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We present a survey of the current state-of-the-art in breast cancer detection and prognosis. We analyze the evolution of Artificial Intelligence-based approaches from using just uni-modal information to multi-modality for detection and how such paradigm shift facilitates the efficacy of detection, consistent with clinical observations. We conclude that interpretable AI-based predictions and ability to handle class imbalance should be considered priority., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Background: Microorganisms inhabit various regions of the human body and significantly contribute to numerous diseases. Predicting the associations between microbes and diseases is crucial for understanding pathogenic mechanisms and informing prevention and treatment strategies. Biological experiments to determine these associations are time-consuming and costly. Therefore, integrating deep learning with biological networks can efficiently identify potential microbe-disease associations on a large scale., Methods: We propose an adversarial regularized autoencoder graph neural network algorithm, named Stacked Adversarial Regularization for Microbe-Disease Associations Prediction (SARMDA), for predicting associations between microbes and diseases. First, we integrate topological structural similarity and functional similarity metrics of microbes and diseases to construct a heterogeneous network. Then, utilizing an autoencoder based on GraphSAGE, we learn both the topological and attribute representations of nodes within the constructed network. Finally, we introduce an adversarial regularized autoencoder graph neural network embedding model to address the inherent limitations of traditional GraphSAGE autoencoders in capturing global information., Results: Under the five-fold cross-validation on microbe-disease pairs, SARMDA was compared with eight advanced methods using the Human Microbe-Disease Association Database (HMDAD) and Disbiome databases. The best area under the ROC curve (AUC) achieved by SARMDA on HMDAD was 0.9891$\pm$0.0057, and the best area under the precision-recall curve (AUPR) was 0.9902$\pm$0.0128. On the Disbiome dataset, the AUC was 0.9328$\pm$0.0072, and the best AUPR was 0.9233$\pm$0.0089, outperforming the other eight MDAs prediction methods. Furthermore, the effectiveness of our model was demonstrated through a detailed analysis of asthma and inflammatory bowel disease cases., (© The Author(s) 2024. Published by Oxford University Press.)

High-throughput screening rapidly tests an extensive array of chemical compounds to identify hit compounds for specific biological targets in drug discovery. However, false-positive results disrupt hit compound screening, leading to wastage of time and resources. To address this, we propose ChemFH, an integrated online platform facilitating rapid virtual evaluation of potential false positives, including colloidal aggregators, spectroscopic interference compounds, firefly luciferase inhibitors, chemical reactive compounds, promiscuous compounds, and other assay interferences. By leveraging a dataset containing 823 391 compounds, we constructed high-quality prediction models using multi-task directed message-passing network (DMPNN) architectures combining uncertainty estimation, yielding an average AUC value of 0.91. Furthermore, ChemFH incorporated 1441 representative alert substructures derived from the collected data and ten commonly used frequent hitter screening rules. ChemFH was validated with an external set of 75 compounds. Subsequently, the virtual screening capability of ChemFH was successfully confirmed through its application to five virtual screening libraries. Furthermore, ChemFH underwent additional validation on two natural products and FDA-approved drugs, yielding reliable and accurate results. ChemFH is a comprehensive, reliable, and computationally efficient screening pipeline that facilitates the identification of true positive results in assays, contributing to enhanced efficiency and success rates in drug discovery. ChemFH is freely available via https://chemfh.scbdd.com/., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Pseudouridine is an RNA modification that is widely distributed in both prokaryotes and eukaryotes, and plays a critical role in numerous biological activities. Despite its importance, the precise identification of pseudouridine sites through experimental approaches poses significant challenges, requiring substantial time and resources.Therefore, there is a growing need for computational techniques that can reliably and quickly identify pseudouridine sites from vast amounts of RNA sequencing data. In this study, we propose fuzzy kernel evidence Random Forest (FKeERF) to identify pseudouridine sites. This method is called PseU-FKeERF, which demonstrates high accuracy in identifying pseudouridine sites from RNA sequencing data. The PseU-FKeERF model selected four RNA feature coding schemes with relatively good performance for feature combination, and then input them into the newly proposed FKeERF method for category prediction. FKeERF not only uses fuzzy logic to expand the original feature space, but also combines kernel methods that are easy to interpret in general for category prediction. Both cross-validation tests and independent tests on benchmark datasets have shown that PseU-FKeERF has better predictive performance than several state-of-the-art methods. This new method not only improves the accuracy of pseudouridine site identification, but also provides a certain reference for disease control and related drug development in the future., (© The Author(s) 2024. Published by Oxford University Press.)

Objectives: Diffusion-weighted MRI (DWI) may provide biologically relevant target volumes for dose-escalated radiotherapy in locally advanced rectal cancer (LARC). This planning study assessed the dosimetric feasibility of delivering hypofractionated boost treatment to intra-tumoural regions of restricted diffusion prior to conventional long-course radiotherapy., Methods: Ten patients previously treated with curative-intent standard long-course radiotherapy (50 Gy/25#) were re-planned. Boost target volumes ( BTVs ) were delineated semi-automatically using 40th centile intra-tumoural apparent diffusion coefficient value with expansions (anteroposterior 11 mm, transverse 7 mm, craniocaudal 13 mm). Biased-dosed combined plans consisted of a single-fraction volumetric modulated arc therapy flattening-filter-free (VMAT-FFF) boost (phase 1) of 5, 7, or 10 Gy before long-course VMAT (phase 2). Phase 1 plans were assessed with reference to stereotactic conformality and deliverability measures. Combined plans were evaluated with reference to standard long-course therapy dose constraints., Results: Phase 1 BTV dose targets at 5/7/10 Gy were met in all instances. Conformality constraints were met with only 1 minor violation at 5 and 7 Gy. All phase 1 and combined phase 1 + 2 plans passed patient-specific quality assurance. Combined phase 1 + 2 plans generally met organ-at-risk dose constraints. Exceptions included high-dose spillage to bladder and large bowel, predominantly in cases where previously administered, clinically acceptable non-boosted plans also could not meet constraints., Conclusions: Targeted upfront LARC radiotherapy dose escalation to DWI-defined is feasible with appropriate patient selection and preparation., Advances in Knowledge: This is the first study to evaluate the feasibility of DWI-targeted upfront radiotherapy boost in LARC. This work will inform an upcoming clinical feasibility study., Competing Interests: None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of the British Institute of Radiology.)

Background: During pre-travel consultations, clinicians and travellers face the challenge of weighing the risks verus benefits of Japanese encephalitis (JE) vaccination due to the high cost of the vaccine, low incidence in travellers (~1 in 1 million), but potentially severe consequences (~30% case-fatality rate). Personalised JE risk assessment based on the travellers' demographics and travel itinerary is challenging using standard risk matrices. We developed an interactive digital tool to estimate risks of JE infection and severe health outcomes under different scenarios to facilitate shared decision-making between clinicians and travellers., Methods: A Bayesian network (conditional probability) model risk-benefit analysis of JE vaccine in travellers was developed. The model considers travellers' characteristics (age, sex, co-morbidities), itinerary (destination, departure date, duration, setting of planned activities) and vaccination status to estimate the risks of JE infection, the development of symptomatic disease (meningitis, encephalitis), clinical outcomes (hospital admission, chronic neurological complications, death) and adverse events following immunization., Results: In low-risk travellers (e.g. to urban areas for <1 month), the risk of developing JE and dying is low (<1 per million) irrespective of the destination; thus, the potential impact of JE vaccination in reducing the risk of clinical outcomes is limited. In high-risk travellers (e.g. to rural areas in high JE incidence destinations for >2 months), the risk of developing symptomatic disease and mortality is estimated at 9.5 and 1.4 per million, respectively. JE vaccination in this group would significantly reduce the risk of symptomatic disease and mortality (by ~80%) to 1.9 and 0.3 per million, respectively., Conclusion: The JE tool may assist decision-making by travellers and clinicians and could increase JE vaccine uptake. The tool will be updated as additional evidence becomes available. Future work needs to evaluate the usability of the tool. The interactive, scenario-based, personalised JE vaccine risk-benefit tool is freely available on www.VaxiCal.com., (© International Society of Travel Medicine 2023. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Objective: To derive a comprehensive implementation framework for clinical AI models within hospitals informed by existing AI frameworks and integrated with reporting standards for clinical AI research., Materials and Methods: (1) Derive a provisional implementation framework based on the taxonomy of Stead et al and integrated with current reporting standards for AI research: TRIPOD, DECIDE-AI, CONSORT-AI. (2) Undertake a scoping review of published clinical AI implementation frameworks and identify key themes and stages. (3) Perform a gap analysis and refine the framework by incorporating missing items., Results: The provisional AI implementation framework, called SALIENT, was mapped to 5 stages common to both the taxonomy and the reporting standards. A scoping review retrieved 20 studies and 247 themes, stages, and subelements were identified. A gap analysis identified 5 new cross-stage themes and 16 new tasks. The final framework comprised 5 stages, 7 elements, and 4 components, including the AI system, data pipeline, human-computer interface, and clinical workflow., Discussion: This pragmatic framework resolves gaps in existing stage- and theme-based clinical AI implementation guidance by comprehensively addressing the what (components), when (stages), and how (tasks) of AI implementation, as well as the who (organization) and why (policy domains). By integrating research reporting standards into SALIENT, the framework is grounded in rigorous evaluation methodologies. The framework requires validation as being applicable to real-world studies of deployed AI models., Conclusions: A novel end-to-end framework has been developed for implementing AI within hospital clinical practice that builds on previous AI implementation frameworks and research reporting standards., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

Objective: To retrieve and appraise studies of deployed artificial intelligence (AI)-based sepsis prediction algorithms using systematic methods, identify implementation barriers, enablers, and key decisions and then map these to a novel end-to-end clinical AI implementation framework., Materials and Methods: Systematically review studies of clinically applied AI-based sepsis prediction algorithms in regard to methodological quality, deployment and evaluation methods, and outcomes. Identify contextual factors that influence implementation and map these factors to the SALIENT implementation framework., Results: The review identified 30 articles of algorithms applied in adult hospital settings, with 5 studies reporting significantly decreased mortality post-implementation. Eight groups of algorithms were identified, each sharing a common algorithm. We identified 14 barriers, 26 enablers, and 22 decision points which were able to be mapped to the 5 stages of the SALIENT implementation framework., Discussion: Empirical studies of deployed sepsis prediction algorithms demonstrate their potential for improving care and reducing mortality but reveal persisting gaps in existing implementation guidance. In the examined publications, key decision points reflecting real-word implementation experience could be mapped to the SALIENT framework and, as these decision points appear to be AI-task agnostic, this framework may also be applicable to non-sepsis algorithms. The mapping clarified where and when barriers, enablers, and key decisions arise within the end-to-end AI implementation process., Conclusions: A systematic review of real-world implementation studies of sepsis prediction algorithms was used to validate an end-to-end staged implementation framework that has the ability to account for key factors that warrant attention in ensuring successful deployment, and which extends on previous AI implementation frameworks., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

Cortical folding patterns are related to brain function, cognition, and behavior. Since the relationship has not been fully explained on a coarse scale, many efforts have been devoted to the identification of finer grained cortical landmarks, such as sulcal pits and gyral peaks, which were found to remain invariant across subjects and ages and the invariance may be related to gene mediated proto-map. However, gyral peaks were only investigated on macaque monkey brains, but not on human brains where the investigation is challenged due to high inter-individual variabilities. To this end, in this work, we successfully identified 96 gyral peaks both on the left and right hemispheres of human brains, respectively. These peaks are spatially consistent across individuals. Higher or sharper peaks are more consistent across subjects. Both structural and functional graph metrics of peaks are significantly different from other cortical regions, and more importantly, these nodal graph metrics are anti-correlated with the spatial consistency metrics within peaks. In addition, the distribution of peaks and various cortical anatomical, structural/functional connective features show hemispheric symmetry. These findings provide new clues to understanding the cortical landmarks, as well as their relationship with brain functions, cognition, behavior in both healthy and aberrant brains., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Study Objectives: Sleep stability can be studied by evaluating the cyclic alternating pattern (CAP) in electroencephalogram (EEG) signals. The present study presents a novel approach for assessing sleep stability, developing an index based on the CAP A-phase characteristics to display a sleep stability profile for a whole night's sleep., Methods: Two ensemble classifiers were developed to automatically score the signals, one for "A-phase" and the other for "non-rapid eye movement" estimation. Both were based on three one-dimension convolutional neural networks. Six different inputs were produced from the EEG signal to feed the ensembles' classifiers. A proposed heuristic-oriented search algorithm individually tuned the classifiers' structures. The outputs of the two ensembles were combined to estimate the A-phase index (API). The models can also assess the A-phase subtypes, their API, and the CAP cycles and rate., Results: Four dataset variations were considered, examining healthy and sleep-disordered subjects. The A-phase average estimation's accuracy, sensitivity, and specificity range was 82%-87%, 72%-80%, and 82%-88%, respectively. A similar performance was attained for the A-phase subtype's assessments, with an accuracy range of 82%-88%. Furthermore, in the examined dataset's variations, the API metric's average error varied from 0.15 to 0.25 (with a median range of 0.11-0.24). These results were attained without manually removing wake or rapid eye movement periods, leading to a methodology suitable to produce a fully automatic CAP scoring algorithm., Conclusions: Metrics based on API can be understood as a new view for CAP analysis, where the goal is to produce and examine a sleep stability profile., (© The Author(s) 2022. Published by Oxford University Press on behalf of Sleep Research Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Objectives: The availability of new techniques may affect surgeons' procedure selection and thereby affect clinical outcomes. This study aimed to evaluate the effect of the availability of virtual-assisted lung mapping (VAL-MAP) on the selection of lung resection methods., Methods: Members of the Japanese Association for Chest Surgeons were invited to participate in a web-based survey. Participants were divided into those who had never used VAL-MAP (group 0), those who had used only VAL-MAP 1.0 (multiple dye marks on the pleural surface; group 1) and those who had used VAL-MAP 2.0 (multiple dye marks and intrabronchial microcoils for three-dimensional mapping; group 2). Participants were shown chest computed tomography images of 6 ground-glass opacity nodules and asked to choose surgical procedures to resect the nodules with sufficient resection margins greater than the lesion diameter or 2 cm., Results: There were 197 surgeons in group 0, 49 in group 1 and 26 in group 2. All groups showed a similar trend of avoiding wedge resection for deeply located nodules. However, group 1 showed a trend of disagreeing with the selection of wedge resection compared with group 0 as measured by a Likert scale (1-5) by -0.21 points (95% confidence interval, -0.41 to -0.008 points, P = 0.042). This tendency disappeared in group 2., Conclusions: The availability of VAL-MAP 1.0 led to the selection of segmentectomy, while the availability of VAL-MAP 2.0 led to aggressive deep wedge resection., (© The Author(s) 2022. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.)

A major challenge for the estimation of crop traits (biophysical variables) from canopy reflectance is the creation of a high-quality training dataset. To address this problem, this research investigated a conceptual framework by integrating a crop growth model with a radiative transfer model to introduce biological constraints in a synthetic training dataset. In addition to the comparison of two datasets without and with biological constraints, we also investigated the effects of observation geometry, retrieval method, and wavelength range on estimation accuracy of four crop traits (leaf area index, leaf chlorophyll content, leaf dry matter, and leaf water content) of wheat. The theoretical analysis demonstrated potential advantages of adding biological constraints in synthetic training datasets as well as the capability of deep learning. Additionally, the predictive models were validated on real unmanned aerial vehicle-based multispectral images collected from wheat plots contrasting in canopy structure. The predictive model trained over a synthetic dataset with biological constraints enabled the prediction of leaf water content from using wavelengths in the visible to near infrared range based on the correlations between crop traits. Our findings presented the potential of the proposed conceptual framework in simultaneously retrieving multiple crop traits from canopy reflectance for applications in precision agriculture and plant breeding., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

In India, strict public health measures to suppress COVID-19 transmission and reduce burden have been rapidly adopted. Pandemic containment and confinement measures impact societies and economies; their costs and benefits must be assessed holistically. This study provides an evolving portrait of the health, economic and social consequences of the COVID-19 pandemic on vulnerable populations in India. Our analysis focuses on 100 days early in the pandemic from 13 March to 20 June 2020. We developed a conceptual framework based on the human right to health and the UN Sustainable Development Goals (SDGs). We analysed people's experiences recorded and shared via mobile phone on the voice platforms operated by the Gram Vaani COVID-19 response network, a service for rural and low-income populations now being deployed to support India's COVID-19 response. Quantitative and visual methods were used to summarize key features of the data and explore relationships between factors. In its first 100 days, the platform logged over 1.15 million phone calls, of which 793 350 (69%) were outbound calls related largely to health promotion in the context of COVID-19. Analysis of 6636 audio recordings by network users revealed struggles to secure the basic necessities of survival, including food (48%), cash (17%), transportation (10%) and employment or livelihoods (8%). Themes were mapped to shortfalls in 10 SDGs and their associated targets. Pre-existing development deficits and weak social safety nets are driving vulnerability during the COVID-19 crisis. For an effective pandemic response and recovery, these must be addressed through inclusive policy design and institutional reforms., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Study Objectives: The presence of flow limitation during sleep is associated with adverse health consequences independent of obstructive sleep apnea (OSA) severity (apnea-hypopnea index, AHI), but remains extremely challenging to quantify. Here we present a unique library and an accompanying automated method that we apply to investigate flow limitation during sleep., Methods: A library of 117,871 breaths (N = 40 participants) were visually classified (certain flow limitation, possible flow limitation, normal) using airflow shape and physiological signals (ventilatory drive per intra-esophageal diaphragm EMG). An ordinal regression model was developed to quantify flow limitation certainty using flow-shape features (e.g. flattening, scooping); breath-by-breath agreement (Cohen's ƙ); and overnight flow limitation frequency (R2, %breaths in certain or possible categories during sleep) were compared against visual scoring. Subsequent application examined flow limitation frequency during arousals and stable breathing, and associations with ventilatory drive., Results: The model (23 features) assessed flow limitation with good agreement (breath-by-breath ƙ = 0.572, p < 0.001) and minimal error (overnight flow limitation frequency R2 = 0.86, error = 7.2%). Flow limitation frequency was largely independent of AHI (R2 = 0.16) and varied widely within individuals with OSA (74[32-95]%breaths, mean[range], AHI > 15/h, N = 22). Flow limitation was unexpectedly frequent but variable during arousals (40[5-85]%breaths) and stable breathing (58[12-91]%breaths), and was associated with elevated ventilatory drive (R2 = 0.26-0.29; R2 < 0.01 AHI v. drive)., Conclusions: Our method enables quantification of flow limitation frequency, a key aspect of obstructive sleep-disordered breathing that is independent of the AHI and often unavailable. Flow limitation frequency varies widely between individuals, is prevalent during arousals and stable breathing, and reveals elevated ventilatory drive. Clinical trial registration: The current observational physiology study does not qualify as a clinical trial., (© Sleep Research Society 2021. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Study Objectives: To assess the relationship between obstructive sleep apnea (OSA) severity and sleep fragmentation, accurate differentiation between sleep and wakefulness is needed. Sleep staging is usually performed manually using electroencephalography (EEG). This is time-consuming due to complexity of EEG setup and the amount of work in manual scoring. In this study, we aimed to develop an automated deep learning-based solution to assess OSA-related sleep fragmentation based on photoplethysmography (PPG) signal., Methods: A combination of convolutional and recurrent neural networks was used for PPG-based sleep staging. The models were trained using two large clinical datasets from Israel (n = 2149) and Australia (n = 877) and tested separately on three-class (wake/NREM/REM), four-class (wake/N1 + N2/N3/REM), and five-class (wake/N1/N2/N3/REM) classification. The relationship between OSA severity categories and sleep fragmentation was assessed using survival analysis of mean continuous sleep. Overlapping PPG epochs were applied to artificially obtain denser hypnograms for better identification of fragmented sleep., Results: Automatic PPG-based sleep staging achieved an accuracy of 83.3% on three-class, 74.1% on four-class, and 68.7% on five-class models. The hazard ratios for decreased mean continuous sleep compared to the non-OSA group obtained with Cox proportional hazards models with 5-s epoch-to-epoch intervals were 1.70, 3.30, and 8.11 for mild, moderate, and severe OSA, respectively. With EEG-based hypnograms scored manually with conventional 30-s epoch-to-epoch intervals, the corresponding hazard ratios were 1.18, 1.78, and 2.90., Conclusions: PPG-based automatic sleep staging can be used to differentiate between OSA severity categories based on sleep continuity. The differences between the OSA severity categories become more apparent when a shorter epoch-to-epoch interval is used., (© Sleep Research Society 2021. Published by Oxford University Press on behalf of the Sleep Research Society.)

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume., (© The Author(s) 2021. Published by Oxford University Press on behalf of GigaScience. 2021.)

Summary: The development of new drugs is costly, time consuming and often accompanied with safety issues. Drug repurposing can avoid the expensive and lengthy process of drug development by finding new uses for already approved drugs. In order to repurpose drugs effectively, it is useful to know which proteins are targeted by which drugs. Computational models that estimate the interaction strength of new drug-target pairs have the potential to expedite drug repurposing. Several models have been proposed for this task. However, these models represent the drugs as strings, which is not a natural way to represent molecules. We propose a new model called GraphDTA that represents drugs as graphs and uses graph neural networks to predict drug-target affinity. We show that graph neural networks not only predict drug-target affinity better than non-deep learning models, but also outperform competing deep learning methods. Our results confirm that deep learning models are appropriate for drug-target binding affinity prediction, and that representing drugs as graphs can lead to further improvements., Availability of Implementation: The proposed models are implemented in Python. Related data, pre-trained models and source code are publicly available at https://github.com/thinng/GraphDTA. All scripts and data needed to reproduce the post hoc statistical analysis are available from https://doi.org/10.5281/zenodo.3603523., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Motivation: Predicting cell locations is important since with the understanding of cell locations, we may estimate the function of cells and their integration with the spatial environment. Thus, the DREAM challenge on single-cell transcriptomics required participants to predict the locations of single cells in the Drosophila embryo using single-cell transcriptomic data., Results: We have developed over 50 pipelines by combining different ways of preprocessing the RNA-seq data, selecting the genes, predicting the cell locations and validating predicted cell locations, resulting in the winning methods which were ranked second in sub-challenge 1, first in sub-challenge 2 and third in sub-challenge 3. In this paper, we present an R package, SCTCwhatateam, which includes all the methods we developed and the Shiny web application to facilitate the research on single-cell spatial reconstruction. All the data and the example use cases are available in the Supplementary data., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Shielded garments are widely recommended for occupational radiation protection in diagnostic and interventional radiology. This study investigated a novel method for efficiently verifying shielded garment integrity while simultaneously acquiring data for lead-equivalence measurements, using two-dimensional topogram images from computed tomography (CT) scanners. This method was tested against more-conventional measurements with superficial and orthovoltage radiotherapy treatment beams, for 12 shielded garments containing 3 different lead-free shielding materials. Despite some energy-dependent results, all shielded garments approximately achieved their specified lead-equivalence for the energy range expected during clinical use for fluoroscopy procedures, except for three shielded skirts that required two layers of material to be overlapped at the front. All lead-equivalence measurements from CT topograms agreed with or conservatively underestimated the kV narrow-beam results. This method is potentially useful for independently assessing the shielding properties of new shielded garments and performing annual checks for damage or degradation of existing shielded garments., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

A common symptom of obstructive sleep apnea (OSA) is excessive daytime sleepiness (EDS). The gold standard test for EDS is the multiple sleep latency test (MSLT). However, due to its high cost, MSLT is not routinely conducted for OSA patients and EDS is instead evaluated using sleep questionnaires. This is problematic however, since sleep questionnaires are subjective and correlate poorly with the MSLT. Therefore, new objective tools are needed for reliable evaluation of EDS. The aim of this study was to test our hypothesis that EDS can be estimated with neural network analysis of previous night polysomnographic signals. We trained a convolutional neural network (CNN) classifier using electroencephalography, electrooculography, and chin electromyography signals from 2,014 patients with suspected OSA. The CNN was trained to classify the patients into four sleepiness categories based on their mean sleep latency (MSL); severe (MSL < 5min), moderate (5 ≤ MSL < 10), mild (10 ≤ MSL < 15), and normal (MSL ≥ 15). The CNN classified patients to the four sleepiness categories with an overall accuracy of 60.6% and Cohen's kappa value of 0.464. In two-group classification scheme with sleepy (MSL < 10 min) and non-sleepy (MSL ≥ 10) patients, the CNN achieved an accuracy of 77.2%, with sensitivity of 76.5%, and specificity of 77.9%. Our results show that previous night's polysomnographic signals can be used for objective estimation of EDS with at least moderate accuracy. Since the diagnosis of OSA is currently confirmed by polysomnography, the classifier could be used simultaneously to get an objective estimate of the daytime sleepiness with minimal extra workload., (© Sleep Research Society 2020. Published by Oxford University Press on behalf of the Sleep Research Society.)

Study Objectives: Accurate identification of sleep stages is essential in the diagnosis of sleep disorders (e.g. obstructive sleep apnea [OSA]) but relies on labor-intensive electroencephalogram (EEG)-based manual scoring. Furthermore, long-term assessment of sleep relies on actigraphy differentiating only between wake and sleep periods without identifying specific sleep stages and having low reliability in identifying wake periods after sleep onset. To address these issues, we aimed to develop an automatic method for identifying the sleep stages from the photoplethysmogram (PPG) signal obtained with a simple finger pulse oximeter., Methods: PPG signals from the diagnostic polysomnographies of susptected OSA patients (n = 894) were utilized to develop a combined convolutional and recurrent neural network. The deep learning model was trained individually for three-stage (wake/NREM/REM), four-stage (wake/N1+N2/N3/REM), and five-stage (wake/N1/N2/N3/REM) classification of sleep., Results: The three-stage model achieved an epoch-by-epoch accuracy of 80.1% with Cohen's κ of 0.65. The four- and five-stage models achieved 68.5% (κ = 0.54), and 64.1% (κ = 0.51) accuracies, respectively. With the five-stage model, the total sleep time was underestimated with a mean bias error (SD) of of 7.5 (55.2) minutes., Conclusion: The PPG-based deep learning model enabled accurate estimation of sleep time and differentiation between sleep stages with a moderate agreement to manual EEG-based scoring. As PPG is already included in ambulatory polygraphic recordings, applying the PPG-based sleep staging could improve their diagnostic value by enabling simple, low-cost, and reliable monitoring of sleep and help assess otherwise overlooked conditions such as REM-related OSA., (© Sleep Research Society 2020. Published by Oxford University Press on behalf of the Sleep Research Society.)

Summary: We define a disease module as a partition of a molecular network whose components are jointly associated with one or several diseases or risk factors thereof. Identification of such modules, across different types of networks, has great potential for elucidating disease mechanisms and establishing new powerful biomarkers. To this end, we launched the 'Disease Module Identification (DMI) DREAM Challenge', a community effort to build and evaluate unsupervised molecular network modularization algorithms. Here, we present MONET, a toolbox providing easy and unified access to the three top-performing methods from the DMI DREAM Challenge for the bioinformatics community., Availability and Implementation: MONET is a command line tool for Linux, based on Docker and Singularity containers; the core algorithms were written in R, Python, Ada and C++. It is freely available for download at https://github.com/BergmannLab/MONET.git., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2020. Published by Oxford University Press.)

Objective: Depression is currently the second most significant contributor to non-fatal disease burdens globally. While it is treatable, depression remains undiagnosed in many cases. As mobile phones have now become an integral part of daily life, this study examines the possibility of screening for depressive symptoms continuously based on patients' mobile usage patterns., Materials and Methods: 412 research participants reported a range of their mobile usage statistics. Beck Depression Inventory-2nd ed (BDI-II) was used to measure the severity of depression among participants. A wide array of machine learning classification algorithms was trained to detect participants with depression symptoms (ie, BDI-II score ≥ 14). The relative importance of individual variables was additionally quantified., Results: Participants with depression were found to have fewer saved contacts on their devices, spend more time on their mobile devices to make and receive fewer and shorter calls, and send more text messages than participants without depression. The best model was a random forest classifier, which had an out-of-sample balanced accuracy of 0.768. The balanced accuracy increased to 0.811 when participants' age and gender were included., Discussions/conclusion: The significant predictive power of mobile usage attributes implies that, by collecting mobile usage statistics, mental health mobile applications can continuously screen for depressive symptoms for initial diagnosis or for monitoring the progress of ongoing treatments. Moreover, the input variables used in this study were aggregated mobile usage metadata attributes, which has low privacy sensitivity making it more likely for patients to grant required application permissions., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Motivation: An important goal of cancer genomics initiatives is to provide the research community with the resources for the unbiased query of cancer mechanisms. Several excellent web platforms have been developed to enable the visual analyses of molecular alterations in cancers from these datasets. However, there are few tools to allow the researchers to mine these resources for mechanisms of cancer processes and their functional interactions in an intuitive unbiased manner., Results: To address this need, we developed SEMA, a web platform for building and testing of models of cancer mechanisms from large multidimensional cancer genomics datasets. Unlike the existing tools for the analyses and query of these resources, SEMA is explicitly designed to enable exploratory and confirmatory analyses of complex cancer mechanisms through a suite of intuitive visual and statistical functionalities. Here, we present a case study of the functional mechanisms of TP53-mediated tumor suppression in various cancers, using SEMA, and identify its role in the regulation of cell cycle progression, DNA repair and signal transduction in different cancers.SEMA is a first-in-its-class web application designed to allow visual data mining and hypothesis testing from the multidimensional cancer datasets. The web application, an extensive tutorial and several video screencasts with case studies are freely available for academic use at https://sema.research.cchmc.org/., Availability and Implementation: SEMA is freely available at https://sema.research.cchmc.org. The web site also contains a detailed Tutorial (also in Supplementary Information), and a link to the YouTube channel for video screencasts of analyses, including the analyses presented here. The Shiny and JavaScript source codes have been deposited to GitHub: https://github.com/msolmazm/sema., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press.)

Motivation: Detection of maximal exact matches (MEMs) between two long sequences is a fundamental problem in pairwise reference-query genome comparisons. To efficiently compare larger and larger genomes, reducing the number of indexed k-mers as well as the number of query k-mers has been adopted as a mainstream approach which saves the computational resources by avoiding a significant number of unnecessary matches., Results: Under this framework, we proposed a new method to detect all MEMs from a pair of genomes. The method first performs a fixed sampling of k-mers on the query sequence, and adds these selected k-mers to a Bloom filter. Then all the k-mers of the reference sequence are tested by the Bloom filter. If a k-mer passes the test, it is inserted into a hash table for indexing. Compared with the existing methods, much less number of query k-mers are generated and much less k-mers are inserted into the index to avoid unnecessary matches, leading to an efficient matching process and memory usage savings. Experiments on large genomes demonstrate that our method is at least 1.8 times faster than the best of the existing algorithms. This performance is mainly attributed to the key novelty of our method that the fixed k-mer sampling must be conducted on the query sequence and the index k-mers are filtered from the reference sequence via a Bloom filter., Availability and Implementation: https://github.com/yuansliu/bfMEM., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Epithelial-mesenchymal transition (EMT) has been a subject of intense scrutiny as it facilitates metastasis and alters drug sensitivity. Although EMT-regulatory roles for numerous miRNAs and transcription factors are known, their functions can be difficult to disentangle, in part due to the difficulty in identifying direct miRNA targets from complex datasets and in deciding how to incorporate 'indirect' miRNA effects that may, or may not, represent biologically relevant information. To better understand how miRNAs exert effects throughout the transcriptome during EMT, we employed Exon-Intron Split Analysis (EISA), a bioinformatic technique that separates transcriptional and post-transcriptional effects through the separate analysis of RNA-Seq reads mapping to exons and introns. We find that in response to the manipulation of miRNAs, a major effect on gene expression is transcriptional. We also find extensive co-ordination of transcriptional and post-transcriptional regulatory mechanisms during both EMT and mesenchymal to epithelial transition (MET) in response to TGF-β or miR-200c respectively. The prominent transcriptional influence of miRNAs was also observed in other datasets where miRNA levels were perturbed. This work cautions against a narrow approach that is limited to the analysis of direct targets, and demonstrates the utility of EISA to examine complex regulatory networks involving both transcriptional and post-transcriptional mechanisms., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Aims: Apnoea-hypopnoea index (AHI), the universal clinical metric of sleep apnoea severity, poorly predicts the adverse outcomes of sleep apnoea, potentially because the AHI, a frequency measure, does not adequately capture disease burden. Therefore, we sought to evaluate whether quantifying the severity of sleep apnoea by the 'hypoxic burden' would predict mortality among adults aged 40 and older., Methods and Results: The samples were derived from two cohort studies: The Outcomes of Sleep Disorders in Older Men (MrOS), which included 2743 men, age 76.3 ± 5.5 years; and the Sleep Heart Health Study (SHHS), which included 5111 middle-aged and older adults (52.8% women), age: 63.7 ± 10.9 years. The outcomes were all-cause and Cardiovascular disease (CVD)-related mortality. The hypoxic burden was determined by measuring the respiratory event-associated area under the desaturation curve from pre-event baseline. Cox models were used to calculate the adjusted hazard ratios for hypoxic burden. Unlike the AHI, the hypoxic burden strongly predicted CVD mortality and all-cause mortality (only in MrOS). Individuals in the MrOS study with hypoxic burden in the highest two quintiles had hazard ratios of 1.81 [95% confidence interval (CI) 1.25-2.62] and 2.73 (95% CI 1.71-4.36), respectively. Similarly, the group in the SHHS with hypoxic burden in the highest quintile had a hazard ratio of 1.96 (95% CI 1.11-3.43)., Conclusion: The 'hypoxic burden', an easily derived signal from overnight sleep study, predicts CVD mortality across populations. The findings suggest that not only the frequency but the depth and duration of sleep related upper airway obstructions, are important disease characterizing features., (Published on behalf of the European Society of Cardiology. All rights reserved. © The Author(s) 2018. For permissions, please email: journals.permissions@oup.com.)

Motivation: MicroRNAs (miRNAs) are small non-coding RNAs with the length of ∼22 nucleotides. miRNAs are involved in many biological processes including cancers. Recent studies show that long non-coding RNAs (lncRNAs) are emerging as miRNA sponges, playing important roles in cancer physiology and development. Despite accumulating appreciation of the importance of lncRNAs, the study of their complex functions is still in its preliminary stage. Based on the hypothesis of competing endogenous RNAs (ceRNAs), several computational methods have been proposed for investigating the competitive relationships between lncRNAs and miRNA target messenger RNAs (mRNAs). However, when the mRNAs are released from the control of miRNAs, it remains largely unknown as to how the sponge lncRNAs influence the expression levels of the endogenous miRNA targets., Results: We propose a novel method to construct lncRNA related miRNA sponge regulatory networks (LncmiRSRNs) by integrating matched lncRNA and mRNA expression profiles with clinical information and putative miRNA-target interactions. Using the method, we have constructed the LncmiRSRNs for four human cancers (glioblastoma multiforme, lung cancer, ovarian cancer and prostate cancer). Based on the networks, we discover that after being released from miRNA control, the target mRNAs are normally up-regulated by the sponge lncRNAs, and only a fraction of sponge lncRNA-mRNA regulatory relationships and hub lncRNAs are shared by the four cancers. Moreover, most sponge lncRNA-mRNA regulatory relationships show a rewired mode between different cancers, and a minority of sponge lncRNA-mRNA regulatory relationships conserved (appearing) in different cancers may act as a common pivot across cancers. Besides, differential and conserved hub lncRNAs may act as potential cancer drivers to influence the cancerous state in cancers. Functional enrichment and survival analysis indicate that the identified differential and conserved LncmiRSRN network modules work as functional units in biological processes, and can distinguish metastasis risks of cancers. Our analysis demonstrates the potential of integrating expression profiles, clinical information and miRNA-target interactions for investigating lncRNA regulatory mechanism., Availability and Implementation: LncmiRSRN is freely available (https://github.com/zhangjunpeng411/LncmiRSRN)., Supplementary Information: Supplementary data are available at Bioinformatics online.

Background and Objectives: Communication difficulties have been reported as one of the most stress-inducing aspects of caring for people with dementia. Notably, with disease progression comes an increase in the frequency of communication difficulty and a reduction in the effectiveness of attempts to remedy breakdowns in communication. The aim of the current research was to evaluate the utility of an automated discourse analysis tool (i.e., Discursis) in distinguishing between different types of trouble and repair signaling behaviors, demonstrated within conversations between people with dementia and their professional care staff., Research Design and Methods: Twenty conversations between people with dementia and their professional care staff were human-coded for instances of interactive/noninteractive trouble and typical/facilitative repair behaviors. Associations were then examined between these behaviors and recurrence metrics generated by Discursis., Results: Significant associations were identified between Discursis metrics, trouble-indicating, and repair behaviors., Discussion and Implications: These results suggest that discourse analysis software is capable of discriminating between different types of trouble and repair signaling behavior, on the basis of term recurrence calculated across speaker turns. The subsequent recurrence metrics generated by Discursis offer a means of automating the analysis of episodes of conversational trouble and repair. This achievement represents the first step toward the future development of an intelligent assistant that can analyze conversations in real time and offers support to people with dementia and their carers during periods of communicative trouble.

Study Objectives: Periodic breathing (PB) is common in newborns and is an obvious manifestation of ventilatory control instability. However, many infants without PB may still have important underlying ventilatory control instabilities that go unnoticed using standard clinical monitoring. Methods to detect infants with "subclinical" ventilatory control instability are therefore required. The current study aimed to assess the degree of ventilatory control instability using simple bedside recordings in preterm infants., Methods: Respiratory inductance plethysmography (RIP) recordings were analyzed from ~20 minutes of quiet sleep in 20 preterm infants at 36 weeks post-menstrual age (median [range]: 36 [34-40]). The percentage time spent in PB was also calculated for each infant (%PB). Spontaneous sighs were identified and breath-by-breath measurements of (uncalibrated) ventilation were derived from RIP traces. Loop gain (LG, a measure of ventilatory control instability) was calculated by fitting a simple ventilatory control model (gain, time-constant, delay) to the post-sigh ventilatory pattern. For comparison, periodic inter-breath variability was also quantified using power spectral analysis (ventilatory oscillation magnitude index [VOMI])., Results: %PB was strongly associated with LG (r2 = 0.77, p < 0.001) and moderately with the VOMI (r2 = 0.21, p = 0.047). LG (0.52 ± 0.05 vs. 0.30 ± 0.03; p = 0.0025) and the VOMI (-8.2 ± 1.1 dB vs. -11.8 ± 0.9 dB; p = 0.026) were both significantly higher in infants that displayed PB vs. those without., Conclusions: LG and VOMI determined from the ventilatory responses to spontaneous sighs can provide a practical approach to assessing ventilatory control instability in preterm infants. Such simple techniques may help identify infants at particular risk for ventilatory instabilities with concomitant hypoxemia and its associated consequences.

Study Objectives: The severity of obstructive sleep apnea (OSA) is known to vary according to sleep stage; however, the pathophysiology responsible for this robust observation is incompletely understood. The objective of the present work was to examine how ventilatory control system sensitivity (i.e. loop gain) varies during sleep in patients with OSA., Methods: Loop gain was estimated using signals collected from standard diagnostic polysomnographic recordings performed in 44 patients with OSA. Loop gain measurements associated with nonrapid eye movement (NREM) stage 2 (N2), stage 3 (N3), and REM sleep were calculated and compared. The sleep period was also split into three equal duration tertiles to investigate how loop gain changes over the course of sleep., Results: Loop gain was significantly lower (i.e. ventilatory control more stable) in REM (Mean ± SEM: 0.51 ± 0.04) compared with N2 sleep (0.63 ± 0.04; p = 0.001). Differences in loop gain between REM and N3 (p = 0.095), and N2 and N3 (p = 0.247) sleep were not significant. Furthermore, N2 loop gain was significantly lower in the first third (0.57 ± 0.03) of the sleep period compared with later second (0.64 ± 0.03, p = 0.012) and third (0.64 ± 0.03, p = 0.015) tertiles. REM loop gain also tended to increase across the night; however, this trend was not statistically significant [F(2, 12) = 3.49, p = 0.09]., Conclusions: These data suggest that loop gain varies between REM and NREM sleep and modestly increases over the course of sleep. Lower loop gain in REM is unlikely to contribute to the worsened OSA severity typically observed in REM sleep, but may explain the reduced propensity for central sleep apnea in this sleep stage.

Background: Despite the widespread use of actigraphy in pediatric sleep studies, there are currently no age-related normative data., Objectives: To systematically review the literature, calculate pooled mean estimates of actigraphy-derived pediatric nighttime sleep variables and to examine the magnitude of change with age., Methods: A systematic search was performed across eight databases of studies that included at least one actigraphy sleep variable from healthy children aged 0-18 years. Data suitable for meta-analysis were confined to ages 3-18 years with seven actigraphy variables analyzed using random effects meta-analysis and meta-regression performed using age as a covariate., Results: In total, 1334 articles did not meet inclusion criteria; 87 had data suitable for review and 79 were suitable for meta-analysis. Pooled mean estimates for overnight sleep duration declined from 9.68 hours (3-5 years age band) to 8.98, 8.85, 8.05, and 7.4 for age bands 6-8, 9-11, 12-14, and 15-18 years, respectively. For continuous data, the best-fit (R2 = 0.74) equation for hours over the 0-18 years age range was 9.02 - 1.04 × [(age/10)^2 - 0.83]. There was a significant curvilinear association between both sleep onset and offset with age (p < .001). Sleep latency was stable at 19.4 min per night. There were significant differences among the older age groups between weekday and weekend/nonschool days (18 studies). Total sleep time in 15-18 years old was 56 min longer, and sleep onset and offset almost 1 and 2 hours later, respectively, on weekend or nonschool days., Conclusion: These normative values have potential application to assist the interpretation of actigraphy measures from nighttime recordings across the pediatric age range, and aid future research.

Study Objectives: Precision medicine for obstructive sleep apnea (OSA) requires noninvasive estimates of each patient's pathophysiological "traits." Here, we provide the first automated technique to quantify the respiratory arousal threshold-defined as the level of ventilatory drive triggering arousal from sleep-using diagnostic polysomnographic signals in patients with OSA., Methods: Ventilatory drive preceding clinically scored arousals was estimated from polysomnographic studies by fitting a respiratory control model (Terrill et al.) to the pattern of ventilation during spontaneous respiratory events. Conceptually, the magnitude of the airflow signal immediately after arousal onset reveals information on the underlying ventilatory drive that triggered the arousal. Polysomnographic arousal threshold measures were compared with gold standard values taken from esophageal pressure and intraoesophageal diaphragm electromyography recorded simultaneously (N = 29). Comparisons were also made to arousal threshold measures using continuous positive airway pressure (CPAP) dial-downs (N = 28). The validity of using (linearized) nasal pressure rather than pneumotachograph ventilation was also assessed (N = 11)., Results: Polysomnographic arousal threshold values were correlated with those measured using esophageal pressure and diaphragm EMG (R = 0.79, p < .0001; R = 0.73, p = .0001), as well as CPAP manipulation (R = 0.73, p < .0001). Arousal threshold estimates were similar using nasal pressure and pneumotachograph ventilation (R = 0.96, p < .0001)., Conclusions: The arousal threshold in patients with OSA can be estimated using polysomnographic signals and may enable more personalized therapeutic interventions for patients with a low arousal threshold., (© Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.)

Summary: Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes, an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization. The input and output of each step in the framework are packaged in the same data format, making it convenience to compare different methods. The package is useful for inferring cancer subtypes from an input genomic dataset, comparing the predictions from different well-known methods and testing new subtype discovery methods, as shown with different application scenarios in the Supplementary Material., Availability and Implementation: The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/CancerSubtypes/)., Contact: thuc.le@unisa.edu.au or jiuyong.li@unisa.edu.au., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com)

Motivation: Cancer is not a single disease and involves different subtypes characterized by different sets of molecules. Patients with different subtypes of cancer often react heterogeneously towards the same treatment. Currently, clinical diagnoses rather than molecular profiles are used to determine the most suitable treatment. A molecular level approach will allow a more precise and informed way for making treatment decisions, leading to a better survival chance and less suffering of patients. Although many computational methods have been proposed to identify cancer subtypes at molecular level, to the best of our knowledge none of them are designed to discover subtypes with heterogeneous treatment responses., Results: In this article we propose the Survival Causal Tree (SCT) method. SCT is designed to discover patient subgroups with heterogeneous treatment effects from censored observational data. Results on TCGA breast invasive carcinoma and glioma datasets have shown that for each subtype identified by SCT, the patients treated with radiotherapy exhibit significantly different relapse free survival pattern when compared to patients without the treatment. With the capability to identify cancer subtypes with heterogeneous treatment responses, SCT is useful in helping to choose the most suitable treatment for individual patients., Availability and Implementation: Data and code are available at https://github.com/WeijiaZhang24/SurvivalCausalTree ., Contact: weijia.zhang@mymail.uinsa.edu.au., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com)

Study Objectives: Upper airway surgery is often recommended to treat patients with obstructive sleep apnea (OSA) who cannot tolerate continuous positive airways pressure. However, the response to surgery is variable, potentially because it does not improve the nonanatomical factors (ie, loop gain [LG] and arousal threshold) causing OSA. Measuring these traits clinically might predict responses to surgery. Our primary objective was to test the value of LG and arousal threshold to predict surgical success defined as 50% reduction in apnea-hypopnea index (AHI) and AHI <10 events/hour post surgery., Methods: We retrospectively analyzed data from patients who underwent upper airway surgery for OSA (n = 46). Clinical estimates of LG and arousal threshold were calculated from routine polysomnographic recordings presurgery and postsurgery (median of 124 [91-170] days follow-up)., Results: Surgery reduced both the AHI (39.1 ± 4.2 vs. 26.5 ± 3.6 events/hour; p < .005) and estimated arousal threshold (-14.8 [-22.9 to -10.2] vs. -9.4 [-14.5 to -6.0] cmH2O) but did not alter LG (0.45 ± 0.08 vs. 0.45 ± 0.12; p = .278). Responders to surgery had a lower baseline LG (0.38 ± 0.02 vs. 0.48 ± 0.01, p < .05) and were younger (31.0 [27.3-42.5] vs. 43.0 [33.0-55.3] years, p < .05) than nonresponders. Lower LG remained a significant predictor of surgical success after controlling for covariates (logistic regression p = .018; receiver operating characteristic area under curve = 0.80)., Conclusions: Our study provides proof-of-principle that upper airway surgery most effectively resolves OSA in patients with lower LG. Predicting the failure of surgical treatment, consequent to less stable ventilatory control (elevated LG), can be achieved in the clinic and may facilitate avoidance of surgical failures., (© Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.)

Recent findings show that coding genes are not the only targets that miRNAs interact with. In fact, there is a pool of different RNAs competing with each other to attract miRNAs for interactions, thus acting as competing endogenous RNAs (ceRNAs). The ceRNAs indirectly regulate each other via the titration mechanism, i.e. the increasing concentration of a ceRNA will decrease the number of miRNAs that are available for interacting with other targets. The cross-talks between ceRNAs, i.e. their interactions mediated by miRNAs, have been identified as the drivers in many disease conditions, including cancers. In recent years, some computational methods have emerged for identifying ceRNA-ceRNA interactions. However, there remain great challenges and opportunities for developing computational methods to provide new insights into ceRNA regulatory mechanisms.In this paper, we review the publically available databases of ceRNA-ceRNA interactions and the computational methods for identifying ceRNA-ceRNA interactions (also known as miRNA sponge interactions). We also conduct a comparison study of the methods with a breast cancer dataset. Our aim is to provide a current snapshot of the advances of the computational methods in identifying miRNA sponge interactions and to discuss the remaining challenges., (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Objective: Australians are among the highest users of antibiotics in the developed world. The primary aim was to determine the 'age' of antibiotic prescriptions at the time of dispensing as a possible contributor to antibiotic misuse and ultimately, resistance. The secondary aim was to test customised software to permit extraction and de-identification of dispensing records for analysis., Methods: Data were extracted and de-identified from computerised dispensing systems in three community pharmacies in Brisbane, Australia, according to a strict ethical protocol. All prescription records dispensed between 1 January 2010 and 31 December 2012 were merged to form a complete dataset of 1 158 871 de-identified dispensing records which were analysed using Microsoft Excel ® . A retrospective drug utilisation study was conducted on a subset of 100 573 antibiotic records. In a substudy conducted at a single pharmacy site, all antibiotic records dispensed over a 4-month (winter) period were examined to determine the age of prescriptions., Key Findings: Nearly one in ten antibiotics (9.0%) was dispensed from prescriptions that were more than a month old, and over one in five (22.1%) were dispensed from a repeat prescription., Conclusions: Health system factors may contribute to inappropriate antibiotic use in Australia, including availability and validity of repeat antibiotic prescriptions. Government health departments, prescribers, pharmacists, other health professionals and consumers have to share the responsibility of ensuring that antibiotics are used appropriately., (© 2016 Royal Pharmaceutical Society.)

Methods for measuring genetic distances in phylogenetics are known to be sensitive to the evolutionary model assumed. However, there is a lack of established methodology to accommodate the trade-off between incorporating sufficient biological reality and avoiding model overfitting. In addition, as traditional methods measure distances based on the observed number of substitutions, their tend to underestimate distances between diverged sequences due to backward and parallel substitutions. Various techniques were proposed to correct this, but they lack the robustness against sequences that are distantly related and of unequal base frequencies. In this article, we present a novel genetic distance estimate based on information theory that overcomes the above two hurdles. Instead of examining the observed number of substitutions, this method estimates genetic distances using Shannon's mutual information. This naturally provides an effective framework for balancing model complexity and goodness of fit. Our distance estimate is shown to be approximately linear to elapsed time and hence is less sensitive to the divergence of sequence data and compositional biased sequences. Using extensive simulation data, we show that our method 1) consistently reconstructs more accurate phylogeny topologies than existing methods, 2) is robust in extreme conditions such as diverged phylogenies, unequal base frequencies data, and heterogeneous mutation patterns, and 3) scales well with large phylogenies., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Objective: The Health Insurance Portability and Accountability Act Privacy Rule enables healthcare organizations to share de-identified data via two routes. They can either 1) show re-identification risk is small (e.g., via a formal model, such as k-anonymity) with respect to an anticipated recipient or 2) apply a rule-based policy (i.e., Safe Harbor) that enumerates attributes to be altered (e.g., dates to years). The latter is often invoked because it is interpretable, but it fails to tailor protections to the capabilities of the recipient. The paper shows rule-based policies can be mapped to a utility (U) and re-identification risk (R) space, which can be searched for a collection, or frontier, of policies that systematically trade off between these goals., Methods: We extend an algorithm to efficiently compose an R-U frontier using a lattice of policy options. Risk is proportional to the number of patients to which a record corresponds, while utility is proportional to similarity of the original and de-identified distribution. We allow our method to search 20 000 rule-based policies (out of 2(700)) and compare the resulting frontier with k-anonymous solutions and Safe Harbor using the demographics of 10 U.S. states., Results: The results demonstrate the rule-based frontier 1) consists, on average, of 5000 policies, 2% of which enable better utility with less risk than Safe Harbor and 2) the policies cover a broader spectrum of utility and risk than k-anonymity frontiers., Conclusions: R-U frontiers of de-identification policies can be discovered efficiently, allowing healthcare organizations to tailor protections to anticipated needs and trustworthiness of recipients., (© The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Summary: Circos plots are graphical outputs that display three dimensional chromosomal interactions and fusion transcripts. However, the Circos plot tool is not an interactive visualization tool, but rather a figure generator. For example, it does not enable data to be added dynamically nor does it provide information for specific data points interactively. Recently, an R-based Circos tool (RCircos) has been developed to integrate Circos to R, but similarly, Rcircos can only be used to generate plots. Thus, we have developed a Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable, it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the Graphical user interface (GUI). J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data., Availability and Implementation: J-circos and its manual are freely available at http://www.australianprostatecentre.org/research/software/jcircos, Contact: j.an@qut.edu.au, Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Motivation: MicroRNAs (miRNAs) play crucial roles in complex cellular networks by binding to the messenger RNAs (mRNAs) of protein coding genes. It has been found that miRNA regulation is often condition-specific. A number of computational approaches have been developed to identify miRNA activity specific to a condition of interest using gene expression data. However, most of the methods only use the data in a single condition, and thus, the activity discovered may not be unique to the condition of interest. Additionally, these methods are based on statistical associations between the gene expression levels of miRNAs and mRNAs, so they may not be able to reveal real gene regulatory relationships, which are causal relationships., Results: We propose a novel method to infer condition-specific miRNA activity by considering (i) the difference between the regulatory behavior that an miRNA has in the condition of interest and its behavior in the other conditions; (ii) the causal semantics of miRNA-mRNA relationships. The method is applied to the epithelial-mesenchymal transition (EMT) and multi-class cancer (MCC) datasets. The validation by the results of transfection experiments shows that our approach is effective in discovering significant miRNA-mRNA interactions. Functional and pathway analysis and literature validation indicate that the identified active miRNAs are closely associated with the specific biological processes, diseases and pathways. More detailed analysis of the activity of the active miRNAs implies that some active miRNAs show different regulation types in different conditions, but some have the same regulation types and their activity only differs in different conditions in the strengths of regulation., Availability and Implementation: The R and Matlab scripts are in the Supplementary materials., (© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Clinical and research staff who work around magnetic resonance imaging (MRI) scanners are exposed to the static magnetic stray fields of these scanners. Although the past decade has seen strong developments in the assessment of occupational exposure to electromagnetic fields from MRI scanners, there is insufficient insight into the exposure variability that characterizes routine MRI work practice. However, this is an essential component of risk assessment and epidemiological studies. This paper describes the results of a measurement survey of shift-based personal exposure to static magnetic fields (SMF) (B) and motion-induced time-varying magnetic fields (dB/dt) among workers at 15 MRI facilities in the Netherlands. With the use of portable magnetic field dosimeters, >400 full-shift and partial shift exposure measurements were collected among various jobs involved in clinical and research MRI. Various full-shift exposure metrics for B and motion-induced dB/dt exposure were calculated from the measurements, including instantaneous peak exposure and time-weighted average (TWA) exposures. We found strong correlations between levels of static (B) and time-varying (dB/dt) exposure (r = 0.88-0.92) and between different metrics (i.e. peak exposure, TWA exposure) to express full-shift exposure (r = 0.69-0.78). On average, participants were exposed to MRI-related SMFs during only 3.7% of their work shift. Average and peak B and dB/dt exposure levels during the work inside the MRI scanner room were highest among technical staff, research staff, and radiographers. Average and peak B exposure levels were lowest among cleaners, while dB/dt levels were lowest among anaesthesiology staff. Although modest exposure variability between workplaces and occupations was observed, variation between individuals of the same occupation was substantial, especially among research staff. This relatively large variability between workers with the same job suggests that exposure classification based solely on job title may not be an optimal grouping strategy for epidemiological purposes., (© The Author 2014. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.)

Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field., Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field., Availability: http://lcb.infotech.monash.edu.au/I-value., Supplementary Information: Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html., (© The Author 2014. Published by Oxford University Press.)

To identify non-coding RNA (ncRNA) signals within genomic regions, a classification tool was developed based on a hybrid random forest (RF) with a logistic regression model to efficiently discriminate short ncRNA sequences as well as long complex ncRNA sequences. This RF-based classifier was trained on a well-balanced dataset with a discriminative set of features and achieved an accuracy, sensitivity and specificity of 92.11%, 90.7% and 93.5%, respectively. The selected feature set includes a new proposed feature, SCORE. This feature is generated based on a logistic regression function that combines five significant features-structure, sequence, modularity, structural robustness and coding potential-to enable improved characterization of long ncRNA (lncRNA) elements. The use of SCORE improved the performance of the RF-based classifier in the identification of Rfam lncRNA families. A genome-wide ncRNA classification framework was applied to a wide variety of organisms, with an emphasis on those of economic, social, public health, environmental and agricultural significance, such as various bacteria genomes, the Arthrospira (Spirulina) genome, and rice and human genomic regions. Our framework was able to identify known ncRNAs with sensitivities of greater than 90% and 77.7% for prokaryotic and eukaryotic sequences, respectively. Our classifier is available at http://ncrna-pred.com/HLRF.htm., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.)

The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method's ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats.

Motivation: microRNAs (miRNAs) are known to play an essential role in the post-transcriptional gene regulation in plants and animals. Currently, several computational approaches have been developed with a shared aim to elucidate miRNA-mRNA regulatory relationships. Although these existing computational methods discover the statistical relationships, such as correlations and associations between miRNAs and mRNAs at data level, such statistical relationships are not necessarily the real causal regulatory relationships that would ultimately provide useful insights into the causes of gene regulations. The standard method for determining causal relationships is randomized controlled perturbation experiments. In practice, however, such experiments are expensive and time consuming. Our motivation for this study is to discover the miRNA-mRNA causal regulatory relationships from observational data., Results: We present a causality discovery-based method to uncover the causal regulatory relationship between miRNAs and mRNAs, using expression profiles of miRNAs and mRNAs without taking into consideration the previous target information. We apply this method to the epithelial-to-mesenchymal transition (EMT) datasets and validate the computational discoveries by a controlled biological experiment for the miR-200 family. A significant portion of the regulatory relationships discovered in data is consistent with those identified by experiments. In addition, the top genes that are causally regulated by miRNAs are highly relevant to the biological conditions of the datasets. The results indicate that the causal discovery method effectively discovers miRNA regulatory relationships in data. Although computational predictions may not completely replace intervention experiments, the accurate and reliable discoveries in data are cost effective for the design of miRNA experiments and the understanding of miRNA-mRNA regulatory relationships.

Study Objectives: Sighs are thought to have a role in regulating breathing control. They may preceed a central apnea (sigh-CA) or a pause (sigh-P), particularly in quiet sleep. Recent techniques characterizing cardiorespiratory synchronization (CRS) provide sensitive measures of cardiorespiratory coupling, which is an important factor in breathing control. We speculated that the strength of CRS and direction of cardiorespiratory coupling (DC), would differ between sigh-P and sigh-CA; before and after a sigh; and with maturation., Design: Prospective study. CRS and DC were calculated from the respiratory signal and heart rate before and after sighs recorded during overnight polysomnography., Setting: Sleep laboratory., Participants: The data were selected from 15 subjects of a prospective cohort of 34 healthy infants at ages 2 weeks, 3 months and 6 months., Interventions: N/A., Measurements and Results: Both CRS and respiratory modulation on heart rate (RMH) (negative DC index) were decreased around sigh-CA compared with sigh-P at all ages. Short-term CRS decreased after both sigh-P and sigh-CA in infants aged 2 weeks and 3 months. Long term CRS did not change before and after sigh-P or sigh-CA. CRS and RMH were increased at 3 months and 6 months compared to 2 weeks., Conclusions: A sigh was not found to be associated with apparent resetting of breathing control in healthy infants less than 6 months of age. Cardiorespiratory coupling appears to be a leading marker of changes in breathing control, preceding central apnea associated with a sigh., Citation: Nguyen CD; Dakin C; Yuill M; Crozier S; Wilson S. The effect of sigh on cardiorespiratory synchronization in healthy sleeping infants. SLEEP 2012;35(12):1643-1650.