Affymetrix probes containing runs of contiguous guanines are not gene-specific

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 the designated probe set will provide a consistent message signifying the gene's presence. However, we demonstrate by data mining thousands of CEL files from NCBI's GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes

Pharmaceutical Surge Requirements for the Prime Vendor Program-Europe in Support of Military Operations Other than War

The U.S. military in Europe often provides medical support to military operations other than war due to unstable situations in that region of the world. The increasing support to peace operations and humanitarian assistance have led the military medical units in Europe to reexamine the pharmaceuticals traditionally maintained to support surges. This research was a qualitative, exploratory study using multiple case study strategy to identify the specific pharmaceuticals utilized in the initial stages of military operations other than war primarily peacekeeping, peace enforcement and humanitarian assistance. The operations chosen as the units of analysis were Operation Provide Promise (Croatia), Operation Support Hope (Rwanda), and Operation Joint Endeavor (Bosnia-Herzegovina). The results of the research show that some unique surge requirements exist for military operations other than war. Taking advantage of existing clauses in its Prime Vendor contracts, the military medical community in Europe can position itself to adequately support surges for MOOTW. Future studies can continue to build on this concept and identify pharmaceutical inventory to support a wide range of contingencies which can be maintained by commercial vendors for immediate access

Pyrimido[1,2-a]-purin-10(3H)-one, M(1)G, is less prone to artifact than base oxidation

Pyrimido[1,2-a]-purin-10(3H)-one (M(1)G) is a secondary DNA damage product arising from primary reactive oxygen species (ROS) damage to membrane lipids or deoxyribose. The present study investigated conditions that might lead to artifactual formation or loss of M(1)G during DNA isolation. The addition of antioxidants, DNA isolation at low temperature or non-phenol extraction methods had no statistically significant effect on the number of M(1)G adducts measured in either control or positive control tissue samples. The number of M(1)G adducts in nuclear DNA isolated from brain, liver, kidney, pancreas, lung and heart of control male rats were 0.8, 1.1, 1.1, 1.1, 1.8 and 4.2 M(1)G/10(8) nt, respectively. In rat liver tissue, the mitochondrial DNA contained a 2-fold greater number of M(1)G adducts compared with nuclear DNA. Overall, the results from this study demonstrated that measuring M(1)G is a reliable way to assess oxidative DNA damage because the number of M(1)G adducts is significantly affected by the amount of ROS production, but not by DNA isolation procedures. In addition, this study confirmed that the background number of M(1)G adducts reported in genomic DNA could have been overestimated by one to three orders of magnitude in previous reports

Evidence of hybrid institutional logics in the U.S. public research university

While the ascendancy of market behaviours in public research universities is well documented, the extent to which universities have transformed themselves into industry-like organisations has been called into question. So to what extent are universities displaying transformation in their core values? The concept of institutional logics, with its focus on the relationship between organisational design and underlying beliefs and values, shows potential to address this question. Yet study of institutional logics at the campus level has to date been limited. This paper presents an empirical analysis of three U.S. research universities’ organising principles as expressed in key mission and planning documents over a fifteen-year period. Of the multiple strategies at play in the universities’ responses to potentially competing values, the creation of new, hybrid logics is of particular interest. The concept of hybrid logics suggests a promising framework for understanding how universities can and do manage tensions in their mission

Decomposing Crude Price Differentials: Domestic Shipping Constraints or the Crude Oil Export Ban?

Over the past five years the U.S. domestic crude benchmark, WTI, diverged considerably from its foreign counterpart, Brent. Some studies pointed to the crude oil export ban as the main culprit for this divergence, but pipeline capacity was also scarce during this time. To understand the drivers of domestic crude oil discounts, we decompose domestic price differentials for multiple crudes into the contributions of shipping and export constraints. We find that scarce pipeline capacity explains the majority of the deviation of mid-continent crude oil prices from their long-run relationship with Brent crude, while refining changes explain very little. This implies that the deleterious effects of the export ban may have been exaggerated

Investigation of the Muffling Problem for Airplane Engines

The experimentation presented in this report falls in two divisions: first, the determination of the relation between back pressure in the exhaust line and consequent power loss, for various combinations of speed and throttle positions of the engine; second, the construction and trial of muffler designs covering both type and size. Report deals with experiments in the development of a muffler designed on the principle which will give the maximum muffling effect with a minimum loss of power. The main body of the work has been done on a Curtiss OX eight-cylinder airplane engine, 4 by 5 inches, rated 70 horsepower at 1,200 revolutions per minute. For estimation of the muffling ability and suppression of "bark" of individual exhausts, the "Ingeco" stationary, single cylinder, 5 1/2 by 10 inch, throttling governed gasoline engine, and occasionally other engines were used

G-spots cause incorrect expression measurement in Affymetrix microarrays

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. We have tested this expectation by examining the correlations between probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. Results: We have identified probes that are not well-correlated with the other probes in their probeset but nevertheless are highly correlated with probes in other probesets. The common element of these highly correlated probes is that they contain a G-spot (a sequence of four or more guanines). Conclusions: 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

Large emergency-response exercises: qualitative characteristics - a survey

Exercises, drills, or simulations are widely used, by governments, agencies and commercial organizations, to simulate serious incidents and train staff how to respond to them. International cooperation has led to increasingly large-scale exercises, often involving hundreds or even thousands of participants in many locations. The difference between ‘large’ and ‘small’ exercises is more than one of size: (a) Large exercises are more ‘experiential’ and more likely to undermine any model of reality that single organizations may create; (b) they create a ‘play space’ in which organizations and individuals act out their own needs and identifications, and a ritual with strong social implications; (c) group-analytic psychotherapy suggests that the emotions aroused in a large group may be stronger and more difficult to control. Feelings are an unacknowledged major factor in the success or failure of exercises; (d) successful large exercises help improve the nature of trust between individuals and the organizations they represent, changing it from a situational trust to a personal trust; (e) it is more difficult to learn from large exercises or to apply the lessons identified; (f) however, large exercises can help develop organizations and individuals. Exercises (and simulation in general) need to be approached from a broader multidisciplinary direction if their full potential is to be realized