Agile and Lean Systems Engineering: Kanban in Systems Engineering

This is the 2nd of two reports that were created for research on this topic funded through SERC. The first report, SERC-TR-032-1 dated March 13, 2012, constituted the 2011-2012 Annual Technical Report and the Final Technical Report of the SERC Research Task RT-6: Software Intensive Systems Data Quality and Estimation Research In Support of Future Defense Cost Analysis. The overall objectives of RT-6 were to use data submitted to DoD in the Software Resources Data Report (SRDR) forms to provide guidance for DoD projects in estimating software costs for future DoD projects. In analyzing the data, the project found variances in productivity data that made such SRDR-based estimates highly variable. The project then performed additional analyses that provided better bases of estimate, but also identified ambiguities in the SRDR data definitions that enabled the project to help the DoD DCARC organization to develop better SRDR data definitions. In SERC-TR-2012-032-1, the resulting Manual provided the guidance elements for software cost estimation performers and users. Several appendices provide further related information on acronyms, sizing, nomograms, work breakdown structures, and references. SERC-TR-2013-032-2 (current report), included the “Software Cost Estimation Metrics Manual.” This constitutes the 2012-2013 Annual Technical Report and the Final Technical Report of the SERC Research Task Order 0024, RT-6: Software Intensive Systems Cost and Schedule Estimation Estimating the cost to develop a software application is different from almost any other manufacturing process. In other manufacturing disciplines, the product is developed once and replicated many times using physical processes. Replication improves physical process productivity (duplicate machines produce more items faster), reduces learning curve effects on people and spreads unit cost over many items. Whereas a software application is a single production item, i.e. every application is unique. The only physical processes are the documentation of ideas, their translation into computer instructions and their validation and verification. Production productivity reduces, not increases, when more people are employed to develop the software application. Savings through replication are only realized in the development processes and on the learning curve effects on the management and technical staff. Unit cost is not reduced by creating the software application over and over again. This manual helps analysts and decision makers develop accurate, easy and quick software cost estimates for different operating environments such as ground, shipboard, air and space. It was developed by the Air Force Cost Analysis Agency (AFCAA) in conjunction with DoD Service Cost Agencies, and assisted by the SERC through involving the University of Southern California and the Naval Postgraduate School. The intent is to improve quality and consistency of estimating methods across cost agencies and program offices through guidance, standardization, and knowledge sharing. The manual consists of chapters on metric definitions, e.g., what is meant by equivalent lines of code, examples of metric definitions from commercially available cost models, the data collection and repository form, guidelines for preparing the data for analysis, analysis results, cost estimating relationships found in the data, productivity benchmarks, future cost estimation challenges and a very large appendix.SERCU.S. Department of DefenseSystems Engineering Research Center (SERC)Systems Engineering Research Center (SERC) Contract H98230-08-D-0171

Prospective Evaluation of Patient Satisfaction, and Surgeon and Patient Trainer Assessment of the Coloplast Titan One Touch Release Three‐Piece Inflatable Penile Prosthesis

Introduction.  A single‐armed, prospective, multicenter international study evaluated the redesigned Coloplast Titan One Touch Release (OTR) pump inflatable penile prosthesis. The OTR pump has a unique release valve that permits deflation of the implant with one squeeze of opposing touch pads. Aims.  To assess the impact of a new penile prosthesis design, the Titan OTR, on patient ease of operation. Furthermore, to assess patient satisfaction, surgeon acceptance, and the ease with which patients were trained in device operation in the clinic setting. Methods.  A total of 113 eligible patients from eight centers were recruited from men presenting with erectile dysfunction without prior prosthetic implantation. The subjects had a mean age of 61 years, and had a number of comorbidities, including diabetes (31.9%), hypertension (34.5%), and Peyronie's disease (23.9%). All underwent implantation of the study device. Main Outcome Measures.  Questionnaires were used to capture patient satisfaction as well as physician feedback on ease of implantation and patient education. A paired analysis was completed for patient satisfaction at 6 (N = 96) and 12 (N = 90) months. Results.  Overall satisfaction with the device was 90.6% and 90.0% at 6 and 12 months, respectively. The primary end point, ease of deflation, was seen in 70.8% and 73.3% at these two time points, with the 12‐month value statistically better than historical controls. Physicians overwhelmingly reported straightforward/simple intraoperative product preparation (97.3%) and equivalent or easier training compared with their previous pump of choice (96.4%). Adverse events for all subjects (N = 113) included removal of the device in four cases (3.5%) for infection and one case for chronic pain (0.8%). Conclusions.  The Titan OTR represents an advance in penile prosthetic technology that is well accepted by patients and physicians. The study design allowed for realistic evaluation of the new technology aimed at enhancing clinical outcomes. Ohl DA, Brock G, Ralph D, Bogache W, Jones L, Munarriz R, Levine L, and Ritenour C. Prospective evaluation of patient satisfaction, and surgeon and patient trainer assessment of the Coloplast Titan One Touch Release three‐piece inflatable penile prosthesis. J Sex Med 2012;9:2467–2474.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/93661/1/j.1743-6109.2012.02819.x.pd

All the queen's horses: statutory authority and HS2

This article focuses on the potential impact of the statutory authority defence on HS2 once the line is put into operation. The defence was forged in the heat of the railway revolution. It protects operators from liability in nuisance in respect of certain harms resulting from exercising the statutory powers under which the scheme is authorised. However, the nineteenth century case law established that the defence would only operate in respect of harms which are the inevitable consequence of using those powers. In common with its Victorian forebears, the HS2 project has been authorised by way of an Act of Parliament. Arguably, the HS2 Act is one of the longest, most detailed and highly scrutinised pieces of legislation in history. Nevertheless, it is argued that the scheme may cause uncompensated losses which are not inevitable. In this respect common law actions may yet have an important role to play

Non-surgical therapy of Peyronie’s disease

Abstract The present paper provides a review of the available non-surgical treatments for Peyronie's disease (PD). A review of published literature on oral, intralesional, external energy and iontophoresis therapies for PD was performed, and the published results of available treatment options reviewed. The authors' recommendations for appropriate non-surgical management of PD are provided. Although there are many published reports that show the efficacy of non-surgical therapies for PD, there is a lack of large scale, multicenter controlled clinical trials, which makes treatment recommendations difficult. Careful review of the literature does suggest that there are treatment options that make scientific sense and appear to stabilize the disease process, reduce deformity, and improve function. Offering no treatment at all will encourage our patients to pursue alternative treatments, which might do harm, and misses the opportunity to do some good. Clearly further work is necessary to develop safe and effective non-surgical treatments for PD

Facial EMG activity levels predict treatment outcome in depression

Higher electromyographic (EMG) activity levels of corrugator and zygomatic face muscles have been reported to be pretreatment predictors of better clinical outcome in depressed patients. We tested this possibility in 29 drug-free, rigorously diagnosed subjects by measuring low-level EMG activity of corrugator and zygomatic muscles during resting and three imagery states (happy, typical day, sad). All patients had major depressive disorder, endogenous subtype. Good responders had significantly higher pretreatment EMG zygomatic values and different EMG profiles. Our findings replicate and expand prior reports.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24620/1/0000030.pd

Update to the Vitamin C, Thiamine and Steroids in Sepsis (VICTAS) protocol: statistical analysis plan for a prospective, multicenter, double-blind, adaptive sample size, randomized, placebo-controlled, clinical trial.

BACKGROUND: Observational research suggests that combined therapy with Vitamin C, thiamine and hydrocortisone may reduce mortality in patients with septic shock. METHODS AND DESIGN: The Vitamin C, Thiamine and Steroids in Sepsis (VICTAS) trial is a multicenter, double-blind, adaptive sample size, randomized, placebo-controlled trial designed to test the efficacy of combination therapy with vitamin C (1.5 g), thiamine (100 mg), and hydrocortisone (50 mg) given every 6 h for up to 16 doses in patients with respiratory or circulatory dysfunction (or both) resulting from sepsis. The primary outcome is ventilator- and vasopressor-free days with mortality as the key secondary outcome. Recruitment began in August 2018 and is ongoing; 501 participants have been enrolled to date, with a planned maximum sample size of 2000. The Data and Safety Monitoring Board reviewed interim results at N = 200, 300, 400 and 500, and has recommended continuing recruitment. The next interim analysis will occur when N = 1000. This update presents the statistical analysis plan. Specifically, we provide definitions for key treatment and outcome variables, and for intent-to-treat, per-protocol, and safety analysis datasets. We describe the planned descriptive analyses, the main analysis of the primary end point, our approach to secondary and exploratory analyses, and handling of missing data. Our goal is to provide enough detail that our approach could be replicated by an independent study group, thereby enhancing the transparency of the study. TRIAL REGISTRATION: ClinicalTrials.gov, NCT03509350. Registered on 26 April 2018

Factors Affecting Repeat Visitation and Flow-on Tourism as Sources of Event Strategy Sustainability

The sustainability of including medium sized one-time sport events in an event portfolio is examined with reference to the capacity of one such event to stimulate flow-on tourism (i.e. tourism activities beyond the event but around the time of the event), a desire to return to the destination, and positive word-of-mouth. Relationships among four motives (socialising, escape, learning about the destination, and learning about athletics), identification with the event (self and social identity), previous visitation to the host destination, information search, tourism activities, and likelihood of recommending and/or returning to the host destination were examined for four categories of attendees at the Pan American Junior Athletics Championships: primary purpose spectators, casual spectators, athletes, and non-athlete participants. All four categories of attendee engaged in some information search and participated in flow-on tourism, but to a low degree. Information search fostered flow-on tourism. Classic tourism activities (e.g. sightseeing, visiting museums) were motivated by a desire to learn about the destination, and encouraged future visitation and likelihood of recommendation. It is concluded that medium-sized one-time sport events can play a sustainable role in event portfolios, but their efficacy requires greater integration of destination experiences with the event. It is suggested that future work should examine the means to cultivate that integration, including creation of more effective alliances between destination marketers and event organizers

The UCSC cancer genomics browser: update 2011

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple data sets can be viewed simultaneously as coordinated ‘heatmap tracks’ to compare across studies or different data modalities. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available data sets. The browser hosts a growing body of publicly available cancer genomics data from a variety of cancer types, including data generated from the Cancer Genome Atlas project. Multiple consortiums use the browser on confidential prepublication data enabled by private installations. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and ‘PARADIGM’ pathway tracks to display integrative pathway activities. The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser’s rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data

Microbiota that affect risk for shigellosis in children in low-income countries

Pathogens in the gastrointestinal tract exist within a vast population of microbes. We examined associations between pathogens and composition of gut microbiota as they relate to Shigella spp./enteroinvasive Escherichia coli infection. We analyzed 3,035 stool specimens (1,735 nondiarrheal and 1,300 moderate-to-severe diarrheal) from the Global Enteric Multicenter Study for 9 enteropathogens. Diarrheal specimens had a higher number of enteropathogens (diarrheal mean 1.4, nondiarrheal mean 0.95; p<0.0001). Rotavirus showed a negative association with Shigella spp. in cases of diarrhea (odds ratio 0.31, 95% CI 0.17–0.55) and had a large combined effect on moderate-to-severe diarrhea (odds ratio 29, 95% CI 3.8–220). In 4 Lactobacillus taxa identified by 16S rRNA gene sequencing, the association between pathogen and disease was decreased, which is consistent with the possibility that Lactobacillus spp. are protective against Shigella spp.–induced diarrhea. Bacterial diversity of gut microbiota was associated with diarrhea status, not high levels of the Shigella spp. ipaH gene.publishedVersio

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts