Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities

Two new species of Marmosopus (Acari: Astigmata) from rodents of the genus Scotinomys (Cricetidae) in Central America

http://deepblue.lib.umich.edu/bitstream/2027.42/57139/1/OP703.pd

Virtual Design of a Four-Bed Molecular Sieve for Exploration

Aboard the International Space Station, CO2 is removed from the cabin atmosphere by a four-bed molecular sieve (4BMS) process called the Carbon Dioxide Removal Assembly (CDRA).1 This 4BMS process operates by passing the CO2-laden air through a desiccant bed to remove any humidity and then passing the dried air through a sorbent bed to remove the CO2. While one pair of beds is in use, the other pair is thermally regenerated to allow for continuous CO2 removal

Interventional Radiology and the Care of the Oncology Patient

Interventional Radiology (IR) is occupying an increasingly prominent role in the care of patients with cancer, with involvement from initial diagnosis, right through to minimally invasive treatment of the malignancy and its complications. Adequate diagnostic samples can be obtained under image guidance by percutaneous biopsy and needle aspiration in an accurate and minimally invasive manner. IR techniques may be used to place central venous access devices with well-established safety and efficacy. Therapeutic applications of IR in the oncology patient include local tumour treatments such as transarterial chemo-embolisation and radiofrequency ablation, as well as management of complications of malignancy such as pain, organ obstruction, and venous thrombosis

Higher Order Correlations in Quantum Chaotic Spectra

The statistical properties of the quantum chaotic spectra have been studied, so far, only up to the second order correlation effects. The numerical as well as the analytical evidence that random matrix theory can successfully model the spectral fluctuatations of these systems is available only up to this order. For a complete understanding of spectral properties it is highly desirable to study the higher order spectral correlations. This will also inform us about the limitations of random matrix theory in modelling the properties of quantum chaotic systems. Our main purpose in this paper is to carry out this study by a semiclassical calculation for the quantum maps; however results are also valid for time-independent systems.Comment: Revtex, Four figures (Postscript files), Phys. Rev E (in press

Object knowledge modulates colour appearance

We investigated the memory colour effect for colour diagnostic artificial objects. Since knowledge about these objects and their colours has been learned in everyday life, these stimuli allow the investigation of the influence of acquired object knowledge on colour appearance. These investigations are relevant for questions about how object and colour information in high-level vision interact as well as for research about the influence of learning and experience on perception in general. In order to identify suitable artificial objects, we developed a reaction time paradigm that measures (subjective) colour diagnosticity. In the main experiment, participants adjusted sixteen such objects to their typical colour as well as to grey. If the achromatic object appears in its typical colour, then participants should adjust it to the opponent colour in order to subjectively perceive it as grey. We found that knowledge about the typical colour influences the colour appearance of artificial objects. This effect was particularly strong along the daylight axis

Quantum Spin Chains and Riemann Zeta Function with Odd Arguments

Riemann zeta function is an important object of number theory. It was also used for description of disordered systems in statistical mechanics. We show that Riemann zeta function is also useful for the description of integrable model. We study XXX Heisenberg spin 1/2 anti-ferromagnet. We evaluate a probability of formation of a ferromagnetic string in the anti-ferromagnetic ground state in thermodynamics limit. We prove that for short strings the probability can be expressed in terms of Riemann zeta function with odd arguments.Comment: LaTeX, 7 page

Rocaglates induce gain-of-function alterations to eIF4A and eIF4F

Rocaglates are a diverse family of biologically active molecules that have gained tremendous interest in recent years due to their promising activities in pre-clinical cancer studies. As a result, this family of compounds has been significantly expanded through the development of efficient synthetic schemes. However, it is unknown whether all of the members of the rocaglate family act through similar mechanisms of action. Here, we present a comprehensive study comparing the biological activities of >200 rocaglates to better understand how the presence of different chemical entities influences their biological activities. Through this, we find that most rocaglates preferentially repress the translation of mRNAs containing purine-rich 5' leaders, but certain rocaglates lack this bias in translation repression. We also uncover an aspect of rocaglate mechanism of action in which the pool of translationally active eIF4F is diminished due to the sequestration of the complex onto RNA.P50 GM067041 - NIGMS NIH HHS; R24 GM111625 - NIGMS NIH HHS; R35 GM118173 - NIGMS NIH HHSPublished versio