qTeller: a tool for comparative multi-genomic gene expression analysis

Motivation: Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses. Results: To address this challenge, we revamped the comparative gene expression tool qTeller to take advantage of the growing number of public RNA-Seq datasets. qTeller allows users to evaluate gene expression data in a defined genomic interval and also perform two-gene comparisons across multiple user-chosen tissues. Though previously unpublished, qTeller has been cited extensively in the scientific literature, demonstrating its importance to researchers. Our new version of qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets. Other new features include support for additional data formats, modernized interface and back-end database and an optimized framework for adoption by other organisms’ databases. Availability and implementation: The source code for qTeller is open-source and available through GitHub (https:// github.com/Maize-Genetics-and-Genomics-Database/qTeller). A maize instance of qTeller is available at the Maize Genetics and Genomics database (MaizeGDB) (https://qteller.maizegdb.org/), where we have mapped over 200 unique datasets from GenBank across 27 maize genomes

Prefigurative politics between ethical practice and absent promise

'Prefigurative politics' has become a popular term for social movements' ethos of unity between means and ends, but its conceptual genealogy has escaped attention. This article disentangles two components: an ethical revolutionary practice, chiefly indebted to the anarchist tradition, which fights domination while directly constructing alternatives; and prefiguration as a recursive temporal framing, unknowingly drawn from Christianity, in which a future radiates backwards on its past. Tracing prefiguration from the Church Fathers to politicised re-surfacings in the Diggers and the New Left, I associate it with Koselleck's 'process of reassurance' in a pre-ordained historical path. Contrasted to recursive prefiguration are the generative temporal framings couching defences of means-ends unity in the anarchist tradition. These emphasised the path dependency of revolutionary social transformation and the ethical underpinnings of anti-authoritarian politics. Misplaced recursive terminology, I argue, today conveniently distracts from the generative framing of means-ends unity, as the promise of revolution is replaced by that of environmental and industrial collapse. Instead of prefiguration, I suggest conceiving of means-ends unity in terms of Bloch's 'concrete utopia', and associating it with 'anxious' and 'catastrophic' forms of hope

Targeting the hypoxic fraction of tumours using hypoxia activated prodrugs

The presence of a microenvironment within most tumours containing regions of low oxygen tension or hypoxia has profound biological and therapeutic implications. Tumour hypoxia is known to promote the development of an aggressive phenotype, resistance to both chemotherapy and radiotherapy and is strongly associated with poor clinical outcome. Paradoxically, it is recognised as a high priority target and one therapeutic strategies designed to eradicate hypoxic cells in tumours are a group of compounds known collectively as hypoxia activated prodrugs (HAPs) or bioreductive drugs. These drugs are inactive prodrugs that require enzymatic activation (typically by 1 or 2 electron oxidoreductases) to generate cytotoxic species with selectivity for hypoxic cells being determined by (i) the ability of oxygen to either reverse or inhibit the activation process and (ii) the presence of elevated expression of oxidoreductases in tumours. The concepts underpinning HAP development were established over 40 years ago and have been refined over the years to produce a new generation of HAPs that are under preclinical and clinical development. The purpose of this article is to describe current progress in the development of HAPs focusing on the mechanisms of action, preclinical properties and clinical progress of leading examples

CMS Distribution Subsystem user`s guide. Software Version 2.0

The Common Mapping Standard (CMS) Data Production System (CDPS) produces and distributes CMS data in compliance with the Common Mapping Standard Interface Control Document. CDPS is composed of two subsystems the CMS Distribution Subsystem (CDS) and the CMS Preprocessing Subsystem (CPS). This guide describes the operation of CDS. CDS is responsible for the management of archived CMS data, the management of production orders, and the generation of theater databases. This subsystem was developed for use on a workstation running Ultrix 4.2, the X Window System Version X11R4, and motif Version 1.1. CDS is organized into seven major functional groups and supports archiving and distributing CMS data for selected products

H2-O2 porous fuel injection in a radical farming scramjet

This paper reports on the experimental testing of oxygen compatible ceramic matrix composite porous injectors in a nominally two-dimensional hydrogen fuelled and oxygen enriched radical farming scramjet in the T4 shock tunnel facility. All experiments were performed at a dynamic pressure of 146 kPa, an equivalent flight Mach number of 9.7, a stagnation pressure and enthalpy of 40MPa and 4.3 MJ/kg respectively and at a fuelling condition that resulted in an average equivalence ratio of 0.472. Oxygen was pre-mixed with the fuel prior to injection to achieve enrichment percentages of approximately 13%, 15% and 17%. These levels ensured that the hydrogen-oxidiser mix injected into the engine always remained too fuel rich to sustain a flame without any additional mixing with the captured air. Addition of pre-mixed oxygen with the fuel was found to significantly alter the performance of the engine; enhancing both combustion and ignition and converting a previously observed limited combustion condition into one with sustained and noticeable combustion induced pressure rise. Increases in the enrichment percentage lead to further increases in combustion levels and acted to reduce ignition lengths within the engine. Suppressed combustion runs, where a nitrogen test gas was used, confirmed that the pressure rise observed in these experiments as attributed to the oxygen enrichment and not associated with the increased mass injected

Work-based learning at higher education level: value, practice and critique

Since the 1980s there has been significant growth in the engagement of higher education with workforce development, with among other things the emergence of a distinct if varied area of provision commonly referred to as work-based learning. Recent examination of practice and literature indicates a growing sophistication in the way that work-based learning is being theorised and facilitated in higher education, with its gradual emergence as a distinct field of practice and study supported by relevant pedagogies and concepts of curriculum. Tensions continue to exist between the demands and opportunities provided by the workplace and the need to develop capable practice, support personal development and maintain academic validity; however, universities are beginning to engage with these issues at a deeper level than that suggested by simple notions of employer engagement and skills development, and the evidence indicates that well-designed work-based programmes are both effective and robust