Ultraplex- A rapid, flexible, all-in-one fastq demultiplexer [version 1; peer review- 1 approved]

BACKGROUND: The first step of virtually all next generation sequencing analysis involves the splitting of the raw sequencing data into separate files using sample-specific barcodes, a process known as “demultiplexing”. However, we found that existing software for this purpose was either too inflexible or too computationally intensive for fast, streamlined processing of raw, single end fastq files containing combinatorial barcodes. RESULTS: Here, we introduce a fast and uniquely flexible demultiplexer, named Ultraplex, which splits a raw FASTQ file containing barcodes either at a single end or at both 5’ and 3’ ends of reads, trims the sequencing adaptors and low-quality bases, and moves unique molecular identifiers (UMIs) into the read header, allowing subsequent removal of PCR duplicates. Ultraplex is able to perform such single or combinatorial demultiplexing on both single- and paired-end sequencing data, and can process an entire Illumina HiSeq lane, consisting of nearly 500 million reads, in less than 20 minutes. CONCLUSIONS: Ultraplex greatly reduces computational burden and pipeline complexity for the demultiplexing of complex sequencing libraries, such as those produced by various CLIP and ribosome profiling protocols, and is also very user friendly, enabling streamlined, robust data processing. Ultraplex is available on PyPi and Conda and via Github

Contralateral Total Hip Arthroplasty After Hindquarter Amputation

We describe the management and outcome of a 62-year old lady who developed severe osteoarthritis of the hip, nine years after a hindquarter amputation for radiation-induced sarcoma of the contralateral pelvis. The difficulties of stabilising the pelvis intraoperatively and the problems of postoperative rehabilitation are outlined. The operation successfully relieved her pain and restored limited mobility

Prostate cancer risk: associations with ultraviolet radiation, tyrosinase and melanocortin-1 receptor genotypes

Exposure to ultraviolet radiation may reduce prostate cancer risk, suggesting that polymorphism in genes that mediate host pigmentation will be associated with susceptibility to this cancer. We studied 210 prostate cancer cases and 155 controls to determine whether vitamin D receptor (VDR, Taql and Fokl variants), tyrosinase (TYR, codon 192 variant) and melanocortin-1 receptor (MC1R, Arg151Cys, Arg160Trp, Val92Met, Asp294His and Asp84Glu variants) genotypes are associated with risk. UV exposure was determined using a questionnaire. MC1R Arg160/Arg160 homozygotes were at increased risk (P = 0.027, odds ratio = 1.94) while TYR A2/A2 homozygotes were at reduced risk of prostate cancer (P = 0.033, odds ratio = 0.48). These associations remained significant after correction for UV-exposure. Stratification of cases and controls by quartiles of exposure, showed that the protective effect of TYR A1A2 (P = 0.006, odds ratio 0.075) and A2A2 (P = 0.003, odds ratio 0.055) was particularly strong in subjects who had received the greatest exposure. Our data show for the first time, that allelism in genes linked with skin pigment synthesis is associated with prostate cancer risk possibly because it mediates the protective effects of UV. Importantly, susceptibility is associated with an interaction between host predisposition and exposure. © 2001 Cancer Research Campaign  http://www.bjcancer.co

RGS4 RNA secondary structure mediates Staufen2 RNP assembly in Neurons

RNA‐binding proteins (RBPs) act as posttranscriptional regulators controlling the fate of target mRNAs. Unraveling how RNAs are recognized by RBPs and in turn are assembled into neuronal RNA granules is therefore key to understanding the underlying mechanism. While RNA sequence elements have been extensively characterized, the functional impact of RNA secondary structures is only recently being explored. Here, we show that Staufen2 binds complex, long‐ranged RNA hairpins in the 3′‐untranslated region (UTR) of its targets. These structures are involved in the assembly of Staufen2 into RNA granules. Furthermore, we provide direct evidence that a defined Rgs4 RNA duplex regulates Staufen2‐dependent RNA localization to distal dendrites. Importantly, disrupting the RNA hairpin impairs the observed effects. Finally, we show that these secondary structures differently affect protein expression in neurons. In conclusion, our data reveal the importance of RNA secondary structure in regulating RNA granule assembly, localization and even-tually translation. It is therefore tempting to speculate that secondary structures represent an important code for cells to control the intracellular fate of their mRNAs

Nyquist method for Wigner-Poisson quantum plasmas

By means of the Nyquist method, we investigate the linear stability of electrostatic waves in homogeneous equilibria of quantum plasmas described by the Wigner-Poisson system. We show that, unlike the classical Vlasov-Poisson system, the Wigner-Poisson case does not necessarily possess a Penrose functional determining its linear stability properties. The Nyquist method is then applied to a two-stream distribution, for which we obtain an exact, necessary and sufficient condition for linear stability, as well as to a bump-in-tail equilibrium.Comment: 6 figure

Glauber dynamics in a single-chain magnet: From theory to real systems

The Glauber dynamics is studied in a single-chain magnet. As predicted, a single relaxation mode of the magnetization is found. Above 2.7 K, the thermally activated relaxation time is mainly governed by the effect of magnetic correlations and the energy barrier experienced by each magnetic unit. This result is in perfect agreement with independent thermodynamical measurements. Below 2.7 K, a crossover towards a relaxation regime is observed that is interpreted as the manifestation of finite-size effects. The temperature dependences of the relaxation time and of the magnetic susceptibility reveal the importance of the boundary conditions.Comment: Submitted to PRL 10 May 2003. Submitted to PRB 12 December 2003; published 15 April 200

Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?

In the past few years, numerous research projects have focused on identifying and understanding scaling properties in the gene content of prokaryote genomes and the intricacy of their regulation networks. Yet, and despite the increasing amount of data available, the origins of these scalings remain an open question. The RAevol model, a digital genetics model, provides us with an insight into the mechanisms involved in an evolutionary process. The results we present here show that (i) our model reproduces qualitatively these scaling laws and that (ii) these laws are not due to differences in lifestyles but to differences in the spontaneous rates of mutations and rearrangements. We argue that this is due to an indirect selective pressure for robustness that constrains the genome size

Long-term effects of a very low carbohydrate compared with a high carbohydrate diet on renal function in individuals with type 2 diabetes: a randomized trial

To compare the long-term effects of a very low carbohydrate, high-protein, low saturated fat (LC) diet with a traditional high unrefined carbohydrate, low-fat (HC) diet on markers of renal function in obese adults with type 2 diabetes (T2DM), but without overt kidney disease.One hundred fifteen adults (BMI 34.6 ± 4.3 kg/m, age 58 ± 7 years, HbA1c 7.3 ± 1.1%, 56 ± 12 mmol/mol, serum creatinine (SCr) 69 ± 15 μmol/L, glomerular filtration rate estimated by the Chronic Kidney Disease Epidemiology Collaboration formula (eGFR 94 ± 12 mL/min/1.73 m)) were randomized to consume either an LC (14% energy as carbohydrate [CHO < 50 g/day], 28% protein [PRO], 58% fat [<10% saturated fat]) or an HC (53% CHO, 17% PRO, 30% fat [<10% saturated fat]) energy-matched, weight-loss diet combined with supervised exercise training (60 min, 3 day/wk) for 12 months. Body weight, blood pressure, and renal function assessed by eGFR, estimated creatinine clearance (Cockcroft-Gault, Salazar-Corcoran) and albumin excretion rate (AER), were measured pre- and post-intervention.Both groups achieved similar completion rates (LC 71%, HC 65%) and reductions in weight (mean [95% CI]; -9.3 [-10.6, -8.0] kg) and blood pressure (-6 [-9, -4]/-6[-8, -5] mmHg), P ≥ 0.18. Protein intake calculated from 24 hours urinary urea was higher in the LC than HC group (LC 120.1 ± 38.2 g/day, 1.3 g/kg/day; HC 95.8 ± 27.8 g/day, 1 g/kg/day), P < 0.001 diet effect. Changes in SCr (LC 3 [1, 5], HC 1 [-1, 3] μmol/L) and eGFR (LC -4 [-6, -2], HC -2 [-3, 0] mL/min/1.73 m) did not differ between diets (P = 0.25). AER decreased independent of diet composition (LC --2.4 [-6, 1.2], HC -1.8 [-5.4, 1.8] mg/24 h, P = 0.24); 6 participants (LC 3, HC 3) had moderately elevated AER at baseline (30-300 mg/24 h), which normalized in 4 participants (LC 2, HC 2) after 52 weeks.Compared with a traditional HC weight loss diet, consumption of an LC high protein diet does not adversely affect clinical markers of renal function in obese adults with T2DM and no preexisting kidney disease.Jeannie Tay, Campbell H. Thompson, Natalie D. Luscombe-Marsh, Manny Noakes, Jonathan D. Buckley, Gary A. Wittert and Grant D. Brinkwort

Anomalous self-diffusion in the ferromagnetic Ising chain with Kawasaki dynamics

We investigate the motion of a tagged spin in a ferromagnetic Ising chain evolving under Kawasaki dynamics. At equilibrium, the displacement is Gaussian, with a variance growing as $A t^{1/2}$. The temperature dependence of the prefactor $A$ is derived exactly. At low temperature, where the static correlation length $\xi$ is large, the mean square displacement grows as $(t/\xi^2)^{2/3}$ in the coarsening regime, i.e., as a finite fraction of the mean square domain length. The case of totally asymmetric dynamics, where $(+)$ (resp. $(-)$) spins move only to the right (resp. to the left), is also considered. In the steady state, the displacement variance grows as $B t^{2/3}$. The temperature dependence of the prefactor $B$ is derived exactly, using the Kardar-Parisi-Zhang theory. At low temperature, the displacement variance grows as $t/\xi^2$ in the coarsening regime, again proportionally to the mean square domain length.Comment: 22 pages, 8 figures. A few minor changes and update