Search results for: Systems and Synthetic Biology

Authors: Tomokazu Shirai, Akihiko Kondo

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Technologies of metabolic engineering or synthetic biology are essential for effective microbial bioproduction. It is especially important to develop an in silico tool for designing a metabolic pathway producing an unnatural and valuable chemical such as fossil materials of fuel or plastics. We here demonstrated two in silico tools for designing novel metabolic pathways: BioProV and HyMeP. Furthermore, we succeeded in creating an artificial metabolic pathway by enzyme engineering.

Keywords: bioinformatics, metabolic engineering, synthetic biology, genome scale model

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: synthetic gene network, network identification, optimization, nonlinear modeling

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Authors: Mehrshad Khosraviani, Sepehr Najjarpour

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Considering the usage of graph-based approaches in systems and synthetic biology, and the various types of ‎the graphs employed by them, a comprehensive graph library based ‎on the three-tier architecture (3TA) was previously introduced for full representation of the biological systems. Although proposing a 3TA-based graph library, three following reasons motivated us to redesign the graph ‎library based on the service-oriented architecture (SOA): (1) Maintaining the accuracy of the data related to an input graph (including its edges, its ‎vertices, its topology, etc.) without involving the end user:‎ Since, in the case of using 3TA, the library files are available to the end users, they may ‎be utilized incorrectly, and consequently, the invalid graph data will be provided to the ‎computer algorithms. However, considering the usage of the SOA, the operation of the ‎graph registration is specified as a service by encapsulation of the library files. In other words, overall control operations needed for registration of the valid data will be the ‎responsibility of the services. (2) Partitioning of the library product into some different parts: Considering 3TA, a whole library product was provided in general. While here, the product ‎can be divided into smaller ones, such as an AND/OR graph drawing service, and each ‎one can be provided individually. As a result, the end user will be able to select any ‎parts of the library product, instead of all features, to add it to a project. (3) Reduction of the complexities: While using 3TA, several other libraries must be needed to add for connecting to the ‎database, responsibility of the provision of the needed library resources in the SOA-‎based graph library is entrusted with the services by themselves. Therefore, the end user ‎who wants to use the graph library is not involved with its complexity. In the end, in order to ‎make ‎the library easier to control in the system, and to restrict the end user from accessing the files, ‎it was preferred to use the service-oriented ‎architecture ‎‎(SOA) over the three-tier architecture (3TA) and to redevelop the previously proposed graph library based on it‎.

Keywords: Bio-Design Automation, Biological System, Graph Library, Service-Oriented Architecture, Systems and Synthetic Biology

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Authors: Eleni Panagiotarakou

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This paper argues that humans have a collective moral responsibility to help wild animals during the Anthropocene era. Seen from the perspective of deontic logic, this moral responsibility did not exist in the Holocene era (ca. 11,700 BC-1945 AD) on account of humanity’s limited impact on the natural environment. By contrast in the Anthropocene, human activities are causing significant disturbances to planetary ecosystems and by inference to wildlife communities. Under these circumstances controversial and deeply regrettable interventional methods such as Managed Relocations (MR) and synthetic biology should be expanded and become policy measures despite their known and unknown risks. The main rationale for the above stems from the fact that traditional management strategies are simply insufficient in the Anthropocene. If the same anthropogenic activities continue unabated they risk triggering a sixth mass species extinction.

Keywords: anthropocene, humanitarian interventions, managed relocations, species extinctions, synthetic biology

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Authors: Keerthi S. Shetty, Annappa Basava

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In recent years, modelling of biological systems represented by biochemical reactions has become increasingly important in Systems Biology. Biological systems represented by biochemical reactions are highly stochastic in nature. Probabilistic model is often used to describe such systems. One of the main challenges in Systems biology is to combine absolute experimental data into probabilistic model. This challenge arises because (1) some molecules may be present in relatively small quantities, (2) there is a switching between individual elements present in the system, and (3) the process is inherently stochastic on the level at which observations are made. In this paper, we describe a novel idea of combining absolute experimental data into probabilistic model using tool R2. Through a case study of the Transcription Process in Prokaryotes we explain how biological systems can be written as probabilistic program to combine experimental data into the model. The model developed is then analysed in terms of intrinsic noise and exact sampling of switching times between individual elements in the system. We have mainly concentrated on inferring number of genes in ON and OFF states from experimental data.

Keywords: systems biology, probabilistic model, inference, biology, model

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Authors: Hiroshi Nakayama, Yuji Ito

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Synthetic cannabinoids have attracted much public attention recently in Japan. 1-pentyl-3-(1-naphthoyl)-indole (JWH-018), 1-pentyl-2-methyl-3-(1-naphthoyl) indole (JWH-015), 1-(5-fluoropentyl)-3- (1-(2,2,3,3- tetramethylcyclopropyl)) indole (XLR-11) and 1-methyl-3- (1-admantyl) indole (JWH-018 adamantyl analog) are known as synthetic cannabinoids and are also considered dangerous illegal drugs in Japan. It has become necessary to develop sensitive and useful methods for detection of synthetic cannabinoids. We produced two monoclonal antibodies (MAb) against synthetic cannabinoids, named NT1 (IgG1) and NT2 (IgG1), using Hybridoma technology. The cross-reactivity of these produced MAbs was evaluated using a competitive enzyme-linked immunosorbent assay (ELISA). In the results, we found both of these antibodies recognize many kinds of synthetic cannabinoids analog. However, neither of these antibodies recognizes naphtoic acid, 1-methyl-indole and indole known as a raw material of synthetic cannabinoid. Thus, the MAbs produced in this study could be a useful tool for the detection of synthetic cannabinoids.

Keywords: ELISA, monoclonal antibody, sensor, synthetic cannabinoid

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Authors: Jerome G. Chandraseelan, Samuel M. D. Oliveira, Antti Häkkinen, Sofia Startceva, Andre S. Ribeiro

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We used live E. coli containing synthetic genetic oscillators to study how the degree of synchrony between the genetic circuits of sister cells changes with temperature. We found that both the mean and the variability of the degree of synchrony between the fluorescence signals from sister cells are affected by temperature. Also, while most pairs of sister cells were found to be highly synchronous in each condition, the number of asynchronous pairs increased with increasing temperature, which was found to be due to disruptions in the oscillations. Finally we provide evidence that these disruptions tend to affect multiple generations as opposed to individual cells. These findings provide insight in how to design more robust synthetic circuits and in how cell division can affect their dynamics.

Keywords: repressilator, robustness, synchrony, synthetic biology

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Authors: Soner Guler, Demet Yavuz, Fuat Korkut

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Synthetic fibers are commonly used in many civil engineering applications because of its some superior characteristics such as non-corrosive and cheapness. This study presents the results of experimental study on compressive strength of synthetic fiber reinforced concretes. Two types of polyamide (PA) synthetic fiber with the length of 12 and 54 mm are used for this study. The fiber volume ratio is kept as 0.25%, 0.75%, and 0.75% in all mixes. The plain concrete compressive strength is 36.2 MPa. The test results clearly show that the increase in compressive strength for synthetic fiber reinforced concretes is significant. The greatest increase in compressive strength is 23% for PA synthetic fiber reinforced concretes with 0.75% fiber volume.

Keywords: synthetic fibers, polyamide fibers, fiber volume, compressive strength

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Authors: Eric Sanchis

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Although there does not exist a definitive consensus on a precise definition of a complex system, it is generally considered that a system is complex by nature. The presented work illustrates a different point of view: a system becomes complex only with regard to the question posed to it, i.e., with regard to the problem which has to be solved. A complex system is a couple (question, object). Because the number of questions posed to a given object can be potentially substantial, complexity does not present a uniform face. Two types of complex systems are clearly identified: first-order complex systems and second-order complex systems. First-order complex systems physically exist. They are well-known because they have been studied by the scientific community for a long time. In second-order complex systems, complexity results from the system composition and its articulation that are partially unknown. For some of these systems, there is no evidence of their existence. Vagueness is the keyword characterizing this kind of systems. Autonomy and free will, two mental productions of the human cognitive system, can be identified as second-order complex systems. A classification based on the properties structure makes it possible to discriminate complex properties from the others and to model this kind of second order complex systems. The final outcome is an implementable synthetic property that distinguishes the solid aspects of the actual property from those that are uncertain.

Keywords: autonomy, free will, synthetic property, vaporous complex systems

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Authors: Lakshmi Prayaga, Chandra Prayaga. Aaron Wade, Gopi Shankar Mallu, Harsha Satya Pola

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Synthetic data generated by Generative Adversarial Networks and Autoencoders is becoming more common to combat the problem of insufficient data for research purposes. However, generating synthetic data is a tedious task requiring extensive mathematical and programming background. Open-source platforms such as the Synthetic Data Vault (SDV) and Mostly AI have offered a platform that is user-friendly and accessible to non-technical professionals to generate synthetic data to augment existing data for further analysis. The SDV also provides for additions to the generic GAN, such as the Gaussian copula. We present the results from two synthetic data sets (CTGAN data and CTGAN with Gaussian Copula) generated by the SDV and report the findings. The results indicate that the ROC and AUC curves for the data generated by adding the layer of Gaussian copula are much higher than the data generated by the CTGAN.

Keywords: synthetic data generation, generative adversarial networks, conditional tabular GAN, Gaussian copula

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Authors: K. Boualem, T. Yahiaoui, A. Azzi

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Numerical investigations are performed to analyze the flow behavior over NACA0015 and to evaluate the efficiency of synthetic jet as active control device. The second objective of this work is to investigate the influence of momentum coefficient of synthetic jet on the flow behaviour. The unsteady Reynolds-averaged Navier-Stokes equations of the turbulent flow are solved using, k-ω SST provided by ANSYS CFX-CFD code. The model presented in this paper is a comprehensive representation of the information found in the literature. Comparison of obtained numerical flow parameters with the experimental ones shows that the adopted computational procedure reflects nearly the real flow nature. Also, numerical results state that use of synthetic jets devices has positive effects on the flow separation, and thus, aerodynamic performance improvement of NACA0015 airfoil. It can also be observed that the use of synthetic jet increases the lift coefficient about 13.3% and reduces the drag coefficient about 52.7%.

Keywords: active control, synthetic jet, NACA airfoil, CFD

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Authors: Faruque Miah, Hafij Ali, Enaya Jannat, Tanmoy Modok Shuvra, M. Niamul Naser

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In this study, breeding biology and induced breeding of freshwater mud eel, Monopterus cuchia was observed during the experimental period from February to June, 2013. Breeding biology of freshwater mud eel, Monopterus cuchia was considered in terms of gonadosomatic index, length-weight relationship of gonad, ova diameter and fecundity. The ova diameter was recorded from 0.3 mm to 4.30 mm and the individual fecundity was recorded from 155 to 1495 while relative fecundity was found from 2.64 to 12.45. The fecundity related to body weight and length of fish was also discussed. A peak of GSI was observed 2.14±0.2 in male and 5.1 ±1.09 in female. Induced breeding of freshwater mud eel, Monopterus cuchia was also practiced with different doses of different inducing agents like pituitary gland (PG), human chorionic gonadotropin (HCG), Gonadotropin releasing hormone (GnRH) and Ovuline-a synthetic hormone in different environmental conditions. However, it was observed that the artificial breeding of freshwater mud eel, Monopterus cuchia was not yet succeeded through inducing agents in captive conditions, rather the inducing agent showed negative impacts on fecundity and ovarian tissues. It was seen that mature eggs in the oviduct were reduced, absorbed and some eggs were found in spoiled condition.

Keywords: breeding biology, induced breeding, Monopterus cuchia, human chorionic gonadotropin

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Authors: Minjin Kim, Jihwan Kim, Bongsoo Kim, Junho Suh

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We demonstrate nanomechanical resonators constructed with synthetic nanowires (NWs) and study their electro-mechanical properties at millikelvin temperatures. Nanomechanical resonators are fabricated using single-crystalline Au NWs and InAs NWs. The mechanical resonance signals are acquired by either magnetomotive or capacitive detection methods. The Au NWs are synthesized by chemical vapor transport method at 1100 °C, and they exhibit clean surface and single-crystallinity with little defects. Due to pristine surface quality, these Au NW mechanical resonators could provide an ideal model system for studying surface-related effects on the mechanical systems. The InAs NWs are synthesized by molecular beam epitaxy or metal organic chemical vapor deposition method. The InAs NWs show electronic conductance modulation resembling Coulomb blockade, which also manifests in the mechanical resonance signals in the form of damping and resonance frequency shift. Our result provides an evidence of strong electro-mechanical coupling in synthetic NW nanomechanical resonators.

Keywords: Au nanowire, InAs nanowire, nanomechanical resonator, synthetic nanowires

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Authors: Genevieve Pugh, Johnathan Burns, Stefan Howorka

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Single-molecule sensing via protein nanopores has achieved a step-change in portable and label-free DNA sequencing. However, protein pores of both natural or engineered origin are not able to produce the tunable diameters needed for effective protein sensing. Here, we describe a generic strategy to build synthetic DNA nanopores that are wide enough to accommodate folded protein. The pores are composed of interlinked DNA duplexes and carry lipid anchors to achieve the required membrane insertion. Our demonstrator pore has a contiguous cross-sectional channel area of 50 nm2 which is 6-times larger than the largest protein pore. Consequently, transport of folded protein across bilayers is possible. The modular design is amenable for different pore dimensions and can be adapted for protein sensing or to create molecular gates in synthetic biology.

Keywords: biosensing, DNA nanotechnology, DNA origami, nanopore sensing

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Authors: Jayson G. Balansag

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An integrated biology and chemistry (iBC) course for freshmen college students was developed in University of Delaware. This course will prepare students to (1) become interdisciplinary thinkers in the field of biology and (2) collaboratively work with others from multiple disciplines in the future. This paper documents and describes the implementation of the course. The information gathered from reading literature, classroom observations, and interviews were used to carry out the purpose of this paper. The major goal of the iBC course is to align the concepts between Biology and Chemistry, so that students can draw science concepts from both disciplines which they can apply in their interdisciplinary researches. This course is offered every fall and spring semesters of each school year. Students enrolled in Biology are also enrolled in Chemistry during the same semester. The iBC is composed of lectures, laboratories, studio sessions, and workshops and is taught by the faculty from the biology and chemistry departments. In addition, the preceptors, graduate teaching assistants, and studio fellows facilitate the laboratory and studio sessions. These roles are interdependent with each other. The iBC can be used as a model for higher education institutions who wish to implement an integrated biology course.

Keywords: integrated biology and chemistry, integration, interdisciplinary research, new biology, undergraduate science education

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Authors: Ava Dodd, Jonathan Adams

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The purpose of this study is to explore the characteristics of developing a machine learning application using synthetic data. The study is structured to develop the application for the purpose of deploying the computer vision model. The findings discuss the realities of attempting to develop a computer vision model for practical purpose, and detail the processes, tools, and techniques that were used to meet accuracy requirements. The research reveals that synthetic data represents another variable that can be adjusted to improve the performance of a computer vision model. Further, a suite of tools and tuning recommendations are provided.

Keywords: computer vision, machine learning, synthetic data, YOLOv4

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Authors: Silvia Moreno, Banu Iyisan, Hannes Gumz, Brigitte Voit, Dietmar Appelhans

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Polymersomes are materials which are considered as artificial counterparts of natural vesicles. The nanotechnology of such smart nanovesicles is very useful to enhance the efficiency of many therapeutic and diagnostic drugs. Those compounds show a higher stability, flexibility, and mechanical strength to the membrane compared to natural liposomes. In addition, they can be designed in detail, the permeability of the membrane can be controlled by different stimuli, and the surface can be functionalized with different biological molecules to facilitate monitoring and target. For this purpose, this study demonstrates the formation of multifunctional and pH sensitive polymersomes and their functionalization with different reactive groups or biomolecules inside and outside of polymersomes´ membrane providing by crossing the membrane and docking/undocking processes for biomedical applications. Overall, they are highly versatile and thus present new opportunities for the design of targeted and selective recognition systems, for example, in mimicking cell functions and in synthetic biology.

Keywords: multifunctionalized, pH stimulus, controllable release, cellular uptake

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Authors: Ontima Yamchuti, Waruntorn Kanitpanyacharoen, Chakkaphan Sutthirat, Wantana Klysuban, Penphitcha Amonpattarakit

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Natural corundum occurs in various colors due to impurities or trace elements in its structure. Sapphire and ruby are essentially the same mineral, corundum, but valued differently due to their red and blue varieties, respectively. Color is one of the critical factors used to determine the value of natural and synthetic corundum. Despite the abundance of research on impurities in natural corundum, little is known about trace elements in synthetic corundum. This project thus aims to quantify trace elements and identify their oxidation states in synthetic corundum. A total of 15 corundum samples in red, blue, and yellow, synthesized by melt growth process, were first investigated by X-ray diffraction (XRD) analysis to determine the composition. Electron probe micro-analyzer (EPMA) was used to identify the types of trace elements. Results confirm that all synthetic corundums contain crystalline Al₂O₃ and a wide variety type of trace element, particularly Cr, Fe, and Ti. In red, yellow, and blue corundums respectively. To further determine their oxidation states, synchrotron X-ray absorption near edge structure spectrometry (XANES) was used to observe absorbing energy of each element. XANES results show that red synthetic corundum has Cr³⁺ as a major trace element (62%). The pre-edge absorption energy of Cr³⁺ is at 6001 eV. In addition, Fe²⁺ and Fe³⁺ are dominant oxidation states of yellow synthetic corundum while Ti³⁺and Ti⁴⁺ are dominant oxidation states of blue synthetic corundum. the average absorption energy of Fe and Ti is 4980 eV and 7113 eV respectively. The presence of Fe²⁺, Fe³⁺, Cr³⁺, Ti³⁺, and Ti⁴⁺ in synthetic corundums in this study is governed by comparison absorption energy edge with standard transition. The results of oxidation states in this study conform with natural corundum. However yellow synthetic corundums show difference oxidation state of trace element compared with synthetic in electron spin resonance spectrometer method which found that Ni³⁺ is a dominant oxidation state.

Keywords: corundum, trace element, oxidation state, XANES technique

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Authors: Baltazar Ndakidemi

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The resource-constrained farmers, especially those in sub-Saharan Africa, encounter significant challenges related to agriculture, notably diseases and pests. The sustainable means of pest management are not well known to farmers. As a result, some farmers use synthetic pesticides whose environmental impacts, ill health, and other negative impacts of synthetic pesticides on natural enemies have posed a great need for more sustainable means of pest management. Pesticidal plant resources can replace synthetic pesticides because their secondary metabolites can exhibit insecticidal activities such as deterrence, repellence, and pests' mortality. Additionally, the volatiles from these plants can have positive effects of attracting populations of natural enemies. Pesticidal plants can be grown as field margin plants or in strips for supporting natural enemies' populations. However, this is practically undetermined. Hence, there is a need to investigate the roles played by pesticidal plants in supporting natural enemies of pests and their applications in different cropping systems such as legumes. This study investigates different pesticidal plants with a high potential for pest control in agricultural fields. The information sheds light on potential plants that can be used for different crop pests.

Keywords: natural enemies, biological control, synthetic pesticides, pesticidal plants, predators, parasitoids

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Authors: Niki K. Burns, James R. Pearson, Paul G. Stevenson, Xavier A. Conlan

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In Australian state Victoria, synthetic cannabinoids have recently been made illegal under an amendment to the drugs, poisons and controlled substances act 1981. Identification of synthetic cannabinoids in popular brands of ‘incense’ and ‘potpourri’ has been a difficult and challenging task due to the sample complexity and changes observed in the chemical composition of the cannabinoids of interest. This study has developed analytical methodology for the targeted extraction and determination of synthetic cannabinoids available pre-ban. A simple solvent extraction and solid phase extraction methodology was developed that selectively extracted the cannabinoid of interest. High performance liquid chromatography coupled with UV‐visible and chemiluminescence detection (acidic potassium permanganate and tris (2,2‐bipyridine) ruthenium(III)) were used to interrogate the synthetic cannabinoid products. Mass spectrometry and nuclear magnetic resonance spectroscopy were used for structural elucidation of the synthetic cannabinoids. The tris(2,2‐bipyridine)ruthenium(III) detection was found to offer better sensitivity than the permanganate based reagents. In twelve different brands of herbal incense, cannabinoids were extracted and identified including UR‐144, XLR 11, AM2201, 5‐F‐AKB48 and A796‐260.

Keywords: electrospray mass spectrometry, high performance liquid chromatography, solid phase extraction, synthetic cannabinoids

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Authors: J. Mohammadpour, G. E. Lau, S. Cheng, A. Lee

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Numerical study was conducted using two synthetic jet actuators attached underneath a micro-channel. By fixing the oscillating frequency and diaphragm amplitude, the effects on the heat transfer within the micro-channel were investigated with two synthetic jets being in-phase and 180° out-of-phase at different orifice spacing. There was a significant benefit identified with two jets being 180° out-of-phase with each other at the orifice spacing of 2 mm. By having this configuration, there was a distinct pattern of vortex forming which disrupts the main channel flow as well as promoting thermal mixing at high velocity within the channel. Therefore, this configuration achieved higher cooling performance compared to the other cases studied in terms of the reduction in the maximum temperature and cooling uniformity in the silicon wafer.

Keywords: synthetic jets, microchannel, electronic cooling, computational fluid dynamics

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Authors: Ibraheem Alzahrani

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The Saudi Arabia ministry of higher education has established 24 universities across various cities in the kingdom. The universities have the mandate of sustaining technological progress in both teaching and learning. The present study explores the statues of teaching in Saudi universities, focusing on biology, a critical curriculum. The paper explores biology teachers’ points of view is several Saudi higher education institutions through questionnaires disseminated via emails. According to the findings, the current teaching methods are traditional and the teachers believe that it is critical to change it. This study also, reviews how biology has been taught in the kingdom over the past, as well as how it is undertaken presently. In addition, some aspects of biology teaching are considered, including the biology curriculum and learning objectives in higher education biology.

Keywords: higher education, teaching style, traditional learning, electronic learning, web 2.0 applications, blended learning

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Authors: Maik Kschischo, Dominik Kahl, Philipp Wendland, Andreas Weber

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Understanding and modelling of real-world complex dynamic systems in biology, engineering and other fields is often made difficult by incomplete knowledge about the interactions between systems states and by unknown disturbances to the system. In fact, most real-world dynamic networks are open systems receiving unknown inputs from their environment. To understand a system and to estimate the state dynamics, these inputs need to be reconstructed from output measurements. Reconstructing the input of a dynamic system from its measured outputs is an ill-posed problem if only a limited number of states is directly measurable. A first requirement for solving this problem is the invertibility of the input-output map. In our work, we exploit the fact that invertibility of a dynamic system is a structural property, which depends only on the network topology. Therefore, it is possible to check for invertibility using a structural invertibility algorithm which counts the number of node disjoint paths linking inputs and outputs. The algorithm is efficient enough, even for large networks up to a million nodes. To understand structural features influencing the invertibility of a complex dynamic network, we analyze synthetic and real networks using the structural invertibility algorithm. We find that invertibility largely depends on the degree distribution and that dense random networks are easier to invert than sparse inhomogeneous networks. We show that real networks are often very difficult to invert unless the sensor nodes are carefully chosen. To overcome this problem, we present a sensor node placement algorithm to achieve invertibility with a minimum set of measured states. This greedy algorithm is very fast and also guaranteed to find an optimal sensor node-set if it exists. Our results provide a practical approach to experimental design for open, dynamic systems. Since invertibility is a necessary condition for unknown input observers and data assimilation filters to work, it can be used as a preprocessing step to check, whether these input reconstruction algorithms can be successful. If not, we can suggest additional measurements providing sufficient information for input reconstruction. Invertibility is also important for systems design and model building. Dynamic models are always incomplete, and synthetic systems act in an environment, where they receive inputs or even attack signals from their exterior. Being able to monitor these inputs is an important design requirement, which can be achieved by our algorithms for invertibility analysis and sensor node placement.

Keywords: data-driven dynamic systems, inversion of dynamic systems, observability, experimental design, sensor node placement

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Authors: L. K. Davis

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The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time-based DNA codes, writing DNA code from scratch

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Authors: N. Nor Azman, M. F. Kamarudin, S. I. Ong, N. Maaulot

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PERMATApintar^® National Gifted Center is, to the author’s best of knowledge, the first center in Malaysia that provides a platform for Malaysian talented students with high ability in thinking. This center has built a teaching and learning biology curriculum that suits the ability of these gifted students. The level of PERMATApintar^® biology curriculum is basically higher than the national biology curriculum. Here, the foundation students are exposed to the PERMATApintar^® biology curriculum at the age of as early as 11 years old. This center practices a 4-time-a-year examination system to monitor the academic performances of the students. Generally, most of the time, male students show no or low interest towards biology subject compared to female students. This study is to investigate the association of students’ gender and their academic performances in biology examination. A total of 39 students’ scores in twelve sets of biology examinations in 3 years have been collected and analyzed by using the statistical analysis. Based on the analysis, there are no significant differences between male and female students against the biology academic performances with a significant level of p = 0.05. This indicates that gender is not associated with the scores of biology examinations among the students. Another result showed that the average score for male studenta was higher than the female students. Future research can be done by comparing the biology academic achievement in Malaysian National Examination (Sijil Pelajaran Malaysia, SPM) between the Foundation 3 students (Grade 9) and Level 2 students (Grade 11) with similar PERMATApintar^® biology curriculum.

Keywords: academic performances, biology, gender differences, gifted students,

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Authors: R. R. Mankbadi

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There are several technologically-important flow situations in which there is a need to control the outcome of the fluid flow. This could include flow separation, drag, noise, as well as particulate separations, to list only a few. One possible approach is the passive control, in which the design geometry is changed. An alternative approach is the Active Flow Control (AFC) technology in which an actuator is embedded in the flow field to change the outcome. Examples of AFC are pulsed jets, synthetic jets, plasma actuators, heating, and cooling, etc. In this work will present an overview of the development of this field. Some examples will include Airfoil Noise Suppression: Large-Eddy Simulations (LES) is used to simulate the effect of synthetic jet actuator on controlling the far field sound of a transitional airfoil. The results show considerable suppression of the noise if the synthetic jet is operated at frequencies. Mixing Enhancement and suppression: Results will be presented to show that imposing acoustic excitations at the nozzle exit can lead to enhancement or reduction of the jet plume mixing. In vertical takeoff of Aircrafts or in Space Launch, we will present results on the effects of water injection on reducing noise, and on protecting the structure and payload from fatigue damage. Other applications will include airfoil-gust interaction and propulsion systems optimizations.

Keywords: aeroacoustics, flow control, aerodynamics, large eddy simulations

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Authors: Ziyan Zhang

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Although the Synthetic Control Method (SCM) is now widely applied, its most commonly- used inference method, placebo test, is often problematic, especially when the treatment is not uniquely assigned. This paper discusses the problems with the placebo test under the multivariate treatment case. And, to improve the power of inferences, I further propose an Andrews-type procedure as it potentially solves some drawbacks of the placebo test. Simulations are conducted to show the Andrews’ test is often valid and powerful, compared with the placebo test.

Keywords: Synthetic Control Method, Multiple treatments, Andrews' test, placebo test

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Authors: Salman Akrokayan

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Synthetic cDNA (ScDNA) of granulocyte colony-stimulating factor (G-CSF) was constructed using a DNA synthesizer with the aim to increase its expression level. 5' end of the ScDNA of G-CSF coding region was modified by decreasing the GC content without altering the predicted amino acids sequence. The identity of the resulting protein from ScDNA was confirmed by the highly specific enzyme-linked immunosorbent assay. In conclusion, a synthetic G-CSF cDNA in combination with the recombinant DNA protocol offers a rapid and reliable strategy for synthesizing the target protein. However, the commercial utilization of this methodology requires rigorous validation and quality control.

Keywords: synthetic cDNA, recombinant G-CSF, cloning, gene expression

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Authors: Ali Kara, Asim Olgun, Sevgi Sozugecer, Sahin Ozel, Kubra Nur Yildiz, P. Sevinç, Abdurrahman Kuresh, Guliz Turhan, Duygu Gulgun

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The synthetic dyes, one of the most hazardous chemical compound classes, are important potential water pollutions since their presence in water bodies reduces light penetration, precluding the photosynthesis of aqueous flora and causing various diseases. Some the synthetic dyes are highly toxic and/or carcinogenic, and their biodegradation can produce even more toxic aromatic amines. The adsorption procedure is one of the most effective means of removing synthetic dye pollutants, and has been described in a number of previous studies by using the functional polymers. In this study, we investigated the removal of synthetic dyes from aqueous solution by using a functional polymer as an adsorbent material. The effect of initial solution concentration, pH, and contact time on the adsorption capacity of the adsorbent were studied in details. The results showed that functional polymer has a potential to be used as cost-effective and efficient adsorbent for the treatment of aqueous solutions from textile industries.

Keywords: functional polymers, synhetic dyes, adsorption, physicochemical parameters

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Authors: Moreblessings Shoko

Abstract:

Polymersomes are materials which are considered as artificial counterparts of natural vesicles. The nanotechnology of such smart nanovesicles is very useful to enhance the efficiency of many therapeutic and diagnostic drugs. Those compounds show a higher stability, flexibility, and mechanical strength to the membrane compared to natural liposomes. Also, they can be designed in detail, the permeability of the membrane can be controlled by different stimuli, and the surface can be functionalized with different biological molecules to facilitate monitoring and target. For this purpose, this study demonstrates the formation of multifunctional and pH sensitive polymersomes and their functionalization with different reactive groups or biomolecules inside and outside of polymersomes´ membrane providing by crossing the membrane and docking/undocking processes for biomedical applications. Overall, they are highly versatile and thus present new opportunities for the design of targeted and selective recognition systems, for example, in mimicking cell functions and in synthetic biology.

Keywords: women, geomatics, challenges, capacity building

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