Agile Methods: Fast-Paced, but How Fast?

What are the roles of time and time pressures in design and performance of agile processes for software development? How do we plan our rapid development activities given the constraints of due dates? What does it mean to be on ‘internet time’? Agile methods are meant to be fast-paced, but are they fast in an effective way? How do time-pressures influence the productivity of a project team and how do they impact the motivations of developers? This paper considers the time issues in agile approaches to managing software projects and posits research propositions to guide further study of this area

Controls in Flexible Software Development

Control and flexibility may appear an unlikely pair. However, we propose that effective flexible software development processes must still provide clear control mechanisms to manage the progress and quality of the resulting software products. This paper presents a conceptual study to understand the types of control found in flexible software development processes, termed controlled-flexible approaches. Control theory is used as a lens to study the control mechanisms found in plan-driven and flexible processes. We extend current thinking to include emergent outcome controls and clan controls for team coordination in our taxonomy of control mechanisms. Several popular flexible processes are analyzed for control mechanisms. We conclude with a brief discussion of future research directions

Dealing with Uncertainties in Asteroid Deflection Demonstration Missions: NEOTwIST

Deflection missions to near-Earth asteroids will encounter non-negligible uncertainties in the physical and orbital parameters of the target object. In order to reliably assess future impact threat mitigation operations such uncertainties have to be quantified and incorporated into the mission design. The implementation of deflection demonstration missions offers the great opportunity to test our current understanding of deflection relevant uncertainties and their consequences, e.g., regarding kinetic impacts on asteroid surfaces. In this contribution, we discuss the role of uncertainties in the NEOTwIST asteroid deflection demonstration concept, a low-cost kinetic impactor design elaborated in the framework of the NEOShield project. The aim of NEOTwIST is to change the spin state of a known and well characterized near-Earth object, in this case the asteroid (25143) Itokawa. Fast events such as the production of the impact crater and ejecta are studied via cube-sat chasers and a flyby vehicle. Long term changes, for instance, in the asteroid's spin and orbit, can be assessed using ground based observations. We find that such a mission can indeed provide valuable constraints on mitigation relevant parameters. Furthermore, the here proposed kinetic impact scenarios can be implemented within the next two decades without threatening Earth's safety.Comment: Accepted for publication in the proceedings of the IAUS 318 - Asteroids: New Observations, New Models, held at the IAU General Assembly in Honolulu, Hawaii, USA 201

DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis

Inflammatory bowel diseases (IBD) are emerging globally, indicating that environmental factors may be important in their pathogenesis. Colonic mucosal epigenetic changes, such as DNA methylation, can occur in response to the environment and have been implicated in IBD pathology. However, mucosal DNA methylation has not been examined in treatment-naïve patients. We studied DNA methylation in untreated, left sided colonic biopsy specimens using the Infinium HumanMethylation450 BeadChip array. We analyzed 22 control (C) patients, 15 untreated Crohn’s disease (CD) patients, and 9 untreated ulcerative colitis (UC) patients from two cohorts. Samples obtained at the time of clinical remission from two of the treatment-naïve UC patients were also included into the analysis. UC-specific gene expression was interrogated in a subset of adjacent samples (5 C and 5 UC) using the Affymetrix GeneChip PrimeView Human Gene Expression Arrays. Only treatment-naïve UC separated from control. One-hundred-and-twenty genes with significant expression change in UC (> 2-fold, P < 0.05) were associated with differentially methylated regions (DMRs). Epigenetically associated gene expression changes (including gene expression changes in the IFITM1, ITGB2, S100A9, SLPI, SAA1, and STAT3 genes) were linked to colonic mucosal immune and defense responses. These findings underscore the relationship between epigenetic changes and inflammation in pediatric treatment-naïve UC and may have potential etiologic, diagnostic, and therapeutic relevance for IBD

Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing

<p>Abstract</p> <p>Background</p> <p>Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.</p> <p>Results</p> <p>Pash 3.0 generally matches the accuracy and speed of niche programs for fast mapping of short reads, and exceeds their performance on longer reads generated by a new generation of massively parallel sequencing technologies. By exploiting longer read lengths, Pash 3.0 maps reads onto the large fraction of genomic DNA that contains repetitive elements and polymorphic sites, including indel polymorphisms.</p> <p>Conclusions</p> <p>We demonstrate the versatility of Pash 3.0 by analyzing the interaction between CpG methylation, CpG SNPs, and imprinting based on publicly available whole-genome shotgun bisulfite sequencing data. Pash 3.0 makes use of gapped k-mer alignment, a non-seed based comparison method, which is implemented using multi-positional hash tables. This allows Pash 3.0 to run on diverse hardware platforms, including individual computers with standard RAM capacity, multi-core hardware architectures and large clusters.</p

Organizational Challenges in Developing One of the Nationwide Health Information Network Trial Implementation Awardees

Health care in the United States is rarely delivered in a coordinated manner. Current methods to share patient information are inefficient and may lead to medical errors, higher readmission rates, and delays in the delivery of needed health services. This qualitative study describes lessons learned concerning the early implementation of one Nationwide Health Information Network (NHIN) site in Long Beach, CA during its first year of operation. The Long Beach Network for Health (LBNH) focused on an incremental effort to exchange health information. Despite a limited concentration on emergency department care, virtually all respondents noted concerns regarding the sustainability, or business case, for the exchange of health information. Nevertheless, respondents were encouraged by progress on technological challenges and user requirements during this first year. The early gains in this process may, in turn, have laid the groundwork for future efforts to expand beyond the emergency department

Prospects for photon blockade in four level systems in the N configuration with more than one atom

We show that for appropriate choices of parameters it is possible to achieve photon blockade in idealised one, two and three atom systems. We also include realistic parameter ranges for rubidium as the atomic species. Our results circumvent the doubts cast by recent discussion in the literature (Grangier et al Phys. Rev Lett. 81, 2833 (1998), Imamoglu et al Phys. Rev. Lett. 81, 2836 (1998)) on the possibility of photon blockade in multi-atom systems.Comment: 8 page, revtex, 7 figures, gif. Submitted to Journal of Optics B: Quantum and Semiclassical Optic

Provider Stakeholders’ Perceived Benefit from a Nascent Health Information Exchange: A Qualitative Analysis

We sought to better understand the perceived costs and benefits of joining a nascent health information exchange (HIE) from the perspective of potential provider organization participants. We therefore conducted semi-structured interviews with organizational representatives. Interview transcriptions were thematically coded, and coded text was subsequently aggregated to summarize the breadth and depth of responses. Although no respondents expected HIE to result in net financial benefit to their organization, all respondents recognized some potential benefits, and some respondents expected HIE to result in overall organizational benefit. Disproportionate benefit was expected for the poorest, sickest patients. Many respondents had concerns about HIE increasing the risk of data security breaches, and these concerns were most pronounced at larger organizations. We found little evidence of organizational concern regarding loss of patients to other organizations or publication of unfavorable quality data. If HIE’s greatest benefactors are indeed the poorest, sickest patients, our current health care financing environment will make it difficult to align HIE costs with benefits. To sustain HIE, state and federal governments may need to consider ongoing subsidies. Furthermore, these governments will need to ensure that policies regulating data exchange have sufficient nationwide coordination and liability limitations that the perceived organizational risks of joining HIEs do not outweigh perceived benefits. HIE founders can address organizational concerns by attempting to coordinate HIE policies with those of their largest founding organizations, particularly for data security policies. Early HIE development and promotional efforts should not only focus on potential benefits, but should also address organizational concerns

Revised Status of Rare and Endangered Unionaea (Mollusca: Margaritiferidae, Unionidae) in Arkansas

Harris and Gordon (1987) reviewed the distribution and status of 18 rare and /or endangered unionacean bivalve species (commonly referred to as clams, mussels, freshwater mussels, naiads) that occur or have occurred in Arkansas. They discussed four species that were federally listed as endangered, four species that were considered endangered or extirpated within Arkansas, four species considered threatened within Arkansas, four species of special concern within Arkansas, and two species for which the conservation status was considered uncertain due to questions regarding taxonomic validity. Numerous unionacean field surveys have been performed during 1986 1996, and a substantial database of new distributional and relative abundance information has been accumulated. Two additional unionacean species have been listed as federally endangered, one additional species has been listed as federally threatened, and one endangered species has been newly discovered within Arkansas bringing the total number of federally protected unionacean species occurring within Arkansas to eight. The conservation status of 16 additional unionacean species occurring in Arkansas is discussed also

The Evolutionary Path to Extraintestinal Pathogenic, Drug-Resistant Escherichia coli Is Marked by Drastic Reduction in Detectable Recombination within the Core Genome

Peer reviewe