TM-MC 2.0: an enhanced chemical database of medicinal materials in Northeast Asian traditional medicine.

BACKGROUND: As chromatographic techniques have advanced, many articles that analyze the constituting compounds of medicinal materials have been published in relation to Northeast Asian traditional medicine, including traditional Chinese medicine (TCM). TM-MC was launched in 2015, providing information about the chemical compounds in medicinal materials from chromatographic articles in PubMed. Since 2015, through continuous curation efforts, we have now released TM-MC 2.0 with significant improvements to the quantity and quality of the data ( https://tm-mc.kr ). DESCRIPTION: TM-MC 2.0 contains 635 medicinal materials, 34,107 chemical compounds (21,306 identified and de-duplicated), 13,992 targets, 27,997 diseases, and 5,075 prescriptions (2,393 de-duplicated by name). The database provides the largest number of identified compounds for medicinal materials listed in the pharmacopoeia compared to all TCM databases. In particular, marker compounds of medicinal materials and many newly discovered compounds were added through the manual curation of recent chromatographic articles. CONCLUSION: TM-MC 2.0 provides the largest collection of information about the chemical compounds of the medicinal materials listed in the Korean, Chinese, and Japanese pharmacopoeias. Our database can be utilized for network pharmacology in traditional medicine and for the compound screening of medicinal materials for modern drug discovery.

Exploring Variations in Sleep Perception: Comparative Study of Chatbot Sleep Logs and Fitbit Sleep Data.

BACKGROUND: Patient-generated health data are important in the management of several diseases. Although there are limitations, information can be obtained using a wearable device and time-related information such as exercise time or sleep time can also be obtained. Fitbits can be used to acquire sleep onset, sleep offset, total sleep time (TST), and wakefulness after sleep onset (WASO) data, although there are limitations regarding the depth of sleep and satisfaction; therefore, the patient's subjective response is still important information that cannot be replaced by wearable devices. OBJECTIVE: To effectively use patient-generated health data related to time such as sleep, it is first necessary to understand the characteristics of the time response recorded by the user. Therefore, the aim of this study was to analyze the characteristics of individuals' time perception in comparison with wearable data. METHODS: Sleep data were acquired for 2 weeks using a Fitbit. Participants' sleep records were collected daily through chatbot conversations while wearing the Fitbit, and the two sets of data were statistically compared. RESULTS: In total, 736 people aged 30-59 years were recruited for this study, and the sleep data of 543 people who wore a Fitbit and responded to the chatbot for more than 7 days on the same day were analyzed. Research participants tended to respond to sleep-related times on the hour or in 30-minute increments, and each participant responded within the range of 60-90 minutes from the value measured by the Fitbit. On average for all participants, the chat responses and the Fitbit data were similar within a difference of approximately 15 minutes. Regarding sleep onset, the participant response was 8 minutes and 39 seconds (SD 58 minutes) later than that of the Fitbit data, whereas with respect to sleep offset, the response was 5 minutes and 38 seconds (SD 57 minutes) earlier. The participants' actual sleep time (AST) indicated in the chat was similar to that obtained by subtracting the WASO from the TST measured by the Fitbit. The AST was 13 minutes and 39 seconds (SD 87 minutes) longer than the time WASO was subtracted from the Fitbit TST. On days when the participants reported good sleep, they responded 19 (SD 90) minutes longer on the AST than the Fitbit data. However, for each sleep event, the probability that the participant's AST was within ±30 and ±60 minutes of the Fitbit TST-WASO was 50.7% and 74.3%, respectively. CONCLUSIONS: The chatbot sleep response and Fitbit measured time were similar on average and the study participants had a slight tendency to perceive a relatively long sleep time if the quality of sleep was self-reported as good. However, on a participant-by-participant basis, it was difficult to predict participants' sleep duration responses with Fitbit data. Individual variations in sleep time perception significantly affect patient responses related to sleep, revealing the limitations of objective measures obtained through wearable devices.

Effect of Trap Behavior on the Reliability Instability of Metamorphic Buffer in InAlAs/InGaAs MHEMT on GaAs.

Our investigation focused on assessing the influence of the metamorphic buffer in metamorphic high-electron-mobility transistors (MHEMT) that were grown on GaAs substrates. While an MHEMT exhibited elevated off-state current levels, its direct current (DC) and radio frequency (RF) traits were found to be comparable to those of InP-based lattice-matched high-electron-mobility transistors (LM-HEMTs). However, the Pulsed I-V measurement results confirmed the presence of the fast transient charging effect, leading to a more substantial degradation in drain current observed in MHEMT. In addition, through the low-frequency noise characteristics, it was confirmed that the dominant trapping location was located in the bulk site. The slope of the 1/f noise measurement indicated that the primary trapping site was in proximity to the bulk traps. The carrier-number-fluctuation (CNF) model was employed to extract the bulk trap density (Nt). For the LM-HEMTs, the value was at 3.27 × 1016 eV-1·cm-3, while for the MHEMT, it was 3.56 × 1017 eV-1·cm-3.

Fabrication and Characterization of In0.53Ga0.47As/InAs/In0.53Ga0.47As Composite Channel Metamorphic HEMTs (mHEMTs) on a GaAs Substrate.

In this work, we successfully demonstrated In0.53Ga0.47As/InAs/In0.53Ga0.47As composite channel metamorphic high electron mobility transistors (mHEMTs) on a GaAs substrate. The fabricated mHEMTs with a 100 nm gate length exhibited excellent DC and logic characteristics such as VT = -0.13 V, gm,max = 949 mS/mm, subthreshold swing (SS) = 84 mV/dec, drain-induced barrier lowering (DIBL) = 89 mV/V, and Ion/Ioff ratio = 9.8 × 103 at a drain-source voltage (VDS) = 0.5 V. In addition, the device exhibited excellent high-frequency characteristics, such as fT/fmax = 261/304 GHz for the measured result and well-matched modeled fT/fmax = 258/309 GHz at VDS = 0.5 V, which is less power consumption compared to other material systems. These high-frequency characteristics are a well-balanced demonstration of fT and fmax in the mHEMT structure on a GaAs substrate.

Acupuncture improves symptoms in patients with mild-to-moderate atopic dermatitis: A randomized, sham-controlled preliminary trial.

OBJECTIVES: To assess the feasibility of a definitive trial investigating the effects of acupuncture on atopic dermatitis symptoms including itching. DESIGN: A randomized, sham-controlled preliminary trial with three arms with a 4-week intervention period and a 4-week follow-up. INTERVENTIONS: Thirty participants were allocated to three arms (the verum acupuncture group 1 [VA1, 3 times weekly for 4 weeks], the verum acupuncture group 2 [VA2, twice weekly for 4 weeks], and the sham acupuncture group [SA, twice weekly for 4 weeks]) at a 1:1:1 ratio. MAIN OUTCOME MEASURES: We determined the visual analogue scale (VAS) for itching and insomnia, SCORing Atopic Dermatitis (SCORAD), Eczema Area and Severity Index (EASI), Patient Oriented Eczema Measure (POEM), and Dermatology Life Quality Index (DLQI) scores over the course of the study. Baseline index score (BIS) comparison according to general symptom was performed. RESULTS: The SCORAD, VAS (Pruritus), VAS (Insomnia), POEM, DLQI, and EASI were significantly improved in the VA groups. Significant BIS mean differences were observed most predominantly in epigastric tenderness and dyspepsia. There was no significant difference between VA1 and VA2 groups in all the main evaluation indices. CONCLUSIONS: For the following research, the authors suggest SCORAD (Total) as primary outcome and SCORAD (objective), VAS (Itch), VAS (insomnia), EASI, POEM, and DLQI as secondary outcomes. Thirty six participants should be conducted a 4-week acupuncture period (twice weekly) and a 4-week follow-up. It is necessary to compare the differences of general symptoms according to presence of epigastric tenderness or dyspepsia at the screening level.

Novel analgesic effects of melanin-concentrating hormone on persistent neuropathic and inflammatory pain in mice.

The melanin-concentrating hormone (MCH) is a peptidergic neuromodulator synthesized by neurons in the lateral hypothalamus and zona incerta. MCHergic neurons project throughout the central nervous system, indicating the involvements of many physiological functions, but the role in pain has yet to be determined. In this study, we found that pMCH-/- mice showed lower baseline pain thresholds to mechanical and thermal stimuli than did pMCH+/+ mice, and the time to reach the maximum hyperalgesic response was also significantly earlier in both inflammatory and neuropathic pain. To examine its pharmacological properties, MCH was administered intranasally into mice, and results indicated that MCH treatment significantly increased mechanical and thermal pain thresholds in both pain models. Antagonist challenges with naltrexone (opioid receptor antagonist) and AM251 (cannabinoid 1 receptor antagonist) reversed the analgesic effects of MCH in both pain models, suggesting the involvement of opioid and cannabinoid systems. MCH treatment also increased the expression and activation of CB1R in the medial prefrontal cortex and dorsolateral- and ventrolateral periaqueductal grey. The MCH1R antagonist abolished the effects induced by MCH. This is the first study to suggest novel analgesic actions of MCH, which holds great promise for the application of MCH in the therapy of pain-related diseases.

The dynamic relationship between emotional and physical states: an observational study of personal health records.

OBJECTIVES: Recently, there has been increasing interest in preventing and managing diseases both inside and outside medical institutions, and these concerns have supported the development of the individual Personal Health Record (PHR). Thus, the current study created a mobile platform called "Mind Mirror" to evaluate psychological and physical conditions and investigated whether PHRs would be a useful tool for assessment of the dynamic relationship between the emotional and physical conditions of an individual. METHODS: Mind Mirror was used to collect 30 days of observational data about emotional valence and the physical states of pain and fatigue from 20 healthy participants, and these data were used to analyze the dynamic relationship between emotional and physical conditions. Additionally, based on the cross-correlations between these three parameters, a multilevel multivariate regression model (mixed linear model [MLM]) was implemented. RESULTS: The strongest cross-correlation between emotional and physical conditions was at lag 0, which implies that emotion and body condition changed concurrently. In the MLM, emotional valence was negatively associated with fatigue (ß =-0.233, P<0.001), fatigue was positively associated with pain (ß =0.250, P<0.001), and pain was positively associated with fatigue (ß =0.398, P<0.001). CONCLUSION: Our study showed that emotional valence and one's physical condition negatively influenced one another, while fatigue and pain positively affected each other. These findings suggest that the mind and body interact instantaneously, in addition to providing a possible solution for the recording and management of health using a PHR on a daily basis.

Spatial Patterns of the Indications of Acupoints Using Data Mining in Classic Medical Text: A Possible Visualization of the Meridian System.

The indications of acupoints are thought to be highly associated with the lines of the meridian systems. The present study used data mining methods to analyze the characteristics of the indications of each acupoint and to visualize the relationships between the acupoints and disease sites in the classic Korean medical text Chimgoogyeongheombang. Using a term frequency-inverse document frequency (tf-idf) scheme, the present study extracted valuable data regarding the indications of each acupoint according to the frequency of the cooccurrences of eight Source points and eighteen disease sites. Furthermore, the spatial patterns of the indications of each acupoint on a body map were visualized according to the tf-idf values. Each acupoint along the different meridians exhibited different constellation patterns at various disease sites. Additionally, the spatial patterns of the indications of each acupoint were highly associated with the route of the corresponding meridian. The present findings demonstrate that the indications of each acupoint were primarily associated with the corresponding meridian system. Furthermore, these findings suggest that the routes of the meridians may have clinical implications in terms of identifying the constellations of the indications of acupoints.

TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine.

BACKGROUND: In traditional medicine, there has been a great deal of research on the effects exhibited by medicinal materials. To study the effects, resources that can systematically describe the chemical compounds in medicinal materials are necessary. In recent years, numerous databases on medicinal materials and constituent compounds have been constructed. However, because these databases provide differing information and the sources of such information are unclear or difficult to verify, it is difficult to decide which database to use. Moreover, there is much overlapping information. The aim of this study was to construct a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine (TM-MC), for which medicinal materials are listed in the Korean, Chinese, and Japanese pharmacopoeias and information on the compound names of medicinal materials can easily be confirmed online. DESCRIPTION: To provide information on the chemical compounds of medicinal materials, chromatography articles from MEDLINE and PubMed Central were searched. After chemical compounds of medicinal materials were extracted by manually investigating the full-text of articles, a database of information on about 14,000 compounds from 536 medicinal materials was built. The database also provides links to the articles from which each medicinal material and chemical compound were extracted. CONCLUSION: TM-MC database provides information on medicinal materials and their chemical compounds from chromatography articles in MEDLINE and PubMed Central. Researchers can easily check relevant information through the links to articles.

A mathematical model for the deficiency-excess mechanism of yin-yang in five viscera.

To raise traditional medicine to a higher level of scientific research, a mathematical model has been proposed using symbolic notations and operators to describe several disease symptoms generally recognized in traditional medicine. Even though this model to a certain degree offers a mathematical approach to identify the relationships between yin-yang and the five viscera, it is not an efficient means of explaining the pathology in traditional medicine due to its use of superfluous notations and definitions. In this paper, we introduce two concise operators, a self-development operator and an action operator: the former describes the effect of a viscus in the unbalanced state on other viscera: the latter explains the engendering and restraining relationships between the two viscera. These tools are useful to elucidate the interactions among the states of the five viscera based on yin-yang and the five elements theory. Our mathematical model with these two operators facilitates description for the scheme of deficiency-excess of yin-yang in the five viscera. Accordingly, we have mathematically refined the existing results and shown clinical applications as well.

Network analysis of acupuncture points used in the treatment of low back pain.

Background. The appropriate selection of acupoints is fundamental to obtain a therapeutic effect from clinical acupuncture. Objective. Using a network analysis method, we investigated the acupoints that are combined to treat low back pain (LBP). Methods. To analyze the patterns of the combinations of acupoints, we used acupoint information from clinical trials to calculate the modified mutual information (MI) value, integrated these data, and visualized the network. Results. Based on the highest MI values, we found two different types of acupoint pairs used in the treatment of LBP: pairs of distant acupoints and pairs of local acupoints. Using modular analysis, we found that three acupoint modules were applied in the treatment of LBP: local acupoints, distant acupoints along the meridian, and distant acupoints based on the symptom differentiations. Conclusion. Using the modified MI technique, we provide a systematic framework for the acupoint combination network, and reveal how the technique of acupoint combination is used in the treatment of LBP. Application of this knowledge in acupuncture research may help clarify the mechanisms underlying acupuncture treatment at the systems level, bridging the gap between traditional medicine and modern science.

Ontology for medicinal materials based on traditional Korean medicine.

UNLABELLED: We are constructing an ontology for traditional Korean medicine, and we started with medicinal materials to express the relationships between patients' symptoms, diseases and treatments. Biological materials and mineral resources have been used traditionally for patient treatments. The ontology includes various data related to these materials, such as their scientific names, parts of materials used, effectiveness and related oriental organ of the human body. AVAILABILITY: http://tkm.kiom.re.kr/ontology/TraditionalKoreanMedicine.rdf-xml.owl (10-20 s using Internet Explorer.)

Detection of cytolethal distending toxin and other virulence characteristics of enteropathogenic Escherichia coli isolates from diarrheal patients in Republic of Korea.

Cytolethal distending toxins (CDTs) represent an emerging family of newly described bacterial products that are produced by a number of pathogens. The genes encoding these toxins have been identified as a cluster of three adjacent genes, cdtA, cdtB, and cdtC, plus 5 cdt genetic variants, designated as cdt-I, cdt-II, cdt-III, cdt-IV, and cdt- V, have been identified to date. In this study, a general multiplex PCR system designed to detect Escherichia coli cdts was applied to investigate the presence of cdt genes among isolates. As a result, among 366 E. coli strains, 2.7% were found to carry the cdtB gene. In addition, the use of type-specific primers revealed the presence of cdt-I, cdtIV, and cdt-V types of the cdt gene, yet no cdt-II or cdt- III strains. The presence of other virulence genes (stx1, stx2, eae, bfp, espA, espB, and espD) was also investigated using a PCR assay. Among the 10 cdtB gene-positive strains, 8 were identified as CDT-producing typical enteropathogenic E. coli (EPEC) strains (eae(+), bfp(+)), whereas 2 were identified as CDT-producing atypical EPEC strains (eae(+), bfp(-)). When comparing the cytotoxic activity of the CDT-producing typical and atypical EPEC strains, the CDT-producing atypical EPEC strains appeared to be less toxic than the CDT-producing typical EPEC strains.

Daily activity recognition system for the elderly using pressure sensors.

As transformed to aging society rapidly, the number of old persons who live alone is drastically increased. Because these old people may have disorder of bodily function, and be suffering from geriatric disease, needs of a health assistance system to make them healthier are strongly increased. In this paper, we propose a daily activity recognition system for an old person using pressure sensors. The target daily activities are MEAL, SLEEP, EXCRETION, GO-OUT, and REST. The proposed system installs pressure sensors to furniture and floors in home, and recognizes daily activities based on the object usage information. By using the proposed system, we can provide a warning sign for unhealthy cases such as skipping meals. And, the families who live in remote place can check that their parent takes a healthy daily living.

Normalization of gene/protein names in biological literatures using Vector-Space Model.

As the number of biological literatures grows exponentially, needs for text mining system are increased. In text mining area, normalization is mapping gene/protein names to a database. It is necessary to combine extracted information from various literatures and to create a database or an ontology using literatures. Previous normalization researches used direct comparison methods between a database and literatures, but it is weak to extremely variational gene/protein names in literatures. Therefore, in this paper, we propose a normalization method using Vector-Space Model. For each gene/protein name, we rank identifiers using Vector-Space Model, and find the most similar identifier with the name. Experimental result shows the proposed method has 70.7% f-measure.

Finding the evidence for protein-protein interactions from PubMed abstracts.

MOTIVATION: Protein-protein interactions play critical roles in biological processes, and many biologists try to find or to predict crucial information concerning these interactions. Before verifying interactions in biological laboratory work, validating them from previous research is necessary. Although many efforts have been made to create databases that store verified information in a structured form, much interaction information still remains as unstructured text. As the amount of new publications has increased rapidly, a large amount of research has sought to extract interactions from the text automatically. However, there remain various difficulties associated with the process of applying automatically generated results into manually annotated databases. For interactions that are not found in manually stored databases, researchers attempt to search for abstracts or full papers. RESULTS: As a result of a search for two proteins, PubMed frequently returns hundreds of abstracts. In this paper, a method is introduced that validates protein-protein interactions from PubMed abstracts. A query is generated from two given proteins automatically and abstracts are then collected from PubMed. Following this, target proteins and their synonyms are recognized and their interaction information is extracted from the collection. It was found that 67.37% of the interactions from DIP-PPI corpus were found from the PubMed abstracts and 87.37% of interactions were found from the given full texts. AVAILABILITY: Contact authors.

BioProber: software system for biomedical relation discovery from PubMed.

The numbers of articles and journals that are published are increasing at a considerable rate, and the published information is growing continuously and fast. Because of this, researches to acquire knowledge automatically have been carried out in the areas of information retrieval, information extraction and text mining. Information retrieval approaches are good for specific topics that the number of related articles is small. But, if the number is bigger, searching skill and knowledge acquisition ability are useless. Though many efforts have been made to extract information from literature, many approaches have concentrated on specific entities, such as proteins, genes and their interactions, and much information is still remained in unstructured text. So, we have developed a system that discovers relations between various categories of biomedical entities. Our system collects abstracts from PubMed by queries representing a topic and visualizes relationship from the collection by automatic information extraction.