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Seismic interrogation of the upper mantle from the base of the crust to the top of the mantle transition zone has revealed discontinuities that are variable in space, depth, lateral extent, amplitude and lack a unified explanation for their origin. Improved constraints on the detectability and properties of mantle discontinuities can be obtained with P-to-S receiver function (Ps-RF) where energy scatters from P to S as seismic waves propagate across discontinuities of interest. However, due to the interference of crustal multiples, uppermost mantle discontinuities are more commonly imaged with lower resolution S-to-P receiver function (Sp-RF). In this study, a new method called CRISP-RF (Clean Receiver-function Imaging using SParse Radon Filters) is proposed, which incorporates ideas from compressive sensing and model-based image reconstruction. The central idea involves applying a sparse Radon transform to effectively decompose the Ps-RF into its underlying wavefield contributions, that is direct conversions, multiples, and noise, based on the phase moveout and coherence. A masking filter is then designed and applied to create a multiple-free and denoised Ps-RF. We demonstrate, using synthetic experiment, that our implementation of the Radon transform using a sparsity-promoting regularization outperforms the conventional least-squares methods and can effectively isolate direct Ps conversions. We further apply the CRISP-RF workflow on real data, including single station data on cratons, common-conversion-point stack at continental margins and seismic data from ocean islands. The application of CRISP-RF to global data sets will advance our understanding of the enigmatic origins of the upper mantle discontinuities like the ubiquitous mid-lithospheric discontinuity and the elusive X-discontinuity. [ABSTRACT FROM AUTHOR]

Resolving the detail of crustal deformation of the seismically and technically active Sichuan-Yunnan block located in the southeast margin of the Tibetan Plateau is crucial for understanding the lateral extrusion of the Tibetan Plateau. Using seismic data from two regional seismograph stations of the China Earthquake Networks Center and twenty recently deployed broad-band temporary stations from the MCD Array (Middle ChuanDian block seismic array), we constrained crustal thickness and seismic anisotropy at the west boundary of the Sichuan-Yunnan block, near the east Himalayan syntaxis by receiver function techniques including CCP stacking and sinusoidal moveout of PmS conversions. Crustal thickness varies significantly across major faults inside the block which increases by >20 km from west to east. East of the Chenghai Fault, a clear positive phase lies above the Moho and is interpreted to be caused by the magma intrusion related to a late Permian Emeishan large igneous province (ELIP). The crustal anisotropy shows strong zoning features and clockwise rotation with respect to due north. To the west of the Lijiang-Xiaojinhe and the Honghe Faults, anisotropic fast orientations are near NS, indicating strong crustal deformation and movement of southward crustal flow along the Nujiang-Lancangjiang Fault; to the east of this fault, anisotropic fast orientations are near NE. The variation of the anisotropic fast orientations indicates that the southeastward crustal flow from the Tibetan Plateau may be prevented by fast velocity anomalies beneath the ELIP. These observations provided new evidence for strong crustal deformation along the tectonic boundary in the southeastern Tibetan Plateau with the expansion of the Tibetan Plateau. [ABSTRACT FROM AUTHOR]

Distress calls, as a type of alarm call, play important roles in expressing bodily condition and conveying information concerning predation threats. In this study, we examined the communication via distress calls in parent–offspring and inter-offspring interactions. First, we used playback of chick distress calls of 2 sympatric breeders, the vinous-throated parrotbill Sinosuthora webbiana and the oriental reed warbler Acrocephalus orientalis , to the adults/chicks of these 2 species, respectively, and measured the responses of conspecifics or heterospecifics. The playback-to-chicks experiment showed that both species of chicks reduced the number of begging calls and begging duration time as a response to conspecific/heterospecific distress calls compared with natural begging and background noise controls. However, reed warbler chicks also reduced beak opening frequency in the response to conspecific distress calls compared with other playback stimuli. Second, the results of the playback-to-adults experiment showed that reed warbler adults could eavesdrop on distress calls of conspecific neighbors and sympatric heterospecifics. Furthermore, the nest-leaving behavior of reed warblers did not differ significantly when they heard the distress calls of conspecifics or parrotbills. Finally, reed warbler adults responded to heterospecific distress calls more quickly than to conspecific distress calls, and parrotbill adults presented the same response. Our results supported the warn-kin hypothesis and show that chick distress calls play an important role in conveying risk and the condition of chicks to enhance individual fitness. In addition, we also found that eavesdropping on distress calls is a congenital behavior that begins in the chick stage. [ABSTRACT FROM AUTHOR]

Objective: Synthetic data are increasingly relied upon to share electronic health record (EHR) data while maintaining patient privacy. Current simulation methods can generate longitudinal data, but the results are unreliable for several reasons. First, the synthetic data drifts from the real data distribution over time. Second, the typical approach to quality assessment, which is based on the extent to which real records can be distinguished from synthetic records using a critic model, often fails to recognize poor simulation results. In this article, we introduce a longitudinal simulation framework, called LS-EHR, which addresses these issues.Materials and Methods: LS-EHR enhances simulation through conditional fuzzing and regularization, rejection sampling, and prior knowledge embedding. We compare LS-EHR to the state-of-the-art using data from 60 000 EHRs from Vanderbilt University Medical Center (VUMC) and the All of Us Research Program. We assess discrimination between real and synthetic data over time. We evaluate the generation process and critic model using the area under the receiver operating characteristic curve (AUROC). For the critic, a higher value indicates a more robust model for quality assessment. For the generation process, a lower value indicates better synthetic data quality.Results: The LS-EHR critic improves discrimination AUROC from 0.655 to 0.909 and 0.692 to 0.918 for VUMC and All of Us data, respectively. By using the new critic, the LS-EHR generation model reduces the AUROC from 0.909 to 0.758 and 0.918 to 0.806.Conclusion: LS-EHR can substantially improve the usability of simulated longitudinal EHR data. [ABSTRACT FROM AUTHOR]

Objective: Deep learning models for clinical event forecasting (CEF) based on a patient's medical history have improved significantly over the past decade. However, their transition into practice has been limited, particularly for diseases with very low prevalence. In this paper, we introduce CEF-CL, a novel method based on contrastive learning to forecast in the face of a limited number of positive training instances.Materials and Methods: CEF-CL consists of two primary components: (1) unsupervised contrastive learning for patient representation and (2) supervised transfer learning over the derived representation. We evaluate the new method along with state-of-the-art model architectures trained in a supervised manner with electronic health records data from Vanderbilt University Medical Center and the All of Us Research Program, covering 48 000 and 16 000 patients, respectively. We assess forecasting for over 100 diagnosis codes with respect to their area under the receiver operator characteristic curve (AUROC) and area under the precision-recall curve (AUPRC). We investigate the correlation between forecasting performance improvement and code prevalence via a Wald Test.Results: CEF-CL achieved an average AUROC and AUPRC performance improvement over the state-of-the-art of 8.0%-9.3% and 11.7%-32.0%, respectively. The improvement in AUROC was negatively correlated with the number of positive training instances (P < .001).Conclusion: This investigation indicates that clinical event forecasting can be improved significantly through contrastive representation learning, especially when the number of positive training instances is small. [ABSTRACT FROM AUTHOR]

Objective: In intensive care units (ICUs), a patient's brain function status can shift from a state of acute brain dysfunction (ABD) to one that is ABD-free and vice versa, which is challenging to forecast and, in turn, hampers the allocation of hospital resources. We aim to develop a machine learning model to predict next-day brain function status changes.Materials and Methods: Using multicenter prospective adult cohorts involving medical and surgical ICU patients from 2 civilian and 3 Veteran Affairs hospitals, we trained and externally validated a light gradient boosting machine to predict brain function status changes. We compared the performances of the boosting model against state-of-the-art models-an ABD predictive model and its variants. We applied Shapley additive explanations to identify influential factors to develop a compact model.Results: There were 1026 critically ill patients without evidence of prior major dementia, or structural brain diseases, from whom 12 295 daily transitions (ABD: 5847 days; ABD-free: 6448 days) were observed. The boosting model achieved an area under the receiver-operating characteristic curve (AUROC) of 0.824 (95% confidence interval [CI], 0.821-0.827), compared with the state-of-the-art models of 0.697 (95% CI, 0.693-0.701) with P < .001. Using 13 identified top influential factors, the compact model achieved 99.4% of the boosting model on AUROC. The boosting and the compact models demonstrated high generalizability in external validation by achieving an AUROC of 0.812 (95% CI, 0.812-0.813).Conclusion: The inputs of the compact model are based on several simple questions that clinicians can quickly answer in practice, which demonstrates the model has direct prospective deployment potential into clinical practice, aiding in critical hospital resource allocation. [ABSTRACT FROM AUTHOR]

Motivation The study of the evolutionary history of biological networks enables deep functional understanding of various bio-molecular processes. Network growth models, such as the Duplication–Mutation with Complementarity (DMC) model, provide a principled approach to characterizing the evolution of protein–protein interactions (PPIs) based on duplication and divergence. Current methods for model-based ancestral network reconstruction primarily use greedy heuristics and yield sub-optimal solutions. Results We present a new Integer Linear Programming (ILP) solution for maximum likelihood reconstruction of ancestral PPI networks using the DMC model. We prove the correctness of our solution that is designed to find the optimal solution. It can also use efficient heuristics from general-purpose ILP solvers to obtain multiple optimal and near-optimal solutions that may be useful in many applications. Experiments on synthetic data show that our ILP obtains solutions with higher likelihood than those from previous methods, and is robust to noise and model mismatch. We evaluate our algorithm on two real PPI networks, with proteins from the families of bZIP transcription factors and the Commander complex. On both the networks, solutions from our ILP have higher likelihood and are in better agreement with independent biological evidence from other studies. Availability and implementation A Python implementation is available at https://bitbucket.org/cdal/network-reconstruction. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Objective: Simulating electronic health record data offers an opportunity to resolve the tension between data sharing and patient privacy. Recent techniques based on generative adversarial networks have shown promise but neglect the temporal aspect of healthcare. We introduce a generative framework for simulating the trajectory of patients' diagnoses and measures to evaluate utility and privacy.Materials and Methods: The framework simulates date-stamped diagnosis sequences based on a 2-stage process that 1) sequentially extracts temporal patterns from clinical visits and 2) generates synthetic data conditioned on the learned patterns. We designed 3 utility measures to characterize the extent to which the framework maintains feature correlations and temporal patterns in clinical events. We evaluated the framework with billing codes, represented as phenome-wide association study codes (phecodes), from over 500 000 Vanderbilt University Medical Center electronic health records. We further assessed the privacy risks based on membership inference and attribute disclosure attacks.Results: The simulated temporal sequences exhibited similar characteristics to real sequences on the utility measures. Notably, diagnosis prediction models based on real versus synthetic temporal data exhibited an average relative difference in area under the ROC curve of 1.6% with standard deviation of 3.8% for 1276 phecodes. Additionally, the relative difference in the mean occurrence age and time between visits were 4.9% and 4.2%, respectively. The privacy risks in synthetic data, with respect to the membership and attribute inference were negligible.Conclusion: This investigation indicates that temporal diagnosis code sequences can be simulated in a manner that provides utility and respects privacy. [ABSTRACT FROM AUTHOR]

Objective: Electronic medical records (EMRs) can support medical research and discovery, but privacy risks limit the sharing of such data on a wide scale. Various approaches have been developed to mitigate risk, including record simulation via generative adversarial networks (GANs). While showing promise in certain application domains, GANs lack a principled approach for EMR data that induces subpar simulation. In this article, we improve EMR simulation through a novel pipeline that (1) enhances the learning model, (2) incorporates evaluation criteria for data utility that informs learning, and (3) refines the training process.Materials and Methods: We propose a new electronic health record generator using a GAN with a Wasserstein divergence and layer normalization techniques. We designed 2 utility measures to characterize similarity in the structural properties of real and simulated EMRs in the original and latent space, respectively. We applied a filtering strategy to enhance GAN training for low-prevalence clinical concepts. We evaluated the new and existing GANs with utility and privacy measures (membership and disclosure attacks) using billing codes from over 1 million EMRs at Vanderbilt University Medical Center.Results: The proposed model outperformed the state-of-the-art approaches with significant improvement in retaining the nature of real records, including prediction performance and structural properties, without sacrificing privacy. Additionally, the filtering strategy achieved higher utility when the EMR training dataset was small.Conclusions: These findings illustrate that EMR simulation through GANs can be substantially improved through more appropriate training, modeling, and evaluation criteria. [ABSTRACT FROM AUTHOR]