be classified according to the program, the proposed method can store a program desired by the user, and thus create and schedule a kind of individual channel. Experimental results show that the proposed method has a higher prediction accuracy; this is accomplished by comparing existing channel recommendation methods with the program recommendation methods proposed in this paper. [ABSTRACT FROM AUTHOR]

This paper proposes a method to predict fluctuations in the prices of cryptocurrencies, which are increasingly used for online transactions worldwide. Little research has been conducted on predicting fluctuations in the price and number of transactions of a variety of cryptocurrencies. Moreover, the few methods proposed to predict fluctuation in currency prices are inefficient because they fail to take into account the differences in attributes between real currencies and cryptocurrencies. This paper analyzes user comments in online cryptocurrency communities to predict fluctuations in the prices of cryptocurrencies and the number of transactions. By focusing on three cryptocurrencies, each with a large market size and user base, this paper attempts to predict such fluctuations by using a simple and efficient method. [ABSTRACT FROM AUTHOR]

An extreme learning machine (ELM) is a novel training method for single-hidden layer feedforward neural networks (SLFNs) in which the hidden nodes are randomly assigned and fixed without iterative tuning. ELMs have earned widespread global interest due to their fast learning speed, satisfactory generalization ability and ease of implementation. In this paper, we extend this theory to hypercomplex space and attempt to simultaneously consider multisource information using a hypercomplex representation. To illustrate the performance of the proposed hypercomplex extreme learning machine (HELM), we have applied this scheme to the task of multispectral palmprint recognition. Images from different spectral bands are utilized to construct the hypercomplex space. Extensive experiments conducted on the PolyU and CASIA multispectral databases demonstrate that the HELM scheme can achieve competitive results. The source code together with datasets involved in this paper can be available for free download at . [ABSTRACT FROM AUTHOR]

Background and objectives: ECG signal is relatively weak and vulnerable to various noise interferences, such as electromyography. There will be robustness problems when detecting the instantaneous heart rate independently. In some cases, multiple human physiologic parameters are monitored to help in heart rate detection. Methods: In this paper, an algorithm that marks the R-wave peaks with the help of simultaneously recorded continuous blood pressure is proposed and tested on two databases. One database, called the challenge database, is provided by the PhysioNet/Computing in Cardiology Challenge 2014, and the other is the MGH/MF waveform database. Results: The final scores of the proposed algorithm are 97.3% for the challenge database and 96.6% for the MGH/MF waveform database. Conclusions: The experimental results show that this algorithm has high detection accuracy and a relatively strong robustness. [ABSTRACT FROM AUTHOR]

Metabolic models can estimate intrinsic product yields for microbial factories, but such frameworks struggle to predict cell performance (including product titer or rate) under suboptimal metabolism and complex bioprocess conditions. On the other hand, machine learning, complementary to metabolic modeling necessitates large amounts of data. Building such a database for metabolic engineering designs requires significant manpower and is prone to human errors and bias. We propose an approach to integrate data-driven methods with genome scale metabolic model for assessment of microbial bio-production (yield, titer and rate). Using engineered E. coli as an example, we manually extracted and curated a data set comprising about 1200 experimentally realized cell factories from ~100 papers. We furthermore augmented the key design features (e.g., genetic modifications and bioprocess variables) extracted from literature with additional features derived from running the genome-scale metabolic model iML1515 simulations with constraints that match the experimental data. Then, data augmentation and ensemble learning (e.g., support vector machines, gradient boosted trees, and neural networks in a stacked regressor model) are employed to alleviate the challenges of sparse, non-standardized, and incomplete data sets, while multiple correspondence analysis/principal component analysis are used to rank influential factors on bio-production. The hybrid framework demonstrates a reasonably high cross-validation accuracy for prediction of E.coli factory performance metrics under presumed bioprocess and pathway conditions (Pearson correlation coefficients between 0.8 and 0.93 on new data not seen by the model). [ABSTRACT FROM AUTHOR]

Web service has become irreplaceable for service-oriented application in both academia and industry in recent years. Quality of Service (QoS) is used to describe the nonfunctional characteristics of Web service. Identifying Web service QoS is crucial for service-oriented application designers because service users may obtain very different QoS performance of the same service in the client-side due to dynamic changes of Internet environment as well as user context. However, evaluating QoS performance of a large scale of Web services requires considerable time and resources in real-world. Existing methods can make a personalized prediction for average QoS values by employing historical data but fail to take into consideration the fluctuation feature of Web service QoS values. To address this issue, this paper proposes a novel method for personalized QoS prediction of dynamic Web Services. First, a novel approach is used to extract feature points of QoS sequences and dynamic time warping distance is used to compute the similarity instead of Euclidean distance. By finding the most similar QoS sequences of the target QoS sequence, the missing QoS values can be predicted without extra Web services invoking. To validate our method, we conduct a large number of experiments based on real-world Web service QoS data set. The experimental studies show that our method has higher accuracy rate compared with the existing methods. [ABSTRACT FROM AUTHOR]

As an important factor for improving recommendations, time information has been introduced to model users’ dynamic preferences in many papers. However, the sequence of users’ behaviour is rarely studied in recommender systems. Due to the users’ unique behavior evolution patterns and personalized interest transitions among items, users’ similarity in sequential dimension should be introduced to further distinguish users’ preferences and interests. In this paper, we propose a new collaborative filtering recommendation method based on users’ interest sequences (IS) that rank users’ ratings or other online behaviors according to the timestamps when they occurred. This method extracts the semantics hidden in the interest sequences by the length of users’ longest common sub-IS (LCSIS) and the count of users’ total common sub-IS (ACSIS). Then, these semantics are utilized to obtain users’ IS-based similarities and, further, to refine the similarities acquired from traditional collaborative filtering approaches. With these updated similarities, transition characteristics and dynamic evolution patterns of users’ preferences are considered. Our new proposed method was compared with state-of-the-art time-aware collaborative filtering algorithms on datasets MovieLens, Flixster and Ciao. The experimental results validate that the proposed recommendation method is effective and outperforms several existing algorithms in the accuracy of rating prediction. [ABSTRACT FROM AUTHOR]

A significant approach for the discovery of biological regulatory rules of genes, protein and their inheritance relationships is the extraction of meaningful patterns from biological sequence data. The existing algorithms of sequence pattern discovery, like MSPM and FBSB, suffice their low efficiency and accuracy. In order to deal with this issue, this paper presents a new algorithm for biological sequence pattern mining abbreviated MpBsmi based on the data index structure. The MpBsmi algorithm employs a sequence position table abbreviated ST and a sequence database index structure named DB-Index for data storing, mining and pattern expansion. The ST and DB-Index of single items are firstly obtained through scanning sequence database once. Then a new algorithm for fast support counting is developed to mine the table ST to identify the frequent single items. Based on a connection strategy, the frequent patterns are expanded and the expanded table ST is updated by scanning the DB-Index. The fast support counting algorithm is used for obtaining the frequent expansion patterns. Finally, a new pruning technique is developed for extended pattern to avoid the generation of unnecessarily large number of candidate patterns. The experiments results on multiple classical protein sequences from the Pfam database validate the performance of the proposed algorithm including the accuracy, stability and scalability. It is showed that the proposed algorithm has achieved the better space efficiency, stability and scalability comparing with MSPM, FBSB which are the two main algorithms for biological sequence mining. [ABSTRACT FROM AUTHOR]

Designing an efficient association rule mining (ARM) algorithm for multilevel knowledge-based transactional databases that is appropriate for real-world deployments is of paramount concern. However, dynamic decision making that needs to modify the threshold either to minimize or maximize the output knowledge certainly necessitates the extant state-of-the-art algorithms to rescan the entire database. Subsequently, the process incurs heavy computation cost and is not feasible for real-time applications. The paper addresses efficiently the problem of threshold dynamic updation for a given purpose. The paper contributes by presenting a novel ARM approach that creates an intermediate itemset and applies a threshold to extract categorical frequent itemsets with diverse threshold values. Thus, improving the overall efficiency as we no longer needs to scan the whole database. After the entire itemset is built, we are able to obtain real support without the need of rebuilding the itemset (e.g. Itemset list is intersected to obtain the actual support). Moreover, the algorithm supports to extract many frequent itemsets according to a pre-determined minimum support with an independent purpose. Additionally, the experimental results of our proposed approach demonstrate the capability to be deployed in any mining system in a fully parallel mode; consequently, increasing the efficiency of the real-time association rules discovery process. The proposed approach outperforms the extant state-of-the-art and shows promising results that reduce computation cost, increase accuracy, and produce all possible itemsets. [ABSTRACT FROM AUTHOR]

Approximate string matching with k-differences has a number of practical applications, ranging from pattern recognition to computational biology. This paper proposes an efficient memory-access algorithm for parallel approximate string matching with k-differences on Graphics Processing Units (GPUs). In the proposed algorithm, all threads in the same GPUs warp share data using warp-shuffle operation instead of accessing the shared memory. Moreover, we implement the proposed algorithm by exploiting the memory structure of GPUs to optimize its performance. Experiment results for real DNA packages revealed that the performance of the proposed algorithm and its implementation archived up to 122.64 and 1.53 times compared to that of sequential algorithm on CPU and previous parallel approximate string matching algorithm on GPUs, respectively. [ABSTRACT FROM AUTHOR]

Double cycling is an efficient tool to increase the efficiency of quay crane (QC) in container terminals. In this paper, an optimization model for double cycling is developed to optimize the operation sequence of multiple QCs. The objective is to minimize the makespan of the ship handling operation considering the ship balance constraint. To solve the model, an algorithm based on Lagrangian relaxation is designed. Finally, we compare the efficiency of the Lagrangian relaxation based heuristic with the branch-and-bound method and a genetic algorithm using instances of different sizes. The results of numerical experiments indicate that the proposed model can effectively reduce the unloading and loading times of QCs. The effects of the ship balance constraint are more notable when the number of QCs is high. [ABSTRACT FROM AUTHOR]

Background and objectives: Heat related mortality is of great concern for public health, and estimates of future mortality under a warming climate are important for planning of resources and possible adaptation measures. Papers providing projections of future heat-related mortality were critically reviewed with a focus on the use of climate model data. Some best practice guidelines are proposed for future research. Methods: The electronic databases Web of Science and PubMed/Medline were searched for papers containing a quantitative estimate of future heat-related mortality. The search was limited to papers published in English in peer-reviewed journals up to the end of March 2017. Reference lists of relevant papers and the citing literature were also examined. The wide range of locations studied and climate data used prevented a meta-analysis. Results: A total of 608 articles were identified after removal of duplicate entries, of which 63 were found to contain a quantitative estimate of future mortality from hot days or heat waves. A wide range of mortality models and climate model data have been used to estimate future mortality. Temperatures in the climate simulations used in these studies were projected to increase. Consequently, all the papers indicated that mortality from high temperatures would increase under a warming climate. The spread in projections of future climate by models adds substantial uncertainty to estimates of future heat-related mortality. However, many studies either did not consider this source of uncertainty, or only used results from a small number of climate models. Other studies showed that uncertainty from changes in populations and demographics, and the methods for adaptation to warmer temperatures were at least as important as climate model uncertainty. Some inconsistencies in the use of climate data (for example, using global mean temperature changes instead of changes for specific locations) and interpretation of the effects on mortality were apparent. Some factors which have not been considered when estimating future mortality are summarised. Conclusions: Most studies have used climate data generated using scenarios with medium and high emissions of greenhouse gases. More estimates of future mortality using climate information from the mitigation scenario RCP2.6 are needed, as this scenario is the only one under which the Paris Agreement to limit global warming to 2°C or less could be realised. Many of the methods used to combine modelled data with local climate observations are simplistic. Quantile-based methods might offer an improved approach, especially for temperatures at the ends of the distributions. The modelling of adaptation to warmer temperatures in mortality models is generally arbitrary and simplistic, and more research is needed to better quantify adaptation. Only a small number of studies included possible changes in population and demographics in their estimates of future mortality, meaning many estimates of mortality could be biased low. Uncertainty originating from establishing a mortality baseline, climate projections, adaptation and population changes is important and should be considered when estimating future mortality. [ABSTRACT FROM AUTHOR]

This paper presents a method for classifying the ancestry of Brazilian surnames based on historical sources. The information obtained forms the basis for applying fuzzy matching and machine learning classification algorithms to more than 46 million workers in 5 categories: Iberian, Italian, Japanese, German and East European. The vast majority (96.7%) of the single surnames were identified using a fuzzy matching and the rest using a method proposed by Cavnar and Trenkle (1994). A comparison of the results of the procedures with data on foreigners in the 1920 Census and with the geographic distribution of non-Iberian surnames underscores the accuracy of the procedure. The study shows that surname ancestry is associated with significant differences in wages and schooling. [ABSTRACT FROM AUTHOR]

In big data area a significant challenge about string similarity join is to find all similar pairs more efficiently. In this paper, we propose a parallel processing framework for efficient string similarity join. First, the input is split into some disjoint small subsets according to the joint frequency distribution and the interval distribution of strings. Then the filter-verification strategy is adopted in the computation of string similarity for each subset so that the number of candidate pairs is reduced before an effective pruning strategy is used to improve the performance. Finally, the operation of string join is executed in parallel. Para-Join algorithm based on the multi-threading technique is proposed to implement the framework in a multi-core system while Pada-Join algorithm based on Spark platform is proposed to implement the framework in a cluster system. We prove that Para-Join and Pada-Join cannot only avoid reduplicate computation but also ensure the completeness of the result. Experimental results show that Para-Join can achieve high efficiency and significantly outperform than state-of-the-art approaches, meanwhile, Pada-Join can work on large datasets. [ABSTRACT FROM AUTHOR]

Information confidentiality is an essential requirement for cyber security in critical infrastructure. Identity-based cryptography, an increasingly popular branch of cryptography, is widely used to protect the information confidentiality in the critical infrastructure sector due to the ability to directly compute the user’s public key based on the user’s identity. However, computational requirements complicate the practical application of Identity-based cryptography. In order to improve the efficiency of identity-based cryptography, this paper presents an effective method to construct pairing-friendly elliptic curves with low hamming weight 4 under embedding degree 1. Based on the analysis of the Complex Multiplication(CM) method, the soundness of our method to calculate the characteristic of the finite field is proved. And then, three relative algorithms to construct pairing-friendly elliptic curve are put forward. 10 elliptic curves with low hamming weight 4 under 160 bits are presented to demonstrate the utility of our approach. Finally, the evaluation also indicates that it is more efficient to compute Tate pairing with our curves, than that of Bertoni et al. [ABSTRACT FROM AUTHOR]

Background: Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to compute protein clusters, to annotate sequence function, and to compute evolutionary relationships among protein sequences. A number of approaches exist for identifying and characterizing protein families based on their domains, and because domains represent conserved portions of a protein sequence, the primary computation involved in protein family characterization is identification of such conserved regions. However, identifying conserved regions from large collections (millions) of protein sequences presents significant challenges. Methods: In this paper we present a new, alignment-free method for detecting conserved regions in protein sequences called NADDA (No-Alignment Domain Detection Algorithm). Our method exploits the abundance of exact matching short subsequences (k-mers) to quickly detect conserved regions, and the power of machine learning is used to improve the prediction accuracy of detection. We present a parallel implementation of NADDA using the MapReduce framework and show that our method is highly scalable. Results: We have compared NADDA with Pfam and InterPro databases. For known domains annotated by Pfam, accuracy is 83%, sensitivity 96%, and specificity 44%. For sequences with new domains not present in the training set an average accuracy of 63% is achieved when compared to Pfam. A boost in results in comparison with InterPro demonstrates the ability of NADDA to capture conserved regions beyond those present in Pfam. We have also compared NADDA with ADDA and MKDOM2, assuming Pfam as ground-truth. On average NADDA shows comparable accuracy, more balanced sensitivity and specificity, and being alignment-free, is significantly faster. Excluding the one-time cost of training, runtimes on a single processor were 49s, 10,566s, and 456s for NADDA, ADDA, and MKDOM2, respectively, for a data set comprised of approximately 2500 sequences. [ABSTRACT FROM AUTHOR]

Cancer driver genes, i.e., oncogenes and tumor suppressor genes, are involved in the acquisition of important functions in tumors, providing a selective growth advantage, allowing uncontrolled proliferation and avoiding apoptosis. It is therefore important to identify these driver genes, both for the fundamental understanding of cancer and to help finding new therapeutic targets or biomarkers. Although the most frequently mutated driver genes have been identified, it is believed that many more remain to be discovered, particularly for driver genes specific to some cancer types. In this paper, we propose a new computational method called LOTUS to predict new driver genes. LOTUS is a machine-learning based approach which allows to integrate various types of data in a versatile manner, including information about gene mutations and protein-protein interactions. In addition, LOTUS can predict cancer driver genes in a pan-cancer setting as well as for specific cancer types, using a multitask learning strategy to share information across cancer types. We empirically show that LOTUS outperforms five other state-of-the-art driver gene prediction methods, both in terms of intrinsic consistency and prediction accuracy, and provide predictions of new cancer genes across many cancer types. [ABSTRACT FROM AUTHOR]

To balance the supply and demand in China's beef market, beef consumption must be scientifically and effectively forecasted. Beef consumption is affected by many factors and is characterized by gray uncertainty. Therefore, gray theory can be used to forecast the beef consumption, In this paper, the structural defects and unreasonable parameter design of the traditional gray model are analyzed. Then, a new gray model termed, EGM(1,1,r), is built, and the modeling conditions and error checking methods of EGM(1,1,r) are studied. Then, EGM(1,1,r) is used to simulate and forecast China’s beef consumption. The results show that both the simulation and prediction precisions of the new model are better than those of other gray models. Finally, the new model is used to forecast China’s beef consumption for the period from 2019–2025. The findings will serve as an important reference for the Chinese government in formulating policies to ensure the balance between the supply and demand for Chinese beef. [ABSTRACT FROM AUTHOR]

Forgery detection is essential to verify the integrity and authenticity of images. Existing block-based detection techniques detect forgery in the same image, most of which use similar frameworks while differ in the feature extraction schemes. These methods have high accuracy in detecting the forged regions, but the computational load is heavy when facing exhaustive search problems. This paper describes a forgery detection method based on local binary pattern residue classes and color regions. An image is divided into overlapped blocks. Local binary pattern residue classes are computed for each block. The plane formed by a dimensional and b dimensional from Lab color space is divided into 16 regions. Similar blocks are searched in the overlapped blocks with the same local binary pattern residue class and color region, then they are grouped into several suspicious regions. Finally, we analyze the multi-region relation of these suspicious regions and their areas to locate the tampered regions. The small hole is filled through the morphologic operation. The results of experiments demonstrated that our method has good performance in that it improved detection accuracy and reduced execution time under various challenging conditions. As the proposed method reduces the search range for similar blocks, it has a higher speed than exhaustive search and has comparable detection results at the same time. [ABSTRACT FROM AUTHOR]

In this paper, we propose a human action recognition method using HOIRM (histogram of oriented interest region motion) feature fusion and a BOW (bag of words) model based on AP (affinity propagation) clustering. First, a HOIRM feature extraction method based on spatiotemporal interest points ROI is proposed. HOIRM can be regarded as a middle-level feature between local and global features. Then, HOIRM is fused with 3D HOG and 3D HOF local features using a cumulative histogram. The method further improves the robustness of local features to camera view angle and distance variations in complex scenes, which in turn improves the correct rate of action recognition. Finally, a BOW model based on AP clustering is proposed and applied to action classification. It obtains the appropriate visual dictionary capacity and achieves better clustering effect for the joint description of a variety of features. The experimental results demonstrate that by using the fused features with the proposed BOW model, the average recognition rate is 95.75% in the KTH database, and 88.25% in the UCF database, which are both higher than those by using only 3D HOG+3D HOF or HOIRM features. Moreover, the average recognition rate achieved by the proposed method in the two databases is higher than that obtained by other methods. [ABSTRACT FROM AUTHOR]

Floating Catchment Area (FCA) methods are a popular tool to investigate accessibility to public facilities, in particular health care services. FCA approaches are attractive because, unlike other accessibility measures, they take into account the potential for congestion of facilities. This is done by 1) considering the population within the catchment area of a facility to calculate a variable that measures level of service, and then 2) aggregating the level of service by population centers subject to catchment area constraints. In this paper we discuss an effect of FCA approaches, an artifact that we term demand and level of service inflation. These artifacts are present in previous implementations of FCA methods. We argue that inflation makes interpretation of estimates of accessibility difficult, which has possible deleterious consequences for decision making. Next, we propose a simple and intuitive approach to proportionally allocate demandand and level of service in FCA calculations. The approach is based on a standardization of the impedance matrix, similar to approaches popular in the spatial statistics and econometrics literature. The result is a more intiuitive measure of accessibility that 1) provides a local version of the provider-to-population ratio; and 2) preserves the level of demand and the level of supply in a system. We illustrate the relevant issues with some examples, and then empirically by means of a case study of accessibility to family physicians in the Hamilton Census Metropolitan Area (CMA), in Ontario, Canada. Results indicate that demand and supply inflation/deflation affect the interpretation of accessibility analysis using existing FCA methods, and that the proposed adjustment can lead to more intuitive results. [ABSTRACT FROM AUTHOR]

Profilin 1 (PFN1) protein plays key roles in neuronal growth and differentiation, membrane trafficking, and regulation of the actin cytoskeleton. Four natural variants of PFN1 were described as related to ALS, the most common adult-onset motor neuron disorder. However, the pathological mechanism of PFN1 in ALS is not yet completely understood. The goal of this work is to thoroughly analyze the effects of the ALS-related mutations on PFN1 structure and function using computational simulations. Here, PhD-SNP, PMUT, PolyPhen-2, SIFT, SNAP, SNPS&GO, SAAP, nsSNPAnalyzer, SNPeffect4.0 and I-Mutant2.0 were used to predict the functional and stability effects of PFN1 mutations. ConSurf was used for the evolutionary conservation analysis, and GROMACS was used to perform the MD simulations. The mutations C71G, M114T, and G118V, but not E117G, were predicted as deleterious by most of the functional prediction algorithms that were used. The stability prediction indicated that the ALS-related mutations could destabilize PFN1. The ConSurf analysis indicated that the mutation C71G, M114T, E117G, and G118V occur in highly conserved positions. The MD results indicated that the studied mutations could affect the PFN1 flexibility at the actin and PLP-binding domains, and consequently, their intermolecular interactions. It may be therefore related to the functional impairment of PFN1 upon C71G, M114T, E117G and G118V mutations, and their involvement in ALS development. We also developed a database, SNPMOL (), containing the results presented on this paper for biologists and clinicians to exploit PFN1 and its natural variants. [ABSTRACT FROM AUTHOR]

The reuse of business processes (BPs) requires similarities between them to be suitably identified. Various approaches have been introduced to address this problem, but many of them feature a high computational cost and a low level of automation. This paper presents a clustering algorithm that groups business processes retrieved from a multimodal search system (based on textual and structural information). The algorithm is based on Incremental Covering Arrays (ICAs) with different alphabets to determine the possible number of groups to be created for each row of the ICA. The proposed algorithm also incorporates Balanced Bayesian Information Criterion to determine the optimal number of groups and the best solution for each query. Experimental evaluation shows that the use of ICAs with strength four (4) and different alphabets reduces the number of solutions needed to be evaluated and optimizes the number of clusters. The proposed algorithm outperforms other algorithms in various measures (precision, recall, and F-measure) by between 12% and 88%. Friedman and Wilcoxon non-parametric tests gave a 90–95% significance level to the obtained results. Better options of repository search for BPs help companies to reuse them. By thus reusing BPs, managers and analysts can more easily get to know the evolution and trajectory of the company processes, a situation that could be expected to lead to improved managerial and commercial decision making. [ABSTRACT FROM AUTHOR]

Due to continuous evolution of biomedical data, biomedical ontologies are becoming larger and more complex, which leads to the existence of many overlapping information. To support semantic inter-operability between ontology-based biomedical systems, it is necessary to identify the correspondences between these information, which is commonly known as biomedical ontology matching. However, it is a challenge to match biomedical ontologies, which dues to: (1) biomedical ontologies often possess tens of thousands of entities, (2) biomedical terminologies are complex and ambiguous. To efficiently match biomedical ontologies, in this paper, an interactive biomedical ontology matching approach is proposed, which utilizes the Evolutionary Algorithm (EA) to implement the automatic matching process, and gets a user involved in the evolving process to improve the matching efficiency. In particular, we propose an Evolutionary Tabu Search (ETS) algorithm, which can improve EA’s performance by introducing the tabu search algorithm as a local search strategy into the evolving process. On this basis, we further make the ETS-based ontology matching technique cooperate with the user in a reasonable amount of time to efficiently create high quality alignments, and make use of EA’s survival of the fittest to eliminate the wrong correspondences brought by erroneous user validations. The experiment is conducted on the Anatomy track and Large Biomedic track that are provided by the Ontology Alignment Evaluation Initiative (OAEI), and the experimental results show that our approach is able to efficiently exploit the user intervention to improve its non-interactive version, and the performance of our approach outperforms the state-of-the-art semi-automatic ontology matching systems. [ABSTRACT FROM AUTHOR]

We generalize the notion of λ-superstrings, presented in a previous paper, to the notion of weighted λ-superstrings. This generalization entails an important improvement in the applications to vaccine designs, as it allows epitopes to be weighted by their immunogenicities. Motivated by these potential applications of constructing short weighted λ-superstrings to vaccine design, we approach this problem in two ways. First, we formalize the problem as a combinatorial optimization problem (in fact, as two polynomially equivalent problems) and develop an integer programming (IP) formulation for solving it optimally. Second, we describe a model that also takes into account good pairwise alignments of the obtained superstring with the input strings, and present a genetic algorithm that solves the problem approximately. We apply both algorithms to a set of 169 strings corresponding to the Nef protein taken from patiens infected with HIV-1. In the IP-based algorithm, we take the epitopes and the estimation of the immunogenicities from databases of experimental epitopes. In the genetic algorithm we take as candidate epitopes all 9-mers present in the 169 strings and estimate their immunogenicities using a public bioinformatics tool. Finally, we used several bioinformatic tools to evaluate the properties of the candidates generated by our method, which indicated that we can score high immunogenic λ-superstrings that at the same time present similar conformations to the Nef virus proteins. [ABSTRACT FROM AUTHOR]

In order to retrieve similar trademarks from large-scale trademark databases, combining the characteristics of trademark images, this paper presents a trademark image retrieval method based on regional and border feature fusion. Based on the target image extraction, the proposed approach describes the target region and border features. The region feature description is mainly based on the concept of partition block statistics. The region is divided into equal-area unit using concentric circles, and feature extraction is performed in each small block unit. For the border feature description, this study first detect corners, and then construct a Delaunay graph and extract features by combining the corner detected and the Delaunay triangulation reconstruction. In the search process, the method also incorporates information such as the trademark's color characteristics, trademark classification, and trademark keywords. The present study carried out image retrieval experiment on CE-SHAPE-1 database containing 1400 MPEG-7 core experimental shape, a classification trademark database containing 2000 images, and a national trademark database containing approximately 4.89 million images. The experimental results show that the proposed approach combines the advantages of region and border feature description, and can choose the best among various local optimizations, which makes the retrieval result more effective, more in line with human visual perception, and improves the retrieval accuracy. [ABSTRACT FROM AUTHOR]

This paper presents a lightweight synthesis algorithm, named adaptive region segmentation based piecewise linear (ARSPL) algorithm, for reconstructing standard 12-lead electrocardiogram (ECG) signals from a 3-lead subset (I, II and V2). Such a lightweight algorithm is particularly suitable for healthcare mobile devices with limited resources for computing, communication and data storage. After detection of R-peaks, the ECGs are segmented by cardiac cycles. Each cycle is further divided into four regions according to different cardiac electrical activity stages. A personalized linear regression algorithm is then applied to these regions respectively for improved ECG synthesis. The proposed ARSPL method has been tested on 39 subjects randomly selected from the PTB diagnostic ECG database and achieved accurate synthesis of remaining leads with an average correlation coefficient of 0.947, an average root-mean-square error of 55.4μV, and an average runtime performance of 114ms. Overall, these results are significantly better than those of the common linear regression method, the back propagation (BP) neural network and the BP optimized using the genetic algorithm. We have also used the reconstructed ECG signals to evaluate the denivelation of ST segment, which is a potential symptom of intrinsic myocardial disease. After ARSPL, only 10.71% of the synthesized ECG cycles are with a ST-level synthesis error larger than 0.1mV, which is also better than those of the three above-mentioned methods. [ABSTRACT FROM AUTHOR]

To predict what products customers will buy in next transaction is an important task. Existing work in next-basket prediction can be summarized into two paradigms. One is the item-centric paradigm, where sequential patterns are mined from customers’ transactional data and leveraged for prediction. However, these approaches usually suffer from the data sparseness problem. The other is the user-centric paradigm, where collaborative filtering techniques have been applied on customers’ historical data. However, these methods ignore the sequential behaviors of customers which is often crucial for next-basket prediction. In this paper, we introduce a hybrid method, namely the Co-Factorization model over Sequential and Historical purchase data (CFSH for short) for next-basket recommendation. Compared with existing methods, our approach conveys the following merits: 1) By mining global sequential patterns, we can avoid the sparseness problem in traditional item-centric methods; 2) By factorizing product-product and customer-product matrices simultaneously, we can fully exploit both sequential and historical behaviors to learn customer and product representations better; 3) By using a hybrid recommendation method, we can achieve better performance in next-basket prediction. Experimental results on three real-world purchase datasets demonstrated the effectiveness of our approach as compared with the state-of-the-art methods. [ABSTRACT FROM AUTHOR]

PubMed is a free search engine for biomedical literature accessed by millions of users from around the world each day. With the rapid growth of biomedical literature—about two articles are added every minute on average—finding and retrieving the most relevant papers for a given query is increasingly challenging. We present Best Match, a new relevance search algorithm for PubMed that leverages the intelligence of our users and cutting-edge machine-learning technology as an alternative to the traditional date sort order. The Best Match algorithm is trained with past user searches with dozens of relevance-ranking signals (factors), the most important being the past usage of an article, publication date, relevance score, and type of article. This new algorithm demonstrates state-of-the-art retrieval performance in benchmarking experiments as well as an improved user experience in real-world testing (over 20% increase in user click-through rate). Since its deployment in June 2017, we have observed a significant increase (60%) in PubMed searches with relevance sort order: it now assists millions of PubMed searches each week. In this work, we hope to increase the awareness and transparency of this new relevance sort option for PubMed users, enabling them to retrieve information more effectively. [ABSTRACT FROM AUTHOR]

Due to recent developments in technologies associated with the Internet of Things (IoT), a large number of people now regularly use smart devices, such as smartwatches and smartphones. However, these devices are prone to data leaks because of security vulnerabilities. In particular, Android devices use permission-based security, which allows users to directly approve permissions requested by an app when installing it. As a result, many malicious apps can obtain and leak private user data by requesting more permissions than are needed. However, it is difficult to identify malicious apps based solely on the requested permissions. A system is hence needed to accurately identify malicious apps and protect private data from them. In this paper, we propose a system for hiding data related to a user’s contacts or providing virtual data according to preconfigured policies when an Android app requests access to them. By hiding data related to the contacts, the proposed system can protect them from malicious apps. By using virtual data, it can even detect malicious apps that leak private data. The system requires less storage and provides faster access to user contacts than prevalent solutions to similar problems. [ABSTRACT FROM AUTHOR]

Motion capture allows accurate recording of human motion, with applications in many fields, including entertainment, medicine, sports science and human computer interaction. A common difficulty with this technology is the occurrence of missing data, due to occlusions, or recording conditions. Various models have been proposed to estimate missing data. Some are based on interpolation, low-rank properties or inter-correlations. Others involve dataset matching or skeleton constraints. While the latter have the advantage of promoting a realistic motion estimation, they require prior knowledge of skeleton constraints, or the availability of a prerecorded dataset. In this article, we propose a probabilistic averaging method of several recovery models (referred to as Probabilistic Model Averaging (PMA) in this paper), based on the likelihoods of the distances between body points. This method has the advantage of being automatic, while allowing an efficient gap data recovery. To support and validate the proposed method, we use a set of four individual recovery models, based on linear/nonlinear regression in local coordinate systems. Finally, we propose two heuristic algorithms to enforce skeleton constraints in the reconstructed motion, which can be used on any individual recovery model. For validation purposes, random gaps were introduced into motion-capture sequences, and the effects of factors such as the number of simultaneous gaps, gap length and sequence duration were analyzed. Results show that the proposed probabilistic averaging method yields better recovery than (i) each of the four individual models and (ii) two recent state-of-the-art models, regardless of gap length, sequence duration and number of simultaneous gaps. Moreover, both of our heuristic skeleton-constraint algorithms significantly improve the recovery for 7 out of 8 tested motion-capture sequences (p < 0.05), for 10 simultaneous gaps of 5 seconds. The code is available for free download at: . [ABSTRACT FROM AUTHOR]

Both in DNA and protein contexts, an important method for modelling motifs is to utilize position weight matrix (PWM) in biological sequences. With the development of genome sequencing technology, the quantity of the sequence data is increasing explosively, so the faster searching algorithms which have the ability to meet the increasingly need are desired to develop. In this paper, we proposed a method for speeding up the searching process of candidate transcription factor binding sites (TFBS), and the users can be allowed to specify p threshold to get the desired trade-off between speed and sensitivity for a particular sequence analysis. Moreover, the proposed method can also be generalized to large-scale annotation and sequence projects. [ABSTRACT FROM AUTHOR]

Non-invasive fetal electrocardiography (ECG) is based on the acquisition of signals from abdominal surface electrodes. The composite abdominal signal consists of the maternal electrocardiogram along with the fetal electrocardiogram and other electrical interferences. These recordings allow for the acquisition of valuable and reliable information that helps ensure fetal well-being during pregnancy. This paper introduces a procedure for fetal heart rate extraction from a single-channel abdominal ECG signal. The procedure is composed of three main stages: a method based on wavelet for signal denoising, a new clustering-based methodology for detecting fetal QRS complexes, and a final stage to correct false positives and false negatives. The novelty of the procedure thus relies on using clustering techniques to classify singularities from the abdominal ECG into three types: maternal QRS complexes, fetal QRS complexes, and noise. The amplitude and time distance of all the local maxima followed by a local minimum were selected as features for the clustering classification. A wide set of real abdominal ECG recordings from two different databases, providing a large range of different characteristics, was used to illustrate the efficiency of the proposed method. The accuracy achieved shows that the proposed technique exhibits a competitve performance when compared to other recent works in the literature and a better performance over threshold-based techniques. [ABSTRACT FROM AUTHOR]

Arabic script is highly sensitive to changes in meaning with respect to the accurate arrangement of diacritics and other related symbols. The most sensitive Arabic text available online is the Digital Qur’an, the sacred book of Revelation in Islam that all Muslims including non-Arabs recite as part of their worship. Due to the different characteristics of the Arabic letters like diacritics (punctuation symbols), kashida (extended letters) and other symbols, it is written and available in different styles like Kufi, Naskh, Thuluth, Uthmani, etc. As social media has become part of our daily life, posting downloaded Qur’anic verses from the web is common. This leads to the problem of authenticating the selected Qur’anic passages available in different styles. This paper presents a residual approach for authenticating Uthmani and plain Qur’an verses using one common database. Residual (difference) is obtained by analyzing the differences between Uthmani and plain Quranic styles using XOR operation. Based on predefined data, the proposed approach converts Uthmani text into plain text. Furthermore, we propose to use the Tuned BM algorithm (BMT) exact pattern matching algorithm to verify the substituted Uthmani verse with a given database of plain Qur’anic style. Experimental results show that the proposed approach is useful and effective in authenticating multi-style texts of the Qur’an with 87.1% accuracy. [ABSTRACT FROM AUTHOR]

The query-template alignment of proteins is one of the most critical steps of template-based modeling methods used to predict the 3D structure of a query protein. This alignment can be interpreted as a temporal classification or structured prediction task and first order Conditional Random Fields have been proposed for protein alignment and proven to be rather successful. Some other popular structured prediction problems, such as speech or image classification, have gained from the use of higher order Conditional Random Fields due to the well known higher order correlations that exist between their labels and features. In this paper, we propose and describe the use of higher order Conditional Random Fields for query-template protein alignment. The experiments carried out on different public datasets validate our proposal, especially on distantly-related protein pairs which are the most difficult to align. [ABSTRACT FROM AUTHOR]

The prediction of protein complexes from protein-protein interactions (PPIs) is a well-studied problem in bioinformatics. However, the currently available PPI data is not enough to describe all known protein complexes. In this paper, we express the problem of determining the minimum number of (additional) required protein-protein interactions as a graph theoretic problem under the constraint that each complex constitutes a connected component in a PPI network. For this problem, we develop two computational methods: one is based on integer linear programming (ILPMinPPI) and the other one is based on an existing greedy-type approximation algorithm (GreedyMinPPI) originally developed in the context of communication and social networks. Since the former method is only applicable to datasets of small size, we apply the latter method to a combination of the CYC2008 protein complex dataset and each of eight PPI datasets (STRING, MINT, BioGRID, IntAct, DIP, BIND, WI-PHI, iRefIndex). The results show that the minimum number of additional required PPIs ranges from 51 (STRING) to 964 (BIND), and that even the four best PPI databases, STRING (51), BioGRID (67), WI-PHI (93) and iRefIndex (85), do not include enough PPIs to form all CYC2008 protein complexes. We also demonstrate that the proposed problem framework and our solutions can enhance the prediction accuracy of existing PPI prediction methods. ILPMinPPI can be freely downloaded from . [ABSTRACT FROM AUTHOR]

RNA-protein binding is critical to gene regulation, controlling fundamental processes including splicing, translation, localization and stability, and aberrant RNA-protein interactions are known to play a role in a wide variety of diseases. However, molecular understanding of RNA-protein interactions remains limited; in particular, identification of RNA motifs that bind proteins has long been challenging, especially when such motifs depend on both sequence and structure. Moreover, although RNA binding proteins (RBPs) often contain more than one binding domain, algorithms capable of identifying more than one binding motif simultaneously have not been developed. In this paper we present a novel pipeline to determine binding peaks in crosslinking immunoprecipitation (CLIP) data, to discover multiple possible RNA sequence/structure motifs among them, and to experimentally validate such motifs. At the core is a new semi-automatic algorithm SARNAclust, the first unsupervised method to identify and deconvolve multiple sequence/structure motifs simultaneously. SARNAclust computes similarity between sequence/structure objects using a graph kernel, providing the ability to isolate the impact of specific features through the bulge graph formalism. Application of SARNAclust to synthetic data shows its capability of clustering 5 motifs at once with a V-measure value of over 0.95, while GraphClust achieves only a V-measure of 0.083 and RNAcontext cannot detect any of the motifs. When applied to existing eCLIP sets, SARNAclust finds known motifs for SLBP and HNRNPC and novel motifs for several other RBPs such as AGGF1, AKAP8L and ILF3. We demonstrate an experimental validation protocol, a targeted Bind-n-Seq-like high-throughput sequencing approach that relies on RNA inverse folding for oligo pool design, that can validate the components within the SLBP motif. Finally, we use this protocol to experimentally interrogate the SARNAclust motif predictions for protein ILF3. Our results support a newly identified partially double-stranded UUUUUGAGA motif similar to that known for the splicing factor HNRNPC. [ABSTRACT FROM AUTHOR]

In this paper, we propose a connectivity-preserving flocking algorithm for multi-agent systems in which the neighbor set of each agent is determined by the hybrid metric-topological distance so that the interaction topology can be represented as the range-limited Delaunay graph, which combines the properties of the commonly used disk graph and Delaunay graph. As a result, the proposed flocking algorithm has the following advantages over the existing ones. First, range-limited Delaunay graph is sparser than the disk graph so that the information exchange among agents is reduced significantly. Second, some links irrelevant to the connectivity can be dynamically deleted during the evolution of the system. Thus, the proposed flocking algorithm is more flexible than existing algorithms, where links are not allowed to be disconnected once they are created. Finally, the multi-agent system spontaneously generates a regular quasi-lattice formation without imposing the constraint on the ratio of the sensing range of the agent to the desired distance between two adjacent agents. With the interaction topology induced by the hybrid distance, the proposed flocking algorithm can still be implemented in a distributed manner. We prove that the proposed flocking algorithm can steer the multi-agent system to a stable flocking motion, provided the initial interaction topology of multi-agent systems is connected and the hysteresis in link addition is smaller than a derived upper bound. The correctness and effectiveness of the proposed algorithm are verified by extensive numerical simulations, where the flocking algorithms based on the disk and Delaunay graph are compared. [ABSTRACT FROM AUTHOR]

In this paper, we introduce sequence-based multiscale modeling for biomolecular data analysis. We employ spectral clustering method in our modeling and reveal the difference between sequence-based global scale clustering and local scale clustering. Essentially, two types of distances, i.e., Euclidean (or spatial) distance and genomic (or sequential) distance, can be used in data clustering. Clusters from sequence-based global scale models optimize spatial distances, meaning spatially adjacent loci are more likely to be assigned into the same cluster. Sequence-based local scale models, on the other hand, result in clusters that optimize genomic distances. That is to say, in these models, sequentially adjoining loci tend to be cluster together. We propose two sequence-based multiscale models (SeqMMs) for the study of chromosome hierarchical structures, including genomic compartments and topological associated domains (TADs). We find that genomic compartments are determined only by global scale information in the Hi-C data. The removal of all the local interactions within a band region as large as 10 Mb in genomic distance has almost no significant influence on the final compartment results. Further, in TAD analysis, we find that when the sequential scale is small, a tiny variation of diagonal band region in a contact map will result in a great change in the predicted TAD boundaries. When the scale value is larger than a threshold value, the TAD boundaries become very consistent. This threshold value is highly related to TAD sizes. By the comparison of our results with those previously obtained using a spectral clustering model, we find that our method is more robust and reliable. Finally, we demonstrate that almost all TAD boundaries from both clustering methods are local minimum of a TAD summation function. [ABSTRACT FROM AUTHOR]

In this paper, we present a research work on a novel methodology of identifying abnormal behaviors at the underlying network monitor layer during runtime based on the execution patterns of Web of Things (WoT) applications. An execution pattern of a WoT application is a sequence of profiled time delays between the invocations of involved Web services, and it can be obtained from WoT platforms. We convert the execution pattern to a time sequence of network flows that are generated when the WoT applications are executed. We consider such time sequences as a whitelist. This whitelist reflects the valid application execution patterns. At the network monitor layer, our applied RETE algorithm examines whether any given runtime sequence of network flow instances does not conform to the whitelist. Through this approach, it is possible to interpret a sequence of network flows with regard to application logic. Given such contextual information, we believe that the administrators can detect and reason about any abnormal behaviors more effectively. Our empirical evaluation shows that our RETE-based algorithm outperforms the baseline algorithm in terms of memory usage. [ABSTRACT FROM AUTHOR]

In this paper, we propose a face recognition algorithm based on a combination of vector quantization (VQ) and Markov stationary features (MSF). The VQ algorithm has been shown to be an effective method for generating features; it extracts a codevector histogram as a facial feature representation for face recognition. Still, the VQ histogram features are unable to convey spatial structural information, which to some extent limits their usefulness in discrimination. To alleviate this limitation of VQ histograms, we utilize Markov stationary features (MSF) to extend the VQ histogram-based features so as to add spatial structural information. We demonstrate the effectiveness of our proposed algorithm by achieving recognition results superior to those of several state-of-the-art methods on publicly available face databases. [ABSTRACT FROM AUTHOR]

DNA-binding proteins play pivotal roles in alternative splicing, RNA editing, methylating and many other biological functions for both eukaryotic and prokaryotic proteomes. Predicting the functions of these proteins from primary amino acids sequences is becoming one of the major challenges in functional annotations of genomes. Traditional prediction methods often devote themselves to extracting physiochemical features from sequences but ignoring motif information and location information between motifs. Meanwhile, the small scale of data volumes and large noises in training data result in lower accuracy and reliability of predictions. In this paper, we propose a deep learning based method to identify DNA-binding proteins from primary sequences alone. It utilizes two stages of convolutional neutral network to detect the function domains of protein sequences, and the long short-term memory neural network to identify their long term dependencies, an binary cross entropy to evaluate the quality of the neural networks. When the proposed method is tested with a realistic DNA binding protein dataset, it achieves a prediction accuracy of 94.2% at the Matthew’s correlation coefficient of 0.961. Compared with the LibSVM on the arabidopsis and yeast datasets via independent tests, the accuracy raises by 9% and 4% respectively. Comparative experiments using different feature extraction methods show that our model performs similar accuracy with the best of others, but its values of sensitivity, specificity and AUC increase by 27.83%, 1.31% and 16.21% respectively. Those results suggest that our method is a promising tool for identifying DNA-binding proteins. [ABSTRACT FROM AUTHOR]

Periplasmic Binding Proteins (PBPs) trap nutrients for their internalization into bacteria by ABC transporters. Ligand binding triggers PBP closure by bringing its two domains together like a Venus flytrap. The atomic determinants that control PBP opening and closure for nutrient capture and release are not known, although it is proposed that opening and ligand release occur while in contact with the ABC transporter for concurrent substrate translocation. In this paper we evaluated the effect of the isomerization of a conserved proline, located near the binding site, on the propensity of PBPs to open and close. ArgT/LAO from Salmonella typhimurium and HisJ from Escherichia coli were studied through molecular mechanics at two different temperatures: 300 and 323 K. Eight microseconds were simulated per protein to analyze protein opening and closure in the absence of the ABC transporter. We show that when the studied proline is in trans, closed empty LAO and HisJ can open. In contrast, with the proline in cis, opening transitions were much less frequent and characterized by smaller changes. The proline in trans also renders the open trap prone to close over a ligand. Our data suggest that the isomerization of this conserved proline modulates the PBP mechanism: the proline in trans allows the exploration of conformational space to produce trap opening and closure, while in cis it restricts PBP movement and could limit ligand release until in productive contact with the ABC transporter. This is the first time that a proline isomerization has been related to the control of a large conformational change like the PBP flytrap mechanism. [ABSTRACT FROM AUTHOR]

This paper introduces a new framework for the segmentation of different brain structures (white matter, gray matter, and cerebrospinal fluid) from 3D MR brain images at different life stages. The proposed segmentation framework is based on a shape prior built using a subset of co-aligned training images that is adapted during the segmentation process based on first- and second-order visual appearance characteristics of MR images. These characteristics are described using voxel-wise image intensities and their spatial interaction features. To more accurately model the empirical grey level distribution of the brain signals, we use a linear combination of discrete Gaussians (LCDG) model having positive and negative components. To accurately account for the large inhomogeneity in infant MRIs, a higher-order Markov-Gibbs Random Field (MGRF) spatial interaction model that integrates third- and fourth- order families with a traditional second-order model is proposed. The proposed approach was tested and evaluated on 102 3D MR brain scans using three metrics: the Dice coefficient, the 95-percentile modified Hausdorff distance, and the absolute brain volume difference. Experimental results show better segmentation of MR brain images compared to current open source segmentation tools. [ABSTRACT FROM AUTHOR]

Proteomic analysis of cancers' stages has provided new opportunities for the development of novel, highly sensitive diagnostic tools which helps early detection of cancer. This paper introduces a new feature ranking approach called FRMT. FRMT is based on the Technique for Order of Preference by Similarity to Ideal Solution method (TOPSIS) which select the most discriminative proteins from proteomics data for cancer staging. In this approach, outcomes of 10 feature selection techniques were combined by TOPSIS method, to select the final discriminative proteins from seven different proteomic databases of protein expression profiles. In the proposed workflow, feature selection methods and protein expressions have been considered as criteria and alternatives in TOPSIS, respectively. The proposed method is tested on seven various classifier models in a 10-fold cross validation procedure that repeated 30 times on the seven cancer datasets. The obtained results proved the higher stability and superior classification performance of method in comparison with other methods, and it is less sensitive to the applied classifier. Moreover, the final introduced proteins are informative and have the potential for application in the real medical practice. [ABSTRACT FROM AUTHOR]

Although recent developments in DNA sequencing have allowed for great leaps in both the quality and quantity of genome assembly projects, de novo assemblies still lack the efficiency and accuracy required for studying genetic variation of individuals. Thus, efficient and accurate methods for calling and genotyping genetic variants are fundamental to studying the genomes of individuals. We study the problem of genotyping insertion variants. We assume that the location of the insertion is given, and the task is to find the insertion sequence. Insertions are the hardest structural variant to genotype, because the insertion sequence must be assembled from the reads, whereas genotyping other structural variants only requires transformations of the reference genome. The current methods for constructing insertion variants are mostly linked to variation calling methods and are only able to construct small insertions. A sub-problem in genome assembly, the gap filling problem, provides techniques that are readily applicable to insertion genotyping. Gap filling takes the context and length of a missing sequence in a genome assembly and attempts to assemble the intervening sequence. In this paper we show how tools and methods for gap filling can be used to assemble insertion variants by modeling the problem of insertion genotyping as filling gaps in the reference genome. We further give a general read filtering scheme to make the method scalable to large data sets. Our results show that gap filling methods are competitive against insertion genotyping tools. We further show that read filtering improves performance of insertion genotyping especially for long insertions. Our experiments show that on long insertions the new proposed method is the most accurate one, whereas on short insertions it has comparable performance as compared against existing tools. [ABSTRACT FROM AUTHOR]