Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection

Background: Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. Each gene is represented on a GeneChip array by a probe-set, consisting of up to 16 probe-pairs. Signal intensities across probe-pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. We have previously developed a technique to study the transcriptomes of heterologous species based on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology. Results: Here we have investigated the effects of hybridising homologous species gDNA to study the transcriptomes of species for which the arrays have been designed. Genomic DNA from Arabidopsis thaliana and rice (Oryza sativa) were hybridised to the Affymetrix Arabidopsis ATH1 and Rice Genome GeneChip arrays respectively. Probe selection based on gDNA hybridisation intensity increased the number of genes identified as significantly differentially expressed in two published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice. Conclusion: This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays

Gamma-herpesvirus latency requires T cell evasion during episome maintenance.

The gamma-herpesviruses persist as latent episomes in a dynamic lymphocyte pool. Their consequent need to express a viral episome maintenance protein presents a potential immune target. The glycine-alanine repeat of the Epstein-Barr virus episome maintenance protein, EBNA-1, limits EBNA-1 epitope presentation to CD8(+) T lymphocytes (CTLs). However, CTL recognition occurs in vitro, so the significance of such evasion for viral fitness is unclear. We used the murine gamma-herpesvirus-68 (MHV-68) to define the in vivo contribution of cis-acting CTL evasion to host colonisation. Although the ORF73 episome maintenance protein of MHV-68 lacks a glycine-alanine repeat, it was equivalent to EBNA-1 in conferring limited presentation on linked epitopes. This was associated with reduced protein synthesis and reduced protein degradation. We bypassed the cis-acting evasion of ORF73 by using an internal ribosome entry site to express in trans-a CTL target from the same mRNA. This led to a severe, MHC class I-restricted and CTL-dependent reduction in viral latency. Thus, despite MHV-68 encoding at least two trans-acting CTL evasion proteins, cis-acting evasion during episome maintenance was essential for normal host colonisation

Should the Psychiatrist Be Hospitalized?

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68096/2/10.1177_002076407502100212.pd

Systems, interactions and macrotheory

A significant proportion of early HCI research was guided by one very clear vision: that the existing theory base in psychology and cognitive science could be developed to yield engineering tools for use in the interdisciplinary context of HCI design. While interface technologies and heuristic methods for behavioral evaluation have rapidly advanced in both capability and breadth of application, progress toward deeper theory has been modest, and some now believe it to be unnecessary. A case is presented for developing new forms of theory, based around generic “systems of interactors.” An overlapping, layered structure of macro- and microtheories could then serve an explanatory role, and could also bind together contributions from the different disciplines. Novel routes to formalizing and applying such theories provide a host of interesting and tractable problems for future basic research in HCI

Apples and Oranges: Comparing the Backgrounds and Academic Trajectories of International Baccalaureate (IB) Students to a Matched Comparison Group

This report presents findings from a retrospective study of the academic histories of International Baccalaureate (IB) students and other students in the state of Florida. The IB Diploma Program is an internationally recognized college-preparatory curriculum designed to provide students with a rigorous and comprehensive academic experience. IB has grown dramatically in recent years and is thought by many to be among the best college-preparatory programs in existence. As such, there is tremendous interest in the potential impacts of IB, but any attempts to examine those impacts must deal with selection bias that results from the voluntary participation of schools and students. Failure to do so makes it impossible to determine whether the performance of participating students was actually influenced by IB, or whether the outcomes for these students would have been just as good without IB. As a critical step in understanding the impacts of IB, the analyses presented in this report examined the selection mechanisms behind IB participation across Florida, the state with the second highest representation of IB programs in the nation. We use longitudinal student and school-level data from 1995 through 2009 from the Florida K-20 Education Data Warehouse (EDW) to characterize individual students’ educational histories from elementary school through high school and into college. To address issues of selection bias, we use propensity score methods (Rosenbaum & Rubin, 1983) to adjust for preexisting differences between IB and non-IB students

Nested solitons in two-field fuzzy dark matter

Dark matter as scalar particles consisting of multiple species is well motivated in string theory where axion fields are ubiquitous. A two-field fuzzy dark matter (FDM) model features two species of ultralight axion particles with different masses, $m_1 \neq m_2$, which is extended from the standard one-field model with $m_a \sim 10^{-22}\,{\rm eV}$. Here we perform numerical simulations to explore the properties of two-field FDM haloes. We find that the central soliton has a nested structure when $m_2 \gg m_1$, which is distinguishable from the generic flat-core soliton in one-field haloes. However, the formation of this nested soliton is subject to many factors, including the density fraction and mass ratio of the two fields. Finally, we study non-linear structure formation in two-field cosmological simulations with self-consistent initial conditions and find that the small-scale structure in two-field cosmology is also distinct from the one-field model in terms of DM halo counts and soliton formation time.Comment: 11 pages, 5 figures. Published versio

Guselkumab provides durable improvement across psoriatic arthritis disease domains: post hoc analysis of a phase 3, randomised, double-blind, placebo-controlled study

Objective Evaluate long-term guselkumab effectiveness across Group for Research and Assessment of Psoriasis and Psoriatic Arthritis (GRAPPA)-recognised domains/related conditions of psoriatic arthritis (PsA). Methods Post hoc analyses used data from DISCOVER-2 (NCT03158285) biologic/Janus-kinase inhibitor-naïve participants with active PsA (≥5 swollen/≥5 tender joints, C-reactive protein ≥0.6 mg/dL), randomised (1:1:1) to guselkumab every 4 or 8 weeks (Q4W/Q8W) or placebo with crossover to guselkumab. Outcomes aligned with key GRAPPA-recognised domains of overall disease activity, peripheral arthritis, axial disease, enthesitis/dactylitis and skin psoriasis (nail psoriasis was not evaluated). PsA-related conditions (inflammatory bowel disease (IBD)/uveitis) were assessed via adverse events through W112. Least squares mean changes from baseline through W100 in continuous outcomes employed repeated measures mixed-effects models adjusting for baseline scores. Binary measure response rates were determined with non-responder imputation for missing data. Results 442/493 (90%) of guselkumab-randomised patients completed treatment through W100. Following early reductions in disease activity with guselkumab, durable improvements were observed across key PsA domains (swollen/tender joints, psoriasis, spinal pain, enthesitis/dactylitis) through W100. Response rates of therapeutically relevant targets generally increased through W100 with guselkumab Q4W/Q8W: Disease Activity Index for PsA low disease activity (LDA) 62%/59%, enthesitis resolution 61%/70%, dactylitis resolution 72%/83%, 100% improvement in Psoriasis Area and Severity Index 59%/53%, Psoriatic Arthritis Disease Activity Score LDA 51%/49% and minimal disease activity 38%/40%. Through W112, no cases of IBD developed among guselkumab-randomised patients and one case of uveitis was reported. Conclusion In biologic-naïve patients with active PsA, guselkumab provided early and durable improvements in key GRAPPA-recognised domains through 2 years, with substantial proportions achieving important treatment targets

In vivo function of the murid herpesvirus-4 ribonucleotide reductase small subunit

The difficulty of eliminating herpesvirus carriage makes host entry a key target for infection control. However, its viral requirements are poorly defined. Murid herpesvirus-4 (MuHV-4) can potentially provide insights into gammaherpesvirus host entry. Upper respiratory tract infection requires the MuHV-4 thymidine kinase (TK) and ribonucleotide reductase large subunit (RNR-L), suggesting a need for increased nucleotide production. However, both TK and RNR-L are likely to be multifunctional. We therefore tested further the importance of nucleotide production by disrupting the MuHV-4 ribonucleotide reductase small subunit (RNR-S). This caused a similar attenuation to RNR-L disruption: despite reduced intra-host spread, invasive inoculations still established infection, whereas a non-invasive upper respiratory tract inoculation did so only at high dose. Histological analysis showed that RNR-S−, RNR-L− and TK− viruses all infected cells in the olfactory neuroepithelium but unlike wild-type virus then failed to spread. Thus captured host nucleotide metabolism enzymes, up to now defined mainly as important for alphaherpesvirus reactivation in neurons, also have a key role in gammaherpesvirus host entry. This seemed to reflect a requirement for lytic replication to occur in a terminally differentiated cell before a viable pool of latent genomes could be established