Programming Juxtacrine-Based Synthetic Signaling Networks in a Cellular Potts Framework.

Synthetic development is a synthetic biology subfield aiming to reprogram higher-order eukaryotic cells for tissue formation and morphogenesis. Reprogramming efforts commonly rely upon implementing custom signaling networks into these cells, but the efficient design of these signaling networks is a substantial challenge. It is difficult to predict the tissue/morphogenic outcome of these networks, and in vitro testing of many networks is both costly and time-consuming. We therefore developed a computational framework with an in silico cell line (ISCL) that sports basic but modifiable features such as adhesion, motility, growth, and division. More importantly, ISCL can be quickly engineered with custom genetic circuits to test, improve, and explore different signaling network designs. We implemented this framework in a free cellular Potts modeling software CompuCell3D. In this chapter, we briefly discuss how to start with CompuCell3D and then go through the steps of how to make and modify ISCL. We then go through the steps of programming custom genetic circuits into ISCL to generate an example signaling network.

Design and mathematical analysis of activating transcriptional amplifiers that enable modular temporal control in synthetic juxtacrine circuits.

The ability to control mammalian cells such that they self-organize or enact therapeutic effects as desired has incredible implications. Not only would it further our understanding of native processes such as development and the immune response, but it would also have powerful applications in medical fields such as regenerative medicine and immunotherapy. This control is typically obtained by synthetic circuits that use synthetic receptors, but control remains incomplete. The synthetic juxtacrine receptors (SJRs) are widely used as they are fully modular and enable spatial control, but they have limited gene expression amplification and temporal control. As these are integral facets to cell control, I therefore designed transcription factor based amplifiers that amplify gene expression and enable unidirectional temporal control by prolonging duration of target gene expression. Using a validated in silico framework for SJR signaling, I combined these amplifiers with SJRs and show that these SJR amplifier circuits can direct spatiotemporal patterning and improve the quality of self-organization. I then show that these circuits can improve chimeric antigen receptor (CAR) T cell tumor killing against various heterogenous antigen expression tumors. These amplifiers are flexible tools that improve control over SJR based circuits with both basic and therapeutic applications.

Impact of a moulded pureed diet on taste, appearance, recognisability, and overall liking among patients in an acute hospital.

Introduction: Hospital meals potentially influence patients' nutritional, physical, and emotional well-being during their admission. Patients on pureed diets report poorer meal satisfaction, due to taste, appearance, and recognisability, potentially impacting on their nutritional status. This study compared whether a moulded pureed diet made from modified maize starch led to improved taste, appearance, recognisability, and overall liking, compared to an unmoulded pureed diet made from potato starch in an acute hospital. Methods: Patients on texture-modified diets were recruited and presented with two pureed diets - unmoulded and moulded. Participants were asked to identify meat and vegetable dishes prior to eating. After the meal, participants indicated their diet preference in terms of appearance, taste, and overall liking. Results: 145 participants were recruited, of which 126 completed data collection. 86% correctly identified moulded meat dishes, 69% correctly identified moulded vegetable dishes, with an overall 77% accuracy in identifying moulded puree side dishes. On unmoulded puree side dishes, participants correctly identified 25% of meat dishes, 4% of vegetable dishes, with an overall accuracy of 14%. In terms of preference, the moulded puree was preferred, with 81% for appearance, 76% for taste and 75% for overall preference. When participants had differing preferences for appearance and taste (e.g., prefers unmoulded puree appearance and moulded puree taste), 95% of them subsequently aligned their overall preference with their taste preference (i.e., overall preferred moulded pureed diet). This suggests that taste has a stronger influence on overall preference compared to appearance. Discussion: Findings indicate that a moulded pureed diet made from modified maize starch led to improved recognisability, taste, appearance, and overall liking compared to an unmoulded pureed diet made from potato starch. Taste had a stronger influence on overall preference compared to appearance. These findings capture patient preferences and may have implications on how hospital pureed diets may be improved, potentially improving patient nutrition and health outcomes.

Synthetic Immunotherapy: Programming Immune Cells with Novel and Sophisticated Logic Capabilities.

The development of chimeric antigen receptor (CAR) T cells began as a means toward specific yet modular therapies against cancer. Recent advancements in several CAR T cell therapies show the promise of cellular immunotherapy in cancer treatment. CAR T cell therapy is still immature, however, and improvements are needed to fully realize its curative potential. The approved CAR T cells are designed with simple logic capabilities; an antigen sensor that, when bound to the target antigen, triggers costimulation domains and native T cell activation. This single-type sensor and native activation design, although capable, also has severe limitations. Reliance on a single-type sensor leads to unwanted toxicity toward antigen-expressing normal tissues, and unmodulated activation leads to unwanted cytokine toxicity. Synthetic biology (SB) offers a powerful solution to these limitations: modular receptors with customizable sensors and output behaviors that enable higher Boolean logic. SB T cells already have shown incredible capabilities, such as multiple-antigen discrimination and improved persistence. In light of these results, cellular immunotherapy may already be branching into a new subfield that we term here as "synthetic immunotherapy." Here we review the current logic capabilities of CAR T cells, the resulting limitations, and the engineering undertaken to address these issues. We then discuss several tools of SB and show how SB CAR T cells pave the way for synthetic immunotherapy.

Parameterized Computational Framework for the Description and Design of Genetic Circuits of Morphogenesis Based on Contact-Dependent Signaling and Changes in Cell-Cell Adhesion.

Synthetic development is a nascent field of research that uses the tools of synthetic biology to design genetic programs directing cellular patterning and morphogenesis in higher eukaryotic cells, such as mammalian cells. One specific example of such synthetic genetic programs was based on cell-cell contact-dependent signaling using synthetic Notch pathways and was shown to drive the formation of multilayered spheroids by modulating cell-cell adhesion via differential expression of cadherin family proteins in a mouse fibroblast cell line (L929). The design method for these genetic programs relied on trial and error, which limited the number of possible circuits and parameter ranges that could be explored. Here, we build a parameterized computational framework that, given a cell-cell communication network driving changes in cell adhesion and initial conditions as inputs, predicts developmental trajectories. We first built a general computational framework where contact-dependent cell-cell signaling networks and changes in cell-cell adhesion could be designed in a modular fashion. We then used a set of available in vitro results (that we call the "training set" in analogy to similar pipelines in the machine learning field) to parameterize the computational model with values for adhesion and signaling. We then show that this parameterized model can qualitatively predict experimental results from a "testing set" of available in vitro data that varied the genetic network in terms of adhesion combinations, initial number of cells, and even changes to the network architecture. Finally, this parameterized model is used to recommend novel network implementation for the formation of a four-layered structure that has not been reported previously. The framework that we develop here could function as a testing ground to identify the reachable space of morphologies that can be obtained by controlling contact-dependent cell-cell communications and adhesion with these molecular tools and in this cellular system. Additionally, we discuss how the model could be expanded to include other forms of communication or effectors for the computational design of the next generation of synthetic developmental trajectories.

Dose-response effects of light therapy on sleepiness and circadian phase shift in shift workers: a meta-analysis and moderator analysis.

Light therapy has been considered to be effective in mitigating sleepiness and regulating circadian phase shift in shift workers. However, the effective treatment dose of light therapy remains undetermined. We performed a meta-analysis of randomized experimental studies to determine the effect of light therapy doses on sleepiness and circadian phase shift in shift workers. An article search was performed in 10 electronic databases from inception to June 2020. Two raters independently screened and extracted data and reached consensus. Twenty-one eligible studies were included. Analyses were performed using random-effects models. Light therapy exerted significantly small to medium effects on sleepiness and large treatment effects on circadian phase shift. Moderator analyses performed with subgroup and metaregression analyses revealed that medium-intensity light therapy for a shorter duration more effectively reduced sleepiness at night, whereas higher-intensity light therapy more effectively induced phase shifting, but the required treatment duration remained inconclusive. This study provides evidence regarding the effect of light therapy in reducing sleepiness and shifting circadian phase in shift workers. Exposure to medium-intensity light for a short duration at night reduced sleepiness, whereas exposure to high-intensity light improved sleep by shifting their circadian phase.

Time-dependent association between mass protests and psychological distress on social media: A text mining study during the 2019 anti-government social unrest in Hong Kong.

BACKGROUND & AIMS: Social media are increasingly pivotal as the platform where activists and observers plan, promote, and respond to collective actions. To examine how mass protests influence psychological wellbeing and distress, this study analyzed their time-dependent association during the 2019 anti-government social unrest in Hong Kong. METHODS: Consecutive day-by-day users-generated content on online forums and social network sites (SNS) from June to November 2019 was obtained. A Cantonese term-list was created to identify terms related to mass protests and psychological distress. The frequency of comments containing such terms was analyzed using time series models. RESULTS: There were 3,572,665 social media comments in the investigation period. As hypothesized, the frequency of comments with mass protest terms was higher on days with mass protests than on days without. Frequency of comments with both mass protest- and psychological distress-terms was also higher on days with protests than days without. Time-lagged effect (responses on the following day) of protest-terms was found on online forums but not on SNS. Our results suggest a positive association between offline protest activities and online psychological reactions. CONCLUSIONS: Social media content reveals discussions of psychological distress stemming from, or exacerbated by, social unrest. The potential mutual influences between mass protests and online reactions, as well as the functional differences between online forums and SNS in this regard are discussed. Street protests and their associated psychological distress can be readily detected on popular online forums. Mental health services should consider, and even make use of, such dynamic relationship between on- and offline activities.

Performing Awake Surgeries in Times of COVID-19 - A Singapore Experience.

INTRODUCTION: It has been 17 years since the severe acute respiratory syndrome outbreak and Singapore is facing yet another daunting pandemic - the novel coronavirus (COVID-19). To date, there are 57,607 cases and 27 casualties. This deadly pandemic requires significant changes especially in the field of awake surgeries for intra-axial tumors that routinely involve long clinic consults, significant interactions between patient and multiple other team members pre, intra, and postoperatively. MATERIALS AND METHODS: A retrospective review of all awake cases done during the COVID-19 pandemic from February to June 2020 was done. In this article, we outline the rigorous measures adopted during the COVID-19 pandemic that has allowed us to proceed with awake surgeries and intraoperative mapping at our institution. RESULTS AND DISCUSSION: We have divided the protocol into various phases of care of patients planned for an awake craniotomy. Preoperatively, teleconsults have been used where possible thereby limiting multiple hospital visits and interaction. Intraoperatively, safety nets have been established during asleep-awake-asleep phases of awake craniotomy for all the team members. Postoperatively, early discharge and teleconsult are being employed for rehabilitation and follow-ups. CONCLUSIONS: Multiple studies have shown that with intraoperative mapping, we can improve neurological outcomes. As the future of the pandemic remains unknown, the authors believe that surgical treatment should not be delayed for intracranial tumors. Awake craniotomies and intraoperative mapping can be safely carried out by adopting the described protocols with combination of multiple checkpoints and usage of telecommunication.

Epidemiology, Mechanical Power, and 3-Year Outcomes in Acute Respiratory Distress Syndrome Patients Using Standardized Screening. An Observational Cohort Study.

Rationale: Limited data on the epidemiology of acute respiratory distress syndrome (ARDS) using a standardized screening program exist.Objectives: To describe the population-based incidence of hypoxemic respiratory failure and ARDS using a prospective standardized screening protocol; and to describe the mechanical ventilation practice and the mechanical power and examine their association with 28-day and 3-year survival outcomes.Methods: A prospective standardized screening program for ARDS, as a quality improvement initiative, was initiated at four adult intensive care units over a 27-month period. An ancillary analysis of this observational cohort was performed. Patients requiring mechanical ventilation for ≥24 hours underwent prospective and consecutive screening using standardized ventilator settings. Patient physiological data and outcomes were collected prospectively through an electronic clinical-information system and retrospectively analyzed to apply Berlin criteria.Results: Screened were 7,944 patients, among which 986 (12.4%) had hypoxemic respiratory failure (arterial oxygen tension to inspired fraction of oxygen ratio ≤300), and 731 (9.2%) met criteria for ARDS. Age-adjusted incidence of hypoxemic respiratory failure and ARDS were 37.7 and 27.6 cases per 100,000 person-years, respectively. Patients sustaining the diagnosis of ARDS had a hospital mortality of 26.5% for mild, 31.8% for moderate, and 60.0% for severe ARDS and a 3-year mortality of 43.5% for mild, 46.9% for moderate, and 71.1% for severe ARDS. Mechanical power >22 J/min was associated with increased 28-day hospital and 3-year mortality. Determinants of mechanical power associated with lower 28-day hospital and 3-year survival included plateau pressure >30 cm H2O and driving pressure >15 cm H2O, but not tidal volumes >8 ml/kg of predicted body weight.Conclusions: Using standardized screening, a large proportion of patients with hypoxemic respiratory failure met criteria for ARDS. Increasing ARDS severity was associated with increased 28-day hospital and 3-year mortality. Increased mechanical power was associated with increased mortality. Potentially modifiable determinants of mechanical power associated with lower survival included plateau pressure and driving pressure.

Synthetic development: building mammalian multicellular structures with artificial genetic programs.

Synthetic biology efforts began in simple single-cell systems, which were relatively easy to manipulate genetically (Cameron et al., 2014). The field grew exponentially in the last two decades, and one of the latest frontiers are synthetic developmental programs for multicellular mammalian systems (Black et al., 2017; Wieland and Fussenegger, 2012) to genetically control features such as patterning or morphogenesis. These programs rely on engineered cell-cell communications, multicellular gene regulatory networks and effector genes. Here, we contextualize the first of these synthetic developmental programs, examine molecular and computational tools that can be used to generate next generation versions, and present the general logic that underpins these approaches. These advances are exciting as they represent a novel way to address both control and understanding in the field of developmental biology and tissue development (Elowitz and Lim, 2010; Velazquez et al., 2018; White et al., 2018; Morsut, 2017). This field is just at the beginning, and it promises to be of major interest in the upcoming years of biomedical research.

Influence of new hire transition workload on insomnia in nurses.

AIMS: In this study, we investigated the relationship of the prevalence and incidence of insomnia with the new hire transition workload in nurses. METHODS: This retrospective study used the clinical diagnosis data of the entire nursing population in Taiwan for 2005 to 2008, drawn from the National Health Insurance Research Database. Adjusted logistic regression and Cox regression models were used to separately analyse factors related to the prevalence and incidence of insomnia. RESULTS: During this period, the prevalence of insomnia increased, whereas its incidence remained stable. After adjustment for demographic variables in the logistic regression models, the higher prevalence of insomnia was associated with a longer employment duration and a higher new hire ratio. In the Cox regression models, a higher incidence of insomnia was associated with a shorter employment duration and a higher new hire ratio. Nurses with a longer employment duration had a higher prevalence, but lower incidence, of insomnia. A higher new hire ratio was associated with a higher prevalence and incidence of insomnia. CONCLUSION: To mitigate the risk of insomnia, we suggest that additional support should be provided to non-new nurses to assist them in the new hire transition.

Dancing attraction: followers of honey bee tremble and waggle dances exhibit similar behaviors.

The function of the honey bee tremble dance and how it attracts signal receivers is poorly understood. We tested the hypothesis that tremble followers and waggle followers exhibit the same dance-following behavior. If correct, this could unify our understanding of dance following, provide insight into dance information transfer, and offer a way to identify the signal receivers of tremble dance information. Followers showed similar initial attraction to and tracking of dancers. However, waggle dancers were faster than tremble dancers, and follower-forward, -sideways, and -angular velocities were generally similar to the velocities of their respective dancers. Waggle dancers attracted followers from 1.3-fold greater distances away than tremble dancers. Both follower types were attracted to the lateral sides of dancers, but tremble followers were more attracted to the dancer's head, and waggle followers were more attracted to the dancer's abdomen. Tremble dancers engaged in 4-fold more brief food exchanges with their followers than waggle dancers. The behaviors of both follower types are therefore relatively conserved. Researchers can now take the next steps, observing tremble followers to determine their subsequent behaviors and testing the broader question of whether follower attraction and tracking is conserved in a wide range of social insects.

Seasonal variations in sleep disorders of nurses.

AIMS AND OBJECTIVES: To investigate the difference between nurses and the general population regarding seasonal variations in sleep disorders during 2004-2008. The effects of season and group interaction on sleep disorders with regard to different comorbidities were also examined. BACKGROUND: Studies on seasonal variations in sleep disorders were mainly conducted in Norway for the general population. Furthermore, whether different comorbidities cause seasonal variations in sleep disorders in nurses remains unknown. DESIGN: A retrospective study. METHODS: Data from the Taiwan National Health Insurance Research Database were used in generalised estimating equation Poisson distribution models to investigate the differences in sleep disorders between nurses and the general population diagnosed with sleep disorders (each n = 7643) as well as the interaction effects of sleep disorders between the groups with respect to different seasons. Furthermore, the interaction effects between groups and seasons on sleep disorders in the subgroups of comorbid anxiety disorders and depressive disorders were studied. RESULTS: Both the nurses and the general population had fewer outpatient visits for sleep disorders in winter than in other seasons. The nurses had fewer outpatient visits for sleep disorders than the general population did in each season. The nurses had more outpatient visits for sleep disorders in winter than in summer compared with the general population in the comorbid depressive disorder subgroup but not in the comorbid anxiety disorder subgroup. CONCLUSIONS: Nurses and the general population exhibited similar seasonal patterns of sleep disorders, but nurses had fewer outpatient visits for sleep disorders than the general population did in each season. For nurses with comorbid depressive disorders, outpatient visits for sleep disorders were more numerous in winter than in summer, potentially because nurses with comorbid depressive disorders are affected by shorter daylight exposure during winter. RELEVANCE TO CLINICAL PRACTICE: Depression and daylight exposure may be considered in mitigating sleep disorders in nurses.

Text Mining of Journal Articles for Sleep Disorder Terminologies.

OBJECTIVE: Research on publication trends in journal articles on sleep disorders (SDs) and the associated methodologies by using text mining has been limited. The present study involved text mining for terms to determine the publication trends in sleep-related journal articles published during 2000-2013 and to identify associations between SD and methodology terms as well as conducting statistical analyses of the text mining findings. METHODS: SD and methodology terms were extracted from 3,720 sleep-related journal articles in the PubMed database by using MetaMap. The extracted data set was analyzed using hierarchical cluster analyses and adjusted logistic regression models to investigate publication trends and associations between SD and methodology terms. RESULTS: MetaMap had a text mining precision, recall, and false positive rate of 0.70, 0.77, and 11.51%, respectively. The most common SD term was breathing-related sleep disorder, whereas narcolepsy was the least common. Cluster analyses showed similar methodology clusters for each SD term, except narcolepsy. The logistic regression models showed an increasing prevalence of insomnia, parasomnia, and other sleep disorders but a decreasing prevalence of breathing-related sleep disorder during 2000-2013. Different SD terms were positively associated with different methodology terms regarding research design terms, measure terms, and analysis terms. CONCLUSION: Insomnia-, parasomnia-, and other sleep disorder-related articles showed an increasing publication trend, whereas those related to breathing-related sleep disorder showed a decreasing trend. Furthermore, experimental studies more commonly focused on hypersomnia and other SDs and less commonly on insomnia, breathing-related sleep disorder, narcolepsy, and parasomnia. Thus, text mining may facilitate the exploration of the publication trends in SDs and the associated methodologies.