Creating cloud platforms for supporting FAIR data management in biomedical research projects.

Biomedical research projects are becoming increasingly complex and require technological solutions that support all phases of the data lifecycle and application of the FAIR principles. At the Berlin Institute of Health (BIH), we have developed and established a flexible and cost-effective approach to building customized cloud platforms for supporting research projects. The approach is based on a microservice architecture and on the management of a portfolio of supported services. On this basis, we created and maintained cloud platforms for several international research projects. In this article, we present our approach and argue that building customized cloud platforms can offer multiple advantages over using multi-project platforms. Our approach is transferable to other research environments and can be easily adapted by other projects and other service providers.

Integrating Laboratory Testing Results at Point-of-Care in Hospital@Home Care Settings: A FHIR-Based Approach.

The care model Hospital@Home offers hospital-level treatment at home, aiming to alleviate hospital strain and enhance patient comfort. Despite its potential, integrating digital health solutions into this care model still remains limited. This paper proposes a concept for integrating laboratory testing at the Point of Care (POC) into Hospital@Home models to improve efficiency and interoperability. METHODS: Using the HL7 FHIR standard and cloud infrastructure, we developed a concept for direct transmission of laboratory data collected at POC. Requirements were derived from literature and discussions with a POC testing device producer. An architecture for data exchange was developed based on these requirements. RESULTS: Our concept enables access to laboratory data collected at POC, facilitating efficient data transfer and enhancing interoperability. A hypothetical scenario demonstrates the concept's feasibility and benefits, showcasing improved patient care and streamlined processes in Hospital@Home settings. CONCLUSIONS: Integration of POC data into Hospital@Home models using the HL7 FHIR standard and cloud infrastructure offers potential to enhance patient care and streamline processes. Addressing challenges such as data security and privacy is crucial for its successful implementation into practice.

PlasCAT: Plasmid Cloud Assembly Tool.

SUMMARY: PlasCAT (Plasmid Cloud Assembly Tool) is an easy-to-use cloud-based bioinformatics tool that enables de novo plasmid sequence assembly from raw sequencing data. Nontechnical users can now assemble sequences from long reads and short reads without ever touching a line of code. PlasCAT uses high-performance computing servers to reduce run times on assemblies and deliver results faster. AVAILABILITY AND IMPLEMENTATION: PlasCAT is freely available on the web at https://sequencing.genofab.com. The assembly pipeline source code and server code are available for download at https://bitbucket.org/genofabinc/workspace/projects/PLASCAT. Click the Cancel button to access the source code without authenticating. Web servers implemented in React.js and Python, with all major browsers supported.

[Using Cloud Healthcare to Improve Home Learning Efficacy in Congenital Heart Disease Infants].

BACKGROUND: During the COVID-19 pandemic, visitation restrictions in line with infection control policies curtailed opportunities for family members to learn essential caregiving skills in the intensive care unit. This limitation decreased satisfaction among family members, possibly indicating their increased difficulties in care due to the lack of face-to-face guidance. Thus, increasing family member understanding of and ability to apply learning content without direct interaction presents a significant and urgent challenge. Moreover, because of lack of caregiving confidence, some family members may be reluctant to facilitate the discharge of critically ill patients, causing delays in discharge planning. These challenges underscore the obstacles faced by nursing health education during the pandemic. PURPOSE: This study was designed to utilize cloud technology to enhance the knowledge and skills of families caring for infants with congenital heart disease at home and to assess their satisfaction with the associated homecare learning platform. RESOLUTION: Based on our hospital's cloud-based health education platform, a series of personalized instructional video materials was developed for families of infants with congenital heart disease. These materials cover comprehensively the entire treatment process, from diagnosis to post-discharge home care skills, for these patients. To facilitate autonomous learning, the videos in this series were made accessible to the families anytime, anywhere via personal devices such as smartphones and tablets. Concurrently, a chatbot tool was integrated to provide guidance on inpatient care for infants with congenital heart disease, including fundamental aspects of newborn care, with the aim of equipping parents and caregivers with the knowledge and skills necessary to provide basic post-discharge care. To ensure the families acquired personalized care skills, after completing the learning modules, practical bedside training sessions incorporating knowledge and skills assessments were organized for family members. RESULTS: After project implementation, the average knowledge score for family members increased significantly from 79.1 to 100 (perfect score). The proportion of family members proficient in executing caregiving techniques autonomously also rose impressively from 30% to 95%. Furthermore, average overall satisfaction with cloud-based technology-assisted caregiving learning among the family members rose 31.4% from 3.5 to 4.6. CONCLUSIONS: This project represents a viable solution to providing clinical nursing guidance independent of the constraints of time and location, and effectively enhances homecare-skill-related learning outcomes in family members, especially with regard to caring for infants with congenital heart disease.

EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics.

DNA methylation analysis based on supervised machine learning algorithms with static reference data, allowing diagnostic tumour typing with unprecedented precision, has quickly become a new standard of care. Whereas genome-wide diagnostic methylation profiling is mostly performed on microarrays, an increasing number of institutions additionally employ nanopore sequencing as a faster alternative. In addition, methylation-specific parallel sequencing can generate methylation and genomic copy number data. Given these diverse approaches to methylation profiling, to date, there is no single tool that allows (1) classification and interpretation of microarray, nanopore and parallel sequencing data, (2) direct control of nanopore sequencers, and (3) the integration of microarray-based methylation reference data. Furthermore, no software capable of entirely running in routine diagnostic laboratory environments lacking high-performance computing and network infrastructure exists. To overcome these shortcomings, we present EpiDiP/NanoDiP as an open-source DNA methylation and copy number profiling suite, which has been benchmarked against an established supervised machine learning approach using in-house routine diagnostics data obtained between 2019 and 2021. Running locally on portable, cost- and energy-saving system-on-chip as well as gpGPU-augmented edge computing devices, NanoDiP works in offline mode, ensuring data privacy. It does not require the rigid training data annotation of supervised approaches. Furthermore, NanoDiP is the core of our public, free-of-charge EpiDiP web service which enables comparative methylation data analysis against an extensive reference data collection. We envision this versatile platform as a useful resource not only for neuropathologists and surgical pathologists but also for the tumour epigenetics research community. In daily diagnostic routine, analysis of native, unfixed biopsies by NanoDiP delivers molecular tumour classification in an intraoperative time frame.

Securing cloud data using secret key 4 optimization algorithm (SK4OA) with a non-linearity run time trend.

Cloud computing alludes to the on-demand availability of personal computer framework resources, primarily information storage and processing power, without the customer's direct personal involvement. Cloud computing has developed dramatically among many organizations due to its benefits such as cost savings, resource pooling, broad network access, and ease of management; nonetheless, security has been a major concern. Researchers have proposed several cryptographic methods to offer cloud data security; however, their execution times are linear and longer. A Security Key 4 Optimization Algorithm (SK4OA) with a non-linear run time is proposed in this paper. The secret key of SK4OA determines the run time rather than the size of the data as such is able to transmit large volumes of data with minimal bandwidth and able to resist security attacks like brute force since its execution timings are unpredictable. A data set from Kaggle was used to determine the algorithm's mean and standard deviation after thirty (30) times of execution. Data sizes of 3KB, 5KB, 8KB, 12KB, and 16 KB were used in this study. There was an empirical analysis done against RC4, Salsa20, and Chacha20 based on encryption time, decryption time, throughput and memory utilization. The analysis showed that SK4OA generated lowest mean non-linear run time of 5.545±2.785 when 16KB of data was executed. Additionally, SK4OA's standard deviation was greater, indicating that the observed data varied far from the mean. However, RC4, Salsa20, and Chacha20 showed smaller standard deviations making them more clustered around the mean resulting in predictable run times.

Transforming Tele-Ophthalmology: Utilizing Cloud Computing for Remote Eye Care.

BACKGROUND: Tele-ophthalmology is gaining recognition for its role in improving eye care accessibility via cloud-based solutions. The Google Cloud Platform (GCP) Healthcare API enables secure and efficient management of medical image data such as high-resolution ophthalmic images. OBJECTIVES: This study investigates cloud-based solutions' effectiveness in tele-ophthalmology, with a focus on GCP's role in data management, annotation, and integration for a novel imaging device. METHODS: Leveraging the Integrating the Healthcare Enterprise (IHE) Eye Care profile, the cloud platform was utilized as a PACS and integrated with the Open Health Imaging Foundation (OHIF) Viewer for image display and annotation capabilities for ophthalmic images. RESULTS: The setup of a GCP DICOM storage and the OHIF Viewer facilitated remote image data analytics. Prolonged loading times and relatively large individual image file sizes indicated system challenges. CONCLUSION: Cloud platforms have the potential to ease distributed data analytics, as needed for efficient tele-ophthalmology scenarios in research and clinical practice, by providing scalable and secure image management solutions.

A provably lightweight and secure DSSE scheme, with a constant storage cost for a smart device client.

Outsourcing data to remote cloud providers is becoming increasingly popular amongst organizations and individuals. A semi-trusted server uses Searchable Symmetric Encryption (SSE) to keep the search information under acceptable leakage levels whilst searching an encrypted database. A dynamic SSE (DSSE) scheme enables the adding and removing of documents by performing update queries, where some information is leaked to the server each time a record is added or removed. The complexity of structures and cryptographic primitives in most existing DSSE schemes makes them inefficient, in terms of storage, and query requests generate overhead costs on the Smart Device Client (SDC) side. Achieving constant storage cost for SDCs enhances the viability, efficiency, and easy user experience of smart devices, promoting their widespread adoption in various applications while upholding robust privacy and security standards. DSSE schemes must address two important privacy requirements: forward and backward privacy. Due to the increasing number of keywords, the cost of storage on the client side is also increasing at a linear rate. This article introduces an innovative, secure, and lightweight Dynamic Searchable Symmetric Encryption (DSSE) scheme, ensuring Type-II backward and forward privacy without incurring ongoing storage costs and high-cost query generation for the SDC. The proposed scheme, based on an inverted index structure, merges the hash table with linked nodes, linking encrypted keywords in all hash tables. Achieving a one-time O(1) storage cost without keyword counters on the SDC side, the scheme enhances security by generating a fresh key for each update. Experimental results show low-cost query generation on the SDC side (6,460 nanoseconds), making it compatible with resource-limited devices. The scheme outperforms existing ones, reducing server-side search costs significantly.

[Design and Development of ECG Monitoring Cloud Platform Based on the Internet of Things Electrocardiograph].

The design and development of electrocardiogram（ECG） monitoring cloud platform based on the Internet of Things（IoT） electrocardiograph is introduced. The platform is mainly composed of ECG acquisition module, algorithm module, diagnostic model comparison module, warning module, positioning module and medical aid system. The ECG acquisition module collects ECG signals of patients and displays them in real time on the mobile terminals. Then they are uploaded to the ECG monitoring cloud platform through the IoT. The algorithm module and the diagnostic model comparison module mark, process, analyze and diagnose the ECG. Meanwhile, the ECG diagnosis and warning results are pushed to patients and 120 emergency centers through the IoT. Furthermore, the cloud platform will guide patients to self-rescue and the emergency platform will open the green channel to save patients in time.The platform realizes from the onset to diagnosis and treatment in one step, and saves lives against time.

recruIT: A cloud-native clinical trial recruitment support system based on Health Level 7 Fast Healthcare Interoperability Resources (HL7 FHIR) and the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM).

BACKGROUND: Clinical trials (CTs) are foundational to the advancement of evidence-based medicine and recruiting a sufficient number of participants is one of the crucial steps to their successful conduct. Yet, poor recruitment remains the most frequent reason for premature discontinuation or costly extension of clinical trials. METHODS: We designed and implemented a novel, open-source software system to support the recruitment process in clinical trials by generating automatic recruitment recommendations. The development is guided by modern, cloud-native design principles and based on Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) as an interoperability standard with the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) being used as a source of patient data. We evaluated the usability using the system usability scale (SUS) after deploying the application for use by study personnel. RESULTS: The implementation is based on the OMOP CDM as a repository of patient data that is continuously queried for possible trial candidates based on given clinical trial eligibility criteria. A web-based screening list can be used to display the candidates and email notifications about possible new trial participants can be sent automatically. All interactions between services use HL7 FHIR as the communication standard. The system can be installed using standard container technology and supports more sophisticated deployments on Kubernetes clusters. End-users (n = 19) rated the system with a SUS score of 79.9/100. CONCLUSION: We contribute a novel, open-source implementation to support the patient recruitment process in clinical trials that can be deployed using state-of-the art technologies. According to the SUS score, the system provides good usability.

Irrigation intelligence-enabling a cloud-based Internet of Things approach for enhanced water management in agriculture.

Advanced sensor technology, especially those that incorporate artificial intelligence (AI), has been recognized as increasingly important in various contemporary applications, including navigation, automation, water under imaging, environmental monitoring, and robotics. Data-driven decision-making and higher efficiency have enabled more excellent infrastructure thanks to integrating AI with sensors. The agricultural sector is one such area that has seen significant promise from this technology using the Internet of Things (IoT) capabilities. This paper describes an intelligent system for monitoring and analyzing agricultural environmental conditions, including weather, soil, and crop health, that uses internet-connected sensors and equipment. This work makes two significant contributions. It first makes it possible to use sensors linked to the IoT to accurately monitor the environment remotely. Gathering and analyzing data over time may give us valuable insights into daily fluctuations and long-term patterns. The second benefit of AI integration is the remote control; it provides for essential activities like irrigation, pest management, and disease detection. The technology can optimize water usage by tracking plant development and health and adjusting watering schedules accordingly. Intelligent Control Systems (Matlab/Simulink Ver. 2022b) use a hybrid controller that combines fuzzy logic with standard PID control to get high-efficiency performance from water pumps. In addition to monitoring crops, smart cameras allow farmers to make real-time adjustments based on soil moisture and plant needs. Potentially revolutionizing contemporary agriculture, this revolutionary approach might boost production, sustainability, and efficiency.

brainlife.io: a decentralized and open-source cloud platform to support neuroscience research.

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.

SensAA-Design and Verification of a Cloud-Based Wearable Biomechanical Data Acquisition System.

Exoskeletons designed to assist patients with activities of daily living are becoming increasingly popular, but still are subject to research. In order to gather requirements for the design of such systems, long-term gait observation of the patients over the course of multiple days in an environment of daily living are required. In this paper a wearable all-in-one data acquisition system for collecting and storing biomechanical data in everyday life is proposed. The system is designed to be cost efficient and easy to use, using off-the-shelf components and a cloud server system for centralized data storage. The measurement accuracy of the system was verified, by measuring the angle of the human knee joint at walking speeds between 3 and 12 km/h in reference to an optical motion analysis system. The acquired data were uploaded to a cloud database via a smartphone application. Verification results showed that the proposed toolchain works as desired. The system reached an RMSE from 2.9° to 8°, which is below that of most comparable systems. The system provides a powerful, scalable platform for collecting and processing biomechanical data, which can help to automize the generation of an extensive database for human kinematics.

Comparison of attribute-based encryption schemes in securing healthcare systems.

E-health has become a top priority for healthcare organizations focused on advancing healthcare services. Thus, medical organizations have been widely adopting cloud services, resulting in the effective storage of sensitive data. To prevent privacy and security issues associated with the data, attribute-based encryption (ABE) has been a popular choice for encrypting private data. Likewise, the attribute-based access control (ABAC) technique has been widely adopted for controlling data access. Researchers have proposed electronic health record (EHR) systems using ABE techniques like ciphertext policy attribute-based encryption (CP-ABE), key policy attribute-based encryption (KP-ABE), and multi authority attribute-based encryption (MA-ABE). However, there is a lack of rigorous comparison among the various ABE schemes used in healthcare systems. To better understand the usability of ABE techniques in medical systems, we performed a comprehensive review and evaluation of the three popular ABE techniques by developing EHR systems using knowledge graphs with the same data but different encryption mechanisms. We have used the MIMIC-III dataset with varying record sizes for this study. This paper can help healthcare organizations or researchers using ABE in their systems to comprehend the correct usage scenario and the prospect of ABE deployment in the most recent technological evolution.

Secure Cloud-Based Electronic Health Records: Cross-Patient Block-Level Deduplication with Blockchain Auditing.

In today's data-driven world, the exponential growth of digital information poses significant challenges in data management. In recent years, the adoption of cloud-based Electronic Health Records (EHR) sharing schemes has yielded numerous advantages like improved accessibility, availability, and enhanced interoperability. However, the centralized nature of cloud storage presents challenges in terms of information storage, privacy protection, and security. Despite several approaches that have been presented to ensure secure deduplication of similar EHRs, the validation of data integrity without a third-party auditor (TPA) remains a persistent task. Because involving a TPA raises concerns about the confidentiality and privacy of crucial healthcare information. To tackle this challenge, a novel cloud storage auditing technique is proposed that incorporates cross-patient block-level deduplication while upholding strong privacy protection, ensuring that EHR is not compromised. Here, we introduced blockchain technology to achieve integrity verification, thus eliminating the need for a TPA by providing a decentralized and transparent mechanism. Additionally, an index for all EHRs has been generated to facilitate block-level duplicate checks and employ a novel strategy to prevent adversaries from acquiring original information saved in the cloud storage. The security of the proposed approach is established against factorization attacks and decrypt exponent attacks. The performance evaluation demonstrates the superior efficiency of the proposed scheme in terms of file authenticator generation, challenge creation, and proof verification to other existing client-side deduplication approaches.

Colabind: A Cloud-Based Approach for Prediction of Binding Sites Using Coarse-Grained Simulations with Molecular Probes.

Binding site prediction is a crucial step in understanding protein-ligand and protein-protein interactions (PPIs) with broad implications in drug discovery and bioinformatics. This study introduces Colabind, a robust, versatile, and user-friendly cloud-based approach that employs coarse-grained molecular dynamics simulations in the presence of molecular probes, mimicking fragments of drug-like compounds. Our method has demonstrated high effectiveness when validated across a diverse range of biological targets spanning various protein classes, successfully identifying orthosteric binding sites, as well as known druggable allosteric or PPI sites, in both experimentally determined and AI-predicted protein structures, consistently placing them among the top-ranked sites. Furthermore, we suggest that careful inspection of the identified regions with a high affinity for specific probes can provide valuable insights for the development of pharmacophore hypotheses. The approach is available at https://github.com/porekhov/CG_probeMD.

Edge Computing Transformers for Fall Detection in Older Adults.

The global trend of increasing life expectancy introduces new challenges with far-reaching implications. Among these, the risk of falls among older adults is particularly significant, affecting individual health and the quality of life, and placing an additional burden on healthcare systems. Existing fall detection systems often have limitations, including delays due to continuous server communication, high false-positive rates, low adoption rates due to wearability and comfort issues, and high costs. In response to these challenges, this work presents a reliable, wearable, and cost-effective fall detection system. The proposed system consists of a fit-for-purpose device, with an embedded algorithm and an Inertial Measurement Unit (IMU), enabling real-time fall detection. The algorithm combines a Threshold-Based Algorithm (TBA) and a neural network with low number of parameters based on a Transformer architecture. This system demonstrates notable performance with 95.29% accuracy, 93.68% specificity, and 96.66% sensitivity, while only using a 0.38% of the trainable parameters used by the other approach.

The ARIA trial protocol: a randomised controlled trial to assess the clinical, technical, and cost-effectiveness of a cloud-based, ARtificially Intelligent image fusion system in comparison to standard treatment to guide endovascular Aortic aneurysm repair.

BACKGROUND: Endovascular repair of aortic aneurysmal disease is established due to perceived advantages in patient survival, reduced postoperative complications, and shorter hospital lengths of stay. High spatial and contrast resolution 3D CT angiography images are used to plan the procedures and inform device selection and manufacture, but in standard care, the surgery is performed using image-guidance from 2D X-ray fluoroscopy with injection of nephrotoxic contrast material to visualise the blood vessels. This study aims to assess the benefit to patients, practitioners, and the health service of a novel image fusion medical device (Cydar EV), which allows this high-resolution 3D information to be available to operators at the time of surgery. METHODS: The trial is a multi-centre, open label, two-armed randomised controlled clinical trial of 340 patient, randomised 1:1 to either standard treatment in endovascular aneurysm repair or treatment using Cydar EV, a CE-marked medical device comprising of cloud computing, augmented intelligence, and computer vision. The primary outcome is procedural time, with secondary outcomes of procedural efficiency, technical effectiveness, patient outcomes, and cost-effectiveness. Patients with a clinical diagnosis of AAA or TAAA suitable for endovascular repair and able to provide written informed consent will be invited to participate. DISCUSSION: This trial is the first randomised controlled trial evaluating advanced image fusion technology in endovascular aortic surgery and is well placed to evaluate the effect of this technology on patient outcomes and cost to the NHS. TRIAL REGISTRATION: ISRCTN13832085. Dec. 3, 2021.

Compact rover surveying and laser scanning for BIM development.

This paper presents a custom made small rover based surveying, mapping and building information modeling solution. Majority of the commercially available mobile surveying systems are larger in size which restricts their maneuverability in the targeted indoor vicinities. Furthermore their functional cost is unaffordable for low budget projects belonging to developing markets. Keeping in view these challenges, an economical indigenous rover based scanning and mapping system has developed using orthogonal integration of two low cost RPLidar A1 laser scanners. All the instrumentation of the rover has been interfaced with Robot Operating System (ROS) for online processing and recording of all sensorial data. The ROS based pose and map estimations of the rover have performed using Simultaneous Localization and Mapping (SLAM) technique. The perceived class 1 laser scans data belonging to distinct vicinities with variable reflective properties have been successfully tested and validated for required structural modeling. Systematically the recorded scans have been used in offline mode to generate the 3D point cloud map of the surveyed environment. Later the structural planes extraction from the point cloud data has been done using Random Sampling and Consensus (RANSAC) technique. Finally the 2D floor plan and 3D building model have been developed using point cloud processing in appropriate software. Multiple interiors of existing buildings and under construction indoor sites have been scanned, mapped and modelled as presented in this paper. In addition, the validation of the as-built models have been performed by comparing with the actual architecture design of the surveyed buildings. In comparison to available surveying solutions present in the local market, the developed system has been found faster, accurate and user friendly to produce more enhanced structural results with minute details.

NCI Cancer Research Data Commons: Cloud-Based Analytic Resources.

The NCI's Cloud Resources (CR) are the analytical components of the Cancer Research Data Commons (CRDC) ecosystem. This review describes how the three CRs (Broad Institute FireCloud, Institute for Systems Biology Cancer Gateway in the Cloud, and Seven Bridges Cancer Genomics Cloud) provide access and availability to large, cloud-hosted, multimodal cancer datasets, as well as offer tools and workspaces for performing data analysis where the data resides, without download or storage. In addition, users can upload their own data and tools into their workspaces, allowing researchers to create custom analysis workflows and integrate CRDC-hosted data with their own. See related articles by Brady et al., p. 1384, Wang et al., p. 1388, and Kim et al., p. 1404.