Academic literature on the topic 'Two-layered and three-layered tissue models'
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Journal articles on the topic "Two-layered and three-layered tissue models"
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Pei, Na, Zhiyan Hao, Sen Wang, et al. "3D Printing of Layered Gradient Pore Structure of Brain-like Tissue." International Journal of Bioprinting 7, no. 3 (2021): 359. http://dx.doi.org/10.18063/ijb.v7i3.359.
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The pathological research and drug development of brain diseases require appropriate brain models. Given the complex, layered structure of the cerebral cortex, as well as the constraints on the medical ethics and the inaccuracy of animal models, it is necessary to construct a brain-like model in vitro. In this study, we designed and built integrated three-dimensional (3D) printing equipment for cell printing/culture, which can guarantee cell viability in the printing process and provide the equipment foundation for manufacturing the layered structures with gradient distribution of pore size. Based on this printing equipment, to achieve the purpose of printing the layered structures with multiple materials, we conducted research on the performance of bio-inks with different compositions and optimized the printing process. By extruding and stacking materials, we can print the layered structure with the uniform distribution of cells and the gradient distribution of pore sizes. Finally, we can accurately print a structure with 30 layers. The line width (resolution) of the printed monolayer structure was about 478 μm, the forming accuracy can reach 97.24%, and the viability of cells in the printed structure is as high as 94.5%.
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Deaconescu, Delia, and Simona Miclăuş. "A Computational Study of 2.4 and 3.7 GHz Radiations Deposition Inside Models Made of Human Tissues Placed Nearby a Microstrip Antenna." International conference KNOWLEDGE-BASED ORGANIZATION 26, no. 3 (2020): 97–102. http://dx.doi.org/10.2478/kbo-2020-0121.
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AbstractThe interest for GHz frequency range in present wireless communication devices is high. Therefore, a continuous need to observe peculiarities of electromagnetic power deposition in human tissues, when they are exposed to signals in this range, is obvious. In this paper, by using an electromagnetic field simulation software, we aimed to highlight the differences between specific absorption rates (SAR) of energy absorption and their geometric distribution in four cases: at two different frequencies and in two tissue models (plane and anthropomorphic). First step was to design and analyse the electromagnetic field provided by a microstrip antenna, and second step was to compute SAR averaged over 10 g of tissue in two models: a three-layered planar model of human tissues and a homogeneous human head. Similarities and differences are discussed, together with observations regarding temperature increase due to exposures and its trend in different layers of tissues.
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Sekine, Waki, Yuji Haraguchi, Tatsuya Shimizu, Masayuki Yamato, Akihiro Umezawa, and Teruo Okano. "Chondrocyte Differentiation of Human Endometrial Gland-Derived MSCs in Layered Cell Sheets." Scientific World Journal 2013 (2013): 1–7. http://dx.doi.org/10.1155/2013/359109.
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Recently, regenerative medicine using engineered three-dimensional (3D) tissues has been focused. In the fields of cell therapy and regenerative medicine, mesenchymal stem cells (MSCs) are attractive autologous cell sources. While, in bioengineered tissues, a 3D environment may affect the differentiation of the stem cells, little is known regarding the effect of 3D environment on cellular differentiation. In this study, MSC differentiation inin vitro3D tissue models was assessed by human endometrial gland-derived MSCs (hEMSCs) and cell sheet technology. hEMSC sheets were layered into cell-dense 3D tissues and were cultured on porous membranes. The tissue sections revealed that chondrocyte-like cells were found within the multilayered cell sheets even at 24 h after layering. Immunostainings of chondrospecific markers were positive within those cell sheet constructs. In addition, sulfated glycosaminoglycan accumulation within the tissues increased in proportion to the numbers of layered cell sheets. The findings suggested that a high cell density and hypoxic environment in 3D tissues by layering cell sheets might accelerate a rapid differentiation of hEMSCs into chondrocytes without the help of chondro-differentiation reagents. These tissue models using cell sheets would give new insights to stem cell differentiation in 3D environment and contribute to the future application of stem cells to cartilage regenerative therapy.
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Nowakowski, Sophia, Freia F. Schmidt, and Petra J. Kluger. "Development of an in vitro three-layered skin wound healing model for pre-clinical testing." Current Directions in Biomedical Engineering 10, no. 4 (2024): 461–64. https://doi.org/10.1515/cdbme-2024-2113.
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Abstract Skin wound healing involves many cell types in a stepwise process of tissue regeneration. Reepithelialization is an essential characteristic of successful healing. In tissue engineering, mimicking the complex process of injury repair in vitro is challenging and requires the development of advanced skin models. In this study, a simple and reproducible method for wounding three-layered skin models on membranes with different pore sizes (0.4, 1, 3 μm) was established. The model allows the investigation of reepithelialization processes in a more complex environment. Hemalaun-eosin (HE) and 3-[4,5-dimethylthiazole-2-yl]-2,5- diphenyltetrazolium bromide (MTT) staining proved sufficient removal of the epidermis directly after wounding. An increasing pore size of the culture membrane delayed the reepithelialization time. Transepithelial electrical resistance (TEER) measurements provided non-invasive monitoring of reepithelialization, showing increasing values 4 days after wounding for the skin models on 0.4 and 1 μm membranes but not for those on 3 μm membranes. Cytokine quantification of interleukin (IL)-6 and IL-8 complemented the TEER results with increasing levels directly after wounding for all skin models. This skin wounding model could be used to simulate different wounding scenarios and test wound matrix materials. Furthermore, it could be adapted by adding immune cells to resemble the in vivo setup more closely.
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Früh, Anton, Bernd Rolauffs, and Michael Seidenstuecker. "Parametric Numerical Modeling and Fabrication of PCL Scaffolds for Bone Tissue Engineering Applications." Applied Sciences 12, no. 23 (2022): 12280. http://dx.doi.org/10.3390/app122312280.
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Bone tissue engineering (BTE) is an interdisciplinary discipline that focuses on bone structure–function relationships for improving the replacement and/or regeneration of bone tissues. Thereby, the architecture and load-bearing capacity of embedded scaffolds play an important role in the generation of artificial tissues. The aim of this study was to develop a parametric numerical model and the accompanying fabrication of polycaprolactone (PCL) scaffolds for BTE applications. Therefore, we manufactured layered PCL-based constructs using three-dimensional (3D) printing. The material properties of PCL and constructs were determined by mechanical testing, and numerical models based on Beam188 Timoshenko elements were developed in the software environment ANSYS. PCL constructs were coated with collagen and seeded with osteoblasts, mesenchymal stem cells (MSCs), MLO-Y4 and MG63 cell types. We demonstrated the successful production of PCL constructs with 3D interconnected pores suitable for BTE applications. Furthermore, we provided for the first time geometrical parametric numerical models that determined the mechanical behavior of layered PCL scaffolds consisting of interconnected compartments for strains up to 3%. The parametric structures of the model allowed us to flexibly study new geometries in silico, which demonstrated its role as an important tool for supporting the fabrication of customized PCL constructs in planning and performing suitable mechanical characterizations for BTE applications.
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Dieterich, C., M. Schandar, M. Noll, et al. "In vitro reconstructed human epithelia reveal contributions of Candida albicans EFG1 and CPH1 to adhesion and invasion." Microbiology 148, no. 2 (2002): 497–506. http://dx.doi.org/10.1099/00221287-148-2-497.
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The individual and synergistic contributions of two transcription factors, EFG1 and CPH1, have been characterized with regard to adhesion to, and invasion of, human epithelia by Candida albicans. For this purpose two in vitro reconstructed tissue models were developed. A multi-layered model of human epidermis was used to simulate superficial infections of the skin, whereas a reconstructed human intestinal model was used to mimic the first steps of systemic infections. It was shown that C. albicans deleted for both transcription factors CPH1 and EFG1, in contrast to the congenic clinical isolate Sc5314, was neither able to adhere to, nor to penetrate, either of the model systems. A strain deleted for EFG1 alone showed significant reduction in adhesion and was not able to penetrate through the stratum corneum. However, strains deleted for CPH1 showed phenotypes paralleling the phenotypes of the clinical isolate Sc5314. Using different types of multi-layered human tissues reconstructed in vitro the individual contributions of Efg1p and Cph1p to two important virulence factors of C. albicans, namely adhesion and invasion, could be defined.
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Nowicki, Andrzej. "Safety of ultrasonic examinations; thermal and mechanical indices." Medical Ultrasonography 22, no. 2 (2020): 203. http://dx.doi.org/10.11152/mu-2372.
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This review article combines the reports on the biophysical effects in ultrasonography and provides the rationale behind the mechanical index (MI) and thermal index (TI) complying with the Output Display Standard (ODS). Safe ultrasonic doses are determined according to specific rules, and the screen displays the associated quantities MI and TI. The introduced indices MI and TI take into account the physical mechanism of interaction between ultrasounds and biological tissue, which depends on the temporal and spatial parameters of the acoustic field generated by ultrasound transducers. The predicted temperature increase is determined using three different tissue models: homogeneous, layered and bone/tissue interface.
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Paolillo, Colombo, Serra, et al. "Stem-like Cancer Cells in a Dynamic 3D Culture System: A Model to Study Metastatic Cell Adhesion and Anti-cancer Drugs." Cells 8, no. 11 (2019): 1434. http://dx.doi.org/10.3390/cells8111434.
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Metastatic spread is mainly sustained by cancer stem cells (CSC), a subpopulation of cancer cells that displays stemness features. CSC are thought to be derived from cancer cells that undergo epithelial to mesenchymal transition (EMT), thus acquiring resistance to anoikis and anti-cancer drugs. After detachment from the primary tumor mass, CSC reach the blood and lymphatic flow, and disseminate to the target tissue. This process is by nature dynamic and in vitro models are quite far from the in vivo situation. In this study, we have tried to reproduce the adhesion process of CSC to a target tissue by using a 3D dynamic cell culture system. We isolated two populations of 3D tumor spheroids displaying CSC-like features from breast carcinoma (MCF-7) and lung carcinoma (A549) cell lines. Human fibroblasts were layered on a polystyrene scaffold placed in a dynamically perfused millifluidic system and then the adhesion of tumor cell derived from spheroids to fibroblasts was investigated under continuous perfusion. After 24 h of perfusion, we found that spheroid cells tightly adhered to fibroblasts layered on the scaffold, as assessed by a scanning electron microscope (SEM). To further investigate mechanisms involved in spheroid cell adhesion to fibroblasts, we tested the effect of three RGD integrin antagonists with different molecular structures on cell adhesion; when injected into the circuit, only cilengitide was able to inhibit cell adhesion to fibroblasts. Although our model needs further refinements and improvements, we do believe this study could represent a promising approach in improving current models to study metastatic infiltration in vitro and a new tool to screen new potential anti-metastatic molecules.
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Ahmad, Ashfaq, Farooq Faisal, Sadiq Ullah, and Dong-You Choi. "Design and SAR Analysis of a Dual Band Wearable Antenna for WLAN Applications." Applied Sciences 12, no. 18 (2022): 9218. http://dx.doi.org/10.3390/app12189218.
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This paper presents the design of three types of dual band (2.5 & 5.2 GHz) wearable microstrip patch antennas. The first one is based on a conventional ground plane, whereas the other two antennas are based on two different types of two-dimensional electromagnetic band gap (EBG) structures. The design of these two different dual-band EBG structures using wearable substrates incorporates several factors in order to improve the performance of the proposed conventional ground plane (dual band) wearable antenna. The second EBG with plus-shaped slots is about 22.7% more compact in size relative to the designed mushroom-like EBG. Subsequently, we have demonstrated that the mushroom-like EBG and the EBG with plus-shaped slots improve the bandwidth by 5.2 MHz and 7.9 MHz at lower resonance frequencies and by 33.6 MHz and 16.7 MHz at higher resonance frequencies, respectively. Furthermore, improvements in gain of 4.33% and 16.5% at a frequency of 2.5 GHz and improvements in gain of 30.43% and 4.57% at 5.2 GHz have been achieved by using the mushroom-like EBG and EBG with plus-shaped slots, respectively. The operation of the conventional ground plane antenna is investigated under different bending conditions, such as wrapped around different rounded body parts. The proposed conventional ground plane antenna is placed over a three-layered (flat body phantom (chest)) and four-layered (rounded body parts) tissue models, and a thorough SAR analysis has been performed. It is concluded that the proposed antenna reduces SAR effects (<2 W/kg) on the human body, thereby making it useful for numerous critical wearable applications.
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Wu, Kevin Y., Rahma Osman, Natalie Kearn, and Ananda Kalevar. "Three-Dimensional Bioprinting for Retinal Tissue Engineering." Biomimetics 9, no. 12 (2024): 733. https://doi.org/10.3390/biomimetics9120733.
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Three-dimensional bioprinting (3DP) is transforming the field of regenerative medicine by enabling the precise fabrication of complex tissues, including the retina, a highly specialized and anatomically complex tissue. This review provides an overview of 3DP’s principles, its multi-step process, and various bioprinting techniques, such as extrusion-, droplet-, and laser-based methods. Within the scope of biomimicry and biomimetics, emphasis is placed on how 3DP potentially enables the recreation of the retina’s natural cellular environment, structural complexity, and biomechanical properties. Focusing on retinal tissue engineering, we discuss the unique challenges posed by the retina’s layered structure, vascularization needs, and the complex interplay between its numerous cell types. Emphasis is placed on recent advancements in bioink formulations, designed to emulate retinal characteristics and improve cell viability, printability, and mechanical stability. In-depth analyses of bioinks, scaffold materials, and emerging technologies, such as microfluidics and organ-on-a-chip, highlight the potential of bioprinted models to replicate retinal disease states, facilitating drug development and testing. While challenges remain in achieving clinical translation—particularly in immune compatibility and long-term integration—continued innovations in bioinks and scaffolding are paving the way toward functional retinal constructs. We conclude with insights into future research directions, aiming to refine 3DP for personalized therapies and transformative applications in vision restoration.
Dissertations / Theses on the topic "Two-layered and three-layered tissue models"
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Sabbir, Md Mainul Hasan. "Accuracy of semi-infinite diffusion theory to estimate tissue hemodynamics in layered slab models." Miami University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=miami1627383040154061.
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Viljoen, Suretha. "Analysis of crosstalk signals in a cylindrical layered volume conductor influence of the anatomy, detection system and physical properties of the tissues /." Diss., Pretoria : [s.n.], 2005. http://upetd.up.ac.za/thesis/available/etd-08082005-113739.
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Tien, Gen-Hao, and 田耕豪. "Quantifying the fluorescence optical properties of two-layered tissue from spectroscopic data using fluorescence information table constructed by fluorescence Monte Carlo model." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/15772491248029081461.
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碩士<br>國立臺灣大學<br>生醫電子與資訊學研究所<br>104<br>This research is to develop an inverse fluorescence spectra fitting tool, using the Monte Carlo model, to quantify the fluorescence optical parameters of tissue, hoping that we can acquire the tissue fluorescence information for analyzing and distinguishing the cancer tissues form normal ones.
We use two different ways, MPG (Method of parameter grid) and MMC (Method of matrix convolution), to build the fluorescence information table, and apply them into our inverse fluorescence spectra fitting tool to reduce the time cost during the parameters extracted process, to make the inverse tool faster.
We use different grid sizes of information table in our inverse fluorescence spectra fitting tool and analyze the correction of extracting parameters to get the ideas how big of information table we should build. When the size of information table is small, we find that MPG needs less memory and time than MMC does to build the information table. However, the result may reverse if the table size keeps increasing.
We also analyze the fluorescence spectra noise depends on the portable spectroscopy we designed and analyze the diffusion optical parameters error which may have an effect on information table searching during parameters extracted process. We find that the former one does not have an obvious influence on the correction of extracting fluorescence optical parameters, while the later one does.
In the future, we will use the inverse fluorescence spectra fitting tool to analyze the in vivo fluorescence spectra measured from our portable spectroscopy, and hoping that the optical parameters we get can help the tumor diagnosis.
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Lee, Yuan-chun Harry. "The simulated effect of the lightning first short stroke current on a multi-layered cylindrical model of the human leg." Thesis, 2015. http://hdl.handle.net/10539/22609.
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A dissertation submitted to the Faculty of Engineering and the Built Environment,
University of the Witwatersrand, Johannesburg, in ful lment of the requirements
for the degree of Master of Science in Engineering.
Johannesburg, 2015<br>This research investigates the e ects of the frequency components of the lightning
First Short Stroke (FSS) on the current pathway through human tissues using frequency
domain analysis. A Double Exponential Function (DEF) is developed to
model the FSS with frequency components in the range 10 Hz 100 kHz. Human
tissues are simulated using Finite Element Analysis (FEA) in COMSOL and
comprises of two types of models: Single Layer Cylindrical Model (SLCM) and
Multi-layered Cylindrical Model (MLCM). The SLCM models 54 human tissues independently
and the MLCM models the human leg with ve tissue layers: bone
marrow, cortical bone, muscle, blood and fat.
Three aspects are analysed: current density, complex impedance and power dissipation.
From the SLCM results, aqueous tissues have the lowest impedances and tissue
heat dissipation is proportional to tissue impedance. Results from the MLCM show
that 85% of the FSS current
ows through muscle, 11%
ows through blood, 3:5%
through fat and the rest through cortical bone and bone marrow. From the results,
frequency dependent equivalent circuit models consisting of resistors and capacitors
connected in series are proposed.
The simulation results are correlated with three main clinical symptoms of lightning
injuries: neurological, cardiovascular and external burns. The results of this work are
applicable to the analysis of High Voltage (HV) injuries at power frequencies.<br>MT2017
Books on the topic "Two-layered and three-layered tissue models"
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La Canna, Giovanni. Heart valve disease (mitral valve disease): anatomy and morphology of the mitral valve. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780198726012.003.0034.
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The mitral valve is a complex anatomical structure that includes the valve tissue (leaflets), the left atrioventricular junction (annulus), and the valve suspension system (chordae tendineae, papillary muscles, and left ventricle). Its functional anatomy can be analysed using two- and three-dimensional transthoracic and transoesophageal echocardiography. Based on certain hallmarks (commissures, clefts), in vivo mitral valve tissue anatomy can be accurately categorized. In addition, three-dimensional reconstruction provides a quantitative model for comprehensive valve analysis. This chapter describes the anatomy and morphology of the mitral valve, including the subvalvular suspension system and functional anatomy and dynamics of the mitral annulus.
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Galderisi, Maurizio, and Sergio Mondillo. Assessment of diastolic function. Oxford University Press, 2011. http://dx.doi.org/10.1093/med/9780199599639.003.0009.
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Modern assessment of left ventricular (LV) diastolic function should be based on the estimation of degree of LV filling pressure (LVFP), which is the true determinant of symptoms/signs and prognosis in heart failure.In order to achieve this goal, standard Doppler assessment of mitral inflow pattern (E/A ratio, deceleration time, isovolumic relaxation time) should be combined with additional manoeuvres and/or ultrasound tools such as: ◆ Valsalva manoeuvre applied to mitral inflow pattern. ◆ Pulmonary venous flow pattern. ◆ Velocity flow propagation by colour M-mode. ◆ Pulsed wave tissue Doppler of mitral annuls (average of septal and lateral E′ velocity).In intermediate doubtful situations, the two-dimensional determination of left atrial (LA) volume can be diagnostic, since LA enlargement is associated with a chronic increase of LVFP in the absence of mitral valve disease and atrial fibrillation.Some new echocardiographic technologies, such as the speckle tracking-derived LV longitudinal strain and LV torsion, LA strain, and even the three-dimensional determination of LA volumes can be potentially useful to add further information. In particular, the reduction of LV longitudinal strain in patients with LV diastolic dysfunction and normal ejection fraction demonstrates that a subclinical impairment of LV systolic function already exists under these circumstances.
Book chapters on the topic "Two-layered and three-layered tissue models"
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Garanto, Alejandro. "Delivery of Antisense Oligonucleotides to the Mouse Retina." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2010-6_22.
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AbstractThe eye is the organ in charge of vision and, given its properties, has become an excellent organ to test genetic therapies, including antisense oligonucleotide (AON) technology. In fact, the first AON receiving FDA and EMA approval was meant to treat an eye condition. Currently, dozens of clinical trials are being conducted for a variety of subtypes of inherited retinal disease. Although most of them are based on gene augmentation therapies, a phase 3 and two phase 1/2 clinical trials using AONs are ongoing. Since the retina is a layered structure of nondividing cells, obtaining human retinal tissue and expanding it in the lab is not possible, unless induced pluripotent stem cell technology is used. Mouse models have helped to elucidate the function of many genes, and the retinal structure is quite similar to that of humans. Thus, drug delivery to the mouse eye can provide valuable information for further optimization of therapies. In this chapter, the protocol for intravitreal injections of AONs is described in detail.
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Soderi, Simone, Mariella Särestöniemi, Syifaul Fuada, Matti Hämäläinen, Marcos Katz, and Jari Iinatti. "Securing Hybrid Wireless Body Area Networks (HyWBAN): Advancements in Semantic Communications and Jamming Techniques." In Communications in Computer and Information Science. Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-59091-7_24.
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AbstractThis paper explores novel strategies to strengthen the security of Hybrid Wireless Body Area Networks (HyWBANs), which are essential in smart healthcare and Internet of Things (IoT) applications. Recognizing the vulnerability of HyWBAN to sophisticated cyber-attacks, we propose an innovative combination of semantic communications and jamming receivers. This dual-layered security mechanism protects against unauthorized access and data breaches, particularly in scenarios involving in-body to on-body communication channels. We conduct comprehensive laboratory measurements to understand hybrid (radio and optical) communication propagation through biological tissues. We utilize these insights to refine a dataset for training a Deep Learning (DL) model. These models, in turn, generate semantic concepts linked to cryptographic keys for enhanced data confidentiality and integrity using a jamming receiver. The proposed model significantly reduces energy consumption compared to traditional cryptographic methods, like Elliptic Curve Diffie-Hellman (ECDH), especially when supplemented with jamming. Our approach addresses the primary security concerns and sets the baseline for future secure biomedical communication systems advancements.
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Mandal, Akash Pradip, and Prashanta Kumar Mandal. "Role of Stent Embedment and Release Kinetics on Two-Phase Binding of Drug in a Three-Layered Arterial Tissue." In Intelligent Systems and Simulation. CRC Press, 2025. https://doi.org/10.1201/9781003638414-10.
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Cardenas, Daviel, Seema Bhalchandra, Hymlaire Lamisere, et al. "Two- and Three-Dimensional Bioengineered Human Intestinal Tissue Models for Cryptosporidium." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9748-0_21.
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Svoren, Martin, Elena Camerini, Merijn van Erp, Feng Wei Yang, Gert-Jan Bakker, and Katarina Wolf. "Approaches to Determine Nuclear Shape in Cells During Migration Through Collagen Matrices." In Cell Migration in Three Dimensions. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2887-4_7.
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AbstractFibrillar collagen is an abundant extracellular matrix (ECM) component of interstitial tissues which supports the structure of many organs, including the skin and breast. Many different physiological processes, but also pathological processes such as metastatic cancer invasion, involve interstitial cell migration. Often, cell movement takes place through small ECM gaps and pores and depends upon the ability of the cell and its stiff nucleus to deform. Such nuclear deformation during cell migration may impact nuclear integrity, such as of chromatin or the nuclear envelope, and therefore the morphometric analysis of nuclear shapes can provide valuable insight into a broad variety of biological processes. Here, we describe a protocol on how to generate a cell-collagen model in vitro and how to use confocal microscopy for the static and dynamic visualization of labeled nuclei in single migratory cells. We developed, and here provide, two scripts that (Fidler, Nat Rev Cancer 3(6):453–458, 2003) enable the semi-automated and fast quantification of static single nuclear shape descriptors, such as aspect ratio or circularity, and the nuclear irregularity index that forms a combination of four distinct shape descriptors, as well as (Frantz et al., J Cell Sci 123 (Pt 24):4195–4200, 2010) a quantification of their changes over time. Finally, we provide quantitative measurements on nuclear shapes from cells that migrated through collagen either in the presence or the absence of an inhibitor of collagen degradation, showing the distinctive power of this approach. This pipeline can also be applied to cell migration studied in different assays, ranging from 3D microfluidics to migration in the living organism.
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Hua, Yihe, Desmond T. B. Yeo, and Thomas K. F. Foo. "Peripheral Nerve Stimulation (PNS) Analysis of MRI Head Gradient Coils with Human Body Models." In Brain and Human Body Modelling 2021. Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-15451-5_3.
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AbstractThe main objective of this chapter is to provide a comprehensive and intuitive introduction to MRI gradient coil related PNS modeling with human body models. We will present the fundamental concepts and analytical processes behind gradient coil-induced peripheral nerve stimulation (PNS) modeling and also show some new results of our work. We first describe the process of performing electromagnetic simulation of a gradient coil, the neurodynamic simulation of nerves, and the gradient coil design. Then, we present improvements of two existing human body models by adding more nerve trajectories in the head and upper body to reduce the discrepancies between the simulated and measured results for PNS thresholds in head gradient coils. Further, we apply the modified human body models to analyze three folded and non-folded gradient coils and reveal the relationship between the eddy current flow in the human body and the gradient coil wire pattern and its impact on the PNS. We also show the connection between concomitant fields and PNS and assess the accuracy of PNS calculations in human body models with simplified tissue properties. Finally, we give our thoughts on the future direction of this work.
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Randall, Sarah, John Schomberg, Andreina Giron, Alice Martino, and Zoe Flyer. "Identification of Molecular Leads for Treatment of Secondary TBI via Analysis of Gene Expression in Models of Traumatic Brain Injury in Combination with Two-Dimensional and Three-Dimensional Drug Library Analysis." In Communications in Computer and Information Science. Springer Nature Switzerland, 2025. https://doi.org/10.1007/978-3-031-88346-0_4.
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Abstract Traumatic brain injury (TBI) is a common and serious clinical problem with high variability in injury severity. Current clinical therapies generally only manage downstream effects of TBI. Thus, there is an increasing interest in finding treatments that can directly address underlying physiological responses such as edema, cell apoptosis, and tissue oxidation. We applied open-source, clinician-accessible informatics methods that identified differentially expressed genes (DEGs) in curated TBI rodent models, found associated hub genes and genetic pathways, and determined novel chemical leads for treatments that target key pathways associated with secondary inflammatory injury in TBI. Differential expression analysis was performed by identifying DEGs between models of TBI and controls. Pathway analysis was completed to determine the up and down regulated genes enriched in each gene pathway and to delineate DEGs in post TBI models over a 48-h recovery period. A molecular similarity search using over 22,000 known molecules was then run against the identified ligands. The pathways determined to be relevant to secondary TBI were inflammation, oxidative stress, cell apoptosis, and angiogenesis, a marker for blood-brain barrier permeability. The similarity search yielded 95 potential ligand matches found in PubChem’s database. 20 ligands were determined to have potential in neuropathological treatment research or were associated with gene pathways relevant to TBI. The methodology reported in this study can be applied to other gene expression datasets to enable clinicians to identify viable treatment leads in rare or neglected diseases.
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Hu Rui, Barner Kenneth E., and Steiner Karl V. "A Generalized Haptic Feedback Approach for Arbitrarily Shaped Objects." In Studies in Health Technology and Informatics. IOS Press, 2011. https://doi.org/10.3233/978-1-60750-706-2-224.
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In surgery procedures, haptic interaction provides surgeons with indispensable information to accurately locate the surgery target. This is especially critical when visual feedback cannot provide sufficient information and tactile interrogation, such as palpating some region of tissue, is required to locate a specific underlying tumor. However, in most current surgery simulators, the haptic interaction model is usually simplified into a contact sphere or rod model, leaving arbitrarily shaped intersection haptic feedback between target tissue and surgery instrument less unreliable. In this paper, a novel haptic feedback algorithm is introduced for generating the feedback forces in surgery simulations. The proposed algorithm initially employs three Layered Depth Images (LDI) to sample the 3D objects in X, Y and Z directions. A secondary analysis scans through two sampled meshes and detects their penetration volume. Based on the principle that interaction force should minimize the penetration volume, the haptic feedback force is derived directly. Additionally, a post-processing technique is developed to render distinct physical tissue properties across different interaction areas. The proposed approach does not require any pre-processing and is applicable for both rigid and deformable objects.
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Oliveira, João Fradinho, José Luis Moyano-Cuevas, J. Blas Pagador, Hugo Capote, and Francisco Miguel Sánchez Margallo. "Preoperative and Intraoperative Spatial Reasoning Support with 3D Organ and Vascular Models." In Medical Imaging. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-0571-6.ch078.
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Different imaging modalities (MRI/CT) are used to analyse/plan complex surgical procedures in order to minimize risks and complications. Although there are numerous computer tools for preoperative assistance (VR/AR simulators, 3D printed implants), intraoperative systems are less common, specifically for soft tissue related interventions. For this reason, this paper is focused on 3D reconstruction. The proposed reconstruction combines a surface approach for organs and a block approach for vascular networks. Layered closed surface(s) represent an organ and stacks of extruded individual contour blocks represent the vascular networks. The authors use IGSTK to show that their approach improves shape and transparency results when compared with other modelling methods and to communicate with trackers. With their method polygon contour correspondence/branching between slices is implicit/automatic, saving time; they show that traditional tiling problems become visually negligible. The authors' novel file format allows polygons segmented by other tools to be reconstructed in their contour annotation tool which uses VTK.
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Grizzle William E., Bell Walter C., and Sexton Katherine C. "Issues in collecting, processing and storing human tissues and associated information to support biomedical research." In Translational Pathology of Early Cancer. IOS Press, 2012. https://doi.org/10.3233/978-1-61499-024-6-531.
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The availability of human tissues to support biomedical research is critical to advance translational research focused on identifying and characterizing approaches to individualized (personalized) medical care. Providing such tissues relies on three acceptable models &ndash; a tissue banking model, a prospective collection model and a combination of these two models. An unacceptable model is the &ldquo;catch as catch can&rdquo; model in which tissues are collected, processed and stored without goals or a plan or without standard operating procedures, i.e., portions of tissues are collected as available and processed and stored when time permits. In the tissue banking model, aliquots of tissues are collected according to SOPs. Usually specific sizes and types of tissues are collected and processed (e.g., 0.1 gm of breast cancer frozen in OCT). Using the banking model, tissues may be collected that may not be used and/or do not meet specific needs of investigators; however, at the time of an investigator request, tissues are readily available as is clinical information including clinical outcomes. In the model of prospective collection, tissues are collected based upon investigator requests including specific requirements of investigators. For example, the investigator may request that two 0.15 gm matching aliquots of breast cancer be minced while fresh, put in RPMI media with and without fetal calf serum, cooled to 4&deg;C and shipped to the investigator on wet ice. Thus, the tissues collected prospectively meet investigator needs, all collected specimens are utilized and storage of specimens is minimized; however, investigators must wait until specimens are collected, and if needed, for clinical outcome. The operation of any tissue repository requires well trained and dedicated personnel. A quality assurance program is required which provides quality control information on the diagnosis of a specimen that is matched specifically to the specimen provided to an investigator instead of an overall diagnosis of the specimen via a surgical pathology report. This is necessary because a specific specimen may not match the diagnosis of the case due to many factors such as necrosis, unsuspected tumor invasion of apparently normal tissue, and areas of fibrosis which are mistaken grossly for tumor. Aliquots for quality control (QC) may or may not be collected at the time of collection and in some cases, QC may not occur until specimens are distributed to investigators. In establishing a tumor repository, multiple issues need to be considered. These include the available resources, long term support, space and equipment. The needs of the potential users need to be identified as to the types of tissues and services needed and the annotation expected. Other specific issues to be considered include collection of specimens potentially infected with blood borne pathogens (e.g., hepatitis B), charge back mechanisms, informatics needs and support, and investigator requirements (e.g., recognition of repository contributions in publications). In general, the repository should not perform the research of the investigators, but should provide the infrastructure necessary to support the research of the investigator. Thus, the goals of the repository must be established. Similarly, ethical and regulatory issues must be evaluated. In general, tissue repositories need ethical (e.g., IRB) and privacy (e.g., HIPAA) review. Also, safety issues need to be considered as well as how biohazards will be addressed by investigator-users. Considerations involving the transfer of specimens to other organization usually require a material transfer agreement (MTA). A MTA should address biohazards as well as indemnification. Thus, many issues must be considered and addressed in order to establish and operate successfully a biorepository.
Conference papers on the topic "Two-layered and three-layered tissue models"
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Chamani, Shaghayegh, Xiaojing Lv, Trevor S. Bird, and Yang Yang. "Exploring a Dual-Port Open-ended Coaxial Cable and a Multi-Layered Tissue Model for Skin Cancer Detection." In 2024 49th International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz). IEEE, 2024. http://dx.doi.org/10.1109/irmmw-thz60956.2024.10697727.
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Wilson, Robert H., Karthik Vishwanath, and Mary-Ann Mycek. "Time-Resolved Reflectance of Two-Layered Tissue Models via Scaling of “White” Monte Carlo Simulations." In Biomedical Topical Meeting. OSA, 2006. http://dx.doi.org/10.1364/bio.2006.me1.
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katmi, Ghazi, and Ola Awad. "Numerical Analysis of Damage Due To Photo-thermal Interaction of Skin." In Frontiers in Optics. Optica Publishing Group, 2022. http://dx.doi.org/10.1364/fio.2022.jw5b.62.
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The purpose of this work is to study the thermal damage of tissue by mathematical models. A three layered tissue structure is modeled using the software package COMSOL Multiphysics. The irradiation of the laser beam is modeled as a Gaussian beam, the effects of laser irradiation time, wavelength, laser intensity, laser beam radius on temperature distribution, during laser irradiation are systematically investigated.
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Mok, Chong-Ian, and Kung-Bin Sung. "Extracting Autofluorescence Spectral Shape and Intensity from Uterine Cervical Mucosa Using Monte-Carlo Based Two-layered Tissue Models." In Clinical and Translational Biophotonics. OSA, 2020. http://dx.doi.org/10.1364/translational.2020.jw3a.6.
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Kushwaha, Sandeep Singh, and P. S. Ghoshdastidar. "Numerical Prediction of the Temperature Distribution Within a Human Eye During Laser Surgery." In ASME 2008 Heat Transfer Summer Conference collocated with the Fluids Engineering, Energy Sustainability, and 3rd Energy Nanotechnology Conferences. ASMEDC, 2008. http://dx.doi.org/10.1115/ht2008-56259.
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In this paper a computational heat transfer model for prediction of the temperature distribution within the human eye during laser surgery is presented. The heat transfer within a tissue is described by the classic Pennes bioheat transfer equation. The intraocular temperature distribution is calculated using finite-difference method. Two types of computational domain have been considered: (i) rectangular parallelepiped and (ii) cylindrical. The eye is modeled as a composite layered structure consisting of four different ocular tissues, namely, cornea, aqueous, lens and vitreous. It is assumed that the eye is symmetrical about the pupillary axis. The absorption probability of ocular tissue is modulated based on the Lambert-Beer’s law to reproduce the exponential attenuation of the laser light with depth within a biomaterial. The heat flow is modeled as transient and three-dimensional for rectangular parallelepiped geometry and two-dimensional (axi-symmetric) for the cylindrical geometry. The results indicate that for the insulation condition imposed on the periphery of the eye the model based on rectangular parallelepiped geometry of the eye at no laser power and at the initial temperature of 25°C predicts temperature closer to in-vitro experimental measurements reported in literature whereas the model based on cylindrical geometry predicts higher temperature. The opposite is true (that is, lower temperature is predicted by the model based on cylindrical geometry) for high laser heat flux (2000 W/m2) and higher initial temperature (37°C). This study also presents changes in eye temperature subjected to intermittent laser source used in laser surgery techniques such as PRK and LASIK. A comparison of the results based on three different boundary conditions such as convection (hb = 10 W/m2K), constant temperature (37°C) and insulation on the eye periphery reveals that the model based on insulation condition predicts results closer to that of in-vitro experiment at no laser power and initial temperature of 25°C whereas at a laser power of 200 W/m2 and at the initial temperature of 37°C insulation boundary condition produces highest temperature followed by that produced by convection and constant temperature conditions. The heat transfer is one-dimensional for the insulated eye periphery whereas multi-dimensional heat flow takes place when the circumferential boundary condition is either convective or isothermal.
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Tourlomousis, Filippos, and Robert C. Chang. "Computational Modeling of 3D Printed Tissue-on-a-Chip Microfluidic Devices as Drug Screening Platforms." In ASME 2014 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/imece2014-38454.
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Physiological tissue-on-a-chip technology is enabled by adapting microfluidics to create micro scale drug screening platforms that replicate the complex drug transport and reaction processes in the human liver. The ability to incorporate three-dimensional (3d) tissue models using layered fabrication approaches into devices that can be perfused with drugs offer an optimal analog of the in vivo scenario. The dynamic nature of such in vitro metabolism models demands reliable numerical tools to determine the optimum tissue fabrication process, flow, material, and geometric parameters for the most effective metabolic conversion of the perfused drug into the liver microenvironment. Thus, in this modeling-based study, the authors focus on modeling of in vitro 3d microfluidic microanalytical microorgan devices (3MD), where the human liver analog is replicated by 3d cell encapsulated alginate hydrogel based tissue-engineered constructs. These biopolymer constructs are hosted in the chamber of the 3MD device serving as walls of the microfluidic array of channels through which a fluorescent drug substrate is perfused into the microfluidic printed channel walls at a specified volumetric flow rate assuring Stokes flow conditions (Re<<1). Due to the porous nature of the hydrogel walls, a metabolized drug product is collected as an effluent stream at the outlet port. A rigorous modeling approached aimed to capture both the macro and micro scale transport phenomena is presented. Initially, the Stokes Flow Equations (free flow regime) are solved in combination with the Brinkman Equations (porous flow regime) for the laminar velocity profile and wall shear stresses in the whole shear mediated flow regime. These equations are then coupled with the Convection-Diffusion Equation to yield the drug concentration profile by incorporating a reaction term described by the Michael-Menten Kinetics model. This effectively yields a convection-diffusion–cell kinetics model (steady state and transient), where for the prescribed process and material parameters, the drug concentration profile throughout the flow channels can be predicted. A key consideration that is addressed in this paper is the effect of cell mechanotransduction, where shear stresses imposed on the encapsulated cells alter the functional ability of the liver cell enzymes to metabolize the drug. Different cases are presented, where cells are incorporated into the geometric model either as voids that experience wall shear stress (WSS) around their membrane boundaries or as solid materials, with linear elastic properties. As a last step, transient simulations are implemented showing that there exists a tradeoff with respect the drug metabolized effluent product between the shear stresses required and the residence time needed for drug diffusion.
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Rosen-Zvi, Michal, and Haim Taitelbaum. "Frequency-Domain Photon Migration in Two-Layered Tissues." In Biomedical Optical Spectroscopy and Diagnostics. Optica Publishing Group, 2006. http://dx.doi.org/10.1364/bosd.1996.ap11.
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We study frequency-domain spectroscopy for reflectance measurements in two-layered tissues, using a random-walk model of photon migration. We study the phase shift of the reflected light as a function of the source-detector separation, and show that there can be as many as three different types of behavior of this quantity, depending on the relation between the modulated frequency and the absorptivities of both layers. As a result, the possibility of determining the absorptivities of the two layers and the upper layer thickness from the phase shift is different in each regime.
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Hielscher, Andreas H., Mohideen Azeez-Jan, and Sebastian Bartel. "Tomographic reconstruction of layered tissue structures." In European Conference on Biomedical Optics. Optica Publishing Group, 2001. http://dx.doi.org/10.1364/ecbo.2001.4431_126.
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In recent years the interest in the determination of optical properties of layered tissue structure has resurfaced. Applications include, for example, studies on layered skin tissue and underlying muscles, imaging of the brain underneath layers of skin, skull, and meninges, and imaging of the fetal head in utero beneath the layered structures of the maternal abdomen. In this work we approach the problem of layered structures in the framework of model-based iterative image reconstruction schemes. These schemes are currently developed to determine the optical properties inside tissue from measurement on the surface. If applied to layered structure these techniques yield substantial improvements over currently available semi-analytical approaches.
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Zhao, Aihong, Ian Owens Pericevic, Kennerly Digges, Cing-Dao Kan, Moji Moatamedi, and Jeffrey S. Augenstein. "FE Modeling of the Orthotropic and Three-Layered Human Thoracic Aorta." In ASME 2006 Pressure Vessels and Piping/ICPVT-11 Conference. ASMEDC, 2006. http://dx.doi.org/10.1115/pvp2006-icpvt-11-93573.
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The human aorta consists of three layers: intima, media and adventitia from the inner to outer layer. Since aortic rupture of victims in vehicle crashes frequently occurs in the intima and the media, latent aortic injuries are difficult to detect at the crash scene or in the emergency room. It is necessary to develop a multi-layer aorta finite element (FE) model to identify and describe the potential mechanisms of injury in various impact modes. In this paper, a novel three-layer FE aortic model was created to study aortic ruptures under impact loading. The orthotropic material model [1] has been implemented into a user-defined material subroutine in the commercial dynamic finite element software LS-DYNA version 970 [2], which was adopted in the aorta FE model. The Arbitrary-Lagrangian Eulerian (ALE) approach was adopted to simulate the interaction between the fluid (blood) and the structure (aorta). Single element verifications for the user-defined subroutine were performed. The mechanical behaviors of aortic tissues under impact loading were simulated by the aorta FE model. The models successfully predicted the rupture of the layers separately. The results provide a basis for a more in-depth investigation of blunt traumatic aortic rupture (BTAR) in vehicle crashes.
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Bayıntır, Hazel, Demet Elmas, Mithat İdemen, Banu Uzun, and Mustafa Karaman. "Thermoacoustic image reconstruction based on layered tissue model." In SPIE Medical Imaging, edited by Neb Duric and Brecht Heyde. SPIE, 2017. http://dx.doi.org/10.1117/12.2250143.
Full textReports on the topic "Two-layered and three-layered tissue models"
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Rafaeli, Ada, Russell Jurenka, and Chris Sander. Molecular characterisation of PBAN-receptors: a basis for the development and screening of antagonists against Pheromone biosynthesis in moth pest species. United States Department of Agriculture, 2008. http://dx.doi.org/10.32747/2008.7695862.bard.
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The original objectives of the approved proposal included: (a) The determination of species- and tissue-specificity of the PBAN-R; (b) the elucidation of the role of juvenile hormone in gene regulation of the PBAN-R; (c) the identificationof the ligand binding domains in the PBAN-R and (d) the development of efficient screening assays in order to screen potential antagonists that will block the PBAN-R. Background to the topic: Moths constitute one of the major groups of pest insects in agriculture and their reproductive behavior is dependent on chemical communication. Sex-pheromone blends are utilised by a variety of moth species to attract conspecific mates. In most of the moth species sex-pheromone biosynthesis is under circadian control by the neurohormone, PBAN (pheromone-biosynthesis-activating neuropeptide). In order to devise ideal strategies for mating disruption/prevention, we proposed to study the interactions between PBAN and its membrane-bound receptor in order to devise potential antagonists. Major conclusions: Within the framework of the planned objectives we have confirmed the similarities between the two Helicoverpa species: armigera and zea. Receptor sequences of the two Helicoverpa spp. are 98% identical with most changes taking place in the C-terminal. Our findings indicate that PBAN or PBAN-like receptors are also present in the neural tissues and may represent a neurotransmitter-like function for PBAN-like peptides. Surprisingly the gene encoding the PBAN-receptor was also present in the male homologous tissue, but it is absent at the protein level. The presence of the receptor (at the gene- and protein-levels), and the subsequent pheromonotropic activity are age-dependent and up-regulated by Juvenile Hormone in pharate females but down-regulated by Juvenile Hormone in adult females. Lower levels of pheromonotropic activity were observed when challenged with pyrokinin-like peptides than with HezPBAN as ligand. A model of the 3D structure of the receptor was created using the X-ray structure of rhodopsin as a template after sequence alignment of the HezPBAN-R with several other GPCRs and computer simulated docking with the model predicted putative binding sites. Using in silico mutagenesis the predicted docking model was validated with experimental data obtained from expressed chimera receptors in Sf9 cells created by exchanging between the three extracellular loops of the HezPBAN-R and the Drosophila Pyrokinin-R (CG9918). The chimera receptors also indicated that the 3ʳᵈ extracellular loop is important for recognition of PBAN or Diapause hormone ligands. Implications: The project has successfully completed all the objectives and we are now in a position to be able to design and screen potential antagonists for pheromone production. The successful docking simulation-experiments encourage the use of in silico experiments for initial (high-throughput) screening of potential antagonists. However, the differential responses between the expressed receptor (Sf9 cells) and the endogenous receptor (pheromone glands) emphasize the importance of assaying lead compounds using several alternative bioassays (at the cellular, tissue and organism levels). The surprising discovery of the presence of the gene encoding the PBAN-R in the male homologous tissue, but its absence at the protein level, launches opportunities for studying molecular regulation pathways and the evolution of these GPCRs. Overall this research will advance research towards the goal of finding antagonists for this important class of receptors that might encompass a variety of essential insect functions.
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Cohen, Yuval, Christopher A. Cullis, and Uri Lavi. Molecular Analyses of Soma-clonal Variation in Date Palm and Banana for Early Identification and Control of Off-types Generation. United States Department of Agriculture, 2010. http://dx.doi.org/10.32747/2010.7592124.bard.
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Date palm (Phoenix dactylifera L.) is the major fruit tree grown in arid areas in the Middle East and North Africa. In the last century, dates were introduced to new regions including the USA. Date palms are traditionally propagated through offshoots. Expansion of modern date palm groves led to the development of Tissue Culture propagation methods that generate a large number of homogenous plants, have no seasonal effect on plant source and provide tools to fight the expansion of date pests and diseases. The disadvantage of this procedure is the occurrence of off-type trees which differ from the original cultivar. In the present project we focused on two of the most common date palm off-types: (1) trees with reduced fruit setting, in which most of the flowers turn into three-carpel parthenocarpic fruits. In a severe form, multi-carpel flowers and fruitlets (with up to six or eight carpels instead of the normal three-carpel flowers) are also formed. (2) dwarf trees, having fewer and shorter leaves, very short trunk and are not bearing fruits at their expected age, compared to the normal trees. Similar off-types occur in other crop species propagated by tissue culture, like banana (mainly dwarf plants) or oil palm (with a common 'Mantled' phenotype with reduced fruit setting and occurrence of supernumerary carpels). Some off-types can only be detected several years after planting in the fields. Therefore, efficient methods for prevention of the generation of off-types, as well as methods for their detection and early removal, are required for date palms, as well as for other tissue culture propagated crops. This research is aimed at the understanding of the mechanisms by which off-types are generated, and developing markers for their early identification. Several molecular and genomic approaches were applied. Using Methylation Sensitive AFLP and bisulfite sequencing, we detected changes in DNA methylation patterns occurring in off-types. We isolated and compared the sequence and expression of candidate genes, genes related to vegetative growth and dwarfism and genes related to flower development. While no sequence variation were detected, changes in gene expression, associated with the severity of the "fruit set" phenotype were detected in two genes - PdDEF (Ortholog of rice SPW1, and AP3 B type MADS box gene), and PdDIF (a defensin gene, highly homologous to the oil palm gene EGAD). We applied transcriptomic analyses, using high throughput sequencing, to identify genes differentially expressed in the "palm heart" (the apical meristem and the region of embryonic leaves) of dwarf vs. normal trees. Among the differentially expressed genes we identified genes related to hormonal biosynthesis, perception and regulation, genes related to cell expansion, and genes related to DNA methylation. Using Representation Difference Analyses, we detected changes in the genomes of off-type trees, mainly chloroplast-derived sequences that were incorporated in the nuclear genome and sequences of transposable elements. Sequences previously identified as differing between normal and off-type trees of oil palms or banana, successfully identified variation among date palm off-types, suggesting that these represent highly labile regions of monocot genomes. The data indicate that the date palm genome, similarly to genomes of other monocot crops as oil palm and banana, is quite unstable when cells pass through a cycle of tissue culture and regeneration. Changes in DNA sequences, translocation of DNA fragments and alteration of methylation patterns occur. Consequently, patterns of gene expression are changed, resulting in abnormal phenotypes. The data can be useful for future development of tools for early identification of off-type as well as for better understanding the phenomenon of somaclonal variation during propagation in vitro.
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Burdman, S., E. Welbaum, R. Walcott, and B. Zhao. erial fruit blotch, elucidating the mechanisms of fruit infection by Acidovorax citrulli. United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134162.bard.
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Bacterial fruit blotch (BFB) of cucurbits is caused by the Gram-negative bacterium Acidovorax citrulli. BFB affects cucurbit production worldwide, and mainly watermelon and melon. Most A. citrulli strains are divided into two genetically differentiated groups: while group I strains have been mainly associated with melon and other non-watermelon cucurbits, group II strains are more aggressive on watermelon. Like many Gram-negative plant-pathogenic bacteria, A. citrulli relies on a functional type III secretion system (T3SS) for pathogenicity. The T3SS is responsible for direct secretion of bacterial protein effectors to the host cell. Type III-secreted effectors (T3Es) contribute to virulence through manipulation of the host cell metabolism and suppression of plant defense. Our previous collaboration showed that group I and II strains significantly differ in their T3E arsenal (Eckshtain-Levi et al., Phytopathology 2014, 104:1152-1162). Using comparative genomics, we also showed that group I and II strains of A. citrulli have substantial differences in their genome content (Eckshtain-Levi et al., Front. Microbiol. 2016, 7:430). Our long-term goals are to identify the genetic determinants that contribute to virulence and host preferential association of the two major groups of A. citrulli, and to exploit these insights to develop effective BFB management strategies. We hypothesize that differences in the arsenal of T3Es, are greatly responsible for the differences in host preferential association between strains belonging to the two groups. The specific objectives of this project were: (1) to investigate the susceptibility of cucurbit species to group I and II strains under field conditions; (2) to assess the contribution of T3Es and other virulence factors to A. citrulli virulence and host preference; and (3) to characterize the mechanisms of action of selected T3Es of A. citrulli. In the frame of objective 1, we carried out three field experiments involving inoculation of several cucurbit crops (watermelon, melon, pumpkin and squash) with group I and II strains. Findings from these experiments confirmed that A. citrulli strains exhibit a preference for watermelon and melon. Moreover, we demonstrated, for the first time under field conditions, host-preferential association of group I and II strains to melon and watermelon, respectively. While host-preferential association was observed in leaves and in fruit tissues, it was more pronounced in the latter. In this part of the project we also developed a duplex PCR assay to differentiate between group I and II strains. In the frame of objective 2, we employed a multifaceted approach combining bioinformatics and experimental methods to elucidate the T3E arsenal of A. citrulli. These experiments led to discovery that A. citrulli strains possess large arsenals with more than 60 T3E genes. Remarkably, we found that ~15% of the T3E genes are group-specific. Advances were achieved on the contribution of selected T3E genes and other virulence determinants to the ability of A. citrulli to colonize the fruit and other tissues of melon and watermelon. Last, in the frame of objective 3, we advanced our understanding on the mode of action of few key T3Es of A. citrulli. We also optimized a virus-induced gene silencing (VIGS) system for functional genomics in melon and watermelon. This system will allow us to test melon and watermelon genes that may have defense or susceptibility roles related to BFB disease. Overall, this collaboration substantially enriched our knowledge on basic aspects of BFB disease. We believe that the fruits of this collaboration will greatly contribute to our ultimate goal, which is generation of durable resistance of melon and watermelon to A. citrulli.
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Chamovitz, A. Daniel, and Georg Jander. Genetic and biochemical analysis of glucosinolate breakdown: The effects of indole-3-carbinol on plant physiology and development. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7597917.bard.
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Genetic and biochemical analysis of glucosinolate breakdown: The effects of indole-3-carbinol on plant physiology and development Glucosinolates are a class of defense-related secondary metabolites found in all crucifers, including important oilseed and vegetable crops in the Brassica genus and the well-studied model plant Arabidopsis thaliana. Upon tissue damage, such as that provided by insect feeding, glucosinolates are subjected to catalysis and spontaneous degradation to form a variety of breakdown products. These breakdown products typically have a deterrent effect on generalist herbivores. Glucosinolate breakdown products also contribute to the anti-carcinogenic effects of eating cabbage, broccoli and related cruciferous vegetables. Indole-3-carbinol, a breakdown product of indol-3-ylmethylglucosinolate, forms conjugates with several other plant metabolites. Although some indole-3-carbinol conjugates have known functions in defense against herbivores and pathogens, most play as yet unidentified roles in plant metabolism, and possibly also plant development. At the outset, our proposal had three main hypotheses: (1) There is a specific detoxification pathway for indole-3-carbinol; (2) Metabolites derived from indole-3-carbinol are phloem-mobile and serve as signaling molecules; and (3) Indole-3-carbinol affects plant cell cycle and cell-differentiation pathways. The experiments were designed to enable us to elucidate how indole-3-carbinol and related metabolites affect plants and their interactions with herbivorous insects. We discovered that indole-3- carbinol rapidly and reversibly inhibits root elongation in a dose-dependent manner, and that this inhibition is accompanied by a loss of auxin activity in the root meristem. A direct interaction between indole-3-carbinol and the auxin perception machinery was suggested, as application of indole-3-carbinol rescued auxin-induced root phenotypes. In vitro and yeast-based protein interaction studies showed that indole-3-carbinol perturbs the auxin-dependent interaction of TIR1 with Aux/IAA proteins, supporting the notion that indole-3-carbinol acts as an auxin antagonist. Furthermore, transcript profiling experiments revealed the influence of indole-3-carbinol on auxin signaling in root tips, and indole-3-carbinol also affected auxin transporters. Brief treatment with indole-3-carbinol led to a reduction in the amount of PIN1 and to mislocalization of PIN2. The results indicate that chemicals induced by herbivory, such as indole-3-carbinol, function not only to repel herbivores, but also as signaling molecules that directly compete with auxin to fine tune plant growth and development, which implies transport of indole-3- carbinol that we are as yet unsuccessful in detecting. Our results indicate that plant defensive metabolites also have secondary functions in regulating aspects of plant metabolism, thereby providing diversity in defense-related plant signaling pathways. Such diversity of of signaling by defensive metabolites would be beneficial for the plant, as herbivores and pathogens would be less likely to mount effective countermeasures. We propose that growth arrest can be mediated directly by the herbivory-induced chemicals, in our case, indole-3-carbinol. Thus, glucosinolate breakdown to I3C following herbivory would have two outcomes: (1) Indole-3-carbinaol would inhibit the herbivore, while (2) at the same time inducing growth arrest within the plant. Thus, our results indicate that I3C is a defensive phytohormone that modulates auxin signaling, leading to growth arrest.
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Wilson, Thomas E., Avraham A. Levy, and Tzvi Tzfira. Controlling Early Stages of DNA Repair for Gene-targeting Enhancement in Plants. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7697124.bard.
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Gene targeting (GT) is a much needed technology as a tool for plant research and for the precise engineering of crop species. Recent advances in this field have shown that the presence of a DNA double-strand break (DSB) in a genomic locus is critical for the integration of an exogenous DNA molecule introduced into this locus. This integration can occur via either non-homologous end joining (NHEJ) into the break or homologous recombination (HR) between the broken genomic DNA and the introduced vector. A bottleneck for DNA integration via HR is the machinery responsible for homology search and strand invasion. Important proteins in this pathway are Rad51, Rad52 and Rad54. We proposed to combine our respective expertise: on the US side, in the design of zincfinger nucleases (ZFNs) for the induction of DNA DSBs at any desired genomic locus and in the integration of DNA molecules via NHEJ; and on the Israeli side in the HR events, downstream of the DSB, that lead to homology search and strand invasion. We sought to test three major pathways of targeted DNA integration: (i) integration by NHEJ into DSBs induced at desired sites by specially designed ZFNs; (ii) integration into DSBs induced at desired sites combined with the use of Rad51, Rad52 and Rad54 proteins to maximize the chances for efficient and precise HR-mediated vector insertion; (iii) stimulation of HR by Rad51, Rad52 and Rad54 in the absence of DSB induction. We also proposed to study the formation of dsT-DNA molecules during the transformation of plant cells. dsT-DNA molecules are an important substrate for HR and NHEJ-mediatedGT, yet the mode of their formation from single stranded T-DNA molecules is still obscure. In addition we sought to develop a system for assembly of multi-transgene binary vectors by using ZFNs. The latter may facilitate the production of binary vectors that may be ready for genome editing in transgenic plants. ZFNs were proposed for the induction of DSBs in genomic targets, namely, the FtsH2 gene whose loss of function can easily be identified in somatic tissues as white sectors, and the Cruciferin locus whose targeting by a GFP or RFP reporter vectors can give rise to fluorescent seeds. ZFNs were also proposed for the induction of DSBs in artificial targets and for assembly of multi-gene vectors. We finally sought to address two important cell types in terms of relevance to plant transformation, namely GT of germinal (egg) cells by floral dipping, and GT in somatic cells by root and leave transformation. To be successful, we made use of novel optimized expression cassettes that enable coexpression of all of the genes of interest (ZFNs and Rad genes) in the right tissues (egg or root cells) at the right time, namely when the GT vector is delivered into the cells. Methods were proposed for investigating the complementation of T-strands to dsDNA molecules in living plant cells. During the course of this research, we (i) designed, assembled and tested, in vitro, a pair of new ZFNs capable of targeting the Cruciferin gene, (ii) produced transgenic plants which expresses for ZFN monomers for targeting of the FtsH2 gene. Expression of these enzymes is controlled by constitutive or heat shock induced promoters, (iii) produced a large population of transgenic Arabidopsis lines in which mutated mGUS gene was incorporated into different genomic locations, (iv) designed a system for egg-cell-specific expression of ZFNs and RAD genes and initiate GT experiments, (v) demonstrated that we can achieve NHEJ-mediated gene replacement in plant cells (vi) developed a system for ZFN and homing endonuclease-mediated assembly of multigene plant transformation vectors and (vii) explored the mechanism of dsTDNA formation in plant cells. This work has substantially advanced our understanding of the mechanisms of DNA integration into plants and furthered the development of important new tools for GT in plants.