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Low‐cost air pollutant sensors suffer several interferences due to the variation of climatic elements. Recent studies look for calibration solutions based on different regression and classification machine learning algorithms. The present work brings together the implementation and extraction of performance metrics from these algorithms in a single open‐source tool. Both the input data and parameters for each algorithm are automatically configured. This feature makes the tool compatible with any input dataset and removes the need to interact with complex codes.In this paper the structure of an open‐source tool is introduced for evaluation of calibration techniques used in low‐cost air pollutant monitors. Different algorithms can be configured and used, such as regression techniques and machine learning classifiers. In addition, this tool was implemented to be compatible with any input dataset. These features remove the need for the user to interact with complex codes. [ABSTRACT FROM AUTHOR]

This paper introduces Detection Metrics, an open-source scientific software for the assessment of deep learning neural network models for visual object detection. This software provides objective performance metrics such as mean average precision and mean inference time. The most relevant international object detection datasets are supported along with the most widely used deep learning frameworks. Different network models, even those built from different frameworks, can be fairly compared in this way. This is very useful when developing deep learning applications or research. A set of tools is provided to manage and work with different datasets and models, including visualization and conversion into several common formats. Detection Metrics may also be used in automatic batch processing for large experimental tests, saving researchers time, and new domain-specific datasets can be easily created from videos or webcams. It is open-source, can be audited, extended, and adapted to particular requirements. It has been experimentally validated. The performance of the most relevant state-of-the-art neural models for object detection has been experimentally compared. In addition, it has been used in several research projects, guiding in selecting the most suitable network model architectures and training procedures. The performance of the different models and training alternatives can be easily measured, even on large datasets. [ABSTRACT FROM AUTHOR]

Computer-aided molecular design (CAMD) studies quantitative structure–property relationships and discovers desired molecules using optimization algorithms. With the emergence of machine learning models, CAMD score functions may be replaced by various surrogates to automatically learn the structure–property relationships. Due to their outstanding performance on graph domains, graph neural networks (GNNs) have recently appeared frequently in CAMD. But using GNNs introduces new optimization challenges. This paper formulates GNNs using mixed-integer programming and then integrates this GNN formulation into the optimization and machine learning toolkit OMLT. To characterize and formulate molecules, we inherit the well-established mixed-integer optimization formulation for CAMD and propose symmetry-breaking constraints to remove symmetric solutions caused by graph isomorphism. In two case studies, we investigate fragment-based odorant molecular design with more practical requirements to test the compatibility and performance of our approaches. • We formulate graph neural networks with mixed-integer programming and break symmetry. • We integrate our formulation into the optimization and machine learning toolkit OMLT. • We develop an application in computer-aided molecular design of odorants. [ABSTRACT FROM AUTHOR]

Recent developments in data science and machine learning have inspired a new wave of research into data-driven modeling for mathematical optimization of process applications. This paper first considers essential conditions for robustness to uncertainties and accurate extrapolation, which are required to integrate surrogates into process optimization. Next we consider two perspectives for developing process engineering surrogates: a surrogate-led and a mathematical programming-led approach. As these data-driven surrogate models must be integrated into a larger process optimization problem, we discuss the verification problem , i.e., checking that the optimum of the surrogate corresponds to the optimum of the truth model. The paper investigates two case studies on surrogate-based optimization for heat exchanger network synthesis and drill scheduling. • We consider essential conditions for robustness to uncertainties and accurate extrapolation. • We investigate two perspectives for developing process engineering surrogates. • For the surrogate-led perspective, we discuss heat exchanger network synthesis. • For the mathematical programming-led approach, we discuss drill scheduling. [ABSTRACT FROM AUTHOR]

Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed “easy to install,” and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software. [ABSTRACT FROM AUTHOR]

Diabetic retinopathy (DR) is a disease which is widely diagnosed using (colour fundus) images. Efficiency and accuracy are critical in diagnosing DR as lack of timely intervention can lead to irreversible visual impairment. In this paper, we examine strategies for scrutinizing images which affect diagnostic performance of medical practitioners via an eye-tracking study. A total of 56 subjects with 0 to 18 years of experience participated in the study. Every subject was asked to detect DR from 40 images. The findings indicate that practitioners use mainly two types of strategies characterized by either higher dwell duration or longer track length. The main findings of the study are that higher dwell-based strategy led to higher average accuracy (> 85%) in diagnosis, irrespective of the expertise of practitioner; whereas, the average obtained accuracy with a long-track length-based strategy was dependent on the expertise of the practitioner. In the second part of the paper, we use the experimental findings to recommend a scanning strategy for fast and accurate diagnosis of DR that can be potentially used by image readers. This is derived by combining the eye-tracking gaze maps of medical experts in a novel manner based on a set of rules. This strategy requires scrutiny of images in a manner which is consistent with spatial preferences found in human perception in general and in the domain of fundus images in particular. The Levenshtein distance-based assessment of gaze patterns also establish the effectiveness of the derived scanning pattern and is thus recommended for image readers. [ABSTRACT FROM AUTHOR]

In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software. However, the actual state of the body of bioinformatics software remains largely unknown. The purpose of this paper is to investigate the state of source code in the bioinformatics community, specifically looking at relationships between code properties, development activity, developer communities, and software impact. To investigate these issues, we curated a list of 1,720 bioinformatics repositories on GitHub through their mention in peer-reviewed bioinformatics articles. Additionally, we included 23 high-profile repositories identified by their popularity in an online bioinformatics forum. We analyzed repository metadata, source code, development activity, and team dynamics using data made available publicly through the GitHub API, as well as article metadata. We found key relationships within our dataset, including: certain scientific topics are associated with more active code development and higher community interest in the repository; most of the code in the main dataset is written in dynamically typed languages, while most of the code in the high-profile set is statically typed; developer team size is associated with community engagement and high-profile repositories have larger teams; the proportion of female contributors decreases for high-profile repositories and with seniority level in author lists; and, multiple measures of project impact are associated with the simple variable of whether the code was modified at all after paper publication. In addition to providing the first large-scale analysis of bioinformatics code to our knowledge, our work will enable future analysis through publicly available data, code, and methods. Code to generate the dataset and reproduce the analysis is provided under the MIT license at . Data are available at . [ABSTRACT FROM AUTHOR]

In business replenishment, discount offers of multi-item may either provide different discount schedules with a single discount type, or provide schedules with multiple discount types. The paper investigates the joint effects of multiple discount schemes on the decisions of multi-item joint replenishment. In this paper, a joint replenishment problem (JRP) model, considering three discount (all-unit discount, incremental discount, total volume discount) offers simultaneously, is constructed to determine the basic cycle time and joint replenishment frequencies of multi-item. To solve the proposed problem, a heuristic algorithm is proposed to find the optimal solutions and the corresponding total cost of the JRP model. Numerical experiment is performed to test the algorithm and the computational results of JRPs under different discount combinations show different significance in the replenishment cost reduction. [ABSTRACT FROM AUTHOR]

The need for improved building performance is global and has led to numerous international collaborations. Since 2000, the International Energy Agency (IEA) Energy in Buildings and Communities Program (EBC, formerly ECBCS ) has completed two building commissioning research annexes, recognizing the role of the building commissioning process in meeting energy conservation goals. Annex 40 established a common understanding of the commissioning process and initiated research that became the basis for the development of national guidelines and automated tools. Subsequently, Annex 47 focused on advancing the use of technology in commissioning and the work developed and ideas exchanged in Annex 47 were foundational in enabling numerous positive impacts internationally. This paper describes research results from these annexes 1 1 Certain commercial entities, equipment, or materials may be identified in this document in order to describe an experimental procedure or concept adequately. Such identification is not intended to imply recommendation or endorsement by the National Institute of Standards and Technology, nor is it intended to imply that the entities, materials, or equipment are necessarily the best available for the purpose. and discusses the impact of both in four areas: 1) commissioning support software tools, 2) cost-benefit methodology, 3) guidelines and standards, and 4) industry associations and research conferences. The paper concludes with a discussion of current commissioning industry research and policy needs. [ABSTRACT FROM AUTHOR]

Single-point incremental forming (SPIF) is a technology that allows incremental manufacturing of complex parts from a flat sheet using simple tools; further, this technology is flexible and economical. Measuring the forming force using this technology helps in preventing failures, determining the optimal processes, and implementing on-line control. In this paper, an experimental study using SPIF is described. This study focuses on the influence of four different process parameters, namely, step size, tool diameter, sheet thickness, and feed rate, on the maximum forming force. For an efficient force predictive model based on an adaptive neuro-fuzzy inference system (ANFIS), an artificial neural network (ANN) and a regressions model were applied. The predicted forces exhibited relatively good agreement with the experimental results. The results indicate that the performance of the ANFIS model realizes the full potential of the ANN model. [ABSTRACT FROM AUTHOR]

The calibration of transient current sensors is fundamental for the reliability of high currents short-circuit tests. The test can be performed with prospective or withstand current, and in both cases, the dynamic behavior of the current sensors has to be investigated, due to their influence on the scale factor (SF) value. The requirements of the IEC 62475 standard can be achieved with a calibration in transient conditions, performed with an approved reference measuring system. In this paper, a more accurate measuring system is presented, for the improvement of the Istituto Nazionale di Ricerca Metrologica high transient current measuring capability. The result is achieved by analyzing the performance in digitalization of a commercial Keysight (former Agilent) multimeter 3458A, with a custom algorithm that can also perform the calculation of Joule integral ($I^{2}t$) on a given amount of time along the acquired signal. The objective of the research is the realization of a measurement system with an uncertainty compatible with the test laboratory requirements, both for the determination of SF and evaluation of the performance in the measurement of $I^{2}t$ in the device under calibration. [ABSTRACT FROM AUTHOR]

The Demographic and Health Surveys (DHS) are a major source for many demographic and health indicators in developing countries. Although these indicators are well defined in the literature, using survey data to calculate some of these indicators has never been an easy task for data users. This paper presents the software, a user-friendly R package developed to calculate fertility indicators, such as the total fertility rate, general fertility rate, and age-specific fertility rates, and childhood mortality indicators, such as the neonatal mortality rate, post-neonatal mortality rate, infant mortality rate, child mortality rate, and under-5 mortality rate, from the DHS data. The package allows for national and subnational indicators. In addition, the package calculates sampling error indicators such as standard error, design effect, relative standard error, and confidence interval for each demographic indicator. The package can also be used to calculate the same indicators from other population surveys such as the Multiple Indicator Cluster Survey (MICS). [ABSTRACT FROM AUTHOR]

A reasonable micro-pits texture has been initially proved that it can improve friction characteristics between wood and cemented carbide surface and reduce surface friction coefficient. In order to study the cutting performance of the micro-texture when it is applied to the cutting tool for cutting wood more effectively, this paper selected micro-pit texture for studying influence of surface micro-texture cutting tool on wood cutting performance and cutting temperature, finding that when micro-pit cemented carbide cutting tool is adopted for turning the northeast China ash (Fraxinus spp.), it can reduce cutting force of turning and surface friction coefficient between rake face and cuttings. Moreover, for type A and type B cutting tools, when the texture parameters are that the diameter of the micro-pit is 80μm, the depth of the micro pit is: 10μm, area occupancy is 20% and the diameter of the micro-pit is 120μm, the depth of the micro-pit is 10μm and the area occupancy is 20%, the effect generated is the best. When a texture cutting tool is used for cutting, the decrease of the highest temperature in the cutting area is not very great, but the average temperature in the cutting area changes a lot, which is mainly caused by that micro-texture is processed at a position of the rake face close to the main cutting edge and that the highest temperature of cutting is mainly generated on the contact point between tool tip and wood. A reasonable micro-texture parameter can form a layer of liquid lubricating film on the up and down contact surfaces such that the direct contact between cemented carbide and northeast China ash is changed into indirect contact between lubricating films formed by the liquid so as to reduce the surface friction coefficient. [ABSTRACT FROM AUTHOR]

Background: Randomized controlled clinical trials require management effort, involving huge organizational, economic and informatics investments. Information technology offers opportunities to approach clinical trial methodology in new ways. However, there are only a few reports of computerized data and drug management systems. Objective: This paper describes a novel software created specifically for the management of a randomized trial of diet and metformin in people with metabolic syndrome (the Me.Me.Me. trial). Methods: Me.Me.Me. is an ongoing phase III randomized controlled trial in healthy people with metabolic syndrome to test the hypothesis that comprehensive lifestyle changes and/or metformin can prevent age-related chronic non-communicable diseases. To manage all the phases of the trial, we created a software which is a state pattern machine, user friendly, web-based, able to maintain the correct balance between randomization groups, and structured in various levels of security in order to guarantee the participant’s privacy and compliance with the study protocol. The software achieves budget savings: drug management is not based on patients’ packs, but on the actual need for drugs according to each participant’s “state”, with strict guidelines for the handling and supply of medication. Results: The trial is ongoing and recruitment will close on August 31, 2018. To date, 11737 bottles of metformin/placebo have been dispensed to 1054 randomized participants, with drug savings of 29.5%. Conclusions: A software which takes into account the “state” of participant might be a powerful resource for developing and managing clinical trials, helping avoid poor treatment allocation, and wastage of drugs and money. Me.Me.Me. trial: EUDRACT no. . ClinicalTrials.gov Identifier: . [ABSTRACT FROM AUTHOR]

The problem of checking the genotype distribution obtained for some diallelic marker for compatibility with the Hardy-Weinberg equilibrium (HWE) condition arises also for loci on the X chromosome. The possible genotypes depend on the sex of the individual in this case: for females, the genotype distribution is trinomial, as in the case of an autosomal locus, whereas a binomial proportion is observed for males. Like in genetic association studies with autosomal SNPs, interest is typically in establishing approximate compatibility of the observed genotype frequencies with HWE. This requires to replace traditional methods tailored for detecting lack of fit to the model with an equivalence testing procedure to be derived by treating approximate compatibility with the model as the alternative hypothesis. The test constructed here is based on an upper confidence bound and a simple to interpret combined measure of distance between true and HWE conforming genotype distributions in female and male subjects. A particular focus of the paper is on the derivation of the asymptotic distribution of the test statistic under null alternatives which is not of the usual Gaussian form. A closed sample size formula is also provided and shown to behave satisfactorily in terms of the approximation error. [ABSTRACT FROM AUTHOR]

This paper presents an open-source package developed in Python that controls and drives a programmable Josephson array to synthesize dc and ac quantum-accurate voltages. Programmable arrays are devices subdivided into independent subsections, each counting a number of series connected Josephson junctions that follows a binary sequence (1, 2, 4, 8, …) to control the output voltage. Our software allows to independently measure the current-voltage characteristics of each subsection by means of a set of arbitrary waveform generators and a nanovoltmeter that measures the voltage across the whole array with high sensitivity. A quantization test tool is also provided to check with sub-microvolt resolution whether the array is operating on its quantum margins. The code is modular and easily expandable with the support of many libraries, allowing prompt reconfiguration for different calibration and testing purposes. It is aimed at being a starting point for cooperation between National Metrology Institutes towards the realization of a shared quantum voltage calibration infrastructure. [ABSTRACT FROM AUTHOR]

The swift evolution of technology has facilitated the access of information through different means which has opened the doors to plagiarism. In today's world of technological outburst, plagiarism is aggravating and has become a serious concern in academia, research and many other fields. To curb this intellectual theft and to ensure academic integrity, efficient software systems to detect them are in urgent need. In this paper, a study on plagiarism is done with the focus on extrinsic text plagiarism detection, which is a fast emerging research area in this domain. The different extrinsic detection techniques and the methodologies involved are reviewed based on the current state of art. Further an overview of some of the available detection software tools, their features and detection efficiency is discussed with some of the output demos. The paper also throws light on the popular PAN competition, which is conducted yearly since 2009 in plagiarism domain and the major tasks involved in it. Further it attempts to identify the problems existing in available tools and the research gaps where immense explorations can be done. [ABSTRACT FROM AUTHOR]

This paper provides a description of how market competitiveness evaluations concerning mechanical equipment can be made in the context of multi-criteria decision environments. It is assumed that, when we are evaluating the market competitiveness, there are limited number of candidates with some required qualifications, and the alternatives will be pairwise compared on a ratio scale. The qualifications are depicted as criteria in hierarchical structure. A hierarchical decision model called PCbHDM was used in this study based on an analysis of its desirable traits. Illustration and comparison shows that the PCbHDM provides a convenient and effective tool for evaluating the market competitiveness of mechanical equipment. The researchers and practitioners might use findings of this paper in application of PCbHDM. [ABSTRACT FROM AUTHOR]

This paper demonstrates the need for and provides an improved fitting of the line parameters when a wide range of frequencies with emphasis on the dc response is the objective. The improved fitting is based on a low-order fitting of a function error for each of the line parameters, that is, the characteristic admittance and propagation function, in the low-frequency range. The function error represents the difference between the analytical evaluation of the line parameters, that is, obtained from a frequency-dependent distributed parameters line model, and their initial rational approximation, for example, given by an electromagnetic transients software tool. The approximated function error, added to the initial rational approximation of the line parameters, provides the enhanced fitted line model. The enhanced fitting improves the dc response of the line and ensures numerical stability in time-domain simulations. This paper applies the proposed fitting approach to the universal line model for time-domain simulations. The simulation results by the enhanced fitting are validated by comparing the results with those obtained from a frequency-domain line model (FDLM). Two case studies are presented to illustrate the proposed fitting approach. [ABSTRACT FROM AUTHOR]

Bugs and vulnerabilities in binary executables threaten cyber security. Current discovery methods, like fuzz testing, symbolic execution and manual analysis, both have advantages and disadvantages when exercising the deeper code area in binary executables to find more bugs. In this paper, we designed and implemented a hybrid automatic bug finding tool—F—on top of fuzz testing and selective symbolic execution. It targets full system software stack testing including both the user space and kernel space. Combining these two mainstream techniques enables us to achieve higher coverage and avoid getting stuck both in fuzz testing and symbolic execution. We also proposed two key optimizations to improve the efficiency of full system testing. We evaluated the efficiency and effectiveness of our method on real-world binary software and 844 memory corruption vulnerable programs in the Juliet test suite. The results show that F can discover software bugs in the full system software stack effectively and efficiently. [ABSTRACT FROM AUTHOR]

Data, including information generated from them by processing and analysis, are an asset with measurable value. The assets that biological research funding produces are the data generated, the information derived from these data, and, ultimately, the discoveries and knowledge these lead to. From the time when Henry Oldenburg published the first scientific journal in 1665 (Proceedings of the Royal Society) to the founding of the United States National Library of Medicine in 1879 to the present, there has been a sustained drive to improve how researchers can record and discover what is known. Researchers’ experimental work builds upon years and (collectively) billions of dollars’ worth of earlier work. Today, researchers are generating data at ever-faster rates because of advances in instrumentation and technology, coupled with decreases in production costs. Unfortunately, the ability of researchers to manage and disseminate their results has not kept pace, so their work cannot achieve its maximal impact. Strides have recently been made, but more awareness is needed of the essential role that biological data resources, including biocuration, play in maintaining and linking this ever-growing flood of data and information. The aim of this paper is to describe the nature of data as an asset, the role biocurators play in increasing its value, and consistent, practical means to measure effectiveness that can guide planning and justify costs in biological research information resources’ development and management. [ABSTRACT FROM AUTHOR]

This paper studies the Retailer Stackelberg game in a supply chain consisting of two manufacturers and one retailer where they compete simultaneously under three factors including price, service and simple price discount contract. It is assumed that the second manufacturer provides service directly to his customers, and the retailer provides service for the first product’s customers, while the retailer buys the first product under price discount from the first manufacturer. The analysis of the optimal equilibrium solutions and the results of the numerical examples show that if a manufacturer chooses the appropriate range of discount rate, he will gain more profit than when there is no discount given to the retailer. This situation can be considered as an effective tool for the coordination of the first manufacturer and the retailer to offer discount by manufacturer and to provide the service by the retailer. We obtain equilibrium solution of Retailer Stackelberg game and analyze the numerical examples under two cases: a) the manufacturers sell their products to the retailer without price discount contract. b) The first manufacturer sells his products to the retailer with the simple price discount contract. The preliminary results show that the service and the price discount contract can improve the performance of supply chain. [ABSTRACT FROM AUTHOR]

The awareness of others’ activities has been widely recognized as essential in facilitating coordination in a team among Computer-Supported Cooperative Work communities. Several field studies of software developers in large software companies such as Microsoft have shown that coworker and artifact awareness are the most common information needs for software developers; however, they are also two of the seven most frequently unsatisfied information needs. To address this problem, we built a workspace awareness tool named TeamWATCH to visualize developer activities using a 3-D city metaphor. In this paper, we discuss the importance of awareness in software development, review existing workspace awareness tools, present the design and implementation of TeamWATCH, and evaluate how it could help detect and resolve conflicts earlier and better maintain group awareness via a controlled experiment. The experimental results showed that the subjects using TeamWATCH performed significantly better with respect to early conflict detection and resolution. [ABSTRACT FROM AUTHOR]

We give an overview of the basic principles of approximate Bayesian computation (ABC), a class of stochastic methods that enable flexible and likelihood-free model comparison and parameter estimation. Our new open-source software called ABrox is used to illustrate ABC for model comparison on two prominent statistical tests, the two-sample t-test and the Levene-Test. We further highlight the flexibility of ABC compared to classical Bayesian hypothesis testing by computing an approximate Bayes factor for two multinomial processing tree models. Last but not least, throughout the paper, we introduce ABrox using the accompanied graphical user interface. [ABSTRACT FROM AUTHOR]

Project management refers to a set of activities that contribute to to achieve a successful project: defining the objectives, establishing the team, planning the tasks and providing the resources and deadlines for completing them, continuous assessing the performance and making adjustments when is necessary. The case study used the PMBOK methodology and software tools to design a website for a recruitment agency. The project was accomplished by a group of master students guided by a teacher, at Software for Project Management class. As future work, the authors of this paper aim to continue this experience by enlarging the research study to other projects and by using different project management methodologies. [ABSTRACT FROM AUTHOR]

In a world where millions of people are dependent on batteries to provide them with convenient and portable energy, battery recycling is of the utmost importance. In this paper, we developed a new method to sort 18650 Lithium-ion batteries in large quantities and in real time for harvesting used cells with enough capacity for battery reuse. Internal resistance and capacity tests were conducted as a basis for comparison with a novel degradation-based method based on X-ray radiographic scanning and digital image contrast computation. The test results indicate that the sorting accuracy of the test cells is about 79% and the execution time of our algorithm is at a level of 200 milliseconds, making our method a potential real-time solution for reusing the remaining capacity in good used cells. [ABSTRACT FROM AUTHOR]

The social functions of urbanized areas are highly dependent on and supported by the convenient access to public transportation systems, particularly for the less privileged populations who have restrained auto ownership. To accurately evaluate the public transit accessibility, it is critical to capture the spatiotemporal variation of transit services. This can be achieved by measuring the shortest paths or minimum travel time between origin-destination (OD) pairs at each time-of-day (e.g. every minute). In recent years, General Transit Feed Specification (GTFS) data has been gaining popularity for between-station travel time estimation due to its interoperability in spatiotemporal analytics. Many software packages, such as ArcGIS, have developed toolbox to enable the travel time estimation with GTFS. They perform reasonably well in calculating travel time between OD pairs for a specific time-of-day (e.g. 8:00 AM), yet can become computational inefficient and unpractical with the increase of data dimensions (e.g. all times-of-day and large network). In this paper, we introduce a new algorithm that is computationally elegant and mathematically efficient to address this issue. An open-source toolbox written in C++ is developed to implement the algorithm. We implemented the algorithm on City of St. George’s transit network to showcase the accessibility analysis enabled by the toolbox. The experimental evidence shows significant reduction on computational time. The proposed algorithm and toolbox presented is easily transferable to other transit networks to allow transit agencies and researchers perform high resolution transit performance analysis. [ABSTRACT FROM AUTHOR]

Background: Microsoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text into dates, scientific notation, and other numerical representations. These conversions lead to subsequent, irreversible, corruption of the imported text. A recent survey of popular genomic literature estimates that one-fifth of all papers with supplementary gene lists suffer from this issue. Results: Here, we present an open-source tool, Escape Excel, which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel. Escape Excel is implemented in a variety of formats (), including a command line based Perl script, a Windows-only Excel Add-In, an OS X drag-and-drop application, a simple web-server, and as a Galaxy web environment interface. Test server implementations are accessible as a Galaxy interface () and simple non-Galaxy web server (). Conclusions: Escape Excel detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Examples of problematic strings include date-like strings, time-like strings, leading zeroes in front of numbers, and long numeric and alphanumeric identifiers that should not be automatically converted into scientific notation. It is hoped that greater awareness of these potential data corruption issues, together with diligent escaping of text files prior to importation into Excel, will help to reduce the amount of Excel-corrupted data in scientific analyses and publications. [ABSTRACT FROM AUTHOR]

Electricity generation presents the biggest opportunity to lower CO 2 emissions and it is foreseen that hydrogen energy technology will play an important role in realising the scenario to cap global warming at 2 °C through replacement of fossil fuels with renewables. The transition to electric power for transport in battery- and fuel-cell-electric vehicles will further increase the need for low-carbon electricity generation. For a successful transition to a renewable energy economy the traditional approach of designing energy systems to meet only goals related to the technology (capacity, availability, reliability) and economics (return on investment, cost to the consumer) must evolve to take on a more holistic viewpoint and be able to take into account other goals addressing environmental and social considerations. This paper reviews approaches for integrating hydrogen energy technology into hybrid energy systems, emphasising electricity generation using a hydrogen fuel cell. Integration of energy storage, sizing methodologies, energy flow management and their associated optimization algorithms and software implementation are addressed. Few published case studies go beyond technical considerations. This reality is discussed in the light of available software packages. A four-dimensional multi-objective meta-heuristic function is proposed with weighting of technical, economic, environmental and socio-political factors to suit the design goals for the energy system. [ABSTRACT FROM AUTHOR]

Author summary: Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010. [ABSTRACT FROM AUTHOR]

Quench heaters are an essential part of the protection of all high-current large hadron collider (LHC) superconducting circuits. About 2000 dipole and quadrupole magnets are equipped with quench heaters in order to protect them against development of excessive voltage and overheating after a resistive transition. The quench heaters are made of stainless steel foil partially plated with copper and connected to 900 V capacitor bank discharge power supplies. During Hardware Commissioning campaigns and machine operation every quench heater discharge event is carefully analysed to detect a possible failure or a precursor of a failure, which could lead to damage of the heater or to the superconducting coils in subsequent discharges. This paper will briefly describe two different ways of quench heater data analysis and will present the heaters performance during the years 2008–2015. A summary of the quench heater fatigue test performed on a spare LHC main dipole magnet will also be given. [ABSTRACT FROM PUBLISHER]

The article discusses rules for considering regarding preprint submission of scientific work in journals. Topics include analysis of published papers undertaken by cell biologist Stephen Royle for estimating the average time from first submission to publication, data mining of the written content for making it better utilizing the knowledge, and encouraging authors to licenses and formats for facilitating reuse while retaining copyright to their work.

As the quality of crucial entities can directly affect that of software, their identification and protection become an important premise for effective software development, management, maintenance and testing, which thus contribute to improving the software quality and its attack-defending ability. Most analysis and evaluation on important entities like codes-based static structure analysis are on the destruction of the actual software running. In this paper, from the perspective of software execution process, we proposed an approach to mine dynamic noteworthy functions (DNFM)in software execution sequences. First, according to software decompiling and tracking stack changes, the execution traces composed of a series of function addresses were acquired. Then these traces were modeled as execution sequences and then simplified so as to get simplified sequences (SFS), followed by the extraction of patterns through pattern extraction (PE) algorithm from SFS. After that, evaluating indicators inner-importance and inter-importance were designed to measure the noteworthiness of functions in DNFM algorithm. Finally, these functions were sorted by their noteworthiness. Comparison and contrast were conducted on the experiment results from two traditional complex network-based node mining methods, namely PageRank and DegreeRank. The results show that the DNFM method can mine noteworthy functions in software effectively and precisely. [ABSTRACT FROM AUTHOR]

Background: The study objectives were to describe the incidence and the nature of patient safety incidents (PSIs) in primary care general practice settings, and to explore the association between these incidents and practice or organizational characteristics. Methods: GPs, randomly selected from a national influenza surveillance network (n = 800) across France, prospectively reported any incidents observed each day over a one-week period between May and July 2013. An incident was an event or circumstance that could have resulted, or did result, in harm to a patient, which the GP would not wish to recur. Primary outcome was the incidence of PSIs which was determined by counting reports per total number of patient encounters. Reports were categorized using existing taxonomies. The association with practice and organizational characteristics was calculated using a negative binomial regression model. Results: 127 GPs (participation rate 79%) reported 317 incidents of which 270 were deemed to be a posteriori judged preventable, among 12,348 encounters. 77% had no consequences for the patient. The incidence of reported PSIs was 26 per 1000 patient encounters per week (95% CI [23‰ -28‰]). Incidents were three times more frequently related to the organization of healthcare than to knowledge and skills of health professionals, and especially to the workflow in the GPs’ offices and to the communication between providers and with patients. Among GP characteristics, three were related with an increased incidence in the final multivariable model: length of consultation higher than 15 minutes, method of receiving radiological results (by fax compared to paper or email), and being in a multidisciplinary clinic compared with sole practitioners. Conclusions: Patient safety incidents (PSIs) occurred in mean once every two days in the sampled GPs and 2% of them were associated with a definite possibility for harm. Studying the association between organizational features of general practices and PSIs remains a major challenge and one of the most important issues for safety in primary care. [ABSTRACT FROM AUTHOR]

This paper introduces a high-throughput software tool framework called sam2bam that enables users to significantly speed up pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156–186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize multiple processors, available memory, high-bandwidth storage, and hardware compression accelerators, if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting input data are provided by using plug-in tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of next generation sequencing (NGS) data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime of NGS data pre-processing from about 20 hours to about nine minutes for a whole-genome sequencing data set on the same system using up to 711 GB of memory. [ABSTRACT FROM AUTHOR]

Cascading failure in electric power systems is a complicated problem for which a variety of models, software tools, and analytical tools have been proposed but are difficult to verify. Benchmarking and validation are necessary to understand how closely a particular modeling method corresponds to reality, what engineering conclusions may be drawn from a particular tool, and what improvements need to be made to the tool in order to reach valid conclusions. The community needs to develop the test cases tailored to cascading that are central to practical benchmarking and validation. In this paper, the IEEE PES working group on cascading failure reviews and synthesizes how benchmarking and validation can be done for cascading failure analysis, summarizes and reviews the cascading test cases that are available to the international community, and makes recommendations for improving the state of the art. [ABSTRACT FROM PUBLISHER]

We propose the architecture of a novel robot system merging biological and artificial intelligence based on a neural controller connected to an external agent. We initially built a framework that connected the dissociated neural network to a mobile robot system to implement a realistic vehicle. The mobile robot system characterized by a camera and two-wheeled robot was designed to execute the target-searching task. We modified a software architecture and developed a home-made stimulation generator to build a bi-directional connection between the biological and the artificial components via simple binomial coding/decoding schemes. In this paper, we utilized a specific hierarchical dissociated neural network for the first time as the neural controller. Based on our work, neural cultures were successfully employed to control an artificial agent resulting in high performance. Surprisingly, under the tetanus stimulus training, the robot performed better and better with the increasement of training cycle because of the short-term plasticity of neural network (a kind of reinforced learning). Comparing to the work previously reported, we adopted an effective experimental proposal (i.e. increasing the training cycle) to make sure of the occurrence of the short-term plasticity, and preliminarily demonstrated that the improvement of the robot’s performance could be caused independently by the plasticity development of dissociated neural network. This new framework may provide some possible solutions for the learning abilities of intelligent robots by the engineering application of the plasticity processing of neural networks, also for the development of theoretical inspiration for the next generation neuro-prostheses on the basis of the bi-directional exchange of information within the hierarchical neural networks. [ABSTRACT FROM AUTHOR]

This paper reports the design and implementation of an innovative and cost-effective imaging management infrastructure suitable for radiology centres in emerging countries. It was implemented in the main referring hospital of Bhutan equipped with a CT, an MRI, digital radiology, and a suite of several ultrasound units. They lacked the necessary informatics infrastructure for image archiving and interpretation and needed a system for distribution of images to clinical wards. The solution developed for this project combines several open source software platforms in a robust and versatile archiving and communication system connected to analysis workstations equipped with a FDA-certified version of the highly popular Open-Source software. The whole system was implemented on standard off-the-shelf hardware. The system was installed in three days, and training of the radiologists as well as the technical and IT staff was provided onsite to ensure full ownership of the system by the local team. Radiologists were rapidly capable of reading and interpreting studies on the diagnostic workstations, which had a significant benefit on their workflow and ability to perform diagnostic tasks more efficiently. Furthermore, images were also made available to several clinical units on standard desktop computers through a web-based viewer. Messages/teaching points : • Open source imaging informatics platforms can provide cost-effective alternatives for PACS • Robust and cost-effective open architecture can provide adequate solutions for emerging countries • Imaging informatics is often lacking in hospitals equipped with digital modalities [ABSTRACT FROM AUTHOR]

RNase H (RNH) is a pivotal domain in retrovirus to cleave the DNA-RNA hybrid for continuing retroviral replication. The crucial role indicates that RNH is a promising drug target for therapeutic intervention. However, annotated RNHs in UniProtKB database have still been insufficient for a good understanding of their statistical characteristics so far. In this work, a computational RNH model was proposed to annotate new putative RNHs (np-RNHs) in the retroviruses. It basically predicts RNH domains through recognizing their start and end sites separately with SVM method. The classification accuracy rates are 100%, 99.01% and 97.52% respectively corresponding to jack-knife, 10-fold cross-validation and 5-fold cross-validation test. Subsequently, this model discovered 14,033 np-RNHs after scanning sequences without RNH annotations. All these predicted np-RNHs and annotated RNHs were employed to analyze the length, hydrophobicity and evolutionary relationship of RNH domains. They are all related to retroviral genera, which validates the classification of retroviruses to a certain degree. In the end, a software tool was designed for the application of our prediction model. The software together with datasets involved in this paper can be available for free download at . [ABSTRACT FROM AUTHOR]

Introduction: Concise visualization is critical to present large amounts of information in a minimal space that can be interpreted quickly. Clinical applications in precision medicine present an important use case due to the time dependent nature of the interpretations, although visualization is increasingly necessary across the life sciences. In this paper we describe the Lollipops software for the presentation of panel or exome sequencing results. Source code and binaries are freely available at . Although other software and web resources exist to produce lollipop diagrams, these packages are less suited to clinical applications. The demands of precision medicine require the ability to easily fit into a workflow and incorporate external information without manual intervention. Results: The Lollipops software provides a simple command line interface that only requires an official gene symbol and mutation list making it easily scriptable. External information is integrated using the publicly available Uniprot and Pfam resources. Heuristics are used to select the most informative components and condense them for a concise plot. The output is a flexible Scalable Vector Graphic (SVG) diagram that can be displayed in a web page or graphic illustration tool. Conclusion: The Lollipops software creates information-dense, publication-quality mutation plots for automated pipelines and high-throughput workflows in precision medicine. The automatic data integration enables clinical data security, and visualization heuristics concisely present knowledge with minimal user configuration. [ABSTRACT FROM AUTHOR]

Resource allocation could be influenced by various dynamic elements, such as the skills of engineers and the growth of skills, which requires managers to find an effective and efficient tool to support their staffing decision-making processes. Rescheduling happens commonly and frequently during the project execution. Control options have to be made when new resources are added or tasks are changed. In this paper we propose a software project staffing model considering dynamic elements of staff productivity with a Genetic Algorithm (GA) and Hill Climbing (HC) based optimizer. Since a newly generated reschedule dramatically different from the initial schedule could cause an obvious shifting cost increase, our rescheduling strategies consider both efficiency and stability. The results of real world case studies and extensive simulation experiments show that our proposed method is effective and could achieve comparable performance to other heuristic algorithms in most cases. [ABSTRACT FROM AUTHOR]

A number of circular regression models have been proposed in the literature. In recent years, there is a strong interest shown on the subject of outlier detection in circular regression. An outlier detection procedure can be developed by defining a new statistic in terms of the circular residuals. In this paper, we propose a new measure which transforms the circular residuals into linear measures using a trigonometric function. We then employ the row deletion approach to identify observations that affect the measure the most, a candidate of outlier. The corresponding cut-off points and the performance of the detection procedure when applied on Down and Mardia’s model are studied via simulations. For illustration, we apply the procedure on circadian data. [ABSTRACT FROM AUTHOR]

The omnipresent need for optimisation requires constant improvements of companies’ business processes (BPs). Minimising the risk of inappropriate BP being implemented is usually performed by simulating the newly developed BP under various initial conditions and “what-if” scenarios. An effectual business process simulations software (BPSS) is a prerequisite for accurate analysis of an BP. Characterisation of an BPSS tool is a challenging task due to the complex selection criteria that includes quality of visual aspects, simulation capabilities, statistical facilities, quality reporting etc. Under such circumstances, making an optimal decision is challenging. Therefore, various decision support models are employed aiding the BPSS tool selection. The currently established decision support models are either proprietary or comprise only a limited subset of criteria, which affects their accuracy. Addressing this issue, this paper proposes a new hierarchical decision support model for ranking of BPSS based on their technical characteristics by employing DEX and qualitative to quantitative (QQ) methodology. Consequently, the decision expert feeds the required information in a systematic and user friendly manner. There are three significant contributions of the proposed approach. Firstly, the proposed hierarchical model is easily extendible for adding new criteria in the hierarchical structure. Secondly, a fully operational decision support system (DSS) tool that implements the proposed hierarchical model is presented. Finally, the effectiveness of the proposed hierarchical model is assessed by comparing the resulting rankings of BPSS with respect to currently available results. [ABSTRACT FROM AUTHOR]

The Rapid Flashover pollution test method (RFO) exposes energized polluted insulators to fog and uses step changes of voltage to identify a minimum flashover voltage. The RFO method reduces test time by a factor of three or more compared to up-and-down voltage application method and is thus time- and cost-effective. In this paper the results from RFO on five ceramic and composite station insulators (line, post and hollow) with median 4.7 m leakage distance are compared closely with duplicate tests using up-anddown procedure. The tests on hydrophobic composite insulators used the preconditioning principles from CIGRE Brochure 555. Full-scale withstand testing of the same five but 420-kV class voltage insulators with median leakage distance 13.3 m are also presented. It is indicated that the flashover test results of RTV-coated station insulators should be specially analyzed and treated. [ABSTRACT FROM PUBLISHER]

Surprisal analysis is increasingly being applied for the examination of transcription levels in cellular processes, towards revealing inner network structures and predicting response. But to achieve its full potential, surprisal analysis should be integrated into a wider range computational tool. The purposes of this paper are to combine surprisal analysis with other important computation procedures, such as easy manipulation of the analysis results – e.g. to choose desirable result sub-sets for further inspection –, retrieval and comparison with relevant datasets from public databases, and flexible graphical displays for heuristic thinking. The whole set of computation procedures integrated into a single practical tool is what we call Computational Surprisal Analysis. This combined kind of analysis should facilitate significantly quantitative understanding of different cellular processes for researchers, including applications in proteomics and metabolomics. Beyond that, our vision is that Computational Surprisal Analysis has the potential to reach the status of a routine method of analysis for practitioners. The resolving power of Computational Surprisal Analysis is here demonstrated by its application to a variety of cellular cancer process transcription datasets, ours and from the literature. The results provide a compact biological picture of the thermodynamic significance of the leading gene expression phenotypes in every stage of the disease. For each transcript we characterize both its inherent steady state weight, its correlation with the other transcripts and its variation due to the disease. We present a dedicated website to facilitate the analysis for researchers and practitioners. [ABSTRACT FROM AUTHOR]

In this paper, we present a tool combining two software applications aimed at optimizing structural design problems of the civil engineering domain. Our approach lies in integrating an application for designing 2D and 3D bar structures, called Ebes, with the jMetal multi-objective optimization framework. The result is a software package that helps civil engineers to create bar structures which can be optimized further with multi-objective metaheuristics according to different goals, such as minimizing the structure weight and minimizing the deformation. The main features of both Ebes and jMetal are described and how they are combined together in one single tool is explained. Finally a case study to illustrate how the application works is presented. [ABSTRACT FROM AUTHOR]

This paper describes a model-driven decision-support system (software tool) implementing a model-based methodology for on-line leakage detection and localization which is useful for a large class of water distribution networks. Since these methods present a certain degree of complexity which limits their use to experts, the proposed software tool focuses on the integration of a method emphasizing its use by water network managers as a decision support system. The proposed software tool integrates a model-based leakage localization methodology based on the use of on-line telemetry information, as well as a water network calibrated hydraulic model. The application of the resulting decision support software tool in a district metered area (DMA) of the Barcelona distribution network is provided and discussed. The obtained results show that the leakage detection and localization may be performed efficiently reducing the required time. [ABSTRACT FROM AUTHOR]

This work describes the set of tools developed, tested, and put into production in the context of the H2020 project Multi-scale Observation and Monitoring of Railway Infrastructure Threats (MOMIT). This project, which ended in 2019, aimed to show how the use of various remote sensing techniques could help to improve the monitoring of railway infrastructures, such as tracks or bridges, and thus, consequently, improve the detection of ground instabilities and facilitate their management. Several lines of work were opened by MOMIT, but the authors of this work concentrated their efforts in the design of tools to help the detection and identification of ground movements using synthetic aperture radar interferometry (InSAR) data. The main output of this activity was a set of tools able to detect the areas labelled active deformation areas (ADA), with the highest deformation rates and to connect them to a geological or anthropogenic process. ADAtools is the name given to the aforementioned set of tools. The description of these tools includes the definition of their targets, inputs, and outputs, as well as details on how the correctness of the applications was checked and on the benchmarks showing their performance. The ADAtools include the following applications: ADAfinder, los2hv, ADAclassifier, and THEXfinder. The toolset is targeted at the analysis and interpretation of InSAR results. Ancillary information supports the semi-automatic interpretation and classification process. Two real use-cases illustrating this statement are included at the end of this paper to show the kind of results that may be obtained with the ADAtools. [ABSTRACT FROM AUTHOR]

Remote and isolated communities in Canada experience gaps in access to stable energy sources and must rely on diesel generators for heat and electricity. However, the cost and environmental impact resulting from the use of fossil fuels, especially in local energy production, heating, industrial processes and transportation are compelling reasons to support the development and deployment of renewable energy hybrid systems. This paper presents a computer model for economic analysis and risk assessment of a wind–diesel hybrid system with compressed air energy storage. The proposed model is developed from the point of view of the project investor and it includes technical, financial, risk and environmental analysis. Robustness is evaluated through sensitivity analysis. The model has been validated by comparing the results of a wind–diesel case study against those obtained using HOMER (National Renewable Energy Laboratory, Golden, CO, United States) and RETScreen (Natural Resources Canada, Government of Canada, Canada) software. The impact on economic performance of adding energy storage system in a wind–diesel hybrid system has been discussed. The obtained results demonstrate the feasibility of such hybrid system as a suitable power generator in terms of high net present value and internal rate of return, low cost of energy, as well as low risk assessment. In addition, the environmental impact is positive since less fuel is used. [ABSTRACT FROM AUTHOR]