Analytical evaluation of mixing efficiencies and nonlinear interactions of turbulence in a stratified flow

Mixing efficiency and nonlinear interactions in stratified turbulence were studied using rapid distortion theory (RDT). Mixing efficiency was predicted in strongly stratified flows for both one and two active scalars. The former used results of Hanazaki and Hunt (1996), while a new analytical solution was derived for the latter. Mixing efficiencies depend on the Schmidt number Sc, Grashof number Gr, and density ratio Rρ. A decrease in the mixing efficiency was observed as Sc increased for the one scalar case and as Rρ decreased for the two scalar case. RDT was also extended in an attempt to better predict behaviors in moderately stratified flows. Extensions using eddy viscosities, simulations, and modification of RDT input parameters were attempted and compared to experimental data, but magnitude and peak timing discrepancies in the vertical flux correlation coefficient curves remained. A different attempt at extending RDT was made by deriving expressions for the neglected nonlinear terms using an approach similar to Kevlahan and Hunt (1997). A model system including the expected form of the nonlinear terms showed that adjustment of coefficients in the nonlinear term had the ability to influence the period and decay of turbulent parameters

A Writer, an Editor, an Instructor, and an Alumna Walk into the Writing Center

As the writing center director, I believe our professional tutors provide valuable expert perspectives to student writers. They also help me mentor the peer tutors and push me to reevaluate our practices. They add staffing stability to the center (whose peer tutors never stay for more than three years). Finally, these trusted writing experts professionalize the writing center’s status among administration, faculty, and students. In the following paragraphs, Amy, Ellen, Chris, and Lindsey illustrate the rich variety of skills and perspectives professional writing tutors can contribute to a writing centerUniversity Writing Cente

Beliefs About Savoring in Older Adulthood: Aging and Perceived Health Affect Temporal Components of Perceived Savoring Ability

The ability to savor positive life events is associated with higher emotional well-being; however, few studies have examined savoring ability in older adults. The present study used a longitudinal design to examine changes in perceived savoring abilities and associations with perceived health in older adulthood. Older adults (N=131) reported on beliefs about savoring and perceived health at baseline and 2½ years later. Perceived anticipation (savoring the future) and reminiscing (savoring the past) abilities declined from baseline to follow-up. Better perceived health at baseline predicted greater perceived reminiscing and anticipation abilities at follow-up. Greater perceived ability to savor the present moment at baseline predicted better perceived health at follow-up. Aging and poorer health focus older adults’ thoughts on present-moment pleasures, which may benefit health, but may also lead to reductions in perceived anticipation and reminiscing abilities

Collecting Diverse Microorganisms from Rover Spacecraft

. The Planetary Protection discipline at NASA’s Jet Propulsion Laboratory develops and implements procedures to prevent both forward and backward contamination between the Earth and solar system bodies. However, there will always be some microorganisms that will be resistant to the strictest of sterilization methods. In order understand the microorganisms found on spacecraft during assembly, and to rapidly identify them, a mass spectrometry approach was developed. As an experimental approach, a custom database was created for a subset of microorganisms in the Planetary Protection Archive. In order to make the database as accurate and efficient as possible, several different procedures have been developed on how to identify and classify each isolate within the database. Building upon previous research in the area, we designed a method characterizing revived isolates with known 16SrRNA gene sequence OTUs (Operational Taxonomy Units) to create MSPs (Mass Spectral Profiles) and RTCs (Real Time Classifications) using MALDI-TOF Mass Spectroscopy. We will use these profiles to enhance the Planetary Protection custom classification database, for immediate and future investigations. This work was carried out at NASA’s Jet Propulsion Laboratory, California Institute of Technology

Conceptual and Measurement Challenges in Research on Cognitive Reserve

Cognitive reserve, broadly conceived, encompasses aspects of brain structure and function that optimize individual performance in the presence of injury or pathology. Reserve is defined as a feature of brain structure and/or function that modifies the relationship between injury or pathology and performance on neuropsychological tasks or clinical outcomes. Reserve is challenging to study for two reasons. The first is: reserve is a hypothetical construct, and direct measures of reserve are not available. Proxy variables and latent variable models are used to attempt to operationalize reserve. The second is: in vivo measures of neuronal pathology are not widely available. It is challenging to develop and test models involving a risk factor (injury or pathology), a moderator (reserve) and an outcome (performance or clinical status) when neither the risk factor nor the moderator are measured directly. We discuss approaches for quantifying reserve with latent variable models, with emphasis on their application in the analysis of data from observational studies. Increasingly latent variable models are used to generate composites of cognitive reserve based on multiple proxies. We review the theoretical and ontological status of latent variable modeling approaches to cognitive reserve, and suggest research strategies for advancing the field

Covalent Inhibitors of Protein-Protein Interactions Targeting Lysine, Tyrosine, or Histidine Residues.

We have recently reported a series of Lys-covalent agents targeting the BIR3 domain of the X-linked inhibitor of apoptosis protein (XIAP) using a benzamide-sulfonyl fluoride warhead. Using XIAP as a model system, we further investigated a variety of additional warheads that can be easily incorporated into binding peptides and analyzed their ability to form covalent adducts with lysine and other amino acids, including tyrosine, histidine, serine, and threonine, using biochemical and biophysical assays. Moreover, we tested aqueous, plasma stability, cell permeability, and cellular efficacy of the most effective agents. These studies identified aryl-fluoro sulfates as likely the most suitable electrophiles to effectively form covalent adducts with Lys, Tyr, and His residues, given that these agents were cell permeable and stable in aqueous buffer and in plasma. Our studies contain a number of general findings that open new possible avenues for the design of potent covalent protein-protein interaction antagonists

A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and commensals

Urinary tract infection is among the most common infections worldwide, typically studied in animals and cell lines with limited uropathogenic strains. Here, we assessed diverse bacterial species in a human urothelial microtissue model exhibiting full stratification, differentiation, innate epithelial responses, and urine tolerance. Several uropathogens invaded intracellularly, but also commensal Escherichia coli, suggesting that invasion is a shared survival strategy, not solely a virulence hallmark. The E. coli adhesin FimH was required for intracellular bacterial community formation, but not for invasion. Other shared lifestyles included filamentation (Gram-negatives), chaining (Gram-positives), and hijacking of exfoliating cells, while biofilm-like aggregates were formed mainly with Pseudomonas and Proteus. Urothelial cells expelled invasive bacteria in Rab-/LC3-decorated structures, while highly cytotoxic/invasive uropathogens, but not commensals, disrupted host barrier function and strongly induced exfoliation and cytokine production. Overall, this work highlights diverse species-/strain-specific infection strategies and corresponding host responses in a human urothelial microenvironment, providing insights at the microtissue, cell, and molecular level

Genomic sequence analysis and characterization of Sneathia amnii sp. nov

Background Bacteria of the genus Sneathia are emerging as potential pathogens of the female reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be part of the normal microbiota of the genitourinary tracts of men and women, but they are also associated with a variety of clinical conditions including bacterial vaginosis, preeclampsia, preterm labor, spontaneous abortion, post-partum bacteremia and other invasive infections. Sneathia species also exhibit a significant correlation with sexually transmitted diseases and cervical cancer. BecauseSneathia species are fastidious and rarely cultured successfully in vitro; and the genomes of members of the genus had until now not been characterized, very little is known about the physiology or the virulence of these organisms. Results Here, we describe a novel species, Sneathia amnii sp. nov, which closely resembles bacteria previously designated Leptotrichia amnionii . As part of the Vaginal Human Microbiome Project at VCU, a vaginal isolate of S. amnii sp. nov. was identified, successfully cultured and bacteriologically cloned. The biochemical characteristics and virulence properties of the organism were examined in vitro, and the genome of the organism was sequenced, annotated and analyzed. The analysis revealed a reduced circular genome of ~1.34 Mbp, containing ~1,282 protein-coding genes. Metabolic reconstruction of the bacterium reflected its biochemical phenotype, and several genes potentially associated with pathogenicity were identified. Conclusions Bacteria with complex growth requirements frequently remain poorly characterized and, as a consequence, their roles in health and disease are unclear. Elucidation of the physiology and identification of genes putatively involved in the metabolism and virulence of S. amnii may lead to a better understanding of the role of this potential pathogen in bacterial vaginosis, preterm birth, and other issues associated with vaginal and reproductive health

Species-level classification of the vaginal microbiome

Background The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species level, is necessary to fully understand the association of the vaginal microbiome with bacterial vaginosis, sexually transmitted infections, pregnancy complications, menopause, and other physiological and infectious conditions. However, most current taxonomic assignment strategies based on metagenomic 16S rDNA sequence analysis provide at best a genus-level resolution. While surveys of 16S rRNA gene sequences are common in microbiome studies, few well-curated, body-site-specific reference databases of 16S rRNA gene sequences are available, and no such resource is available for vaginal microbiome studies. Results We constructed the Vaginal 16S rDNA Reference Database, a comprehensive and non-redundant database of 16S rDNA reference sequences for bacterial taxa likely to be associated with vaginal health, and we developed STIRRUPS, a new method that employs the USEARCH algorithm with a curated reference database for rapid species-level classification of 16S rDNA partial sequences. The method was applied to two datasets of V1-V3 16S rDNA reads: one generated from a mock community containing DNA from six bacterial strains associated with vaginal health, and a second generated from over 1,000 mid-vaginal samples collected as part of the Vaginal Human Microbiome Project at Virginia Commonwealth University. In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment. Conclusions This database and method provide accurate species-level classifications of metagenomic 16S rDNA sequence reads that will be useful for analysis and comparison of microbiome profiles from vaginal samples. STIRRUPS can be used to classify 16S rDNA sequence reads from other ecological niches if an appropriate reference database of 16S rDNA sequences is available