| 1. |
- Damiati, Laila A., et al.
(author)
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Developments in the use of microfluidics in synthetic biology
- 2022
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In: New Frontiers and Applications of Synthetic Biology. - : Elsevier BV. ; , s. 423-435
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Book chapter (other academic/artistic)abstract
- Biomimetics aims to copy and imitate natural elements and systems in a simpler form to overcome the limitations of complex biological elements and systems. The construction of biomimetic platforms to investigate physiological conditions requires an understanding of the native structure of cells and tissues and their interactions. Thus synthetic biology effectively connects biology and engineering. The engineering of custom cells/organs involves the construction of seminatural models that either perform existing functions in a modified manner or perform functions that do not exist naturally. In addition to providing an understanding of biological approaches, artificial models allow the mimicking of human physiology and diseases, facilitating the discovery of new drugs. Microfluidics is one of the most advanced technologies that allow the studying, mimicking, and manipulation of biological behaviors. Microfluidic devices are miniaturized devices that are functionally integrated on a single platform. The continuous development of microfluidic technology has led to the generation of artificial cells/organs that are based on in vivo mimetic models. Hence, it offers promising approaches for drug analysis, investigation of diseases and toxicity pathways, and construction of artificial models and even synthetic cell/organ chassis. This chapter presents microfluidic innovations for cell-like and organ-like architectures that were developed to simplify the complex networks of cells and organs. The merging of synthetic biology and microfluidics has led to the successful generation of artificial cells and organ-on-a-chip models. These biomimetic microfluidic environments have reduced the technical difficulties that acted as obstacles to studying cellular biology, have allowed the investigation of cell-cell, cell-tissue, and organ-like interfaces, and have aided the discovery of new therapeutic agents.
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| 2. |
- Damiati, Safa A., et al.
(author)
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Artificial intelligence application for rapid fabrication of size-tunable PLGA microparticles in microfluidics
- 2020
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 10:1
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Journal article (peer-reviewed)abstract
- In this study, synthetic polymeric particles were effectively fabricated by combining modern technologies of artificial intelligence (AI) and microfluidics. Because size uniformity is a key factor that significantly influences the stability of polymeric particles, therefore, this work aimed to establish a new AI application using machine learning technology for prediction of the size of poly(d,l-lactide-co-glycolide) (PLGA) microparticles produced by diverse microfluidic systems either in the form of single or multiple particles. Experimentally, the most effective factors for tuning droplet/particle sizes are PLGA concentrations and the flow rates of dispersed and aqueous phases in microfluidics. These factors were utilized to develop five different and simple in structure artificial neural network (ANN) models that are capable of predicting PLGA particle sizes produced by different microfluidic systems either individually or jointly merged. The systematic development of ANN models allowed ultimate construction of a single in silico model which consists of data for three different microfluidic systems. This ANN model eventually allowed rapid prediction of particle sizes produced using various microfluidic systems. This AI application offers a new platform for further rapid and economical exploration of polymer particles production in defined sizes for various applications including biomimetic studies, biomedicine, and pharmaceutics.
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| 3. |
- Damiati, Safa A., et al.
(author)
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Microfluidic Synthesis of Indomethacin-Loaded PLGA Microparticles Optimized by Machine Learning
- 2021
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In: Frontiers in Molecular Biosciences. - : Frontiers Media SA. - 2296-889X. ; 8
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Journal article (peer-reviewed)abstract
- Several attempts have been made to encapsulate indomethacin (IND), to control its sustained release and reduce its side effects. To develop a successful formulation, drug release from a polymeric matrix and subsequent biodegradation need to be achieved. In this study, we focus on combining microfluidic and artificial intelligence (AI) technologies, alongside using biomaterials, to generate drug-loaded polymeric microparticles (MPs). Our strategy is based on using Poly (D,L-lactide-co-glycolide) (PLGA) as a biodegradable polymer for the generation of a controlled drug delivery vehicle, with IND as an example of a poorly soluble drug, a 3D flow focusing microfluidic chip as a simple device synthesis particle, and machine learning using artificial neural networks (ANNs) as an in silico tool to generate and predict size-tunable PLGA MPs. The influence of different polymer concentrations and the flow rates of dispersed and continuous phases on PLGA droplet size prediction in a microfluidic platform were assessed. Subsequently, the developed ANN model was utilized as a quick guide to generate PLGA MPs at a desired size. After conditions optimization, IND-loaded PLGA MPs were produced, and showed larger droplet sizes than blank MPs. Further, the proposed microfluidic system is capable of producing monodisperse particles with a well-controllable shape and size. IND-loaded-PLGA MPs exhibited acceptable drug loading and encapsulation efficiency (7.79 and 62.35%, respectively) and showed sustained release, reaching approximately 80% within 9 days. Hence, combining modern technologies of machine learning and microfluidics with biomaterials can be applied to many pharmaceutical applications, as a quick, low cost, and reproducible strategy.
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| 4. |
- Budreviciute, Aida, et al.
(author)
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Management and Prevention Strategies for Non-communicable Diseases (NCDs) and Their Risk Factors
- 2020
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In: Frontiers In Public Health. - : Frontiers Media SA. - 2296-2565. ; 8
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Research review (peer-reviewed)abstract
- Non-communicable diseases (NCDs) are of increasing concern for society and national governments, as well as globally due to their high mortality rate. The main risk factors of NCDs can be classified into the categories of self-management, genetic factors, environmental factors, factors of medical conditions, and socio-demographic factors. The main focus is on the elements of self-management and to reach a consensus about the influence of food on risk management and actions toward the prevention of NCDs at all stages of life. Nutrition interventions are essential in managing the risk of NCDs. As they are of the utmost importance, this review highlights NCDs and their risk factors and outlines several common prevention strategies. We foresee that the best prevention management strategy will include individual (lifestyle management), societal (awareness management), national (health policy decisions), and global (health strategy) elements, with target actions, such as multi-sectoral partnership, knowledge and information management, and innovations. The most effective preventative strategy is the one that leads to changes in lifestyle with respect to diet, physical activities, cessation of smoking, and the control of metabolic disorders.
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| 5. |
- Bungon, Theodore, et al.
(author)
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Graphene FET Sensors for Alzheimer's Disease Protein Biomarker Clusterin Detection
- 2021
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In: Frontiers in Molecular Biosciences. - : Frontiers Media SA. - 2296-889X. ; 8
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Journal article (peer-reviewed)abstract
- We report on the fabrication and characterisation of graphene field-effect transistor (GFET) biosensors for the detection of Clusterin, a prominent protein biomarker of Alzheimer's disease (AD). The GFET sensors were fabricated on Si/SiO2 substrate using photolithographic patterning and metal lift-off techniques with evaporated chromium and sputtered gold contacts. Raman Spectroscopy was performed on the devices to determine the quality of the graphene. The GFETs were annealed to improve their performance before the channels were functionalized by immobilising the graphene surface with linker molecules and anti-Clusterin antibodies. Concentration of linker molecules was also independently verified by absorption spectroscopy using the highly collimated micro-beam light of Diamond B23 beamline. The detection was achieved through the binding reaction between the antibody and varying concentrations of Clusterin antigen from 1 to 100 pg/mL, as well as specificity tests using human chorionic gonadotropin (hCG), a glycoprotein risk biomarker of certain cancers. The GFETs were characterized using direct current (DC) 4-probe electrical resistance (4-PER) measurements, which demonstrated a limit of detection of the biosensors to be similar to 300 fg/mL (4 fM). Comparison with back-gated Dirac voltage shifts with varying concentration of Clusterin show 4-PER measurements to be more accurate, at present, and point to a requirement for further optimisation of the fabrication processes for our next generation of GFET sensors. Thus, we have successfully fabricated a promising set of GFET biosensors for the detection of Clusterin protein biomarker. The developed GFET biosensors are entirely generic and also have the potential to be applied to a variety of other disease detection applications such as Parkinson's, cancer, and cardiovascular.
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| 6. |
- Damiati, Samar
(author)
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Acoustic Biosensors for Cell Research
- 2021
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In: Handbook of Cell Biosensors. - Cham : Springer Nature. ; , s. 537-568
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Book chapter (other academic/artistic)abstract
- Drawing inspiration from nature and applying natural principles can support the continuous improvement of sensing technologies in various fields, such as medicine, pharmacy, and environmental applications. It is difficult to directly connect a sensing system to a complex biological system. Thus, finding a suitable technique that simplifies and interprets complicated biological information to generate readable signals is in high demand. Acoustic technology appears to be a promising sensing model. The monitoring of the biochemical processes or the quantification of a captured analyte can be performed utilizing acoustic wave devices that rely on gravimetric sensing of materials adsorbed onto the sensor surface. Considering nature as a toolkit that provides individual puzzle pieces that can be assembled carefully into a sensory system offers a rich source to build selective and sensitive biosensors. The natural toolbox includes biological components such as DNA, RNA, sugar, amino acids, proteins, and lipids, in addition to nonbiological components such as graphene, carbon nanotubes, and metals. These molecules can be assembled together onto piezoelectric substrates to enhance the functionality of fabricated acoustic devices. This chapter has classified acoustic biosensors into four classes for various cell applications. First, lipid membrane-based biosensors are biomimetic models constructed by natural biological materials to simplify the complexity of biological cell membranes and enable investigations of membrane proteins in a native-like environment. These bioarchitectures also offer a good opportunity to investigate the interactions of lipids and proteins under controlled conditions. Second, whole cell-based biosensors are fabricated to enable investigations of cellular behaviors such as cell adhesion and cell-substrate interactions. Third, detection biosensors are also attracting attention due to their high sensitivity, ability to track cells in real time without labeling, and ability to differentiate between viable and nonviable cells. Finally, recent advancements in the fabrication of acoustic biosensors have enabled cells themselves to act as biosensors to detect analytes. All designed acoustic platforms are aimed at studying the cell, the basic unit of life, from different perspectives. The facts discussed in this chapter are based on phenomena that cannot be visualized by the eye, such as cellular interactions, or factors present in such small quantities, but they can be heard by tracking their acoustic sounds.
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| 7. |
- Damiati, Samar, et al.
(author)
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Electrochemical Biosensors Based on S-Layer Proteins
- 2020
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In: Sensors. - : MDPI AG. - 1424-8220. ; 20:6
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Research review (peer-reviewed)abstract
- Designing and development of electrochemical biosensors enable molecule sensing and quantification of biochemical compositions with multitudinous benefits such as monitoring, detection, and feedback for medical and biotechnological applications. Integrating bioinspired materials and electrochemical techniques promote specific, rapid, sensitive, and inexpensive biosensing platforms for (e.g., point-of-care testing). The selection of biomaterials to decorate a biosensor surface is a critical issue as it strongly affects selectivity and sensitivity. In this context, smart biomaterials with the intrinsic self-assemble capability like bacterial surface (S-) layer proteins are of paramount importance. Indeed, by forming a crystalline two-dimensional protein lattice on many sensors surfaces and interfaces, the S-layer lattice constitutes an immobilization matrix for small biomolecules and lipid membranes and a patterning structure with unsurpassed spatial distribution for sensing elements and bioreceptors. This review aims to highlight on exploiting S-layer proteins in biosensor technology for various applications ranging from detection of metal ions over small organic compounds to cells. Furthermore, enzymes immobilized on the S-layer proteins allow specific detection of several vital biomolecules. The special features of the S-layer protein lattice as part of the sensor architecture enhances surface functionalization and thus may feature an innovative class of electrochemical biosensors.
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| 8. |
- Damiati, Samar, et al.
(author)
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Flex Printed Circuit Board Implemented Grapene-Based DNA Sensor for Detection of SARS-CoV-2
- 2021
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In: IEEE Sensors Journal. - : Institute of Electrical and Electronics Engineers (IEEE). - 1530-437X .- 1558-1748. ; 21:12, s. 13060-13067
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Journal article (peer-reviewed)abstract
- Since the COVID-19 outbreak was declared a pandemic by the World Health Organization (WHO) in March 2020, ongoing efforts have been made to develop sensitive diagnostic platforms. Detection of viral RNA provides the highest sensitivity and specificity for detection of early and asymptomatic infections. Thus, this work aimed at developing a label-free genosensor composed of graphene as a working electrode that could be embedded into a flex printed circuit board (FPCB) for the rapid, sensitive, amplification-free and label-free detection of SARS-CoV-2. To facilitate liquid handling and ease of use, the developed biosensor was embedded with a user-friendly reservoir chamber. As a proof-of-concept, detection of a synthetic DNA strand matching the sequence of ORF1ab was performed as a two-step strategy involving the immobilization of a biotinylated complementary sequence on a streptavidin-modified surface, followed by hybridization with the target sequence recorded by the differential pulse voltammetric (DPV) technique in the presence of a ferro/ferricyanide redox couple. The effective design of the sensing platform improved its selectivity and sensitivity and allowed DNA quantification ranging from 100 fg/mL to 1 mu g/mL. Combining the electrochemical technique with FPCB enabled rapid detection of the target sequence using a small volume of the sample (5-20 mu L). We achieved a limit-of-detection of 100 fg/mL, whereas the predicted value was similar to 33 fg/mL, equivalent to approximately 5 x 10(5) copies/mL and comparable to sensitivities provided by isothermal nucleic acid amplification tests. We believe that the developed approach proves the ability of an FPCB-implemented DNA sensor to act as a potentially simpler and more affordable diagnostic assay for viral infections in Point-Of-Care (POC) applications.
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| 9. |
- Damiati, Samar
(author)
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In Situ Microfluidic Preparation and Solidification of Alginate Microgels
- 2020
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In: Macromolecular Research. - : Polymer Society of Korea. - 1598-5032 .- 2092-7673.
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Journal article (peer-reviewed)abstract
- Biomimetic fabrication of alginate beads has promising applications in the field of synthetic bioarchitecture. Combining microfluidic technology with in situ gelation enables the creation of alginate microgels with precisely tunable size, as well as allowing control of the crosslinking process. Owing to the wide range of applications of alginate microgel beads, this study aimed to develop various microfluidic models for the generation of such beads by investigating the influence of several parameters on their morphologies and dispersity. Four types of glass microfluidic chips with flow focusing or co-flowing droplet generators were used to continuously form alginate droplets, with the possibility of either internal or external alginate gelation by a cross-linking agent supplied by a microfluidic channel. In all four models, alginate was used at a fixed concentration, Span 80 was used as a surfactant to improve the long-term stability of the beads, either mineral oil or oleic acid was used as a continuous phase, and either calcium carbonate (CaCO3) or calcium chloride (CaCl2) was used as a crosslinking agent. The generated beads exhibited various architectures, including individual monodisperse or polydisperse beads, small clusters, and multicompartment systems. The results of the study revealed the importance of microfluidic design and gelation strategy for the generation of stable polymeric architectures. The current study proposes a simple user’s guide to create alginate microgels in various architectures. The fabricated biomimetic models in the form of polymeric-based vesicles can be further exploited in several applications, including cell-like structures, tissue engineering, and cell and drug encapsulation. Additional investigations will be needed, however, to improve these models so that they more closely resemble the natural structures of cells and tissues. [Figure not available: see fulltext.].
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| 10. |
- Schweiker, Marcel, et al.
(author)
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Evaluating assumptions of scales for subjective assessment of thermal environments – Do laypersons perceive them the way, we researchers believe?
- 2020
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In: Energy and Buildings. - : Elsevier BV. - 0378-7788. ; 211
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Journal article (peer-reviewed)abstract
- People's subjective response to any thermal environment is commonly investigated by using rating scales describing the degree of thermal sensation, comfort, and acceptability. Subsequent analyses of results collected in this way rely on the assumption that specific distances between verbal anchors placed on the scale exist and that relationships between verbal anchors from different dimensions that are assessed (e.g. thermal sensation and comfort) do not change. Another inherent assumption is that such scales are independent of the context in which they are used (climate zone, season, etc.). Despite their use worldwide, there is indication that contextual differences influence the way the scales are perceived and therefore question the reliability of the scales’ interpretation. To address this issue, a large international collaborative questionnaire study was conducted in 26 countries, using 21 different languages, which led to a dataset of 8225 questionnaires. Results, analysed by means of robust statistical techniques, revealed that only a subset of the responses are in accordance with the mentioned assumptions. Significant differences appeared between groups of participants in their perception of the scales, both in relation to distances of the anchors and relationships between scales. It was also found that respondents’ interpretations of scales changed with contextual factors, such as climate, season, and language. These findings highlight the need to carefully consider context-dependent factors in interpreting and reporting results from thermal comfort studies or post-occupancy evaluations, as well as to revisit the use of rating scales and the analysis methods used in thermal comfort studies to improve their reliability.
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| 11. |
- Schweiker, Marcel, et al.
(author)
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The Scales Project, a cross-national dataset on the interpretation of thermal perception scales
- 2019
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In: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 6:1
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Journal article (peer-reviewed)abstract
- Thermal discomfort is one of the main triggers for occupants' interactions with components of the built environment such as adjustments of thermostats and/or opening windows and strongly related to the energy use in buildings. Understanding causes for thermal (dis-)comfort is crucial for design and operation of any type of building. The assessment of human thermal perception through rating scales, for example in post-occupancy studies, has been applied for several decades; however, long-existing assumptions related to these rating scales had been questioned by several researchers. The aim of this study was to gain deeper knowledge on contextual influences on the interpretation of thermal perception scales and their verbal anchors by survey participants. A questionnaire was designed and consequently applied in 21 language versions. These surveys were conducted in 57 cities in 30 countries resulting in a dataset containing responses from 8225 participants. The database offers potential for further analysis in the areas of building design and operation, psycho-physical relationships between human perception and the built environment, and linguistic analyses.
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| 12. |
- Zayni, Sonja, et al.
(author)
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Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence-An Experimental Study of the Human Voltage-Dependent Anion Channel
- 2021
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In: Membranes. - : MDPI AG. - 2077-0375. ; 11:10
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Journal article (peer-reviewed)abstract
- Membrane proteins are involved in many aspects of cellular biology; for example, they regulate how cells interact with their environment, so such proteins are important drug targets. The rapid advancement in the field of immune effector cell therapy has been expanding the horizons of synthetic membrane receptors in the areas of cell-based immunotherapy and cellular medicine. However, the investigation of membrane proteins, which are key constituents of cells, is hampered by the difficulty and complexity of their in vitro synthesis, which is of unpredictable yield. Cell-free synthesis is herein employed to unravel the impact of the expression construct on gene transcription and translation, without the complex regulatory mechanisms of cellular systems. Through the systematic design of plasmids in the immediacy of the start of the target gene, it was possible to identify translation initiation and the conformation of mRNA as the main factors governing the cell-free expression efficiency of the human voltage-dependent anion channel (VDAC), which is a relevant membrane protein in drug-based therapy. A simple translation initiation model was developed to quantitatively assess the expression potential for the designed constructs. A scoring function that quantifies the feasibility of the formation of the translation initiation complex through the ribosome-mRNA hybridization energy and the accessibility of the mRNA segment binding to the ribosome is proposed. The scoring function enables one to optimize plasmid sequences and semi-quantitatively predict protein expression efficiencies. This scoring function is publicly available as webservice XenoExpressO at University of Vienna, Austria.
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