Source Files Research Articles

The wavelet transfer function of a human body–seat system

In the analysis of vibration systems, classical transfer functions are used. Usually, it is the ratio of Fourier or Laplace transforms. The wavelet transfer function is proposed in this work. In this paper, the wavelets transfer function is the ratio of output and input wavelet transforms. It is considered as a distinctive correlation of the output and input system signals. The wavelet transform consists of coefficients, where the first is a scale and second time shift. To get input and output signals in the human body–seat system the dedicated test stand was made. The stand consists of a seat, moved by special shaker, which is used as a mechanical vibration device. The control program included in the source file is taken to imitate angular position of the engine. Motor shaft is connected with exciter’s moving parts and stand base, which influences directly on the seat position. The disturbance signal usually simulates a horizontal road influence on a driver. It can be considered as a low-frequency signal. It is measured by accelerometers called inertial sensors, which are placed on the platform of the shaker. The output signal is measured by an accelerometer placed on a seat and on the human head. Both signals are recorded by the Inertia Studio software wireless in the real time. After the measurement, the signals are transformed into wavelet coefficients by using Matlab package functions. The transfer function and its visualization are presented in two dimensions scale-time. The scale is related to frequency (pseudo-frequency). By the transfer function it is possible to analyze the systems, evaluate safety, compare the systems, and many more.

CGManalyzer: an R package for analyzing continuous glucose monitoring studies.

The R package CGManalyzer contains functions for analyzing data from a continuous glucose monitoring (CGM) study. It covers a wide and comprehensive range of data analysis methods including reading a series of datasets, obtaining summary statistics of glucose levels, plotting data, transforming the time stamp format, fixing missing values, evaluating the mean of daily difference and continuous overlapping net glycemic action, calculating multiscale sample entropy, conducting pairwise comparison, displaying results using various plots including a new type of plot called an antenna plot, etc. This package has been developed from our work in directly analyzing data from various CGM devices such as the FreeStyle Libre, Glutalor, Dexcom and Medtronic CGM. Thus, this package should greatly facilitate the analysis of various CGM studies. The package for Windows is available from CRAN: http://cran.r-project.org/mirrors.html. The source file CGManalyzer_1.0.tar.gz is available in the Supplementary Material and at the website of Zhang's lab https://quantitativelab.fhs.umac.mo/analytic-tool/. douglaszhang@umac.mo. Supplementary data are available at Bioinformatics online.

Towards Implementation of OMOP in a German University Hospital Consortium

Background In 2015, the German Federal Ministry of Education and Research initiated a large data integration and data sharing research initiative to improve the reuse of data from patient care and translational research. The Observational Medical Outcomes Partnership (OMOP) common data model and the Observational Health Data Sciences and Informatics (OHDSI) tools could be used as a core element in this initiative for harmonizing the terminologies used as well as facilitating the federation of research analyses across institutions. Objective To realize an OMOP/OHDSI-based pilot implementation within a consortium of eight German university hospitals, evaluate the applicability to support data harmonization and sharing among them, and identify potential enhancement requirements. Methods The vocabularies and terminological mapping required for importing the fact data were prepared, and the process for importing the data from the source files was designed. For eight German university hospitals, a virtual machine preconfigured with the OMOP database and the OHDSI tools as well as the jobs to import the data and conduct the analysis was provided. Last, a federated/distributed query to test the approach was executed. Results While the mapping of ICD-10 German Modification succeeded with a rate of 98.8% of all terms for diagnoses, the procedures could not be mapped and hence an extension to the OMOP standard terminologies had to be made. Overall, the data of 3 million inpatients with approximately 26 million conditions, 21 million procedures, and 23 million observations have been imported.A federated query to identify a cohort of colorectal cancer patients was successfully executed and yielded 16,701 patient cases visualized in a Sunburst plot. Conclusion OMOP/OHDSI is a viable open source solution for data integration in a German research consortium. Once the terminology problems can be solved, researchers can build on an active community for further development.

On a Class of Multi-Source Distributed Storage With Exact Repair

In future communication networks, say 5G networks and Internet of Things, users may need to obtain messages from multiple available sources in a distributed manner, which requires distributed storage in the network. One essential issue in distributed storage is how to repair a failed storage node. In conventional distributed storage model with exact repair, source files are stored in many nodes in a distributed manner and the contents of a failed node are exactly recovered by the surviving nodes. Further, all files can be reconstructed when a decoder has access to a certain number of storage nodes. So, the underlying reconstruction network is equivalent to a single-source multicast problem. This paper considers a variant of the exact repair problem, where the underlying reconstruction network is the independent distributed source coding system, a type of multi-source multicast problem. As the first non-trivial case with two sources and three encoders, the storage-repair tradeoff regions are proved for all the 33 non-isomorphic instances, and it is shown that binary codes are optimal.

Generating Correct, Compact, and Efficient PLC Code from Scenario-based Assume-Guarantee Specifications

Cyber-physical systems can be found in many areas, e.g., manufacturing, health care or smart cities. They consist of many distributed components cooperating to provide increasingly complex functionality. The design and development of such a system is difficult and error-prone. To help engineers overcome these challenges we created a formal, scenario-based specification language. Short scenarios, i.e., event sequences, specify requirements and the desired behaviors by describing how components may, must, or must not behave. Scenarios provide an intuitive way for creating formal assume-guarantee (GR(1)) specifications, giving engineers easy access to simulation, for validating the specified behavior, and controller synthesis, for creating controller software which is correct by construction. In this paper we present an approach for generating Programmable Logic Controller (PLC) code from a scenario-based specification. Previous code generation efforts, including our own, created large, verbose source files causing some tools, e.g., compilers or editors, to perform slowly or even become unresponsive. Our new approach creates compact files, shifting significant amounts of code from executable instructions to data, to reduce the burden on the compiler and other tools. The generated code is efficient and introduces minimal to no latency between the occurrence of an event and the system’s reaction to it.

Anisotropic peridynamic model—Formulation and implementation

In this work, anisotropy is introduced in a peridynamic model. The spherical influence function is replaced by an ellipsoidal influence function. The model is mathematically formulated and implemented into the source files of LAMMPS, extending the program in a straight-forward manner. The extension ca be applied to other peridynamic model and here it is introduced into elastoplastic peridynamic model in LAMMPS. The implemented model is tested through simulating beams loaded in compression. The model is found to alter the material behavior in the simulations compared to the original isotropic mode. A clear qualitative and quantitative difference in behavior is shown independently of pre-existing simulation parameters. The model is shown to be internally consistent. Finally we also demonstrated that the model can easily be extended to include several preferable direction opening for application as modeling elasticplastic deformation of anisotropic heterogeneous crystalline matter.

All-Cause Mortality for Life Insurance Applicants with a Family History of Coronary Artery Disease Before 60.

-To determine the all-cause mortality of life insurance applicants having a family history of coronary artery disease (CAD) before age 60. -Epidemiological studies have shown that a family history of premature CAD is an independent risk factor for CAD events. The strength of the association between family history and CAD is greatest with earlier age of presentation of CAD in the family member and when multiple family members are affected. Despite earlier insurance studies on this relationship, there is sparse current data on the association between family history of CAD and all-cause mortality in life insurance applicants. -Life insurance applicants with reported family history of Coronary Artery Disease (CAD) were extracted from data covering United States residents between October 2009 and October 2016. Information about these applicants was matched to the Social Security Death Master (SSDMF) file for deaths occurring from 2009 to 2012 and to another commercially available death source file (Other Death Source, ODS) for deaths occurring from 2009 to 2016 to determine vital status. Actual to Expected (A/E) mortality ratios were calculated using the Society of Actuaries 2015 Valuation Basic Table (2015VBT), select and ultimate table (age last birthday). All expected bases were not smoker distinct. Confidence bands around these mortality ratios were calculated. The variables of interest were applicant age, gender, number of family members with CAD before age 60, and the presence of cardiac or cardiovascular conditions. -Overall, the mortality of applicants with family members with a history of CAD before age 60 was slightly lower than expected mortality based on the 2015 VBT. Applicants with a cardiac or cardiovascular comorbid condition had a significantly higher mortality ratio. For applicants aged 25-54 and 65-75 with cardiac comorbid conditions, the mortality ratio was 2 times that of those without a cardiac comorbid condition. For those aged 55-64 with cardiovascular comorbid conditions, the mortality ratio was 2.9 times that of those without a cardiovascular comorbid condition. Females had a slightly higher mortality ratio for all age groups, number of family members with CAD before age 60, and cardiovascular conditions. -A family history of CAD before the age of 60 in an insurance applicant may be associated with increased all-cause mortality. Overall in this study, life insurance applicants had a mortality slightly lower than the expected mortality based on the 2015 VBT. However, applicants with a positive family history and a cardiac or cardiovascular comorbid condition had a significantly higher mortality ratio.

Reducing calling convention overhead in object-oriented programming on embedded ARM thumb-2 platforms

This paper examines the causes and extent of code size overhead caused by the ARM calling convention in Thumb-2 binaries. We show that binaries generated from C++ source files generally have higher amounts of calling convention overhead, and present a binary file optimizer to eliminate some of that overhead. Calling convention overhead can negatively impact power consumption, flash memory costs, and chip size in embedded or otherwise resource-constrained domains. This is particularly true on platforms using "compressed" instruction sets, such as the 16-bit ARM Thumb and Thumb-2 instruction sets, used in virtually all smartphones and in many other smaller-scale embedded devices. In this paper, we examine the extent of calling convention overhead in practical software, and compare the results of C and C++ programs, and find that C++ programs generally have a higher percentage of calling-convention overhead. Finally, we demonstrate a tool capable of eliminating some of this overhead, particularly in the case of C++ programs, by modifying the calling conventions on a per-procedure basis.

An efficient scheduling multimedia transcoding method for DASH streaming in cloud environment

As a result of technological evolution, streaming service providers have been dealing with the problem of delivery multimedia content to the diversity of devices with different resolutions. This issue can be solved by using dynamic adaptive streaming over hypertext (DASH) transfer protocol. However, a transcoding job in DASH requires a lot of computation resource which could lead to delaying the starting of multimedia streaming. Recently, new studies have addressed novel scheduling methods on video transcoding, but those research did not solve the problem entirely, such as the solution did not concern server performance or speed connection between a server and its requested users. Moreover, the load and speed connection status of the data servers is often unstable, leading to increasing the starting delay. So in this article, we solve such problem by modeling transcoding jobs in the form of an optimization problem and propose an algorithm to find an optimal schedule to transcode video source files. In which, we use moving average method to find average points for a short period to deal with server state changes. In the experiment, we implement our proposed method with DASH to demonstrate the effectiveness of the optimization scheduling method. In the system, we create several servers running on the Docker platform to simulate a cloud environment. Experimental results show that our methodology reduces the time of the transcoding process up to 30% compared to existing research.

Expression and significance of long non-coding RNA metastasis associated in lung denocarcinoma transcript 1 in the process of hyperoxia-induced lung injury in preterm infants

Objective To explore the protective effect of long non-coding RNA (lncRNA) metastasis associated in lung denocarcinoma transcript 1 (MALAT1) involved in hyperoxia-induced lung injury in preterm infants. Methods This study had downloaded chip data set GSE25286 (Mouse GEO Genome 430 2.0 Array) from gene expression database gene expression omnibus (GEO), according to the state of hyperoxia exposure, the MALAT1 mRNA expression in rats normal lung tissues and hyperoxic lung tissues was compared at day 14th and 29th.In chip data set GSE43830(Human Exon 1.0 ST Arrays) from GEO, the expression of multiple genes[cell division cycle 6(CDC6), death effector domain containing 2(DEDD2), and Cyclin B1(CCNB1)] in WI38 cells (lung fibroblasts) was compared before and after MALAT1 was knockout.At the same time, the peripheral blood samples of premature infants were collected to verify.Totally 40 premature infants were hospitalized in the department of neonatology in our hospital from Jan 2015 to Dec 2016, the peripheral blood samples of 40 premature infants were collected.RNA was extracted and Real time-PCR was performed after reverse transcription, clinical data of these 40 cases were retrospectively analyzed. Results (1) By using Affymetrix Expression console and Affymetrix Transcriptome analysis console software source files of the chip of pretreatment and difference expression gene screening, the expression of lncRNA MALAT1 gene in lung tissues of hyperoxia lung injury mice significantly upregulated[fold change(FC)=2.33, P=0.001]. (2) After MALAT1 in WI38 cell was knockout, MALAT1 expression was significantly reduced(FC=-15.6, P=0.000), the expression of CDC6(FC=-2.37, P=0.001) and CCNB1(FC=-2.16, P=0.002) were down regulated, DEDD2 expression was up regulated(FC=2.46, P=0.000). (3) The results of peripheral blood samples from preterm infants showed that the expression of MALAT1 was significantly increased in preterm infants with hyperoxia-induced lung injury(0.375 5±0.081 9, t=4.634, P=0.015), compared with normal preterm infants(0.273 4±0.067 3). Conclusion Through inhibiting cell apoptosis, lncRNA MALAT1 can protect preterm infants with hyperoxia-induced lung injury, it may provide a new strategy for prevention and treatment of hyperoxia-induced lung injury in premature infants. Key words: Long noncoding RNA; Neonates; Lung injury; Metastasis associated in lung denocarcinoma transcript 1; Hyperoxia

An Evaluation of Coding Violation Focusing on Change History and Authorship of Source File

This paper focuses on an evaluation of coding violation warned by a static code analysis tool while considering the change history of violation and the authorship of source file. Through an empirical study with data collected from seven open source software projects, the following findings are reported: (1) the variety and the evaluation of a coding violation tend to vary accroding to the authoring type of the source file; (2) while important violations tend to vary from project to project, about 30% of violations are commonly disregarded by many programmers.

DFMDEF18: A C-code for the double folding interaction potential of a spherical nucleus with deformed nucleus

DFMDEF18: A C-code for the double folding interaction potential of a spherical nucleus with deformed nucleus

On the value of a prioritization scheme for resolving Self-admitted technical debt

Programmers tend to leave incomplete, temporary workarounds and buggy codes that require rework in software development and such pitfall is referred to as Self-admitted Technical Debt (SATD). Previous studies have shown that SATD negatively affects software project and incurs high maintenance overheads. In this study, we introduce a prioritization scheme comprising mainly of identification, examination and rework effort estimation of prioritized tasks in order to make a final decision prior to software release. Using the proposed prioritization scheme, we perform an exploratory analysis on four open source projects to investigate how SATD can be minimized. Four prominent causes of SATD are identified, namely code smells (23.2%), complicated and complex tasks (22.0%), inadequate code testing (21.2%) and unexpected code performance (17.4%). Results show that, among all the types of SATD, design debts on average are highly prone to software bugs across the four projects analysed. Our findings show that a rework effort of approximately 10 to 25 commented LOC per SATD source file is needed to address the highly prioritized SATD (vital few) tasks. The proposed prioritization scheme is a novel technique that will aid in decision making prior to software release in an attempt to minimize high maintenance overheads.

A solid-discrete-based method for extracting the cutter-workpiece engagement in five-axis flank milling

Five-axis flank milling has been widely used in industry because of its high material removal rate, low tool loss, and achievement of good surface quality. The cutting force, which is the basis for studying the milling process, is mainly determined by the cutting coefficients, spindle speed, feed rate, and cutter-workpiece engagement (CWE). However, due to the complex spatial motion of the cutting tool, extracting the CWE with high precision and efficiency in five-axis flank milling has become a challenging topic. This paper proposes a novel and integrated solid-discrete-based method to identify the CWE data in a flank milling workpiece with ruled surfaces. In this method, the tool path and cutting location source (CLS) file of certain tool/workpiece combinations are obtained by commercial CAM software. Two cutting types, first cut and following cut, are considered. First, the point cloud data of the machining surface are extracted, and the instantaneous contact profile of the tool and the workpiece is obtained according to the tool geometry information at different cutting location points. The feasible contact surface is then constructed based on an analysis of the surface normal and instantaneous feed direction at the arbitrary tool point. After trimming the contact profile by the feasible contact boundary, the exact CWE can finally be extracted. Compared with the existing methods for CWE extraction, the proposed method replaces the solid model with discrete coordinate points in the calculation process and is thus more suitable for system integration. Experiments and applications show that this method has high accuracy and computational efficiency.

Retrieving and classifying instances of source code plagiarism

Automatic detection of source code plagiarism is an important research field for both the commercial software industry and within the research community. Existing methods of plagiarism detection primarily involve exhaustive pairwise document comparison, which does not scale well for large software collections. To achieve scalability, we approach the problem from an information retrieval (IR) perspective. We retrieve a ranked list of candidate documents in response to a pseudo-query representation constructed from each source code document in the collection. The challenge in source code document retrieval is that the standard bag-of-words (BoW) representation model for such documents is likely to result in many false positives being retrieved, because of the use of identical programming language specific constructs and keywords. To address this problem, we make use of an abstract syntax tree (AST) representation of the source code documents. While the IR approach is efficient, it is essentially unsupervised in nature. To further improve its effectiveness, we apply a supervised classifier (pre-trained with features extracted from sample plagiarized source code pairs) on the top ranked retrieved documents. We report experiments on the SOCO-2014 dataset comprising 12K Java source files with almost 1M lines of code. Our experiments confirm that the AST based approach produces significantly better retrieval effectiveness than a standard BoW representation, i.e., the AST based approach is able to identify a higher number of plagiarized source code documents at top ranks in response to a query source code document. The supervised classifier, trained on features extracted from sample plagiarized source code pairs, is shown to effectively filter and thus further improve the ranked list of retrieved candidate plagiarized documents.

Just enough semantics: An information theoretic approach for IR-based software bug localization

ContextSoftware systems are often shipped with defects. Whenever a bug is reported, developers use the information available in the associated report to locate source code fragments that need to be modified in order to fix the bug. However, as software systems evolve in size and complexity, bug localization can become a tedious and time-consuming process. To minimize the manual effort, contemporary bug localization tools utilize Information Retrieval (IR) methods for automated support. IR methods exploit the textual content of bug reports to automatically capture and rank relevant buggy source files. ObjectiveIn this paper, we propose a new paradigm of information-theoretic IR methods to support bug localization tasks in software systems. These methods, including Pointwise Mutual Information (PMI) and Normalized Google Distance (NGD), exploit the co-occurrence patterns of code terms in the software system to reveal hidden textual semantic dimensions that other methods often fail to capture. Our objective is establish accurate semantic similarity relations between source code and bug reports. MethodFive benchmark datasets from different application domains are used to conduct our analysis. The proposed methods are compared against classical IR methods that are commonly used in bug localization research. ResultsThe results show that information-theoretic IR methods significantly outperform classical IR methods, providing a semantically aware, yet, computationally efficient solution for bug localization in large and complex software systems. (A replication package is available at: http://seel.cse.lsu.edu/data/ist17.zip). ConclusionsInformation-theoretic co-occurrence methods provide “just enough semantics” necessary to establish relations between bug reports and code artifacts, achieving a balance between simple lexical methods and computationally-expensive semantic IR methods that require substantial amounts of data to function properly.

Astro: Auto-Generation of Synthetic Traces Using Scaling Pattern Recognition for MPI Workloads

Performance modeling of scale-out MPI workloads is critical in assessing trade-offs for high-performance system designs. Traces and workload skeletons are the two main vehicles used to date to accomplish this task. However, the ever-increasing scale and complexity of MPI workloads makes it difficult, sometimes infeasible, to collect the traces and/or skeletonize the workloads, dueto the constraints of computing resources or the unavailability of workload source code. This paper presents Astro , a framework that leverages machine learning techniques to automatically recognize the scaling patterns from training traces, and generate high-quality synthetic traces which mimic original trace behavior and extrapolate it to arbitrary scale. Experimental results show that compared with original traces, the synthetic traces yield less than 15 percent error against a range of metrics for up to 8 K MPI ranks. This framework enables large-scale performance modeling with limited computing resources, and allows modeling proprietary workloads in a portable and secure way. Author: There was a discrepancy in Bibliography in the PDF and the source file. We have followed the source file. ?>

A Generic Multi-Axis Post-Processor Engine for Optimal CNC Data Creation and Intelligent Surface Machining

This paper focuses on the development of a multi-axis post-processor engine with a curvature-based feed adaptation module, capable of extracting generic CNC data for high precision machining. The motivation of this work stems from the drawback of standard and commercial post-processors to modify their internal source codes so as to be implemented to newly-developed functions which integrate modern CNC units. The multi-axis post-processor proposed in this work operates as a stand-alone function of an artificial intelligent module that optimizes machining parameters for standard swept cut multi-axis surface tool-paths. The post-processor developed receives APT source files previously been optimized by means of a genetic algorithm that handles cutting tool selection; radial cut engagement; maximum discretization step; lead and tilt angles. The algorithm optimizes the aforementioned machining parameters towards the minimization of the number of cutter locations found in a specific APT source file as well as the surface machining error as a combined effect of chordal deviation and scallop height. The final APT output is then properly handled by the post-processor engine so as to extract the final ISO code for a double-pivoted head 5-axis CNC machine and compute optimal values for feed rate in each NC block considering the interpolation error and curvature analysis given the surface properties. To simulate and verify our proposals, the MAZAK Vortex 1000 gantry-type 5-axis CNC machine tool equipped with a Fanuc 15i CNC unit has been selected as the manufacturing resource corresponding to the final CNC output that the proposed post-processor computes. A benchmark sculptured part is created and used for the virtual material removal simulation in CATIA® V5 R18. For that part, both the proposed post-processor engine and a commercially available post-processor were employed to extract G-code data whilst it was shown that identical outputs were obtained.

Augmenting Bug Localization with Part-of-Speech and Invocation

Bug localization represents one of the most expensive, as well as time-consuming, activities during software maintenance and evolution. To alleviate the workload of developers, numerous methods have been proposed to automate this process and narrow down the scope of reviewing buggy files. In this paper, we present a novel buggy source-file localization approach, using the information from both the bug reports and the source files. We leverage the part-of-speech features of bug reports and the invocation relationship among source files. We also integrate an adaptive technique to further optimize the performance of the approach. The adaptive technique discriminates Top 1 and Top N recommendations for a given bug report and consists of two modules. One module is to maximize the accuracy of the first recommended file, and the other one aims at improving the accuracy of the fixed defect file list. We evaluate our approach on six large-scale open source projects, i.e. ASpectJ, Eclipse, SWT, Zxing, Birt and Tomcat. Compared to the previous work, empirical results show that our approach can improve the overall prediction performance in all of these cases. Particularly, in terms of the Top 1 recommendation accuracy, our approach achieves an enhancement from 22.73% to 39.86% for ASpectJ, from 24.36% to 30.76% for Eclipse, from 31.63% to 46.94% for SWT, from 40% to 55% for ZXing, from 7.97% to 21.99% for Birt, and from 33.37% to 38.90% for Tomcat.

Multimedia file forensics system exploiting file similarity search

With the fast increase of multimedia contents, efficient forensics investigation methods for multimedia files have been required. In multimedia files, the similarity means that the identical media (audio and video) data are existing among multimedia files. This paper proposes an efficient multimedia file forensics system based on file similarity search of video contents. The proposed system needs two key techniques. First is a media-aware information detection technique. The first critical step for the similarity search is to find the meaningful keyframes or key sequences in the shots through a multimedia file, in order to recognize altered files from the same source file. Second is a video fingerprint-based technique (VFB) for file similarity search. The byte for byte comparison is an inefficient similarity searching method for large files such as multimedia. The VFB technique is an efficient method to extract video features from the large multimedia files. It also provides an independent media-aware identification method for detecting alterations to the source video file (e.g., frame rates, resolutions, and formats, etc.). In this paper, we focus on two key challenges: to generate robust video fingerprints by finding meaningful boundaries of a multimedia file, and to measure video similarity by using fingerprint-based matching. Our evaluation shows that the proposed system is possible to apply to realistic multimedia file forensics tools.