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In this paper, we analyze and discuss the performance limits of optical clock recovery systems using a phase-locked loop (PLL) structure with nonlinear two-photon absorption (TPA) phase detection scheme. The motivation in analyzing the aforementioned optical PLL with TPA receiver structure is due to a recent successful experiment reported in . We characterize the mathematical structure of PLLs with TPA, so as to evaluate the performance limits on optical clock recovery mechanism. More specifically, we identify two intrinsic sources of phase noise in the system namely, the on- off nature of the incoming data pulses and the detector's shot noise that ultimately limit the performance of the aforementioned optical clock recovery system. In our characterization of the clock recovery system, we obtain the power spectral densities (PSDs) of the signals involved in the PLL and use the PSDs to obtain a mathematical expression for the variance of the timing jitter inherently associated with the recovered clock. We examine the variance of the introduced timing jitter as a function of different system parameters such as power, bit rate, and pulsewidth of the data and clock signals. An interesting result is that the duty cycle factor near 4 in return to zero optical pulses is optimal in the sense that it minimizes the variance of the system phase noise. [ABSTRACT FROM PUBLISHER]

Significance: The skin's mechanical properties are tightly regulated. Various pathologies can affect skin stiffness, and understanding these changes is a focus in tissue engineering. Ex vivo skin scaffolds are a robust platform for evaluating the effects of various genetic and molecular interactions on the skin. Transforming growth factor-beta ( TGF - β ) is a critical signaling molecule in the skin that can regulate the amount of collagen and elastin in the skin and, consequently, its mechanical properties., Aim: This study investigates the biomechanical properties of bio-engineered skin scaffolds, focusing on the influence of TGF - β , a signaling molecule with diverse cellular functions., Approach: The TGF - β receptor I inhibitor, galunisertib, was employed to assess the mechanical changes resulting from dysregulation of TGF - β . Skin scaffold samples, grouped into three categories (control, TGF - β -treated, and TGF - β + galunisertib-treated), were prepared in two distinct culture media-one with aprotinin (AP) and another without. Two optical elastography techniques, namely wave-based optical coherence elastography (OCE) and Brillouin microscopy, were utilized to quantify the biomechanical properties of the tissues., Results: Results showed significantly higher wave speed (with AP, p < 0.001 ; without AP, p < 0.001 ) and Brillouin frequency shift (with AP, p < 0.001 ; without AP, p = 0.01 ) in TGF - β -treated group compared with the control group. The difference in wave speed between the control and TGF - β + galunisertib with ( p = 0.10 ) and without AP ( p = 0.36 ) was not significant. Moreover, the TGF - β + galunisertib-treated group exhibited lower wave speed without and with AP and reduced Brillouin frequency shift than the TGF - β -treated group without AP, further strengthening the potential role of TGF - β in regulating the mechanical properties of the samples., Conclusions: These findings offer valuable insights into TGF - β -induced biomechanical alterations in bio-engineered skin scaffolds, highlighting the potential of OCE and Brillouin microscopy in the development of targeted therapies in conditions involving abnormal tissue remodeling and fibrosis., (© 2024 The Authors.)

There is a critical need for physiologically relevant, robust, and ready-to-use in vitro cellular assay platforms to rapidly model the infectivity of emerging viruses and develop new antiviral treatments. Here we describe the cellular complexity of human alveolar and tracheobronchial air liquid interface (ALI) tissue models during SARS-CoV-2 and influenza A virus (IAV) infections. Our results showed that both SARS-CoV-2 and IAV effectively infect these ALI tissues, with SARS-CoV-2 exhibiting a slower replication peaking at later time-points compared to IAV. We detected tissue-specific chemokine and cytokine storms in response to viral infection, including well-defined biomarkers in severe SARS-CoV-2 and IAV infections such as CXCL10, IL-6, and IL-10. Our single-cell RNA sequencing analysis showed similar findings to that found in vivo for SARS-CoV-2 infection, including dampened IFN response, increased chemokine induction, and inhibition of MHC Class I presentation not observed for IAV infected tissues. Finally, we demonstrate the pharmacological validity of these ALI tissue models as antiviral drug screening assay platforms, with the potential to be easily adapted to include other cell types and increase the throughput to test relevant pathogens., (© 2022. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic, resulting millions of infections and deaths with few effective interventions available. Here, we demonstrate that SARS-CoV-2 evades interferon (IFN) activation in respiratory epithelial cells, resulting in a delayed response in bystander cells. Since pretreatment with IFNs can block viral infection, we reasoned that pharmacological activation of innate immune pathways could control SARS-CoV-2 infection. To identify potent antiviral innate immune agonists, we screened a panel of 75 microbial ligands that activate diverse signaling pathways and identified cyclic dinucleotides (CDNs), canonical STING agonists, as antiviral. Since CDNs have poor bioavailability, we tested the small molecule STING agonist diABZI, and found that it potently inhibits SARS-CoV-2 infection of diverse strains including variants of concern (B.1.351) by transiently stimulating IFN signaling. Importantly, diABZI restricts viral replication in primary human bronchial epithelial cells and in mice in vivo. Our study provides evidence that activation of STING may represent a promising therapeutic strategy to control SARS-CoV-2., (Copyright © 2021, American Association for the Advancement of Science.)

Cells and tissues sense, respond to and translate mechanical forces into biochemical signals through mechanotransduction, which governs individual cell responses that drive gene expression, metabolic pathways and cell motility, and determines how cells work together in tissues. Mechanotransduction often depends on cytoskeletal networks and their attachment sites that physically couple cells to each other and to the extracellular matrix. One way that cells associate with each other is through Ca 2+ -dependent adhesion molecules called cadherins, which mediate cell-cell interactions through adherens junctions, thereby anchoring and organizing the cortical actin cytoskeleton. This actin-based network confers dynamic properties to cell sheets and developing organisms. However, these contractile networks do not work alone but in concert with other cytoarchitectural elements, including a diverse network of intermediate filaments. This Review takes a close look at the intermediate filament network and its associated intercellular junctions, desmosomes. We provide evidence that this system not only ensures tissue integrity, but also cooperates with other networks to create more complex tissues with emerging properties in sensing and responding to increasingly stressful environments. We will also draw attention to how defects in intermediate filament and desmosome networks result in both chronic and acquired diseases., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2020. Published by The Company of Biologists Ltd.)

Extracellular matrix stiffness has a profound effect on the behavior of many cell types. Adherent cells apply contractile forces to the material on which they adhere and sense the resistance of the material to deformation-its stiffness. This is dependent on both the elastic modulus and the thickness of the material, with the corollary that single cells are able to sense underlying stiff materials through soft hydrogel materials at low (<10 μm) thicknesses. Here, we hypothesized that cohesive colonies of cells exert more force and create more hydrogel deformation than single cells, therefore enabling them to mechanosense more deeply into underlying materials than single cells. To test this, we modulated the thickness of soft (1 kPa) elastic extracellular-matrix-functionalized polyacrylamide hydrogels adhered to glass substrates and allowed colonies of MG63 cells to form on their surfaces. Cell morphology and deformations of fluorescent fiducial-marker-labeled hydrogels were quantified by time-lapse fluorescence microscopy imaging. Single-cell spreading increased with respect to decreasing hydrogel thickness, with data fitting to an exponential model with half-maximal response at a thickness of 3.2 μm. By quantifying cell area within colonies of defined area, we similarly found that colony-cell spreading increased with decreasing hydrogel thickness but with a greater half-maximal response at 54 μm. Depth-sensing was dependent on Rho-associated protein kinase-mediated cellular contractility. Surface hydrogel deformations were significantly greater on thick hydrogels compared to thin hydrogels. In addition, deformations extended greater distances from the periphery of colonies on thick hydrogels compared to thin hydrogels. Our data suggest that by acting collectively, cells mechanosense rigid materials beneath elastic hydrogels at greater depths than individual cells. This raises the possibility that the collective action of cells in colonies or sheets may allow cells to sense structures of differing material properties at comparatively large distances., (Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Cell migration is an essential part of many (patho)physiological processes, including keratinocyte re-epithelialization of healing wounds. Physical forces and mechanical cues from the wound bed (in addition to biochemical signals) may also play an important role in the healing process. Previously, we explored this possibility and found that polyacrylamide (PA) gel stiffness affected human keratinocyte behaviour and that mechanical deformations in soft (approx. 1.2 kPa) PA gels produced by neighbouring cells appeared to influence the process of de novo epithelial sheet formation. To clearly demonstrate that keratinocytes do respond to such deformations, we conducted a series of experiments where we observed the response of single keratinocytes to a prescribed local substrate deformation that mimicked a neighbouring cell or evolving multicellular aggregate via a servo-controlled microneedle. We also examined the effect of adding either Y27632 or blebbistatin on cell response. Our results indicate that keratinocytes do sense and respond to mechanical signals comparable to those that originate from substrate deformations imposed by neighbouring cells, a finding that could have important implications for the process of keratinocyte re-epithelialization that takes place during wound healing. Furthermore, the Rho/ROCK pathway and the engagement of NM II are both essential to substrate deformation-directed keratinocyte migration., (© 2018 The Author(s).)

Introduction: Traditionally thought to serve active vs. passive mechanical functions, respectively, a growing body of evidence suggests that actin microfilament and keratin intermediate filament (IF) networks, together with their associated cell-cell and cell-matrix anchoring junctions, may have a large degree of functional interdependence. Therefore, we hypothesized that the loss of keratin IFs in a knockout mouse keratinocyte model would affect the kinematics of colony formation, i.e., the spatiotemporal process by which individual cells join to form colonies and eventually a nascent epithelial sheet., Methods: Time-lapse imaging and deformation tracking microscopy was used to observe colony formation for both wild type (WT) and keratin-deficient knockout (KO) mouse keratinocytes over 24 h. Cells were cultured under high calcium conditions on collagen-coated substrates with nominal stiffnesses of ~ 1.2 kPa (soft) and 24 kPa (stiff). Immunofluorescent staining of actin and selected adhesion proteins was also performed., Results: The absence of keratin IFs markedly affected cell morphology, spread area, and cytoskeleton and adhesion protein organization on both soft and stiff substrates. Strikingly, an absence of keratin IFs also significantly reduced the ability of mouse keratinocytes to mechanically deform the soft substrate. Furthermore, KO cells formed colonies more efficiently on stiff vs. soft substrates, a behavior opposite to that observed for WT keratinocytes., Conclusions: Collectively, these data are strongly supportive of the idea that an interdependence between actin microfilaments and keratin IFs does exist, while further suggesting that keratin IFs may represent an important and under-recognized component of keratinocyte mechanosensation and the force generation apparatus., (© Biomedical Engineering Society 2018.)

The aim of this study was to measure the impact of genetic data in improving the prediction of type 2 diabetes (T2D) in the Malmö Diet and Cancer Study cohort. The current study was performed in 3,426 Swedish individuals and utilizes of a set of genetic and environmental risk data. We first validated our environmental risk model by comparing it to both the Finnish Diabetes Risk Score and the T2D risk model derived from the Framingham Offspring Study. The area under the curve (AUC) for our environmental model was 0.72 [95% CI, 0.69-0.74], which was significantly better than both the Finnish (0.64 [95% CI, 0.61-0.66], p-value < 1 x 10-4) and Framingham (0.69 [95% CI, 0.66-0.71], p-value = 0.0017) risk scores. We then verified that the genetic data has a statistically significant positive correlation with incidence of T2D in the studied population. We also verified that adding genetic data slightly but statistically increased the AUC of a model based only on environmental risk factors (RFs, AUC shift +1.0% from 0.72 to 0.73, p-value = 0.042). To study the dependence of the results on the environmental RFs, we divided the population into two equally sized risk groups based only on their environmental risk and repeated the same analysis within each subpopulation. While there is a statistically significant positive correlation between the genetic data and incidence of T2D in both environmental risk categories, the positive shift in the AUC remains statistically significant only in the category with the lower environmental risk. These results demonstrate that genetic data can be used to increase the accuracy of T2D prediction. Also, the data suggests that genetic data is more valuable in improving T2D prediction in populations with lower environmental risk. This suggests that the impact of genetic data depends on the environmental risk of the studied population and thus genetic association studies should be performed in light of the underlying environmental risk of the population.

Goal: In computational biology, selecting a small subset of informative genes from microarray data continues to be a challenge due to the presence of thousands of genes. This paper aims at quantifying the dependence between gene expression data and the response variables and to identifying a subset of the most informative genes using a fast and scalable multivariate algorithm., Methods: A novel algorithm for feature selection from gene expression data was developed. The algorithm was based on the Hilbert-Schmidt independence criterion (HSIC), and was partly motivated by singular value decomposition (SVD)., Results: The algorithm is computationally fast and scalable to large datasets. Moreover, it can be applied to problems with any type of response variables including, biclass, multiclass, and continuous response variables. The performance of the proposed algorithm in terms of accuracy, stability of the selected genes, speed, and scalability was evaluated using both synthetic and real-world datasets. The simulation results demonstrated that the proposed algorithm effectively and efficiently extracted stable genes with high predictive capability, in particular for datasets with multiclass response variables., Conclusion/significance: The proposed method does not require the whole microarray dataset to be stored in memory, and thus can easily be scaled to large datasets. This capability is an important attribute in big data analytics, where data can be large and massively distributed.

Restoration of epidermal organization and function in response to a variety of pathophysiological insults is critically dependent on coordinated keratinocyte migration, proliferation, and stratification during the process of wound healing. These processes are mediated by the reconfiguration of both cell-cell (desmosomes, adherens junctions) and cell-matrix (focal adhesions, hemidesmosomes) junctions and the cytoskeletal filament networks that they serve to interconnect. In this study, we investigated the role of substrate elasticity (stiffness) on keratinocyte colony formation in vitro during the process of nascent epithelial sheet formation as triggered by the calcium switch model of keratinocyte culture. Keratinocytes cultured on pepsin digested type I collagen coated soft (nominal E = 1.2 kPa) polyacrylamide gels embedded with fluorescent microspheres exhibited (i) smaller spread contact areas, (ii) increased migration velocities, and (iii) increased rates of colony formation with more cells per colony than did keratinocytes cultured on stiff (nominal E = 24 kPa) polyacrylamide gels. As assessed by tracking of embedded microsphere displacements, keratinocytes cultured on soft substrates generated large local substrate deformations that appeared to recruit adjacent keratinocytes into joining an evolving colony. Together with the observed differences in keratinocyte kinematics and substrate deformations, we developed two ad hoc analyses, termed distance rank (DR) and radius of cooperativity (RC), that help to objectively ascribe what we perceive as increasingly cooperative behavior of keratinocytes cultured on soft versus stiff gels during the process of colony formation. We hypothesize that the differences in keratinocyte colony formation observed in our experiments could be due to cell-cell mechanical signaling generated via local substrate deformations that appear to be correlated with the increased expression of β4 integrin within keratinocytes positioned along the periphery of an evolving cell colony.

Background: Radiofrequency (RF) is a new technique to treat facial wrinkles. This study was designed to assess the efficacy of Accent RF in wrinkle reduction of different areas of the face., Materials and Methods: Patients with mild to severe facial wrinkles were treated with Accent using RF energies of 35-145 W. The average energy used in this study was 83.11 W. Patients received four subsequent weekly RF sessions. Wrinkle improvement was rated by two physicians comparing 6-month post treatment photographs with pretreatment photos. Moreover, patient satisfaction was assessed at 1 and 6 months after the last session of the treatment., Results: A total of 45 women participated in this study. In terms of patient satisfaction one month after the last treatment, 8.9% of the patients declared their dissatisfaction, 53.3% were somehow satisfied, 33.3% were satisfied, and 4.4% were very satisfied. At 6 months, patient satisfaction was as follows: 4.4% dissatisfied, 31.1% somehow satisfied, 46.7% satisfied, and 17.8% very satisfied. Patient satisfaction 6 months after the last treatment was significantly higher than 1 month post treatment (P = 0.006). At 6 months, patient satisfaction was not more than 75% in any treatment areas of the face., Conclusion: The results of this study suggest that Accent RF may be considered as a possible effective option for facial skin rejuvenation although its efficacy and safety needs to be evaluated further in randomized controlled trials.

In this manuscript, we use genetic data to provide a three-faceted analysis on the links between molecular subclasses of glioblastoma, epithelial-to-mesenchymal transition (EMT) and CD133 cell surface protein. The contribution of this paper is three-fold: First, we use a newly identified signature for epithelial-to-mesenchymal transition in human mammary epithelial cells, and demonstrate that genes in this signature have significant overlap with genes differentially expressed in all known GBM subtypes. However, the overlap between genes up regulated in the mesenchymal subtype of GBM and in the EMT signature was more significant than other GBM subtypes. Second, we provide evidence that there is a negative correlation between the genetic signature of EMT and that of CD133 cell surface protein, a putative marker for neural stem cells. Third, we study the correlation between GBM molecular subtypes and the genetic signature of CD133 cell surface protein. We demonstrate that the mesenchymal and neural subtypes of GBM have the strongest correlations with the CD133 genetic signature. While the mesenchymal subtype of GBM displays similarity with the signatures of both EMT and CD133, it also exhibits some differences with each of these signatures that are partly due to the fact that the signatures of EMT and CD133 are inversely related to each other. Taken together these data shed light on the role of the mesenchymal transition and neural stem cells, and their mutual interaction, in molecular subtypes of glioblastoma multiforme.