G-spots cause incorrect expression measurement in Affymetrix microarrays

Abstract Background High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene's probe set will provide a consistent message signifying the gene's presence. However, probes that contain a G-spot (a sequence of four or more guanines) behave abnormally and it has been suggested that these probes are responding to some biochemical effect such as the formation of G-quadruplexes. Results We have tested this expectation by examining the correlation coefficients between pairs of probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. We confirm the finding that G-spot probes are poorly correlated with others in their probesets and reveal that, by contrast, they are highly correlated with one another. We demonstrate that the correlation is most marked when the G-spot is at the 5' end of the probe. Conclusion Since these G-spot probes generally show little correlation with the other members of their probesets they are not fit for purpose and their values should be excluded when calculating gene expression values. This has serious implications, since more than 40% of the probesets in the HG-U133A GeneChip contain at least one such probe. Future array designs should avoid these untrustworthy probes. </jats:sec

A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia

We have previously discovered that probes containing runs of four or more contiguous guanines are not reliable for measuring gene expression in the Human HG_U133A Affymetrix GeneChip data. These probes are not correlated with other members of their probe set, but they are correlated with each other. We now extend our analysis to different3′GeneChip designs of mouse, rat, and human. We find that, in all these chip designs, the G-stack probes (probes with a run of exactly four consecutive guanines) are correlated highly with each other, indicating that such probes are not reliable measures of gene expression in mammalian studies. Furthermore, there is no specific position of G-stack where the correlation is highest in all the chips. We also find that the latest designs of rat and mouse chips have significantly fewer G-stack probes compared to their predecessors, whereas there has not been a similar reduction in G-stack density across the changes in human chips. Moreover, we find significant changes in RMA values (after removing G-stack probes) as the number of G-stack probes increases.</jats:p

Fluid and Diffusion Limits for Bike Sharing Systems

Bike sharing systems have rapidly developed around the world, and they are served as a promising strategy to improve urban traffic congestion and to decrease polluting gas emissions. So far performance analysis of bike sharing systems always exists many difficulties and challenges under some more general factors. In this paper, a more general large-scale bike sharing system is discussed by means of heavy traffic approximation of multiclass closed queueing networks with non-exponential factors. Based on this, the fluid scaled equations and the diffusion scaled equations are established by means of the numbers of bikes both at the stations and on the roads, respectively. Furthermore, the scaling processes for the numbers of bikes both at the stations and on the roads are proved to converge in distribution to a semimartingale reflecting Brownian motion (SRBM) in a $N^{2}$-dimensional box, and also the fluid and diffusion limit theorems are obtained. Furthermore, performance analysis of the bike sharing system is provided. Thus the results and methodology of this paper provide new highlight in the study of more general large-scale bike sharing systems.Comment: 34 pages, 1 figure

Chemical potential oscillations from a single nodal pocket in the underdoped high-Tc superconductor YBa2Cu3O6+x

The mystery of the normal state in the underdoped cuprates has deepened with the use of newer and complementary experimental probes. While photoemission studies have revealed solely `Fermi arcs' centered on nodal points in the Brillouin zone at which holes aggregate upon doping, more recent quantum oscillation experiments have been interpreted in terms of an ambipolar Fermi surface, that includes sections containing electron carriers located at the antinodal region. To address the question of whether an ambipolar Fermi surface truly exists, here we utilize measurements of the second harmonic quantum oscillations, which reveal that the amplitude of these oscillations arises mainly from oscillations in the chemical potential, providing crucial information on the nature of the Fermi surface in underdoped YBa2Cu3O6+x. In particular, the detailed relationship between the second harmonic amplitude and the fundamental amplitude of the quantum oscillations leads us to the conclusion that there exists only a single underlying quasi-two dimensional Fermi surface pocket giving rise to the multiple frequency components observed via the effects of warping, bilayer splitting and magnetic breakdown. A range of studies suggest that the pocket is most likely associated with states near the nodal region of the Brillouin zone of underdoped YBa2Cu3O6+x at high magnetic fields.Comment: 7 pages, 4 figure

Execution of the SimSET Monte Carlo PET/SPECT Simulator in the Condor Distributed Computing Environment

SimSET is a package for simulation of emission tomography data sets. Condor is a popular distributed computing environment. Simple C/C++ applications and shell scripts are presented which allow the execution of SimSET on the Condor environment. This is accomplished without any modification to SimSET by executing multiple instances and using its combinebin utility. This enables research facilities without dedicated parallel computing systems to utilize the idle cycles of desktop workstations to greatly reduce the run times of their SimSET simulations. The necessary steps to implement this approach in other environments are presented along with sample results

Single-plant chambers to control humidity for pathological studies

The construction of a set of controlled-humidity chambers for single plants is described. Accurate control of relative humidity (r.h.) between 40% and 99% was achieved by mixing dry air with a saturated air stream using solenoid valves controlled by a programmable data logger. At values of r.h. >90%, mean values over periods greater than 1 min were constant to within ±0-1% and spot measurements at 3 s intervals were within 0-3% of the mean value. The system responded to a step change of r.h. in about 6-10 min and diurnal changes of r.h. were reproduced, similar to those observed in nature. The stability of control made it possible to differentiate between the requirement of liquid water and very high humidity (98% r.h.) for conidial germination and subsequent infection of groundnut by Phaeoisariopsis personata, the cause of late leaf spot disease

Annular pigment band on the posterior capsule following blunt ocular trauma: a case report

BACKGROUND: To report an unusual case of annular pigment band on the posterior capsule following blunt ocular trauma. CASE PRESENTATION: We describe an annular pigment band on the posterior capsule following blunt ocular trauma in a 28-year old male patient. Repeat examinations revealed no evidence of other signs of blunt ocular trauma or pigment dispersion syndrome in either eye. CONCLUSION: The annular pigment band in this case corresponds to the adherence of the hyaloideocapsulare ligament to the posterior capsule and reconfirms its rare visualization in the living eye. This finding may be an isolated sign of blunt ocular trauma and a compromised integrity of the vitreolenticular interface should be strongly suspected. We recommend careful documentation in context of future cataract surgery in these eyes

A mathematical modelling study of an athlete's sprint time when towing a weighted sled

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s12283-013-0114-2.This study used a mathematical model to examine the effects of the sled, the running surface, and the athlete on sprint time when towing a weighted sled. Simulations showed that ratio scaling is an appropriate method of normalising the weight of the sled for athletes of different body size. The relationship between sprint time and the weight of the sled was almost linear, as long as the sled was not excessively heavy. The athlete’s sprint time and rate of increase in sprint time were greater on running surfaces with a greater coefficient of friction, and on any given running surface an athlete with a greater power-to-weight ratio had a lower rate of increase in sprint time. The angle of the tow cord did not have a substantial effect on an athlete’s sprint time. This greater understanding should help coaches set the training intensity experienced by an athlete when performing a sled-towing exercise

Simulating quantum statistics with entangled photons: a continuous transition from bosons to fermions

In contrast to classical physics, quantum mechanics divides particles into two classes-bosons and fermions-whose exchange statistics dictate the dynamics of systems at a fundamental level. In two dimensions quasi-particles known as 'anyons' exhibit fractional exchange statistics intermediate between these two classes. The ability to simulate and observe behaviour associated to fundamentally different quantum particles is important for simulating complex quantum systems. Here we use the symmetry and quantum correlations of entangled photons subjected to multiple copies of a quantum process to directly simulate quantum interference of fermions, bosons and a continuum of fractional behaviour exhibited by anyons. We observe an average similarity of 93.6\pm0.2% between an ideal model and experimental observation. The approach generalises to an arbitrary number of particles and is independent of the statistics of the particles used, indicating application with other quantum systems and large scale application.Comment: 10 pages, 5 figure

Surgical Treatment of Iatrogenic Ventral Glottic Stenosis Using a Mucosal Flap Technique

OBJECTIVE: To describe a novel surgical technique for correcting postoperative ventral glottic stenosis (cicatrix or web formation) and the outcome in 2 Thoroughbred racehorses. STUDY DESIGN: Retrospective case report. ANIMALS: Thoroughbreds diagnosed with ventral glottic stenosis (n=2). METHODS: Horses presenting with iatrogenic ventral glottic stenosis and resultant exercise intolerance and abnormal exercise‐related noise were anesthetized and a midline sagittal skin incision was made over the ventral larynx and between the sternohyoideus muscles overlying the cricothyroid notch. The cricothyroid ligament, attached laryngeal cicatrix, and overlying mucosa were sagittally sectioned at the dorsal aspect of the cicatrix on the left side. The laryngeal mucosa, cicatrix, and underlying cricothyroid ligament immediately rostral and caudal to the cicatrix were sectioned in a medial (axial) direction as far as the right side of the cricothyroid notch. After resection of the majority of the attached cicatrix tissue, the residual mucosal flap (attached to the right side of the larynx) was reflected ventrally and sutured to the attachment of the cricothyroid ligament on the right side of the cricothyroid notch, creating an intact mucosal layer on the right side of the ventral larynx. RESULTS: Both horses had good intralaryngeal wound healing with minimal redevelopment of ventral glottic stenosis at 5 and 9 months postoperatively and were successfully returned to racing with complete absence of abnormal respiratory noise. CONCLUSION: The unique laryngeal anatomy of horses, with a cartilage‐free ventral laryngeal area (cricothyroid notch), allowed the use of this novel surgical technique to successfully treat ventral glottic stenosis