Thirty-Three Stata Tips

Since 2003, the Stata Journal has published Stata Tips on special issues in data analysis with Stata. Now Thirty-three Stata Tips compiles these useful guides into a compact tome for ease of reference. In keeping with the Stata spirit, Tips are from Stata users and StataCorp employees alike and will serve as guideposts for both new and experienced users.data management, statistics, graphics, Stata

A conversation with William Gould

William Gould is President of StataCorp. He was born in Burbank, California, on January 21, 1952. He received a B.A. in economics from UCLA in 1974 and a C.Phil. in economics from UCLA in 1977, after initially majoring in physics and then engineering. He studied economics in the Ph.D. program at UCLA and was simultaneously a Research Fellow at The Rand Corporation. He did not turn in his dissertation in labor economics before becoming a Senior Research Associate at the National Bureau of Economic Research in Stanford, California, in 1977. In 1979, he become a Senior Economist at Unicon Research Corporation in Los Angeles, a company that he helped to found. He cofounded and served as Vice-President of Computing Resource Center in 1982, the company that went on to develop Stata. Bill became President of CRC in 1990 and, in 1993, CRC was renamed StataCorp. Copyright 2005 by StataCorp LP.

Sewage reflects the microbiomes of human populations

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 6 (2015): e02574-14, doi:10.1128/mBio.02574-14.Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome.Funding for this work was provided by the NIH grant R01AI091829-01A1 to S.L.M. and M.L.S

A single genus in the gut microbiome reflects host preference and specificity

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 90–100, doi:10.1038/ismej.2014.97.Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, a single microbial genus that is important for nutrient assimilation as preliminary work suggested host-related patterns within members of this genus. In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping. Our analysis revealed 13 host-specific oligotypes that occurred exclusively in fecal samples of humans (three oligotypes), swine (six oligotypes), cows (one oligotype), deer (one oligotype), or chickens (two oligotypes). We identified an additional 171 oligotypes that exhibited differential abundance patterns among all the host species. Blautia oligotypes in the human population obtained from sewage and fecal samples displayed remarkable continuity. Oligotypes from only 10 Brazilian human fecal samples collected from individuals in a rural village encompassed 97% of all Blautia oligotypes found in a Brazilian sewage sample from a city of three million people. Further, 75% of the oligotypes in Brazilian human fecal samples matched those in US sewage samples, implying that a universal set of Blautia strains may be shared among culturally and geographically distinct human populations. Such strains can serve as universal markers to assess human fecal contamination in environmental samples. Our results indicate that host-specificity and host-preference patterns of organisms within this genus are driven by host physiology more than dietary habits.This study was funded by the NIH grant R01AI091829-01A1 to SLM

Inertial frame rotation induced by rotating gravitational waves

We calculate the rotation of the inertial frames within an almost flat cylindrical region surrounded by a pulse of non-axially-symmetric gravitational waves that rotate about the axis of our cylindrical polar coordinates. Our spacetime has only one Killing vector. It is along the z-axis and hypersurface orthogonal. We solve the Einstein equations to first order in the wave amplitude and superpose such linearized solutions to form a wave pulse. We then solve the relevant Einstein equation to second order in the amplitude to find the rotation of inertial frames produced by the pulse. The rotation is without time delay. The influence of gravitational wave angular momentum on the inertial frame demonstrates that Mach's principle can not be expressed in terms of the influence of the stress-energy-momentum tensor alone but must involve also influences of gravitational wave energy and angular momentum.Comment: Scheduled to appear in Class. and Quantum Grav. July 2008, "inertial" added in titl

Climatic patterns in the establishment of wintering areas by North American migratory birds

Long-distance migration in birds is relatively well studied in nature; however, one aspect of this phenomenon that remains poorly understood is the pattern of distribution presented by species during arrival to and establishment of wintering areas. Some studies suggest that the selection of areas in winter is somehow determined by climate, given its influence on both the distribution of bird species and their resources. We analyzed whether different migrant passerine species of North America present climatic preferences during arrival to and departure from their wintering areas. We used ecological niche modeling to generate monthly potential climatic distributions for 13 migratory bird species during the winter season by combining the locations recorded per month with four environmental layers. We calculated monthly coefficients of climate variation and then compared two GLM (generalized linear models), evaluated with the AIC (Akaike information criterion), to describe how these coefficients varied over the course of the season, as a measure of the patterns of establishment in the wintering areas. For 11 species, the sites show nonlinear patterns of variation in climatic preferences, with low coefficients of variation at the beginning and end of the season and higher values found in the intermediate months. The remaining two species analyzed showed a different climatic pattern of selective establishment of wintering areas, probably due to taxonomic discrepancy, which would affect their modeled winter distribution. Patterns of establishment of wintering areas in the species showed a climatic preference at the macroscale, suggesting that individuals of several species actively select wintering areas that meet specific climatic conditions. This probably gives them an advantage over the winter and during the return to breeding areas. As these areas become full of migrants, alternative suboptimal sites are occupied. Nonrandom winter area selection may also have consequences for the conservation of migratory bird species, particularly under a scenario of climate change

Can exercise suppress tumour growth in advanced prostate cancer patients with sclerotic bone metastases? A randomised, controlled study protocol examining feasibility, safety and efficacy

Introduction Exercise may positively alter tumour biology through numerous modulatory and regulatory mechanisms in response to a variety of modes and dosages, evidenced in preclinical models to date. Specifically, localised and systemic biochemical alterations produced during and following exercise may suppress tumour formation, growth and distribution by virtue of altered epigenetics and endocrine–paracrine activity. Given the impressive ability of targeted mechanical loading to interfere with metastasis-driven tumour formation in human osteolytic tumour cells, it is of equal interest to determine whether a similar effect is observed in sclerotic tumour cells. The study aims to (1) establish the feasibility and safety of a combined modular multimodal exercise programme with spinal isometric training in advanced prostate cancer patients with sclerotic bone metastases and (2) examine whether targeted and supervised exercise can suppress sclerotic tumour growth and activity in spinal metastases in humans. Methods and analysis A single-blinded, two-armed, randomised, controlled and explorative phase I clinical trial combining spinal isometric training with a modular multimodal exercise programme in 40 men with advanced prostate cancer and stable sclerotic spinal metastases. Participants will be randomly assigned to (1) the exercise intervention or (2) usual medical care. The intervention arm will receive a 3-month, supervised and individually tailored modular multimodal exercise programme with spinal isometric training. Primary endpoints (feasibility and safety) and secondary endpoints (tumour morphology; biomarker activity; anthropometry; musculoskeletal health; adiposity; physical function; quality of life; anxiety; distress; fatigue; insomnia; physical activity levels) will be measured at baseline and following the intervention. Statistical analyses will include descriptive characteristics, t-tests, effect sizes and two-way (group × time) repeated-measures analysis of variance (or analysis of covariance) to examine differences between groups over time. The data-set will be primarily examined using an intention-to-treat approach with multiple imputations, followed by a secondary sensitivity analysis to ensure data robustness using a complete cases approach. Ethics and dissemination Ethics approval was obtained from the Human Research Ethics Committee (HREC) of Edith Cowan University and the Sir Charles Gairdner and Osborne Park Health Care Group. If proven to be feasible and safe, this study will form the basis of future phase II and III trials in human patients with advanced cancer. To reach a maximum number of clinicians, practitioners, patients and scientists, outcomes will be disseminated through national and international clinical, conference and patient presentations, as well as publication in high-impact, peer-reviewed academic journals

Differential expression analysis with global network adjustment

<p>Background: Large-scale chromosomal deletions or other non-specific perturbations of the transcriptome can alter the expression of hundreds or thousands of genes, and it is of biological interest to understand which genes are most profoundly affected. We present a method for predicting a gene’s expression as a function of other genes thereby accounting for the effect of transcriptional regulation that confounds the identification of genes differentially expressed relative to a regulatory network. The challenge in constructing such models is that the number of possible regulator transcripts within a global network is on the order of thousands, and the number of biological samples is typically on the order of 10. Nevertheless, there are large gene expression databases that can be used to construct networks that could be helpful in modeling transcriptional regulation in smaller experiments.</p> <p>Results: We demonstrate a type of penalized regression model that can be estimated from large gene expression databases, and then applied to smaller experiments. The ridge parameter is selected by minimizing the cross-validation error of the predictions in the independent out-sample. This tends to increase the model stability and leads to a much greater degree of parameter shrinkage, but the resulting biased estimation is mitigated by a second round of regression. Nevertheless, the proposed computationally efficient “over-shrinkage” method outperforms previously used LASSO-based techniques. In two independent datasets, we find that the median proportion of explained variability in expression is approximately 25%, and this results in a substantial increase in the signal-to-noise ratio allowing more powerful inferences on differential gene expression leading to biologically intuitive findings. We also show that a large proportion of gene dependencies are conditional on the biological state, which would be impossible with standard differential expression methods.</p> <p>Conclusions: By adjusting for the effects of the global network on individual genes, both the sensitivity and reliability of differential expression measures are greatly improved.</p&gt

Exercise Preserves Physical Function in Prostate Cancer Patients with Bone Metastases

The presence of bone metastases has excluded participation of cancer patients in exercise interventions and is a relative contraindication to supervised exercise in the community setting due to concerns of fragility fracture. We examined the efficacy and safety of a modular multi-modal exercise program in prostate cancer patients with bone metastases.Between 2012 and 2015, 57 prostate cancer patients (70.0±8.4 years; BMI 28.7±4.0 kg/m) with bone metastases (pelvis 75.4%, femur 40.4%, rib/thoracic spine 66.7%, lumbar spine 43.9%, humerus 24.6%, other sites 70.2%) were randomised to multi-modal supervised aerobic, resistance and flexibility exercises undertaken thrice weekly (EX, n=28) or usual care (CON, n=29) for 3 months. Physical function subscale of the SF-36 was the primary endpoint as an indicator of patient-rated physical functioning. Secondary endpoints included objective measures of physical function, lower body muscle strength, body composition and fatigue. Safety was assessed by recording the incidence and severity of any adverse events, skeletal complications, and bone pain throughout the intervention.There was a significant difference between groups for self-reported physical functioning (3.2 points, 95% CI 0.4-6.0 points; p=0.028) and lower body muscle strength (6.6 kg, 95% CI 0.6-12.7; p =0.033) at 3 months favouring EX. However, there was no difference between groups for lean mass (p=0.584), fat mass (p=0.598), or fatigue (p=0.964). There were no exercise-related adverse events or skeletal fractures and no differences in bone pain between EX and CON (p=0.507).Multi-modal modular exercise in prostate cancer patients with bone metastases led to self-reported improvements in physical function and objectively measured lower body muscle strength with no skeletal complications or increased bone pain.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal

Where constructionism and critical realism converge: interrogating the domain of epistemological relativism

The paper interrogates the status, nature and significance of epistemological relativism as a key element of constructionism and critical realism. It finds that epistemological relativism is espoused by authorities in critical realism and marginalized or displaced in the field of management and organization studies, resulting in forms of analysis that are empirically, but not fully critically, realist. This evaluation prompts reflection on the question of whether, how and with what implications epistemological relativism might be recast at the heart of critical realist studies of management and organization