On-premise containerized, light-weight software solutions for Biomedicine

Bioinformatics software systems are critical tools for analysing large-scale biological data, but their design and implementation can be challenging due to the need for reliability, scalability, and performance. This thesis investigates the impact of several software approaches on the design and implementation of bioinformatics software systems. These approaches include software patterns, microservices, distributed computing, containerisation and container orchestration. The research focuses on understanding how these techniques affect bioinformatics software systems’ reliability, scalability, performance, and efficiency. Furthermore, this research highlights the challenges and considerations involved in their implementation. This study also examines potential solutions for implementing container orchestration in bioinformatics research teams with limited resources and the challenges of using container orchestration. Additionally, the thesis considers microservices and distributed computing and how these can be optimised in the design and implementation process to enhance the productivity and performance of bioinformatics software systems. The research was conducted using a combination of software development, experimentation, and evaluation. The results show that implementing software patterns can significantly improve the code accessibility and structure of bioinformatics software systems. Specifically, microservices and containerisation also enhanced system reliability, scalability, and performance. Additionally, the study indicates that adopting advanced software engineering practices, such as model-driven design and container orchestration, can facilitate efficient and productive deployment and management of bioinformatics software systems, even for researchers with limited resources. Overall, we develop a software system integrating all our findings. Our proposed system demonstrated the ability to address challenges in bioinformatics. The thesis makes several key contributions in addressing the research questions surrounding the design, implementation, and optimisation of bioinformatics software systems using software patterns, microservices, containerisation, and advanced software engineering principles and practices. Our findings suggest that incorporating these technologies can significantly improve bioinformatics software systems’ reliability, scalability, performance, efficiency, and productivity.Bioinformatische Software-Systeme stellen bedeutende Werkzeuge für die Analyse umfangreicher biologischer Daten dar. Ihre Entwicklung und Implementierung kann jedoch aufgrund der erforderlichen Zuverlässigkeit, Skalierbarkeit und Leistungsfähigkeit eine Herausforderung darstellen. Das Ziel dieser Arbeit ist es, die Auswirkungen von Software-Mustern, Microservices, verteilten Systemen, Containerisierung und Container-Orchestrierung auf die Architektur und Implementierung von bioinformatischen Software-Systemen zu untersuchen. Die Forschung konzentriert sich darauf, zu verstehen, wie sich diese Techniken auf die Zuverlässigkeit, Skalierbarkeit, Leistungsfähigkeit und Effizienz von bioinformatischen Software-Systemen auswirken und welche Herausforderungen mit ihrer Konzeptualisierungen und Implementierung verbunden sind. Diese Arbeit untersucht auch potenzielle Lösungen zur Implementierung von Container-Orchestrierung in bioinformatischen Forschungsteams mit begrenzten Ressourcen und die Einschränkungen bei deren Verwendung in diesem Kontext. Des Weiteren werden die Schlüsselfaktoren, die den Erfolg von bioinformatischen Software-Systemen mit Containerisierung, Microservices und verteiltem Computing beeinflussen, untersucht und wie diese im Design- und Implementierungsprozess optimiert werden können, um die Produktivität und Leistung bioinformatischer Software-Systeme zu steigern. Die vorliegende Arbeit wurde mittels einer Kombination aus Software-Entwicklung, Experimenten und Evaluation durchgeführt. Die erzielten Ergebnisse zeigen, dass die Implementierung von Software-Mustern, die Zuverlässigkeit und Skalierbarkeit von bioinformatischen Software-Systemen erheblich verbessern kann. Der Einsatz von Microservices und Containerisierung trug ebenfalls zur Steigerung der Zuverlässigkeit, Skalierbarkeit und Leistungsfähigkeit des Systems bei. Darüber hinaus legt die Arbeit dar, dass die Anwendung von SoftwareEngineering-Praktiken, wie modellgesteuertem Design und Container-Orchestrierung, die effiziente und produktive Bereitstellung und Verwaltung von bioinformatischen Software-Systemen erleichtern kann. Zudem löst die Implementierung dieses SoftwareSystems, Herausforderungen für Forschungsgruppen mit begrenzten Ressourcen. Insgesamt hat das System gezeigt, dass es in der Lage ist, Herausforderungen im Bereich der Bioinformatik zu bewältigen und stellt somit ein wertvolles Werkzeug für Forscher in diesem Bereich dar. Die vorliegende Arbeit leistet mehrere wichtige Beiträge zur Beantwortung von Forschungsfragen im Zusammenhang mit dem Entwurf, der Implementierung und der Optimierung von Software-Systemen für die Bioinformatik unter Verwendung von Prinzipien und Praktiken der Softwaretechnik. Unsere Ergebnisse deuten darauf hin, dass die Einbindung dieser Technologien die Zuverlässigkeit, Skalierbarkeit, Leistungsfähigkeit, Effizienz und Produktivität bioinformatischer Software-Systeme erheblich verbessern kann

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*

Effects of dietary tryptophan on cannibalism, survival and growth of Wallago attu (Bloch & Schneider, 1801) juveniles

This study aims to evaluate the effects of supplemented commercial diets with tryptophan (TRP) on plasma serotonin, cannibalism, survival rate, and growth of Wallago attu (helicopter catfish). After one week of acclimation, 3,200 juveniles of helicopter catfish (BW = 2.5 ± 0.27 g, total length = 5.6 ± 0.43 cm) were randomly assigned for the experiment in fifteen plastic tanks (200 L). The experiment was conducted with five treatments (CT – 0 g TRP/kg – control group, T1 – 5 g TRP/kg, T2 – 10 g TRP/kg, T3 – 20 g TRP/kg, and T4 – 40 g TRP/kg) in a completely randomized design with three replications for four weeks. The results from the enzyme-linked immunosorbent assay reveal that TRP-supplemented diets effectively increased the serotonin level (5-HT) in the plasma of the catfish. The serotonin level increased with the dose of TRP added to the feed. Furthermore, a higher TRP level significantly decreased cannibalism and improved the final survival of the fish. However, the fish’s growth rate among treatments T1, T2, T3, and T4 was not significantly different, but there was a statistical difference between the experimental treatments and the CT treatment. The findings of this study suggest that TRP could be supplemented at a dose of 20 g·kg–1 to the feed to reduce cannibalism and improve the final survival of helicopter catfish

CHANGES IN PLASMA LEVELS OF STEROID HORMONES DURING SEXUAL MATURATION OF MALE HELICOPTER CATFISH (WALLAGO ATTU) IN CAPTIVITY

In order to provide reliable indicators of the spawning season of captive helicopter catfish (Wallago attu), this study evaluated the temporal variation in gonadosomatic index (GSI), plasma levels of testosterone (T), and 11-ketotestosterone (11-KT) in male broodstock in captivity. GSI was estimated as the percentage of the relative weight of testis to total body weight. Plasma levels of sex steroids were determined by enzyme-linked immunosorbent assay (EIA). Testis samples were dehydrated and embedded in paraffin, then sectioned at 5 μm thickness. The highest level of T (402.1 ± 16.7 pg/mL) was found in June, followed by a peak in 11-KT level (76.9 ± 4.7 pg/mL) in May. Testes containing the highest concentrations of spermatozoa were observed from June to August. The GSI of males increased significantly from January to June and peaked in July (2.14%). Taken together, we conclude that the spawning season of captive helicopter catfish occurs from June to August. These results will contribute to the basic knowledge of the reproductive biology of helicopter catfish, which can be useful in artificial breeding

Asymptotic periodic solutions of differential equations with infinite delay

In this paper, by using the spectral theory of functions and properties of evolution semigroups, we establish conditions on the existence, and uniqueness of asymptotic 1-periodic solutions to a class of abstract differential equations with infinite delay of the form \begin{equation*} \frac{d u(t)}{d t}=A u(t)+L(u_t)+f(t) \end{equation*} where $A$ is the generator of a strongly continuous semigroup of linear operators, $L$ is a bounded linear operator from a phase space $\mathscr{B}$ to a Banach space $X$, $u_t$ is an element of $\mathscr{B}$ which is defined as $u_t(\theta)=u(t+\theta)$ for $\theta \leq 0$ and $f$ is asymptotic 1-periodic in the sense that $\lim\limits_{t \rightarrow \infty}(f(t+1)-$ $f(t))=0$. A Lotka-Volterra model with diffusion and infinite delay is considered to illustrate our results.Comment: 13 page