Performance Assessment of the Network Reconstruction Approaches on Various Interactomes

Beyond the list of molecules, there is a necessity to collectively consider multiple sets of omic data and to reconstruct the connections between the molecules. Especially, pathway reconstruction is crucial to understanding disease biology because abnormal cellular signaling may be pathological. The main challenge is how to integrate the data together in an accurate way. In this study, we aim to comparatively analyze the performance of a set of network reconstruction algorithms on multiple reference interactomes. We first explored several human protein interactomes, including PathwayCommons, OmniPath, HIPPIE, iRefWeb, STRING, and ConsensusPathDB. The comparison is based on the coverage of each interactome in terms of cancer driver proteins, structural information of protein interactions, and the bias toward well-studied proteins. We next used these interactomes to evaluate the performance of network reconstruction algorithms including all-pair shortest path, heat diffusion with flux, personalized PageRank with flux, and prize-collecting Steiner forest (PCSF) approaches. Each approach has its own merits and weaknesses. Among them, PCSF had the most balanced performance in terms of precision and recall scores when 28 pathways from NetPath were reconstructed using the listed algorithms. Additionally, the reference interactome affects the performance of the network reconstruction approaches. The coverage and disease- or tissue-specificity of each interactome may vary, which may result in differences in the reconstructed networks

Diabetic gastroparesis in association with autonomic neuropathy and microvasculopathy.

Gastroparesis is a frequent and sometimes life-threatening complication of diabetes mellitus. Autonomic neuropathy seems to be one of the most important mechanisms underlying this entity, together with the other probable pathologies. The present study was performed in order to identify an alternative to gastric scintigraphy as a screening test. The gastric emptying times of 60 subjects (Group 1: 20 insulin-dependent patients, Group 2: 20 non-insulin-dependent diabetes mellitus patients, and Group 3: 20 healthy volunteers) were monitored by gastric scintigraphy. Perception thresholds for cold, heat, and vibration were tested by a quantitative sensory test, and QTc dispersions were calculated from standard electrocardiography recordings. In addition, fasting blood glucose, hemoglobin A1c and urine beta2-microglobulin and microalbumin concentrations were determined for the patient groups. Funduscopic examination was performed by an independent ophthalmologist. Gastroparesis was determined in both patient groups, regardless of fasting blood glucose and hemoglobin A1c concentrations. A strong correlation was observed between nephropathy, retinopathy, and cardiac autonomic denervation (QTc) and gastroparesis. In conclusion, retinal and renal microvasculopathy parameters and cardiac autonomic function tests may be useful for screening diabetic patients for gastroparesis.</p

Thai lexical tone perception in native speakers of Thai, English and Mandarin Chinese: An event-related potentials training study

<p>Abstract</p> <p>Background</p> <p>Tone languages such as Thai and Mandarin Chinese use differences in fundamental frequency (F₀, pitch) to distinguish lexical meaning. Previous behavioral studies have shown that native speakers of a non-tone language have difficulty discriminating among tone contrasts and are sensitive to different F₀dimensions than speakers of a tone language. The aim of the present ERP study was to investigate the effect of language background and training on the non-attentive processing of lexical tones. EEG was recorded from 12 adult native speakers of Mandarin Chinese, 12 native speakers of American English, and 11 Thai speakers while they were watching a movie and were presented with multiple tokens of low-falling, mid-level and high-rising Thai lexical tones. High-rising or low-falling tokens were presented as deviants among mid-level standard tokens, and vice versa. EEG data and data from a behavioral discrimination task were collected before and after a two-day perceptual categorization training task.</p> <p>Results</p> <p>Behavioral discrimination improved after training in both the Chinese and the English groups. Low-falling tone deviants versus standards elicited a mismatch negativity (MMN) in all language groups. Before, but not after training, the English speakers showed a larger MMN compared to the Chinese, even though English speakers performed worst in the behavioral tasks. The MMN was followed by a late negativity, which became smaller with improved discrimination. The High-rising deviants versus standards elicited a late negativity, which was left-lateralized only in the English and Chinese groups.</p> <p>Conclusion</p> <p>Results showed that native speakers of English, Chinese and Thai recruited largely similar mechanisms when non-attentively processing Thai lexical tones. However, native Thai speakers differed from the Chinese and English speakers with respect to the processing of late F₀contour differences (high-rising versus mid-level tones). In addition, native speakers of a non-tone language (English) were initially more sensitive to F₀onset differences (low-falling versus mid-level contrast), which was suppressed as a result of training. This result converges with results from previous behavioral studies and supports the view that attentive as well as non-attentive processing of F₀contrasts is affected by language background, but is malleable even in adult learners.</p

Trajectories of charged particles trapped in Earth's magnetic field

I outline the theory of relativistic charged-particle motion in the magnetosphere in a way suitable for undergraduate courses. I discuss particle and guiding center motion, derive the three adiabatic invariants associated with them, and present particle trajectories in a dipolar field. I provide twelve computational exercises that can be used as classroom assignments or for self-study. Two of the exercises, drift-shell bifurcation and Speiser orbits, are adapted from active magnetospheric research. The Python code provided in the supplement can be used to replicate the trajectories and can be easily extended for different field geometries.Comment: 10 pages, 7 figures. Submitted to American Journal of Physic

Numerical Investigation of Dam-Break Flow over a Bottom Obstacle Using Eulerian Finite Element Method

Dam-break flows can cause major destructions in case settlements located atthe downstream area. Since many people live in the settlements, investigations regarding the dam-break flow have great importance.Dam break flow characteristics can become variousbased on different downstream conditions. In this study, an investigation was made relating tothe dam break flow in a channel with symmetrical triangular-shaped bottom obstacle using Finite Element Method (FEM) formulation. Numerical results of the present study were compared with experimental results. It was concluded that numerical and experimental results are in good agreement

Students' Reluctance to Attend Office Hours: Reasons and Suggested Solutions

This paper focuses on investigating students’ reasons for their reluctance to attend faculty members’ office hours. Study participants included 500 male and female students from the Colleges of Engineering (n = 248) and Arts and Social Sciences (CASS) (n = 252) at Sultan Qaboos University (SQU). The study followed a descriptive-analytical approach, and a questionnaire was utilized to collect people’s views. The results of the study indicate that the rates of SQU students’ attendance to office hours were low, and some students (11.2%) do not attend at all as they consider these office hours a waste of time. The main reasons behind the students’ lack of interest in office hours were busy student timetables, conflicts between faculty office hours and students’ timetables, and easier and faster ways of getting information than visiting faculty members. Additional reasons were related to faculty members’ personalities and their discouraging attitudes toward attending office hours. The researchers recommend that SQU adopt a new strategy for encouraging faculty members to hold office hours, familiarizing students with the importance of office hours and assigning part of a course’s grades to meeting with faculty members’ office hours

Effects of Extremely Low Frequency Magnetic Field on the Lens of the Rats

The present aim of the study is to evaluate the effects of extremely low frequency magnetic field (ELF MF) on lens epithelial cells. Twenty adult female Spraque Dawley rats were divided into two groups, each containing 10 rats. The experimental group received magnetic field 2 hours/day for 7 days. The second group receiving standard laboratory care, was used as a control. The specimens were evaluated for cataractogenesis alteretion of lens and histological changes in lens epithelial cells.On biomicroscopic examination, no pathological damage to the lens was detected. In addition, on microscopic examination of materials in the controls, there were also no changes in lens fibrils and lens epithelial cells. In experimental group, however, only a slight pleomorphism was determined at the surface of epithelial cells.In the study, it is cocluded that ELF MF exposure do might not lead to histopathological alterations of the lens fibrils and lens epithelial cells