Probabilistic uncertainty quantification and experiment design for nonlinear models: Applications in systems biology

Despite the ever-increasing interest in understanding biology at the system level, there are several factors that hinder studies and analyses of biological systems. First, unlike systems from other applied fields whose parameters can be effectively identified, biological systems are usually unidentifiable, even in the ideal case when all possible system outputs are known with high accuracy. Second, the presence of multivariate bifurcations often leads the system to behaviors that are completely different in nature. In such cases, system outputs (as function of parameters/inputs) are usually discontinuous or have sharp transitions across domains with different behaviors. Finally, models from systems biology are usually strongly nonlinear with large numbers of parameters and complex interactions. This results in high computational costs of model simulations that are required to study the systems, an issue that becomes more and more problematic when the dimensionality of the system increases. Similarly, wet-lab experiments to gather information about the biological model of interest are usually strictly constrained by research budget and experimental settings. The choice of experiments/simulations for inference, therefore, needs to be carefully addressed. ^ The work presented in this dissertation develops strategies to address theoretical and practical limitations in uncertainty quantification and experimental design of non-linear mathematical models, applied in the context of systems biology. This work resolves those issues by focusing on three separate but related approaches: (i) the use of probabilistic frameworks for uncertainty quantification in the face of unidentifiability (ii) the use of behavior discrimination algorithms to study systems with discontinuous model responses and (iii) the use of effective sampling schemes and optimal experimental design to reduce the computational/experimental costs. ^ This cumulative work also places strong emphasis on providing theoretical foundations for the use of the proposed framework: theoretical properties of algorithms at each step in the process are investigated carefully to give more insights about how the algorithms perform, and in many cases, to provide feedback to improve the performance of existing approaches. Through the newly developed procedures, we successfully created a general probabilistic framework for uncertainty quantification and experiment design for non-linear models in the face of unidentifiability, sharp model responses with limited number of model simulations, constraints on experimental setting, and even in the absence of data. The proposed methods have strong theoretical foundations and have also proven to be effective in studies of expensive high-dimensional biological systems in various contexts

Quality of Water used at pig farms in the Red River delta

peer reviewedA research was carried out to evaluate water quality using at 12 different pig farms in Bac Ninh, Hung Yen and Hai Duong provinces. Water samples were taken in two periods from October to December 2006 and from March to April 2007. Physical and chemical parameters were analysed at the laboratory of the Department of Veterinary Parasitology-Inspection and Hygiene - Hanoi University of Agriculture. The results showed that, all water sources using the pig farms came from underground and a half of which was not processed. Contents of COD(H+), COD(OH-), CO2, Cl- in water in Hai Duong and Bac Ninh were exceeded the hygiene standard. Iron content in water in all three provinces was exceeded the hygiene standard. After using a processed system including artificial rain, H2O2 supplement and filter the content of DO, CO2 and Fe in the water reached the permitted hygiene standard

Impact of sea level rise on current and wave in Van Uc coastal area

This paper presents the results of analysis, comparison of some characteristics of current, wave at Van Uc estuary area when being affected by sea level rise due to climate change based on Delft3D model. Scenario groups are established: The current scenario and the scenarios simulating effect of sea level rise 0.5 m and 1.0 m. The results of calculation and simulation show that the velocity values change locally when sea level rises: Rise in the northern and southern areas (0.2–5 cm/s); decrease in the navigation channel (0.6–30 cm/s). Sea level rise causes the increase of wave height in the coastal area (13.5–43.8% in the dry season and 20–40% in the rainy season) and fewer changes in the outer area

Quality comparison of Y-shape joints by tube hydroforming with and without counterforce

The design capability, strength, and structural rigidity provided by tube hydroforming (THF) are successfully used in many applications to produce high-strength parts and assemblies with improved mechanical properties, optimized service life, and weight features. In tubular metal forming, output parameters such as branch height, distribution of tube wall material thickness, distribution of damage factor, metal flow, effective stress, and effective strain significantly affect the quality of the product after the forming process. Therefore, this paper aims to evaluate the manufacturing quality of Y-shape joints from AISI304 material steel tube through output parameters of THF process with and without counter punch force on numerical simulation base. The Finite Element Method (FEM) has become an established feature of metal forming technology. The objective of FEM is to replace costly and elaborate experimental testing with fast, low-cost computer simulation. The simulation study uses finite element method-based virtual prototyping techniques to characterize output parameters, gain insight into strain mechanics, and predict mechanical properties of shaped components. The research results are presented clearly and unambiguously through the evaluation of 7 criteria to compare the quality of the specimens hydroformed by two surveyed cases and optimize the crucial input process parameters. And these data can be applied in experiments, more efficient product and process design, calculation, and control of input parameters avoiding costly trial and error in industrial production. The findings can help technologists optimize process parameters in the hydroforming process of products with protrusion from a tubular blan

Characterization of pig farms in Hung Yen, Hai Duong and Bac Ninh provinces

peer reviewedIn order to characterization of pig farms in the Red River Delta, a study was conducted on 90 pig farms in Hung Yen, Hai Duong and Bac Ninh provinces from June to December 2006. Results show that most of the pig farms had been built for five years with a small size (0.5 hectare per farm). The invested capital was about 300-400 millions VND per farm. Four main sow groups used in the farms included crossbred exotic sows (51.1%), crossbred sow between local and exotic breeds (14.4%), purebred Landrace and Yorkshire breeds (15.6 and 18.9%, respectively). The boars were various (Duroc 30%, Yorkshire 21%, Landrace 13%, PiÐtrain × Duroc 36% and others). The pigs farms were faced with several difficulties such as limited land, lack of invested capital, uncontrolled quality of breeding pigs, high costs of feed, poor hygiene condition and diseases

Primary Evaluation on Growth Performances of Stress Negative Piétrain Pigs Raised in Hai Phong Province of Vietnam

peer reviewedThe present study was carried out on 19 stress negative Piétrain pigs (Pietrain ReHal), consisting of 13 gilts and 6 young boars imported from Belgium, raised in the livestock farm of Dong Hiep (Hai Phong) in order to evaluate growth performances and their adaptability in the North of Vietnam. Results showed that the average body weight of the whole herd at 2, 4, 5.5, and 8.5 months old was 19.05, 51.05, 85.82, and 119.47 kg, respectively. During the growing periods, except the first stage, the male grew faster than the female and the pigs of the CT genotype grew faster than those of CC genotype although the difference was not significant (P>0.05). The average daily gain (ADG) was 528.56 grams for the whole herd. The ADG was higher for the male (546.48 grams) than for the female (520.29 grams), and its was higher for the CT than the CC, but the difference was not statistically significant (P>0.05). The feed conversion ratio (FCR) was 2.69 kg. The estimated lean percentage at 8.5 months old was 64.08%. The results indicate that Piétrain stress negative pigs could develop well on the farm conditions in Hai Phong, Vietnam

The impact of intraspecific competition on tree growth in planted Korean pine forest

The aim of this study was to explore the correlation of competition indices (CIs) on individual tree growth for Korean pine (Pinus koraiensis) plantation using partial correlation analysis and generalized linear models. The data were collected from 15 permanent plots in Mengjiagang forestry farm, Northeast China. The results showed that the distance dependent CIs have a higher predictive capacity for individual growth of pine trees. The control index of competitive trees number (CI1) combined with the selection fixed competitor trees (M2) was found to be the most well correlated competition measure with five - years diameter increment. Thus, the competition index (CI1- M2) was recommended for developing individual tree growth models. The subject tree diameter at breast height, crown width, height to crown base, tree volume and basal area all showed a significantly linear correlation with tree competition intensity (P 0,05). Diameter at breast height, crown width, tree volume and basal area all decreased with increasing competition intensity, whereas the height to crown base increased. There was no significant relationship between competition intensity and tree height (P 0,05). The optimal model of predicting individual growth with logarithm of diameter at breast height and CIs as the independent variables due to the best fitting performance. This results also showed considerable improvement in predicting individual tree periodic growth when including competition indices that the mean absolute error is reduced in the range of 22−25%.

Evaluation of Anterior Chamber Depth and Anterior Chamber Angle Changing After Phacoemulsification in the Primary Angle Close Suspect Eyes

BACKGROUND: Phacoemulsification surgery has the ability to deeply alter the segment anterior morphology, especially in eye with shallow anterior chamber (AC), narrow anterior chamber angle (ACA). However, the changes of anterior chamber depth (ACD) and ACA on the close angle suspect eyes after phacoemulsification have not been mentioned in many studies. So, we conduct this research. AIM: To evaluate the alteration in the ACA and ACD after phacoemulsification in the close angle suspect eyes. METHODS: Interventional study with no control group. Subjects were the primary angle closure suspect (PACS) eyes, that were operated by phacoemulsification with intraocular lens (IOL) at Glaucoma Department of VNIO from December 2017 to October 2018. RESULTS: 29 PACS eyes with cataract were operated by phacoemulsification with intraocular lens. After 3 months of monitoring, the average ACD augmented from 2.082 ± 0.244 to 3.673 ± 0.222 mm. AOD500 increase from 0.183 ± 0.088 to 0.388 ± 0.132 μm, AOD750 increased from 0.278 ± 0.105 to 0.576 ± 0.149 μm. The TISA500 enlarged from 0.068 ± 0.033 to 0.140 ± 0.052 mm2, TISA750 enlarged from 0.125 ± 0.052 to 0.256 ± 0.089 mm2 at the third month (p < 0.01). CONCLUSION: Phacoemulsification surgery increases the ACD and enlarged the angle in the PACS eyes

The use of metaverse in maritime sector – a combination of social communication, hands on experiencing and digital twins

COVID-19 has caused challenges in traveling, sales activities, and teleconferencing is at the moment the main communication tool in industry. Various technologies have been introduced during the last a couple of years to increase the immersion of remote presence. Technologies, that can be called as a virtual reality social platform (VRSP) such as Glue, MootUp, Breakroom, LearnBrite, Virtway Events, Engage, AltspaceVR, and VirBELA are robust solutions for a small group of people to participate in the same event. In July 2021, both Microsoft CEO and Facebook CEO published their visions for remote presence, teleconferencing, and much more. Microsoft plans to build an enterprise metaverse (combining technologies such as AltspaceVR, Mesh, Teams, and HoloLens). Facebook in turn intends to transit their business from social media platform to metaverse provider. In February 2021, much before the metaverse enhancement of the big tech giants, Turku University of Applied Sciences started the development of its own metaverse technology. According to Nevelsteen (2018) metaverse is a virtual universe shared amongst its users allowing them to interact with each other within the boundaries of the platform. For TUAS the metaverse concept is a combination of social communication, hands on experiencing and digital twin integration. None of the mentioned VRSP technologies include all these three features neither Microsoft or Facebook have this type of vision. Moreover existing VRSP technologies typically have challenges such as update management, number of simultaneous users, usability, user experience, license policies, customization but also limited user interaction and user data gathering. In this paper, we will introduce our own metaverse technology. Research conducted at TUAS tested existing VRSPs, compared Unity and Unreal game engines in metaverse development and based on industry trend analysis revealed that Epic Games intends to focus on metaverse software development tools. On the other hand the use of Unreal limits user groups for VR and PC users. This research approach presented in this paper provides metaverse experiences to be used with various ways from VR/AR/XR to PCs and mobile phones. This way, users who have limited resources available are able to participate in metaverse applications where the user experience will vary based the available device. This paper introduces the TUAS metaverse technology, the first experiences of developing it and how the first prototype version of this technology has been used in various maritime sector projects. To demonstrate the technology a harbor area has been selected as a test environment. In the first test, AltspaceVR technology was used to develop the environment itself with features needed in virtual exhibition called Match XR. This will be followed by an experiment where the harbor environment with same functionalities will be moved to the TUAS metaverse technology. Finally, the paper reports how multiplayer concepts such as MarISOT command bridge training scenarios can be developed utilizing the TUAS metaverse technology