Faculty and Staff Publications

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(1 + ε) moments suffice to characterise the GFF
(Electronic Journal of Probability, 2021) Berestycki, Nathanaël; Powell, Ellen; Ray, Gourab
We show that there is “no stable free field of index α∈ (1,2)”, in the following sense. It was proved in [4] that subject to a fourth moment assumption, any random generalised function on a domain D of the plane, satisfying conformal invariance and a natural domain Markov property, must be a constant multiple of the Gaussian free field. In this article we show that the existence of (1+𝜀) moments is sufficient for the same conclusion. A key idea is a new way of exploring the field, where (instead of looking at the more standard circle averages) we start from the boundary and discover averages of the field with respect to a certain “hitting density” of Itô excursions.
A 10 kW ZVS Integrated Boost Dual Three-Phase Bridge DC–DC Resonant Converter for a Linear Generator-Based Wave-Energy System: Design and Simulation
(Electronics, 2019) Harischandrappa, Nagendrappa; Bhat, Ashoka K. S.
The design and performance analysis of a 10 kW three-phase DC–DC LCL-type resonant converter having a built-in boost function were carried out. This high-power converter is proposed for its application in grid-interfacing a linear generator (LG)-based wave-energy system. Fixed-frequency control is used, and the converter was designed to operate with a lagging power factor. It is shown that all switches turn on with zero-voltage switching (ZVS) for wide input voltage and load variations. This results in reduced switching losses and stresses, which is very important in large-power applications. The performance of the converter was studied through PSIM simulation software. Theoretical and simulation results are presented for comparison. Power-loss break-down analysis of the designed converter was carried out and the summary of results is presented.
13,000 years of fire history derived from soil charcoal in a British Columbia coastal temperate rain forest
(Ecosphere, 2016) Hoffman, Kira M.; Gavin, D. G.; Lertzman, K. P.; Smith, D. J.; Starzomski, Brian M.
Little is known regarding the fire history of high‐latitude coastal temperate rain forests in the Pacific Northwest (PNW) of North America. While reconstructing historical fire regimes typically requires dendrochronological records from fire‐scarred trees or stratigraphically preserved lake sediment data, this type of information is virtually non‐existent in this region. To describe the long‐term fire history of a site on the central coast of British Columbia, Canada, we radiocarbon‐dated 52 pieces of charcoal. Charcoal ages ranged from 12,670 to 70 yr BP. Fires occurred regularly since 12,670 yr BP, with the exception of a distinct fire‐free period at 7500–5500 yr BP. Time since fire (TSF) estimates from soil charcoal and fire‐scarred trees ranged from 12,670 to 100 yr BP (median = 327 yr), and 70% of the sites examined had burned within the past 1000 yr. An increase in fire frequency in the late Holocene is consistent with the widely held hypothesis that anthropogenic fires were common across the PNW. We evaluate TSF distributions and discuss the difficulties in assigning actual fire dates from charcoal fragments with large inbuilt ages in a coastal temperate rain forest setting. We determine that a comprehensive approach using soil charcoal and fire scar analyses is necessary to reconstruct general trends in fire activity throughout the Holocene in this region.
13-moment-equations from nonequilibrium thermodynamics and kinetic theory: Comparison for non-linear one-dimensional flows
(Physics of Fluids, 2025) Bell, Luke; Struchtrup, Henning
The GENERIC-13 moment equations (general equation for the non-equilibrium reversible-irreversible coupling) [Struchtrup & Öttinger, Phys. Fluids 34, 017105 (2022)] were developed to have complete thermodynamic structure, in contrast to Grad’s 13-moment equations which are not accompanied by a suitable formulation of the second law of thermodynamics and loose hyperbolicity for larger deviations from equilibrium. With GENERIC-13 constructed to agree with Grad-13 to second order in the Knudsen number, both sets are considered and compared for hyperbolicity and plane heat transfer, and Couette and Poiseuille flows. It is shown that the GENERIC-13 equations are unconditionally hyperbolic. Jump and slip boundary conditions for GENERIC-13 are developed from the second law with coefficients adapted from kinetic theory. Additional asymptotically vanishing boundary conditions are constructed such that solutions of the GENERIC-13 equations reduce to those of Grad-13 to second and of Navier–Stokes–Fourier equations to first order in the Knudsen number.
16p11.2 haploinsufficiency reduces mitochondrial biogenesis in brain endothelial cells and alters brain metabolism in adult mice
(Cell Reports, 2023) Béland-Millar, Alexandria; Kirby, Alexia; Truong, Yen; Ouellette, Julie; Yandiev, Sozerko; Bouyakdan, Khalil; Pileggi, Chantal; Naz, Shama; Yin, Melissa; Carrier, Micaël; Kotchetkov, Pavel; St-Pierre, Marie-Kim; Tremblay, Marie-Ève; Courchet, Julien; Harper, Mary-Ellen; Alquier, Thierry; Messier, Claude; Shuhendler, Adam J.; Lacoste, Baptiste
Summary Neurovascular abnormalities in mouse models of 16p11.2 deletion autism syndrome are reminiscent of alterations reported in murine models of glucose transporter deficiency, including reduced brain angiogenesis and behavioral alterations. Yet, whether cerebrovascular alterations in 16p11.2df/+ mice affect brain metabolism is unknown. Here, we report that anesthetized 16p11.2df/+ mice display elevated brain glucose uptake, a phenomenon recapitulated in mice with endothelial-specific 16p11.2 haplodeficiency. Awake 16p11.2df/+ mice display attenuated relative fluctuations of extracellular brain glucose following systemic glucose administration. Targeted metabolomics on cerebral cortex extracts reveals enhanced metabolic responses to systemic glucose in 16p11.2df/+ mice that also display reduced mitochondria number in brain endothelial cells. This is not associated with changes in mitochondria fusion or fission proteins, but 16p11.2df/+ brain endothelial cells lack the splice variant NT-PGC-1α, suggesting defective mitochondrial biogenesis. We propose that altered brain metabolism in 16p11.2df/+ mice is compensatory to endothelial dysfunction, shedding light on previously unknown adaptative responses.
A 1D microphysical cloud model for Earth, and Earth-like exoplanets Liquid water and water ice clouds in the convective troposphere
(Elsevier, 2013) Zsom, Andras; Kaltnegger, Lisa; Goldblatt, Colin
One significant difference between the atmospheres of stars and exoplanets is the presence of condensed particles (clouds or hazes) in the atmosphere of the latter. In current 1D models clouds and hazes are treated in an approximate way by raising the surface albedo, or adopting measured Earth cloud properties. The former method introduces errors to the modeled spectra of the exoplanet, as clouds shield the lower atmosphere and thus modify the spectral features. The latter method works only for an exact Earth-analog, but it is challenging to extend to other planets. The main goal of this paper is to develop a self-consistent microphysical cloud model for 1D atmospheric codes, which can reproduce some observed properties of Earth, such as the average albedo, surface temperature, and global energy budget. The cloud model is designed to be computationally efficient, simple to implement, and applicable for a wide range of atmospheric parameters for planets in the habitable zone. We use a 1D, cloud-free, radiative-convective, and photochemical equilibrium code originally developed by Kasting, Pavlov, Segura, and collaborators as basis for our cloudy atmosphere model. The cloud model is based on models used by the meteorology community for Earth’s clouds. The free parameters of the model are the relative humidity and number density of condensation nuclei, and the precipitation efficiency. In a 1D model, the cloud coverage cannot be self-consistently determined, thus we treat it as a free parameter. We apply this model to Earth (aerosol number density 100 cm−3, relative humidity 77 %, liquid cloud fraction 40%, and ice cloud fraction 25%) and find that a precipitation efficiency of 0.8 is needed to reproduce the albedo, average surface temperature and global energy budget of Earth. We perform simulations to determine how the albedo and the climate of a planet is influenced by the free parameters of the cloud model. We find that the planetary climate is most sensitive to changes in the liquid water cloud fraction and precipitation efficiency. The advantage of our cloud model is that the cloud height and the droplet sizes are self-consistently calculated, both of which influence the climate and albedo of exoplanets.
A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate
(Marine Genomics, 2018) Messmer, Amber M.; Leong, Jong S.; Rondeau, Eric B.; Mueller, Anita; Despins, Cody A.; Minkley, David R.; Kent, Matthew P.; Lien, Sigbjørn; Boyce, Brad; Morrison, Diane; Fast, Mark D.; Norman, Joseph D.; Danzmann, Roy G.; Koop, Ben F.
Antiparasitic drugs such as emamectin benzoate (EMB) are relied upon to reduce the parasite load, particularly of the sea louse Lepeophtheirus salmonis, on farmed salmon. The decline in EMB treatment efficacy for this purpose is an important issue for salmon producers around the world, and particularly for those in the Atlantic Ocean where widespread EMB tolerance in sea lice is recognized as a significant problem. Salmon farms in the Northeast Pacific Ocean have not historically experienced the same issues with treatment efficacy, possibly due to the relatively large population of endemic salmonid hosts that serve to both redistribute surviving lice and dilute populations potentially under selection by introducing naïve lice to farms. Frequent migration of lice among farmed and wild hosts should limit the effect of farm-specific selection pressures on changes to the overall allele frequencies of sea lice in the Pacific Ocean. A previous study using microsatellites examined L. salmonis oncorhynchi from 10 Pacific locations from wild and farmed hosts and found no population structure. Recently however, a farm population of sea lice was detected where EMB bioassay exposure tolerance was abnormally elevated. In response, we have developed a Pacific louse draft genome that complements the previously-released Atlantic louse sequence. These genomes were combined with whole-genome re-sequencing data to design a highly sensitive 201,279 marker SNP array applicable for both subspecies (90,827 validated Pacific loci; 153,569 validated Atlantic loci). Notably, kmer spectrum analysis of the re-sequenced samples indicated that Pacific lice exhibit a large within-individual heterozygosity rate (average of 1 in every 72 bases) that is markedly higher than that of Atlantic individuals (1 in every 173 bases). The SNP chip was used to produce a high-density map for Atlantic sea louse linkage group 5 that was previously shown to be associated with EMB tolerance in Atlantic lice. Additionally, 478 Pacific louse samples from farmed and wild hosts obtained between 2005 and 2014 were also genotyped on the array. Clustering analysis allowed us to detect the apparent emergence of an otherwise rare genotype at a high frequency among the lice collected from two farms in 2013 that had reported elevated EMB tolerance. This genotype was not observed in louse samples collected from the same farm in 2010, nor in any lice sampled from other locations prior to 2013. However, this genotype was detected at low frequencies in louse samples from farms in two locations reporting elevated EMB tolerance in 2014. These results suggest that a rare genotype present in Pacific lice may be locally expanded in farms after EMB treatment. Supporting this hypothesis, 437 SNPs associated with this genotype were found to be in a region of linkage group 5 that overlaps the region associated with EMB resistance in Atlantic lice. Finally, five of the top diagnostic SNPs within this region were used to screen lice that had been subjected to an EMB survival assay, revealing a significant association between these SNPs and EMB treatment outcome. To our knowledge this work is the first report to identify a genetic link to altered EMB efficacy in L. salmonis in the Pacific Ocean.
The 2019–2020 Khalili (Iran) Earthquake Sequence—Anthropogenic Seismicity in the Zagros Simply Folded Belt?
(Journal of Geophysical Research: solid Earth, 2021-12) Jamalreyhani, Mohammadreza; Pousse-Beltran, Léa; Büyükakpınar, Pınar; Cesca, Simone; Nissen, Edwin; Ghods, Abdolreza; López-Comino, José Ángel; Rezapour, Mehdi; Najafi, Mahdi
We investigate the origin of a long-lived earthquake cluster in the Fars arc of the Zagros Simply Folded Belt that is colocated with the major Shanul natural gas field. The cluster emerged in January 2019 and initially comprised small events of Mn ∼ 3–4. It culminated on 9 June 2020 with a pair of Mw 5.4 and 5.7 earthquakes, which was followed by >100 aftershocks. We assess the spatiotemporal evolution of the earthquake sequence using multiple event hypocenter relocations, waveform inversions, and Sentinel-1 Interferometric Synthetic Aperture Radar (InSAR) measurements and models. We find that the early part of the sequence is spatially distinct from the 9 June 2020 earthquakes and their aftershocks. Moment tensors, centroid depths, and source parameter uncertainties of 15 of the largest (Mn ≥ 4.0) events show that the sequence is dominated by reverse faulting at shallow depths (mostly ≤4 km) within the sedimentary cover. InSAR modeling shows that the Mw 5.7 mainshock occurred at depths of 2–8 km with a rupture length and maximum slip of ∼20 km and ∼0.5 m, respectively. Our results suggest that the 2019–2020 Khalili earthquake sequence was likely influenced by operation of the Shanul field, though elevated natural seismicity in the Zagros makes the association difficult to prove. Understanding how to distinguish man-made from natural seismicity is helpful for hazard and risk assessment, notably in the Zagros, which is both seismically active and rich in oil and gas reserves.
2023 Study Leave Report
(Christine Walde, 2024-02-16) Walde, Christine
A report on the 3-month study leave of Fine Arts and Grants and Awards librarian Christine Walde.
365 Days of Openness: The Emergence of OER at the University of Cape town
(Open Educational Resources: Innovation, Research and Practice, 2013) Hodgkinson-Williams, Cheryl; Paskevicius, Michael; Cox, Glenda; Shaikh, Shihaam; Czerniewicz, Laura; Lee-Pan, Samantha
Historically, resources such as books, journals, newspapers, audio and video recordings have been fairly well curated in university libraries. However, the same cannot be said for teaching and learning materials, unless they have been included in a textbook or study guide. With the growth in digital media, libraries have been extending their curation of scholarly resources to include electronic journals, digital books and reference guides, broadening access to these beyond the physical walls of the library. While the growth in digital technology has prompted academics to create their own customised and contextually specific digital media for use in their teaching in the form of PowerPoint presentations, manuals, handbooks, guides, media resources and websites, these resources are most often stored on personal hard drives, on departmental servers or within password-protected institutional learning management systems. Access to these digital materials is usually limited to registered students undertaking specific courses within specific institutions and usually only disseminated by individual academics or departments.
A 3D analysis revealed complexe mitochondria morphologies in porcine cumulus cells
(Scientific Reports, 2022) Lounas, Amel; Lebrun, Ariane; Laflamme, Isabelle; Vernoux, Nathalie; Savage, Julie; Tremblay, Marie-Ève; Germain, Marc; Richard, François J.
In the ovarian follicle, a bilateral cell-to-cell communication exists between the female germ cell and the cumulus cells which surround the oocyte. This communication allows the transit of small size molecules known to impact oocyte developmental competence. Pyruvate derivatives produced by mitochondria, are one of these transferred molecules. Interestingly, mitochondria may adopt a variety of morphologies to regulate their functions. In this study, we described mitochondrial morphologies in porcine cumulus cells. Active mitochondria were stained with TMRM (Tetramethylrhodamine, Methyl Ester, Perchlorate) and observed with 2D confocal microscopy showing mitochondria of different morphologies such as short, intermediate, long, and very long. The number of mitochondria of each phenotype was quantified in cells and the results showed that most cells contained elongated mitochondria. Scanning electron microscopy (SEM) analysis confirmed at nanoscale resolution the different mitochondrial morphologies including round, short, intermediate, and long. Interestingly, 3D visualisation by focused ion-beam scanning electron microscopy (FIB-SEM) revealed different complex mitochondrial morphologies including connected clusters of different sizes, branched mitochondria, as well as individual mitochondria. Since mitochondrial dynamics is a key regulator of function, the description of the mitochondrial network organisation will allow to further study mitochondrial dynamics in cumulus cells in response to various conditions such as in vitro maturation.
A 3D analysis revealed complexe mitochondria morphologies in porcine cumulus cells
(Scientific Reports, 2022) Lounas, Amel; Lebrun, Ariane; Laflamme, Isabelle; Vernoux, Nathalie; Savage, Julie; Tremblay, Marie-Ève; Germain, Marc; Richard, François J.
In the ovarian follicle, a bilateral cell-to-cell communication exists between the female germ cell and the cumulus cells which surround the oocyte. This communication allows the transit of small size molecules known to impact oocyte developmental competence. Pyruvate derivatives produced by mitochondria, are one of these transferred molecules. Interestingly, mitochondria may adopt a variety of morphologies to regulate their functions. In this study, we described mitochondrial morphologies in porcine cumulus cells. Active mitochondria were stained with TMRM (Tetramethylrhodamine, Methyl Ester, Perchlorate) and observed with 2D confocal microscopy showing mitochondria of different morphologies such as short, intermediate, long, and very long. The number of mitochondria of each phenotype was quantified in cells and the results showed that most cells contained elongated mitochondria. Scanning electron microscopy (SEM) analysis confirmed at nanoscale resolution the different mitochondrial morphologies including round, short, intermediate, and long. Interestingly, 3D visualisation by focused ion-beam scanning electron microscopy (FIB-SEM) revealed different complex mitochondrial morphologies including connected clusters of different sizes, branched mitochondria, as well as individual mitochondria. Since mitochondrial dynamics is a key regulator of function, the description of the mitochondrial network organisation will allow to further study mitochondrial dynamics in cumulus cells in response to various conditions such as in vitro maturation.
3D bioprinted coaxial testis model using human induced pluripotent stem cells: A step toward bicompartmental cytoarchitecture and functionalization
(Advanced Healthcare Materials) Robinson, Meghan A.; Kung, Sonia H.; Youssef, Khaled Y.; Scheck, Kali M.; Bell, Robert H.; Sar, Funda; Haegert, Anne M.; Asmae, M. Mahdi; Cheng, Changfeng; Yeack, Salina V.; Mathur, Bhairvi T.; Jiang, Feng; Collins, Colin C.; Hach, Farach; Willerth, Stephanie M.; Flannigan, Ryan K.
Fertility preservation following pediatric cancer therapy programs has become a major avenue of infertility research. In vitro spermatogenesis (IVS) aims to generate sperm from banked prepubertal testicular tissues in a lab setting using specialized culture conditions. While successful using rodent tissues, progress with human tissues is limited by the scarcity of human prepubertal testicular tissues for research. This study posits that human induced pluripotent stem cells (hiPSCs) can model human prepubertal testicular tissue to facilitate the development of human IVS conditions. Testicular cells derived from hiPSCs are characterized for phenotype markers and profiled transcriptionally. HiPSC-derived testicular cells are bioprinted into core�shell constructs representative of testis cytoarchitecture and found to capture functional aspects of prepubertal testicular tissues within 7 days under xeno-free conditions. Moreover, hiPSC-derived Sertoli cells illustrate the capacity to mature under pubertal-like conditions. The utility of the model is tested by comparing 2 methods of supplementing retinoic acid (RA), the vitamin responsible for inducing spermatogenesis. The model reveals a significant gain in activity under microsphere-released RA compared to RA medium supplementation, indicating that the fragility of free RA in vitro may be a contributing factor to the molecular dysfunction observed in human IVS studies to date.
3D Bioprinting Human Induced Pluripotent Stem Cell-Derived Neural Tissues Using a Novel Lab-on-a-Printer Technology
(Applied Sciences, 2018-11) De la Vega, Laura; Gómez, Diego A. Rosas; Abelseth, Emily; Abelseth, Laila; Allisson da Silva, Victor; Willerth, Stephanie M.
Most neurological diseases and disorders lack true cures, including spinal cord injury (SCI). Accordingly, current treatments only alleviate the symptoms of these neurological diseases and disorders. Engineered neural tissues derived from human induced pluripotent stem cells (hiPSCs) can serve as powerful tools to identify drug targets for treating such diseases and disorders. In this work, we demonstrate how hiPSC-derived neural progenitor cells (NPCs) can be bioprinted into defined structures using Aspect Biosystems’ novel RX1 bioprinter in combination with our unique fibrin-based bioink in rapid fashion as it takes under 5 min to print four tissues. This printing process preserves high levels of cell viability (>81%) and their differentiation capacity in comparison to less sophisticated bioprinting methods. These bioprinted neural tissues expressed the neuronal marker, βT-III (45 ± 20.9%), after 15 days of culture and markers associated with spinal cord (SC) motor neurons (MNs), such as Olig2 (68.8 ± 6.9%), and HB9 (99.6 ± 0.4%) as indicated by flow cytometry. The bioprinted neural tissues expressed the mature MN marker, ChaT, after 30 days of culture as indicated by immunocytochemistry. In conclusion, we have presented a novel method for high throughput production of mature hiPSC-derived neural tissues with defined structures that resemble those found in the SC.
3D Bioprinting Mesenchymal Stem Cell-Derived Neural Tissues Using a Fibrin-Based Bioink
(Biomolecules, 2021) Restan Perez, Milena; Sharma, Ruchi; Zeina Masri, Nadia; Willerth, Stephanie
Current treatments for neurodegenerative diseases aim to alleviate the symptoms experienced by patients; however, these treatments do not cure the disease nor prevent further degeneration. Improvements in current disease-modeling and drug-development practices could accelerate effective treatments for neurological diseases. To that end, 3D bioprinting has gained significant attention for engineering tissues in a rapid and reproducible fashion. Additionally, using patient-derived stem cells, which can be reprogrammed to neural-like cells, could generate personalized neural tissues. Here, adipose tissue-derived mesenchymal stem cells (MSCs) were bioprinted using a fibrin-based bioink and the microfluidic RX1 bioprinter. These tissues were cultured for 12 days in the presence of SB431542 (SB), LDN-193189 (LDN), purmorphamine (puro), fibroblast growth factor 8 (FGF8), fibroblast growth factor-basic (bFGF), and brain-derived neurotrophic factor (BDNF) to induce differentiation to dopaminergic neurons (DN). The constructs were analyzed for expression of neural markers, dopamine release, and electrophysiological activity. The cells expressed DN-specific and early neuronal markers (tyrosine hydroxylase (TH) and class III beta-tubulin (TUJ1), respectively) after 12 days of differentiation. Additionally, the tissues exhibited immature electrical signaling after treatment with potassium chloride (KCl). Overall, this work shows the potential of bioprinting engineered neural tissues from patient-derived MSCs, which could serve as an important tool for personalized disease models and drug-screening.
3D printed hydrogel microneedle arrays for interstitial fluid biomarker extraction and colorimetric detection
(Polymers, 2023) Razzaghi, Mahmood; Seyfoori, Amir; Pagan, Erik; Askari, Esfandyar; Najafabadi, Alireza Hassani; Akbari, Mohsen
To treat and manage chronic diseases, it is necessary to continuously monitor relevant biomarkers and modify treatment as the disease state changes. Compared to other bodily fluids, interstitial skin fluid (ISF) is a good choice for identifying biomarkers because it has a molecular composition most similar to blood plasma. Herein, a microneedle array (MNA) is presented to extract ISF painlessly and bloodlessly. The MNA is made of crosslinked poly(ethylene glycol) diacrylate (PEGDA), and an optimal balance of mechanical properties and absorption capability is suggested. Besides, the effect of needles’ cross-section shape on skin penetration is studied. The MNA is integrated with a multiplexed sensor that provides a color change in a biomarker concentration-dependent manner based on the relevant reactions for colorimetric detection of pH and glucose biomarkers. The developed device enables diagnosis by visual inspection or quantitative red, green, and blue (RGB) analysis. The outcomes of this study show that MNA can successfully identify biomarkers in interstitial skin fluid in a matter of minutes. The home-based long-term monitoring and management of metabolic diseases will benefit from such practical and self-administrable biomarker detection.
3D Printing Breast Tissue Models: A Review of Past Work and Directions for Future Work
(Micromachines, 2019) Cleversey, Chantell; Robinson, Meghan; Willerth, Stephanie M.
Breast cancer often results in the removal of the breast, creating a need for replacement tissue. Tissue engineering offers the promise of generating such replacements by combining cells with biomaterial scaffolds and serves as an attractive potential alternative to current surgical repair methods. Such engineered tissues can also serve as important tools for drug screening and provide in vitro models for analysis. 3D bioprinting serves as an exciting technology with significant implications and applications in the field of tissue engineering. Here we review the work that has been undertaken in hopes of generating the recognized in-demand replacement breast tissue using different types of bioprinting. We then offer suggestions for future work needed to advance this field for both in vitro and in vivo applications.
3D Printing for Medical Applications: Current State of the Art and Perspectives during the COVID-19 Crisis
(Surgeries, 2021) Hagen, Andrew; Chisling, Megan; House, Kevin; Katz, Tal; Abelseth, Laila; Fraser, Ian; Bradley, Stephen; Kirsch, Rebecca; Morris, Jacob; Giles, Joshua W.; Willerth, Stephanie M.
The coronavirus SARS-CoV-2 pandemic has affected over one hundred million people worldwide and has resulted in over two million deaths. In addition to the toll that coronavirus takes on the health of humans infected with the virus and the potential long term effects of infection, the repercussions of the pandemic on the economy as well as on the healthcare system have been enormous. The global supply of equipment necessary for dealing with the pandemic experienced extreme stress as healthcare systems around the world attempted to acquire personal protective equipment for their workers and medical devices for treating COVID-19. This review describes how 3D printing is currently being used in life saving surgeries such as heart and lung surgery and how 3D printing can address some of the worldwide shortage of personal protective equipment, by examining recent trends of the use of 3D printing and how these technologies can be applied during and after the pandemic. We review the use of 3D printed models for treating the long term effects of COVID-19. We then focus on methods for generating face shields and different types of respirators. We conclude with areas for future investigation and application of 3D printing technology.
3D-Printed Tumor-on-a-Chip Model for Investigating the Effect of Matrix Stiffness on Glioblastoma Tumor Invasion
(Biomimetics, 2023) Amereh, Meitham; Seyfoori, Amir; Dallinger, Briana; Azimzadeh, Mostafa; Stefanek, Evan; Akbari, Mohsen
Glioblastoma multiform (GBM) tumor progression has been recognized to be correlated with extracellular matrix (ECM) stiffness. Dynamic variation of tumor ECM is primarily regulated by a family of enzymes which induce remodeling and degradation. In this paper, we investigated the effect of matrix stiffness on the invasion pattern of human glioblastoma tumoroids. A 3D-printed tumor-on-a-chip platform was utilized to culture human glioblastoma tumoroids with the capability of evaluating the effect of stiffness on tumor progression. To induce variations in the stiffness of the collagen matrix, different concentrations of collagenase were added, thereby creating an inhomogeneous collagen concentration. To better understand the mechanisms involved in GBM invasion, an in silico hybrid mathematical model was used to predict the evolution of a tumor in an inhomogeneous environment, providing the ability to study multiple dynamic interacting variables. The model consists of a continuum reaction–diffusion model for the growth of tumoroids and a discrete model to capture the migration of single cells into the surrounding tissue. Results revealed that tumoroids exhibit two distinct patterns of invasion in response to the concentration of collagenase, namely ring-type and finger-type patterns. Moreover, higher concentrations of collagenase resulted in greater invasion lengths, confirming the strong dependency of tumor behavior on the stiffness of the surrounding matrix. The agreement between the experimental results and the model’s predictions demonstrates the advantages of this approach in investigating the impact of various extracellular matrix characteristics on tumor growth and invasion.
A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.)
(BioMed Central, 2011-03-29) Jantzen, Stuart G.; Sanderson, Dan S.; Von Schalburg, Kristian Robert; Yasuike, Motoshige; Marass, Francesco; Koop, Benjamin F.
Background: Atlantic salmon (Salmo salar L.) is an environmentally and economically important organism and its gene content is reasonably well characterized. From a transcriptional standpoint, it is important to characterize the changes in gene expression over the course of unperturbed early development, from fertilization through to the parr stage. Findings: S. salar samples were taken at 17 time points from 2 to 89 days post fertilization. Total RNA was extracted and cRNA was synthesized and hybridized to a newly developed 44K oligo salmonid microarray platform. Quantified results were subjected to preliminary data analysis and submitted to NCBI’s Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE25938. http://www.ncbi.nlm.nih.gov/geo/query/acc. cgi?acc=GSE25938 Conclusions: Throughout the entire period of development, several thousand genes were found to be differentially regulated. This work represents the trancriptional characterization of a very large geneset that will be extremely valuable in further examination of the transcriptional changes in Atlantic salmon during the first few months of development. The expression profiles can help to annotate salmon genes in addition to being used as references against any number of experimental variables to which developing salmonids might be subjected.

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