Unifying Gene Expression Complexity and Cellular Operational Efficiency: Application of the Locality and Caching Principles via a Cell-to-Computer Analogy

Gene expression is time-consuming, and the delay from transcription activation to produced proteins is sequentially longer from bacteria to yeast and to humans. How human cells bypass the delay and attain operational efficiency, i.e., quick proteomic response to signals, is not well understood. The computer has endured the same system latency issue due to much slower information retrieval (hard drive (HD) to memory and to CPU) than CPU execution, and mitigated it via efficient memory management, namely, the spatiotemporal locality principles that control specialized user functions and the permanent caching of core system functions, the operating system (OS) kernel. Thus, in this study, we unified gene expression and HD-memory-CPU information flow as instances of the Shannon information theory, both supporting the respective system operations and consisting of three components: information storage, the execution/decoding step, and the channel for the dynamic storage-to-execution information flow; the gene expression machinery and their regulators, and the OS kernel, were deemed as the respective channels. This abstraction prompted a multi-omic comparative analysis, generating experimental evidence that transcriptome regulation shares the computer memory management principles. First, the temporal locality principle explains the mRNA stabilization-by-translation regulatory mechanism and controls specialized cellular functions. Second, the caching principle explains cytoplasmic mRNA sequestration and the defiance of the locality principle by highly sequestered mRNAs. Third, strikingly, in both systems, the caching principle controls the information channels; similar to permanent caching of OS kernel, basic translation/transcription machinery and their regulators are the top most sequestered mRNAs. Summarily, the locality and the caching principles differentially regulate specialized functions and core system functions, respectively, integrating the complexity of transcriptome regulation with cellular operational latency mitigation.

EagleImp: Fast and Accurate Genome-wide Phasing and Imputation in a Single Tool

Background: Reference-based phasing and genotype imputation algorithms have been developed with sublinear theoretical runtime behaviour, but runtimes are still high in practice when large genome-wide reference datasets are used. Methods: We developed EagleImp, a software with algorithmic and technical improvements and new features for accurate and accelerated phasing and imputation in a single tool. Results: We compared accuracy and runtime of EagleImp with Eagle2, PBWT and prominent imputation servers using whole-genome sequencing data from the 1000 Genomes Project, the Haplotype Reference Consortium and simulated data with more than 1 million reference genomes. EagleImp is 2 to 10 times faster (depending on the single or multiprocessor configuration selected) than Eagle2/PBWT, with the same or better phasing and imputation quality in all tested scenarios. For common variants investigated in typical GWAS studies, EagleImp provides same or higher imputation accuracy than the Sanger Imputation Service, Michigan Imputation Server and the newly developed TOPMed Imputation Server, despite larger (not publicly available) reference panels. It has many new features, including automated chromosome splitting and memory management at runtime to avoid job aborts, fast reading and writing of large files, and various user-configurable algorithm and output options. Conclusions: Due to the technical optimisations, EagleImp can perform fast and accurate reference-based phasing and imputation for future very large reference panels with more than 1 million genomes. EagleImp is freely available for download from https://github.com/ikmb/eagleimp.

Refresh Rate Identification Strategy for Optimal Page Replacement Algorithms for Virtual Memory Management

Operating system offers a service known as memory management which manages and guides primary memory. It moves processes between disk and main memory during the execution back and forth. The process in which we provisionally moves process from primary memory to the hard disk so the memory is available for other processes. This process is known as swapping. Page replacement techniques are the methods by which the operating system concludes which memory pages to be swapped out and write to disk, whenever a page of main memory is required to be allocated. There are different policies regarding how to select a page to be swapped out when a page fault occurs to create space for new page. These Policies are called page replacement algorithms. In this paper the strategy for identifying the refresh rate for ‘Aging’ page replacement algorithm is presented and evaluated. Keywords: Aging algorithm, page replacement algorithm, refresh rate, virtual memory management.

Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer

This study aimed to provide efficient recognition of bacterial strains on personal computers from MinION (Nanopore) long read data. Thanks to the fall in sequencing costs, the identification of bacteria can now proceed by whole genome sequencing. MinION is a fast, but highly error-prone sequencing device and it is a challenge to successfully identify the strain content of unknown simple or complex microbial samples. It is heavily constrained by memory management and fast access to the read and genome fragments. Our strategy involves three steps: indexing of known genomic sequences for a given or several bacterial species; a request process to assign a read to a strain by matching it to the closest reference genomes; and a final step looking for a minimum set of strains that best explains the observed reads. We have applied our method, called ORI, on 77 strains of Streptococcus thermophilus . We worked on several genomic distances and obtained a detailed classification of the strains, together with a criterion that allows merging of what we termed ‘sibling’ strains, only separated by a few mutations. Overall, isolated strains can be safely recognized from MinION data. For mixtures of several non-sibling strains, results depend on strain abundance.

Killing Processes or Killing Flash? Escaping from the Dilemma Using Lightweight, Compression-Aware Swap for Mobile Devices

Android apps become increasingly memory-demanding as software vendors add more and more new features to their apps. In the mean time, Android users often launch multiple apps and conveniently switch back and forth among the apps. Although running multiple apps imposes a high pressure on memory management, virtual-memory swap, an essential feature to improve the degree of multitasking, is disabled in fear of premature retirement of flash-based storage devices. Instead, Android employs a termination-based, process-level memory reclaiming method. We observed that process killing is, unfortunately, not effective in memory reclaiming and is highly negative to user experience. In this study, we advocate re-thinking using swap in Android for improved user experience with managed write stress on flash storage. Based on a series of empirical analyses of swap activities, we propose an enhanced page replacement policy and a page-compressing frontswap module. The proposed page replacement policy jointly considers page activeness and compressibility to boost the compression ratio of swap writes. A sampled-based method for page compressibility prediction is introduced so that decisions on page replacement can be made without compressing every page. We also design a frontswap module that strategically organizes compressed pages in the swap space for reducing the overhead of swap I/O operations. Experimental results showed that compared with process killing, our method improved the app launching time and energy consumption by 58% and 19%, respectively; compared with the original swap, our approach reduced the swap write stress by 65%.

Design of computer aided translation system for English communication language based on grey clustering evaluation

In order to facilitate communication and communication, this paper studies the optimization of the current computer-aided translation system, and proposed a design method of English communication language computer-aided translation system based on grey clustering evaluation. By optimizing the hardware configuration and algorithm function keys of the system, the English translation mechanism of multilanguage interaction, the design idea of editing and modifying after English translation and knowledge database management are realized, and the system function framework was constructed, including the system transceiver unit, automatic translation unit, manual correction unit, task management unit and memory management unit, the performance of task management unit and memory management unit is analyzed. On this basis, the specific work flow of the design system mainly includes the English translation service flow integrating multilanguage interaction and the project-based multilanguage interaction English translation service flow design, which realizes the English translation online assistance under the multilanguage interaction environment. The experimental results show that the design system has the advantages of high online translation speed, pronunciation success rate and multilanguage translation success rate.