Innovative Approaches in the Discovery of Aquatic Mycobacteriophages

Bacteriophages (phages), viruses that infect bacteria, have many applications in medicine, agriculture, molecular biology, and other fields. As antibiotic resistance becomes an increasing problem, interest in phages has grown. The traditional techniques of phage discovery are successful for some phages, but others require modified procedures to achieve detectable host infection. Mycobacterium is a diverse bacterial genus characterized by a unique cell wall containing mycolic acids, which aids in survival and pathogenesis. The aims of the present research were to isolate mycobacteriophages, use bioinformatics techniques to analyze mycobacterial prophages, and combine genetic analysis with multi-well plate host range studies to identify phages that may infect M. marinum, M. fortuitum, or M. chelonae, aquatic pathogens with importance to aquaculture, zoonotic infections, and more. Firstly, three phage discovery procedures were adapted to a multi-well plate format using the host M. smegmatis mc2155 as a model organism; the 96-well plate detection assay was at least as sensitive as the traditional plaque assay and a technique was developed for the purification of single phage types from mixed cultures in liquid medium. Secondly, phage enrichment from various environmental sources and prophage induction using a variety of techniques did not result in confirmed phage isolation for several tested strains of M. marinum, M. fortuitum, and M. chelonae, demonstrating the difficulty of phage isolation for these species. Thirdly, the emergence and evolution of prophages was investigated in 49 sequenced genomes of the M. ulcerans-M. marinum complex (MuMC), resulting in 134 identified prophages in nine genomic insertion sites. Lastly, phages from a pre-existing phage collection were used in host range studies against 10 strains of mycobacteria, using both plaque assays and multi-well plate turbidity assays (MuMC, M. fortuitum, and M. chelonae). As phages become more extensively used in medicine and other fields, it will become increasingly important to efficiently isolate phages that can infect the bacterium of interest and that have the appropriate qualities for each specific application. Phages are already known to be diverse in their morphology, physiology, and ecological roles, and it is now becoming clearer that the techniques to manipulate them must also be diverse

A computer program for the calculation of laminar and turbulent boundary layer flows

The results are presented of a study to produce a computer program to calculate laminar and turbulent boundary layer flows. The program is capable of calculating the following types of flow: (1) incompressible or compressible, (2) two dimensional or axisymmetric, and (3) flows with significant transverse curvature. Also, the program can handle a large variety of boundary conditions, such as blowing or suction, arbitrary temperature distributions and arbitrary wall heat fluxes. The program has been specialized to the calculation of equilibrium air flows and all of the thermodynamic and transport properties used are for air. For the turbulent transport properties, the eddy viscosity approach has been used. Although the eddy viscosity models are semi-empirical, the model employed in the program has corrections for pressure gradients, suction and blowing and compressibility. The basic method of approach is to put the equations of motion into a finite difference form and then solve them by use of a digital computer. The program is written in FORTRAN 4 and requires small amounts of computer time on most scientific machines. For example, most laminar flows can be calculated in less than one minute of machine time, while turbulent flows usually require three or four minutes

The Risk of Cancer from CT Scans and Other Sources of Low-Dose Radiation: A Critical Appraisal of Methodologic Quality

AbstractIntroduction: Concern exists that radiation exposure from computerized tomography (CT) will cause thousands of malignancies. Other experts share the same perspective regarding the risk from additional sources of low-dose ionizing radiation, such as the releases from Three Mile Island (1979; Pennsylvania USA) and Fukushima (2011; Okuma, Fukushima Prefecture, Japan) nuclear power plant disasters. If this premise is false, the fear of cancer leading patients and physicians to avoid CT scans and disaster responders to initiate forcedevacuations is unfounded.Study Objective: This investigation provides a quantitative evaluation of the methodologic quality of studies to determine the evidentiary strength supporting or refuting a causal relationshipbetween low-dose radiation and cancer. It will assess the number of higher qualitystudies that support or question the role of low-dose radiation in oncogenesis.Methods: This investigation is a systematic, methodologic review of articles published from 1975–2017 examining cancer risk from external low-dose x-ray and gamma radiation, defined as less than 200 millisievert (mSv). Following the PRISMA guidelines, the authors performed a search of the PubMed, Cochrane, Scopus, and Web of Science databases. Methodologies of selected articles were scored using the Newcastle Ottawa Scale (NOS) and a tool identifying 11 lower quality indicators. Manuscript methodologies were rankedas higher quality if they scored no lower than seven out of nine on the NOS and contained no more than two lower quality indicators. Investigators then characterized articles as supporting or not supporting a causal relationship between low-dose radiation and cancer.Results: Investigators identified 4,382 articles for initial review. A total of 62 articles met all inclusion/exclusion criteria and were evaluated in this study. Quantitative evaluation of the manuscripts’ methodologic strengths found 25 studies met higher quality criteria while 37 studies met lower quality criteria. Of the 25 studies with higher quality methods, 21 out of 25did not support cancer induction by low-dose radiation (P = .0003).Conclusions: A clear preponderance of articles with higher quality methods found no increased risk of cancer from low-dose radiation. The evidence suggests that exposure to multiple CT scans and other sources of low-dose radiation with a cumulative dose up to 100 mSv (approximately 10 scans), and possibly as high as 200 mSv (approximately 20 scans), does not increase cancer risk

Modified NASA-Lewis chemical equilibrium code for MHD applications

A substantially modified version of the NASA-Lewis Chemical Equilibrium Code was recently developed. The modifications were designed to extend the power and convenience of the Code as a tool for performing combustor analysis for MHD systems studies. The effect of the programming details is described from a user point of view

Directed and Elliptic Flow in 158 AGeV Pb+Pb Collisions

Directed and elliptic flow of protons and positively charged pions has been studied in the target fragmentation region using the Plastic Ball detector in the WA98 experiment. The results exhibit a strong dependence on centrality, rapidity, and transverse momentum. The rapidity dependence can be described by a Gaussian distribution. The model comparisons reveal a large discrepancy of the flow strength obtained from the data and the simulations.Comment: 4 pages, 4 eps figures, talk at Quark Matter 99, see also http://qgp.uni-muenster.de/WA98/qm99/flo

Introduction to The Special Issue: Advances in Methods and Measurement in Family Psychology

This special issue presents a collection of reports that highlight recent advances in methods and measurement and also shed light on the complexity of family psychology. The importance of theory in guiding solid family science is evident throughout these reports. The reports include guides for researchers who incorporate direct observation into their research protocols and the ever-expanding field of tele-health interventions. Advanced analytic approaches are offered in the areas of grid sequence analysis, latent fixed-effects models, and the Factors of Curves Model (FOCUS). These sophisticated analytic approaches may be applied to advance systemic thinking in family psychology. The last set of articles illustrate how complex and innovative methodologies are applied to address important societal issues. Work experiences and marital relationships in African American couples address the importance of spillover effects in contemporary families. The creation of biobehavioral plasticity index has the potential to inform gene x environment contributions to family functioning. Finally, the unique methodological issues that are particularly germane to the diverse nature of stepfamilies and nonresident fathers are addressed. We hope that readers of this special issue will return to these reports as resources and examples of theory-driven methods and measurements

Hybrid Method for Digits Recognition using Fixed-Frame Scores and Derived Pitch

This paper presents a procedure of frame normalization based on the traditional dynamic time warping (DTW) using the LPC coefficients. The redefined method is called as the DTW frame-fixing method (DTW-FF), it works by normalizing the word frames of the input against the reference frames. The enthusiasm to this study is due to neural network limitation that entails a fix number of input nodes for when processing multiple inputs in parallel. Due to this problem, this research is initiated to reduce the amount of computation and complexity in a neural network by reducing the number of inputs into the network. In this study, dynamic warping process is used, in which local distance scores of the warping path are fixed and collected so that their scores are of equal number of frames. Also studied in this paper is the consideration of pitch as a contributing feature to the speech recognition. Results showed a good performance and improvement when using pitch along with DTW-FF feature. The convergence rate between using the steepest gradient descent is also compared to another method namely conjugate gradient method. Convergence rate is also improved when conjugate gradient method is introduced in the back-propagation algorithm

Microscopic calculations of stopping and flow from 160AMeV to 160AGeV

The behavior of hadronic matter at high baryon densities is studied within Ultrarelativistic Quantum Molecular Dynamics (URQMD). Baryonic stopping is observed for Au+Au collisions from SIS up to SPS energies. The excitation function of flow shows strong sensitivities to the underlying equation of state (EOS), allowing for systematic studies of the EOS. Effects of a density dependent pole of the $\rho$-meson propagator on dilepton spectra are studied for different systems and centralities at CERN energies.Comment: Proceedings of the Quark Matter '96 Conference, Heidelberg, German