Co-expression networks in generation of induced pluripotent stem cells.

We developed an adenoviral vector, in which Yamanaka's four reprogramming factors (RFs) were controlled by individual CMV promoters in a single cassette (Ad-SOcMK). This permitted coordinated expression of RFs (SOX2, OCT3/4, c-MYC and KLF4) in a cell for a transient period of time, synchronizing the reprogramming process with the majority of transduced cells assuming induced pluripotent stem cell (iPSC)-like characteristics as early as three days post-transduction. These reprogrammed cells resembled human embryonic stem cells (ESCs) with regard to morphology, biomarker expression, and could be differentiated into cells of the germ layers in vitro and in vivo. These iPSC-like cells, however, failed to expand into larger iPSC colonies. The short and synchronized reprogramming process allowed us to study global transcription changes within short time intervals. Weighted gene co-expression network analysis (WGCNA) identified sixteen large gene co-expression modules, each including members of gene ontology categories involved in cell differentiation and development. In particular, the brown module contained a significant number of ESC marker genes, whereas the turquoise module contained cell-cycle-related genes that were downregulated in contrast to upregulation in human ESCs. Strong coordinated expression of all four RFs via adenoviral transduction may constrain stochastic processes and lead to silencing of genes important for cellular proliferation

The Enantioselective Construction of Tetracyclic Diterpene Skeletons with Friedel-Crafts Alkylation and Palladium-catalyzed Cycloalkenylation Reactions

Due to the profound extent to which natural products inspire medicinal chemists in drug discovery, there is demand for innovative syntheses of these often complex materials. This article describes the synthesis of tricarbocyclic natural product architectures through an extension of the enantioselective Birch-Cope sequence with intramolecular Friedel-Crafts alkylation reactions. Additionally, palladium-catalyzed enol silane cycloalkenylation of the tricarbocyclic structures afforded the challenging bicyclo[3.2.1]octane C/D ring system found in the gibberellins and the ent-kauranes, two natural products with diverse medicinal value. In the case of the ent-kaurane derivative, an unprecedented alkene rearrangement converted four alkene isomers to one final product

Using Semantic Waves to Analyse the Effectiveness of Unplugged Computing Activities

We apply the notion of ‘semantic waves’ from Legitimation Code Theory (LCT), a powerful educational framework, to Computer Science Education. We consider two case studies exploring how a simple analysis can help improve learning activities. The case studies focus on unplugged activities used in the context of both teaching school students and teacher continuing professional development. We used a simple method based on LCT to analyse the activities in terms of their ‘semantic profiles’: changes in the context-dependence and complexity of the knowledge being taught.This led to improvements to the activities. We argue that ‘semantic waves’, or moves back and forth between concrete/simpler and abstract/complex knowledge, help show ways that an unplugged activity might be effective or not, and how small changes to the activities can make a difference in potentially offering a more fruitful learning experienc

Semantic representation of neural circuit knowledge in Caenorhabditis elegans.

In modern biology, new knowledge is generated quickly, making it challenging for researchers to efficiently acquire and synthesise new information from the large volume of primary publications. To address this problem, computational approaches that generate machine-readable representations of scientific findings in the form of knowledge graphs have been developed. These representations can integrate different types of experimental data from multiple papers and biological knowledge bases in a unifying data model, providing a complementary method to manual review for interacting with published knowledge. The Gene Ontology Consortium (GOC) has created a semantic modelling framework that extends individual functional gene annotations to structured descriptions of causal networks representing biological processes (Gene Ontology-Causal Activity Modelling, or GO-CAM). In this study, we explored whether the GO-CAM framework could represent knowledge of the causal relationships between environmental inputs, neural circuits and behavior in the model nematode C. elegans [C. elegans Neural-Circuit Causal Activity Modelling (CeN-CAM)]. We found that, given extensions to several relevant ontologies, a wide variety of author statements from the literature about the neural circuit basis of egg-laying and carbon dioxide (C

Mixing, scalar boundedness, and numerical dissipation in large-eddy simulations

Numerical schemes for scalar transport and mixing in turbulent flows must be high-order accurate, and observe conservation and boundedness constraints. Discretization accuracy can be evaluated from the truncation error, and assessed by its dispersion and dissipation properties. Dispersion errors can cause violation of physical scalar bounds, whereas numerical dissipation is key to mitigating those violations. Numerical dissipation primarily alters the energy at small scales that are critical to turbulent mixing. Influence of additional dissipation on scalar mixing in large-eddy simulations (LES) of incompressible temporally evolving shear flow is examined in terms of the resolved passive-scalar field, z. Scalar fields in flows with different mixing behavior, exhibiting both uniform and non-uniform mixed-fluid composition across a shear layer, are compared for different grid resolutions, subgrid-scale models, and scalar-convection schemes. Scalar mixing is assessed based on resolved passive scalar probability density function (PDF), variance, and spectra. The numerical-dissipation influence on mixing is found to depend on the nature of the flow. Mixing metrics sensitive to numerical dissipation are applied to examine the performance of limiting methods employed to mitigate unphysical scalar excursions. Two approaches, using a linear-scaling limiter for finite-volume schemes and a monotonicity-preserving limiter for finite-difference schemes, are studied. Their performance with respect to accuracy, conservation, and boundedness is discussed

Going beyond 20 μm-sized channels for studying red blood cell phase separation in microfluidic bifurcations

Despite the development of microfluidics, experimental challenges are considerable for achieving a quantitative study of phase separation, i.e., the non-proportional dis- tribution of Red Blood Cells (RBCs) and suspending fluid, in microfluidic bifurca- tions with channels smaller than 20lm. Yet, a basic understanding of phase separation in such small vessels is needed for understanding the coupling between microvascular network architecture and dynamics at larger scale. Here, we present the experimental methodologies and measurement techniques developed for that pur- pose for RBC concentrations (tube hematocrits) ranging between 2% and 20%. The maximal RBC velocity profile is directly measured by a temporal cross-correlation technique which enables to capture the RBC slip velocity at walls with high resolu- tion, highlighting two different regimes (flat and more blunted ones) as a function of RBC confinement. The tube hematocrit is independently measured by a photometric technique. The RBC and suspending fluid flow rates are then deduced assuming the velocity profile of a Newtonian fluid with no slip at walls for the latter. The accuracy of this combination of techniques is demonstrated by comparison with reference measurements and verification of RBC and suspending fluid mass conservation at individual bifurcations. The present methodologies are much more accurate, with less than 15% relative errors, than the ones used in previous in vivo experiments. Their potential for studying steady state phase separation is demonstrated, highlight- ing an unexpected decrease of phase separation with increasing hematocrit in symmetrical, but not asymmetrical, bifurcations and providing new reference data in regimes where in vitro results were previously lacking. Published by AIP Publishin

Results of an Indo-Swiss programme for qualification and testing of a 300-kW IISc-Dasag gasifier

The paper describes the performance and operational experience in India on a high efficiency, low tar, woody biomass gasifier developed at Indian Institute of Science, Bangalore. This development is also of interest to Switzerland, which has a substantial potential of biomass energy. The test scheme included measurements on tar and particulates and the effluents along with necessary measurements for the mass and energy balance. The results indicate a low tar level to meet the engine specifications and the effluents issuing out of the system could be treated using simpler techniques, as the levels are low

Model-based autonomous system for performing dexterous, human-level manipulation tasks

This article presents a model based approach to autonomous dexterous manipulation, developed as part of the DARPA Autonomous Robotic Manipulation Software (ARM-S) program. Performing human-level manipulation tasks is achieved through a novel combination of perception in uncertain environments, precise tool use, forceful dual-arm planning and control, persistent environmental tracking, and task level verification. Deliberate interaction with the environment is incorporated into planning and control strategies, which, when coupled with world estimation, allows for refinement of models and precise manipulation. The system takes advantage of sensory feedback immediately with little open-loop execution, attempting true autonomous reasoning and multi-step sequencing that adapts in the face of changing and uncertain environments. A tire change scenario utilizing human tools, discussed throughout the article, is used to described the system approach. A second scenario of cutting a wire is also presented, and is used to illustrate system component reuse and generality.United States. Defense Advanced Research Projects Agency. Autonomous Robotic Manipulation Progra

Identification of bradycardia following remdesivir administration through the US Food and Drug Administration American College of Medical Toxicology COVID-19 Toxic Pharmacovigilance Project

IMPORTANCE: The rapid spread and mortality associated with COVID-19 emphasized a need for surveillance system development to identify adverse events (AEs) to emerging therapeutics. Bradycardia is a remdesivir infusion-associated AE listed in the US Food and Drug Administration-approved prescribing information. OBJECTIVE: To evaluate the magnitude and duration of bradycardic events following remdesivir administration. DESIGN, SETTING, AND PARTICIPANTS: A multicenter cohort study of patients with recorded heart rate less than 60 beats per minute within 24 hours after administration of a remdesivir dose was conducted between November 23, 2020, and October 31, 2021. Participants included patients hospitalized with COVID-19 at 15 medical centers across the US. Patients excluded had AEs unrelated to bradycardia, AEs in addition to bradycardia, or first onset of bradycardia after 5 remdesivir doses. EXPOSURES: Remdesivir administration. MAIN OUTCOMES AND MEASURES: Linear mixed-effect models for the minimum HR before starting remdesivir and within 24 hours of each dose included doses as fixed effects. Baseline covariates were age (≥65 years vs \u3c65 years), sex (male vs female), cardiovascular disease history (yes vs no), and concomitant use of bradycardia-associated medications. The interactions between variables and doses were considered fixed-effects covariates to adjust models. RESULTS: A total of 188 patients were included in the primary analysis and 181 in the secondary analysis. The cohort included 108 men (57.4%); 75 individuals (39.9%) were non-Hispanic White and mean (SD) age was 61.3 (15.4) years. Minimum HR after doses 1 to 5 was lower than before remdesivir. Mean minimum HR was lowest after dose 4, decreasing by -15.2 beats per minute (95% CI, -17.4 to -13.1; P \u3c .001) compared with before remdesivir administration. Mean (SD) minimum HR was 55.6 (10.2) beats per minute across all 5 doses. Of 181 patients included in time-to-event analysis, 91 had their first episode of bradycardia within 23.4 hours (95% CI, 20.1-31.5 hours) and 91 had their lowest HR within 60.7 hours (95% CI, 54.0-68.3 hours). Median time to first bradycardia after starting remdesivir was shorter for patients aged 65 years or older vs those younger than 65 years (18.7 hours; 95% CI, 16.8-23.7 hours vs 31.5 hours; 95% CI, 22.7-39.3 hours; P = .04). Median time to lowest HR was shorter for men vs women (54.2 hours; 95% CI, 47.3-62.0 hours vs 71.0 hours; 95% CI, 59.5-79.6 hours; P = .02). CONCLUSIONS AND RELEVANCE: In this cohort study, bradycardia occurred during remdesivir infusion and persisted. Given the widespread use of remdesivir, practitioners should be aware of this safety signal