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https://digitalcommons.library.umaine.edu/mmb-vp/1583/thumbnail.jp

A Selective Advantage for Conservative Viruses

In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses interacting with a realistic semi-conservatively replicating immune system. The conservative virus is found to have a selective advantage in the form of an ability to survive in regions with a wider range of mutation rates than its semi-conservative counterpart. This may help explain the existence of a rich range of viruses with conservatively replicating genomes, a trait which is found nowhere else in nature.Comment: 4 pages, 2 figure

Correcting for sequence biases in present/absent calls

Correction of non-specific binding for both PM and MM probes using probe-sequence models can partially remove the probe-sequence bias in Affymetrix microarray experiments and result in better performance of the MAS 5.0 algorithm

Estimation and correction of non-specific binding in a large-scale spike-in experiment

A combined statistical analysis using the MAS5 PM-MM, GC-NSB and PDNN methods to generate probeset values from microarray data results in an improved ability to detect differential expression and estimates of false discovery rates compared with the individual methods

Black Carbon Concentration from Worldwide Aerosol Robotic Network (AERONET) Measurements

The carbon emissions inventories used to initialize transport models and general circulation models are highly parameterized, and created on the basis of multiple sparse datasets (such as fuel use inventories and emission factors). The resulting inventories are uncertain by at least a factor of 2, and this uncertainty is carried forward to the model output. [Bond et al., 1998, Bond et al., 2004, Cooke et al., 1999, Streets et al., 2001] Worldwide black carbon concentration measurements are needed to assess the efficacy of the carbon emissions inventory and transport model output on a continuous basis

Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in mice

Dietary restriction (DR) is the most widely studied non-genetic intervention capable of extending lifespan across multiple taxa. Modulation of genes, primarily within the insulin/insulin-like growth factor signalling (IIS) and the mechanistic target of rapamycin (mTOR) signalling pathways also act to extend lifespan in model organisms. For example, mice lacking insulin receptor substrate-1 (IRS1) are long-lived and protected against several age-associated pathologies. However, it remains unclear how these particular interventions act mechanistically to produce their beneficial effects. Here, we investigated transcriptional responses in wild-type and IRS1 null mice fed an ad libitum diet (WTAL and KOAL) or fed a 30% DR diet (WTDR or KODR). Using an RNAseq approach we noted a high correlation coefficient of differentially expressed genes existed within the same tissue across WTDR and KOAL mice and many metabolic features were shared between these mice. Overall, we report that significant overlap exists in the tissue-specific transcriptional response between long-lived DR mice and IRS1 null mice. However, there was evidence of disconnect between transcriptional signatures and certain phenotypic measures between KOAL and KODR, in that additive effects on body mass were observed but at the transcriptional level DR induced a unique set of genes in these already long-lived mice

Black Carbon Concentration from Worldwide Aerosol Robotic Network (AERONET)

Worldwide black carbon concentration measurements are needed to assess the efficacy of the carbon emissions inventory and transport model output. This requires long-term measurements in many regions, as model success in one region or season does not apply to all regions and seasons. AERONET is an automated network of more than 180 surface radiometers located throughout the world. The sky radiance measurements obtained by AERONET are inverted to provide column-averaged aerosol refractive indices and size distributions for the AERONET database, which we use to derive column-averaged black carbon concentrations and specific absorptions that are constrained by the measured radiation field. This provides a link between AERONET sky radiance measurements and the elemental carbon concentration of transport models without the need for an optics module in the transport model. Knowledge of both the black carbon concentration and aerosol absorption optical depth (i.e., input and output of the optics module) will enable improvements to the transport model optics module

Evolutionary conservation of regulated longevity assurance mechanisms

Short abstract: A multi-level cross-species comparative analysis of gene-expression changes accompanying increased longevity in mutant nematodes, fruit flies and mice with reduced insulin/IGF-1 signaling revealed candidate conserved mechanisms

Bayesian penalised likelihood reconstruction (Q.Clear) of 18F-fluciclovine PET for imaging of recurrent prostate cancer: semi-quantitative and clinical evaluation

Objective: 18F-Fluciclovine (FACBC) is an amino acid PET radiotracer approved for recurrent prostate cancer imaging. We investigate the use of Bayesian penalised likelihood (BPL) reconstruction for 18F-fluciclovine PET. Methods: 15 18F-fluciclovine scans were reconstructed using ordered subset expectation maximisation (OSEM), OSEM + point spread function (PSF) modelling and BPL using β-values 100–600. Lesion maximum standardised uptake value (SUVmax), organ SUVmean and standard deviation were measured. Deidentified reconstructions (OSEM, PSF, BPL using β200–600) from 10 cases were visually analysed by two readers who indicated their most and least preferred reconstructions, and scored overall image quality, noise level, background marrow image quality and lesion conspicuity. Results: Comparing BPL to OSEM, there were significant increments in lesion SUVmax and signal-to-background up to β400, with highest gain in β100 reconstructions (mean ΔSUVmax 3.9, p < 0.0001). Organ noise levels increased on PSF, β100 and β200 reconstructions. Across BPL reconstructions, there was incremental reduction in organ noise with increasing β, statistically significant beyond β300–500 (organ-dependent). Comparing with OSEM and PSF, lesion signal-to-noise was significantly increased in BPL reconstructions where β ≥ 300 and ≥ 200 respectively. On visual analysis, β 300 had the first and second highest scores for image quality, β500 and β600 equal highest scores for marrow image quality and least noise, PSF and β 200 had first and second highest scores for lesion conspicuity. For overall preference, one reader preferred β 300 in 9/10 cases and the other preferred β 200 in all cases. Conclusion: BPL reconstruction of 18F-fluciclovine PET images improves signal-to-noise ratio, affirmed by overall reader preferences. On balance, β300 is suggested for 18F-fluciclovine whole body PET image reconstruction using BPL. Advances in knowledge: The optimum β is different to that previously published for 18F-fluorodeoxyglucose, and has practical implications for a relatively new tracer in an environment with modern reconstruction technologies