Robustly detecting differential expression in RNA sequencing data using observation weights

A popular approach for comparing gene expression levels between (replicated) conditions of RNA sequencing data relies on counting reads that map to features of interest. Within such count-based methods, many flexible and advanced statistical approaches now exist and offer the ability to adjust for covariates (e.g. batch effects). Often, these methods include some sort of ‘sharing of information' across features to improve inferences in small samples. It is important to achieve an appropriate tradeoff between statistical power and protection against outliers. Here, we study the robustness of existing approaches for count-based differential expression analysis and propose a new strategy based on observation weights that can be used within existing frameworks. The results suggest that outliers can have a global effect on differential analyses. We demonstrate the effectiveness of our new approach with real data and simulated data that reflects properties of real datasets (e.g. dispersion-mean trend) and develop an extensible framework for comprehensive testing of current and future methods. In addition, we explore the origin of such outliers, in some cases highlighting additional biological or technical factors within the experiment. Further details can be downloaded from the project website: http://imlspenticton.uzh.ch/robinson_lab/edgeR_robus

Spectroscopic Evidence That the Extreme Properties of IRAS F10214+4724 are due to Gravitational Lensing

The extreme bolometric luminosity of IRAS F10214+4724, and in particular the huge mass in molecular gas inferred from the CO line fluxes have led to suggestions that this is a giant galaxy in the process of formation. An arc-like structure and the closeness of a second object suggest, however, that gravitational lensing may be responsible for its anomalously high luminosity and mass. In this paper, we use an optical spectrum taken in conditions of 0.7-arcsec seeing to provide further evidence that F10214+4724 is a gravitationally lensed system. We measure tentative redshifts of 0.896 and 0.899 for galaxies projected $\approx 1$ and $\approx 3$ arcsec from IRAS F10214+4724 respectively. Identifying the former as the lensing galaxy we obtain a mass:light ratio consistent with those derived for other lenses, and find that its luminosity is consistent with the velocity dispersion deduced from the radius of the Einstein ring. If lensed, our models suggest magnification by a factor $\sim 10$, and hence an intrinsic bolometric luminosity for F10214+4724 similar to local ULIRGs.Comment: 5 pages, uuencoded compressed PostScript, 3 figures included. Accepted for publication in MNRAS pink pages; submitted 1 May 199

An evaluation of methods used to assess fat cover in live cattle

[Summary]: Five methods of assessing subcutaneous fat cover were compared using male and female Bos indicus - Bos taurus beef cattle. None of the methods was able to accurately predict fat depth. The ESTD FAT technique has the greatest potential because it requires minimal handling. Use of the TRANS site may assist to improve accuracy with the ESTD FAT technique

A tactile method modified to assess the finish of beef cattle in marketable condition in north Queensland

Three methods of assessing the fat finish of marketable beef cattle were compared using Bos indicus crossbred cattle. The methods were: the Queensland Livestock Market Reporting Service, the National Beef Recording Scheme and a modified tactile method (MT) of the Meat and Livestock Commission. None of the three methods was able to predict accurately the fat depth at the 13th rib of the carcass. The highest correlation between finish score and fat depth was r = 0.568 for one operator using the MT method. However, wehn data from the MT method were examined it was found that mean fat depth at the 13th rib increased (P<0.05) with increasing finish score in two of the three liveweight categories studied. It is suggested that scoring individual animals on finish is no more accurate than weighing and allocating them to finish categories on the basis of liveweight

The Influence of Motion and Stress on Optical Fibers

We report on extensive testing carried out on the optical fibers for the VIRUS instrument. The primary result of this work explores how 10+ years of simulated wear on a VIRUS fiber bundle affects both transmission and focal ratio degradation (FRD) of the optical fibers. During the accelerated lifetime tests we continuously monitored the fibers for signs of FRD. We find that transient FRD events were common during the portions of the tests when motion was at telescope slew rates, but dropped to negligible levels during rates of motion typical for science observation. Tests of fiber transmission and FRD conducted both before and after the lifetime tests reveal that while transmission values do not change over the 10+ years of simulated wear, a clear increase in FRD is seen in all 18 fibers tested. This increase in FRD is likely due to microfractures that develop over time from repeated flexure of the fiber bundle, and stands in contrast to the transient FRD events that stem from localized stress and subsequent modal diffusion of light within the fibers. There was no measurable wavelength dependence on the increase in FRD over 350 nm to 600 nm. We also report on bend radius tests conducted on individual fibers and find the 266 microns VIRUS fibers to be immune to bending-induced FRD at bend radii of R > 10cm. Below this bend radius FRD increases slightly with decreasing radius. Lastly, we give details of a degradation seen in the fiber bundle currently deployed on the Mitchell Spectrograph (formally VIRUS-P) at McDonald Observatory. The degradation is shown to be caused by a localized shear in a select number of optical fibers that leads to an explosive form of FRD. In a few fibers, the overall transmission loss through the instrument can exceed 80%.Comment: 19 pages, 22 figure

The Disconnect Between the Guidelines, the Appropriate Use Criteria, and Reimbursement Coverage Decisions The Ultimate Dilemma

Recently, the American College of Cardiology Foundation in collaboration with the Heart Rhythm Society published appropriate use criteria (AUC) for implantable cardioverter-defibrillators and cardiac resynchronization therapy. These criteria were developed to critically review clinical situations that may warrant implantation of an implantable cardioverter-defibrillator or cardiac resynchronization therapy device, and were based on a synthesis of practice guidelines and practical experience from a diverse group of clinicians. When the AUC was drafted, the writing committee recognized that some of the scenarios that were deemed “appropriate” or “may be appropriate” were discordant with the clinical requirements of many payers, including the Medicare National Coverage Determination (NCD). To charge Medicare for a procedure that is not covered by the NCD may be construed as fraud. Discordance between the guidelines, the AUC, and the NCD places clinicians in the difficult dilemma of trying to do the “right thing” for their patients, while recognizing that the “right thing” may not be covered by the payer or insurer. This commentary addresses these issues. Options for reconciling this disconnect are discussed, and recommendations to help clinicians provide the best care for their patients are offered