bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of classifier performance for multiclass phenotype discrimination in untargeted metabolomics
Authors: Trainor Patrick J. , DeFilippis Andrew P. , Rai Shesh N. 
Published: May 2017

AbstractStatistical classification is a critical component of utilizing metabolomics data for examining the molecular determinants of phenotypes and for furnishing diagnostic and prognostic phenotype predictions in medicine. Despite this, a comprehensive and rigorous evaluation of classification techniques for phenotype discrimination given metabolomics data has not been conducted. We conducted such an evaluation using both simulated and real metabolomics data, comparing Partial Least Squares-Discriminant Analysis (PLS-DA), Sparse PLS-DA, Random Forests, Support Vector Machines, and Neural Network classification techniques for discriminating phenotype. We evaluated the techniques on simulated data generated to mimic global untargeted metabolomics data by incorporating realistic block-wise correlation and partial correlation structures for mimicking the correlations and metabolite clustering generated by biological processes. Over the simulation studies, covariance structures, means, and effect sizes were randomly simulated to provide consistent estimates of classifier performance over a wide range of possible scenarios. The presence of non-normal error distributions and the effect of prior-significance filtering (dimension reduction) were evaluated. In each simulation, classifier parameters (such as the number of hidden nodes in a neural network) were tuned by cross-validation to minimize the probability of detecting spurious results due to poorly tuned classifiers. Classifier performance was then evaluated using real clinical metabolomics datasets of varying sample medium, sample size, and experimental design. We report that in the scenarios without a significant presence of non-normal error distributions over metabolite clusters, Neural Network and PLS-DA classifiers performed poorly relative to Sparse PLS-DA (sPLS-DA), Support Vector Machine (SVM), and Random Forest classifiers. When non-normal error distributions were introduced, the performance of PLS-DA classifiers deteriorated further relative to the remaining techniques. Simultaneously, while the relative performance of Neural Network classifiers improved relative to PLS-DA classifiers, Neural Network classifier performance remained poor compared sPLS-DA, SVM, and Random Forest classifiers. Over the real datasets, a trend of better performance of SVM and Random Forest classifier performance was observed.
Purification of the mammalian NgBR/hCITcis-prenyltransferase complex: Identification of a conserved carboxyterminal RxG motif crucial for enzymatic activity
Authors: Grabińska Kariona A. , Edani Ban H. , Park Eon Joo , Kraehling Jan R. , Sessa William C. 
Published: May 2017

SummaryCis-Prenyltransferases (cisPTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. In eukaryotes and archaea,cisPT is the first enzyme committed to the synthesis of dolichyl-phosphate (DolP). DolP is obligate lipid carrier in protein glycosylation reactions in mammals. The homodimeric bacterial enzyme, undecaprenyl diphosphate synthase (UPPS) generates 11 isoprene units and has been structurally and mechanistically characterized in great detail. Recently our group discovered that unlike UPPS, mammaliancisPT is a heteromer consisting of NgBR (NUS1) and hCIT (DHDDS) subunits and this composition has been confirmed in plants and fungalcisPTs. Here, we establish the first purification system for heteromericcisPT and show that both NgBR and hCIT subunits function in catalysis and substrate binding. Finally, we identified a critical RxG sequence in the C-terminal tail of NgBR that is conserved and essential for enzyme activity across phyla.
Cohesin loss eliminates all loop domains, leading to links among superenhancers and downregulation of nearby genes
Authors: Rao Suhas S. P. , Huang Su-Chen , Glenn St Hilair Brian , Engreitz Jesse M. , Perez Elizabeth M. , Kieffer-Kwon Kyong-Rim , Sanborn Adrian L. , Johnstone Sarah E. , Bochkov Ivan D. , Huang Xingfan , Shamim Muhammad S. , Omer Arina D. , Bernstein Bradley E. , Casellas Rafael , Lander Eric S. , Lieberman Aiden Erez 
Published: May 2017

SUMMARYThe human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci - almost always bound by CTCF and cohesin – lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loci in different compartments that had been in the same loop domain become more segregated. Loss of loop domains does not lead to widespread ectopic gene activation, but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes, and affecting the regulation of nearby genes. Cohesin restoration quickly reverses these effects, consistent with a model where loop extrusion is rapid.
Calculation of Lorentz force in planar EMAT for thickness measurement of steel plate
Authors: Tu Jun , Chen Tao , Xiong Zhi , Song Xiaochun , Huang Songling 
Published: May 2017

Purpose
The aim of this paper is to better understand the generation and transmission mechanism of the electromagnetic acoustic transducer (EMAT).

Design/methodology/approach
A semi-analytical method was used to calculate the Lorentz force. Both the hypothetical magnetic field mirror method and the diffusion equation were adopted to solve the eddy current distribution by variables separation method in time domain. A three-dimension magnetostatic finite element model was used to calculate the static magnetic field and the relative permeability. And an experimental platform with a piezoelectric probe to generate and an EMAT to receive, the ultrasonic wave was set up to verify the distribution of the Lorentz force.

Findings
The Lorentz force at different time and in different positions of the steel plate can be easily calculated. The experimental results show a good agreement with the analytical results.

Originality/value
The accurate prediction of the Lorentz force provides an insight into the physical phenomenon of EMAT and a powerful tool to design optimum EMAT.
Reinforcement learning based PID controller design for LFC in a microgrid
Authors: Esmaeili Mehran , Shayeghi Hossein , Mohammad Nejad Hamid , Younesi Abdollah 
Published: May 2017

Purpose
This paper aims to propose an improved reinforcement learning-based fuzzy-PID controller for load frequency control (LFC) of an island microgrid.

Design/methodology/approach
To evaluate the performance of the proposed controller, three different types of controllers including optimal proportional-integral-derivative (PID) controller, optimal fuzzy PID controller and the proposed reinforcement learning-based fuzzy-PID controller are compared. Optimal PID controller and classic fuzzy-PID controller parameters are tuned using Non-dominated Sorting Genetic Algorithm-II algorithm to minimize overshoot, settling time and integral square error over a wide range of load variations. The simulations are carried out using MATLAB/SIMULINK package.

Findings
Simulation results indicated the superiority of the proposed reinforcement learning-based controller over fuzzy-PID and optimal-PID controllers in the same operational conditions.

Originality/value
In this paper, an improved reinforcement learning-based fuzzy-PID controller is proposed for LFC of an island microgrid. The main advantage of the reinforcement learning-based controllers is their hardiness behavior along with uncertainties and parameters variations. Also, they do not need any knowledge about the system under control; thus, they can control any large system with high nonlinearities.
Analysis of AFPM machines with cylindrically shaped magnets using quasi-3D method
Authors: Rostami Naghi , Rostami Majid 
Published: May 2017

Purpose
The purpose of this paper is the fast and accurate modelling of surface-mounted Axial-Flux Permanent-Magnet (AFPM) machines equipped with cylindrical magnets using quasi-3D approach. Furthermore, the accuracy of the method is improved by using leakage coefficient, saturation coefficient and an appropriate permeance function.

Design/methodology/approach
Quasi-3D approach is used for fast and accurate modelling of AFPM machines. Air-gap flux density distribution, induced back EMF, and produced cogging torque are calculated using the proposed method with reasonable accuracy.

Findings
The results obtained by quasi-3D approach compared to Finite-Element-Analyses (FEA) shows how accurate, fast and efficient this method is. It is proved that, this method can be successfully applied to evaluate the performance of the AFPM machines.

Originality/value
Effectiveness and accuracy of quasi-3D approach is assessed on different AFPM machines. Furthermore, to increase the accuracy of computations, the effects of the magnetic potential drop at iron parts of the machine are taken into account by using a saturation coefficient. Besides, the influence of the slot opening on the flux density distribution is taken into account by using an appropriate relative permeance function.
GPU-based parallelization for bubble mesh generation
Authors: Dinh Van Quang , Marechal Yves 
Published: May 2017

Purpose
In FEM computations, the mesh quality improves the accuracy of the approximation solution and reduces the computation time. The dynamic bubble system meshing technique can provide high-quality meshes, but the packing process is time-consuming. This paper aims to improve the running time of the bubble meshing by using the advantages of parallel computing on graphics processing unit (GPU).

Design/methodology/approach
This paper is based on the analysis of the processing time on CPU. A massively parallel computing-based CUDA architecture is proposed to improve the bubble displacement and database updating. Constraints linked to hardware considerations are taken into account. Finally, speedup factors are provided on test cases and real scale examples.

Findings
The numerical experiences show the efficiency of parallel performance reaches a speedup of 35 compared to the serial implementation.

Research limitations/implications
This contribution is so far limited to two-dimensional (2D) geometries although the extension to three-dimension (3D) is straightforward regarding the meshing technique itself and the GPU implementation. The authors’ works are based on a CUDA environment which is widely used by developers. C\C++ and Java were the programming languages used. Other languages may of course lead to slightly different implementations.

Practical implications
This approach makes it possible to use bubble meshing technique for both initial design and optimization, as excellent meshes can be built in few seconds.

Originality/value
Compared to previous works, this contribution shows that the scalability of the bubble meshing technique needs to solve two key issues: reach a T(N) global cost of the implementation and reach a very fast size map interpolation strategy.
A simple turn-on and turn-off angles searching method for copper loss minimization of the switched reluctance motor
Authors: Chen Hai-Jin , Li Jin-Yang 
Published: May 2017

Purpose
The purpose of this paper is to present a simple and effective method to search the optimal turn-on and turn-off angles on-line for the control of the switched reluctance motor (SRM). The optimal turn-on and turn-off angles are defined as the ones that can meet torque production requirements with minimum copper loss.

Design/methodology/approach
The optimal turn-on and turn-off angles are first defined based on the analysis of the SRM losses and torque production principles. Then the algorithm for optimal angles searching is developed, and the searching parameters are determined through analytical computation. The optimal angles are approached on-line with iterative process. Simulation and experiments are finally performed to verify the proposed method.

Findings
The presented method can meet torque production requirements while copper loss is minimized. The optimal turn-on and turn-off angles are generally approached within five phase cycles for most of the SRM operation modes. Furthermore, the SRM drive system using the presented method exhibits good dynamics during starting and sudden load operations.

Practical implications
The presented method is simple, and implementation of it is easy. It is an eligible candidate for industrial applications where energy conversion efficiency is crucial.

Originality/value
The optimal turn-off angle definition that considers both torque production and copper loss minimization is proposed. The turn-on and turn-off angles are searched independently on-line with little SRM geometrical information. The searching steps are derived through analytical computation and qualitative analysis so that both the searching speed and algorithm convergence are balanced.
Analysis of surface insulation resistance related failures in electronics by circuit simulation
Authors: Verdingovas Vadimas , Joshy Salil , Jellesen Morten Stendahl , Ambat Rajan 
Published: May 2017

Purpose
The purpose of this study is to show that the humidity levels for surface insulation resistance (SIR)-related failures are dependent on the type of activators used in no-clean flux systems and to demonstrate the possibility of simulating the effects of humidity and contamination on printed circuit board components and sensitive parts if typical SIR data connected to a particular climatic condition are available. This is shown on representative components and typical circuits.

Design/methodology/approach
A range of SIR values obtained on SIR patterns with 1,476 squares was used as input data for the circuit analysis. The SIR data were compared to the surface resistance values observable on a real device printed circuit board assembly. SIR issues at the component and circuit levels were analysed on the basis of parasitic circuit effects owing to the formation of a water layer as an electrical conduction medium.

Findings
This paper provides a summary of the effects of contamination with various weak organic acids representing the active components in no-clean solder flux residue, and demonstrates the effect of humidity and contamination on the possible malfunctions and errors in electronic circuits. The effect of contamination and humidity is expressed as drift from the nominal resistance values of the resistors, self-discharge of the capacitors and the errors in the circuits due to parasitic leakage currents (reduction of SIR).

Practical/implications
The methodology of the analysis of the circuits using a range of empirical leakage resistance values combined with the knowledge of the humidity and contamination profile of the electronics can be used for the robust design of a device, which is also important for electronic products relying on low current consumption for long battery lifetime.

Originality/value
Examples provide a basic link between the combined effect of humidity and contamination and the performance of electronic circuits. The methodology shown provides the possibility of addressing the climatic reliability of an electronic device at the early stage of device design by using typical SIR data representing the possible climate exposure.
Information systems architecture for fire emergency response
Authors: Prasanna Raj , Yang Lili , King Malcolm , Huggins Thomas J. 
Published: May 2017

Purpose
There has been a lack of meaningful information systems architecture, which comprehensively conceptualise the essential components and functionality of an information system for fire emergency response addressing needs of different job roles. The purpose of this paper is to propose a comprehensive information systems architecture which would best support four of the key firefighter job roles.

Design/methodology/approach
The study has built on the outcomes of two previous preliminary studies on information and human-computer interaction needs of core firefighter job roles. Scenario-based action research was conducted with firefighters in a range of roles, to evaluate human-computer interaction needs while using various technology platforms.

Findings
Several key themes were identified and led us to propose several layers of an integrated architecture, their composition and interactions.

Research limitations/implications
The selected fire scenarios may not represent every type of fire expected in high-risk built environments.

Practical implications
The current paper represents a shared discussion between end users, system architects and designers, to understand and improve essential components. It therefore provides a reference point for the development of information system architecture for fire emergency response.

Originality/value
The proposed information system architecture is novel because it outlines specific architectural elements required to meet the specific situation awareness needs of different firefighters job roles.
Promoting integration within the public health domain of physical activity promotion
Authors: Whitelaw Sandy , Topping Chris , McCoy Michele , Turpie Lindsay 
Published: May 2017

Purpose
The purpose of this paper is to report and critically reflect on the methodological processes involved in a formal attempt to promote health and social integration in the rarely reported public health domain of physical activity promotion.

Design/methodology/approach
A quality improvement (QI) methodology was deployed, comprising three elements: a diagnostic tool that assessed strategic and practice positions; a half-day workshop that brought senior leaders together for to reflect this evidence; and a structured process that sought to generate proposals for future integrated action. A mixed-method evaluative approach was used, capturing insights of the integration processes via quantitative and qualitative data collection pre-event, in-event, immediate post-event and at six-month follow-up.

Findings
Insights suggested that despite some critical concerns, this QI process can be considered as robust, offering pointers to elements required to successfully promote integration in this domain, including the significance of leadership, the preparatory contribution of a diagnostic tool and position paper, the opportunities for active exchange and planning within a workshop situation and the initiation of a process of integrated work via tangible “pledges”.

Originality/value
The paper offers originality in two respects. Generally, it describes and reflects on the relationship between theoretical and empirical dimensions of a model of integration promotion. Specifically, in offering an account of integrative public health work across health service, local authority and third sector partners, it addressed an area that has received relatively limited prior attention.
One Ilfracombe
Authors: Beacham Andrea 
Published: May 2017

Purpose
The purpose of this paper is to report the findings of a horizontal integration programme in the South West of England. The programme was unusual insofar as it included the full range of public services being provided in a single town. It was a place-based system framed by the concept that a person’s wellbeing includes their health, economic status and living environment and that they are inextricably linked. As well as aiming for broader system integration, the programme utilised a person-centred approach using service-user perceptions to influence design. It was implemented through a local governance structure using a set of collaborative principles.

Design/methodology/approach
The paper presents personal reflections of the programme manager about the efficacy of the model, its sustainability and the problems encountered. It sets out the principles defining the model and the extent to which the principles were followed in practice.

Findings
Creating a holistic public service based on integration to tackle deep seated problems within a population requires reducing complexity at the interface between citizens and services. A local system model that includes all public services allows for collective responsibility for meeting the service needs of the population augmenting the connections and bridging the gaps between services. There was a recognition amongst participants that service redesign does not require wholesale organisational restructuring but does require creating shared aims and objectives and the participation of leaders with the ability to implement change within their services. A user-led, bottom-up approach provides deeper understanding and traction on the ground but should be combined with top-down strategic support to provide structural sustainability and the ability to scale out.

Originality/value
The paper demonstrates that horizontal service integration based on the concept of wellbeing is possible but faces significant challenges. The benefits and complexities of inter-agency collaboration multiply when enhancing the outcome focus from improving population health to general wellbeing. New theories of implementation and transformation are needed that relate to this important emerging service theme.
Care transitions as street-level work
Authors: Foster Michele , Harvey Desley , Quigley Rachel , Strivens Edward 
Published: May 2017

Purpose
Quality care transitions of older people across acute, sub-acute and primary care are critical to safety and cost, which is the reason interventions to improve practice are a priority. Yet, given the complexity of providers and services involved it is often difficult to know the types of tensions that arise in day-to-day transition work or how front-line workers will respond. To that end, this innovative study differs from the largely descriptive studies by conceptualising care transitions as street-level work in order to capture how transition practice takes shape within the complexities and dynamics of the local setting. The paper aims to discuss these issues.

Design/methodology/approach
Data were collected from 23 hospital health professionals and community service providers across primary, sub-acute and acute care through focus groups. A thematic analysis and interrogation of themes using street-level concepts derived three key themes.

Findings
The themes of risk logics and dilemmas of fragmentation make explicit both the local constraints and opportunities of care transitions and how these intersect to engender a particular logic of practice. By revealing the various discretionary tactics adopted by front-line providers, the third theme simultaneously highlights how discretionary spaces might represent both possibilities and problematics for balancing organisational and patient needs.

Originality/value
The study contributes to the knowledge of street-level work in health settings and specifically, the nature of transition work. Importantly, it benefits policy and practice by uncovering mechanisms that could facilitate and impede quality transitions in discrete settings.