The robustness of persistent homology of brain networks to data acquisition-related non-neural variability in resting state fMRI.

There is increasing interest in investigating brain function based on functional connectivity networks (FCN) obtained from resting-state functional magnetic resonance imaging (fMRI). FCNs, typically obtained using measures of time series association such as Pearson's correlation, are sensitive to data acquisition parameters such as sampling period. This introduces non-neural variability in data pooled from different acquisition protocols and MRI scanners, negating the advantages of larger sample sizes in pooled data. To address this, we hypothesize that the topology or shape of brain networks must be preserved irrespective of how densely it is sampled, and metrics which capture this topology may be statistically similar across sampling periods, thereby alleviating this source of non-neural variability. Accordingly, we present an end-to-end pipeline that uses persistent homology (PH), a branch of topological data analysis, to demonstrate similarity across FCNs acquired at different temporal sampling periods. PH, as a technique, extracts topological features by capturing the network organization across all continuous threshold values, as opposed to graph theoretic methods, which fix a discrete network topology by thresholding the connectivity matrix. The extracted topological features are encoded in the form of persistent diagrams that can be compared against one another using the earth-moving metric, also popularly known as the Wasserstein distance. We extract topological features from three data cohorts, each acquired at different temporal sampling periods and demonstrate that these features are statistically the same, hence, empirically showing that PH may be robust to changes in data acquisition parameters such as sampling period.

UALCAN: An update to the integrated cancer data analysis platform.

Cancer genomic, transcriptomic, and proteomic profiling has generated extensive data that necessitate the development of tools for its analysis and dissemination. We developed UALCAN to provide a portal for easy exploring, analyzing, and visualizing these data, allowing users to integrate the data to better understand the gene, proteins, and pathways perturbed in cancer and make discoveries. UALCAN web portal enables analyzing and delivering cancer transcriptome, proteomics, and patient survival data to the cancer research community. With data obtained from The Cancer Genome Atlas (TCGA) project, UALCAN has enabled users to evaluate protein-coding gene expression and its impact on patient survival across 33 types of cancers. The web portal has been used extensively since its release and received immense popularity, underlined by its usage from cancer researchers in more than 100 countries. The present manuscript highlights the task we have undertaken and updates that we have made to UALCAN since its release in 2017. Extensive user feedback motivated us to expand the resource by including data on a) microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and promoter DNA methylation from TCGA and b) mass spectrometry-based proteomics from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). UALCAN provides easy access to pre-computed, tumor subgroup-based gene/protein expression, promoter DNA methylation status, and Kaplan-Meier survival analyses. It also provides new visualization features to comprehend and integrate observations and aids in generating hypotheses for testing. UALCAN is accessible at http://ualcan.path.uab.edu.

A Privacy-Preserving Mobile and Fog Computing Framework to Trace and Prevent COVID-19 Community Transmission.

To slow down the spread of COVID-19, governments worldwide are trying to identify infected people, and contain the virus by enforcing isolation, and quarantine. However, it is difficult to trace people who came into contact with an infected person, which causes widespread community transmission, and mass infection. To address this problem, we develop an e-government Privacy-Preserving Mobile, and Fog computing framework entitled PPMF that can trace infected, and suspected cases nationwide. We use personal mobile devices with contact tracing app, and two types of stationary fog nodes, named Automatic Risk Checkers (ARC), and Suspected User Data Uploader Node (SUDUN), to trace community transmission alongside maintaining user data privacy. Each user's mobile device receives a Unique Encrypted Reference Code (UERC) when registering on the central application. The mobile device, and the central application both generate Rotational Unique Encrypted Reference Code (RUERC), which broadcasted using the Bluetooth Low Energy (BLE) technology. The ARCs are placed at the entry points of buildings, which can immediately detect if there are positive or suspected cases nearby. If any confirmed case is found, the ARCs broadcast pre-cautionary messages to nearby people without revealing the identity of the infected person. The SUDUNs are placed at the health centers that report test results to the central cloud application. The reported data is later used to map between infected, and suspected cases. Therefore, using our proposed PPMF framework, governments can let organizations continue their economic activities without complete lockdown.