Dissimilarities in alignment-free methods for phylogenetic analysis based on genomes

Whole genome sequences are generally accepted as excellent tools for studying evolutionary relationships. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignments could not be directly applied to the whole-genome comparison and phylogenomic studies. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. The “distances” used in these alignment-free methods are not proper distance metrics in the strict mathematical sense. In this study, we first review them in a more general frame — dissimilarity. Then we propose some new dissimilarities for phylogenetic analysis. Last three genome datasets are employed to evaluate these dissimilarities from a biological point of view.

VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

Methods for constructing uncertainty intervals for queries of Bayesian nets

In this paper the issue of finding uncertainty intervals for queries in a Bayesian Network is reconsidered. The investigation focuses on Bayesian Nets with discrete nodes and finite populations. An earlier asymptotic approach is compared with a simulation-based approach, together with further alternatives, one based on a single sample of the Bayesian Net of a particular finite population size, and another which uses expected population sizes together with exact probabilities. We conclude that a query of a Bayesian Net should be expressed as a probability embedded in an uncertainty interval. Based on an investigation of two Bayesian Net structures, the preferred method is the simulation method. However, both the single sample method and the expected sample size methods may be useful and are simpler to compute. Any method at all is more useful than none, when assessing a Bayesian Net under development, or when drawing conclusions from an ‘expert’ system.

Missing in space: An evaluation of imputation methods for missing data in spatial analysis of risk factors for type II diabetes

Background Spatial analysis is increasingly important for identifying modifiable geographic risk factors for disease. However, spatial health data from surveys are often incomplete, ranging from missing data for only a few variables, to missing data for many variables. For spatial analyses of health outcomes, selection of an appropriate imputation method is critical in order to produce the most accurate inferences. Methods We present a cross-validation approach to select between three imputation methods for health survey data with correlated lifestyle covariates, using as a case study, type II diabetes mellitus (DM II) risk across 71 Queensland Local Government Areas (LGAs). We compare the accuracy of mean imputation to imputation using multivariate normal and conditional autoregressive prior distributions. Results Choice of imputation method depends upon the application and is not necessarily the most complex method. Mean imputation was selected as the most accurate method in this application. Conclusions Selecting an appropriate imputation method for health survey data, after accounting for spatial correlation and correlation between covariates, allows more complete analysis of geographic risk factors for disease with more confidence in the results to inform public policy decision-making.

Hybrid metaheuristic techniques for optimising sugarcane rail operations

Mixed integer programming and parallel-machine job shop scheduling are used to solve the sugarcane rail transport scheduling problem. Constructive heuristics and metaheuristics were developed to produce a more efficient scheduling system and so reduce operating costs. The solutions were tested on small and large size problems. High-quality solutions and improved CPU time are the result of developing new hybrid techniques which consist of different ways of integrating simulated annealing and Tabu search techniques.

Multipurpose nanoporous alumina-carbon nanowall bi-dimensional nano-hybrid platform via catalyzed and catalyst-free plasma CVD

Simple, rapid, plasma-assisted synthesis of large-area arrays of vertically-aligned carbon nanowalls on highly-porous, transparent bare and gold-coated alumina membranes with the two pore sizes is reported. It is demonstrated that the complex patterns of vertically aligned nanowalls can nucleate and form different morphologies in the low-temperature plasmas. The process is stable, and the twofold change in the gas flow (10 and 20 sccm) does not noticeably influence the morphology of the nanowall pattern. Application of a thin (5 nm) gold layer to nanoporous membrane prior to the nanowall growth allows controlling the network morphology.

Impacts of tillage and application methods on atrazine and alachlor losses from upland fields: Research paper

The effects of tillage practises and the methods of chemical application on atrazine and alachlor losses through run-off were evaluated for five treatments: conservation (untilled) and surface (US), disk and surface, plow and surface, disk and preplant-incorporated, and plow and preplant-incorporated treatments. A rainfall simulator was used to create 63.5 mm h^-1 of rainfall for 60 min and 127 mm h^-1 for 15 min. Rainfall simulation occurred 24-36 h after chemical application. There was no significant difference in the run-off volume among the treatments but the untilled treatment significantly reduced erosion loss. The untilled treatments had the highest herbicide concentration and the disk treatments were higher than the plow treatments. The surface treatments showed a higher concentration than the incorporated treatments. The concentration of herbicides in the water decreased with time. Among the experimental sites, the one with sandy loam soil produced the greatest losses, both in terms of the run-off volume and herbicide loss. The US treatments had the highest loss and the herbicide incorporation treatments had smaller losses through run-off as the residue cover was effective in preventing herbicide losses. Incorporation might be a favorable method of herbicide application to reduce the herbicide losses by run-off.

“I understand. I am a participant”: Navigating the ‘fuzzy’ boundaries of visual methods in qualitative longitudinal research

In this chapter we discuss how utilising the participatory visual methodology, photovoice, in an aged care context with its unique communal setting raised several ‘fuzzy boundary’ ethical dilemmas. To illustrate these challenges, we draw on immersive field notes from an ongoing qualitative longitudinal research (QLR) exploring the lived experience of aged care from the perspective of older residents, and focus on interactions with one participant, 81 year old Cassie. We explore how the camera, which is integral to the photovoice method, altered the researcher/participant ethical dynamics by becoming a continual ‘connector’ to the researcher. The camera took on a distinct agency, acting as a non-threatening ‘portal’ that lengthened contact, provided informal opportunities to alter the relationship dynamics and enabled unplanned participant revelation.

Colonoscopy preparation in children: Safety, efficacy, and tolerance of high- versus low-volume cleansing methods

Background: The use of large-volume electrolyte balanced solutions as preparation for colonoscopy often results in poor patient compliance and acceptance. The tolerance, safety, and efficacy of high-versus low volume colon-cleansing methods as preparation for colonoscopy in children were compared by randomized operator-blinded trial. Methods: Twenty-nine children ages 3.6-14.6 years had either high-volume nasogastric balanced polyethylene glycol electrolyte lavage (20 ml/kg/h) until the effluent was clear (n = 15), or two oral doses of sodium phosphate solution (22.5-45 ml) separated by oral fluid intake (n = 14). Results: Both preparations were equally effective. The low-volume preparation was better tolerated and caused less discomfort that the high-volume preparation, judging by serial nurse observations. The incidence of abdominal symptoms, diarrhea, sleep disturbance, and vomiting was not significantly different between the two groups. Both groups had a small reduction in mean hematocrit and serum calcium levels. The sodium phosphate preparation caused increases in mean serum sodium concentrations from 140 to 145 mmol/L and serum phosphate concentrations from 1.41 to 2.53 mmol/L. Ten hours after the commencement of the preanesthetic fast, these concentrations had returned to normal. Conclusions: There are advantages in terms of tolerance, discomfort, and case of administration with acceptable colonic cleansing with the use of the less-invasive oral sodium phosphate low-volume colon-cleansing preparation in children. Safe use requires ensuring an adequate oral fluid intake during the preparation time and avoidance of use in patients with renal insufficiency.

Spatio-temporal modelling of cancer data in Queensland using Bayesian methods

Cancer is the leading contributor to the disease burden in Australia. This thesis develops and applies Bayesian hierarchical models to facilitate an investigation of the spatial and temporal associations for cancer diagnosis and survival among Queenslanders. The key objectives are to document and quantify the importance of spatial inequalities, explore factors influencing these inequalities, and investigate how spatial inequalities change over time. Existing Bayesian hierarchical models are refined, new models and methods developed, and tangible benefits obtained for cancer patients in Queensland. The versatility of using Bayesian models in cancer control are clearly demonstrated through these detailed and comprehensive analyses.

Synthesis and vesicle formation from hybrid bolaphile/amphiphile ion-pairs. Evidence of membrane property modulation by molecular design

Four new hybrid (bolaphile/amphiphile) ion-pairs were synthesized. Electron microscopy indicated that each of these forms bilayer membranes upon dispersion in aqueous media. Membrane properties have also been examined by differential scanning calorimetry, microcalorimetry, temperature-dependent fluorescence anisotropy measurements, and UV-vis spectroscopy. The T-m values for the vesicular 1, 2, 3, 4, and 5 were 38, 12, 85, 31.3, and 41.6 degrees C, respectively. Interestingly the T-m values for 1 and 3 were found to depend on their concentration. The entrapment of small solute and the release capability have also been examined to demonstrate that these bilayers form enclosed vesicles. X-ray diffraction of the cast films has been performed to understand the nature and the thickness of these membrane organizations. The membrane widths ranged from 33 to 47 Angstrom. Finally, the above observations have been analyzed in light of the results obtained from molecular modeling studies. Thus we have demonstrated that membrane properties can be modulated by simple structural changes at the amphiphile level. It was shown that by judicious incorporation of central, isomeric, disubstituted aromatic units as structural anchors into different bolaphiles, one can modulate the properties of the resulting vesicles.

Real-World Extensions To Scheduling Algorithms Based On Lagrangian Relaxation

Recently, efficient scheduling algorithms based on Lagrangian relaxation have been proposed for scheduling parallel machine systems and job shops. In this article, we develop real-world extensions to these scheduling methods. In the first part of the paper, we consider the problem of scheduling single operation jobs on parallel identical machines and extend the methodology to handle multiple classes of jobs, taking into account setup times and setup costs, The proposed methodology uses Lagrangian relaxation and simulated annealing in a hybrid framework, In the second part of the paper, we consider a Lagrangian relaxation based method for scheduling job shops and extend it to obtain a scheduling methodology for a real-world flexible manufacturing system with centralized material handling.

Hybrid stiff-string-polynomial basis functions for vibration analysis of high speed rotating beams

A new finite element is developed for free vibration analysis of high speed rotating beams using basis functions which use a linear combination of the solution of the governing static differential equation of a stiff-string and a cubic polynomial. These new shape functions depend on rotation speed and element position along the beam and account for the centrifugal stiffening effect. The natural frequencies predicted by the proposed element are compared with an element with stiff-string, cubic polynomial and quintic polynomial shape functions. It is found that the new element exhibits superior convergence compared to the other basis functions.

Hybrid framework iron(II) phosphate-oxalates

Two inorganic-organic hybrid framework iron phosphate-oxalates, I, [N2C4H12](0.5)[Fe-2(HPO4)(C2O4)(1.5)] and II, [Fe-2(OH2)PO4(C2O4)(0.5)] have been synthesized by hydrothermal means and the structures determined by X-ray crystallography. Crystal Data: compound I, monoclinic, spacegroup = P2(1)/c (No. 14), a=7.569(2) Angstrom, b=7.821(2) Angstrom, c=18.033(4) Angstrom, beta=98.8(1)degrees, V=1055.0(4) Angstrom(3), Z=4, M=382.8, D-calc=2.41 g cm(-3) MoK alpha, R-F=0.02; compound II, monoclinic, spacegroup=P2(1)/c (No. 14), a=10.240(1) b=6.375(3) Angstrom, 9.955(1) Angstrom, beta=117.3(1)degrees, V=577.4(1) Angstrom(3), Z=4, M=268.7, D-calc=3.09 g cm(-3) MoK alpha, R-F=0.03. These materials contain a high proportion of three-coordinated oxygens and [Fe2O9] dimeric units, besides other interesting structural features. The connectivity of Fe2O9 is entirely different in the two materials resulting in the formation of a continuous chain of Fe-O-Fe in II. The phosphate-oxalate containing the amine, I, forms well-defined channels. Magnetic susceptibility measurements show Fen to be in the high-spin state (t(2g)(4)e(g)(2)) in II, and in the intermediate-spin state (t(2g)(5)e(g)(1)) in I.