Differential expression analysis for sequence count data

*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. 

*Availability:* A free open-source R software package, _DESeq_, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq

Responses of plant species diversity and soil physical-chemical-microbial properties to Phragmites australis invasion along a density gradient

Abstract The invasion of ecosystems by strongly colonising plants such as Phragmites australis is viewed as one of the greatest threats to plant diversity and soil properties. This study compared a range of diversity measures including soil properties and mycorrhizal potential under different degrees of Phragmites density among three populations in coastal wetland, Victoria, Australia. Species richness, evenness and Shanon-Wiener index had significantly higher values in low degree of Phragmites density in all populations. Higher densities had the lowest diversity, with Shannon-Wiener index = 0 and Simpson’s index = 1 indicating its mono-specificity. Significant alterations in soil properties associated with different degrees of Phragmites density were noticed. These had interactive effects (population × density) on water content, dehydrogenase activity, microbial biomass (C, N and P) but not on pH, electrical conductivity, phenolics, organic carbon, and spore density. Furthermore, the study elucidated decrease of competitive abilities of native plants, by interfering with formation of mycorrhizal associations and biomass. Overall, our results suggest that significant ecological alterations in vegetation and soil variables (including mycorrhizal potential) were strongly dependent on Phragmites density. Such changes may lead to an important role in process of Phragmites invasion through disruption of functional relationships amongst those variables

For which side the bell tolls: The laterality of approach-avoidance associative networks

The two hemispheres of the brain appear to play different roles in emotion and/or motivation. A great deal of previous research has examined the valence hypothesis (left hemisphere = positive; right = negative), but an increasing body of work has supported the motivational hypothesis (left hemisphere = approach; right = avoidance) as an alternative. The present investigation (N = 117) sought to provide novel support for the latter perspective. Left versus right hemispheres were briefly activated by neutral lateralized auditory primes. Subsequently, participants categorized approach versus avoidance words as quickly and accurately as possible. Performance in the task revealed that approach-related thoughts were more accessible following left-hemispheric activation, whereas avoidance-related thoughts were more accessible following right-hemispheric activation. The present results are the first to examine such lateralized differences in accessible motivational thoughts, which may underlie more “downstream” manifestations of approach and avoidance motivation such as judgments, decision making, and behavior

Total Body Photography and Sequential Digital Dermoscopy Imaging for Melanoma Surveillance in Patients Starting Natalizumab for Multiple Sclerosis

Introduction: Natalizumab is an integrin receptor antagonist that has been approved by the Food and Drug Administration to treat multiple sclerosis and Crohn’s disease. The drug has been linked to an increased risk of melanoma. This brief report highlights an innovative clinical approach for monitoring the skin of patients prescribed natalizumab. Methods: We include 2 cases from our skin oncology clinic and a literature review on the incidence of melanoma in patients prescribed natalizumab between 2004 and 2019. Results: In addition to our 2 cases, we found 193 reports of patients with melanoma who were prescribed natalizumab. We propose an innovative and proactive approach using total body photography and sequential digital dermoscopy imaging before starting and while treating patients with natalizumab. Discussion: Given the mechanism of action of natalizumab, many of the melanomas diagnosed likely arose from preexisting melanocytic nevi. Using total body photography before starting this high-risk medication and then sequential digital dermoscopy imaging will increase a dermatologist’s ability to recognize new and preexisting skin lesions that have evolved since the patient began taking natalizumab. Conclusions: Using the latest non-invasive technology to detect skin cancer supports systematic and objective monitoring of changing melanocytic growths in patients prescribed natalizumab, resulting in earlier detection of melanoma and greater cure rates