Protograph-Based LDPC Code Design for Probabilistic Shaping with On-Off Keying

This work investigates protograph-based LDPC codes for the AWGN channel with OOK modulation. A non-uniform distribution of the OOK modulation symbols is considered to improve the power efficiency especially for low SNRs. To this end, a specific transmitter architecture based on time sharing is proposed that allows probabilistic shaping of (some) OOK modulation symbols. Tailored protograph-based LDPC code designs outperform standard schemes with uniform signaling and off-the-shelf codes by 1.1 dB for a transmission rate of 0.25 bits/channel use.Comment: Invited Paper for CISS 201

First experimental evidence of hop fibres in historical textiles

Hop (Humulus lupulus) has been used in Scandinavia since at least the ninth century AD, as documented through archaeological findings and written, historical records. The written records are mainly focused on the use of cone-shaped flowers for beer brewing and medical purposes, but there are also records, for example, from the famous Swedish botanist Carl von Linne, who mentions the use of hop fibres for textile production. However, until now no experimental investigations have been published on the use of hop fibres in cultural heritage objects. A major reason for this has been the lack of a suitable characterization method. Hop is a bast fibre, just as flax and hemp and bast fibres cannot be distinguished from each other by simple optical inspection. Recently a new identification method for hop fibres was published by the authors of this article. Here we apply the new method in an investigation of two Swedish cultural heritage objects: (i) a woman’s garment from the nineteenth century, which was labelled as having an upper section made from coarse linen and a bottom section made of hemp and hop and (ii) a textile fragment from an eighteenth-century textile sample book, which was labelled as being made from hop. We show that the woman’s garment is made with hop and hemp fibres and the textile fragment from the textile sample book is made with hop. Our work provides the first direct proof that hop fibres were used for textiles in the past.publishedVersio

AIA Pavilion

Each template was cut from PETG (glycol-modified polyethylene terephthalate) sheets, before being thermoformed into shape using a neatly designed adaptable mould. This material can either be produced from recycled plastic, or more pertinent to this location, from sugar cane: a plant that has been an integral part of the culture of Louisiana for over 200 years.https://openscholarship.wustl.edu/bcs/1169/thumbnail.jp

Some aspects of a large deviations theory

SIGLEAvailable from British Library Document Supply Centre-DSC:DXN019854 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

PENGARUH LAMA FERMENTASI DENGAN Lentinus edodes TERHADAP KANDUNGAN BAHAN KERING, PROTEIN KASAR DAN RETENSI NITROGEN DARI CAMPURAN LIMBAH PEMIPILAN JAGUNG DAN AMPAS TAHU

Penelitian ini dilakukan untuk mengetahui pengaruh lama fermentasi dengan Lentinus edodes terhadap kandungan bahan kering, protein kasar dan retensi nitrogen dari campuran limbah buah jagung dan ampas tahu. Penelitian ini menggunakan metode eksperimen dengan Rancangan Acak Lengkap (RAL) 4 perlakuan yaitu : L5 = lama fermentasi 5 hari, L10 = lama fermentasi 10 hari , L15 = lama fermentasi 15 hari, L20 = lama fermentasi 20 hari dengan 5 kali ulangan.Parameter yang diukur adalah kandungan bahan kering (%), protein kasar (%) dan retensi nitrogen (%). Hasil uji sidik ragam menunjukkan bahwa lama fermentasi campuran limbah pemipilan jagung dan ampas tahu dengan Lentinus edodes memberikan pengaruh yang berbeda sangat nyata (P<0,01) terhadap kandungan bahan kering ,kandungan protein kasar dan retensi nitrogen. Dari hasil penelitian ini dapat disimpulkan bahwa lama fermentasi 10 hari merupakan hasil terbaik dengan kandungan bahan kering yang diperoleh 36,63%, protein kasar 19,98% dan retensi nitrogen 52,69%. Kata kunci : Ampas tahu, Lentinus edodes, Limbah pemipilan jagung dan kualitas protei

Development of an in vitro rat proximal tubule cell model as a platform for drug transporter and drug-drug interaction studies

PhD ThesisThe kidney plays a vital role in the elimination of many endogenous metabolites and xenobiotics. Drug transporters expressed in the proximal tubule cells are key factors in the ability of the organ to successfully carry out its function. Previously, primary human proximal tubule cells have been shown to retain a remarkable degree of differentiation in culture and provide a realistic model of the proximal tubule. To address the challenge of extrapolation of drug transporter data from animal and human, this project was set out to develop a parallel rat proximal tubule cell model. This would allow direct comparison of the handling of candidate drugs in both species, and provide better understanding of the mechanisms of drug transport. A technique to isolate primary rat proximal tubule cells (PTCs) was successfully developed using a collagenase digest/Percoll gradient approach. Rat PTCs cultured for 6 days were shown to exhibit cobberstone morphology, typical of many epithelial cells. A range of transport proteins including Mdr1a/b, Bcrp, Mrp2, Oat1, Oct2, Oatp4c1, Slc2a9, Urat1, Mate1, and Mct1 were detected at the mRNA level in these cells. Functional expression of Mdr1a/b, Bcrp, Mrp2, Oct2 and Mct1 was also detected using fluorescence substrate retention assays. In addition, Mdr1a/b, Bcrp and Mrp2 transporters were found localised on the apical membrane of polarised rat PTC monolayer, and Oct2 was found on the basolateral membrane. The handling of urate by rat PTC monolayers was investigated. The monolayers showed absorptive and secretory pathways for urate, although the absorptive pathway was 3.2-fold higher in magnitude. Similarly, 3.4-times more urate was predominant across the apical than across the basolateral membrane. Oat1 and Bcrp were deduced as the transporters responsible for the secretory pathway, and Urat1 and Slc2a9 in the absorptive pathway. This was in accordance with the human PTC monolayers, and both models were representative of urate transport in vivo. Digoxin transport exhibited a net absorptive flux in rat PTC monolayers; absorptive flux was 1.7-fold higher in magnitude than the secretory flux. In contrast, in human PTC monolayers, digoxin secretory flux was 4.2-fold higher than the absorptive flux. In human PTC monolayers, digoxin secretion consisted of OATP4C1-mediated digoxin uptake by the basolateral membrane and MDR1-mediated efflux across the apical membrane. In rat PTC monolayers in addition to these pathways, a significant Oatp-mediated absorptive flux of digoxin located on the apical membrane of rat PTC monolayer was identified as the difference between rat and human digoxin handling, resulting in a dominant absorptive flux of digoxin in rat compared to net secretion in human PTC monolayers. These data alone highlight the importance of developing realistic in vitro human and rat PTC models to understand species difference in renal drug handling

CPEB and miR-15/16 Co-Regulate Translation of Cyclin E1 mRNA during Xenopus Oocyte Maturation.

Cell cycle transitions spanning meiotic maturation of the Xenopus oocyte and early embryogenesis are tightly regulated at the level of stored inactive maternal mRNA. We investigated here the translational control of cyclin E1, required for metaphase II arrest of the unfertilised egg and the initiation of S phase in the early embryo. We show that the cyclin E1 mRNA is regulated by both cytoplasmic polyadenylation elements (CPEs) and two miR-15/16 target sites within its 3'UTR. Moreover, we provide evidence that maternal miR-15/16 microRNAs co-immunoprecipitate with CPE-binding protein (CPEB), and that CPEB interacts with the RISC component Ago2. Experiments using competitor RNA and mutated cyclin E1 3'UTRs suggest cooperation of the regulatory elements to sustain repression of the cyclin E1 mRNA during early stages of maturation when CPEB becomes limiting and cytoplasmic polyadenylation of repressed mRNAs begins. Importantly, injection of anti-miR-15/16 LNA results in the early polyadenylation of endogenous cyclin E1 mRNA during meiotic maturation, and an acceleration of GVBD, altogether strongly suggesting that the proximal CPEB and miRNP complexes act to mutually stabilise each other. We conclude that miR-15/16 and CPEB co-regulate cyclin E1 mRNA. This is the first demonstration of the co-operation of these two pathways.This study was supported by the Biotechnology and Biological Sciences Research Council (BB/E016316/1). AG was funded by Cancer Research UK and the RATHER consortium, and JA was funded by the Cambridge Overseas Trust and the Parke Davis Bursary (Downing College).This is the final version of the article. It first appeared from PLOS via https://doi.org/10.1371/journal.pone.014679

Geometry of vectorial martingale optimal transport and robust option pricing

This paper addresses robust finance, which is concerned with the development of models and approaches that account for market uncertainties. Specifically, we investigate the Vectorial Martingale Optimal Transport (VMOT) problem, the geometry of its solutions, and its application with robust option pricing problems in finance. To this end, we consider two-period market models and show that when the spatial dimension $d$ (the number of underlying assets) is 2, the extremal model for the cap option with a sub- or super-modular payout reduces to a single factor model in the first period, but not in general when $d > 2$. The result demonstrates a subtle relationship between spatial dimension, cost function supermodularity, and their effect on the geometry of solutions to the VMOT problem. We investigate applications of the model to financial problems and demonstrate how the dimensional reduction caused by monotonicity can be used to improve existing computational methods

An improved protocol for small RNA library construction using High Definition adapters

Next generation sequencing of small RNA (sRNA) libraries is widely used for studying sRNAs in various biological systems. However, cDNA libraries of sRNAs are biased for molecules that are ligated to adapters more or less efficiently than other molecules. One approach to reduce this ligation bias is to use a pool of adapters instead of a single adapter sequence, which allows many sRNAs to be ligated efficiently. We previously developed High Definition (HD) adapters for the Illumina sequencing platform, which contain degenerate nucleotides at the ligating ends of the adapters. However, the current commercial kits produced a large amount of 5’ adapter – 3’ adapter ligation product without the cDNA insert when HD adapters were used to replace the kit adapters. Here, we report a protocol to generate sRNA libraries using HD adapters with dramatically reduced adapter-adapter product. This protocol was developed from the procedure invented by Vaidyanathan et al. The libraries can be completed within two days and can be used for various biological and clinical samples. As examples for using this protocol, we constructed sRNA libraries using total RNA extracted from cultured mammalian cells and plant leaf tissue. The PCR products contained a very small amount of adapter-adapter product. Bioinformatic analysis of the sequencing data revealed sRNAs with diverse sequences and many different miRNA families

Enzyme- and gene-specific biases in reverse transcription of RNA raise concerns for evaluating gene expression

Abstract: Reverse transcription is the first step of most analyses of gene expression, yet the quantitative biases it introduces are largely overlooked. Following a series of purpose-designed systematic experiments we cherry-pick examples of various biases introduced by reverse transcription, and alert the “gene expression community” to the pitfalls and improved practice of this fundamental technique