Software Foundation Research Articles

Transactive Energy Market for Energy Management in Microgrids: The Monash Microgrid Case Study

Transactive energy is a novel approach for energy management and trading, which can be used in microgrids to facilitate the integration of distributed energy resources (DERs) in existing networks. The key feature in transactive energy is using market-based solutions for energy management. Hence, an appropriate transactive energy market (TEM) framework should be designed to enable and incentivize DER owners to participate in different markets. The efficient implementation of TEM for microgrid energy management encompasses the application of a variety of design principles. In this rapidly developing area, this paper presents a complete proposal of the TEM as a framework for the design, implementation, and deployment of transactive energy solutions for energy management in microgrids. In particular, we outline the requirements to design an effective market mechanism for the TEM. The applicability of this perspective is demonstrated through the introduction of the Monash Microgrid as a real-world implementation of a TEM solution, where a complete hardware and software foundation is presented as a platform to deploy a market-based solution for microgrid energy management. This is further illustrated through an example scenario, where the application of TEM is discussed to demonstrate the impact of considered design choices on achieving desired objectives.

Quadritherapy vs standard tritherapy immunosuppressant regimen after heart transplantation: A propensity score-matched cohort analysis.

After heart transplant, adding everolimus (EVL) to standard immunosuppressive regimen mostly relies on converting calcineurin inhibitors (CNIs) into EVL. The aim of this study was to describe the effects of combining low-dose EVL and CNIs in maintenance immunosuppression regimen (quadritherapy) and compare it with standard tritherapy associating standard-dose CNIs, mycophenolate mofetil, and corticosteroids. In the 3-year registry cohort of heart transplanted patients, those who received quadritherapy were compared with those who received tritherapy. EVL was added after 3months posttransplant. Three analyses were performed to control for confounders: propensity score matching, multivariable survival, and inverse probability score weighting analyses. Among 213 patients who were included (75 with quadritherapy), propensity score matching selected 64 unique pairs of patients with similar characteristics. In the matched cohort (n=128), quadritherapy was associated with fewer deaths (3 [4.7%] vs 17 [21.9%], P=.007) and biopsy-proven acute rejections (15 [23.4%] vs 31 [48.4%], P=.002). These results were confirmed in the overall cohort (n=213), after multivariable and inverse probability score weighting analyses. Renal function and donor-specific HLA-antibodies remained similar in both groups. Low-dose combination quadritherapy was associated with fewer deaths and rejections, compared with standard immunosuppression tritherapy.

Fish maintain tissue pH despite CO2 blast

![Figure][1] Tambaqui ( Colossoma macropomum ), Leipzig Zoo, Germany. Photo credit: Tino Straus, GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation. Even though lake and river CO2 levels never near the fizzy heights found inside a can

Programming language foundations in Agda

• PLFA is an online textbook, available at plfa.inf.ed.ac.uk . • The proofs for a textbook on programming languages can be written in Agda, without a separate scripting language. • Constructive proofs of preservation and progress give rise to a prototype evaluator. • Using raw terms with a separate typing relation is far less perspicuous than using inherently-typed terms. • An online final examination with access to a proof assistant can lead to flawless student performance. One of the leading textbooks for formal methods is Software Foundations (SF), written by Benjamin Pierce in collaboration with others, and based on Coq. After five years using SF in the classroom, we came to the conclusion that Coq is not the best vehicle for this purpose, as too much of the course needs to focus on learning tactics for proof derivation, to the cost of learning programming language theory. Accordingly, we have written a new textbook, Programming Language Foundations in Agda (PLFA). PLFA covers much of the same ground as SF, although it is not a slavish imitation. What did we learn from writing PLFA? First, that it is possible. One might expect that without proof tactics that the proofs become too long, but in fact proofs in PLFA are about the same length as those in SF. Proofs in Coq require an interactive environment to be understood, while proofs in Agda can be read on the page. Second, that constructive proofs of preservation and progress give immediate rise to a prototype evaluator. This fact is obvious in retrospect but it is not exploited in SF (which instead provides a separate normalise tactic) nor can we find it in the literature. Third, that using extrinsically-typed terms is far less perspicuous than using intrinsically-typed terms. SF uses the former presentation, while PLFA presents both; the former uses about 1.6 as many lines of Agda code as the latter, roughly the golden ratio. The textbook is written as a literate Agda script, and can be found here: http://plfa.inf.ed.ac.uk

OnlineStats.jl: A Julia package for statistics on data streams.

SummaryThe growing prevalence of big and streaming data requires a new generation of tools. Data often has infinite size in the sense that new observations are continually arriving daily, hourly, etc. In recent years, several new technologies such as Kafka (Apache Software Foundation, n.d.-a) and Spark Streaming (Apache Software Foundation, n.d.-b) have been introduced for processing streaming data. Statistical tools for data streams, however, are under-developed and offer only basic functionality. The majority of statistical software can only operate on finite batches and require re-loading possibly large datasets for seemingly simple tasks such as incorporating a few more observations into an analysis.OnlineStats is a Julia (Bezanson, Edelman, Karpinski, & Shah, 2017) package for high-performance online algorithms. The OnlineStats framework is easily extensible, includes a large catalog of algorithms, provides primitives for parallel computing, and offers a weighting mechanism that allows new observations have a higher relative influence over the value of the statistic/model/visualization.

Open Geospatial Software and Data: A Review of the Current State and A Perspective into the Future

All over the world, organizations are increasingly considering the adoption of open source software and open data. In the geospatial domain, this is no different, and the last few decades have seen significant advances in this regard. We review the current state of open source geospatial software, focusing on the Open Source Geospatial Foundation (OSGeo) software ecosystem and its communities, as well as three kinds of open geospatial data (collaboratively contributed, authoritative and scientific). The current state confirms that openness has changed the way in which geospatial data are collected, processed, analyzed, and visualized. A perspective on future developments, informed by responses from professionals in key organizations in the global geospatial community, suggests that open source geospatial software and open geospatial data are likely to have an even more profound impact in the future.

A Distribution of Nodes in Big Data using Hadoop Open Source System

Apache Hadoop is an free open source Java framework under Apache Software Foundation. It provides storage of large amount of data efficiently with low costing. Hadoop has two main core components one is HDFS (Hadoop Distributed File System) and second Map Reduce. It is basically a file system and has capability of high fault-tolerant and while deploying supports less cost hardware. It. provides the high speed admittance to the relevance data. The Hadoop architecture is based on cluster, which consist of two nodes named as Data -Node and Name-Node which perform the internal activity known as heart beat to process data storage on distributed file system and Map reducing is performed internally to show the clustering of distributed data on localhost of ssh serverwebsite. Large quantity of data is needed to store in distributed file structure, for this Hadoop has played important role. Maintaining the large volume storage, making data duplicity for providing security and recovery of big data for its analysis and prediction.

First-trimester screening for fetal growth restriction using Doppler color flow analysis of the uterine artery and serum PAPP-A levels in unselected pregnancies

Purpose To explore an early diagnostic model for fetal growth restriction (FGR) at 11–13 (+6 days) gestational weeks using Doppler analysis of the uterine artery and measurements of pregnancy-associated plasma protein-A (PAPP-A). Methods This was a prospective study which included 1796 singleton pregnant women, who received routine pregnancy examination at 11–13 (+6 days) gestational weeks in Shanghai Changning Maternity and Infant Health Hospital between 1 June 2017 and 31 July 2018. Uterine artery pulsatility index (PI), uterine resistance index (RI), and notching were recorded using the Doppler ultrasound detector (Voluson E8; GE Healthcare, Kretztechnik, Zipf, Austria). Maternal serum PAPP-A was assayed using time-resolved fluorescence immunoassay (Perkin-Elmer Life Sciences, Waltham, MA, USA) and analyzed using Fetal Medicine Foundation software. Maternal and neonatal outcomes were followed. Results Out of 1796 pregnant women aged 18–42 years, 76 (4.2%) mothers had FGR fetus. In the FGR fetuses, the mean uterine artery PI and RI were higher, the PAPP-A levels were 0.42-fold lower (all p values < .05), and notching was 40% higher (p < .0001) than in non-FGR fetuses. The sensitivity and specificity of early diagnosis of FGR and the area under the curve for the combination of uterine artery PI and PAPP-A were 0.788 (95% CI: 0.735, 0.842), 0.816, and 0.758, respectively. A combination of PAPP-A and Doppler analysis of uterine artery was better than individual measurements for predicting FGR (all p values < .05), and the specificity was significantly improved after including serum PAPP-A. Conclusion The combination of uterine artery PI and PAPP-A measured at 11–13 (+6 days) gestational weeks provides a sensitive and specific predictor for early diagnosis of FGR.

Orderly Charging Control Module Design

This paper introduces the design of an orderly charging module. This paper analyzes the system structure of the orderly charging module, the embedded software architecture and business implementation mode of the orderly charging module, and introduces the hardware framework and implementation method of the orderly charging module. This design is mainly used in the charging pile of electric vehicle, which is used to realize intelligent and orderly charging, optimize energy management, provide various forms of Internet of things access scheme, and provide the software and hardware technology foundation for the reasonable management of energy.

The Validity of using a Single-Question Self-Report of Erectile Dysfunction as a Screening Tool among Men with Type 2 Diabetes Mellitus

Background and objectiveThis study aimed to determine the validity of using a single-question self-report of erectile dysfunction (ED) as a screening tool among Saudi men with type 2 diabetes mellitus (T2DM). Materials and methodsA cross-sectional study was conducted using a single-question self-report questionnaire to determine the association between the risk of ED and poor glycemic control among men with T2DM. The study was conducted in a hospital-based diabetes clinic in Riyadh, Saudi Arabia. Married adults (aged >18 years) suffering from T2DM for at least 1 year were included in the study. All statistical analy-ses were performed using SAS version 9.2 and R software (Foundation for Statistical Computing, Vienna, Austria). ResultsWith 86% response rate, 293 participants were included in this study. Over half (53.9%) of the partic-ipants were below 60 years of age. More than half (55.3%) were suffering from uncontrolled diabetes (i.e., HbA1c > 7%). There was significant correlation between the International Index of Erectile Function (IIEF) and self-reported question in terms of duration of T2DM (p < 0.001), type of treatment (p = 0.004), income of the participants (p = 0.005), age (p < 0.001), education level (p = 0.032), and occupation (p < 0.001). However, there was no significant correlation between IIEF and self-reported question in terms of body mass index (p = 743) and smoking. Regarding overall diagnostic accuracy of IIEF score to predict self-reported ED, receiver operating characteristic curve showed area under curve as 89.4%, which is sta-tistically significant. ConclusionSingle-question self-report of ED is a valid and reliable tool to screen diabetic patients suffering from sexual problems. Such tool may help to identify ED in diabetic patients and warrant early management.

New developments in cost modeling for the LHC computing

The increase in the scale of LHC computing during Run 3 and Run 4 (HL-LHC) will certainly require radical changes to the computing models and the data processing of the LHC experiments. The working group established by WLCG and the HEP Software Foundation to investigate all aspects of the cost of computing and how to optimise them has continued producing results and improving our understanding of this process. In particular, experiments have developed more sophisticated ways to calculate their resource needs, we have a much more detailed process to calculate infrastructure costs. This includes studies on the impact of HPC and GPU based resources on meeting the computing demands. We have also developed and perfected tools to quantitatively study the performance of experiments workloads and we are actively collaborating with other activities related to data access, benchmarking and technology cost evolution. In this contribution we expose our recent developments and results and outline the directions of future work.

Modern Software Stack Building for HEP

High-Energy Physics has evolved a rich set of software packages that need to work harmoniously to carry out the key software tasks needed by experiments. The problem of consistently building and deploying these packages as a coherent software stack is one that is shared across the HEP community. To that end the HEP Software Foundation Packaging Working Group has worked to identify common solutions that can be used across experiments, with an emphasis on consistent, reproducible builds and easy deployment into CernVM-FS or containers via CI systems. We based our approach on well-identified use cases and requirements from many experiments. In this paper we summarise the work of the group in the last year and how we have explored various approaches based on package managers from industry and the scientific computing community. We give details about a solution based on the Spack package manager which has been used to build the software required by the SuperNEMO and FCC experiments and trialled for a multi-experiment software stack, Key4hep. We shall discuss changes that needed to be made to Spack to satisfy all our requirements. We show how support for a build environment for software developers is provided.

Bridging the Collaboration Gap: Real-time Identification of Clinical Specimens for Biomedical Research

Introduction: Biomedical and translational research often relies on the evaluation of patients or specimens that meet specific clinical or laboratory criteria. The typical approach used to identify biospecimens is a manual, retrospective process that exists outside the clinical workflow. This often makes biospecimen collection cost prohibitive and prevents the collection of analytes with short stability times. Emerging data architectures offer novel approaches to enhance specimen-identification practices. To this end, we present a new tool that can be deployed in a real-time environment to automate the identification and notification of available biospecimens for biomedical research. Methods: Real-time clinical and laboratory data from Cloverleaf (Infor, NY, NY) were acquired within our computational health platform, which is built on open-source applications. Study-specific filters were developed in NiFi (Apache Software Foundation, Wakefield, MA, USA) to identify the study-appropriate specimens in real time. Specimen metadata were stored in Elasticsearch (Elastic N. V., Mountain View, CA, USA) for visualization and automated alerting. Results: Between June 2018 and December 2018, we identified 2992 unique specimens belonging to 2815 unique patients, split between two different use cases. Based on laboratory policy for specimen retention and study-specific stability requirements, secure E-mail notifications were sent to investigators to automatically notify of availability. The assessment of throughput on commodity hardware demonstrates the ability to scale to approximately 2000 results per second. Conclusion: This work demonstrates that real-world clinical data can be analyzed in real time to increase the efficiency of biospecimen identification with minimal overhead for the clinical laboratory. Future work will integrate additional data types, including the analysis of unstructured data, to enable more complex cases and biospecimen identification.

Um recorte da história do software livre no estado brasileiro: um estudo de caso do programa de software livre do SERPRO

Resumo: Este artigo apresenta resultados de uma pesquisa de mestrado interdisciplinar que buscou compreender como se deu o processo de construção de um software livre por usuários e desenvolvedores de uma empresa estatal brasileira de tecnologia da informação no período de 2003 a 2018, durante o qual vigorou um programa que tinha, entre seus objetivos, o fomento do mercado nacional de software. Como uma das motivações, são apresentados questionamentos sobre a efetividade de projetos estatais de software livre, feitas por Birkinbine (2016), Oram(2016), e representantes do mercado brasileiro de software. Nessa pesquisa, qualitativa, exploratória e descritiva foram utilizados dados primários coletados a partir de um estudo de caso e dados secundários coletados a partir de pesquisa de documentos compilados ou feitos por outros autores. O estudo de caso consistiu de observação direta intensiva pelo instrumento da entrevista. Foram objetos da pesquisa tanto atores humanos (usuários e desenvolvedores) quanto não-humanos (o software selecionado). Para a análise dos resultados foi utilizado o conceito de software livre da Free Software Foundation – FSF e contribuições da Teoria Crítica da Tecnologia de Feenberg(2013). A pesquisa assumiu como premissas a existência de intersecções entre os conjuntos de características do software livre, da economia solidária e da tecnologia social. Nas considerações finais, abordamos contradições encontradas nos discursos favoráveis e contrários à produção de software livre pelo Estado. Os resultados indicaram que entre mais de 800 projetos de software criados pela empresa e classificados por ela como softwares livres, apenas 4 eram softwares livres de acordo com a FSF.&#x0D; Palavras-chave: Economia Solidária. Empresa Estatal. Empresa Pública. Software Livre. Tecnologia Social.

Performance of Fetal Medicine Foundation Software for Pre-Eclampsia Prediction Upon Marker Customization: Cross-Sectional Study.

BackgroundFMF2012 is an algorithm developed by the Fetal Medicine Foundation (FMF) to predict pre-eclampsia on the basis of maternal characteristics combined with biophysical and biochemical markers. Afro-Caribbean ethnicity is the second risk factor, in magnitude, found in populations tested by FMF, which was not confirmed in a Brazilian setting.ObjectiveThis study aimed to analyze the performance of pre-eclampsia prediction software by customization of maternal ethnicity.MethodsThis was a cross-sectional observational study, with secondary evaluation of data from FMF first trimester screening tests of singleton pregnancies. Risk scores were calculated from maternal characteristics and biophysical markers, and they were presented as the risk for early pre-eclampsia (PE34) and preterm pre-eclampsia (PE37). The following steps were followed: (1) identification of women characterized as black ethnicity; (2) calculation of early and preterm pre-eclampsia risk, reclassifying them as white, which generated a new score; (3) comparison of the proportions of women categorized as high risk between the original and new scores; (4) construction of the receiver operator characteristic curve; (5) calculation of the area under the curve, sensitivity, and false positive rate; and (6) comparison of the area under the curve, sensitivity, and false positive rate of the original with the new risk by chi-square test.ResultsA total of 1531 cases were included in the final sample, with 219 out of 1531 cases (14.30; 95% CI 12.5-16.0) and 182 out of 1531 cases (11.88%; 95% CI 10.3-13.5) classified as high risk for pre-eclampsia development, originally and after recalculating the new risk, respectively. The comparison of FMF2012 predictive model performance between the originally estimated risks and the estimated new risks showed that the difference was not significant for sensitivity and area under the curve, but it was significant for false positive rate.ConclusionsWe conclude that black ethnicity classification of Brazilian pregnant women by the FMF2012 algorithm increases the false positive rate. Suppressing ethnicity effect did not improve the test sensitivity. By modifying demographic characteristics, it is possible to improve some performance aspects of clinical prediction tests.

Trustworthy Health-Related Tweets on Social Media in Saudi Arabia: Tweet Metadata Analysis

BackgroundSocial media platforms play a vital role in the dissemination of health information. However, evidence suggests that a high proportion of Twitter posts (ie, tweets) are not necessarily accurate, and many studies suggest that tweets do not need to be accurate, or at least evidence based, to receive traction. This is a dangerous combination in the sphere of health information.ObjectiveThe first objective of this study is to examine health-related tweets originating from Saudi Arabia in terms of their accuracy. The second objective is to find factors that relate to the accuracy and dissemination of these tweets, thereby enabling the identification of ways to enhance the dissemination of accurate tweets. The initial findings from this study and methodological improvements will then be employed in a larger-scale study that will address these issues in more detail.MethodsA health lexicon was used to extract health-related tweets using the Twitter application programming interface and the results were further filtered manually. A total of 300 tweets were each labeled by two medical doctors; the doctors agreed that 109 tweets were either accurate or inaccurate. Other measures were taken from these tweets’ metadata to see if there was any relationship between the measures and either the accuracy or the dissemination of the tweets. The entire range of this metadata was analyzed using Python, version 3.6.5 (Python Software Foundation), to answer the research questions posed.ResultsA total of 34 out of 109 tweets (31.2%) in the dataset used in this study were classified as untrustworthy health information. These came mainly from users with a non-health care background and social media accounts that had no corresponding physical (ie, organization) manifestation. Unsurprisingly, we found that traditionally trusted health sources were more likely to tweet accurate health information than other users. Likewise, these provisional results suggest that tweets posted in the morning are more trustworthy than tweets posted at night, possibly corresponding to official and casual posts, respectively. Our results also suggest that the crowd was quite good at identifying trustworthy information sources, as evidenced by the number of times a tweet’s author was tagged as favorited by the community.ConclusionsThe results indicate some initially surprising factors that might correlate with the accuracy of tweets and their dissemination. For example, the time a tweet was posted correlated with its accuracy, which may reflect a difference between professional (ie, morning) and hobbyist (ie, evening) tweets. More surprisingly, tweets containing a kashida—a decorative element in Arabic writing used to justify the text within lines—were more likely to be disseminated through retweets. These findings will be further assessed using data analysis techniques on a much larger dataset in future work.

Skin Microbiota Perturbations Are Distinct and Disease Severity–Dependent in Hidradenitis Suppurativa

Skin Microbiota Perturbations Are Distinct and Disease Severity–Dependent in Hidradenitis Suppurativa

Pieces of contextual information suitable for predicting co-changes? An empirical study

Models that predict software artifact co-changes have been proposed to assist developers in altering a software system and they often rely on coupling. However, developers have not yet widely adopted these approaches, presumably because of the high number of false recommendations. In this work, we conjecture that the contextual information related to software changes, which is collected from issues (e.g., issue type and reporter), developers’ communication (e.g., number of issue comments, issue discussants and words in the discussion), and commit metadata (e.g., number of lines added, removed, and modified), improves the accuracy of co-change prediction. We built customized prediction models for each co-change and evaluated the approach on 129 releases from a curated set of 10 Apache Software Foundation projects. Comparing our approach with the widely used association rules as a baseline, we found that contextual information models and association rules provide a similar number of co-change recommendations, but our models achieved a significantly higher F-measure. In particular, we found that contextual information significantly reduces the number of false recommendations compared to the baseline model. We conclude that contextual information is an important source for supporting change prediction and may be used to warn developers when they are about to miss relevant artifacts while performing a software change.

Is Requirements-Engineering Research Delivering What It Promised?: A Review of Its Accomplishments and Opportunities After 10 Years

In the 1990s, it was recognized that requirements engineering (RE) laid the foundation for high-quality software. Since then, a substantial research community has formed and set out to enable pract it ioners in the 21st century to systematically adopt proven strategies to solve common development challenges and to enable the engineering of innovative solutions and product features. But is contemporary RE research producing what it set out to deliver? In this article, we provide a brief overview over the accomplishments of the past 10 years and identify open opportunities.

An alliance for biodiversity knowledge: Rethinking international collaboration in biodiversity informatics

There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and non-governmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. The first Global Biodiversity Informatics Conference (GBIC) in 2012 delivered the Global Biodiversity Informatics Outlook (GBIO, Hobern et al. 2012), an architectural vision for the major components of a distributed global infrastructure for biodiiversity information, but realigning the work of existing organisations and projects to achieve this vision remains challenging. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for multiple stakeholders with decentralised funding and independent governance to combine resources and develop sustainable solutions that address common needs. GBIF was asked to coordinate next steps following GBIC2, including publication of a paper, Connecting data and expertise: a new alliance for biodiversity knowledge (Hobern et al. 2019). The supplementary materials for the paper include PDF brochures explaining the concept in eleven languages. During 2019, GBIF is coordinating further consultations to establish an optimal model for the governance and operations of the alliance and to advance collaboration around some of the major building blocks of the GBIO. Collaboration at this scale, and across all aspects of biodiversity information, is essential for effective delivery of important information products such as the Essential Biodiversity Variables and the planned pan-European natural history collections infrastructure, DiSSCo. This presentation explains the goals for this alliance and updates on progress during 2019 in operationalising the concept.