Empowering statistical methods for cellular and molecular biologists.

We provide guidelines for using statistical methods to analyze the types of experiments reported in cellular and molecular biology journals such as Molecular Biology of the Cell. Our aim is to help experimentalists use these methods skillfully, avoid mistakes, and extract the maximum amount of information from their laboratory work. We focus on comparing the average values of control and experimental samples. A Supplemental Tutorial provides examples of how to analyze experimental data using R software

Assessing user preferences for sexually transmitted infection testing services: a discrete choice experiment

Objective: To assess user preferences for different aspects of sexually transmitted infection (STI) testing services. Design: A discrete choice experiment. Setting: 14 centres offering tests for STIs in East Sussex, England. Participants: People testing for STIs. Main outcome measure: (Adjusted) ORs in relation to preferred service characteristics. Results: 3358 questionnaires were returned; mean age 26 (SD 9.4) years. 70% (2366) were recruited from genitourinary medicine (GUM) clinics. The analysis suggested that the most important characteristics to users were whether 'staff had specialist STI knowledge' compared with 'staff without it' (OR 2.55; 95% CI 2.47 to 2.63) and whether 'tests for all STIs' were offered rather than 'some' (OR 2.19; 95% CI 2.12 to 2.25). They remained the most important two service characteristics despite stratifying the analysis by variables such as age and sex. Staff levels of expertise were viewed as particularly important by people attending CASH centres, women and non-men who have sex with men. A 'text or call to a mobile phone' and 'dropping in and waiting' were generally the preferred methods of results reporting and appointment system, respectively. Conclusions: This study suggests that people testing for STIs place particular importance on testing for all infections rather than some and staff with specialist STI knowledge. Thus, targets based purely on waiting up to 48 h for an appointment are misguided from a user perspectiv

The use of systems biology and immunological big data to guide vaccine development

High-throughput technologies applied to the analysis of vaccine responses are likely to reveal the mechanisms responsible for vaccine-induced protection, aid understanding of vaccine safety and help accelerate vaccine development and clinical trials

Distressed conversions

Thesis (S.M. in Real Estate Development)--Massachusetts Institute of Technology, Program in Real Estate Development in Conjunction with the Center for Real Estate, 2012.This thesis was scanned as part of an electronic thesis pilot project.Cataloged from PDF version of thesis. This thesis was scanned as part of an electronic thesis pilot project.Includes bibliographical references (p. 115-123).This thesis analyzes condominium and apartment development in the downtown Chicago residential market between 1997 and 2011. Specifically, it focuses on developments that converted from apartments to condominiums mainly during the boom years between 1997 and 2007 and developments that converted from condominiums to apartments during the bust years between 2008 and 2011. In the case of the latter, this thesis seeks to determine the reason or reasons that these developments had to convert from condominiums to apartments through a detailed analysis of four such developments. This analysis addresses development drivers including timing, pricing, and location. Additionally, this thesis considers the overall market conditions including supply, demand, economics, and demographics to determine what caused the boom and the ultimate bust of the market and these developments.by Canan Ceylan Safar and Daniel Pollard.S.M.in Real Estate Developmen

Correction: Benchmarking tools for the alignment of functional noncoding DNA

AbstractIn follow-up studies to this work [1], we have identified an error in a single line of code responsible for parsing BLASTZ [2] alignments that affects our previously published results for this alignment tool. This error resulted in a reduction in overall alignment coverage, with a concomitant underestimation of alignment sensitivity and overestimation of alignment specificity. As BLASTZ is an important and widely used alignment tool, we present here the revised results of our performance evaluations for BLASTZ together with previously reported results for the other alignment tools studied, which have been subsequently verified (Figures 1-4). The general conclusions presented in [1] remain unchanged, although the following sections concerning BLASTZ performance must be modified in light of our recent findings. The true overall alignment coverage for BLASTZ with and without insertion/deletion evolution and with and without blocks of constraint is shown in Figure 1, and reveals increased overall coverage in the presence of constrained blocks for intermediate to high divergence distances (Figures 1C & 1D) relative to previous results ([1] Figures 3C & 3D). As a consequence, the true overall sensitivity for BLASTZ is increased for intermediate to high divergence distances, especially in the presence of insertion/deletion evolution and constrained blocks (Figure 2D) relative to previous results ([1] Figure 4D). The most important revisions to [1] concern BLASTZ performance in interspersed blocks of constrained sequences (Figures 3, 4). Figure 3 shows that the true constraint coverage, and therefore constraint sensitivity, of BLASTZ is much improved relative to previous results for intermediate to high divergence distances ([1], Figure 5). Thus BLASTZ has increased constraint coverage relative to overall coverage (cp. Figures 1C & 1D with 3A & 3B), indicating that BLASTZ local alignments preferentially occur in constrained sequences for intermediate to high divergence distances, overturning claims on page 6 of [1] to the contrary. Likewise, the claim that BLASTZ has a "dramatic decrease in constraint sensitivity in the presence of indel evolution" on page 10 of [1] is incorrect. The increase in overall coverage, however, decreases the constraint specificity of BLASTZ for intermediate to high divergence distances (Figure 4A & 4B) relative to previous results ([1] Figure 6A & 6B). This decrease in constraint specificity requires reconsideration of the use of BLASTZ local alignments as specific detectors of constrained noncoding sequences discussed page 10 of [1]. Revised performance statistics for BLASTZ are posted along with previous results at [3]. We apologize for any misconception or inconvenience this error may have caused. References: 1. Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5:6. 2. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-7. 3. AlignmentBenchmarking [http://rana.lbl.gov/AlignmentBenchmarking

Understanding patient choices for attending sexually transmitted infection testing services: a qualitative study

Objectives: To establish which aspects of sexually transmitted infection (STI) testing services are important to STI testing service users. Methods: 10 focus groups consisting of previous or existing users of STI testing services were conducted in community settings in the south east of England. Groups were quota sampled based on age, gender and sexual orientation. Data were analysed using Framework Analysis. Results: 65 respondents (58% men) participated. Perceived expertise of staff was the key reason for attendance at genitourinary medicine services rather than general practice. Although some respondents voiced a willingness to test for STIs within general practice, the apparent limited range of tests available in general practice and the perceived lack of expertise around sexual health appeared to discourage attendance at general practice. The decision of where to test for STIs was also influenced by past experience of testing, existing relationships with general practice, method of receiving test results and whether the patient had other medical conditions such as HIV. Conclusions: No one type of STI testing service is suitable for all patients. This is recognised by policymakers, and it now requires commissioners and providers to make services outside of genitourinary medicine clinics more acceptable and attractive to patients, in particular to address the perceived lack of expertise and limited range of STIs tests available at alternative testing sites

Finite group actions on reductive groups and buildings and tamely-ramified descent in Bruhat-Tits theory

The purpose of the paper is to give a new approach to tamely-ramified descent in Bruhat-Tits theory. This descent was first studied by Guy Rousseau in his thesis.Comment: 28 pages. arXiv admin note: text overlap with arXiv:1611.0743

Cost-effectiveness of structured education in children with type-1 diabetes mellitus

Objectives: Kids in Control OF Food (KICk-OFF) is a 5-day structured education program for 11- to 16-year-olds with type 1 diabetes mellitus (T1DM) who are using multiple daily insulin injections. This study evaluates the cost-effectiveness of the KICk-OFF education program compared with the usual care using data from the KICk-OFF trial. Methods: The short-term within-trial analysis covers the 2-year postintervention period. Data on glycated hemoglobin (HbA1c), severe hypoglycemia, and diabetic ketoacidosis (DKA) were collected over a 2-year follow-up period. Sub-group analyses have been defined on the basis of baseline HbA1c being below 7.5 percent (58.5 mmol/mol) (low group), between 7.5 percent and 9.5 percent (80.3 mmol/mol) (medium group), and over 9.5 percent (high group). The long-term cost-effectiveness evaluation has been conducted by using The Sheffield Type 1 Diabetes Policy Model, which is a patient-level simulation model on T1DM. It includes long-term microvascular (retinopathy, neuropathy, and nephropathy) and macrovascular (myocardial infarction, stroke, revascularization, and angina) diabetes-related complications and acute adverse events (severe hypoglycemia and DKA). Results: The most favorable within-trial scenario for the KICk-OFF arm led to an incremental cost-effectiveness ratio (ICER) of £23,688 (base year 2009) with a cost-effectiveness probability of 41.3 percent. Simulating the long-term complications using the full cohort data, the mean ICER for the base case was £28,813 (base year 2011) and the probability of the KICk-OFF intervention being cost-effective at £20,000/QALY threshold was 42.6 percent, with considerable variation due to treatment effect duration. For the high HbA1c sub-group, the KICk-OFF arm was “dominant” (meaning it provided better health gains at lower costs than usual care) over the usual care arm in each scenario considered. Conclusions: For the whole study population, the cost-effectiveness of KICk-OFF depends on the assumption for treatment effect duration. For the high baseline HbA1c sub-group, KICk-OFF arm was estimated to be dominant over the usual care arm regardless of the assumption on the treatment effect duration

Cryostratigraphy and the Sublimation Unconformity in Permafrost from an Ultraxerous Environment, University Valley, McMurdo Dry Valleys of Antarctica

The cryostratigraphy of permafrost in ultraxerous environments is poorly known. In this study, icy permafrost cores from University Valley (McMurdo Dry Valleys, Antarctica) were analyzed for sediment properties, ground-ice content, types and distribution of cryostructures, and presence of unconformities. No active layer exists in the valley, but the ice table, a sublimation unconformity, ranges from 0 to 60 cm depth. The sediments are characterized as a medium sand, which classifies them as low to non-frost susceptible. Computed tomography (CT) scan images of the icy permafrost cores revealed composite cryostructures that included the structureless, porous visible, suspended and crustal types. These cryostructures were observed irrespective of ground-ice origin (vapour deposited and freezing of snow meltwater), suggesting that the type and distribution of cryostructures could not be used as a proxy to infer the mode of emplacement of ground ice. Volumetric ice content derived from the CT scan images underestimated measured volumetric ice content, but approached measured excess ice content. A palaeo-sublimation unconformity could not be detected from a change in cryostructures, but could be inferred from an increase in ice content at the maximum predicted ice table depth. This study highlights some of the unique ground-ice processes and cryostructures in ultraxerous environments

Datathons and Software to Promote Reproducible Research

Background: Datathons facilitate collaboration between clinicians, statisticians, and data scientists in order to answer important clinical questions. Previous datathons have resulted in numerous publications of interest to the critical care community and serve as a viable model for interdisciplinary collaboration. Objective: We report on an open-source software called Chatto that was created by members of our group, in the context of the second international Critical Care Datathon, held in September 2015. Methods: Datathon participants formed teams to discuss potential research questions and the methods required to address them. They were provided with the Chatto suite of tools to facilitate their teamwork. Each multidisciplinary team spent the next 2 days with clinicians working alongside data scientists to write code, extract and analyze data, and reformulate their queries in real time as needed. All projects were then presented on the last day of the datathon to a panel of judges that consisted of clinicians and scientists. Results: Use of Chatto was particularly effective in the datathon setting, enabling teams to reduce the time spent configuring their research environments to just a few minutes—a process that would normally take hours to days. Chatto continued to serve as a useful research tool after the conclusion of the datathon. Conclusions: This suite of tools fulfills two purposes: (1) facilitation of interdisciplinary teamwork through archiving and version control of datasets, analytical code, and team discussions, and (2) advancement of research reproducibility by functioning postpublication as an online environment in which independent investigators can rerun or modify analyses with relative ease. With the introduction of Chatto, we hope to solve a variety of challenges presented by collaborative data mining projects while improving research reproducibility