Categorizing Host-Dependent RNA Viruses by Principal Component Analysis of Their Codon Usage Preferences

ABSTRACT Viruses have to exploit host transcription and translation mechanisms to replicate in a hostile host cellular environment, and therefore, it is likely that the infected host may impose pressure on viral evolution. In this study, we investigated differences in codon usage preferences among the highly mutable single strain RNA viruses which infect vertebrate or invertebrate hosts, respectively. We incorporate principal component analysis (PCA) and k-mean methods to clustering viruses infected with different type of hosts. The relative synonymous codon usage (RSCU) indices of all genes in 32 RNA viruses were calculated, and the correlation of the RSCU indices among different viruses was analyzed by the PCA. Our results show a positive correlation in codon usage preferences among viruses that target the same host category. Results of k-means clustering analysis further confirmed the statistical significance of this study, demonstrating that viruses infecting vertebrate hosts have different codon usage preferences to those of invertebrate viruses. Based on the analysis of the effective number of codons (ENC) in relation to the GC-content at the synonymous third codon position (GC3s), we further identified that mutational pressure was the dominant evolution driving force in making the different codon usage preferences. This study suggests a new and effective way to characterize host-dependent RNA viruses based on the codon usage pattern

Using BPMN to Model a Patient Safety Promulgation Service Based on a Clinical Process

In this paper, we used business process modeling standards to enhance the development of a patient-safety promulgation process with a web service. A web service that is related to a work process is typically in an organization that has been designed, built and stored in a web service repository. The purpose of using a web service is that it can be shared with multiple functional units within an organization via an Intranet. This paper further develops this approach and discusses the use of a visual modeling language to describe a clinical workflow clearly. The final outcome is business process re-engineering and is presented as a business process modeling notation. The workflow management we designed integrates a process for each functional unit in the organization to customize the workflow requirements that suit their needs. 748 cases had been notified among 13 months, the system play its role well even when notify proceeding had been changed.&nbsp

Novel Hierarchical Fall Detection Algorithm Using a Multiphase Fall Model

Falls are the primary cause of accidents for the elderly in the living environment. Reducing hazards in the living environment and performing exercises for training balance and muscles are the common strategies for fall prevention. However, falls cannot be avoided completely; fall detection provides an alarm that can decrease injuries or death caused by the lack of rescue. The automatic fall detection system has opportunities to provide real-time emergency alarms for improving the safety and quality of home healthcare services. Two common technical challenges are also tackled in order to provide a reliable fall detection algorithm, including variability and ambiguity. We propose a novel hierarchical fall detection algorithm involving threshold-based and knowledge-based approaches to detect a fall event. The threshold-based approach efficiently supports the detection and identification of fall events from continuous sensor data. A multiphase fall model is utilized, including free fall, impact, and rest phases for the knowledge-based approach, which identifies fall events and has the potential to deal with the aforementioned technical challenges of a fall detection system. Seven kinds of falls and seven types of daily activities arranged in an experiment are used to explore the performance of the proposed fall detection algorithm. The overall performances of the sensitivity, specificity, precision, and accuracy using a knowledge-based algorithm are 99.79%, 98.74%, 99.05% and 99.33%, respectively. The results show that the proposed novel hierarchical fall detection algorithm can cope with the variability and ambiguity of the technical challenges and fulfill the reliability, adaptability, and flexibility requirements of an automatic fall detection system with respect to the individual differences

A Web-Based Solution for Viewing Large-Sized Microscopic Images

[[abstract]]This paper demonstrates a pure web-based solution enabling the presentation of scanned pathologic microscopic images on the web. For each slide, an entire specimen is scanned, and a high-resolution digital image (in the order of giga-pixels) is reconstructed. These huge images are then tiled into many 256 x 256-pixel blocks with different resolutions, and information about the blocks of each scanned slide is included in an extensible markup language metafile. Based on the data, a virtual microscopy system is created for viewing the scanned pathologic slides on web. The functionalities (changing viewing resolution, location adjustment, and multimedia annotation presentation) of our virtual slide viewing system are accomplished using pure hypertext markup language (HTML) and JavaScript. We show that there is no need to add plug-in components to browsers in order to handle virtual slides on the web. In a heterogeneous healthcare environment, methods using pure HTML and JavaScript to deal with pathologic content are more appropriate than using proprietary technologies supported only by specific browsers

Emotional tones of voice affect the acoustics and perception of Mandarin tones.

Lexical tones and emotions are conveyed by a similar set of acoustic parameters; therefore, listeners of tonal languages face the challenge of processing lexical tones and emotions in the acoustic signal concurrently. This study examined how emotions affect the acoustics and perception of Mandarin tones. In Experiment 1, Mandarin tones were produced by professional actors with angry, fear, happy, sad, and neutral tones of voice. Acoustic analyses on mean F0, F0 range, mean amplitude, and duration were conducted on syllables excised from a carrier phrase. The results showed that emotions affect Mandarin tone acoustics to different degrees depending on specific Mandarin tones and specific emotions. In Experiment 2, selected syllables from Experiment 1 were presented in isolation or in context. Listeners were asked to identify the Mandarin tones and emotions of the syllables. The results showed that emotions affect Mandarin tone identification to a greater extent than Mandarin tones affect emotion recognition. Both Mandarin tones and emotions were identified more accurately in syllables presented with the carrier phrase, but the carrier phrase affected Mandarin tone identification and emotion recognition to different degrees. These findings suggest that lexical tones and emotions interact in complex but systematic ways

Classification of Vascular Hotspots and Micro-Vessel Flow Velocity Waveforms in Low-Grade Squamous Intraepithelial Lesions and HPV Condyloma of the Cervix

To assess hotspot micro-vessel flow velocity waveforms in human papillomavirus (HPV) cervical infections using transvaginal power Doppler ultrasound (TV-PDU) and to explore the associations of these sonographic parameters with HPV condyloma and low-grade squamous intraepithelial lesions (LSIL) of the cervix. A total of 39 patients with cervical HPV infections with abnormal cytology and colposcopy results (26 cases of LSIL; 13 cases of HPV condyloma) were enrolled to assess the vascular classification of the cervix and micro-vessel flow velocity using TV-PDU before treatment; 40 individuals with a pathologically normal cervix were used as the control group; seven parameters were measured, including vascular grading classification (Class I, Class II, and Class III), lowest pulsatility index (PI), resistance index (RI), peak systolic velocity (PS), end-diastolic velocity (ED), time average maximum velocity (TAMV), and the vascular index (VI = PS/ED). According to vascular classification, most LSILs were class I (69.2%, 18/26), followed by class II (26.9%, 7/26) and class III (3.8%, 1/26). Most HPV condylomas were class I (92.3%, 12/13), and one was class II (7.7%, 1/13). PI, RI, VI (p < 0.0001), and the PSs (p < 0.05) were significantly lower in these cases than in the controls. The ED and TAMV were not significantly different between the patients and controls (p = 0.4985 and p = 0.1564). No sonographic parameter was significantly different between LSIL and HPV condyloma. The mean PI, RI, and VI were significantly lower in LSIL than in the controls. For HPV condyloma, a PI of 1.07 had an 84.6% sensitivity, 85.0% specificity, and an AUC of 88.8%; for LSIL, a PI of 1.08 had a 100% sensitivity, 85% specificity, and an AUC of 94.2%; for HPV infection (HPV condyloma + LSIL), a PI of 1.08 had a 94.9% sensitivity, 85% specificity, and an AUC of 92.4%. Hotspot vascular classification and micro-vessel flow velocity waveforms may provide a potential practical method for the auxiliary diagnosis of cervical HPV infection. The PI may represent a valuable index for distinguishing the micro-vessel flow velocity waveforms in LSIL and HPV condyloma. Since the case numbers were limited in the current study, further validation is needed