Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.

BackgroundTo reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.ResultsLog::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.AvailabilityThe source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).ConclusionUsing Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research

TRACING THE EFFECTS OF AGRICULTURAL COMMODITY PRICES ON FOOD PROCESSING COSTS

Although food processing sector production is inherently linked to the availability and prices of agricultural materials (MA), this link appears to be weakening due to adaptations in input costs, technology, and food consumption patterns. This study assesses the roles of these changes on food processors costs and output prices, with a focus on the demand for primary agricultural commodities. Our analysis of the 4-digit U.S. food processing industries for 1972-1992 is based on a cost-function framework, augmented by a profit maximization specification of output pricing, and a virtual price representation for agricultural materials and capital. We find that falling virtual prices of MA and input substitution have provided a stimulus for MA demand. However, scale effects have been MA-saving relative to intermediate food products, and disembodied technical change has strongly contributed to declining primary agricultural materials demand relative to most other inputs.Demand and Price Analysis, Industrial Organization,

Current-induced torques due to compensated antiferromagnets

We analyse the influence of current induced torques on the magnetization configuration of a ferromagnet in a circuit containing a compensated antiferromagnet. We argue that these torques are generically non-zero and support this conclusion with a microscopic NEGF calculation for a circuit containing antiferromagnetic NiMn and ferromagnetic Co layers. Because of symmetry dictated differences in the form of the current-induced torque, the phase diagram which expresses the dependence of ferromagnet configuration on current and external magnetic field differs qualitatively from its ferromagnet-only counterpart.Comment: 4 pages, 5 figure

Alien Registration- Macdonald, Paul M. (Woolwich, Sagadahoc County)

https://digitalmaine.com/alien_docs/9169/thumbnail.jp

Translational Repression by Bicoid Competition for the Cap

Eggs and embryos have proven to be fertile grounds for discovery and characterization of a variety of mechanisms used in posttranscriptional control of gene expression, mechanisms that are central to embryonic patterning and development. In this issue of Cell, Cho et al. (2005) solve a puzzle surrounding the action of the Drosophila Bicoid morphogen in formation of the Caudal protein gradient and in doing so describe a novel mechanism of translational repression

Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method

BACKGROUND: MicroRNAs (miRNAs) mediate a form of translational regulation in animals. Hundreds of animal miRNAs have been identified, but only a few of their targets are known. Prediction of miRNA targets for translational regulation is challenging, since the interaction with the target mRNA usually occurs via incomplete and interrupted base pairing. Moreover, the rules that govern such interactions are incompletely defined. RESULTS: MovingTargets is a software program that allows a researcher to predict a set of miRNA targets that satisfy an adjustable set of biological constraints. We used MovingTargets to identify a high-likelihood set of 83 miRNA targets in Drosophila, all of which adhere to strict biological constraints. We tested and verified 3 of these predictions in cultured cells, including a target for the Drosophila let-7 homolog. In addition, we utilized the flexibility of MovingTargets by relaxing the biological constraints to identify and validate miRNAs targeting tramtrack, a gene also known to be subject to translational control dependent on the RNA binding protein Musashi. CONCLUSION: MovingTargets is a flexible tool for the accurate prediction of miRNA targets in Drosophila. MovingTargets can be used to conduct a genome-wide search of miRNA targets using all Drosophila miRNAs and potential targets, or it can be used to conduct a focused search for miRNAs targeting a specific gene. In addition, the values for a set of biological constraints used to define a miRNA target are adjustable, allowing the software to incorporate the rules used to characterize a miRNA target as these rules are experimentally determined and interpreted

Predictors of survival in a cohort of patients with polymyositis and dermatomyositis: effect of corticosteroids, methotrexate and azathioprine

Introduction: The idiopathic inflammatory myopathies are rare diseases for which data regarding the natural history, response to therapies and factors affecting mortality are needed. We performed this study to examine the effects of treatment and clinical features on survival in polymyositis and dermatomyositis patients. Methods: A total of 160 consecutive patients (77 with polymyositis and 83 with dermatomyositis) seen at the University of Michigan from 1997 to 2003 were included. Medical records were abstracted for clinical, laboratory and therapeutic data, including initial steroid regimen and immunosuppressive use. State vital records were utilized to derive mortality and cause of death data. Survival was modeled by left-truncated Kaplan-Meier estimation and Cox regression. Results: The 5- and 10-year survival estimates were 77% (95% CI = 66 to 85), and 62% (95% CI = 48 to 73), respectively, and the rates were similar for polymyositis and dermatomyositis. Survival between the sexes was similar through 5 years and significantly lower thereafter for males (10-year survival: 18% male, 73% female; P = 0.002 for 5- to 10-year interval). The sex disparity was restricted to the polymyositis group. Increased age at diagnosis and non-Caucasian race were associated with lower survival. Intravenous versus oral corticosteroid use was associated with a higher risk of death among Caucasians (HR = 10.6, 95% CI = 2.1 to 52.8). Early survival between patients treated with methotrexate versus azathioprine was similar, but survival at 10 years was higher for the methotrexate-treated group (76% vs 52%, P = 0.046 for 5- to 10-year interval). Conclusions: Patients treated initially with intravenous corticosteroids had higher mortality, which was likely related to disease severity. Both methotrexate and azathioprine showed similar early survival benefits as first-line immunosuppressive drugs. Survival was higher between 5 and 10 years in the methotrexate-treated group, but could not be confirmed in multivariable modeling for the full follow-up period. Other important predictors of longterm survival included younger age, female sex and Caucasian race.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90025/1/IIM_ART2012.pdf1611

RNA Localization Goes Direct

AbstractDirect injection of RNA provides a new view of localization during Drosophila oogenesis

Community effects in regulation of translation

Certain forms of translational regulation, and translation itself, rely on long-range interactions between proteins bound to the different ends of mRNAs. A widespread assumption is that such interactions occur only in cis, between the two ends of a single transcript. However, certain translational regulatory defects of the Drosophila oskar (osk) mRNA can be rescued in trans. We proposed that inter-transcript interactions, promoted by assembly of the mRNAs in particles, allow regulatory elements to act in trans. Here we confirm predictions of that model and show that disruption of PTB-dependent particle assembly inhibits rescue in trans. Communication between transcripts is not limited to different osk mRNAs, as regulation imposed by cis-acting elements embedded in the osk mRNA spreads to gurken mRNA. We conclude that community effects exist in translational regulation

Eigenvalue Separation in Some Random Matrix Models

The eigenvalue density for members of the Gaussian orthogonal and unitary ensembles follows the Wigner semi-circle law. If the Gaussian entries are all shifted by a constant amount c/Sqrt(2N), where N is the size of the matrix, in the large N limit a single eigenvalue will separate from the support of the Wigner semi-circle provided c > 1. In this study, using an asymptotic analysis of the secular equation for the eigenvalue condition, we compare this effect to analogous effects occurring in general variance Wishart matrices and matrices from the shifted mean chiral ensemble. We undertake an analogous comparative study of eigenvalue separation properties when the size of the matrices are fixed and c goes to infinity, and higher rank analogues of this setting. This is done using exact expressions for eigenvalue probability densities in terms of generalized hypergeometric functions, and using the interpretation of the latter as a Green function in the Dyson Brownian motion model. For the shifted mean Gaussian unitary ensemble and its analogues an alternative approach is to use exact expressions for the correlation functions in terms of classical orthogonal polynomials and associated multiple generalizations. By using these exact expressions to compute and plot the eigenvalue density, illustrations of the various eigenvalue separation effects are obtained.Comment: 25 pages, 9 figures include