Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Controlled hypercapnia and neonatal cerebral artery Doppler ultrasound waveforms

Eleven normal term infants undergoing respiratory assessment involving rebreathing to produce progressive hypercapnia were studied by Doppler ultrasound examination of an anterior cerebral artery during the procedure. A linear increase in end tidal carbon dioxide concentration from 4.5% to a maximum of 8.5% was documented during a period of 4-5 min rebreathing. A corresponding elevation of transcutaneous carbon dioxide tension was shown in the two infants monitored in this way. In all cases the Pourcelot index fell with rising end tidal carbon dioxide concentration. This fall in Pourcelot index was due to an increase in the diastolic frequency of the Doppler waveform. These results are consistent with the view that Pourcelot index correlates with cerebral vascular resistance distal to the site of recording

The concept of the absent curriculum: the case of the Muslim contribution and the English National Curriculum for history

This paper introduces the concept of the absent curriculum on the premise that the study of curriculum has been prone to privileging curricular presence to the exclusion of curricular absence. In order to address this imbalance and to articulate a theory of absence in the curriculum, the paper applies ideas derived from the philosophy of critical realism—‘absence’ and ‘totality’—to curriculum theory to conceive of the absent curriculum. The paper outlines three components of the absent curriculum: the null curriculum at the level of national curricular policy, the unselected curriculum at the level of school curricular planning and the unenacted curriculum at the classroom level of teacher delivery. This conceptual framework is illustrated by a case example of how the absence of the history of Muslim contribution from the teaching of the National Curriculum for history in four English schools formed an absent curriculum which prompted some of the research sample of 295 British Muslim boys to disengage from their learning of history. The paper concludes that the absent curriculum is a hidden curriculum that suggests to groups whose histories are missing from the national curricula that they are relatively insignificant citizens in the community of the nation

Helping Muslim boys succeed: the case for history education

Recent research suggests that Muslim boys have become the ‘New Folk Devils’ of British education, who are characterised by resistance to formal education, especially at secondary level, and under‐achievement. Since the 1990s, British Muslim boys would appear to have become increasingly alienated from compulsory schooling, especially in the humanities subjects which lack obvious instrumental value. This mixed‐methods study of the performance of 295 secondary school British Muslim boys in their compulsory school history provides evidence which interrupts this narrative of the academic under‐achievement and educational dis‐engagement of Muslim boys, especially in the humanities subjects. When viewed through the prism of a laminated, non‐reductive model of educational success, this indicative sample of British Muslim boys could be considered to have had significant success at a traditional humanities subject such as history intellectually, spiritually, emotionally, instrumentally and civically. This paper therefore proposes that history can provide a vital meaning‐making tool to generate the success of Muslim boys in a variety of significant dimensions both in and out of school. It suggests how history can be more fully and effectively harnessed by teachers, parents and policy‐planners to encourage internal integration and external social engagement in British Muslim pupils