Optimal renormalization of multiscale systems.

While model order reduction is a promising approach in dealing with multiscale time-dependent systems that are too large or too expensive to simulate for long times, the resulting reduced order models can suffer from instabilities. We have recently developed a time-dependent renormalization approach to stabilize such reduced models. In the current work, we extend this framework by introducing a parameter that controls the time decay of the memory of such models and optimally select this parameter based on limited fully resolved simulations. First, we demonstrate our framework on the inviscid Burgers equation whose solution develops a finite-time singularity. Our renormalized reduced order models are stable and accurate for long times while using for their calibration only data from a full order simulation before the occurrence of the singularity. Furthermore, we apply this framework to the three-dimensional (3D) Euler equations of incompressible fluid flow, where the problem of finite-time singularity formation is still open and where brute force simulation is only feasible for short times. Our approach allows us to obtain a perturbatively renormalizable model which is stable for long times and includes all the complex effects present in the 3D Euler dynamics. We find that, in each application, the renormalization coefficients display algebraic decay with increasing resolution and that the parameter which controls the time decay of the memory is problem-dependent.

CsrA-Controlled Proteins Reveal New Dimensions of Acinetobacter baumannii Desiccation Tolerance.

Hospital environments are excellent reservoirs for the opportunistic pathogen Acinetobacter baumannii in part because it is exceptionally tolerant to desiccation. We found that relative to other A. baumannii strains, the virulent strain AB5075 was strikingly desiccation resistant at 2% relative humidity (RH), suggesting that it is a good model for studies of the functional basis of this trait. Consistent with results from other A. baumannii strains at 40% RH, we found the global posttranscriptional regulator CsrA to be critically important for desiccation tolerance of AB5075 at 2% RH. Proteomics experiments identified proteins that were differentially present in wild-type and csrA mutant cells. Subsequent analysis of mutants in genes encoding some of these proteins revealed six genes that were required for wild-type levels of desiccation tolerance. These include genes for catalase, a universal stress protein, a hypothetical protein, and a biofilm-associated protein. Two genes of unknown function had very strong desiccation phenotypes, with one of the two genes predicting an intrinsically disordered protein (IDP) that binds to DNA. Intrinsically disordered proteins are widespread in eukaryotes but less so in prokaryotes. Our results suggest there are new mechanisms underlying desiccation tolerance in bacteria and identify several key functions involved. IMPORTANCE Acinetobacter baumannii is found in terrestrial environments but can cause nosocomial infections in very sick patients. A factor that contributes to the prevalence of A. baumannii in hospital settings is that it is intrinsically resistant to dry conditions. Here, we established the virulent strain A. baumannii AB5075 as a model for studies of desiccation tolerance at very low relative humidity. Our results show that this trait depends on two proteins of unknown function, one of which is predicted to be an intrinsically disordered protein. This category of protein is critical for the small animals named tardigrades to survive desiccation. Our results suggest that A. baumannii may have novel strategies to survive desiccation that have not previously been seen in bacteria.

Loneliness in the Daily Lives of People With Mood and Psychotic Disorders.

BACKGROUND AND HYPOTHESIS: Loneliness, the subjective experience of feeling alone, is associated with physical and psychological impairments. While there is an extensive literature linking loneliness to psychopathology, limited work has examined loneliness in daily life in those with serious mental illness. We hypothesized that trait and momentary loneliness would be transdiagnostic and relate to symptoms and measures of daily functioning. STUDY DESIGN: The current study utilized ecological momentary assessment and passive sensing to examine loneliness in those with schizophrenia (N = 59), bipolar disorder (N = 61), unipolar depression (N = 60), remitted unipolar depression (N = 51), and nonclinical comparisons (N = 82) to examine relationships of both trait and momentary loneliness to symptoms and social functioning in daily life. STUDY RESULTS: Findings suggest that both trait and momentary loneliness are higher in those with psychopathology (F(4,284) = 28.00, P < .001, ηp2 = 0.27), and that loneliness significantly relates to social functioning beyond negative symptoms and depression (ß = -0.44, t = 6.40, P < .001). Furthermore, passive sensing measures showed that greater movement (ß = -0.56, t = -3.29, P = .02) and phone calls (ß = -0.22, t = 12.79, P = .04), but not text messaging, were specifically related to decreased loneliness in daily life. Individuals higher in trait loneliness show stronger relationships between momentary loneliness and social context and emotions in everyday life. CONCLUSIONS: These findings provide further evidence pointing to the importance of loneliness transdiagnostically and its strong relation to social functioning. Furthermore, we show that passive sensing technology can be used to measure behaviors related to loneliness in daily life that may point to potential treatment implications or early detection markers of loneliness.

Application of aerobic kenaf granules for biological nutrient removal in a full-scale continuous flow activated sludge system.

Aerobic granular sludge (AGS) is a biofilm technology that offers more treatment capacity in comparison to activated sludge. The integration of AGS into existing continuous-flow activated sludge systems is of great interest as process intensification can be achieved without the use of plastic-based biofilm carriers. Such integration should allow good separation of granules/flocs and ideally with minor retrofitting, making it an ongoing challenge. This study utilized an all-organic media carrier made of porous kenaf plant stalks with high surface areas to facilitate biofilm attachment and granule development. A 5-stage Bardenpho plant was upgraded with the addition of kenaf media and a rotary drum screen to retain the larger particles from the secondary clarifier underflow whereas flocs were selectively wasted. Startup took 5 months with a sludge volume index (SVI) reduction from >200 to 50 mL g-1. Most of the kenaf granules fell in the size range of 600-1400 µm and had a clear biofilm layer. The wet biomass density, SVI30, and SVI30/SVI5 of the kenaf granules were 1035 g L-1, 30.6 mL g-1, and 1.0, respectively, which met the standards of aerobic granules. Improved stability of biological phosphorus removal performance enabled a 25% reduction in sodium aluminate usage. Microbial activities of kenaf granules were compared with aerobic granules, showing comparable N and P removal rates and presence of ammonium-oxidizing bacteria and polyphosphate-accumulating organisms in the outer 50-60 µm layer of the granule. This work is the first viable example for integrating fully organic biofilm particles in existing continuous-flow systems.

Remarkable diversity in the enzymes catalyzing the last step in synthesis of the pimelate moiety of biotin.

Biotin synthesis in Escherichia coli requires the functions of the bioH and bioC genes to synthesize the precursor pimelate moiety by use of a modified fatty acid biosynthesis pathway. However, it was previously noted that bioH has been replaced with bioG or bioK within the biotin synthetic gene clusters of other bacteria. We report that each of four BioG proteins from diverse bacteria and two cyanobacterial BioK proteins functionally replace E. coli BioH in vivo. Moreover, purified BioG proteins have esterase activity against pimeloyl-ACP methyl ester, the physiological substrate of BioH. Two of the BioG proteins block biotin synthesis when highly expressed and these toxic proteins were shown to have more promiscuous substrate specificities than the non-toxic BioG proteins. A postulated BioG-BioC fusion protein was shown to functionally replace both the BioH and BioC functions of E. coli. Although the BioH, BioG and BioK esterases catalyze a common reaction, the proteins are evolutionarily distinct.