Multi-class protein fold classification using a new ensemble machine learning approach.

Protein structure classification represents an important process in understanding the associations between sequence and structure as well as possible functional and evolutionary relationships. Recent structural genomics initiatives and other high-throughput experiments have populated the biological databases at a rapid pace. The amount of structural data has made traditional methods such as manual inspection of the protein structure become impossible. Machine learning has been widely applied to bioinformatics and has gained a lot of success in this research area. This work proposes a novel ensemble machine learning method that improves the coverage of the classifiers under the multi-class imbalanced sample sets by integrating knowledge induced from different base classifiers, and we illustrate this idea in classifying multi-class SCOP protein fold data. We have compared our approach with PART and show that our method improves the sensitivity of the classifier in protein fold classification. Furthermore, we have extended this method to learning over multiple data types, preserving the independence of their corresponding data sources, and show that our new approach performs at least as well as the traditional technique over a single joined data source. These experimental results are encouraging, and can be applied to other bioinformatics problems similarly characterised by multi-class imbalanced data sets held in multiple data sources

Integrative machine learning approach for multi-class SCOP protein fold classification

Classification and prediction of protein structure has been a central research theme in structural bioinformatics. Due to the imbalanced distribution of proteins over multi SCOP classification, most discriminative machine learning suffers the well-known ‘False Positives ’ problem when learning over these types of problems. We have devised eKISS, an ensemble machine learning specifically designed to increase the coverage of positive examples when learning under multiclass imbalanced data sets. We have applied eKISS to classify 25 SCOP folds and show that our learning system improved over classical learning methods

Bronchial thermoplasty: implementing best practice in the era of cost containment.

Increasing dependence on advanced technologies in the 21st century has created a dilemma between the practice and business of medicine. From information technology to robotic surgery, new technologies have expanded treatment possibilities and have potentially improved patient outcomes and safety. Simultaneously, their escalating costs limit access for certain patients and health care facilities. Nevertheless, medical decisions should not simply be based on cost. Input from physicians and other health care specialists as well as adherence to best practice position statements, are vital to implementing truly cost-effective strategies in medicine. Bronchial thermoplasty (BT), a US Food and Drug Administration approved bronchoscopy procedure in difficult-to-control persistent asthma, is a prime example of a new technology facing cost and implementation challenges. We discuss the specific indications and contraindications for BT and review recent real-world experiences that can provide the foundation for building a comprehensive asthma program that provides BT for difficult-to-control asthma patients who fail national guideline treatment recommendations after an adequate clinical trial of one. We also offer insight into the barriers to implementing a successful BT program and strategies for overcoming them

Exciton and biexciton energies in bilayer systems

We report calculations of the energies of excitons and biexcitons in ideal two-dimensional bilayer systems within the effective-mass approximation with isotropic electron and hole masses. The exciton energies are obtained by a simple numerical integration technique, while the biexciton energies are obtained from diffusion quantum Monte Carlo calculations. The exciton binding energy decays as the inverse of the separation of the layers, while the binding energy of the biexciton with respect to dissociation into two separate excitons decays exponentially

The effect of manganese oxide on the sinterability of hydroxyapatite

The sinterability of manganese oxide (MnO2) doped hydroxyapatite (HA) ranging from 0.05 to 1 wt% was investigated. Green samples were prepared and sintered in air at temperatures ranging from 1000 to 1400 °C. Sintered bodies were characterized to determine the phase stability, grain size, bulk density, hardness, fracture toughness and Young's modulus. XRD analysis revealed that the HA phase stability was not disrupted throughout the sintering regime employed. In general, samples containing less than 0.5 wt% MnO2 and when sintered at lower temperatures exhibited higher mechanical properties than the undoped HA. The study revealed that all the MnO2-doped HA achieved >99% relative density when sintered at 1100–1250 °C as compared to the undoped HA which could only attained highest value of 98.9% at 1150 °C. The addition of 0.05 wt% MnO2 was found to be most beneficial as the samples exhibited the highest hardness of 7.58 GPa and fracture toughness of 1.65 MPam1/2 as compared to 5.72 GPa and 1.22 MPam1/2 for the undoped HA when sintered at 1000 °C. Additionally, it was found that the MnO2-doped samples attained E values above 110 GPa when sintered at temperature as low as 1000 °C if compared to 1050 °C for the undoped HA

Implementation of Design Changes Towards a More Reliable, Hands-off Magnetron Ion Source

As the main $H^{-}$ ion source for the accelerator complex, magnetron ion sources have been used at Fermilab since the 1970s. At the offline test stand, new R&D is carried out to develop and upgrade the present magnetron-type sources of $H^{-}$ ions of up to 80 mA and 35 keV beam energy in the context of the Proton Improvement Plan. The aim of this plan is to provide high-power proton beams for the experiments at FNAL. In order to reduce the amount of tuning and monitoring of these ion sources, a new electronic system consisting of a current-regulated arc discharge modulator allow the ion source to run at a constant arc current for improved beam output and operation. A solenoid-type gas valve feeds $H_{2}$ gas into the source precisely and independently of ambient temperature. This summary will cover several studies and design changes that have been tested and will eventually be implemented on the operational magnetron sources at Fermilab. Innovative results for this type of ion source include cathode geometries, solenoid gas valves, current controlled arc pulser, cesium boiler redesign, gas mixtures of hydrogen and nitrogen, and duty factor reduction, with the aim to improve source lifetime, stability, and reducing the amount of tuning needed. In this summary, I will highlight the advances made in ion sources at Fermilab and will outline the directions of the continuing R&D effort.Comment: 4 pp. arXiv admin note: substantial text overlap with arXiv:1701.0175

Improvements on the Stability and Operation of a Magnetron H- Ion Source

The magnetron H- ion sources developed in the 1970s currently in operation at Fermilab provide beam to the rest of the accelerator complex. A series of modifications to these sources have been tested in a dedicated offline test stand with the aim of improving different operational issues. The solenoid type gas valve was tested as an alternative to the piezoelectric gas valve in order to avoid its temperature dependence. A new cesium oven was designed and tested in order to avoid glass pieces that were present with the previous oven, improve thermal insulation and fine tune its temperature. A current-regulated arc modulator was developed to run the ion source at a constant arc current, providing very stable beam outputs during operations. In order to reduce beam noise, the addition of small amounts of N2 gas was explored, as well as testing different cathode shapes with increasing plasma volume. This paper summarizes the studies and modifications done in the source over the last three years with the aim of improving its stability, reliability and overall performance.Comment: 8 pages, 19 figure