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Standardized Data, Scalable Documentation, Sustainable Storage - EnzymeML as a Basis for FAIR Data Management in Biocatalysis

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CHEMCATCHEM 2021年第18期13卷 3909-3913页

作者： Pleiss, Juergen Univ Stuttgart Inst Biochem & Tech Biochem Allmandring 31 D-70569 Stuttgart Germany

The often reported reproducibility crisis in the biomedical sciences also applies to enzymology and biocatalysis, and mainly results from incomplete reporting of reaction conditions. In this Concept article, an infrastructure based on EnzymeML is sketched, which enables reporting, exchange, and storage of enzymatic data according to the FAIR data principles. EnzymeML is a novel data exchange format for enzymology and biocatalysis, which facilitates the application of the STRENDA Guidelines and thus makes data on enzyme-catalyzed reactions findable, accessible, interoperable, and reusable. EnzymeML enables the comprehensive documentation of metadata, thus fostering reproducibility and replicability in enzymology and biocatalysis. An EnzymeML application programming interface integrates electronic lab notebooks with modelling platforms and databases on enzymatic reactions, and thus enables the seamless flow of enzymatic data from measurement to modelling to publication, without the need for manual intervention such as reformatting or editing. EnzymeML serves as a valuable tool for the design of biocatalytic experiments and contributes to the vision of a unified research data infrastructure for catalysis research.

关键词： application programming interface enzymatic reactions FAIR data principles reproducibility crisis STRENDA Guidelines

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Computed tomography-based automated measurement of abdominal aortic aneurysm using semantic segmentation with active learning

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SCIENTIFIC REPORTS 2024年第1期14卷 1-13页

作者： Kim, Taehun On, Sungchul Gwon, Jun Gyo Kim, Namkug Univ Ulsan Asan Med Inst Convergence Sci & Technol Asan Med Ctr Dept Convergence MedColl Med 88Olympic Ro 43 Gil Seoul 05505 South Korea Korea Inst Sci & Technol Artificial Intelligence & Robot Inst Seoul South Korea Univ Ulsan Asan Med Inst Convergence Sci & Technol Asan Med Ctr Dept Biomed EngnColl Med Seoul South Korea Univ Ulsan Coll Med Asan Med Ctr Div Vasc SurgDept Surg 88Olympic Ro 43 Gil Seoul 05505 South Korea Univ Ulsan Coll Med Asan Med Ctr Dept Radiol Seoul South Korea

Accurate measurement of abdominal aortic aneurysm is essential for selecting suitable stent-grafts to avoid complications of endovascular aneurysm repair. However, the conventional image-based measurements are inaccurate and time-consuming. We introduce the automated workflow including semantic segmentation with active learning (AL) and measurement using an application programming interface of computer-aided design. 300 patients underwent CT scans, and semantic segmentation for aorta, thrombus, calcification, and vessels was performed in 60-300 cases with AL across five stages using UNETR, SwinUNETR, and nnU-Net consisted of 2D, 3D U-Net, 2D-3D U-Net ensemble, and cascaded 3D U-Net. 7 clinical landmarks were automatically measured for 96 patients. In AL stage 5, 3D U-Net achieved the highest dice similarity coefficient (DSC) with statistically significant differences (p < 0.01) except from the 2D-3D U-Net ensemble and cascade 3D U-Net. SwinUNETR excelled in 95% Hausdorff distance (HD95) with significant differences (p < 0.01) except from UNETR and 3D U-Net. DSC of aorta and calcification were saturated at stage 1 and 4, whereas thrombus and vessels were continuously improved at stage 5. The segmentation time between the manual and AL-corrected segmentation using the best model (3D U-Net) was reduced to 9.51 +/- 1.02, 2.09 +/- 1.06, 1.07 +/- 1.10, and 1.07 +/- 0.97 min for the aorta, thrombus, calcification, and vessels, respectively (p < 0.001). All measurement and tortuosity ratio measured - 1.71 +/- 6.53 mm and - 0.15 +/- 0.25. We developed an automated workflow with semantic segmentation and measurement, demonstrating its efficiency compared to conventional methods.

关键词： Abdominal aortic aneurysm Active learning application programming interface Computer-aided design Deep learning Endovascular abdominal repair stent graft

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Enhancing whole building life cycle assessment through building information modelling: Principles and best practices

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ENERGY AND BUILDINGS 2023年第1期296卷

作者： Klumbyte, Egle Georgali, Phoebe-Zoe Spudys, Paulius Giama, Effrosyni Morkunaite, Lina Pupeikis, Darius Jurelionis, Andrius Fokaides, Paris Kaunas Univ Technol Fac Civil Engn & Architecture Kaunas Lithuania Frederick Univ Frederick Res Ctr Sch Engn Nicosia Cyprus Aristotle Univ Thessaloniki Dept Mech Engn Thessaloniki Greece

The building physics research community is facing a challenge in evaluating the sustainability of modern buildings using digital tools and methods. Achieving carbon neutrality, the primary objective of the building industry, requires incorporating Industry 4.0 tools into current building evaluation procedures. To address this need, this research presents an application programming interface (API) designed to facilitate Life Cycle Assessment (LCA) for entire buildings using information from Building Information Modelling (BIM) files. The study outlines the steps involved in developing a BIM-LCA API, including code development and validation with commercial software. The research identifies challenges in creating a uniform database platform for BIM-LCA, and the need for region-specific databases to provide automated material classification for measuring potential environmental consequences. The study also emphasizes the importance of establishing market-level sustainability standards through the development of relevant tools, training techniques, and procedures, and the need for national rating systems to align with these standards to achieve European climate adaptation and circularity goals. The assessment also identifies future challenges in the field and highlights the expected role of the European Union (EU) Level(s) sustainability scheme.

关键词： Building information modelling Life cycle assessment application programming interface Level(s) Industry 4.0

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Conducting smart energy audits of buildings with the use of building information modelling

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ENERGY AND BUILDINGS 2023年 285卷

作者： Spudys, Paulius Jurelionis, Andrius Fokaides, Paris Kaunas Univ Technol Fac Civil Engn & Architecture Student u St 48 LT-51367 Kaunas Lithuania Frederick Univ Sch Engn 7 Y Frederickou St CY-1036 Nicosia Cyprus

Energy audits are an integral part of the overall energy savings strategy in the building sector. The significance of energy audits was confirmed both by their adoption by the European Energy Savings Directive (2012/27) as well as by the development and issuance of a large number of European standards (standard series EN16247, EN 15378, EN 16798, EN 16946, EN 16947 etc.), related to the energy audit of buildings and building systems. However, current practices for conducting energy audits in buildings do not adopt the latest developments in the field of Industry 4.0 practices, resulting in the general belief within the engineering community of building physics that energy auditing can be further updated and improved. This work aims to introduce a novel approach for the improvement of existing building energy audit practices with the adaptation of building information models and associated data. The study presents the potential of evaluation process utilizing building information models for constituent energy audit procedure - assessment of building energy consumption related to building envelope. The question of whether there is room for further adoption of digitization practices in carrying out energy audits, as well as the possibilities of developing new tools in this area are addressed. Following this, the main outcome of this study is the overview and analysis of Industry Foundation Classes schema building information model data structure and its interrelationships with the aim of using the extracted information to digitize energy audit procedures. Research approach covers digitization of building energy consumption assessment influenced by building envelope characteristics, as well as evaluation of economic and energy aspects for possible building shell optimization scenarios. The study also presents the results of a case study evaluation carried out with the developed tool using building envelope modification feature for various environment and economic parame

关键词： Energy audit Building application programming interface Building Information Modelling

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Step Into the Digital Age with Python

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CHEMICAL ENGINEERING PROGRESS 2021年第9期117卷 47-53页

作者： Albrecht, Jacob Sage Bionetworks Benchmarking & Data Challenges Seattle WA 98109 USA

The Python programming language is free, is considered easy to learn, and offers flexibility for nearly any digital task. It is maintained by the nonprofit Python Software Foundation. Python was first released in 1991 as an easy-to-use programming language that would have broad appeal. The language is 30 years old, but Python has seen incredible growth in just the past decade, driven by some key application areas, such as data science and machine learning. Here, Albrecht describes the many ways Python can be used for chemical engineering work in the digital age.

关键词： Language Software Chemical engineering programming languages application programming interface Flexibility Automation Machine learning Popularity Engineers Skills

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kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes

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BMC BIOINFORMATICS 2023年第1期24卷 78-78页

作者： Huckvale, Erik Moseley, Hunter N. B. Univ Kentucky Markey Canc Ctr Lexington KY 40536 USA Univ Kentucky Dept Mol & Cellular Biochem Lexington KY 40536 USA Univ Kentucky Inst Biomed Informat Lexington KY 40536 USA

BackgroundThe Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and knowledge that is reasonably current and highly useful for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be findable, accessible, interoperable, and reusable (FAIR) by providing RESTful access to their database entries via their web-accessible KEGG API. However, the overall FAIRness of KEGG is often limited by the library and software package support available in a given programming language. While R library support for KEGG is fairly strong, Python library support has been lacking. Moreover, there is no software that provides extensive command line level support for KEGG access and *** present kegg_pull, a package implemented in the Python programming language that provides better KEGG access and utilization functionality than previous libraries and software packages. Not only does kegg_pull include an application programming interface (API) for Python programming, it also provides a command line interface (CLI) that enables utilization of KEGG for a wide range of shell scripting and data analysis pipeline use-cases. As kegg_pull's name implies, both the API and CLI provide versatile options for pulling (downloading and saving) an arbitrary (user defined) number of database entries from the KEGG API. Moreover, this functionality is implemented to efficiently utilize multiple central processing unit cores as demonstrated in several performance tests. Many options are provided to optimize fault-tolerant performance across a single or multiple processes, with recommendations provided based on extensive testing and practical network *** new kegg_pull package enables new flexible KEGG retrieval use cases not available in previous software packages. The most notable new feature that kegg_pull provides is its ability to robustly pull an arbitrary number o

关键词： KEGG REST application programming interface Python programming language Command line interface

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Reducing Falls from Heights through BIM: A Dedicated System for Visualizing Safety Standards

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BUILDINGS 2023年第3期13卷 671页

作者： Tariq, Ali Ali, Babar Ullah, Fahim Alqahtani, Fahad K. Politecn Milan Dipartimento Ingn Civile Ambientale Piazza Leonardo Vinci 32 I-20133 Milan Italy Natl Univ Technol NUTECH Civil Engn Dept Islamabad 44000 Pakistan Univ Melbourne Fac Architecture Bldg & Planning Melbourne Vic 3010 Australia Univ Southern Queensland Sch Surveying & Built Environm Springfield Qld 4300 Australia King Saud Univ Coll Engn Dept Civil Engn POB 800 Riyadh 11421 Saudi Arabia

Falls from height (FFH) are common safety hazards on construction sites causing monetary and human loss. Accordingly, ensuring safety at heights is a prerequisite for implementing a strong safety culture in the construction industry. However, despite multiple safety management systems, FFH are still rising, indicating that compliance with safety standards and rules remains low or neglected. Building information modelling (BIM) is used in this study to develop a safety clauses visualization system using Autodesk Revit's application programming interface (API). The prototype digitally stores and views clauses of safety standards, such as the Operational Health and Safety Rules 2022 and Introduction to Health and Safety in Construction by NEBOSH 2008, in the BIM environment. This facilitates the safety manager's ability to ensure that the precautionary measures needed to work at different heights are observed. The developed prototype underwent a focus group evaluation involving nine experts to assess its effectiveness in preventing FFH. It successfully created a comprehensive safety clause library that allows safety managers to provide relevant safety equipment to workers before work execution. It also enhances the awareness of construction workers of all safety requirements vis-a-vis heights. Moreover, it creates a database of safety standards that can be viewed and expanded in future by adding more safety standards to ensure wider applicability.

关键词： falls from height OSHA health and safety in construction BIM application programming interface safety clause

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API Refactoring to Patterns: Catalog, Template and Tools for Remote interface Evolution 23

API Refactoring to Patterns: Catalog, Template and Tools for...

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Proceedings of the 28th European Conference on Pattern Languages of Programs

作者： Mirko Stocker Olaf Zimmermann Institute for Software Eastern Switzerland University of Applied Sciences Switzerland

ISBN: (纸本)9798400700408

Refactoring is an essential agile practice for software evolution. While program-internal code-level refactoring is well established, architecture-level refactoring has been researched but not yet widely adopted in practice. As a result, application programming interface (API) refactoring is not well understood, and practitioners consequently struggle with the evolution of distributed systems using Web APIs and other remoting technologies. To fill this knowledge gap, we propose to apply refactoring to the problem of designing and developing adaptive APIs. This paper introduces an interface Refactoring Catalog (IRC) and presents eight of its refactorings. IRC has been available online since 2021 and collects 22 refactorings at present. Eleven of these patterns leverage Patterns for API Design, originating from our previous work; the remaining ones deal with the number and size of API endpoints and their operations, cover renaming of these API building blocks and message representation elements, and deal with architectural change.

关键词： application programming interface cloud computing design patterns enterprise application integration refactoring

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Development of an Interactive Medical Knowledge Graph Based Tool Set

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Procedia Computer Science 2023年 221卷 578-584页

作者： Xiaowei Xu Xuwen Wang Meng Wu Hetong Ma Liu Shen Jiao Li Institute of Medical Information & Library Chinese Academy of Medical Sciences& Peking Union Medical College Beijing 100020 China Key Laboratory of Medical Information Intelligent Technology Chinese Academy of Medical Sciences Beijing 100020 China

The field of clinical research has reached a turning point in terms of the range and diversity of available data and their potential to improve human health and well-being. However, due to discipline-specific variances in terminology and representation, the data is often compartmentalized, disorganized, and inaccessible to a broad audience. In response to these challenges, we designed and evaluated a pilot knowledge graph-based MedKaaS tool capable of integrating existing clinical datasets and translating those data into insights intended to augment human reasoning and accelerate scientific research. In this paper, we present the architecture and performance of our system, which has been applied to several real-world use cases in collaboration with subject-matter specialists. The MedKaaS Tools are actively developed, with regular updates to performance and features. Our future plans include developing a more user-friendly interface and expanding the visualization capabilities for knowledge exploration.

关键词： knowledge graph visualization application programming interface biomedical data

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Examining the impact of spatial accessibility to rehabilitation facilities on the degree of disability: A heterogeneity perspective

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SSM-POPULATION HEALTH 2023年 23卷 101489页

作者： Qiu, Ning Zhang, Tianjie Cheng, Jianquan Shandong Jianzhu Univ Sch Architecture & Urban Planning Jinan Peoples R China Tianjin Univ Sch Architecture Tianjin Peoples R China Manchester Metropolitan Univ Dept Nat Sci Manchester Lancs England

The positive effect of healthcare facilities on residents' health has been extensively studied. However, few studies have focused on the role of rehabilitation services as unique healthcare services for persons with disabilities. This study aimed to examine the relationship between the spatial accessibility of rehabilitation facilities and the degree of disability. To this end, an approach of measuring the spatial accessibility of rehabilitation facilities to persons with disabilities was proposed. This approach integrates multiple key elements including the characteristics of facilities (i.e., the capacity, frequency of use and service radius), characteristics of the mobility of persons with disabilities (i.e., the mode of travel, escort support, transportation fee and barrier-free environment requirements) and travel time obtained from a routing application programme interface. The accessibility of rehabilitation facilities was calculated at the neighbourhood level within the Central Urban Area of Tianjin Municipality. The ordinal logistic regression analysis revealed that higher accessibility to rehabilitation facilities generally corresponded to lower severity of disability. However, the impact varied depending on the type of disability. Increased accessibility was associated with greater severity of intellectual disability, whereas it was linked to reduced severity of visual, hearing, limb, mental and speech disabilities. It is suggested to incorporate disability diversity and the accessibility of rehabilitation facilities into spatial planning and governance.

关键词： Spatial accessibility of rehabilitation facilities Monetization of travel costs Degree of disability Diversity of disability application programming interface Barrier-free facilities

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