Tongue feature dataset construction and real-time detection.

BACKGROUND: Tongue diagnosis in traditional Chinese medicine (TCM) provides clinically important, objective evidence from direct observation of specific features that assist with diagnosis. However, the current interpretation of tongue features requires a significant amount of manpower and time. TCM physicians may have different interpretations of features displayed by the same tongue. An automated interpretation system that interprets tongue features would expedite the interpretation process and yield more consistent results. MATERIALS AND METHODS: This study applied deep learning visualization to tongue diagnosis. After collecting tongue images and corresponding interpretation reports by TCM physicians in a single teaching hospital, various tongue features such as fissures, tooth marks, and different types of coatings were annotated manually with rectangles. These annotated data and images were used to train a deep learning object detection model. Upon completion of training, the position of each tongue feature was dynamically marked. RESULTS: A large high-quality manually annotated tongue feature dataset was constructed and analyzed. A detection model was trained with average precision (AP) 47.67%, 58.94%, 71.25% and 59.78% for fissures, tooth marks, thick and yellow coatings, respectively. At over 40 frames per second on a NVIDIA GeForce GTX 1060, the model was capable of detecting tongue features from any viewpoint in real time. CONCLUSIONS/SIGNIFICANCE: This study constructed a tongue feature dataset and trained a deep learning object detection model to locate tongue features in real time. The model provided interpretability and intuitiveness that are often lacking in general neural network models and implies good feasibility for clinical application.

Does Weekends Effect Exist in Asia? Analysis of Endovascular Thrombectomy for Acute Ischemic Stroke in A Medical Center.

BACKGROUND: Discussing the quality measurements based on interrupted time series in ischemic stroke, delays are often attributed to weekends effect. This study compared the metrics and outcomes of emergent endovascular thrombectomy (EST) during working hours versus non-working hours in the emergency department of an Asian medical center. METHODS: A total of 297 patients who underwent EST between January 2015 and December 2018 were retrospectively included, with 52.5% of patients presenting during working hours and 47.5% presenting during nights, weekends, or holidays. RESULTS: Patients with diabetes were more in non-working hours than in working hours (53.9% vs. 41.0%; p=0.026). It took longer during nonworking hours than working hours in door-to -image times (13 min vs. 12 min; p=0.04) and door-to-groin puncture times (median: 112 min vs. 104 min; p=0.042). Significant statistical differences were not observed between the two groups in neurological outcomes, including successful reperfusion and complications such as intracranial hemorrhage and mortality. However, the change in National Institute of Health Stroke Scale (NIHSS) scores in 24 hours was better in the working-hour group than in the nonworking-hour group (4 vs. 2; p=0.058). CONCLUSION: This study revealed that nonworking-hour effects truly exist in patients who received EST. Although delays in door-to-groin puncture times were noticed during nonworking hours, significant differences in neurological functions and mortality were not observed between working and non-working hours. Nevertheless, methods to improve the process during non-working hours should be explored in the future.

A method for the process of collagen modified polyester from fish scales waste.

In this study, we introduced a novel polymerization method of polyester using collagen peptides derived from fish scale waste. After the extraction process of collagen peptide from fish scales, putting collagen peptide, ethylene glycol and Benzenedicarboxylic acid into a container, and mixing them to form a mixture; heating the mixture for executing an esterification reaction, to product esters and water; heating the esters, and stirring the esters via a mixer; in a specific period, decreasing the pressure in the container for executing a polycondensation reaction; decreasing the pressure in the container to a second pressure, and stirring the esters via the mixer, to produce a collagen modified polyester. Collagen peptides are rich in glycine, proline, and hydroxyproline, and by forming a triple helix structure, such as that of the copolyester, gain better hydrophilicity, antistaticity, and ductility. As a result, the produced collagen modified polyester fiber keeps the characteristics of the traditional polyethylene terephthalate fibers including strength, durability, and resistance to wrinkle and shrink. However, the supramolecular collagen modified polyester containing animal collagen peptides has naturally a soft touch and champagne-like color. Consequently, it can be used as a suitable material for skin-friendly functional clothes with or without additional dying. In brief,•This study introduces a novel method for collagen modified polyester.•Upcycled fish scale waste brings the sustainable benefits of circular economy.•Collagen modified polyester provides a new direction for future technological development in the textile industry.

A system for reporting and evaluating adverse drug reactions of herbal medicine in Taiwan from 1998 to 2016.

The Taiwan Adverse Drug Reaction Reporting System for Herbal Medicine (TADRRS-HM) has systematically documented suspected adverse events from adverse drug reaction (ADR) reports from 1998 (prior to its formal establishment in 2001) and evaluates safety profiles of herbal medicines. This article describes findings from 2079 ADR reports filed between 1998 and 2016: 941 reports involved single herbs and 87 involved folk herbals; 842 were generated from clinical trials, while 209 ADR reports involving foods, health foods, dietary supplement foods and herbal cuisine were grouped as Other. Severity assessments using the Modified Hartwig and Siegel scale classified 72.4% of ADRs as mild, 17.4% as moderate and 6.5% as severe. System Organ Class classification of the ADRs identified gastrointestinal system disorders as the most common (33.4%), followed by skin and subcutaneous tissue disorders (21.2%). The TADRRS-HM records indicate that herbal medicines may cause a wide range of ADRs. Aconiti Radix, Xiao-Qing-Long-Tang, and Datura suaveolens were the most commonly reported single herb, herbal formula, and folk herbal, respectively. The data indicate that herbal medicines may cause a wide range of ADRs. This system will confer long-term benefits for the development of Taiwan's herbal medicines adverse reaction database and facilitate epidemiological analysis.

Analysis of Exercise-Induced Periodic Breathing Using an Autoregressive Model and the Hilbert-Huang Transform.

Evaluation of exercise-induced periodic breathing (PB) in cardiopulmonary exercise testing (CPET) is one of important diagnostic evidences to judge the prognosis of chronic heart failure cases. In this study, we propose a method for the quantitative analysis of measured ventilation signals from an exercise test. We used an autoregressive (AR) model to filter the breath-by-breath measurements of ventilation from exercise tests. Then, the signals before reaching the most ventilation were decomposed into intrinsic mode functions (IMF) by using the Hilbert-Huang transform (HHT). An IMF represents a simple oscillatory pattern which catches a part of original ventilation signal in different frequency band. For each component of IMF, we computed the number of peaks as the feature of its oscillatory pattern denoted by Δ i . In our experiment, 61 chronic heart failure patients with or without PB pattern were studied. The computed peaks of the third and fourth IMF components, Δ3 and Δ4, were statistically significant for the two groups (both p values < 0.02). In summary, our study shows a close link between the HHT analysis and level of intrinsic energy for pulmonary ventilation. The third and fourth IMF components are highly potential to indicate the prognosis of chronic heart failure.

Corrigendum: The Core Pattern Analysis on Chinese Herbal Medicine for Sjögren's syndrome: A Nationwide Population-Based Study.

This corrects the article DOI: 10.1038/srep09541.

Transcriptome Sequencing for the Detection of Chimeric Transcripts.

The occurrence of chimeric transcripts has been reported in many cancer cells and seen as potential biomarkers and therapeutic targets. Modern high-throughput sequencing technologies offer a way to investigate individual chimeric transcripts and the systematic information of associated gene expressions about underlying genome structural variations and genomic interactions. The detection methods of finding chimeric transcripts from massive amount of short read sequence data are discussed here. Both assembly-based and alignment-based methods are used for the investigation of chimeric transcripts.

The Core Pattern Analysis on Chinese Herbal Medicine for Sjögren's syndrome: A Nationwide Population-Based Study.

This large-scale survey aimed to evaluate frequencies and patterns of Chinese herbal medicine (CHM) used for Sjögren's syndrome (SS) in Taiwan by analyzing the National Health Insurance Research Database (NHIRD) for cases in which CHM was used as an alternative therapy to Western medicine for improving patients' discomforts. We analyzed cases of SS principal diagnosis (ICD-9:710.2) with a catastrophic illness certificate (CIC) in traditional Chinese medicine (TCM) outpatient clinics from three cohorts of the Longitudinal Health Insurance Database (LHID) in the NHIRD between 2002 and 2011. CHM prescription patterns for SS were evaluated from claimed visitation files and corresponding prescription files. There were 15,914 SS patients with CIC (SS/CIC), and we found only 130 SS/CIC cases visiting TCM clinics in LHID2000, 133 in LHID2005, and 126 in LHID2010. After removing duplicate data, 366 SS/CIC and 4,867 visits were analyzed. The 50-59 year age group showed the highest ratio (29.51%) in both women and men. "Qi-Ju-Di-Huang-Wan" and "Xuan-Shen" (Scrophularia ningpoensis Hemsl.) was the most commonly used formula and single herb, respectively. "Qi-Ju-Di-Huang-Wan, Gan-Lu-Yin, Xuan-Shen, Mai-Men-Dong (Ophiopogon japonicus (L. f.) Ker-Gawl.), and Sheng-Di-Huang (raw Rehmannia glutinosa Libosch)" were the core pattern prescriptions in treating SS/CIC.

Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data.

BACKGROUND: Neutrophil antigens are involved in a variety of clinical conditions including transfusion-related acute lung injury (TRALI) and other transfusion-related diseases. Recently, there are five characterized groups of human neutrophil antigen (HNA) systems, the HNA1 to 5. Characterization of all neutrophil antigens from whole genome sequencing (WGS) data may be accomplished for revealing complete genotyping formats of neutrophil antigens collectively at genome level with molecular variations which may respectively be revealed with available genotyping techniques for neutrophil antigens conventionally. RESULTS: We developed a computing method for the genotyping of human neutrophil antigens. Six samples from two families, available from the 1000 Genomes projects, were used for a HNA typing test. There are 500 ~ 3000 reads per sample filtered from the adopted human WGS datasets in order for identifying single nucleotide polymorphisms (SNPs) of neutrophil antigens. The visualization of read alignment shows that the yield reads from WGS dataset are enough to cover all of the SNP loci for the antigen system: HNA1, HNA3, HNA4 and HNA5. Consequently, our implemented Bioinformatics tool successfully revealed HNA types on all of the six samples including sequence-based typing (SBT) as well as PCR sequence-specific oligonucleotide probes (SSOP), PCR sequence-specific primers (SSP) and PCR restriction fragment length polymorphism (RFLP) along with parentage possibility. CONCLUSIONS: The next-generation sequencing technology strives to deliver affordable and non-biased sequencing results, hence the complete genotyping formats of HNA may be reported collectively from mining the output data of WGS. The study shows the feasibility of HNA genotyping through new WGS technologies. Our proposed algorithmic methodology is implemented in a HNATyping software package with user's guide available to the public at http://sourceforge.net/projects/hnatyping/.

SeqEntropy: genome-wide assessment of repeats for short read sequencing.

BACKGROUND: Recent studies on genome assembly from short-read sequencing data reported the limitation of this technology to reconstruct the entire genome even at very high depth coverage. We investigated the limitation from the perspective of information theory to evaluate the effect of repeats on short-read genome assembly using idealized (error-free) reads at different lengths. METHODOLOGY/PRINCIPAL FINDINGS: We define a metric H(k) to be the entropy of sequencing reads at a read length k and use the relative loss of entropy ΔH(k) to measure the impact of repeats for the reconstruction of whole-genome from sequences of length k. In our experiments, we found that entropy loss correlates well with de-novo assembly coverage of a genome, and a score of ΔH(k)>1% indicates a severe loss in genome reconstruction fidelity. The minimal read lengths to achieve ΔH(k)<1% are different for various organisms and are independent of the genome size. For example, in order to meet the threshold of ΔH(k)<1%, a read length of 60 bp is needed for the sequencing of human genome (3.2 10(9) bp) and 320 bp for the sequencing of fruit fly (1.8×10(8) bp). We also calculated the ΔH(k) scores for 2725 prokaryotic chromosomes and plasmids at several read lengths. Our results indicate that the levels of repeats in different genomes are diverse and the entropy of sequencing reads provides a measurement for the repeat structures. CONCLUSIONS/SIGNIFICANCE: The proposed entropy-based measurement, which can be calculated in seconds to minutes in most cases, provides a rapid quantitative evaluation on the limitation of idealized short-read genome sequencing. Moreover, the calculation can be parallelized to scale up to large euakryotic genomes. This approach may be useful to tune the sequencing parameters to achieve better genome assemblies when a closely related genome is already available.

EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

MOTIVATION: High-accuracy de novo assembly of the short sequencing reads from RNA-Seq technology is very challenging. We introduce a de novo assembly algorithm, EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This algorithm uses an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data. RESULTS: EBARDenovo resolves the complications of RNA-Seq assembly arising from sequencing errors, repetitive sequences and aberrant chimeric amplicons. In a series of assembly experiments, our algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases. AVAILABILITY AND IMPLEMENTATION: EBARDenovo is available at http://ebardenovo.sourceforge.net/. This software package (with patent pending) is free of charge for academic use only. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.

BACKGROUND: Mitochondrial dysfunction is associated with various aging diseases. The copy number of mtDNA in human cells may therefore be a potential biomarker for diagnostics of aging. Here we propose a new computational method for the accurate assessment of mtDNA copies from whole genome sequencing data. RESULTS: Two families of the human whole genome sequencing datasets from the HapMap and the 1000 Genomes projects were used for the accurate counting of mitochondrial DNA copy numbers. The results revealed the parental mitochondrial DNA copy numbers are significantly lower than that of their children in these samples. There are 8%~21% more copies of mtDNA in samples from the children than from their parents. The experiment demonstrated the possible correlations between the quantity of mitochondrial DNA and aging-related diseases. CONCLUSIONS: Since the next-generation sequencing technology strives to deliver affordable and non-biased sequencing results, accurate assessment of mtDNA copy numbers can be achieved effectively from the output of whole genome sequencing. We implemented the method as a software package MitoCounter with the source code and user's guide available to the public at http://sourceforge.net/projects/mitocounter/.

RFID-initiated workflow control to facilitate patient safety and utilization efficiency in operation theater.

OBJECTIVE: To control the workflow for surgical patients, we in-cooperate radio-frequency identification (RFID) technology to develop a Patient Advancement Monitoring System (PAMS) in operation theater. METHODS: The web-based PAMS is designed to monitor the whole workflow for the handling of surgical patients. The system integrates multiple data entry ports Across the multi-functional surgical teams. Data are entered into the system through RFID, bar code, palm digital assistance (PDA), ultra-mobile personal computer (UMPC), or traditional keyboard at designated checkpoints. Active radio-frequency identification (RFID) tag can initiate data demonstration on the computer screens upon a patient's arrival at any particular checkpoint along the advancement pathway. RESULTS: The PAMS can manage the progress of operations, patient localization, identity verification, and peri-operative care. The workflow monitoring provides caregivers' instant information sharing to enhance management efficiency. CONCLUSION: RFID-initiate surgical workflow control is valuable to meet the safety, quality, efficiency requirements in operation theater.

A quantitative analysis of monochromaticity in genetic interaction networks.

BACKGROUND: A genetic interaction refers to the deviation of phenotypes from the expected when perturbing two genes simultaneously. Studying genetic interactions help clarify relationships between genes, such as compensation and masking, and identify gene groups of functional modules. Recently, several genome-scale experiments for measuring quantitative (positive and negative) genetic interactions have been conducted. The results revealed that genes in the same module usually interact with each other in a consistent way (pure positive or negative); this phenomenon was designated as monochromaticity. Monochromaticity might be the underlying principle that can be utilized to unveil the modularity of cellular networks. However, no appropriate quantitative measurement for this phenomenon has been proposed. RESULTS: In this study, we propose the monochromatic index (MCI), which is able to quantitatively evaluate the monochromaticity of potential functional modules of genes, and the MCI was used to study genetic landscapes in different cellular subsystems. We demonstrated that MCI not only amend the deficiencies of MP-score but also properly incorporate the background effect. The results showed that not only within-complex but also between-complex connections present significant monochromatic tendency. Furthermore, we also found that significantly higher proportion of protein complexes are connected by negative genetic interactions in metabolic network, while transcription and translation system adopts relatively even number of positive and negative genetic interactions to link protein complexes. CONCLUSION: In summary, we demonstrate that MCI improves deficiencies suffered by MP-score, and can be used to evaluate monochromaticity in a quantitative manner. In addition, it also helps to unveil features of genetic landscapes in different cellular subsystems. Moreover, MCI can be easily applied to data produced by different types of genetic interaction methodologies such as Synthetic Genetic Array (SGA), and epistatic miniarray profile (E-MAP).