Coarse-grained simulation of polymer translocation through an artificial nanopore

The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of semiconductor--based nanopore devices for ultra--fast DNA sequencing. The polymer is represented by a simple bead--spring model designed to yield an appropriate coarse-grained description of the phosphate backbone of DNA in salt--free aqueous solution. A detailed analysis of single translocation event is presented to assess whether the passage of individual ions through the pore can be detected by a nanoscale field--effect transistor by measuring variations in electrostatic potential during polymer translocation. We find that it is possible to identify single events corresponding to the passage of counterions through the pore, but that discrimination of individual ions on the polymer chain based on variations in electrostatic potential is problematic. Several distinct stages in the translocation process are identified, characterized by changes in polymer conformation and by variations in the magnitude and direction of the internal electric field induced by the fluctuating charge distribution. The dependence of the condensed fraction of counterions on Bjerrum length leads to significant changes in polymer conformation, which profoundly affect the dynamics of electrophoresis and translocation.Comment: 37 pages Revtex, 11 postscript figure

Systematic review of grounded theory studies in physiotherapy

Aim: This systematic review aimed at appraising the methodological rigor of grounded theory research published in the field of physiotherapy to assess how the methodology is understood and applied. A secondary aim was to provide research implications drawn from the findings to guide future grounded theory methodology research. Methods: A systematic search was conducted in MEDLINE, CINHAL, SPORT Discus, Science Direct, PubMed, Scopus and Web of Science to identify studies in the field of physiotherapy that reported using grounded theory methodology and/or methods in the study title and/or abstract. The descriptive characteristics and methodological quality of eligible studies were examined using the assessment guidelines developed by Hutchison, Johnston and Breckon (2011). Findings: The review included sixty-eight studies conducted between 1998 and 2017. The findings showed that grounded theory methodology is becoming increasingly used by physiotherapy researchers. Thirty-six studies (53%) demonstrated a good understanding and appropriate application of grounded theory methodology. Thirty-two studies (47%) presented descriptive findings and were considered to be of poor methodological quality. Conclusions: There are several key tenets of grounded theory methodology that are integral to the iterative process of qualitative theorizing and need to be applied throughout all research practices including sampling, data collection and analysis

Capturing the essence of grounded theory: the importance of understanding commonalities and variants

This paper aims to capture the essence of grounded theory (GT) by setting out its commonalities and variants and, importantly, the implications of the latter for the implementation of the former, and for the truth claims and the contributions to knowledge that a GT study might make. Firstly, three ontological and epistemological variants of GT are outlined. Secondly, the commonalities of GT are set out as eight core elements of GT methodology that are individually necessary, but only sufficient collectively, to define a GT study. These elements are: an iterative process; theoretical sampling; theoretical sensitivity; codes, memos and concepts; constant comparison; theoretical saturation; fit, work, relevance and modifiability; and substantive theory. Thirdly, the implications of the ontological and epistemological variants of GT for, firstly, the implementation of the core common elements of the methodology and, secondly, the truth claims and contributions to knowledge that might be made, are discussed. Finally, the paper concludes by arguing that published GT studies in sport, exercise and health research have not always explicitly demonstrated a full understand of the commonalities and variants of GT, and that researchers publishing GT studies must take responsibility for doing this

Compressible flow structures interaction with a two-dimensional ejector: a cold-flow study

An experimental study has been conducted to examine the interaction of compressible flow structures such as shocks and vortices with a two-dimensional ejector geometry using a shock-tube facility. Three diaphragm pressure ratios ofP4 =P1 = 4, 8, and 12 have been employed, whereP4 is the driver gas pressure andP1 is the pressure within the driven compartment of the shock tube. These lead to incident shock Mach numbers of Ms = 1:34, 1.54, and 1.66, respectively. The length of the driver section of the shock tube was 700 mm. Air was used for both the driver and driven gases. High-speed shadowgraphy was employed to visualize the induced flowfield. Pressure measurements were taken at different locations along the test section to study theflow quantitatively. The induced flow is unsteady and dependent on the degree of compressibility of the initial shock wave generated by the rupture of the diaphragm

Path Integral Solubility of a General Two-Dimensional Model

The solubility of a general two dimensional model, which reduces to various models in different limits, is studied within the path integral formalism. Various subtleties and interesting features are pointed out.Comment: 7 pages, UR1386, ER40685-83

Tumor site immune markers associated with risk for subsequent basal cell carcinomas.

BackgroundBasal cell carcinoma (BCC) tumors are the most common skin cancer and are highly immunogenic.ObjectiveThe goal of this study was to assess how immune-cell related gene expression in an initial BCC tumor biopsy was related to the appearance of subsequent BCC tumors.Materials and methodsLevels of mRNA for CD3ε (a T-cell receptor marker), CD25 (the alpha chain of the interleukin (IL)-2 receptor expressed on activated T-cells and B-cells), CD68 (a marker for monocytes/macrophages), the cell surface glycoprotein intercellular adhesion molecule-1 (ICAM-1), the cytokine interferon-γ (IFN-γ) and the anti-inflammatory cytokine IL-10 were measured in BCC tumor biopsies from 138 patients using real-time PCR.ResultsThe median follow-up was 26.6 months, and 61% of subjects were free of new BCCs two years post-initial biopsy. Patients with low CD3ε CD25, CD68, and ICAM-1 mRNA levels had significantly shorter times before new tumors were detected (p = 0.03, p = 0.02, p = 0.003, and p = 0.08, respectively). Furthermore, older age diminished the association of mRNA levels with the appearance of subsequent tumors.ConclusionsOur results show that levels of CD3ε, CD25, CD68, and ICAM-1 mRNA in BCC biopsies may predict risk for new BCC tumors

The challenges of staying together while moving fast

We report on the results of an empirical study conducted with 35 experienced software developers from 22 high-tech companies, including Google, Facebook, Microsoft, Intel, and others. The goal of the study was to elicit challenges that these developers face, potential solutions that they envision to these challenges, and research initiatives that they think would deliver useful results. Challenges identified by the majority of the study participants relate to the collaborative nature of the work: the availability and discoverability of information, communication, collaborative planning and integration with work of others. Almost all participants also addressed the advantages and disadvantages of the current "fast to the market" trend, and the toll it takes on the quality of the software that they are able to deliver and on their professional and personal satisfaction as software engineers. We describe in depth the identified challenges, supporting our findings with explicit quotes from the study participants. We also put these findings in context of work done by the software engineering community and outline a roadmap for possible future research initiatives

Discourse revisited : dimensions and employment of first-order strategy discourse during institutional adoption

Despite decades of research on strategy, we still know little about what the concept of strategy means to actual strategists and how they use it in practice. Working at the intersections of institutional and practice theories, we use exploratory interviews with strategy directors and a longitudinal case study to uncover four dimensions of first-order strategy discourse: functional, contextual, identity, and metaphorical. We also reveal three phases in the interrelation between first-order strategy discourse and institutional work: shaping, settling, and selling and a differential emphasis (selective focusing) on dimensions of the first-order strategy discourse during the institutional adoption process. We contribute to a deeper understanding of the concept of strategy in practice, the process of institutional adoption, and of the role of discourse in this process