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Cataracts are a prevalent ophthalmic disease worldwide, and research on the risk factors for cataracts occurrence is actively being conducted. This study aimed to investigate the relationship between nutrient intake and cataracts in the older adult population in Korea. We analyzed data from Korean adults over the age of 60 years (cataract: 2137, non-cataract: 3497) using the Korean National Health and Nutrition Examination Survey. We performed univariate simple and multiple logistic regressions, adjusting for socio-demographic, medical history, and lifestyle, to identify the associations between nutrient intake and cataracts. A higher intake of vitamin B1 in the male group was associated with a lower incidence of cataracts. A lower intake of polyunsaturated fatty acids and vitamin A, and a higher intake of vitamin B2 in the female group were associated with a higher incidence of cataracts. Our study demonstrated that polyunsaturated fatty acids, vitamin A, and vitamin B2 could affect the incidence of cataracts according to sex. The findings could be used to control nutrient intake for cataract prevention.

BACKGROUND The prevalence of cataract among the Korean older adult population is rapidly increasing. To prevent the disease at the individual level through diet control, it is important to examine which nutrients are highly associated with cataract. OBJECTIVE This study aimed to investigate the relationship between nutrient intake and cataract in the older adult population in Korea. METHODS We analyzed data from 5,634 Korean adults over the age of 60 years using the Korean National Health and Nutrition Examination Survey. We performed univariate simple and multiple logistic regressions to identify the associations between nutrient intake and cataracts. Additionally, multiple logistic regression was applied to the factor analysis results to identify the associations between sets of nutrient variables and cataracts. RESULTS The study sample included 2,137 individuals (764 men and 1,373 women) with cataract and 3,497 individuals (1,662 men and 1,835 women) without cataracts. The intake of polyunsaturated fatty acids, phosphorus, and vitamin B1 were statistically significant (P CONCLUSIONS Our study demonstrated that polyunsaturated fatty acids, monounsaturated fatty acids, phosphorus, sugar, vitamin B1, and vitamin A can affect the incidence of cataracts by sex. The findings of this study could be used to control nutrient intake for cataract prevention based on sex and age.

Atrial fibrillation (AF) is a well-known risk factor for stroke. Predicting the risk is important to prevent the first and secondary attacks of cerebrovascular diseases by determining early treatment. This study aimed to predict the ischemic stroke in AF patients based on the massive and complex Korean National Health Insurance (KNHIS) data through a machine learning approach.We extracted 65-dimensional features, including demographics, health examination, and medical history information, of 754,949 patients with AF from KNHIS. Logistic regression was used to determine whether the extracted features had a statistically significant association with ischemic stroke occurrence. Then, we constructed the ischemic stroke prediction model using an attention-based deep neural network. The extracted features were used as input, and the occurrence of ischemic stroke after the diagnosis of AF was the output used to train the model.We found 48 features significantly associated with ischemic stroke occurrence through regression analysis (As part of preventive medicine, this study could help AF patients prepare for ischemic stroke prevention based on predicted stoke associated features and risk scores.

Genetic interactions (GIs), such as the synthetic lethal interaction, are promising therapeutic targets in precision medicine. However, despite extensive efforts to characterize GIs by large-scale perturbation screening, considerable false positives have been reported in multiple studies. We propose a new computational approach for improved precision in GI identification by applying constraints that consider actual biological phenomena. In this study, GIs were characterized by assessing mutation, loss of function, and expression profiles in the DEPMAP database. The expression profiles were used to exclude loss-of-function data for nonexpressed genes in GI characterization. More importantly, the characterized GIs were refined based on Kyoto Encyclopedia of Genes and Genomes (KEGG) or protein–protein interaction (PPI) networks, under the assumption that genes genetically interacting with a certain mutated gene are adjacent in the networks. As a result, the initial GIs characterized with CRISPR and RNAi screenings were refined to 65 and 23 GIs based on KEGG networks and to 183 and 142 GIs based on PPI networks. The evaluation of refined GIs showed improved precision with respect to known synthetic lethal interactions. The refining process also yielded a synthetic partner network (SPN) for each mutated gene, which provides insight into therapeutic strategies for the mutated genes, specifically, exploring the SPN of mutated BRAF revealed ELAVL1 as a potential target for treating BRAF-mutated cancer, as validated by previous research. We expect that this work will advance cancer therapeutic research.

The number of digital healthcare mobile applications in the market is exponentially increasing owing to the development of mobile networks and widespread usage of smartphones. However, only few of these applications have been adequately validated. Like many mobile applications, in general, the use of healthcare applications is considered safe; thus, developers and end users can easily exchange them in the marketplace. However, existing platforms are unsuitable for collecting reliable data for evaluating the effectiveness of the applications. Moreover, these platforms reflect only the perspectives of developers and experts, and not of end users. For instance, typical clinical trial data collection methods are not appropriate for participant-driven assessment of healthcare applications because of their complexity and high cost. Thus, we identified the need for a participant-driven data collection platform for end users that is interpretable, systematic, and sustainable, as a first step to validate the effectiveness of the applications. To collect reliable data in the participatory trial format, we defined distinct stages for data preparation, storage, and sharing. The interpretable data preparation consists of a protocol database system and semantic feature retrieval method that allow a person without professional knowledge to create a protocol. The systematic data storage stage includes calculation of the collected data reliability weight. For sustainable data collection, we integrated a weight method and a future reward distribution function. We validated the methods through statistical tests involving 718 human participants. The results of a validation experiment demonstrate that the compared methods differ significantly and prove that the choice of an appropriate method is essential for reliable data collection, to facilitate effectiveness validation of digital healthcare applications. Furthermore, we created a Web-based system for our pilot platform to collect reliable data in an integrated pipeline. We compared the platform features using existing clinical and pragmatic trial data collection platforms.

Several epidemics, such as the Black Death and the Spanish flu, have threatened human life throughout history, however, it is unclear if humans will remain safe from the sudden and fast spread of epidemic diseases. Moreover, the transmission characteristics of epidemics remain undiscovered. In this study, we present the results of an epidemic simulation experiment revealing the relationship between epidemic parameters and pandemic risk. To analyze the time-dependent risk and impact of epidemics, we considered two parameters for infectious diseases: the recovery time from infection and the transmission rate of the disease. Based on the epidemic simulation, we identified two important aspects of human safety with regard to the threat of a pandemic. First, humans should be safe if the fatality rate is below 100%. Second, even when the fatality rate is 100%, humans would be safe if the average degree of human social networks is below a threshold value. Nevertheless, certain diseases can potentially infect all nodes in the human social networks, and these diseases cause a pandemic when the average degree is larger than the threshold value. These results indicated that certain infectious diseases lead to human extinction and can be prevented by minimizing human contact.

While several studies have explored nutrient intake and dietary habits associated with depression, few studies have reflected recent trends and demographic factors. Therefore, we examined how nutrient intake and eating habits are associated with depression, according to gender and age. We performed simple and multiple regressions using nationally representative samples of 10,106 subjects from the Korea National Health and Nutrition Examination Survey. The results indicated that cholesterol, dietary fiber, sodium, frequency of breakfast, lunch, dinner, and eating out were significantly associated with depression (p-value &lt, 0.05). Moreover, depression was associated with nutrient intake and dietary habits by gender and age group: sugar, breakfast, lunch, and eating out frequency in the young women’s group, sodium and lunch frequency among middle-age men, dietary fibers, breakfast, and eating out frequency among middle-age women, energy, moisture, carbohydrate, lunch, and dinner frequency in late middle-age men, breakfast and lunch frequency among late middle-age women, vitamin A, carotene, lunch, and eating out frequency among older age men, and fat, saturated fatty acids, omega-3 fatty acid, omega-6 fatty acid, and eating out frequency among the older age women’s group (p-value &lt, 0.05). This study can be used to establish dietary strategies for depression prevention, considering gender and age.

Atrial fibrillation (AF) is a well-known risk factor for stroke. Predicting the risk is important to prevent the first attack and re-attack of cerebrovascular diseases by determining the medication. Although several statistical methods have been developed to assess the stroke risk in AF patients, considerable improvement is needed in predictive performance. We propose a machine learning-based approach based on the massive and complex Korean National Health Insurance (KNHIS) data. We extracted 72-dimensional features, including demographics, health examination, and medical history information, of 754,949 patients with AF from KNHIS. Logistic regression was used to determine whether the extracted features had a statistically significant association with stroke occurrence. Then, we constructed the stroke risk prediction model based on a deep neural network. The extracted features were used as input, and the occurrence of stroke after the diagnosis of AF was the output used to train the model. When the proposed deep learning model was applied to 150,989 AF patients, it was confirmed that stroke risk was predicted with high accuracy, sensitivity, and specificity. As part of preventive medicine, this study could help AF patients prepare for stroke prevention based on predicted stoke associated feature and risk scores.

Over a decade, as a specialized workshop in the field of text mining applied to biomedical informatics, DTMBIO (ACM international workshop on Data and Text Mining in Biomedical Informatics) has been held annually in conjunction with one of the largest data management conferences, CIKM. The purpose of DTMBIO is to foster discussions regarding the state-of-the-art applications of data and text mining on biomedical research problems. To address our purpose, we bring together researchers working on computer science and bio/medical informatics area including text mining and high throughput genomic data analysis, such as the next generation Sequencing (NGS) data. DTMBIO 2020 will help scientists navigate emerging trends and opportunities in the evolving area of informatics related techniques and problems in the context of biomedical research.

A clinical trial protocol defines the procedures that should be performed during a clinical trial. Every clinical trial begins with the design of its protocol. While designing the protocol, most researchers refer to electronic databases and extract protocol elements using a keyword search. However, state-of-the-art retrieval systems only offer text-based searches for user-entered keywords. In this study, we present an interactive retrieval system with a context-dependent and protocol-element-selection function for successfully designing a clinical trial protocol. To do this, we first introduce a database for a protocol retrieval system constructed from individual protocol data extracted from 184,634 clinical trials and 13,210 frame structures of clinical trial protocols. The database contains various semantic information that enables the protocols to be filtered during the search operation. Based on the database, we developed a web application called the clinical trial protocol database system (CLIPS; available at https://corus.kaist.edu/clips), which enables an interactive search by utilizing protocol elements. CLIPS provides the options to select the next element according to the previous element in the form of a connected tree, thus enabling an interactive search for combinations of protocol elements. The validation results show that our method achieves better performance than existing databases in predicting phenotypic features.

Researchers have been interested in probing how the environmental factors associated with allergic diseases affect the use of medical services. Considering this demand, we have constructed a database, named the Allergic Disease Database, based on the National Health Insurance Database (NHID). The NHID contains information on demographic and medical service utilization for approximately 99% of the Korean population. This study targeted 3 major allergic diseases, including allergic rhinitis, atopic dermatitis, and asthma. For the target diseases, our database provides daily medical service information, including the number of daily visits from 2013 and 2017, categorized by patients’ characteristics such as address, sex, age, and duration of residence. We provide additional information, including yearly population, a number of patients, and averaged geocoding coordinates by eup, myeon, and dong district code (the smallest-scale administrative units in Korea). This information enables researchers to analyze how daily changes in the environmental factors of allergic diseases (e.g., particulate matter, sulfur dioxide, and ozone) in certain regions would influence patients’ behavioral patterns of medical service utilization. Moreover, researchers can analyze long-term trends in allergic diseases and the health effects caused by environmental factors such as daily climate and pollution data. The advantages of this database are easy access to data, additional levels of geographic detail, time-efficient data-refining and processing, and a de-identification process that minimizes the exposure of identifiable personal information. All datasets included in the Allergic Disease Database can be downloaded by accessing the National Health Insurance Service data sharing webpage (https://nhiss.nhis.or.kr).

The number of digital healthcare mobile apps on the market is increasing exponentially owing to the development of the mobile network and widespread usage of smartphones. However, only a few of these apps have undergone adequate validation. As with many mobile apps, healthcare apps are generally considered safe to use, making them easy for developers and end-users to exchange them in the marketplace. The existing platforms are not suitable to collect reliable data for evaluating the effectiveness of the apps. Moreover, these platforms only reflect the perspectives of developers and experts, not of end-users. For instance, data collection methods typical of clinical trials are not appropriate for participant-driven assessment of healthcare apps because of their complexity and high cost. Thus, we identified a need for a participant-driven data collection platform for end-users that is interpretable, systematic, and sustainable —as a first step to validate the effectiveness of the apps. To collect reliable data in the participatory trial format, we defined distinct stages for data preparation, storage, and sharing. Interpretable data preparation consists of a protocol database system and semantic feature retrieval method to create a protocol without professional knowledge. Collected data reliability weight calculation belongs to the systematic data storage stage. For sustainable data collection, we integrated the weight method and the future reward distribution function. We validated the methods through statistical tests conducted on 718 human participants. The validation results demonstrate that the methods have significant differences in the comparative experiment and prove that the choice of the right method is essential for reliable data collection. Furthermore, we created a web-based system for our pilot platform to collect reliable data in an integrated pipeline. We validate the platform features with existing clinical and pragmatic trial data collection platforms. In conclusion, we show that the method and platform support reliable data collection, forging a path to effectiveness validation of digital healthcare apps.

Although natural compounds have provided a wealth of leads and clues in drug development, the process of identifying their pharmacological effects is still a challenging task. Over the last decade, many in vitro screening methods have been developed to identify the pharmacological effects of natural compounds, but they are still costly processes with low productivity. Therefore, in silico methods, primarily based on molecular information, have been proposed. However, large-scale analysis is rarely considered, since many natural compounds do not have molecular structure and target protein information. Empirical knowledge of medicinal plants can be used as a key resource to solve the problem, but this information is not fully exploited and is used only as a preliminary tool for selecting plants for specific diseases. Here, we introduce a novel method to identify pharmacological effects of natural compounds from herbal medicine based on phenotype-oriented network analysis. In this study, medicinal plants with similar efficacy were clustered by investigating hierarchical relationships between the known efficacy of plants and 5,021 phenotypes in the phenotypic network. We then discovered significantly enriched natural compounds in each plant cluster and mapped the averaged pharmacological effects of the plant cluster to the natural compounds. This approach allows us to predict unexpected effects of natural compounds that have not been found by molecular analysis. When applied to verified medicinal compounds, our method successfully identified their pharmacological effects with high specificity and sensitivity.

Background Natural products have been widely investigated in the drug development field. Their traditional use cases as medicinal agents and their resemblance of our endogenous compounds show the possibility of new drug development. Many researchers have focused on identifying therapeutic effects of natural products, yet the resemblance of natural products and human metabolites has been rarely touched. Methods We propose a novel method which predicts therapeutic effects of natural products based on their similarity with human metabolites. In this study, we compare the structure, target and phenotype similarities between natural products and human metabolites to capture molecular and phenotypic properties of both compounds. With the generated similarity features, we train support vector machine model to identify similar natural product and human metabolite pairs. The known functions of human metabolites are then mapped to the paired natural products to predict their therapeutic effects. Results With our selected three feature sets, structure, target and phenotype similarities, our trained model successfully paired similar natural products and human metabolites. When applied to the natural product derived drugs, we could successfully identify their indications with high specificity and sensitivity. We further validated the found therapeutic effects of natural products with the literature evidence. Conclusions These results suggest that our model can match natural products to similar human metabolites and provide possible therapeutic effects of natural products. By utilizing the similar human metabolite information, we expect to find new indications of natural products which could not be covered by previous in silico methods.

Combinations of natural products have been used as important sources of disease treatments. Existing databases contain information about prescriptions, herbs, and compounds and their relationships with phenotypes, but they do not have information on the use of combinations of natural product compounds. In this paper, we identified large-scale associations between natural product combinations and phenotypes by applying an association rule mining technique to integrated information on herbal medicine, combination drugs, functional foods, molecular compounds, and target genes. The rationale behind this approach is that natural products commonly found in medicinal multicomponent mixtures have statistically significant associations with the therapeutic effects of the multicomponent mixtures. Based on a molecular network analysis and an external literature validation, we show that the inferred associations are valuable information for identifying medicinal combinations of natural products since they have statistically significant closeness proximity in the molecular layer and have much experimental evidence. All results are available through the workbench site at http://biosoft.kaist.ac.kr/coconut to facilitate the investigation of the medicinal use of natural products and their combinations.

Identifying the health benefits of phytochemicals is an essential step in drug and functional food development. While many in vitro screening methods have been developed to identify the health effects of phytochemicals, there is still room for improvement because of high cost and low productivity. Therefore, researchers have alternatively proposed in silico methods, primarily based on three types of approaches, utilizing molecular, chemical or ethnopharmacological information. Although each approach has its own strength in analyzing the characteristics of phytochemicals, previous studies have not considered them all together. Here, we apply an integrated in silico analysis to identify the potential health benefits of phytochemicals based on molecular analysis and chemical properties as well as ethnopharmacological evidence. From the molecular analysis, we found an average of 415.6 health effects for 591 phytochemicals. We further investigated ethnopharmacological evidence of phytochemicals and found that on average 129.1 (31%) of the predicted health effects had ethnopharmacological evidence. Lastly, we investigated chemical properties to confirm whether they are orally bio-available, drug available or effective on certain tissues. The evaluation results indicate that the health effects can be predicted more accurately by cooperatively considering the molecular analysis, chemical properties and ethnopharmacological evidence.

Background Verifying the proteins that are targeted by compounds of natural herbs will be helpful to select natural herb-based drug candidates. However, this entails a great deal of effort to clarify the interaction throughout in vitro or in vivo experiments. In this light, in silico prediction of the interactions between compounds and target proteins can help ease the efforts. Results In this study, we performed in silico predictions of herbal compound target identification. First, data related to compounds, target proteins, and interactions between them are taken from the DrugBank database. Then we characterized six classes of compound-target interaction in humans including G-protein-coupled receptors (GPCRs), ion channel, enzymes, receptors, transporters, and other proteins. Also, classification-prediction models that predict the interactions between compounds and target proteins through a machine learning method were constructed using these matrices. As a result, AUC values of six classes are 0.94, 0.93, 0.90, 0.89, 0.91, and 0.76 respectively. Finally, the interactions of compounds from natural products were predicted using the constructed classification models. Furthermore, from our predicted results, we confirmed that several important disease related proteins were predicted as targets of natural herbal compounds. Conclusions We constructed classification-prediction models that predict the interactions between compounds and target proteins. The constructed models showed good prediction performances, and numbers of potential natural compounds target proteins were predicted from our results.

Natural products used in dietary supplements, complementary and alternative medicine (CAM) and conventional medicine are composites of multiple chemical compounds. These chemical compounds potentially offer an extensive source for drug discovery with accumulated knowledge of efficacy and safety. However, existing natural product related databases have drawbacks in both standardization and structuralization of information. Therefore, in this work, we construct an integrated database of natural products by mapping the prescription, herb, compound, and phenotype information to international identifiers and structuralizing the efficacy information through database integration and text-mining methods. We expect that the constructed database could serve as a fundamental resource for the natural products research.

Electronic Medical Records (EMRs) enable the sharing of patient medical data whenever it is needed and also are used as a tool for building new medical technology and patient recommendation systems. Since EMRs include patients' private data, access is restricted to researchers. Thus, an anonymizing technique is necessary that keeps patients' private data safe while not damaging useful medical information. k-member clustering anonymization approaches k-anonymization as a clustering issue. The objective of the k-member clustering problem is to gather records that will minimize the data distortion during data generalization. Most of the previous clustering techniques include random seed selection. However, randomly selecting a cluster seed will provide inconsistent performance. The authors propose a k-member cluster seed selection algorithm (KMCSSA) that is distinct from the previous clustering methods. Instead of randomly selecting a cluster seed, the proposed method selects the seed based on the closeness centrality to provide consistent information loss (IL) and to reduce the information distortion. An adult database from University of California Irvine Machine Learning Repository was used for the experiment. By comparing the proposed method with two previous methods, the experimental results shows that KMCSSA provides superior performance with respect to information loss. The authors provide a privacy protection algorithm that derives consistent information loss and reduces the overall information distortion.

Electronic Health Records (EHRs) enable the sharing of patients’ medical data. Since EHRs include patients’ private data, access by researchers is restricted. Therefore k-anonymity is necessary to keep patients’ private data safe without damaging useful medical information. However, k-anonymity cannot prevent sensitive attribute disclosure. An alternative, l-diversity, has been proposed as a solution to this problem and is defined as: each Q-block (ie, each set of rows corresponding to the same value for identifiers) contains at least l well-represented values for each sensitive attribute. While l-diversity protects against sensitive attribute disclosure, it is limited in that it focuses only on diversifying sensitive attributes. The aim of the study is to develop a k-anonymity method that not only minimizes information loss but also achieves diversity of the sensitive attribute. This paper proposes a new privacy protection method that uses conditional entropy and mutual information. This method considers both information loss as well as diversity of sensitive attributes. Conditional entropy can measure the information loss by generalization, and mutual information is used to achieve the diversity of sensitive attributes. This method can offer appropriate Q-blocks for generalization. We used the adult database from the UCI Machine Learning Repository and found that the proposed method can greatly reduce information loss compared with a recent l-diversity study. It can also achieve the diversity of sensitive attributes by counting the number of Q-blocks that have leaks of diversity. This study provides a privacy protection method that can improve data utility and protect against sensitive attribute disclosure. The method is viable and should be of interest for further privacy protection in EHR applications.