Exploring One-Cell Inversion Method for Transient Transport on GPU

To find deterministic solutions to the transient $S_N$ neutron transport equation, iterative schemes are typically used to treat the scattering (and fission) source terms. We explore the one-cell inversion iteration scheme to do this on the GPU and make comparisons to a source iteration scheme. We examine convergence behavior, through the analysis of spectral radii, of both one-cell inversion and source iterations. To further boost the GPU parallel efficiency, we derive a higher-order discretization method, simple corner balance (in space) and multiple balance (in time), to add more work to the threads and gain accuracy. Fourier analysis on this higher-order numerical method shows that it is unconditionally stable, but it can produce negative flux alterations that are critically damped through time. We explore a whole-problem (in all angle and all cell) sparse linear algebra framework, for both iterative schemes, to quickly produce performant code for GPUs. Despite one-cell inversion requiring additional iterations to convergence, those iterations can be done faster to provide a significant speedup over source iteration in quadrature sets at or below $S_{128}$. Going forward we will produce a two-dimensional implementation of this code to experiment with memory and performance impacts of a whole-problem framework including methods of synthetic acceleration and pre-conditioners for this scheme, then we will begin making direct comparisons to traditionally implemented source iteration in production code.Comment: 11 pages, 4 figures, M\&C 2023 ANS conferenc

Tracking the evolution of alternatively spliced exons within the Dscam family

BACKGROUND: The Dscam gene in the fruit fly, Drosophila melanogaster, contains twenty-four exons, four of which are composed of tandem arrays that each undergo mutually exclusive alternative splicing (4, 6, 9 and 17), potentially generating 38,016 protein isoforms. This degree of transcript diversity has not been found in mammalian homologs of Dscam. We examined the molecular evolution of exons within this gene family to locate the point of divergence for this alternative splicing pattern. RESULTS: Using the fruit fly Dscam exons 4, 6, 9 and 17 as seed sequences, we iteratively searched sixteen genomes for homologs, and then performed phylogenetic analyses of the resulting sequences to examine their evolutionary history. We found homologs in the nematode, arthropod and vertebrate genomes, including homologs in several vertebrates where Dscam had not been previously annotated. Among these, only the arthropods contain homologs arranged in tandem arrays indicative of mutually exclusive splicing. We found no homologs to these exons within the Arabidopsis, yeast, tunicate or sea urchin genomes but homologs to several constitutive exons from fly Dscam were present within tunicate and sea urchin. Comparing the rate of turnover within the tandem arrays of the insect taxa (fruit fly, mosquito and honeybee), we found the variants within exons 4 and 17 are well conserved in number and spatial arrangement despite 248–283 million years of divergence. In contrast, the variants within exons 6 and 9 have undergone considerable turnover since these taxa diverged, as indicated by deeply branching taxon-specific lineages. CONCLUSION: Our results suggest that at least one Dscam exon array may be an ancient duplication that predates the divergence of deuterostomes from protostomes but that there is no evidence for the presence of arrays in the common ancestor of vertebrates. The different patterns of conservation and turnover among the Dscam exon arrays provide a striking example of how a gene can evolve in a modular fashion rather than as a single unit

Joint Genome-Wide Profiling of miRNA and mRNA Expression in Alzheimer's Disease Cortex Reveals Altered miRNA Regulation

Although microRNAs are being extensively studied for their involvement in cancer and development, little is known about their roles in Alzheimer's disease (AD). In this study, we used microarrays for the first joint profiling and analysis of miRNAs and mRNAs expression in brain cortex from AD and age-matched control subjects. These data provided the unique opportunity to study the relationship between miRNA and mRNA expression in normal and AD brains. Using a non-parametric analysis, we showed that the levels of many miRNAs can be either positively or negatively correlated with those of their target mRNAs. Comparative analysis with independent cancer datasets showed that such miRNA-mRNA expression correlations are not static, but rather context-dependent. Subsequently, we identified a large set of miRNA-mRNA associations that are changed in AD versus control, highlighting AD-specific changes in the miRNA regulatory system. Our results demonstrate a robust relationship between the levels of miRNAs and those of their targets in the brain. This has implications in the study of the molecular pathology of AD, as well as miRNA biology in general

The Use of Social Media in Endourology: An Analysis of the 2013 World Congress of Endourology Meeting

Objective: To examine the use of social media within Endourology by reporting on its utilization during the 2013 World Congress of Endourology (WCE) annual meeting. Materials and Methods: Two social media platforms were analyzed for this study: Twitter (San Francisco, CA) and LinkedIn (Mountain View, CA). For Twitter, a third-party analysis service (Tweetreach) was used to quantitatively analyze all tweets with the hashtags #WCE2013 and #WCE13 during a 7-day period surrounding the WCE. Two reviewers independently classified tweet content using a predefined Twitter-specific classification system. Tweet sentiment was determined using sentiment analysis software (Semantria, Inc., Amherst, MA). Finally, the penetration of Twitter and LinkedIn within the WCE faculty was assessed by means of a manual search. Results: During the study period, 335 tweets had the hashtag #WCE2013 or #WCE13. Content originated from 68 users resulting in a mean of 47 tweets/day and 4.9 tweets/contributor. Conference-related tweets had a reach of 38,141 unique Twitter accounts and an online exposure of 188,629 impressions. Physicians generated the majority of the content (63%), of which 55.8% were not attending the meeting. More tweets were informative (56.7%) versus uninformative (43.3%), and 17.9% had links to an external web citation. The mean sentiment score was 0.13 (range ?0.90 to 1.80); 13.1%, 57.0%, and 29.9% of tweets were negative, neutral, and positive in sentiment, respectively. Of 302 WCE meeting faculty, 150 (49.7%) had registered LinkedIn accounts while only 52 (17.2%) had Twitter accounts, and only 19.2% tweeted during the meeting. Conclusions: Despite a relatively low number of Twitter users, tweeting about the WCE meeting dramatically increased its online exposure with dissemination of content that was mostly informative including engagement with physicians not attending the conference. While half of faculty at WCE 2013 had LinkedIn accounts, their social media footprint in Twitter was limited.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140078/1/end.2014.0329.pd

Correlation between cribriform/intraductal prostatic adenocarcinoma and percent Gleason pattern 4 to a 22‐gene genomic classifier

BackgroundThe Decipher test measures expression of 22 RNA biomarkers associated with aggressive prostate cancer used to improve risk stratification of patients to help guide management. To date, Decipher’s genomic classification has not been extensively correlated with specific histologic growth patterns in prostatic adenocarcinoma. With a growing understanding of the clinical aggressiveness associated with cribriform growth pattern (CF), intraductal carcinoma (IDC), and percent Gleason pattern 4 (G4%), we sought to determine if their presence was associated with an increased genomic risk as measured by the Decipher assay.DesignClinical use of the Decipher assay was performed on the highest Gleason score (GS) tumor nodule of prostatectomy specimens from a prospective cohort of 48 patients, with GS varying from 7 through 9 to help guide clinical risk stratification. The tumors were reviewed for CF, IDC, and G4%, which were then compared to the Decipher score (0‐1) and risk stratification (high vs not high).ResultsThe presence of CF/IDC was significantly associated with Decipher risk score (P = .007), with a high‐risk Decipher score in 22% vs 56% of patients without or with CF/IDC. On binary logistic regression analysis, G4% (odds ratio [OR] 1.04 per percent increase [95% confidence interval [CI], 1.02‐1.06]; P = .0004) and CF predominant (OR, 9.60 [95%CI, 1.48‐62.16]; P = .02) were significantly associated with a high‐risk GC score. IDC did not reach significance (OR, 1.92 [95%CI, 0.65‐5.67]; P = .24).ConclusionsOur findings add to an expanding knowledge base that supports G4% and CF/IDC as molecularly unique and clinically relevant features in prostatic adenocarcinoma. These histologic features should be standardly reported as they are associated with more aggressive prostate cancer. Future work should determine the independent information of these histologic findings that are relative to genomic assessment on long‐term outcomes.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153011/1/pros23926.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153011/2/pros23926_am.pd

Differential Responses of Progesterone Receptor Membrane Component-1 (Pgrmc1) and the Classical Progesterone Receptor (Pgr) to 17β-Estradiol and Progesterone in Hippocampal Subregions that Support Synaptic Remodeling and Neurogenesis

Progesterone (P4) and estradiol (E2) modulate neurogenesis and synaptic remodeling in the hippocampus during the rat estrous cycle and in response to deafferenting lesions, but little is known about the steroidal regulation of hippocampal progesterone receptors associated with these processes. We examined the neuronal expression of progesterone receptor membrane component-1 (Pgrmc1) and the classical progesterone receptor (Pgr), by in situ hybridization and immunohistochemistry. Pgr, a transcription factor, has been associated with synaptic remodeling and other major actions of P4, whereas Pgrmc1 is implicated in P4-dependent proliferation of adult neuroprogenitor cells and with rapid P4 effects on membranes. Ovariectomized adult rats were given E2, P4, or E2+P4 on two schedules: a 4-d model of the rodent estrous cycle and a 30-d model of postmenopausal hormone therapy. Pgr was hormonally responsive only in CA1 pyramidal neurons, and the induction of Pgr by E2 was partly antagonized by P4 only on the 30-d schedule. In CA3 pyramidal and dentate gyrus (DG) neurons, Pgr was largely unresponsive to all hormone treatments. In contrast to Pgr, Pgrmc1 was generally induced by E2 and/or P4 throughout the hippocampus in CA1, CA3, and DG neurons. In neuroprogenitor cells of the DG (immunopositive for bromodeoxyuridine and doublecortin), both Pgrmc1 and Pgr were detected. The differential regulation of hippocampal Pgrmc1 and Pgr by E2 and P4 may guide drug development in hormonal therapy for support of neurogenesis and synaptic regeneration.This work was supported by National Institute on Aging Grants 1PO1 AG026572 (to R.D.B.); Project 4 (to C.E.F. and T.E.M.), Animal Core A (to T.E.M.), and Analytic Core C (to L.Z.)

Nanoparticulate matter exposure results in white matter damage and an inflammatory microglial response in an experimental murine model

Exposure to ambient air pollution has been associated with white matter damage and neurocognitive decline. However, the mechanisms of this injury are not well understood and remain largely uncharacterized in experimental models. Prior studies have shown that exposure to particulate matter (PM), a sub-fraction of air pollution, results in neuroinflammation, specifically the upregulation of inflammatory microglia. This study examines white matter and axonal injury, and characterizes microglial reactivity in the corpus callosum of mice exposed to 10 weeks (150 hours) of PM. Nanoscale particulate matter (nPM, aerodynamic diameter ≤200 nm) consisting primarily of traffic-related emissions was collected from an urban area in Los Angeles. Male C57BL/6J mice were exposed to either re-aerosolized nPM or filtered air for 5 hours/day, 3 days/week, for 10 weeks (150 hours; n = 18/group). Microglia were characterized by immunohistochemical double staining of ionized calcium-binding protein-1 (Iba-1) with inducible nitric oxide synthase (iNOS) to identify pro-inflammatory cells, and Iba-1 with arginase-1 (Arg) to identify anti-inflammatory/ homeostatic cells. Myelin injury was assessed by degraded myelin basic protein (dMBP). Oligodendrocyte cell counts were evaluated by oligodendrocyte transcription factor 2 (Olig2). Axonal injury was assessed by axonal neurofilament marker SMI-312. iNOS-expressing microglia were significantly increased in the corpus callosum of mice exposed to nPM when compared to those exposed to filtered air (2.2 fold increase; p\u3c0.05). This was accompanied by an increase in dMBP (1.4 fold increase; p\u3c0.05) immunofluorescent density, a decrease in oligodendrocyte cell counts (1.16 fold decrease; p\u3c0.05), and a decrease in neurofilament SMI-312 (1.13 fold decrease; p\u3c0.05) immunofluorescent density. Exposure to nPM results in increased inflammatory microglia, white matter injury, and axonal degradation in the corpus callosum of adult male mice. iNOS-expressing microglia release cytokines and reactive oxygen/ nitrogen species which may further contribute to the white matter damage observed in this model

Continuous versus Cyclic Progesterone Exposure Differentially Regulates Hippocampal Gene Expression and Functional Profiles

This is the published version. Copyright 2012 Public Library of Science.This study investigated the impact of chronic exposure to continuous (CoP4) versus cyclic progesterone (CyP4) alone or in combination with 17β-estradiol (E2) on gene expression profiles targeting bioenergetics, metabolism and inflammation in the adult female rat hippocampus. High-throughput qRT-PCR analyses revealed that ovarian hormonal depletion induced by ovariectomy (OVX) led to multiple significant gene expression alterations, which were to a great extent reversed by co-administration of E2 and CyP4. In contrast, co-administration of E2 and CoP4 induced a pattern highly resembling OVX. Bioinformatics analyses further revealed clear disparities in functional profiles associated with E2+CoP4 and E2+CyP4. Genes involved in mitochondrial energy (ATP synthase α subunit; Atp5a1), redox homeostasis (peroxiredoxin 5; Prdx5), insulin signaling (insulin-like growth factor I; Igf1), and cholesterol trafficking (liver X receptor α subtype; Nr1h3), differed in direction of regulation by E2+CoP4 (down-regulation relative to OVX) and E2+CyP4 (up-regulation relative to OVX). In contrast, genes involved in amyloid metabolism (β-secretase; Bace1) differed only in degree of regulation, as both E2+CoP4 and E2+CyP4 induced down-regulation at different efficacy. E2+CyP4-induced changes could be associated with regulation of progesterone receptor membrane component 1(Pgrmc1). In summary, results from this study provide evidence at the molecular level that differing regimens of hormone therapy (HT) can induce disparate gene expression profiles in brain. From a translational perspective, confirmation of these results in a model of natural menopause, would imply that the common regimen of continuous combined HT may have adverse consequences whereas a cyclic combined regimen, which is more physiological, could be an effective strategy to maintain neurological health and function throughout menopausal aging

Competition of nuclear factor-erythroid 2 factors related transcription factor isoforms, Nrf1 and Nrf2, in antioxidant enzyme induction

AbstractAlthough the Nrf2 (nuclear factor-erythroid 2 p45 subunit-related factor 2) regulated expression of multiple antioxidant and cytoprotective genes through the electrophile responsive element (EpRE) is well established, interaction of Nrf2/EpRE with Nrf1, a closely-related transcription factor, is less well understood. Due to either proteolysis or alternative translation, Nrf1 has been found as proteins of varying size, p120, p95, and p65, which have been described as either activators of EpRE or competitive inhibitors of Nrf2. We investigated the effect of Nrf1 on EpRE-regulated gene expression using the catalytic and modifier subunits of glutamate cysteine ligase (GCLC and GCLM) as models and explored the potential role of Nrf1 in altering their expression in aging and upon chronic exposure to airborne nano-sized particulate matter (nPM). Nrf1 knockout resulted in the increased expression of GCLC and GCLM in human bronchial epithelial (HBE1) cells. Overexpression Nrf2 in combination with either p120 or p65 diminished or failed to further increase the GCLC- and GLCM-EpRE luciferase activity. All known forms of Nrf1 protein, remained unchanged in the lungs of mice with age or in response to nPM. Our study shows that Nrf1 could inhibit EpRE activity in vitro, whereas the precise role of Nrf1 in vivo requires further investigations. We conclude that Nrf1 may not be directly responsible for the loss of Nrf2-dependent inducibility of antioxidant and cytoprotective genes observed in aged animals