MGACA-Net: a novel deep learning based multi-scale guided attention and context aggregation for localization of knee anterior cruciate ligament tears region in MRI images

Anterior cruciate ligament (ACL) tears are a common knee injury that can have serious consequences and require medical intervention. Magnetic resonance imaging (MRI) is the preferred method for ACL tear diagnosis. However, manual segmentation of the ACL in MRI images is prone to human error and can be time-consuming. This study presents a new approach that uses deep learning technique for localizing the ACL tear region in MRI images. The proposed multi-scale guided attention-based context aggregation (MGACA) method applies attention mechanisms at different scales within the DeepLabv3+ architecture to aggregate context information and achieve enhanced localization results. The model was trained and evaluated on a dataset of 917 knee MRI images, resulting in 15265 slices, obtaining state-of-the-art results with accuracy scores of 98.63%, intersection over union (IOU) scores of 95.39%, Dice coefficient scores (DCS) of 97.64%, recall scores of 97.5%, precision scores of 98.21%, and F1 Scores of 97.86% on validation set data. Moreover, our method performed well in terms of loss values, with binary cross entropy combined with Dice loss (BCE_Dice_loss) and Dice_loss values of 0.0564 and 0.0236, respectively, on the validation set. The findings suggest that MGACA provides an accurate and efficient solution for automating the localization of ACL in knee MRI images, surpassing other state-of-the-art models in terms of accuracy and loss values. However, in order to improve robustness of the approach and assess its performance on larger data sets, further research is needed.

Diaporthe sp. F18; a new source of camptothecin-producing endophytic fungus from Nothapodytes nimmoniana growing in Sri Lanka

An endophytic fungus producing camptothecin (CPT) was isolated from the leaf of Nothapodytes nimmoniana (Sri Lanka), and culture conditions were optimised to enhance the yield of CPT. The TLC, HPLC-PDA, LC-MS/MS and spectroscopic data were used to identify and quantify CPT. Solvent extraction (chloroform: methanol 4:1 v/v) of submerged cultures in Sabouraud Dextrose Broth (SDB) detected CPT in the mycelial extract but not in the culture broth. The fungus was (KX212080) closely related to Diaporthe guangxiensis (MK335772) with 99% sequence similarity, thus tentatively identified as Diaporthe sp. F18. A significantly high CPT content (72.0 ± 0.2 µg/g) was produced in SDB, pH, 5.6 incubated at 30 °C under shake flask condition (150 rpm) for 14 days. Tryptophan significantly (p > 0.05) enhanced CPT production while ethanol increased it by 8-fold. This endophytic source produced higher CPT content than what has been reported hitherto in the literature, with fairly stable production up to sixth subculture generations.

Hybrid-Enhanced Siamese Similarity Models in Ligand-Based Virtual Screen

Information technology has become an integral aspect of the drug development process. The virtual screening process (VS) is a computational technique for screening chemical compounds in a reasonable amount of time and cost. The similarity search is one of the primary tasks in VS that estimates a molecule’s similarity. It is predicated on the idea that molecules with similar structures may also have similar activities. Many techniques for comparing the biological similarity between a target compound and each compound in the database have been established. Although the approaches have a strong performance, particularly when dealing with molecules with homogenous active structural, they are not enough good when dealing with structurally heterogeneous compounds. The previous works examined many deep learning methods in the enhanced Siamese similarity model and demonstrated that the Enhanced Siamese Multi-Layer Perceptron similarity model (SMLP) and the Siamese Convolutional Neural Network-one dimension similarity model (SCNN1D) have good outcomes when dealing with structurally heterogeneous molecules. To further improve the retrieval effectiveness of the similarity model, we incorporate the best two models in one hybrid model. The reason is that each method gives good results in some classes, so combining them in one hybrid model may improve the retrieval recall. Many designs of the hybrid models will be tested in this study. Several experiments on real-world data sets were conducted, and the findings demonstrated that the new approaches outperformed the previous method.

Convolutional Neural Network Model Based on 2D Fingerprint for Bioactivity Prediction

Determining and modeling the possible behaviour and actions of molecules requires investigating the basic structural features and physicochemical properties that determine their behaviour during chemical, physical, biological, and environmental processes. Computational approaches such as machine learning methods are alternatives to predicting the physiochemical properties of molecules based on their structures. However, the limited accuracy and high error rates of such predictions restrict their use. In this paper, a novel technique based on a deep learning convolutional neural network (CNN) for the prediction of chemical compounds' bioactivity is proposed and developed. The molecules are represented in the new matrix format Mol2mat, a molecular matrix representation adapted from the well-known 2D-fingerprint descriptors. To evaluate the performance of the proposed methods, a series of experiments were conducted using two standard datasets, namely the MDL Drug Data Report (MDDR) and Sutherland, datasets comprising 10 homogeneous and 14 heterogeneous activity classes. After analysing the eight fingerprints, all the probable combinations were investigated using the five best descriptors. The results showed that a combination of three fingerprints, ECFP4, EPFP4, and ECFC4, along with a CNN activity prediction process, achieved the highest performance of 98% AUC when compared to the state-of-the-art ML algorithms NaiveB, LSVM, and RBFN.

Machine Learning-Based Performance Comparison to Diagnose Anterior Cruciate Ligament Tears

In recent times, knee joint pains have become severe enough to make daily tasks difficult. Knee osteoarthritis is a type of arthritis and a leading cause of disability worldwide. The middle of the knee contains a vital portion, the anterior cruciate ligament (ACL). It is necessary to diagnose the ACL ruptured tears early to avoid surgery. The study aimed to perform a comparative analysis of machine learning models to identify the condition of three ACL tears. In contrast to previous studies, this study also considers imbalanced data distributions as machine learning techniques struggle to deal with this problem. The paper applied and analyzed four machine learning classification models, namely, random forest (RF), categorical boosting (Cat Boost), light gradient boosting machines (LGBM), and highly randomized classifier (ETC) on the balanced, structured dataset of ACL. After oversampling a hyperparameter adjustment, the above four models have achieved an average accuracy of 95.72%, 94.98%, 94.98%, and 98.26%. There are 2070 observations and eight features in the collection of three diagnosis ACL classes after oversampling. The area under curve value was approximately 0.998, respectively. Experiments were performed using twelve machine learning algorithms with imbalanced and balanced datasets. However, the accuracy of the imbalanced dataset has remained under 76% for all twelve models. After oversampling, the proposed model may contribute to the investigation of ACL tears on magnetic resonance imaging and other knee ligaments efficiently and automatically without involving radiologists.

Automated Knee MR Images Segmentation of Anterior Cruciate Ligament Tears

The anterior cruciate ligament (ACL) is one of the main stabilizer parts of the knee. ACL injury leads to causes of osteoarthritis risk. ACL rupture is common in the young athletic population. Accurate segmentation at an early stage can improve the analysis and classification of anterior cruciate ligaments tears. This study automatically segmented the anterior cruciate ligament (ACL) tears from magnetic resonance imaging through deep learning. The knee mask was generated on the original Magnetic Resonance (MR) images to apply a semantic segmentation technique with convolutional neural network architecture U-Net. The proposed segmentation method was measured by accuracy, intersection over union (IoU), dice similarity coefficient (DSC), precision, recall and F1-score of 98.4%, 99.0%, 99.4%, 99.6%, 99.6% and 99.6% on 11451 training images, whereas on the validation images of 3817 was, respectively, 97.7%, 93.8%,96.8%, 96.5%, 97.3% and 96.9%. We also provide dice loss of training and test datasets that have remained 0.005 and 0.031, respectively. The experimental results show that the ACL segmentation on JPEG MRI images with U-Nets achieves accuracy that outperforms the human segmentation. The strategy has promising potential applications in medical image analytics for the segmentation of knee ACL tears for MR images.

Similarity-Based Virtual Screen Using Enhanced Siamese Deep Learning Methods

Traditional drug production is a long and complex process that leads to new drug production. The virtual screening technique is a computational method that allows chemical compounds to be screened at an acceptable time and cost. Several databases contain information on various aspects of biologically active substances. Simple statistical tools are difficult to use because of the enormous amount of information and complex data samples of molecules that are structurally heterogeneous recorded in these databases. Many techniques for capturing the biological similarity between a test compound and a known target ligand in LBVS have been established. However, despite the good performances of the above methods compared to their prior, especially when dealing with molecules that have homogeneous active structural elements, they are not satisfied when dealing with molecules that are structurally heterogeneous. Deep learning models have recently achieved considerable success in a variety of disciplines due to their powerful generalization and feature extraction capabilities. Also, the Siamese network has been used in similarity models for more complicated data samples, especially with heterogeneous data samples. The main aim of this study is to enhance the performance of similarity searching, especially with molecules that are structurally heterogeneous. The Siamese architecture will be enhanced using two similarity distance layers with one fusion layer to further improve the similarity measurements between molecules and then adding many layers after the fusion layer for some models to improve the retrieval recall. In this architecture, several methods of deep learning have been used, which are long short-term memory (LSTM), gated recurrent unit (GRU), convolutional neural network-one dimension (CNN1D), and convolutional neural network-two dimensions (CNN2D). A series of experiments have been carried out on real-world data sets, and the results have shown that the proposed methods outperformed the existing methods.

Improved Deep Convolutional Neural Network to Classify Osteoarthritis from Anterior Cruciate Ligament Tear Using Magnetic Resonance Imaging

Anterior cruciate ligament (ACL) tear is caused by partially or completely torn ACL ligament in the knee, especially in sportsmen. There is a need to classify the ACL tear before it fully ruptures to avoid osteoarthritis. This research aims to identify ACL tears automatically and efficiently with a deep learning approach. A dataset was gathered, consisting of 917 knee magnetic resonance images (MRI) from Clinical Hospital Centre Rijeka, Croatia. The dataset we used consists of three classes: non-injured, partial tears, and fully ruptured knee MRI. The study compares and evaluates two variants of convolutional neural networks (CNN). We first tested the standard CNN model of five layers and then a customized CNN model of eleven layers. Eight different hyper-parameters were adjusted and tested on both variants. Our customized CNN model showed good results after a 25% random split using RMSprop and a learning rate of 0.001. The average evaluations are measured by accuracy, precision, sensitivity, specificity, and F1-score in the case of the standard CNN using the Adam optimizer with a learning rate of 0.001, i.e., 96.3%, 95%, 96%, 96.9%, and 95.6%, respectively. In the case of the customized CNN model, using the same evaluation measures, the model performed at 98.6%, 98%, 98%, 98.5%, and 98%, respectively, using an RMSprop optimizer with a learning rate of 0.001. Moreover, we also present our results on the receiver operating curve and area under the curve (ROC AUC). The customized CNN model with the Adam optimizer and a learning rate of 0.001 achieved 0.99 over three classes was highest among all. The model showed good results overall, and in the future, we can improve it to apply other CNN architectures to detect and segment other ligament parts like meniscus and cartilages.

Similarity-Based Virtual Screen Using Enhanced Siamese Multi-Layer Perceptron

Traditional drug development is a slow and costly process that leads to the production of new drugs. Virtual screening (VS) is a computational procedure that measures the similarity of molecules as one of its primary tasks. Many techniques for capturing the biological similarity between a test compound and a known target ligand have been established in ligand-based virtual screens (LBVSs). However, despite the good performances of the above methods compared to their predecessors, especially when dealing with molecules that have structurally homogenous active elements, they are not satisfied when dealing with molecules that are structurally heterogeneous. The main aim of this study is to improve the performance of similarity searching, especially with molecules that are structurally heterogeneous. The Siamese network will be used due to its capability to deal with complicated data samples in many fields. The Siamese multi-layer perceptron architecture will be enhanced by using two similarity distance layers with one fused layer, then multiple layers will be added after the fusion layer, and then the nodes of the model that contribute less or nothing during inference according to their signal-to-noise ratio values will be pruned. Several benchmark datasets will be used, which are: the MDL Drug Data Report (MDDR-DS1, MDDR-DS2, and MDDR-DS3), the Maximum Unbiased Validation (MUV), and the Directory of Useful Decoys (DUD). The results show the outperformance of the proposed method on standard Tanimoto coefficient (TAN) and other methods. Additionally, it is possible to reduce the number of nodes in the Siamese multilayer perceptron model while still keeping the effectiveness of recall on the same level.

Efficient Detection of Knee Anterior Cruciate Ligament from Magnetic Resonance Imaging Using Deep Learning Approach

The most commonly injured ligament in the human body is an anterior cruciate ligament (ACL). ACL injury is standard among the football, basketball and soccer players. The study aims to detect anterior cruciate ligament injury in an early stage via efficient and thorough automatic magnetic resonance imaging without involving radiologists, through a deep learning method. The proposed approach in this paper used a customized 14 layers ResNet-14 architecture of convolutional neural network (CNN) with six different directions by using class balancing and data augmentation. The performance was evaluated using accuracy, sensitivity, specificity, precision and F1 score of our customized ResNet-14 deep learning architecture with hybrid class balancing and real-time data augmentation after 5-fold cross-validation, with results of 0.920%, 0.916%, 0.946%, 0.916% and 0.923%, respectively. For our proposed ResNet-14 CNN the average area under curves (AUCs) for healthy tear, partial tear and fully ruptured tear had results of 0.980%, 0.970%, and 0.999%, respectively. The proposing diagnostic results indicated that our model could be used to detect automatically and evaluate ACL injuries in athletes using the proposed deep-learning approach.

Improved Deep Learning Based Method for Molecular Similarity Searching Using Stack of Deep Belief Networks

Virtual screening (VS) is a computational practice applied in drug discovery research. VS is popularly applied in a computer-based search for new lead molecules based on molecular similarity searching. In chemical databases similarity searching is used to identify molecules that have similarities to a user-defined reference structure and is evaluated by quantitative measures of intermolecular structural similarity. Among existing approaches, 2D fingerprints are widely used. The similarity of a reference structure and a database structure is measured by the computation of association coefficients. In most classical similarity approaches, it is assumed that the molecular features in both biological and non-biologically-related activity carry the same weight. However, based on the chemical structure, it has been found that some distinguishable features are more important than others. Hence, this difference should be taken consideration by placing more weight on each important fragment. The main aim of this research is to enhance the performance of similarity searching by using multiple descriptors. In this paper, a deep learning method known as deep belief networks (DBN) has been used to reweight the molecule features. Several descriptors have been used for the MDL Drug Data Report (MDDR) dataset each of which represents different important features. The proposed method has been implemented with each descriptor individually to select the important features based on a new weight, with a lower error rate, and merging together all new features from all descriptors to produce a new descriptor for similarity searching. Based on the extensive experiments conducted, the results show that the proposed method outperformed several existing benchmark similarity methods, including Bayesian inference networks (BIN), the Tanimoto similarity method (TAN), adapted similarity measure of text processing (ASMTP) and the quantum-based similarity method (SQB). The results of this proposed multi-descriptor-based on Stack of deep belief networks method (SDBN) demonstrated a higher accuracy compared to existing methods on structurally heterogeneous datasets.

Cesarean Law: a turning point in the fight against the Brazilian epidemic of cesarean section?

In the opposite direction to the process that had been gradually changing birth forms and indicators in Brazil, in 2019 the State of São Paulo (located in southeastern Brazil) enacted Law 17. 137, which guarantees all pregnant women the choice of a cesarean section from the 39 weeks of pregnancy, regardless of the obstetric indication. That is a preliminary qualitative analysis of a doctoral investigation, we are looking for show some points of inflection of this law to combat the cesarean epidemic. Affiliated to the theoretical-methodological approach of discursive practices and the production of meanings in daily, it investigates the discourses that support the current policies to encourage humanized obstetric care based on scientific evidence, built over the last 20 years, and those who supported the approval of this legal norm, known as the Cesarean Law. One of the inflection points of Law concerns the quality of prenatal care and the way that women receive information about childbirth during pregnancy. Because lack of information and insecurity are important factors in the choice of women by the type of delivery. Iatrogenic prematurity is one of the biggest problems of Brazilian cesarean section epidemic. Thus, even after 39 weeks of pregnancy, there is no guarantee of baby's maturity. Since the 90's, the Brazilian government had been encouraging the insertion of midwives and nurse midwives in the childbirth care of all women at regular risk and encouraged the creating of childbirth centers as well an adequate classification of gestational risk. At this point, the law affronts the current organization of the system, as it prioritizes attendance by doctors over professional midwives. The cesarean rates and other health indicators are not available yet after the approval of the law in São Paulo state. However, we can postulate that it will mean a setback in the fight against the epidemic of cesarean sections in Brazil.

Key messages

The Cesarean law approved in the state of São Paulo / BR presents inflection points in the fight against the cesarean section epidemic. The Cesarean law approved in the state of São Paulo / BR ignores important issues in the Brazilian obstetric scenario.

[Repetitive resection and intrasurgery radiation therapy of brain malignant gliomas: history of question and modern state of problem]

Numerous studies have shown that the degree of primary resection of malignant gliomas of the brain (MG) directly correlates with rates of relapse-free and overall patient survival. Currently, there is no unequivocal opinion regarding the indications and effectiveness of repeated resection in relapse of MG after combined treatment. Surgical intervention, taking into account the pathomorphological features of these tumors, is not healing and should be supplemented with certain methods of adjuvant treatment. The article reviews and analyzes publications devoted to repeated resection and various methods of intraoperative radiation therapy in the treatment of MG. Based on the analysis, the authors of the article came to the conclusion that it is advisable to start their own research on the use of intraoperative balloon brachytherapy in the treatment of recurrent MG based on modern technological solutions.

High-intensity interval training induced PGC-1∝ and AdipoR1 gene expressions and improved insulin sensitivity in obese individuals

INTRODUCTION

High-intensity interval training (HIIT) has been found to improve cardiometabolic health outcome as compared to moderate-intensity continuous exercise. However, there is still limited data on the benefits of HIIT on the expression of regulatory proteins that are linked to skeletal muscle metabolism and insulin sensitivity in obese adults. This study investigated the effects of HIIT intervention on expressions of peroxisome proliferatoractivated receptor-γ coactivator 1-∝ (PGC-1∝) and adiponectin receptor-1 (AdipoR1), insulin sensitivity (HOMAIR index), and body composition in overweight/obese individuals.

METHODS

Fifty overweight/obese individuals aged 22-29 years were assigned to either no-exercise control (n=25) or HIIT (n=25) group. The HIIT group underwent a 12-week intervention, three days/week, with intensity of 65-80% of age-based maximum heart rate. Anthropometric measurements, homeostatic model of insulin resistance (HOMA-IR) and gene expression analysis were conducted at baseline and post intervention.

RESULTS

Significant time-by-group interactions (p<0.001) were found for body weight, BMI, waist circumference and body fat percentage. The HIIT group had lower body weight (2.3%, p<0.001), BMI (2.7%, p<0.001), waist circumference (2.4%, p<0.001) and body fat percentage (4.3%, p<0.001) post intervention. Compared to baseline, expressions of PGC-1∝ and AdipoR1 were increased by approximately three-fold (p=0.019) and two-fold (p=0.003) respectively, along with improved insulin sensitivity (33%, p=0.019) in the HIIT group.

CONCLUSION

Findings suggest that HIIT possibly improved insulin sensitivity through modulation of PGC-1∝ and AdipoR1. This study also showed that improved metabolic responses can occur despite modest reduction in body weight in overweight/obese individuals undergoing HIIT intervention.

Acute anti-inflammatory and anti-nociceptive activities of crude extracts, alkaloid fraction and evolitrine from Acronychia pedunculata leaves

ETHNOPHARMACOLOGICAL RELEVANCE

Acronychia pedunculata (family: Rutaceae) is one of the commonly used medicinal plants in Sri Lankan traditional medicine. Different parts of this plant are used for the treatment of inflammatory conditions in the form of medicinal oils and herbal porridge.

AIM OF THE STUDY

The present study aimed to evaluate the anti-nociceptive activity and anti-inflammatory activity with their mechanisms and the acute toxicity of crude extracts of the fresh leaves of A. pedunculata for scientific validation of the ethnopharmacological claims for this plant. Further, attention has been focused on the isolation of active compounds from active fractions of the crude extracts.

MATERIALS AND METHODS

The acute anti-inflammatory effect of the aqueous (AELA) and 70% ethanol crude extracts (EELA) and alkaloid fraction of A. pedunculata leaves were evaluated by the determination of inhibition of hind paw oedema induced by carrageenan in Wistar rats. Evolitrine was identified as the major alkaloid with significant bioactivities by column chromatography and NMR. The anti-nociceptive and anti-histamine activities of EELA and evolitrine were evaluated by acetic acid induced writhing and wheal formation tests respectively. In addition, in-vitro (2, 2-diphenyl-1-picrylhydrazyl (DPPH) assay) and in-vivo (lipid peroxidation assay) anti-oxidant activity, nitric oxide (NO) inhibitory activity and acute toxicity of EELA were evaluated.

RESULTS

Acute anti-inflammatory activity of AELA and EELA were dose-dependent. EELA was more active than AELA. The 200 mg/kg body weight (b. w.) dose of EELA was found as the minimum effective dose with maximum inhibition (78%) of oedema at 5th hour compared to the negative control (p < 0.05). Evolitrine was isolated and identified as an active anti-inflammatory and analgesic compound from active alkaloid fraction of EELA. Evolitrine showed activity enhancement when compared with crude EELA. The anti-inflammatory and analgesic activities of evolitrine (50 mg/kg b. w.) were comparable to that of reference drugs indomethacin (5 mg/kg b. w) and acetylsalicylic acid (100 mg/kg b. w.). The significant (p < 0.05) anti-histamine activity, DPPH scavenging in-vitro anti-oxidant activity, in-vivo lipid peroxidation inhibitory activity in-vivo, NO inhibitory activity of EELA as compared with relevant negative controls, were identified as probable mechanisms which mediated its anti-inflammatory action. Further, EELA showed a high safety margin in the limited dose acute toxicity study.

CONCLUSION

The findings of the current study rationalize the usage of leaves of A. pedunculata in Sri Lankan traditional medicine as an analgesic and anti-inflammatory agent. Possible mechanisms mediating this activity included anti-histamine, anti-oxidant and NO inhibitory activities. Evolitrine is the major analgesic and anti-inflammatory compound isolated from the active alkaloid fraction of EELA.

Aspect extraction on user textual reviews using multi-channel convolutional neural network

Aspect extraction is a subtask of sentiment analysis that deals with identifying opinion targets in an opinionated text. Existing approaches to aspect extraction typically rely on using handcrafted features, linear and integrated network architectures. Although these methods can achieve good performances, they are time-consuming and often very complicated. In real-life systems, a simple model with competitive results is generally more effective and preferable over complicated models. In this paper, we present a multichannel convolutional neural network for aspect extraction. The model consists of a deep convolutional neural network with two input channels: a word embedding channel which aims to encode semantic information of the words and a part of speech (POS) tag embedding channel to facilitate the sequential tagging process. To get the vector representation of words, we initialized the word embedding channel and the POS channel using pretrained word2vec and one-hot-vector of POS tags, respectively. Both the word embedding and the POS embedding vectors were fed into the convolutional layer and concatenated to a one-dimensional vector, which is finally pooled and processed using a Softmax function for sequence labeling. We finally conducted a series of experiments using four different datasets. The results indicated better performance compared to the baseline models.

Successful Data Science Projects: Lessons Learned from Kaggle Competition

The workflow from data understanding to deployment of an analytical model of a data science project begins at framing the problem at hand, a task that is typically business-oriented and requires human-to-human interaction. However, the next three steps: data understanding, feature extraction, and model building that come next in the pipeline are the key to successful data science projects. Failing to fully understand the requirements of each of these three steps can negatively affect the performance of the proposed system. Hence, the current study tries to answer the following question “What are the requirements of a successful data science project?” To answer this question, we will use the solution that we built to measure the relevance of local search results of small online e-businesses and submitted to Kaggle data science platform to shed light on why our solution did not achieve a top position among other competitors. Evaluation of the design that we submitted to the competition is going to be carried out in the spirit of the three winning submissions. Our results revealed that well-performed data preprocessing, well-defined features, and model ensembling are critical for building successful data science projects. Such a clarification provides insight into specific aspects of model design to help others including Kagglers avoid possible mistakes while approaching their data science projects.

Semantic concept model using Wikipedia semantic features

Wikipedia has become a high coverage knowledge source which has been used in many research areas such as natural language processing, text mining and information retrieval. Several methods have been introduced for extracting explicit or implicit relations from Wikipedia to represent semantics of concepts/words. However, the main challenge in semantic representation is how to incorporate different types of semantic relations to capture more semantic evidences of the associations of concepts. In this article, we propose a semantic concept model that incorporates different types of semantic features extracting from Wikipedia. For each concept that corresponds to an article, four semantic features are introduced: template links, categories, salient concepts and topics. The proposed model is based on the probability distributions that are defined for these semantic features of a Wikipedia concept. The template links and categories are the document-level features which are directly extracted from the structured information included in the article. On the other hand, the salient concepts and topics are corpus-level features which are extracted to capture implicit relations among concepts. For the salient concepts feature, the distributional-based method is utilised on the hypertext corpus to extract this feature for each Wikipedia concept. Then, the probability product kernel is used to improve the weight of each concept in this feature. For the topic feature, the Labelled latent Dirichlet allocation is adapted on the supervised multi-label of Wikipedia to train the probabilistic model of this feature. Finally, we used the linear interpolation for incorporating these semantic features into the probabilistic model to estimate the semantic relation probability of the specific concept over Wikipedia articles. The proposed model is evaluated on 12 benchmark datasets in three natural language processing tasks: measuring the semantic relatedness of concepts/words in general and in the biomedical domain, semantic textual relatedness measurement and measuring the semantic compositionality of noun compounds. The model is also compared with five methods that depends on separate semantic features in Wikipedia. Experimental results show that the proposed model achieves promising results in three tasks and outperforms the baseline methods in most of the evaluation datasets. This implies that incorporation of explicit and implicit semantic features is useful for representing semantics of concepts in Wikipedia.

Quantum probability ranking principle for ligand-based virtual screening

Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP). The QPRP ranking criteria would make an attempt to draw an analogy between the physical experiment and molecular structure ranking process for 2D fingerprints in ligand based virtual screening (LBVS). The development of QPRP criteria in LBVS has employed the concepts of quantum at three different levels, firstly at representation level, this model makes an effort to develop a new framework of molecular representation by connecting the molecular compounds with mathematical quantum space. Secondly, estimate the similarity between chemical libraries and references based on quantum-based similarity searching method. Finally, rank the molecules using QPRP approach. Simulated virtual screening experiments with MDL drug data report (MDDR) data sets showed that QPRP outperformed the classical ranking principle (PRP) for molecular chemical compounds.

Recognition of side effects as implicit-opinion words in drug reviews

Purpose

Many opinion-mining systems and tools have been developed to provide users with the attitudes of people toward entities and their attributes or the overall polarities of documents. In addition, side effects are one of the critical measures used to evaluate a patient’s opinion for a particular drug. However, side effect recognition is a challenging task, since side effects coincide with disease symptoms lexically and syntactically. The purpose of this paper is to extract drug side effects from drug reviews as an integral implicit-opinion words.

Design/methodology/approach

This paper proposes a detection algorithm to a medical-opinion-mining system using rule-based and support vector machines (SVM) algorithms. A corpus from 225 drug reviews was manually annotated by a medical expert for training and testing.

Findings

The results show that SVM significantly outperforms a rule-based algorithm. However, the results of both algorithms are encouraging and a good foundation for future research. Obviating the limitations and exploiting combined approaches would improve the results.

Practical implications

An automatic extraction for adverse drug effects information from online text can help regulatory authorities in rapid information screening and extraction instead of manual inspection and contributes to the acceleration of medical decision support and safety alert generation.

Originality/value

The results of this study can help database curators in compiling adverse drug effects databases and researchers to digest the huge amount of textual online information which is growing rapidly.

The Power of Implicit Social Relation in Rating Prediction of Social Recommender Systems

The explosive growth of social networks in recent times has presented a powerful source of information to be utilized as an extra source for assisting in the social recommendation problems. The social recommendation methods that are based on probabilistic matrix factorization improved the recommendation accuracy and partly solved the cold-start and data sparsity problems. However, these methods only exploited the explicit social relations and almost completely ignored the implicit social relations. In this article, we firstly propose an algorithm to extract the implicit relation in the undirected graphs of social networks by exploiting the link prediction techniques. Furthermore, we propose a new probabilistic matrix factorization method to alleviate the data sparsity problem through incorporating explicit friendship and implicit friendship. We evaluate our proposed approach on two real datasets, Last.Fm and Douban. The experimental results show that our method performs much better than the state-of-the-art approaches, which indicates the importance of incorporating implicit social relations in the recommendation process to address the poor prediction accuracy.

Adapting Document Similarity Measures for Ligand-Based Virtual Screening

Quantifying the similarity of molecules is considered one of the major tasks in virtual screening. There are many similarity measures that have been proposed for this purpose, some of which have been derived from document and text retrieving areas as most often these similarity methods give good results in document retrieval and can achieve good results in virtual screening. In this work, we propose a similarity measure for ligand-based virtual screening, which has been derived from a text processing similarity measure. It has been adopted to be suitable for virtual screening; we called this proposed measure the Adapted Similarity Measure of Text Processing (ASMTP). For evaluating and testing the proposed ASMTP we conducted several experiments on two different benchmark datasets: the Maximum Unbiased Validation (MUV) and the MDL Drug Data Report (MDDR). The experiments have been conducted by choosing 10 reference structures from each class randomly as queries and evaluate them in the recall of cut-offs at 1% and 5%. The overall obtained results are compared with some similarity methods including the Tanimoto coefficient, which are considered to be the conventional and standard similarity coefficients for fingerprint-based similarity calculations. The achieved results show that the performance of ligand-based virtual screening is better and outperforms the Tanimoto coefficients and other methods.

Arrhythmia recognition and classification using combined linear and nonlinear features of ECG signals

Arrhythmia is a cardiac condition caused by abnormal electrical activity of the heart, and an electrocardiogram (ECG) is the non-invasive method used to detect arrhythmias or heart abnormalities. Due to the presence of noise, the non-stationary nature of the ECG signal (i.e. the changing morphology of the ECG signal with respect to time) and the irregularity of the heartbeat, physicians face difficulties in the diagnosis of arrhythmias. The computer-aided analysis of ECG results assists physicians to detect cardiovascular diseases. The development of many existing arrhythmia systems has depended on the findings from linear experiments on ECG data which achieve high performance on noise-free data. However, nonlinear experiments characterize the ECG signal more effectively sense, extract hidden information in the ECG signal, and achieve good performance under noisy conditions. This paper investigates the representation ability of linear and nonlinear features and proposes a combination of such features in order to improve the classification of ECG data. In this study, five types of beat classes of arrhythmia as recommended by the Association for Advancement of Medical Instrumentation are analyzed: non-ectopic beats (N), supra-ventricular ectopic beats (S), ventricular ectopic beats (V), fusion beats (F) and unclassifiable and paced beats (U). The characterization ability of nonlinear features such as high order statistics and cumulants and nonlinear feature reduction methods such as independent component analysis are combined with linear features, namely, the principal component analysis of discrete wavelet transform coefficients. The features are tested for their ability to differentiate different classes of data using different classifiers, namely, the support vector machine and neural network methods with tenfold cross-validation. Our proposed method is able to classify the N, S, V, F and U arrhythmia classes with high accuracy (98.91%) using a combined support vector machine and radial basis function method.

A Quantum-Based Similarity Method in Virtual Screening

One of the most widely-used techniques for ligand-based virtual screening is similarity searching. This study adopted the concepts of quantum mechanics to present as state-of-the-art similarity method of molecules inspired from quantum theory. The representation of molecular compounds in mathematical quantum space plays a vital role in the development of quantum-based similarity approach. One of the key concepts of quantum theory is the use of complex numbers. Hence, this study proposed three various techniques to embed and to re-represent the molecular compounds to correspond with complex numbers format. The quantum-based similarity method that developed in this study depending on complex pure Hilbert space of molecules called Standard Quantum-Based (SQB). The recall of retrieved active molecules were at top 1% and top 5%, and significant test is used to evaluate our proposed methods. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints. Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.

Existing plagiarism detection techniques

Purpose

– The purpose of this paper is to analyse the state-of-the-art techniques used to detect plagiarism in terms of their limitations, features, taxonomies and processes.

Design/methodology/approach

– The method used to execute this study consisted of a comprehensive search for relevant literature via six online database repositories namely; IEEE xplore, ACM Digital Library, ScienceDirect, EI Compendex, Web of Science and Springer using search strings obtained from the subject of discussion.

Findings

– The findings revealed that existing plagiarism detection techniques require further enhancements as existing techniques are incapable of efficiently detecting plagiarised ideas, figures, tables, formulas and scanned documents.

Originality/value

– The contribution of this study lies in its ability to have exposed the current trends in plagiarism detection researches and identify areas where further improvements are required so as to complement the performances of existing techniques.

Weighted voting-based consensus clustering for chemical structure databases

The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures.

Condorcet and borda count fusion method for ligand-based virtual screening

Background

It is known that any individual similarity measure will not always give the best recall of active molecule structure for all types of activity classes. Recently, the effectiveness of ligand-based virtual screening approaches can be enhanced by using data fusion. Data fusion can be implemented using two different approaches: group fusion and similarity fusion. Similarity fusion involves searching using multiple similarity measures. The similarity scores, or ranking, for each similarity measure are combined to obtain the final ranking of the compounds in the database.

Results

The Condorcet fusion method was examined. This approach combines the outputs of similarity searches from eleven association and distance similarity coefficients, and then the winner measure for each class of molecules, based on Condorcet fusion, was chosen to be the best method of searching. The recall of retrieved active molecules at top 5% and significant test are used to evaluate our proposed method. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints.

Conclusions

Simulated virtual screening experiments with the standard two data sets show that the use of Condorcet fusion provides a very simple way of improving the ligand-based virtual screening, especially when the active molecules being sought have a lowest degree of structural heterogeneity. However, the effectiveness of the Condorcet fusion was increased slightly when structural sets of high diversity activities were being sought.

Chemical named entities recognition: a review on approaches and applications

The rapid increase in the flow rate of published digital information in all disciplines has resulted in a pressing need for techniques that can simplify the use of this information. The chemistry literature is very rich with information about chemical entities. Extracting molecules and their related properties and activities from the scientific literature to "text mine" these extracted data and determine contextual relationships helps research scientists, particularly those in drug development. One of the most important challenges in chemical text mining is the recognition of chemical entities mentioned in the texts. In this review, the authors briefly introduce the fundamental concepts of chemical literature mining, the textual contents of chemical documents, and the methods of naming chemicals in documents. We sketch out dictionary-based, rule-based and machine learning, as well as hybrid chemical named entity recognition approaches with their applied solutions. We end with an outlook on the pros and cons of these approaches and the types of chemical entities extracted.

Combining multiple clusterings of chemical structures using cluster-based similarity partitioning algorithm

Many types of clustering techniques for chemical structures have been used in the literature, but it is known that any single method will not always give the best results for all types of applications. Recent work on consensus clustering methods is motivated because of the successes of combining multiple classifiers in many areas and the ability of consensus clustering to improve the robustness, novelty, consistency and stability of individual clusterings. In this paper, the Cluster-based Similarity Partitioning Algorithm (CSPA) was examined for improving the quality of chemical structures clustering. The effectiveness of clustering was evaluated based on the ability to separate active from inactive molecules in each cluster and the results were compared with the Ward&#39;s clustering method. The chemical dataset MDL Drug Data Report (MDDR) database was used for experiments. The results, obtained by combining multiple clusterings, showed that the consensus clustering method can improve the robustness, novelty and stability of chemical structures clustering.

Prediction of new bioactive molecules using a Bayesian belief network

Natural products and synthetic compounds are a valuable source of new small molecules leading to novel drugs to cure diseases. However identifying new biologically active small molecules is still a challenge. In this paper, we introduce a new activity prediction approach using Bayesian belief network for classification (BBNC). The roots of the network are the fragments composing a compound. The leaves are, on one side, the activities to predict and, on another side, the unknown compound. The activities are represented by sets of known compounds, and sets of inactive compounds are also used. We calculated a similarity between an unknown compound and each activity class. The more similar activity is assigned to the unknown compound. We applied this new approach on eight well-known data sets extracted from the literature and compared its performance to three classical machine learning algorithms. Experiments showed that BBNC provides interesting prediction rates (from 79% accuracy for high diverse data sets to 99% for low diverse ones) with a short time calculation. Experiments also showed that BBNC is particularly effective for homogeneous data sets but has been found to perform less well with structurally heterogeneous sets. However, it is important to stress that we believe that using several approaches whenever possible for activity prediction can often give a broader understanding of the data than using only one approach alone. Thus, BBNC is a useful addition to the computational chemist's toolbox.

Alteration of cell cytoskeleton and functions of cell recovery of normal human osteoblast cells caused by factors associated with real space flight

Experiments involving short-term space flight have shown an adverse effect on the physiology, morphology and functions of cells investigated. The causes for this effect on cells are: microgravity, temperature fluctuations, mechanical stress, hypergravity, nutrient restriction and others. However, the extent to which these adverse effects can be repaired by short-term space flown cells when recultured in conditions of normal gravity remains unclear. Therefore this study aimed to investigate the effect of short-term spaceflight on cytoskeleton distribution and recovery of cell functions of normal human osteoblast cells. The ultrastructure was evaluated using ESEM. Fluorescent staining was done using Hoechst, Mito Tracker CMXRos and Tubulin Tracker Green for cytoskeleton. Gene expression of cell functions was quantified using qPCR. As a result, recovered cells did not show any apoptotic markers when compared with control. Tubulin volume density (p<0.001) was decreased significantly when compared to control, while mitochondria volume density was insignificantly elevated. Gene expression for IL-6 (p<0.05) and sVCAM-1 (p<0.001) was significantly decreased while alkaline phosphatase (p<0.001), osteocalcin and sICAM (p<0.05) were significantly increased in the recovered cells compared to the control ones. The changes in gene and protein expression of collagen 1A, osteonectin, osteoprotegerin and beta-actin, caused by short-term spaceflight, were statistically not significant. These data indicate that short term space flight causes morphological changes in osteoblast cells which are consistent with hypertrophy, reduced cell differentiation and increased release of monocyte attracting proteins. The long-term effect of these changes on bone density and remodeling requires more detailed studies.

Consensus methods for combining multiple clusterings of chemical structures

The goal of consensus clustering methods is to find a consensus partition that optimally summarizes an ensemble and improves the quality of clustering compared with single clustering algorithms. In this paper, an enhanced voting-based consensus method was introduced and compared with other consensus clustering methods, including co-association-based, graph-based, and voting-based consensus methods. The MDDR and MUV data sets were used for the experiments and were represented by three 2D fingerprints: ALOGP, ECFP_4, and ECFC_4. The results were evaluated based on the ability of the clustering method to separate active from inactive molecules in each cluster using four criteria: F-measure, Quality Partition Index (QPI), Rand Index (RI), and Fowlkes-Mallows Index (FMI). The experiments suggest that the consensus methods can deliver significant improvements for the effectiveness of chemical structures clustering.

Information Theory and Voting Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures

Many consensus clustering methods have been applied in different areas such as pattern recognition, machine learning, information theory and bioinformatics. However, few methods have been used for chemical compounds clustering. In this paper, an information theory and voting based algorithm (Adaptive Cumulative Voting-based Aggregation Algorithm A-CVAA) was examined for combining multiple clusterings of chemical structures. The effectiveness of clusterings was evaluated based on the ability of the clustering method to separate active from inactive molecules in each cluster, and the results were compared with Ward's method. The chemical dataset MDL Drug Data Report (MDDR) and the Maximum Unbiased Validation (MUV) dataset were used. Experiments suggest that the adaptive cumulative voting-based consensus method can improve the effectiveness of combining multiple clusterings of chemical structures.

Graph-Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures

Consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics. In this paper, consensus clustering is used for combining the clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster. Two graph-based consensus clustering methods were examined. The Quality Partition Index method (QPI) was used to evaluate the clusterings and the results were compared to the Ward's clustering method. Two homogeneous and heterogeneous subsets DS1-DS2 of MDL Drug Data Report database (MDDR) were used for experiments and represented by two 2D fingerprints. The results, obtained by a combination of multiple runs of an individual clustering and a single run of multiple individual clusterings, showed that graph-based consensus clustering methods can improve the effectiveness of chemical structures clusterings.

Voting-based consensus clustering for combining multiple clusterings of chemical structures

BACKGROUND

Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few consensus clustering methods have been applied for combining multiple clusterings of chemical structures. It is known that any individual clustering method will not always give the best results for all types of applications. So, in this paper, three voting and graph-based consensus clusterings were used for combining multiple clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster.

RESULTS

The cumulative voting-based aggregation algorithm (CVAA), cluster-based similarity partitioning algorithm (CSPA) and hyper-graph partitioning algorithm (HGPA) were examined. The F-measure and Quality Partition Index method (QPI) were used to evaluate the clusterings and the results were compared to the Ward's clustering method. The MDL Drug Data Report (MDDR) dataset was used for experiments and was represented by two 2D fingerprints, ALOGP and ECFP_4. The performance of voting-based consensus clustering method outperformed the Ward's method using F-measure and QPI method for both ALOGP and ECFP_4 fingerprints, while the graph-based consensus clustering methods outperformed the Ward's method only for ALOGP using QPI. The Jaccard and Euclidean distance measures were the methods of choice to generate the ensembles, which give the highest values for both criteria.

CONCLUSIONS

The results of the experiments show that consensus clustering methods can improve the effectiveness of chemical structures clusterings. The cumulative voting-based aggregation algorithm (CVAA) was the method of choice among consensus clustering methods.

Ligand-based virtual screening using Bayesian inference network and reweighted fragments

Many of the similarity-based virtual screening approaches assume that molecular fragments that are not related to the biological activity carry the same weight as the important ones. This was the reason that led to the use of Bayesian networks as an alternative to existing tools for similarity-based virtual screening. In our recent work, the retrieval performance of the Bayesian inference network (BIN) was observed to improve significantly when molecular fragments were reweighted using the relevance feedback information. In this paper, a set of active reference structures were used to reweight the fragments in the reference structure. In this approach, higher weights were assigned to those fragments that occur more frequently in the set of active reference structures while others were penalized. Simulated virtual screening experiments with MDL Drug Data Report datasets showed that the proposed approach significantly improved the retrieval effectiveness of ligand-based virtual screening, especially when the active molecules being sought had a high degree of structural heterogeneity.

Outcome of corticosteroid injection versus physiotherapy in the treatment of mild trigger fingers

We compared the effectiveness of physiotherapy and corticosteroid injection treatment in the management of mild trigger fingers. Mild trigger fingers are those with mild crepitus, uneven finger movements and actively correctable triggering. This is a single-centred, prospective, block randomized study with 74 patients; 39 patients for steroid injection and 35 patients for physiotherapy. The study duration was from Jun 2009 until August 2010. Evaluation was done at 6 weeks, 3 months and 6 months post-treatment. At 3 months, the success rate (absence of pain and triggering) for those receiving steroid injection was 97.4% and physiotherapy 68.6%. The group receiving steroid injection also had lower pain score, higher rate of satisfaction, stronger grip strength and early recovery to near normal function (findings were all significant, p < 0.05). At 6 months, only those who were successfully treated were further questioned on recurrence (presence of pain and triggering). Those who received corticosteroid injections had a significant recurrence rate of pain but not triggering. The physiotherapy group had no recurrence of pain or triggering due to the type of triggering responsive to physiotherapy or possibly due to awareness of physiotherapy exercises. Perhaps they were able to institute self-treatment on early onset of symptoms of trigger fingers. We conclude that corticosteroid injection has a better outcome compared to physiotherapy in the treatment of mild trigger fingers but physiotherapy may have a role in prevention of recurrence.