Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs

Background: MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs. Here, we introduce a novel method based on a heterogeneous network that not only considers miRNAs but also the corresponding target genes in the network model. Results: Instead of constructing homogeneous miRNA networks, we built heterogeneous miRNA networks consisting of both miRNAs and their target genes, using databases of known miRNA-target gene interactions. In addition, as recent studies demonstrated reciprocal regulatory relations between miRNAs and their target genes, we considered these heterogeneous miRNA networks to be undirected, assuming mutual miRNA-target interactions. Next, we introduced a novel method (RWRMTN) operating on these mutual heterogeneous miRNA networks to rank candidate disease-related miRNAs using a random walk with restart (RWR) based algorithm. Using both known disease-associated miRNAs and their target genes as seed nodes, the method can identify additional miRNAs involved in the disease phenotype. Experiments indicated that RWRMTN outperformed two existing state-of-the-art methods: RWRMDA, a network-based method that also uses a RWR on homogeneous (rather than heterogeneous) miRNA networks, and RLSMDA, a machine learning-based method. Interestingly, we could relate this performance gain to the emergence of "disease modules" in the heterogeneous miRNA networks used as input for the algorithm. Moreover, we could demonstrate that RWRMTN is stable, performing well when using both experimentally validated and predicted miRNA-target gene interaction data for network construction. Finally, using RWRMTN, we identified 76 novel miRNAs associated with 23 disease phenotypes which were present in a recent database of known disease-miRNA associations. Conclusions: Summarizing, using random walks on mutual miRNA-target networks improves the prediction of novel disease-associated miRNAs because of the existence of "disease modules" in these networks

Approximation of mild solutions of the linear and nonlinear elliptic equations

In this paper, we investigate the Cauchy problem for both linear and semi-linear elliptic equations. In general, the equations have the form $$\frac{\partial^{2}}{\partial t^{2}}u\left(t\right)=\mathcal{A}u\left(t\right)+f\left(t,u\left(t\right)\right),\quad t\in\left[0,T\right],$$ where $\mathcal{A}$ is a positive-definite, self-adjoint operator with compact inverse. As we know, these problems are well-known to be ill-posed. On account of the orthonormal eigenbasis and the corresponding eigenvalues related to the operator, the method of separation of variables is used to show the solution in series representation. Thereby, we propose a modified method and show error estimations in many accepted cases. For illustration, two numerical examples, a modified Helmholtz equation and an elliptic sine-Gordon equation, are constructed to demonstrate the feasibility and efficiency of the proposed method.Comment: 29 pages, 16 figures, July 201

Diversity of plant-parasitic nematodes on medicinal plants in Melinh station for biodiversity, Vinh Phuc Province, Vietnam

Plant-parasitic nematodes are known as one of the most important pests attacking various plants in the world, and investigating the nematode component is very essential for management of this pest and prevent damage to plants in general. Our survey of plant-parasitic nematodes on medicinal plants in Melinh Station for Biodiversity, a place for conservation of precious plants and animals in Vietnam, identified ten species that belong to nine genera, five families, and two orders of plant-parasitic nematodes parasitizing six medicinal plants. Excoecaria cochinchinensis was parasitized by the highest number of nematode genera (5 genera, including Xiphinema, Discocriconemella, Meloidogyne, Helicotylenchus, and Hemicriconemoides), while Hymenocallis littoralis was associated with the highest number of plant-parasitic nematodes (2060 nematodes/250g soil). The results also showed that Discocriconemella limitanea was found to be a dominant species with the highest number of individuals on 6 medicinal plants, and the genus Helicotylenchus had the highest frequency of appearance (5/6 plants or 83.3%). These nematodes caused symptoms such as yellowing leaves, root galls, and root lesions, which directly affect the quality and yield of medicinal plants. Based on the results, this study showed that plant-parasitic nematodes are a potential threat to the cultivation of medicinal plants in Melinh Station for Biodiversity, and thus, control measures should be applied to ensure sustainable cultivation of medicinal plants in this place

Adherence to highly active antiretroviral therapy among people living with HIV and associated high-risk behaviours and clinical characteristics: A cross-sectional survey in Vietnam

Although Vietnam has promoted the utilisation of highly active antiretroviral therapy (HAART) towards HIV elimination targets, adherence to treatment has remained under-investigated. We aimed to describe high-risk behaviours and clinical characteristics by adherence status and to identify the factors associated with non-adherence. We included 426 people living with HIV (PLWH) currently or previously involved in HAART. Most participants were men (75.4%), young (33.6 years), with low income and low education levels. Non-adherent PLWH (11.5%) were more likely to have a larger number of sex partners (p-value = 0.053), sex without condom use (p-value = 0.007) and not receive result at hospital or voluntary test centre (p-value = 0.001). Multiple logistic regression analysis showed that demographic (education levels), sexual risk behaviours (multiple sex partners and sex without using condom) and clinical characteristics (time and facility at first time received HIV-positive result) were associated with HAART non-adherence. There are differences in associated factors between women (education levels and place of HIV testing) and men (multiple sex partners). Gender-specific programs, changing risky behaviours and reducing harms among PLWH may benefit adherence. We highlight the need to improve the quantity and quality of HIV/AIDS services in Vietnam, especially in pre- and post-test counselling, to achieve better HAART adherence, working towards ending AIDS in 2030. © The Author(s) 2021. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Huy Nguyen” is provided in this record*

Discovering Water Quality Changes and Patterns of the Endangered Thi Vai Estuary in Southern Vietnam through Trend and Multivariate Analysis

Temporal and spatial water quality data are essential to evaluate human health risks. Understanding the interlinking variations between water quality and socio-economic development is the key for integrated pollution management. In this study, we applied several multivariate approaches, including trend analysis, cluster analysis, and principal component analysis, to a 15-year dataset of water quality monitoring (1999 to 2013) in the Thi Vai estuary, Southern Vietnam. We discovered a rapid improvement for most of the considered water quality parameters (e.g., DO, NH4, and BOD) by step trend analysis, after the pollution abatement in 2008. Nevertheless, the nitrate concentration increased significantly at the upper and middle parts and decreased at the lower part of the estuary. Principal component (PC) analysis indicates that nowadays the water quality of the Thi Vai is influenced by point and diffuse pollution. The first PC represents soil erosion and stormwater loads in the catchment (TSS, PO4, and Fetotal); the second PC (DO, NO2, and NO3) determines the influence of DO on nitrification and denitrification; and the third PC (pH and NH4) determines point source pollution and dilution by seawater. Therefore, this study demonstrated the need for stricter pollution abatement strategies to restore and to manage the water quality of the Thi Vai Estuary

Application of directional derivative method to determine boundary of magnetic sources by total magnetic anomalies

This paper presents the Directional Derivative method to determine location and boundaries of the magnetic directional structure sources through a new function DG (Directional Gradient - DG). Algorithm and computer program are made a code by Matlab language to attempt to calculate on 3D models in the compare with Horizontal derivative method (HG). A new function DG also applied to determine the boundary of magnetic sources by the total magnetic anomalies of Tuan Giao region. The result shows that with the application of new function DG, the boundaries of magnetic sources are exactly defined although they have a directional structure and small horizontal size. Moreover, because it does not depend on directions of magnetization, so in the computation, the transformation of the magnetic field to the pole can ignore, thus, reduce transient error. Alternatively, with the application of new function DG, the interferences in case the sources distributed close together are overcome. This usefulness affirms the possibility of application of the this method in the analysis and interpretation of magnetic data in Vietnam.ReferencesBhaskara Rao D. and N. Ramesh Babu, 1993. A fortran 77 computer program for tree dimensional inversion of magnetic anomalies resulting from multiple prismatic bodies, Computer Geosciences, 19(8), 781-801.Beiki M., David A. Clark, James R. Austin, and Clive A. Foss, 2012. Estimating source location using normalized magnetic source strength calculated from magnetic gradient tensor data. Geophysics, 77(6), J23-J37. Blakely R.J., and R. W. Simpson, 1986. Approximating edges of source bodies from magnetic or gravity anomalies: Geophysics, 51, 1494 -1498. Blakely R.J., 1995. Potential theory in gravity and magnetic applications, Cambridge University Press. Cao Dinh Trieu, Pham Huy Long, 2002. Tectonic fault in Vietnam. Publisher of Science and Engineering. Debeglia N. and J. Corpel, 1997. Automatic 3-D interpretation of potential field data using analytic signal derivatives. Geophysics, 62, 87-96.Geological and Mineral resources map on 1:200,000. Seriesof Tay Bac, sheets of Muong Kha - Son La (F-48-XXV-F-48-XXVI), Phong Sa Ly - Dien Bien Phu (F-48-XIX-F-48-XX), Kim Binh - Lao Cai (F-48-VIII-F-48-XIV), 2005. Published and copyringt by Department of Geology and Minerals of Vietnam, Hanoi. Le Huy Minh, Luu Viet Hung, Cao Dinh Trieu, 2001. Some modern methods of the interpretation aeromagnetic data applied for Tuan Giao region. Vietnam Journal of Earth Sciences, 22(3), 207-216. Le Huy Minh, Luu Viet Hung, Cao Dinh Trieu, 2002. Using the maximum horizontal gradient vector to interpret magnetic and gravity data in Vietnam. Vietnam Journal of Earth Sciences, 24(1), 67-80. Nabighian M.N., 1972. The analytic signal of two-dimensional magnetic bodies with polygonal cross-section: Its properties and use of automated anomaly interpretation: Geophysics, 37, 507-517. Nabighian M.N., 1974. Additional comments on the analytic signal of two-dimensionalmagnetic bodies with polygonal cross-section. Geophysics, 39, 85-92. Roest W. R., J. Verhoef and  M. Pilkington, 1992. Magnetic interpretation using the 3-D analytic signal: Geophysics, 57, 116-125. Vo Thanh Son, Le Huy Minh, Luu Viet Hung, 2005. Three-dimensional analytic signal method and its application in interpretation of aeromagnetic anomaly maps in the Tuan Giao region. Proceedings of the 4th geophysical scientific and technical conference of Vietnam, Publisher of Science and Engineering 2005. Vo Thanh Son, Le Huy Minh, Luu Viet Hung, 2005. Determining the horizontal position and depth of the density discontinuties in Red River Delta by using the vertical derivative and Euler deconvolution for the gravity anomaly data, Journal of Geology, Series A, 287(3-4), 39-52.Vo Thanh Son, et al., 2007. Determining the location and depth of contrast magnetic boundaries by using 3D analytics signal method and higher derivatives. Proceeding of the 5th geophysical scientific and technical conference of Vietnam.