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  1. Free, publicly-accessible full text available April 30, 2024
  2. Free, publicly-accessible full text available June 1, 2024
  3. Abstract Background There is growing evidence indicating that a number of functional connectivity networks are disrupted at each stage of the full clinical Alzheimer’s disease spectrum. Such differences are also detectable in cognitive normal (CN) carrying mutations of AD risk genes, suggesting a substantial relationship between genetics and AD-altered functional brain networks. However, direct genetic effect on functional connectivity networks has not been measured. Methods Leveraging existing AD functional connectivity studies collected in NeuroSynth, we performed a meta-analysis to identify two sets of brain regions: ones with altered functional connectivity in resting state network and ones without. Then with the brain-wide gene expression data in the Allen Human Brain Atlas, we applied a new biclustering method to identify a set of genes with differential co-expression patterns between these two set of brain regions. Results Differential co-expression analysis using biclustering method led to a subset of 38 genes which showed distinctive co-expression patterns between AD-related and non AD-related brain regions in default mode network. More specifically, we observed 4 sub-clusters with noticeable co-expression difference, where the difference in correlations is above 0.5 on average. Conclusions This work applies a new biclustering method to search for a subset of genes with altered co-expression patterns in AD-related default mode network regions. Compared with traditional differential expression analysis, differential co-expression analysis yielded many more significant hits with extra insights into the wiring mechanism between genes. Particularly, the differential co-expression pattern was observed between two sets of genes, suggesting potential upstream genetic regulators in AD development. 
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  4. SUMMARY

    Seismograms contain multiple sources of seismic waves, from distinct transient signals such as earthquakes to continuous ambient seismic vibrations such as microseism. Ambient vibrations contaminate the earthquake signals, while the earthquake signals pollute the ambient noise’s statistical properties necessary for ambient-noise seismology analysis. Separating ambient noise from earthquake signals would thus benefit multiple seismological analyses. This work develops a multitask encoder–decoder network named WaveDecompNet to separate transient signals from ambient signals directly in the time domain for 3-component seismograms. We choose the active-volcanic Big Island in Hawai’i as a natural laboratory given its richness in transients (tectonic and volcanic earthquakes) and diffuse ambient noise (strong microseism). The approach takes a noisy 3-component seismogram as input and independently predicts the 3-component earthquake and noise waveforms. The model is trained on earthquake and noise waveforms from the STandford EArthquake Dataset (STEAD) and on the local noise of seismic station IU.POHA. We estimate the network’s performance by using the explained variance metric on both earthquake and noise waveforms. We explore different neural network designs for WaveDecompNet and find that the model with long-short-term memory (LSTM) performs best over other structures. Overall, we find that WaveDecompNet provides satisfactory performance down to a signal-to-noise ratio (SNR) of 0.1. The potential of the method is (1) to improve broad-band SNR of transient (earthquake) waveforms and (2) to improve local ambient noise to monitor the Earth’s structure using ambient noise signals. To test this, we apply a short-time average to a long-time average filter and improve the number of detected events. We also measure single-station cross-correlation functions of the recovered ambient noise and establish their improved coherence through time and over different frequency bands. We conclude that WaveDecompNet is a promising tool for a broad range of seismological research.

     
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  5. Abstract A large number of genetic variations have been identified to be associated with Alzheimer’s disease (AD) and related quantitative traits. However, majority of existing studies focused on single types of omics data, lacking the power of generating a community including multi-omic markers and their functional connections. Because of this, the immense value of multi-omics data on AD has attracted much attention. Leveraging genomic, transcriptomic and proteomic data, and their backbone network through functional relations, we proposed a modularity-constrained logistic regression model to mine the association between disease status and a group of functionally connected multi-omic features, i.e. single-nucleotide polymorphisms (SNPs), genes and proteins. This new model was applied to the real data collected from the frontal cortex tissue in the Religious Orders Study and Memory and Aging Project cohort. Compared with other state-of-art methods, it provided overall the best prediction performance during cross-validation. This new method helped identify a group of densely connected SNPs, genes and proteins predictive of AD status. These SNPs are mostly expression quantitative trait loci in the frontal region. Brain-wide gene expression profile of these genes and proteins were highly correlated with the brain activation map of ‘vision’, a brain function partly controlled by frontal cortex. These genes and proteins were also found to be associated with the amyloid deposition, cortical volume and average thickness of frontal regions. Taken together, these results suggested a potential pathway underlying the development of AD from SNPs to gene expression, protein expression and ultimately brain functional and structural changes. 
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  6. Abstract

    Detecting slow slip events (SSEs) at offshore subduction zones is important to understand the slip behavior on offshore subduction megathrusts, where tsunamis can be generated. The most widely used method to detect SSEs is to measure the vertical seafloor deformation caused by SSEs using seafloor pressure data. However, due to the small signal‐to‐noise ratio and instrumental drift, such detection is very difficult. In this study, we trained a machine learning model using synthetic data to detect SSEs and applied it to real pressure data in New Zealand between 2014 and 2015. Our method detected five events, two of which are confirmed by the onshore GPS records. Besides, our model performs better than the traditional matched filter method. We conclude that machine learning could be used to detect SSEs in real seafloor pressure data. The method can be applied to other regions, especially where near trench GPS is not available.

     
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  7. Abstract

    Given recent advances in geodetic data, interseismic locking models along the megathrust now become useful to qualitatively evaluate future earthquake potential. However, an individual earthquake's true rupture potential is challenging, as it depends on more than just a static image of prior locking. Here, we test the determinism of interseismic locking models using spontaneous rupture simulations and the well‐resolved processes associated with the 2012 moment magnitude (Mw) 7.6 Nicoya earthquake. To do so, we estimate initial megathrust stress from locking by assuming that the entire slip deficit will be released in the next megathrust earthquake. Then we initiate spontaneous ruptures at the hypocenter of the 2012 Nicoya earthquake. We find scenarios that approximate the same coseismic slip distribution and final earthquake moment magnitude as obtained from seismic and geodetic observations, demonstrating that deriving potential rupture scenarios from interseismic locking is feasible. We also find that spontaneous rupture scenarios from different locking models differ in moment rate duration and thus ground motion prediction, although the final slip distribution and moment magnitude were similar. The results highlight that quantifying rupture scenarios and ground motions from reliable locking models by dynamic rupture simulations can be an effective tool for seismic hazard assessment in subduction zones.

     
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