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in Architecture & Planning
Periodicals

Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.

Architecture & Planning• 2013• Public Library of Science
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Periodicals

Blockchain-Based Agri-Food Supply Chain: A Complete Solution

Supply chains are evolving into automated and highly complex networks and are becoming an important source of potential benefits in the modern world. At the same time, consumers are now more interested in food product quality. However, it is challenging to track the provenance of data and maintain its traceability throughout the supply chain network. The traditional supply chains are centralized and they depend on a third party for trading. These centralized systems lack transparency, accountability and auditability. In our proposed solution, we have presented a complete solution for blockchain-based Agriculture and Food (Agri-Food) supply chain. It leverages the key features of blockchain and smart contracts, deployed over ethereum blockchain network. Although blockchain provides immutability of data and records in the network, it still fails to solve some major problems in supply chain management like credibility of the involved entities, accountability of the trading process and traceability of the products. Therefore, there is a need of a reliable system that ensures traceability, trust and delivery mechanism in Agri-Food supply chain. In the proposed system, all transactions are written to blockchain which ultimately uploads the data to Interplanetary File Storage System (IPFS). The storage system returns a hash of the data which is stored on blockchain and ensures efficient, secure and reliable solution. Our system provides smart contracts along with their algorithms to show interaction of entities in the system. Furthermore, simulations and evaluation of smart contracts along with the security and vulnerability analyses are also presented in this work.

Architecture & Planning• 2020• Institute of Electrical and Electronics Engineers
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Periodicals

Overview of the PALM model system 6.0

Abstract. In this paper, we describe the PALM model system 6.0. PALM (formerly an abbreviation for Parallelized Large-eddy Simulation Model and now an independent name) is a Fortran-based code and has been applied for studying a variety of atmospheric and oceanic boundary layers for about 20 years. The model is optimized for use on massively parallel computer architectures. This is a follow-up paper to the PALM 4.0 model description in Maronga et al. (2015). During the last years, PALM has been significantly improved and now offers a variety of new components. In particular, much effort was made to enhance the model with components needed for applications in urban environments, like fully interactive land surface and radiation schemes, chemistry, and an indoor model. This paper serves as an overview paper of the PALM 6.0 model system and we describe its current model core. The individual components for urban applications, case studies, validation runs, and issues with suitable input data are presented and discussed in a series of companion papers in this special issue.

Architecture & Planning• 2020• Copernicus Publications
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Periodicals

Predictive Maintenance and Intelligent Sensors in Smart Factory: Review

With the arrival of new technologies in modern smart factories, automated predictive maintenance is also related to production robotisation. Intelligent sensors make it possible to obtain an ever-increasing amount of data, which must be analysed efficiently and effectively to support increasingly complex systems' decision-making and management. The paper aims to review the current literature concerning predictive maintenance and intelligent sensors in smart factories. We focused on contemporary trends to provide an overview of future research challenges and classification. The paper used burst analysis, systematic review methodology, co-occurrence analysis of keywords, and cluster analysis. The results show the increasing number of papers related to key researched concepts. The importance of predictive maintenance is growing over time in relation to Industry 4.0 technologies. We proposed Smart and Intelligent Predictive Maintenance (SIPM) based on the full-text analysis of relevant papers. The paper's main contribution is the summary and overview of current trends in intelligent sensors used for predictive maintenance in smart factories.

Architecture & Planning• 2021• Multidisciplinary Digital Publishing Institute
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Periodicals

Multimodal Brain Tumor Classification Using Deep Learning and Robust Feature Selection: A Machine Learning Application for Radiologists

Manual identification of brain tumors is an error-prone and tedious process for radiologists; therefore, it is crucial to adopt an automated system. The binary classification process, such as malignant or benign is relatively trivial; whereas, the multimodal brain tumors classification (T1, T2, T1CE, and Flair) is a challenging task for radiologists. Here, we present an automated multimodal classification method using deep learning for brain tumor type classification. The proposed method consists of five core steps. In the first step, the linear contrast stretching is employed using edge-based histogram equalization and discrete cosine transform (DCT). In the second step, deep learning feature extraction is performed. By utilizing transfer learning, two pre-trained convolutional neural network (CNN) models, namely VGG16 and VGG19, were used for feature extraction. In the third step, a correntropy-based joint learning approach was implemented along with the extreme learning machine (ELM) for the selection of best features. In the fourth step, the partial least square (PLS)-based robust covariant features were fused in one matrix. The combined matrix was fed to ELM for final classification. The proposed method was validated on the BraTS datasets and an accuracy of 97.8%, 96.9%, 92.5% for BraTs2015, BraTs2017, and BraTs2018, respectively, was achieved.

Architecture & Planning• 2020• Multidisciplinary Digital Publishing Institute
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Networks and the Epidemiology of Infectious Disease

The science of networks has revolutionised research into the dynamics of interacting elements. It could be argued that epidemiology in particular has embraced the potential of network theory more than any other discipline. Here we review the growing body of research concerning the spread of infectious diseases on networks, focusing on the interplay between network theory and epidemiology. The review is split into four main sections, which examine: the types of network relevant to epidemiology; the multitude of ways these networks can be characterised; the statistical methods that can be applied to infer the epidemiological parameters on a realised network; and finally simulation and analytical methods to determine epidemic dynamics on a given network. Given the breadth of areas covered and the ever-expanding number of publications, a comprehensive review of all work is impossible. Instead, we provide a personalised overview into the areas of network epidemiology that have seen the greatest progress in recent years or have the greatest potential to provide novel insights. As such, considerable importance is placed on analytical approaches and statistical methods which are both rapidly expanding fields. Throughout this review we restrict our attention to epidemiological issues.

Architecture & Planning• 2010• Lancaster University
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Periodicals

Flourishing in nature: A review of the benefits of connecting with nature and its application as a wellbeing intervention

From the increasing number of people living in urban areas to the continued degradation of the natural environment, many of us appear to be physically and psychologically disconnected from nature. We consider the theoretical explanations and present evidence for why this state of affairs might result in suboptimal levels of hedonic and eudaimonic wellbeing by reviewing the large body of research on the mental health benefits of connecting with nature. The advantages of contact with nature as a potential wellbeing intervention are discussed, and examples of how this research is being applied to reconnect individuals to nature and improve wellbeing are given. We conclude by considering the limitations of, and proposing future directions for, research in this area. Overall, evidence suggests that connecting with nature is one path to flourishing in life.

Architecture & Planning• 2015• International Journal of Wellbeing
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Periodicals

Latin American Squatter Settlements: A Problem and a Solution

Squatter settlements have formed around large cities throughout the world, mushrooming particularly since the end of World War II. In an excellent preview to a forthcoming book, Turner (1966) has discussed some common features among squatter settlements in Latin America, Asia, Africa, and Europe. Morse (1965a) has also referred to squatter communities and to general characteristics of Latin American urbanization in an article in this journal. Without repeating the work of Turner and Morse I would like to present a preliminary survey of Latin American squatter settlements with a model of their formation, growth, and social development that contradicts many views held by planners, politicians, newspapermen, and much of the general population, including many residents of the settlements themselves. Several writers have referred to various local names given to squatter communities: colonies proletarias in Mexico, barriadas brujas in Panama, ranchos in Venezuela, barriadas in Peru, callampas in Chile, cantegriles in Uruguay, favelas in Brazil, and, in other places, marginal areas, clandestine urbanizations, barrios of invasion, parachutists, phantom towns, etc. There are no general works on the subject, but some good descriptions of local conditions do exist. The major sources used are listed by country in note 2. Not many sources are available and, unfortunately, several appear only in mimeographed form. The reports point out that squatter populations consist mainly of low income families but all of the authors distinguish between squatter settlements and other types of lower class housing in tenements, alleys (callejones), shack yards tcoralones, jacales), and rented slum buildings. They agree, sometimes to their own surprise, that it is difficult to describe squatter settlements as slums. The differentiation of squatter settlements from inner-city slums is, in fact, one of the first breaks from the widely shared mythology about them. (See, for example, Patch, 1961; Mangin, 1965.) The purpose in noting this mythology is not merely to set up a straw man for the paper. A review of the “Chaos, Crisis, Revolution and Wither Now Latin America” literature, or, of most governmental, United Nations, or AID reports, or, of most newspapers and magazines in Latin America will show that it is the predominant position on squatter settlements.

Architecture & Planning• 1967• Cambridge University Press
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Periodicals

Triple Negative Breast Cancer Treatment Options and Limitations: Future Outlook

Triple negative breast cancer (TNBC) has a negative expression of estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptors (HER2). The survival rate for TNBC is generally worse than other breast cancer subtypes. TNBC treatment has made significant advances, but certain limitations remain. Treatment for TNBC can be challenging since the disease has various molecular subtypes. A variety of treatment options are available, such as chemotherapy, immunotherapy, radiotherapy, and surgery. Chemotherapy is the most common of these options. TNBC is generally treated with systemic chemotherapy using drugs such as anthracyclines and taxanes in neoadjuvant or adjuvant settings. Developing resistance to anticancer drugs and off-target toxicity are the primary hindrances to chemotherapeutic solutions for cancer. It is imperative that researchers, clinicians, and pharmaceutical companies work together to develop effective treatment options for TNBC. Several studies have suggested nanotechnology as a potential solution to the problem of suboptimal TNBC treatment. In this review, we summarized possible treatment options for TNBC, including chemotherapy, immunotherapy, targeted therapy, combination therapy, and nanoparticle-based therapy, and some solutions for the treatment of TNBC in the future. Moreover, we gave general information about TNBC in terms of its characteristics and aggressiveness.

Architecture & Planning• 2023• Multidisciplinary Digital Publishing Institute
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Periodicals

Revolution 4.0: Industry vs. Agriculture in a Future Development for SMEs

The present review retraces the steps of the industrial and agriculture revolution that have taken place up to the present day, giving ideas and considerations for the future. This paper analyses the specific challenges facing agriculture along the farming supply chain to permit the operative implementation of Industry 4.0 guidelines. The subsequent scientific value is an investigation of how Industry 4.0 approaches can be improved and be pertinent to the agricultural sector. However, industry is progressing at a much faster rate than agriculture. In fact, already today experts talk about Industry 5.0. On the other hand, the 4.0 revolution in agriculture is still limited to a few innovative firms. For this reason, this work deals with how technological development affects different sectors (industry and agriculture) in different ways. In this innovative background, despite the advantages of industry or agriculture 4.0 for large enterprises, small- and medium-sized enterprises (SMEs) often face complications in such innovative processes due to the continuous development in innovations and technologies. Policy makers should propose strategies, calls for proposals with aim of supporting SMEs to invest on these technologies and making them more competitive in the marketplace.

Architecture & Planning• 2019• Multidisciplinary Digital Publishing Institute
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Systemic resilience: principles and processes for a science of change in contexts of adversity

Despite the increasing popularity of discussions of resilience in disciplines as diverse as ecology, psychology, economics, architecture, and genetics (among many others), researchers still lack a conceptual model to explain how the resilience of one system relates to the resilience of other cooccurring systems. Models that explain resilience within a single system are more robust and better studied. Although some researchers argue that both ontological and epistemological weaknesses prevent such an integrated model from being developed (the incommensurability hypothesis), others have carried out metasyntheses using techniques like network citation analysis to identify common principles and processes that are associated with resilience across disciplines. Although useful, metasyntheses have yet to identify sufficient commonalities across bodies of research to account for a single model of resilience. This paper adapts methods used for the thematic synthesis of qualitative data to critically analyze metasyntheses of resilience and identify principles that explain patterns of resilience of different systems (biological, psychological, social, cultural, economic, legal, communication, and ecological systems are all considered). Sixteen purposefully selected published syntheses were reviewed, along with dozens of other supporting peer-reviewed articles and book chapters, supplemented by consultations with knowledge experts. Seven common principles across systems were identified. These include: (1) resilience occurs in contexts of adversity; (2) resilience is a process; (3) there are trade-offs between systems when a system experiences resilience; (4) a resilient system is open, dynamic, and complex; (5) a resilient system promotes connectivity; (6) a resilient system demonstrates experimentation and learning; and (7) a resilient system includes diversity, redundancy, and participation. Where evidence refutes a principle, discordant findings are highlighted. Together, these principles account for resilience as a sequence of systemic interdependent interactions through which actors (whether persons, organisms, or ecosystems) secure the resources required for sustainability in stressed environments.

Architecture & Planning• 2018• Resilience Alliance
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A Survey of Multi-Objective Optimization in Wireless Sensor Networks: Metrics, Algorithms, and Open Problems

Wireless sensor networks (WSNs) have attracted substantial research interest, especially in the context of performing monitoring and surveillance tasks. However, it is challenging to strike compelling tradeoffs amongst the various conflicting optimization criteria, such as the network's energy dissipation, packet-loss rate, coverage, and lifetime. This paper provides a tutorial and survey of recent research and development efforts addressing this issue by using the technique of multi-objective optimization (MOO). First, we provide an overview of the main optimization objectives used in WSNs. Then, we elaborate on various prevalent approaches conceived for MOO, such as the family of mathematical programming-based scalarization methods, the family of heuristics/metaheuristics-based optimization algorithms, and a variety of other advanced optimization techniques. Furthermore, we summarize a range of recent studies of MOO in the context of WSNs, which are intended to provide useful guidelines for researchers to understand the referenced literature. Finally, we discuss a range of open problems to be tackled by future research.

Architecture & Planning• 2016• Institute of Electrical and Electronics Engineers
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Genetic Architecture of Complex Traits and Accuracy of Genomic Prediction: Coat Colour, Milk-Fat Percentage, and Type in Holstein Cattle as Contrasting Model Traits

Prediction of genetic merit using dense SNP genotypes can be used for estimation of breeding values for selection of livestock, crops, and forage species; for prediction of disease risk; and for forensics. The accuracy of these genomic predictions depends in part on the genetic architecture of the trait, in particular number of loci affecting the trait and distribution of their effects. Here we investigate the difference among three traits in distribution of effects and the consequences for the accuracy of genomic predictions. Proportion of black coat colour in Holstein cattle was used as one model complex trait. Three loci, KIT, MITF, and a locus on chromosome 8, together explain 24% of the variation of proportion of black. However, a surprisingly large number of loci of small effect are necessary to capture the remaining variation. A second trait, fat concentration in milk, had one locus of large effect and a host of loci with very small effects. Both these distributions of effects were in contrast to that for a third trait, an index of scores for a number of aspects of cow confirmation ("overall type"), which had only loci of small effect. The differences in distribution of effects among the three traits were quantified by estimating the distribution of variance explained by chromosome segments containing 50 SNPs. This approach was taken to account for the imperfect linkage disequilibrium between the SNPs and the QTL affecting the traits. We also show that the accuracy of predicting genetic values is higher for traits with a proportion of large effects (proportion black and fat percentage) than for a trait with no loci of large effect (overall type), provided the method of analysis takes advantage of the distribution of loci effects.

Architecture & Planning• 2010• Public Library of Science
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Periodicals

Jointly Learning Heterogeneous Features for RGB-D Activity Recognition

In this paper, we focus on heterogeneous features learning for RGB-D activity recognition. We find that features from different channels (RGB, depth) could share some similar hidden structures, and then propose a joint learning model to simultaneously explore the shared and feature-specific components as an instance of heterogeneous multi-task learning. The proposed model formed in a unified framework is capable of: 1) jointly mining a set of subspaces with the same dimensionality to exploit latent shared features across different feature channels, 2) meanwhile, quantifying the shared and feature-specific components of features in the subspaces, and 3) transferring feature-specific intermediate transforms (i-transforms) for learning fusion of heterogeneous features across datasets. To efficiently train the joint model, a three-step iterative optimization algorithm is proposed, followed by a simple inference model. Extensive experimental results on four activity datasets have demonstrated the efficacy of the proposed method. A new RGB-D activity dataset focusing on human-object interaction is further contributed, which presents more challenges for RGB-D activity benchmarking.

Architecture & Planning• 2016• IEEE Computer Society
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Fruit recognition from images using deep learning

In this paper we introduce a new, high-quality, dataset of images containing fruits. We also present the results of some numerical experiment for training a neural network to detect fruits. We discuss the reason why we chose to use fruits in this project by proposing a few applications that could use such classifier.

Architecture & Planning• 2018
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Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations

Recent advances in scanning transmission electron and scanning probe microscopies have opened exciting opportunities in probing the materials structural parameters and various functional properties in real space with angstrom-level precision. This progress has been accompanied by an exponential increase in the size and quality of data sets produced by microscopic and spectroscopic experimental techniques. These developments necessitate adequate methods for extracting relevant physical and chemical information from the large data sets, for which a priori information on the structures of various atomic configurations and lattice defects is limited or absent. Here we demonstrate an application of deep neural networks to extract information from atomically resolved images including location of the atomic species and type of defects. We develop a "weakly supervised" approach that uses information on the coordinates of all atomic species in the image, extracted via a deep neural network, to identify a rich variety of defects that are not part of an initial training set. We further apply our approach to interpret complex atomic and defect transformation, including switching between different coordination of silicon dopants in graphene as a function of time, formation of peculiar silicon dimer with mixed 3-fold and 4-fold coordination, and the motion of molecular "rotor". This deep learning-based approach resembles logic of a human operator, but can be scaled leading to significant shift in the way of extracting and analyzing information from raw experimental data.

Architecture & Planning• 2017• American Chemical Society
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Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data

Artificial neural networks (ANN) are computing architectures with many interconnections of simple neural-inspired computing elements, and have been applied to biomedical fields such as imaging analysis and diagnosis. We have developed a new ANN framework called Cox-nnet to predict patient prognosis from high throughput transcriptomics data. In 10 TCGA RNA-Seq data sets, Cox-nnet achieves the same or better predictive accuracy compared to other methods, including Cox-proportional hazards regression (with LASSO, ridge, and mimimax concave penalty), Random Forests Survival and CoxBoost. Cox-nnet also reveals richer biological information, at both the pathway and gene levels. The outputs from the hidden layer node provide an alternative approach for survival-sensitive dimension reduction. In summary, we have developed a new method for accurate and efficient prognosis prediction on high throughput data, with functional biological insights. The source code is freely available at https://github.com/lanagarmire/cox-nnet.

Architecture & Planning• 2018• Public Library of Science
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Implementation of a MIMO OFDM-Based Wireless LAN System

The combination of multiple-input multiple-output (MIMO) signal processing with orthogonal frequency division multiplexing (OFDM) is regarded as a promising solution for enhancing the data rates of next-generation wireless communication systems operating in frequency-selective fading environments. To realize this extension of OFDM with MIMO, a number of changes are required in the baseband signal processing. An overview is given of the necessary changes, including time and frequency synchronization, channel estimation, synchronization tracking, and MIMO detection. As a test case, the OFDM-based wireless local area network (WLAN) standard IEEE 802.11a is considered, but the results are applicable more generally. The complete MIMO OFDM processing is implemented in a system with three transmit and three receive antennas, and its performance is evaluated with both simulations and experimental test results. Results from measurements with this MIMO OFDM system in a typical office environment show, on average, a doubling of the system throughput, compared with a single antenna OFDM system. An average expected tripling of the throughput was most likely not achieved due to coupling between the transmitter and receiver branches.

Architecture & Planning• 2004• Institute of Electrical and Electronics Engineers
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A Survey on Technologies, Standards and Open Challenges in Satellite IoT

The Internet of Things (IoT) is expected to bring new opportunities for improving several services for the Society, from transportation to agriculture, from smart cities to fleet management. In this framework, massive connectivity represents one of the key issues. This is especially relevant when IoT systems are expected to cover a large geographical area or a region not reached by terrestrial network connections. In such scenarios, the usage of satellites might represent a viable solution for providing wide area coverage and connectivity in a flexible and affordable manner. Our paper presents a survey on current solutions for the deployment of IoT services in remote/rural areas by exploiting satellites. Several architectures and technical solutions are analyzed, underlining their features and limitations, and real test cases are presented. It has been highlighted that low-orbit satellites offer an efficient solution to support long-range IoT services, with a good trade-off in terms of coverage and latency. Moreover, open issues, new challenges, and innovative technologies have been focused, carefully considering the perimeter that current IoT standardization framework will impose to the practical implementation of future satellite based IoT systems.

Architecture & Planning• 2021• Institute of Electrical and Electronics Engineers
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The Importance of Respiratory Rate Monitoring: From Healthcare to Sport and Exercise

Respiratory rate is a fundamental vital sign that is sensitive to different pathological conditions (e.g., adverse cardiac events, pneumonia, and clinical deterioration) and stressors, including emotional stress, cognitive load, heat, cold, physical effort, and exercise-induced fatigue. The sensitivity of respiratory rate to these conditions is superior compared to that of most of the other vital signs, and the abundance of suitable technological solutions measuring respiratory rate has important implications for healthcare, occupational settings, and sport. However, respiratory rate is still too often not routinely monitored in these fields of use. This review presents a multidisciplinary approach to respiratory monitoring, with the aim to improve the development and efficacy of respiratory monitoring services. We have identified thirteen monitoring goals where the use of the respiratory rate is invaluable, and for each of them we have described suitable sensors and techniques to monitor respiratory rate in specific measurement scenarios. We have also provided a physiological rationale corroborating the importance of respiratory rate monitoring and an original multidisciplinary framework for the development of respiratory monitoring services. This review is expected to advance the field of respiratory monitoring and favor synergies between different disciplines to accomplish this goal.

Architecture & Planning• 2020• Multidisciplinary Digital Publishing Institute
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