IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

Transmitting Chinese Medicine: Changing Perceptions of Body, Pathology, and Treatment in Late Imperial China

Historians of Chinese medicine acknowledge the plurality of Chinese medicine along both synchronic and diachronic dimensions. Yet, there remains a tendency to think of tradition as being defined by some unchanging features. The Chinese medical body is a case in point. This is assumed to have been formalised by the late Han dynasty around a system of internal organs, conduits, collaterals, and associated body structures. Although criticism was voiced from time to time, this body and the micro/ macrocosmic cosmological resonances that underpin it are seen to persist until the present day. I challenge this view by attending to attempts by physicians in China and Japan in the period from the mid 16th to the late 18th century to reimagine this body. Working within the domain of cold damage therapeutics and combining philological scholarship, empirical observations, and new hermeneutic strategies these physicians worked their way towards a new territorial understanding of the body and of medicine as warfare that required an intimate familiarity with the body’s topography. In late imperial China this new view of the body and medicine was gradually re-absorbed into the mainstream. In Japan, however, it led to a break with this orthodoxy that in the Republican era became influential in China once more. I argue that attending further to the innovations of this period—commonly portrayed as one of decline—from a transnational perspective may help to go beyond the modern insistence to frame East Asian medicines as traditional.

Performance of an adaptive homodyne receiver in the presence of multipath, Rayleigh-fading and time-varying quadrature errors

In this paper, we carry out a detailed performance analysis of the blind source separation based I/Q corrector operating at the baseband. Performance of the digital I/Q corrector is evaluated not only under time-varying phase and gain errors but also in the presence of multipath and Rayleigh fading channels. Performance under low-SNR and different modulation formats and constellation sizes is also evaluated. What is more, BER improvement after correction is illustrated. The results indicate that the adaptive algorithm offers adequate performance for most communication applications hence, reducing the matching requirements of the analog front-end enabling higher levels of integration.

Affective Computing to Enhance E-Learning in Segregated Societies

According to UN Women, to build stronger economies, it is essential to empower women to participate fully in economic life across all sectors. Increasing women and girls’ education enhances their chances to participate in the labor market. In certain cultures, like in Saudi Arabia, women contribution to the public economy growth is very limited. According to the World Bank, less than 20 percent of the female population participate in the labor force. This low participation rate has many reasons. One of them, is the educational level and educational quality for females. Although Saudi Arabia has about thirty three universities, opportunities are still limited for women because of the restrictions of access put upon them. A mixture of local norms, traditions, social beliefs, and principles preventing women from receiving full benefits from the educational system. Gender segregation is one of the challenges that limits the women access for education. It causes a problem due to the shortage of female faculty throughout the country. To overcome this problem, male faculty are allowed to teach female students under certain regulations and following a certain method of education delivery and interaction. However, most of these methods lack face-to-face communication between the teacher and students, which lowers the interactivity level and, accordingly, the students’ engagement, and increases the need for other alternatives. The e-learning model is one of high benefit for female students in such societies. Recognizing the students’ engagement is not straightforward in the e-learning model. To measure the level of engagement, the learner’s mood or emotions should be taken into consideration to help understanding and judging the level of engagement. This paper is to investigate the relationship between emotions and engagement in the e-learning environment, and how recognizing the learner’s emotions and change the content delivery accordingly can affect the efficiency of the e-learning process. The proposed experiment alluded to herein should help to find ways to increase the engagement of the learners, hence, enhance the efficiency of the learning process and the quality of learning, which will increase the chances and opportunities for women in such societies to participate more effectively in the labor market.