Adjoint error estimation and spatial adaptivity for EHL-like models

The use of adjoint error estimation techniques is described for a model problem that is a simplified version of an EHL line contact. Quantities of interest, such as friction, may be dependent upon the accuracy of the Solution in some parts of the domain more than in others. The use of an inexpensive extra solve to calculate an adjoint solution is described for estimating the intergrid error in the value of friction calculated, and as a basis for local refinement. It is demonstrated that this enables an accurate estimate for the quantity of interest to be obtained from a less accurate solution of the model problem

The microbiome in wound repair and tissue fibrosis

Bacterial colonization occurs in all wounds, chronic or acute, and the break in epithelium integrity that defines a wound impairs the forces that shape and constrain the microbiome at that site. This review highlights the interactions between bacterial communities in the wound and the ultimate resolution of the wound or development of fibrotic lesions. Chronic wounds support complex microbial communities comprising a wide variety of bacterial phyla, genera, and species, including some fastidious anaerobic bacteria not identified using culture‐based methods. Thus, the complexity of bacterial communities in wounds has historically been underestimated. There are a number of intriguing possibilities to explain these results that may also provide novel insights into changes and adaptation of bacterial metabolic networks in inflamed and wounded mucosa, including the critical role of biofilm formation. It is well accepted that the heightened state of activation of host cells in a wound that is driven by the microbiota can certainly lead to detrimental effects on wound regeneration, but the microbiota of the wound may also have beneficial effects on wound healing. Studies in experimental systems have clearly demonstrated a beneficial effect for members of the gut microbiota on regulation of systemic inflammation, which could also impact wound healing at sites outside the gastrointestinal tract. The utilization of culture‐independent microbiology to characterize the microbiome of wounds and surrounding mucosa has raised many intriguing questions regarding previously held notions about the cause and effect relationships between bacterial colonization and wound repair and mechanisms involved in this symbiotic relationship.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95009/1/path4118.pd

A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141495/1/jlb0943.pd

Millimeter Wave Localization: Slow Light and Enhanced Absorption

We exploit millimeter wave technology to measure the reflection and transmission response of random dielectric media. Our samples are easily constructed from random stacks of identical, sub-wavelength quartz and Teflon wafers. The measurement allows us to observe the characteristic transmission resonances associated with localization. We show that these resonances give rise to enhanced attenuation even though the attenuation of homogeneous quartz and Teflon is quite low. We provide experimental evidence of disorder-induced slow light and superluminal group velocities, which, in contrast to photonic crystals, are not associated with any periodicity in the system. Furthermore, we observe localization even though the sample is only about four times the localization length, interpreting our data in terms of an effective cavity model. An algorithm for the retrieval of the internal parameters of random samples (localization length and average absorption rate) from the external measurements of the reflection and transmission coefficients is presented and applied to a particular random sample. The retrieved value of the absorption is in agreement with the directly measured value within the accuracy of the experiment.Comment: revised and expande

A protein quality control pathway at the mitochondrial outer membrane.

Maintaining the essential functions of mitochondria requires mechanisms to recognize and remove misfolded proteins. However, quality control (QC) pathways for misfolded mitochondrial proteins remain poorly defined. Here, we establish temperature-sensitive (ts-) peripheral mitochondrial outer membrane (MOM) proteins as novel model QC substrates in Saccharomyces cerevisiae. The ts- proteins sen2-1HAts and sam35-2HAts are degraded from the MOM by the ubiquitin-proteasome system. Ubiquitination of sen2-1HAts is mediated by the ubiquitin ligase (E3) Ubr1, while sam35-2HAts is ubiquitinated primarily by San1. Mitochondria-associated degradation (MAD) of both substrates requires the SSA family of Hsp70s and the Hsp40 Sis1, providing the first evidence for chaperone involvement in MAD. In addition to a role for the Cdc48-Npl4-Ufd1 AAA-ATPase complex, Doa1 and a mitochondrial pool of the transmembrane Cdc48 adaptor, Ubx2, are implicated in their degradation. This study reveals a unique QC pathway comprised of a combination of cytosolic and mitochondrial factors that distinguish it from other cellular QC pathways

Investigation of incoherent scatter radar spectra features with stimulated electromagnetic emissions at EISCAT

Electromagnetic (EM) and electrostatic (ES) emissions can be generated in the ionosphere by high-power high-frequency (HF) radio waves transmitted from the ground. The signatures of the EM emissions observed on the ground are known as Stimulated Electromagnetic Emissions (SEE) and can be employed for remote measurement of ionospheric parameters. The experimental data from recent HF heating experiments near the fourth electron gyro-frequency (4f ce ) at EISCAT are presented. This paper compares the temporal behavior of SEE within a few Hertz up to 50 kHz of the transmission frequency to the time evolution of enhanced ion line (EHIL) in the incoherent scatter radar (ISR) spectrum. The correlation of Wideband SEE (WSEE) spectral lines within 1 kHz to 100 kHz such as the downshifted maximum (DM), downshifted peak (DP), and broad upshifted maximum (BUM), with HF enhanced ion lines (EHIL) is shown. It is shown that WSEE spectral lines can be used to reproduce the EHIL characteristics including altitude range, rise and decay time, maximum and minimum amplitude. A data reduction technique is developed to derive ionospheric parameters such as the electron density profile near the interaction altitude, magnetic field strength B 0 as well as the altitude profile of the EHIL using the temporal evolution of WSEE spectral lines near nf ce . © 2019 COSPA

Vancomycin-induced deletion of the methicillin resistance gene mecA in Staphylococcus aureus

Objective: To elucidate factors that contribute to the development of vancomycin resistance in methicillin-resistant Staphylococcus aureus (MRSA). Methods: Forty-nine MRSA isolates were subjected to passage selection with vancomycin to isolate mutants with reduced susceptibility to vancomycin. One mutant was chosen for detailed molecular and biochemical characterization. Results: Five vancomycin-resistant mutants (vancomycin MICs, 6-12 mg/L) were obtained in vitro from five MRSA parent isolates. Upon acquisition of vancomycin resistance, all mutants showed a concomitant decrease in oxacillin resistance. In one particular MRSA strain, selection for vancomycin resistance repeatedly produced deletions and rearrangements, including loss of the mecA gene. Pleiotropic phenotypical changes, such as yellow pigment formation, loss of haemolysis, thickened cell wall, increased resistance to lysostaphin and reduced cell wall turnover were observed in this mutant. Conclusion: Acquisition of vancomycin resistance in one MRSA strain triggered mecA deletion suggesting that this deletion, coupled to other rearrangements and/or mutations, may be responsible for the increased vancomycin resistance phenotyp

Differential Response of Bacterial Microdiversity to Simulated Global Change

ACKNOWLEDGMENTS UC Irvine and the LRGCE are located on the ancestral homelands of the Indigenous Kizh and Acjachemen nations. We thank Alejandra Rodriguez Verdugo, Katrine Whiteson, Kendra Walters, Cynthia Rodriguez, Kristin Barbour, Alberto Barron Sandoval, Joanna Wang, Joia Kai Capocchi, Pauline Uyen Phuong Nguyen, Khanh Thuy Huynh, and Clara Barnosky for their input on analyses and previous drafts and for laboratory help. This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research grants DE-SC0016410 and DE-SC0020382.Peer reviewedPublisher PD