Caching and Visualizing Statistical Analyses

We present the cacher and CodeDepends packages for R, which provide tools for (1) caching and analyzing the code for statistical analyses and (2) distributing these analyses to others in an efficient manner over the web. The cacher package takes objects created by evaluating R expressions and stores them in key-value databases. These databases of cached objects can subsequently be assembled into “cache packages” for distribution over the web. The cacher package also provides tools to help readers examine the data and code in a statistical analysis and reproduce, modify, or improve upon the results. In addition, readers can easily conduct alternate analyses of the data. The CodeDepends package provides complementary tools for analyzing and visualizing the code for a statistical analysis and this functionality has been integrated into the cacher package. In this chapter we describe the cacher and CodeDepends packages and provide examples of how they can be used for reproducible research.

Seasonal Analyses of Air Pollution and Mortality in 100 U.S. Cities

Time series models relating short-term changes in air pollution levels to daily mortality counts typically assume that the effects of air pollution on the log relative rate of mortality do not vary with time. However, these short-term effects might plausibly vary by season. Changes in the sources of air pollution and meteorology can result in changes in characteristics of the air pollution mixture across seasons. The authors develop Bayesian semi-parametric hierarchical models for estimating time-varying effects of pollution on mortality in multi-site time series studies. The methods are applied to the updated National Morbidity and Mortality Air Pollution Study database for the period 1987--2000, which includes data for 100 U.S. cities. At the national level, a 10 micro-gram/m3 increase in PM(10) at lag 1 is associated with a 0.15 (95% posterior interval: -0.08, 0.39),0.14 (-0.14, 0.42), 0.36 (0.11, 0.61), and 0.14 (-0.06, 0.34) percent increase in mortality for winter, spring, summer, and fall, respectively. An analysis by geographical regions finds a strong seasonal pattern in the northeast (with a peak in summer) and little seasonal variation in the southern regions of the country. These results provide useful information for understanding particle toxicity and guiding future analyses of particle constituent data.

Bibliographic study showed improving methodology of meta-analyses published in leading journals 1993-2002

OBJECTIVE: To assess the methodology of meta-analyses published in leading general and specialist medical journals over a 10-year period. STUDY DESIGN AND SETTING: Volumes 1993-2002 of four general medicine journals and four specialist journals were searched by hand for meta-analyses including at least five controlled trials. Characteristics were assessed using a standardized questionnaire. RESULTS: A total of 272 meta-analyses, which included a median of 11 trials (range 5-195), were assessed. Most (81%) were published in general medicine journals. The median (range) number of databases searched increased from 1 (1-9) in 1993/1994 to 3.5 (1-21) in 2001/2002, P<0.0001. The proportion of meta-analyses including searches by hand (10% in 1993/1994, 25% in 2001/2002, P=0.005), searches of the grey literature (29%, 51%, P=0.010 by chi-square test), and of trial registers (10%, 32%, P=0.025) also increased. Assessments of the quality of trials also became more common (45%, 70%, P=0.008), including whether allocation of patients to treatment groups had been concealed (24%, 60%, P=0.001). The methodological and reporting quality was consistently higher in general medicine compared to specialist journals. CONCLUSION: Many meta-analyses published in leading journals have important methodological limitations. The situation has improved in recent years but considerable room for further improvements remains.

Grey literature in meta-analyses of randomized trials of health care interventions

BACKGROUND: The inclusion of grey literature (i.e. literature that has not been formally published) in systematic reviews may help to overcome some of the problems of publication bias, which can arise due to the selective availability of data. OBJECTIVES: To review systematically research studies, which have investigated the impact of grey literature in meta-analyses of randomized trials of health care interventions. SEARCH STRATEGY: We searched the Cochrane Methodology Register (The Cochrane Library Issue 3, 2005), MEDLINE (1966 to 20 May 2005), the Science Citation Index (June 2005) and contacted researchers who may have carried out relevant studies. SELECTION CRITERIA: A study was considered eligible for this review if it compared the effect of the inclusion and exclusion of grey literature on the results of a cohort of meta-analyses of randomized trials. DATA COLLECTION AND ANALYSIS: Data were extracted from each report independently by two reviewers. The main outcome measure was an estimate of the impact of trials from the grey literature on the pooled effect estimates of the meta-analyses. Information was also collected on the area of health care, the number of meta-analyses, the number of trials, the number of trial participants, the year of publication of the trials, the language and country of publication of the trials, the number and type of grey and published literature, and methodological quality. MAIN RESULTS: Five studies met the inclusion criteria. All five studies showed that published trials showed an overall greater treatment effect than grey trials. This difference was statistically significant in one of the five studies. Data could be combined for three of the five studies. This showed that, on average, published trials showed a 9% greater treatment effect than grey trials (ratio of odds ratios for grey versus published trials 1.09; 95% CI 1.03-1.16). Overall there were more published trials included in the meta-analyses than grey trials (median 224 (IQR 108-365) versus 45(IQR 40-102)). Published trials had more participants on average. The most common types of grey literature were abstracts (55%) and unpublished data (30%). There is limited evidence to show whether grey trials are of poorer methodological quality than published trials. AUTHORS' CONCLUSIONS: This review shows that published trials tend to be larger and show an overall greater treatment effect than grey trials. This has important implications for reviewers who need to ensure they identify grey trials, in order to minimise the risk of introducing bias into their review.

Germline NF1 mutational spectra and loss-of-heterozygosity analyses in patients with pheochromocytoma and neurofibromatosis type 1

BACKGROUND: Neurofibromatosis type 1 (NF1) is a pheochromocytoma-associated syndrome. Because of the low prevalence of pheochromocytoma in NF1, we ascertained subjects by pheochromocytoma that also had NF1 in the hope of describing the germline NF1 mutational spectra of NF1-related pheochromocytoma. MATERIALS AND METHODS: An international registry for NF1-pheochromocytomas was established. Mutation scanning was performed using denaturing HPLC for intragenic variation and quantitative PCR for large deletions. Loss-of-heterozygosity analysis using markers in and around NF1 was performed. RESULTS: There were 37 eligible subjects (ages 14-70 yr). Of 21 patients with corresponding tumor available, 67% showed somatic loss of the nonmutated allele at the NF1 locus vs. 0 of 12 sporadic tumors (P = 0.0002). Overall, 86% of the 37 patients had exonic or splice site mutations, 14% large deletions or duplications; 79% of the mutations are novel. The cysteine-serine rich domain (CSR) was affected in 35% but the RAS GTPase activating protein domain (RGD) in only 13%. There did not appear to be an association between any clinical features, particularly pheochromocytoma presentation and severity, and NF1 mutation genotype. CONCLUSIONS: The germline NF1 mutational spectra comprise intragenic mutations and deletions in individuals with pheochromocytoma and NF1. NF1 mutations tended to cluster in the CSR over the RAS-GAP domain, suggesting that CSR plays a more prominent role in individuals with NF1-pheochromocytoma than in NF1 individuals without this tumor. Loss-of-heterozygosity of NF1 markers in NF1-related pheochromocytoma was significantly more frequent than in sporadic pheochromocytoma, providing further molecular evidence that pheochromocytoma is a true component of NF1.

Comparison of amplification methods for transcriptomic analyses of low abundance prokaryotic RNA sources

Microarrays have established as instrumental for bacterial detection, identification, and genotyping as well as for transcriptomic studies. For gene expression analyses using limited numbers of bacteria (derived from in vivo or ex vivo origin, for example), RNA amplification is often required prior to labeling and hybridization onto microarrays. Evaluation of the fidelity of the amplification methods is crucial for the robustness and reproducibility of microarray results. We report here the first utilization of random primers and the highly processive Phi29 phage polymerase to amplify material for transcription profiling analyses. We compared two commercial amplification methods (GenomiPhi and MessageAmp kits) with direct reverse-transcription as the reference method, focusing on the robustness of mRNA quantification using either microarrays or quantitative RT-PCR. Both amplification methods using either poly-A tailing followed by in vitro transcription, or direct strand displacement polymerase, showed appreciable linearity. Strand displacement technique was particularly affordable compared to in vitro transcription-based (IVT) amplification methods and consisted in a single tube reaction leading to high amplification yields. Real-time measurements using low-, medium-, and highly expressed genes revealed that this simple method provided linear amplification with equivalent results in terms of relative messenger abundance as those obtained by conventional direct reverse-transcription.

Experimental model to evaluate in vivo and in vitro cartilage MR imaging by means of histological analyses

OBJECTIVES: Implementation of an experimental model to compare cartilage MR imaging by means of histological analyses. MATERIAL AND METHODS: MRI was obtained from 4 patients expecting total knee replacement at 1.5 and/or 3T prior surgery. The timeframe between pre-op MRI and knee replacement was within two days. Resected cartilage-bone samples were tagged with Ethi((R))-pins to reproduce the histological cutting course. Pre-operative scanning at 1.5T included following parameters for fast low angle shot (FLASH: TR/TE/FA=33ms/6ms/30 degrees , BW=110kHz, 120mmx120mm FOV, 256x256 matrix, 0.65mm slice-thickness) and double echo steady state (DESS: TR/TE/FA=23.7ms/6.9ms/40 degrees , BW=130kHz, 120x120mm FOV, 256x256 matrix, 0.65mm slice-thickness). At 3T, scan parameters were: FLASH (TR/TE/FA=12.2ms/5.1ms/10 degrees , BW=130kHz, 170x170mm FOV, 320x320, 0.5mm slice-thickness) and DESS (TR/TE/FA=15.6ms/4.5ms/25 degrees , BW=200kHz, 135mmx150mm FOV, 288x320matrix, 0.5mm slice-thickness). Imaging of the specimens was done the same day at 1.5T. MRI (Noyes) and histological (Mankin) score scales were correlated using the paired t-test. Sensitivity and specificity for the detection of different grades of cartilage degeneration were assessed. Inter-reader and intra-reader reliability was determined using Kappa analysis. RESULTS: Low correlation (sensitivity, specificity) was found for both sequences in normal to mild Mankin grades. Only moderate to severe changes were diagnosed with higher significance and specificity. The use of higher field-strengths was advantageous for both protocols with sensitivity values ranging from 13.6% to 93.3% (FLASH) and 20.5% to 96.2% (DESS). Kappa values ranged from 0.488 to 0.944. CONCLUSIONS: Correlating MR images with continuous histological slices was feasible by using three-dimensional imaging, multi-planar-reformat and marker pins. The capability of diagnosing early cartilage changes with high accuracy could not be proven for both FLASH and DESS.

Exigencies for engaging undergraduates in rhetorical problem solving : insights from engineering managers and A3 report analyses

Undergraduate education has a historical tradition of preparing students to meet the problem-solving challenges they will encounter in work, civic, and personal contexts. This thesis research was conducted to study the role of rhetoric in engineering problem solving and decision making and to pose pedagogical strategies for preparing undergraduate students for workplace problem solving. Exploratory interviews with engineering managers as well as the heuristic analyses of engineering A3 project planning reports suggest that Aristotelian rhetorical principles are critical to the engineer's success: Engineers must ascertain the rhetorical situation surrounding engineering problems; apply and adapt invention heuristics to conduct inquiry; draw from their investigation to find innovative solutions; and influence decision making by navigating workplace decision-making systems and audiences using rhetorically constructed discourse. To prepare undergraduates for workplace problem solving, university educators are challenged to help undergraduates understand the exigence and realize the kairotic potential inherent in rhetorical problem solving. This thesis offers pedagogical strategies that focus on mentoring learning communities in problem-posing experiences that are situated in many disciplinary, work, and civic contexts. Undergraduates build a flexible rhetorical technê for problem solving as they navigate the nuances of relevant problem-solving systems through the lens of rhetorical practice.

Eruptive history of Maderas volcano using new 40Ar/39Ar ages and geochemical analyses

Maderas volcano is a small, andesitic stratovolcano located on the island of Ometepe, in Lake Nicaragua, Nicaragua with no record of historic activity. Twenty-one samples were collected from lava flows from Maderas in 2010. Selected samples were analyzed for whole-rock geochemical data using ICP-AES and/or were dated using the 40Ar/39Ar method. The results of these analyses were combined with previously collected data from Maderas as well as field observations to determine the eruptive history of the volcano and create a geologic map. The results of the geochemical analyses indicate that Maderas is a typical Central American andesitic volcano similar to other volcanoes in Nicaragua and Costa Rica and to its nearest neighbor, Concepción volcano. It is different from Concepción in one important way – higher incompatible elements. Determined age dates range from 176.8 ± 6.1 ka to 70.5 ± 6.1 ka. Based on these ages and the geomorphology of the volcano which is characterized by a bisecting graben, it is proposed that Maderas experienced two clear generations of development with three separate phases of volcanism: initial build-up of the older cone, pre-graben lava flows, and post-graben lava flows. The ages also indicate that Maderas is markedly older than Concepción which is historically active. Results were also analyzed regarding geologic hazards. The 40Ar/39Ar ages indicate that Maderas has likely been inactive for tens of thousands of years and the risk of future volcanic eruptions is low. However, earthquake, lahar and landslide hazards exist for the communities around the volcano. The steep slopes of the eroded older cone are the most likely source of landslide and lahar hazards.

PHYLOGENETIC ANALYSES, GENE DOSAGE EFFECT AND SELECTION IN MEMBERS OF THE LATERAL BOUNDARY DOMAIN (LBD) GENES TRANSCRIPTION FACTOR FAMILY

Wood formation is an economically and environmentally important process and has played a significant role in the evolution of terrestrial plants. Despite its significance, the molecular underpinnings of the process are still poorly understood. We have previously shown that four Lateral Boundary Domain (LBD) transcription factors have important roles in the regulation of wood formation with two (LBD1 and LBD4) involved in secondary phloem and ray cell development and two (LBD15 and LBD18) in secondary xylem formation. Here, we used comparative phylogenetic analyses to test potential roles of the four LBD genes in the evolution of woodiness. We studied the copy number and variation in DNA and amino acid sequences of the four LBDs in a wide range of woody and herbaceous plant taxa with fully sequenced and annotated genomes. LBD1 showed the highest gene copy number across the studied species, and LBD1 gene copy number was strongly and significantly correlated with the level of ray seriation. The lianas, cucumber and grape, with multiseriate ray cells showed the highest gene copy number (12 and 11, respectively). Because lianas’ growth habit requires significant twisting and bending, the less lignified ray parenchyma cells likely facilitate stem flexibility and maintenance of xylem conductivity. We further demonstrate conservation of amino acids in the LBD18 protein sequences that are specific to woody taxa. Neutrality tests showed evidence for strong purifying selection on these gene regions across various orders, indicating adaptive convergent evolution of LBD18. Structural modeling demonstrates that the conserved amino acids have a significant impact on the tertiary protein structure and thus are likely of significant functional importance.

Disagreements in meta-analyses using outcomes measured on continuous or rating scales: observer agreement study

OBJECTIVE: To study the inter-observer variation related to extraction of continuous and numerical rating scale data from trial reports for use in meta-analyses. DESIGN: Observer agreement study. DATA SOURCES: A random sample of 10 Cochrane reviews that presented a result as a standardised mean difference (SMD), the protocols for the reviews and the trial reports (n=45) were retrieved. DATA EXTRACTION: Five experienced methodologists and five PhD students independently extracted data from the trial reports for calculation of the first SMD result in each review. The observers did not have access to the reviews but to the protocols, where the relevant outcome was highlighted. The agreement was analysed at both trial and meta-analysis level, pairing the observers in all possible ways (45 pairs, yielding 2025 pairs of trials and 450 pairs of meta-analyses). Agreement was defined as SMDs that differed less than 0.1 in their point estimates or confidence intervals. RESULTS: The agreement was 53% at trial level and 31% at meta-analysis level. Including all pairs, the median disagreement was SMD=0.22 (interquartile range 0.07-0.61). The experts agreed somewhat more than the PhD students at trial level (61% v 46%), but not at meta-analysis level. Important reasons for disagreement were differences in selection of time points, scales, control groups, and type of calculations; whether to include a trial in the meta-analysis; and data extraction errors made by the observers. In 14 out of the 100 SMDs calculated at the meta-analysis level, individual observers reached different conclusions than the originally published review. CONCLUSIONS: Disagreements were common and often larger than the effect of commonly used treatments. Meta-analyses using SMDs are prone to observer variation and should be interpreted with caution. The reliability of meta-analyses might be improved by having more detailed review protocols, more than one observer, and statistical expertise.