Search results for: Hoc Khiem Trieu

Authors: Deybith Venegas-Rojas, Jens Budde, Dominik Nörz, Manfred Jücker, Hoc Khiem Trieu

Abstract:

Microfluidics is a promising approach for biomedicine cell culture experiments with microfluidic bioreactors (MBR), which can provide high precision in volume and time control over mass transport and microenvironments in small-scale studies. Nevertheless, shear stress and oxygen concentration are important factors that affect the microenvironment and then the cell culture. It is presented a novel MBR design in which differences in geometry, shear stress, and oxygen concentration were studied and optimized for cell culture. The aim is to mimic the in vivo condition with biocompatible materials and continuous perfusion of nutrients, a healthy shear stress, and oxygen concentration. The design consists of a capture system of PDMS micropillars which keep cells in place, so it is not necessary any hydrogel or complicated scaffolds for cells immobilization. Besides, the design allows continuous supply with nutrients or even any other chemical for cell experimentation. Finite element method simulations were used to study and optimize the effect of parameters such as flow rate, shear stress, oxygen concentration, micropillars shape, and dimensions. The micropillars device was fabricated with microsystem technology such as soft-lithography, deep reactive ion etching, self-assembled monolayer, replica molding, and oxygen plasma bonding. Eight different geometries were fabricated and tested, with different flow rates according to the simulations. During the experiments, it was observed the effect of micropillars size, shape, and configuration for stability and shear stress control when increasing flow rate. The device was tested with several successful HepG2 3D cell cultures. With this MBR, the aforementioned parameters can be controlled in order to keep a healthy microenvironment according to specific necessities of different cell types, with no need of hydrogels and can be used for a wide range of experiments with cells.

Keywords: cell culture, micro-bioreactor, microfluidics, micropillars, oxygen concentration, shear stress

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Authors: Deybith Venegas-Rojas, Sercan Keskin, Svenja Riekeberg, Sana Azim, Stephanie Manz, R. J. Dwayne Miller, Hoc Khiem Trieu

Abstract:

Liquid Transmission Electron Microscopy (TEM) is a growing area with a broad range of applications from physics and chemistry to material engineering and biology, in which it is possible to image in-situ unseen phenomena. For this, a nanofluidic device is used to insert the nanoflow with the sample inside the microscope in order to keep the liquid encapsulated because of the high vacuum. In the last years, Si3N4 windows have been widely used because of its mechanical stability and low imaging contrast. Nevertheless, the pressure difference between the inside fluid and the outside vacuum in the TEM generates bulging in the windows. This increases the imaged fluid volume, which decreases the signal to noise ratio (SNR), limiting the achievable spatial resolution. With the proposed device, the membrane is fortified with a microstructure capable of stand higher pressure differences, and almost removing completely the bulging. A theoretical study is presented with Finite Element Method (FEM) simulations which provide a deep understanding of the membrane mechanical conditions and proves the effectiveness of this novel concept. Bulging and von Mises Stress were studied for different membrane dimensions, geometries, materials, and thicknesses. The microfabrication of the device was made with a thin wafer coated with thin layers of SiO2 and Si3N4. After the lithography process, these layers were etched (reactive ion etching and buffered oxide etch (BOE) respectively). After that, the microstructure was etched (deep reactive ion etching). Then the back side SiO2 was etched (BOE) and the array of free-standing micro-windows was obtained. Additionally, a Pyrex wafer was patterned with windows, and inlets/outlets, and bonded (anodic bonding) to the Si side to facilitate the thin wafer handling. Later, a thin spacer is sputtered and patterned with microchannels and trenches to guide the nanoflow with the samples. This approach reduces considerably the common bulging problem of the window, improving the SNR, contrast and spatial resolution, increasing substantially the mechanical stability of the windows, allowing a larger viewing area. These developments lead to a wider range of applications of liquid TEM, expanding the spectrum of possible experiments in the field.

Keywords: liquid cell, liquid transmission electron microscopy, nanofluidics, nanofluidic cell, thin films

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Authors: Van Trieu, Shouhuai Xu, Yusheng Feng

Abstract:

Tracking attack trajectories can be difficult, with limited information about the nature of the attack. Even more difficult as attack information is collected by Intrusion Detection Systems (IDSs) due to the current IDSs having some limitations in identifying malicious and anomalous traffic. Moreover, IDSs only point out the suspicious events but do not show how the events relate to each other or which event possibly cause the other event to happen. Because of this, it is important to investigate new methods capable of performing the tracking of attack trajectories task quickly with less attack information and dependency on IDSs, in order to prioritize actions during incident responses. This paper proposes a two-level graph causality framework for tracking attack trajectories in internet networks by leveraging observable malicious behaviors to detect what is the most probable attack events that can cause another event to occur in the system. Technically, given the time series of malicious events, the framework extracts events with useful features, such as attack time and port number, to apply to the conditional independent tests to detect the relationship between attack events. Using the academic datasets collected by IDSs, experimental results show that the framework can quickly detect the causal pairs that offer meaningful insights into the nature of the internet network, given only reasonable restrictions on network size and structure. Without the framework’s guidance, these insights would not be able to discover by the existing tools, such as IDSs. It would cost expert human analysts a significant time if possible. The computational results from the proposed two-level graph network model reveal the obvious pattern and trends. In fact, more than 85% of causal pairs have the average time difference between the causal and effect events in both computed and observed data within 5 minutes. This result can be used as a preventive measure against future attacks. Although the forecast may be short, from 0.24 seconds to 5 minutes, it is long enough to be used to design a prevention protocol to block those attacks.

Keywords: causality, multilevel graph, cyber-attacks, prediction

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Authors: Trieu Anh Ngoc, Nguyen Quang Kim

Abstract:

Located at the downstream of the Mekong Delta, the Vietnamese Mekong Delta is well-known as 'rice bowl' of Vietnam. The Vietnamese Mekong Delta experiences widespread flooding annually where is habitat for about 17 million people. The economy of this region mainly depends on the agricultural productivities. The suspended sediment load in the Mekong River plays an important role in carrying contaminants and nutrients to the delta and changing the geomorphology of the delta river system. In many past decades, flooding and suspended sediment were considered as indispensable factors in agricultural cultivations. Although flooding in the wet season caused serious inundation in paddy field and affected livelihoods, it is an effective facility for flushing acid and saline to this area - alluvial soil heavily contaminated with acid and salt intrusion. In addition, sediment delivery to this delta contained rich-nutrients distributed and deposited on the fields through flooding process. In recent decades, the changing of flow and sediment transport have been strongly and clearly occurring due to upstream dam development and climate change. However, effects of sediment delivery on agricultural cultivations were less attention. This study investigated the impacts of upstream flow on sediment distribution in the Vietnamese Mekong Delta. Flow fluctuation and sediment distribution were simulated by the Mike 11 model, including hydrodynamics model and advection-dispersion model. Various scenarios were simulated based on anticipated upstream discharges. Our findings indicated that sediment delivery into the Vietnamese Mekong Delta come from not only Tien River but also border of Cambodia floodplains. Sediment distribution in the Vietnamese Mekong Delta is dramatically changed by the distance from the main rivers and the secondary channels. The dam development in the upstream is one of the major factors leading a decrease in sediment discharge as well as sediment deposition. Moreover, sea level rise partially contributed to decrease in sediment transport and change of sediment distribution between upstream and downstream of the Vietnamese Mekong Delta.

Keywords: sediment transport, sea level rise, climate change, Mike Model

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Authors: Khiem M. Nguyen, Ming C. Yang

Abstract:

Chloroplast pigments are extremely important during photosynthesis since they play essential roles in light absorption and energy transfer. Therefore, understanding the efficiency of chlorophyll (Chl) biosynthesis could facilitate enhancement in photo-assimilates accumulation, and ultimately, in crop yield. The Chl-deficient mutants have been used extensively to study the Chl biosynthetic pathways and the biogenesis of the photosynthetic apparatus. Rice (Oryza sativa L.) is one of the most leading food crops, serving as staple food for many parts of the world. To author’s best knowledge, Chl b–lacking rice has been found; however the molecular mechanism of Chl biosynthesis still remains unclear compared to wild-type rice. In this study, the ultrastructure analysis, photosynthetic properties, and transcriptome profile of wild-type rice (Norin No.8, N8) and its Chl b-lacking mutant (Chlorina 1, C1) were examined. The finding concluded that total Chl content and Chl b content in the C1 leaves were strongly reduced compared to N8 leaves, suggesting that reduction in the total Chl content contributes to leaf color variation at the physiological level. Plastid ultrastructure of C1 possessed abnormal thylakoid membranes with loss of starch granule, large number of vesicles, and numerous plastoglobuli. The C1 rice also exhibited thinner stacked grana, which was caused by a reduction in the number of thylakoid membranes per granum. Thus, the different Chl a/b ratio of C1 may reflect the abnormal plastid development and function. Transcriptional analysis identified 23 differentially expressed genes (DEGs) and 671 transcription factors (TFs) that were involved in Chl metabolism, chloroplast development, cell division, and photosynthesis. The transcriptome profile and DEGs revealed that the gene encoding PsbR (PSII core protein) was down-regulated, therefore suggesting that the lower in light-harvesting complex proteins are responsible for the lower photosynthetic capacity in C1. In addition, expression level of cell division protein (FtsZ) genes were significantly reduced in C1, causing chloroplast division defect. A total of 19 DEGs were identified based on KEGG pathway assignment involving Chl biosynthesis pathway. Among these DEGs, the GluTR gene was down-regulated, whereas the UROD, CPOX, and MgCH genes were up-regulated. Observation through qPCR suggested that later stages of Chl biosynthesis were enhanced in C1, whereas the early stages were inhibited. Plastid structure analysis together with transcriptomic analysis suggested that the Chl a/b ratio was amplified both by the reduction in Chl contents accumulation, owning to abnormal chloroplast development, and by the enhanced conversion of Chl b to Chl a. Moreover, the results indicated the same Chl-cycle pattern in the wild-type and C1 rice, indicating another Chl b degradation pathway. Furthermore, the results demonstrated that normal grana stacking, along with the absence of Chl b and greatly reduced levels of Chl a in C1, provide evidence to support the conclusion that other factors along with LHCII proteins are involved in grana stacking. The findings of this study provide insight into the molecular mechanisms that underlie different Chl a/b ratios in rice.

Keywords: Chl-deficient mutant, grana stacked, photosynthesis, RNA-Seq, transcriptomic analysis

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