MOTIVATION: Spatial transcriptomics (ST) can reveal the existence and extent of spatial variation of gene expression in complex tissues. Such analyses could help identify spatially localized processes underlying a tissue's function. Existing tools to detect spatially variable genes assume a constant noise variance across spatial locations. This assumption might miss important biological signals when the variance can change across locations. RESULTS: In this article, we propose NoVaTeST, a framework to identify genes with location-dependent noise variance in ST data. NoVaTeST models gene expression as a function of spatial location and allows the noise to vary spatially. NoVaTeST then statistically compares this model to one with constant noise and detects genes showing significant spatial noise variation. We refer to these genes as "noisy genes." In tumor samples, the noisy genes detected by NoVaTeST are largely independent of the spatially variable genes detected by existing tools that assume constant noise, and provide important biological insights into tumor microenvironments. AVAILABILITY AND IMPLEMENTATION: An implementation of the NoVaTeST framework in Python along with instructions for running the pipeline is available at https://github.com/abidabrar-bracu/NoVaTeST.

Demand for fast data sharing among smart devices is rapidly increasing. This trend creates challenges towards ensuring essential security for online shared data while maintaining the resource usage at a reasonable level. Existing research studies attempt to leverage compression based encryption for enabling such secure and fast data transmission replacing the traditional resource-heavy encryption schemes. Current compression-based encryption methods mainly focus on error insensitive digital data formats and prone to be vulnerable to different attacks. Therefore, in this paper, we propose and implement a new Huffman compression based Encryption scheme using lightweight dynamic Order Statistic tree (HEliOS) for digital data transmission. The core idea of HEliOS involves around finding a secure encoding method based on a novel notion of Huffman coding, which compresses the given digital data using a small sized "secret" (called as secret_intelligence in our study). HEliOS does this in such a way that, without the possession of the secret intelligence, an attacker will not be able to decode the encoded compressed data. Hence, by encrypting only the small-sized intelligence, we can secure the whole compressed data. Moreover, our rigorous real experimental evaluation for downloading and uploading digital data to and from a personal cloud storage Dropbox server validates efficacy and lightweight nature of HEliOS.

An antigen is a protein capable of triggering an effective immune system response. Protective antigens are the ones that can invoke specific and enhanced adaptive immune response to subsequent exposure to the specific pathogen or related organisms. Such proteins are therefore of immense importance in vaccine preparation and drug design. However, the laboratory experiments to isolate and identify antigens from a microbial pathogen are expensive, time consuming and often unsuccessful. This is why Reverse Vaccinology has become the modern trend of vaccine search, where computational methods are first applied to predict protective antigens or their determinants, known as epitopes. In this paper, we propose a novel, accurate computational model to identify protective antigens efficiently. Our model extracts features directly from the protein sequences, without any dependence on functional domain or structural information. After relevant features are extracted, we have used Random Forest algorithm to rank the features. Then Recursive Feature Elimination (RFE) and minimum redundancy maximum relevance (mRMR) criterion were applied to extract an optimal set of features. The learning model was trained using Random Forest algorithm. Named as Antigenic, our proposed model demonstrates superior performance compared to the state-of-the-art predictors on a benchmark dataset. Antigenic achieves accuracy, sensitivity and specificity values of 78.04%, 78.99% and 77.08% in 10-fold cross-validation testing respectively. In jackknife cross-validation, the corresponding scores are 80.03%, 80.90% and 79.16% respectively. The source code of Antigenic, along with relevant dataset and detailed experimental results, can be found at https://github.com/srautonu/AntigenPredictor. A publicly accessible web interface has also been established at: http://antigenic.research.buet.ac.bd.

In this paper, we propose techniques for dynamically adjusting heartbeat or keep-alive interval of long-lived TCP connections, particularly the ones that are used in push notification service in mobile platforms. When a device connects to a server using TCP, often times the connection is established through some sort of middle-box, such as NAT, proxy, firewall, and so on. When such a connection is idle for a long time, it may get torn down due to binding timeout of the middle-box. To keep the connection alive, the client device needs to send keep-alive packets through the connection when it is otherwise idle. To reduce resource consumption, the keep-alive packet should preferably be sent at the farthest possible time within the binding timeout. Due to varied settings of different network equipments, the binding timeout will not be identical in different networks. Hence, the heartbeat rate used in different networks should be changed dynamically. We propose a set of iterative probing techniques, namely binary, exponential, and composite search, that detect the middle-box binding timeout with varying degree of accuracy; and in the process, keeps improving the keep-alive interval used by the client device. We also analytically derive performance bounds of these techniques. To the best of our knowledge, ours is the first work that systematically studies several techniques to dynamically improve keep-alive interval. To this end, we run experiments in simulation as well as make a real implementation on android to demonstrate the proof-of-concept of the proposed schemes.