This thesis formulates versions of observability, reconstructibility, controllability, and reachability for stochastic linear and nonlinear systems. The concepts of observability and reconstructibility concern whether the measurements of a system suffice to construct a complete characterization of the system behavior while the concepts of controllability and reachability concern whether the actuation of the system suffices to cause the system to behave according to various user specifications. Thus, these concepts are fundamental to the design of control algorithms. In deterministic linear systems, linear algebraic conditions specify whether an unknown state can be exactly reconstructed from the measurements over a finite time interval, and whether there exists an input sequence over a finite time interval which can steer the state to a desired endpoint; thus, the concepts of observability, reconstructibility, controllability, and reachability are straightforwardly defined. The extension to linear stochastic systems is not obvious. While the deterministic matrix conditions have significance in applications such as Kalman filtering and linear-quadratic -optimal control, the presence of noise generally prevents exact reconstruction of the state via the measurements and exact placement of the state via the control inputs. This ambiguity in interpreting the matrix conditions has lead to a multitude of extensions in the literature. Nonlinear behavior introduces further difficulties; even in nonlinear deterministic systems, the generalization of the linear conditions is not immediate; for instance, whereas observability and reconstructibility does not depend on the control input in linear systems, this separation of control and estimation questions need not hold for nonlinear systems. Our purpose is to make precise the stochastic versions of observability, reconstructibility, controllability, and reachability; in the process, we obtain the expected matrix conditions for stochastic linear systems, which arise both in deterministic linear systems analysis and in Kalman filtering theory and linear -quadratic-optimal-control theory. Perhaps unexpectedly, we also obtain an analogous rank condition for the finite- state hidden Markov model. We show important roles of reconstructibility: in linear systems, it corresponds to minimality of the Kalman filter; in nonlinear systems, it is necessary for performance improvement via output feedback over open-loop control. The role of observability in the stability of optimal filters is discussed. Additionally, we demonstrate a connection between stochastic controllability/reachability and Granger causality and its generalizations from the statistics and econometrics literature. The ideas are explored via simulation of a finite-state hidden Markov model for the network congestion control problem

In mammals, the suprachiasmatic nucleus (SCN) is the central pacemaker organizing circadian rhythms of behavior and physiology. At the cellular level, the mammalian clock consists of autoregulatory feedback loops involving a set of "clock genes," including the Cryptochrome (Cry) genes, Cry1 and Cry2. Experimental evidence suggests that Cry1 and Cry2 play distinct roles in circadian clock function. In mice, Cry1 is required for sustained circadian rhythms in dissociated SCN neurons or fibroblasts but not in organotypic SCN slices or at the behavioral level, whereas Cry2 is not required at any of these levels. It has been argued that coupling among SCN cellular oscillators compensates for clock gene defects to preserve oscillatory function. Here we test this hypothesis in Cry1(-/-) mice by first disrupting intercellular coupling in vivo using constant light (resulting in behavioral arrhythmicity) and then examining circadian clock gene expression in SCN slices at the single cell level. In this manner, we were able to test the role of intercellular coupling without drugs and while preserving tissue organization, avoiding the confounding influences of more invasive manipulations. Cry1(-/-) mice (as well as control Cry2(-/-) mice) bearing the PER2::LUC knock-in reporter were transferred from a standard light:dark cycle to constant bright light (~650 lux) to induce arrhythmic locomotor patterns. In SCN slices from these animals, we used bioluminescence imaging to monitor PER2::LUC expression in single cells. We show that SCN slices from rhythmic Cry1(-/-) and Cry2(-/-) mice had similarly high percentages of functional single-cell oscillators. In contrast, SCN slices from arrhythmic Cry1(-/-) mice had significantly fewer rhythmic cells than SCN slices from arrhythmic Cry2(-/-) mice. Thus, constant light in vivo disrupted intercellular SCN coupling to reveal a cell-autonomous circadian defect in Cry1(-/-) cells that is normally compensated by intercellular coupling in vivo.

Objective

The utilization of video telemedicine has dramatically increased due to the COVID-19 pandemic. However, significant social and technological barriers have led to disparities in access. We aimed to identify factors associated with patient inability to successfully initiate a video visit across a high-volume urologic practice.

Materials and methods

Video visit completion rates and patient characteristics were extracted from the electronic medical record and linked with census-level socioeconomic data. Associations between video visit failure were identified using multivariate regression modeling and random forest ensemble classification modeling.

Results

Six thousand eighty six patients and their first video visits were analyzed. On multivariate logistic regression analysis, Hispanic or Latino patients (OR 0.52, 95%CI 0.31-0.89), patients insured by Medicare (OR 0.46, 95%CI 0.26-0.79) or Medicaid (OR 0.50, 95%CI 0.29-0.87), patients of low socioeconomic status (OR 0.98, 95%CI 0.98-0.99), patients with an un-activated MyChart patient portal (OR 0.43, 95%CI 0.29-0.62), and patients unconfirmed at appointment reminder (OR 0.68, 95%CI 0.48-0.96) were significantly associated with video visit failure. Patients with primary diagnosis category of men's health (OR 47.96, 95%CI 10.24-856.35), and lower urinary tract syndromes (OR 2.69, 95%CI 1.66-4.51) were significantly associated with video visit success. Random forest analyses identified insurance status and socioeconomic status as the top predictors of video visit failure.

Conclusion

An analysis of a urology video telemedicine cohort reveals clinical and demographic disparities in video visit completion and priorities for future interventions to ensure equity of access. Our study further suggests that specific urologic indications may play a role in success or failure of video visits.

Non-steroidal anti-inflammatory drugs are not only potent analgesics and antipyretics but also nephrotoxins, and may cause electrolyte disarray. In addition to the commonly expected effects, including hyperkalemia, hyponatremia, acute renal injury, renal cortical necrosis, and volume retention, glomerular disease with or without nephrotic syndrome or nephritis can occur as well including after years of seemingly safe administration. Minimal change disease, secondary membranous glomerulonephritis, and acute interstitial nephritis are all reported glomerular lesions seen with non-steroidal anti-inflammatory use. We report a patient who used non-steroidal anti-inflammatory drugs for years without diabetes, chronic kidney disease, or proteinuria; he then developed severe nephrotic range proteinuria with 7 g of daily urinary protein excretion. Renal biopsy showed minimal change nephropathy, a likely secondary membranous glomerulonephritis, and acute interstitial nephritis present simultaneously in one biopsy. Cessation of non-steroidal anti-inflammatory drug use along with steroid treatment resulted in a moderate improvement in renal function, though residual impairment remained. Urine heavy metal screen returned with elevated levels of urine copper, but with normal ceruloplasmin level. Workup suggested that the elevated copper levels were due to cirrhosis from non-alcoholic fatty liver disease. The membranous glomerulonephritis is possibly linked to non-steroidal anti-inflammatory drug exposure, and possibly to heavy metal exposure, and is clinically and pathologically much less likely to be a primary membranous glomerulonephritis with negative serological markers.

The mammalian circadian clockwork is composed of a core PER/CRY feedback loop and additional interlocking loops. In particular, the ROR/REV/Bmal1 loop, consisting of ROR activators and REV-ERB repressors that regulate Bmal1 expression, is thought to "stabilize" core clock function. However, due to functional redundancy and pleiotropic effects of gene deletions, the role of the ROR/REV/Bmal1 loop has not been accurately defined. In this study, we examined cell-autonomous circadian oscillations using combined gene knockout and RNA interference and demonstrated that REV-ERBalpha and beta are functionally redundant and are required for rhythmic Bmal1 expression. In contrast, the RORs contribute to Bmal1 amplitude but are dispensable for Bmal1 rhythm. We provide direct in vivo genetic evidence that the REV-ERBs also participate in combinatorial regulation of Cry1 and Rorc expression, leading to their phase-delay relative to Rev-erbalpha. Thus, the REV-ERBs play a more prominent role than the RORs in the basic clock mechanism. The cellular genetic approach permitted testing of the robustness of the intracellular core clock function. We showed that cells deficient in both REV-ERBalpha and beta function, or those expressing constitutive BMAL1, were still able to generate and maintain normal Per2 rhythmicity. Our findings thus underscore the resilience of the intracellular clock mechanism and provide important insights into the transcriptional topologies underlying the circadian clock. Since REV-ERB function and Bmal1 mRNA/protein cycling are not necessary for basic clock function, we propose that the major role of the ROR/REV/Bmal1 loop and its constituents is to control rhythmic transcription of clock output genes.

BACKGROUND: Inflammatory bowel disease (IBD) is a chronic condition that requires close monitoring. Digital health virtual care platforms can enable self-monitoring and allow providers to remotely surveil patients and efficiently identify those with active disease. OBJECTIVES: The primary aim was to design and implement an IBD remote monitoring program, identify predictors of patient engagement, and determine who found the chat to be a valuable tool. METHODS: We developed the IBD Virtual Care Chat, an electronic health record (EHR)-integrated chat to monitor electronic patient reported outcomes (ePROs), medication changes, and disease activity, and subsequently report concerning findings to providers via the EHR. All patients in the IBD practice over age 18 with a clinical encounter in the preceding 12 months were eligible to be enrolled. The primary aim was to identify predictors of patient engagement and determine who found the chat to be a valuable tool. RESULTS: Between May 2021 and March 2022, 2,934 patients were enrolled. A total of 1,160 engaged at least once and 687 (23.4%) continually engaged, submitting at least three ePROs. Disease severity (based on Harvey-Bradshaw Index or Simple Clinical Colitis Activity Index) did not impact ePRO submissions. Patients were significantly more likely to be continually engaged if they self-reported the presence of extraintestinal manifestations (7%, 95% confidence interval: 0.01-0.14; p = 0.04). Patient satisfaction remained moderately high with a median score of 8 (interquartile range: 5-10) on a scale of 1 (poor) to 10 (good). CONCLUSION: Our program demonstrates the potential for EHR-integrated digital health as part of routine IBD care to achieve sustained engagement with high patient satisfaction.

The molecular circadian clock in mammals is generated from transcriptional activation by the bHLH-PAS transcription factor CLOCK-BMAL1 and subsequent repression by PERIOD and CRYPTOCHROME (CRY). The mechanism by which CRYs repress CLOCK-BMAL1 to close the negative feedback loop and generate 24-h timing is not known. Here we show that, in mouse fibroblasts, CRY1 competes for binding with coactivators to the intrinsically unstructured C-terminal transactivation domain (TAD) of BMAL1 to establish a functional switch between activation and repression of CLOCK-BMAL1. TAD mutations that alter affinities for co-regulators affect the balance of repression and activation to consequently change the intrinsic circadian period or eliminate cycling altogether. Our results suggest that CRY1 fulfills its role as an essential circadian repressor by sequestering the TAD from coactivators, and they highlight regulation of the BMAL1 TAD as a critical mechanism for establishing circadian timing.

In animals, circadian rhythms in physiology and behavior result from coherent rhythmic interactions between clocks in the brain and those throughout the body. Despite the many tissue specific clocks, most understanding of the molecular core clock mechanism comes from studies of the suprachiasmatic nuclei (SCN) of the hypothalamus and a few other cell types. Here we report establishment and genetic characterization of three cell-autonomous mouse clock models: 3T3 fibroblasts, 3T3-L1 adipocytes, and MMH-D3 hepatocytes. Each model is genetically tractable and has an integrated luciferase reporter that allows for longitudinal luminescence recording of rhythmic clock gene expression using an inexpensive off-the-shelf microplate reader. To test these cellular models, we generated a library of short hairpin RNAs (shRNAs) against a panel of known clock genes and evaluated their impact on circadian rhythms. Knockdown of Bmal1, Clock, Cry1, and Cry2 each resulted in similar phenotypes in all three models, consistent with previous studies. However, we observed cell type-specific knockdown phenotypes for the Period and Rev-Erb families of clock genes. In particular, Per1 and Per2, which have strong behavioral effects in knockout mice, appear to play different roles in regulating period length and amplitude in these peripheral systems. Per3, which has relatively modest behavioral effects in knockout mice, substantially affects period length in the three cellular models and in dissociated SCN neurons. In summary, this study establishes new cell-autonomous clock models that are of particular relevance to metabolism and suitable for screening for clock modifiers, and reveals previously under-appreciated cell type-specific functions of clock genes.

Carbon dioxide (CO2) must be removed from the atmosphere to mitigate the negative effects of climate change. However, the most scalable methods for removing CO2 from the air require heat from fossil-fuel combustion to produce pure CO2 and continuously regenerate the sorbent. Bipolar-membrane electrodialysis (BPM-ED) is a promising technology that uses renewable electricity to dissociate water into acid and base to regenerate bicarbonate-based CO2 capture solutions, such as those used in chemical loops of direct-air-capture (DAC) processes, and in direct-ocean capture (DOC) to promote atmospheric CO2 drawdown via decarbonization of the shallow ocean. In this study, we develop an experimentally validated 1D model for the electrochemical regeneration of CO2 from bicarbonate-based carbon capture solutions and seawater using BPM-ED. For DAC, our experimental and computational results demonstrate that pH swings induced by BPM water dissociation drive the formation of CO2 at the cation-exchange layer|catholyte interface with energy-intensities of less than 150 kJ mol−1. However, high rates of bubble formation increase energy intensity at current densities >100 mA cm−2. Correspondingly, accelerating water dissociation catalysis and enacting bubble removal could enable CO2 recovery at energy intensities <100 kJ mol−1 and current densities >100 mA cm−2. For DOC, mass transport limitations associated with low carbon concentrations in oceanwater suggest that DOC is best suited for clean production of acid and base usable in downstream processes. These results provide design principles for industrial-scale CO2 recovery using BPM-ED.