Performing Two-Way Analysis of Variance Under Variance Heterogeneity

Small sample properties of the method proposed by Brunner et al. (1997) for performing two-way analysis of variance are compared to those of the normal based ANOVA method for factorial arrangements. Different effect sizes, sample sizes, and error structures are utilized in a simulation study to compare type I error rates and power of the two methods. An SAS program is also presented to assist those wishing to implement the Brunner method to real data

DELAYED ONSET MUSCLE SORENESS AND PROPRIOCEPTION

J. Rupp, E. Payton, & S. O. Henry Pacific University, Forest Grove, OR Although some effects of delayed onset muscle soreness (DOMS) are well documented, the impact of DOMS on proprioception – awareness of body and limb position in space and time has not yet been investigated. Delayed onset muscle soreness may affect neuromuscular sensory receptors and neural pathways due to microtears in the muscle, which could reduce proprioceptive abilities. PURPOSE: Investigate effects of DOMS on three selected measures of proprioception. METHODS: Using digital inclinometers, and data acquisition system; proprioception was assessed by participants’ (n = 19) ability to actively replicate a target angle (actively-determined reference) and ability to replicate joint angle velocity of knee flexion and extension. Force gradation, the ability to produce a target sub-maximal isometric force (25%, 50%, or 75% maximal voluntary isometric contraction), was assessed via force transducer. All testing trials were conducted in a random and repeated design and without immediate visual or auditory augmented feedback. After establishing baseline sensitivity and proprioceptive abilities, one leg was chosen at random to undergo a customized resistance training regimen, to induce DOMS, using the contralateral leg as the control. Post-testing followed approximately 48hrs post exercise regimen. For each set of proprioceptive test absolute error and percent error (from reference value) were calculated; percent error was used for analysis. RESULTS: Two-way repeated measures ANOVA (α=0.05) revealed no differences amongst the PrePost, ConExp, or PrePost* ContExp main effects for joint angle replication, joint movement velocity replication, or force gradation. **Table can be found in the downloadable pdf version** CONCLUSION: Delayed onset muscle soreness had no effect on ability to replicate a target joint angle, joint velocity, or ability to scale submaximal force

JMASM8: Using SAS To Perform Two-Way Analysis Of Variance Under Variance Heterogeneity

We present SAS code to implement the method proposed by Brunner et al. (1997) for performing two-way analysis of variance under variance heterogeneity

USING RANKS TO PERFORM EXACT AND ESTIMATED EXACT TESTS IN DESIGNED EXPERIMENTS

A procedure is studied that uses rank transformed data to perform exact and estimated exact tests which is an alternative to the commonly used F-ratio test procedure. First, a common parametric test statistic is computed using rank transformed data, where two methods of ranking - ranks taken of the original observations, and ranks taken after aligning the observations - are studied. Significance is then determined using either the exact permutation distribution of the statistic or an estimate of this distribution based on a random sample of all possible permutations. Simulation studies compare the performance of this method to both the normal theory parametric F-test and the traditional rank transform procedure. Power and nominal type-I error rates are compared under conditions when normal theory assumptions are satisfied as well as when these assumptions are violated. The method is studied for a two factor factorial arrangement of treatments in a completely randomized design and also for a split-unit experiment

Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

Failure of the ERBE scanner instrument aboard NOAA 10 spacecraft and results of failure analysis

The Earth Radiation Budget Experiment (ERBE) scanner instrument on the NOAA 10 spacecraft malfunctioned on May 22, 1989, after more than 4 years of in-flight operation. After the failure, all instrument operational mode commands were tested and the resulting data analyzed. Details of the tests and analysis of output data are discussed therein. The radiometric and housekeeping data appear to be valid. However, the instrument will not correctly execute operational scan mode commands or the preprogrammed calibration sequences. The data indicate the problem is the result of a failure in the internal address decoding circuity in one of the ROM (read only memory) chips of the instrument computer

Identification of transcriptional regulatory networks specific to pilocytic astrocytoma.

BackgroundPilocytic Astrocytomas (PAs) are common low-grade central nervous system malignancies for which few recurrent and specific genetic alterations have been identified. In an effort to better understand the molecular biology underlying the pathogenesis of these pediatric brain tumors, we performed higher-order transcriptional network analysis of a large gene expression dataset to identify gene regulatory pathways that are specific to this tumor type, relative to other, more aggressive glial or histologically distinct brain tumours.MethodsRNA derived from frozen human PA tumours was subjected to microarray-based gene expression profiling, using Affymetrix U133Plus2 GeneChip microarrays. This data set was compared to similar data sets previously generated from non-malignant human brain tissue and other brain tumour types, after appropriate normalization.ResultsIn this study, we examined gene expression in 66 PA tumors compared to 15 non-malignant cortical brain tissues, and identified 792 genes that demonstrated consistent differential expression between independent sets of PA and non-malignant specimens. From this entire 792 gene set, we used the previously described PAP tool to assemble a core transcriptional regulatory network composed of 6 transcription factor genes (TFs) and 24 target genes, for a total of 55 interactions. A similar analysis of oligodendroglioma and glioblastoma multiforme (GBM) gene expression data sets identified distinct, but overlapping, networks. Most importantly, comparison of each of the brain tumor type-specific networks revealed a network unique to PA that included repressed expression of ONECUT2, a gene frequently methylated in other tumor types, and 13 other uniquely predicted TF-gene interactions.ConclusionsThese results suggest specific transcriptional pathways that may operate to create the unique molecular phenotype of PA and thus opportunities for corresponding targeted therapeutic intervention. Moreover, this study also demonstrates how integration of gene expression data with TF-gene and TF-TF interaction data is a powerful approach to generating testable hypotheses to better understand cell-type specific genetic programs relevant to cancer

The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis: transcript classification and analysis

BACKGROUND: The cellular response of plants to water-deficits has both economic and evolutionary importance directly affecting plant productivity in agriculture and plant survival in the natural environment. Genes induced by water-deficit stress have been successfully enumerated in plants that are relatively sensitive to cellular dehydration, however we have little knowledge as to the adaptive role of these genes in establishing tolerance to water loss at the cellular level. Our approach to address this problem has been to investigate the genetic responses of plants that are capable of tolerating extremes of dehydration, in particular the desiccation-tolerant bryophyte, Tortula ruralis. To establish a sound basis for characterizing the Tortula genome in regards to desiccation tolerance, we analyzed 10,368 expressed sequence tags (ESTs) from rehydrated rapid-dried Tortula gametophytes, a stage previously determined to exhibit the maximum stress induced change in gene expression. RESULTS: The 10, 368 ESTs formed 5,563 EST clusters (contig groups representing individual genes) of which 3,321 (59.7%) exhibited similarity to genes present in the public databases and 2,242 were categorized as unknowns based on protein homology scores. The 3,321 clusters were classified by function using the Gene Ontology (GO) hierarchy and the KEGG database. The results indicate that the transcriptome contains a diverse population of transcripts that reflects, as expected, a period of metabolic upheaval in the gametophyte cells. Much of the emphasis within the transcriptome is centered on the protein synthetic machinery, ion and metabolite transport, and membrane biosynthesis and repair. Rehydrating gametophytes also have an abundance of transcripts that code for enzymes involved in oxidative stress metabolism and phosphorylating activities. The functional classifications reflect a remarkable consistency with what we have previously established with regards to the metabolic activities that are important in the recovery of the gametophytes from desiccation. A comparison of the GO distribution of Tortula clusters with an identical analysis of 9,981 clusters from the desiccation sensitive bryophyte species Physcomitrella patens, revealed, and accentuated, the differences between stressed and unstressed transcriptomes. Cross species sequence comparisons indicated that on the whole the Tortula clusters were more closely related to those from Physcomitrella than Arabidopsis (complete genome BLASTx comparison) although because of the differences in the databases there were more high scoring matches to the Arabidopsis sequences. The most abundant transcripts contained within the Tortula ESTs encode Late Embryogenesis Abundant (LEA) proteins that are normally associated with drying plant tissues. This suggests that LEAs may also play a role in recovery from desiccation when water is reintroduced into a dried tissue. CONCLUSION: The establishment of a rehydration EST collection for Tortula ruralis, an important plant model for plant stress responses and vegetative desiccation tolerance, is an important step in understanding the genome level response to cellular dehydration. The type of transcript analysis performed here has laid the foundation for more detailed functional and genome level analyses of the genes involved in desiccation tolerance in plants

An integrated approach to use genetic resources for resurrection plants to enhance drought tolerance in breeding-extension programs [abstract]

Only abstract of poster available.Track V: BiomassThe ultimate goals of this project are to gain a basic understanding of the unique gene and gene regulatory networks that are necessary and sufficient for vegetative tissues to withstand dehydration and then rapidly recover upon rehydration and to use the knowledge gained to develop crops, maize and forage grasses that maintain biomass production under drought condition. Our approach is to combine comparative genomics and phylogenetics to identify genes and gene networks that are adaptive and central to the tolerance of cellular dehydration. This involves the use of resurrection species as models for dehydration tolerance coupled with a suite of comparative bioinformatic tools that allows for the phylogenetic assessment of gene expression patterns in response to dehydration and rehydration. Once the key genetic elements have been identified and assessed we will use a transgenic functional assessment of their involvement in the phenotype, both at a molecular and physiological level, of drought tolerance. One of our key resurrection species is the South African grass Sporobolus stapfianus, which is capable of surviving -240 MPa of water deficit (a hundred times lower than most crop plants). This plant not only serves as a model for monocot crops such as maize and switchgrass, our major targets for crop improvement, but also serves as a direct possibility for an alternate forage grass and biomass source. The improvement of biomass production under drought conditions is not only important for sustainable biofuel production but also for food and energy security. Funded by a CSREES-NRI Grant of $450,000 over three years to PI Mel Oliver USDA-ARS-PGRU Columbia, CoPIs Robert Sharp, University of Missouri; John Cushman, University of Nevada, Reno; Paxton Payton, USDA-ARS-PSRU Lubbock