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.

Image features of spinning regular black holes based on a locality principle

To understand the true nature of black holes, fundamental theoretical developments should be linked all the way to observational features of black holes in their natural astrophysical environments. Here, we take several steps to establish such a link. We construct a family of spinning, regular black-hole spacetimes based on a locality principle for new physics and analyze their shadow images. We identify characteristic image features associated to regularity (increased compactness and relative stretching) and to the locality principle (cusps and asymmetry) that persist in the presence of a simple analytical disk model. We conjecture that these occur as universal features of distinct classes of regular black holes based on different sets of construction principles for the corresponding spacetimes.

Locality and professional life

The locality principle extends beyond computer memories. It teaches us something about being human.

Hercules: Intelligent Coupling of Dual-Mode Flash Memory and Hard Disk Drive

The write performance of multi-level cell (MLC) is several times slower than single-level cell (SLC); however, the cost per bit of MLC is much lower than SLC. Dual-mode flash (the medium can be partially switched to SLC mode by programming only 1 bit in some cells) can combine SLC and MLC to provide trading density opportunity for performance. In this paper, we present Hercules—a hybrid storage system that couples dual-mode flash memory and hard drive disk (HDD)—based on the content locality principle for high storage performance. The data are divided into two types: the reference data for read operation and the delta data for write operation. The reference data are stored in SLC and the delta data in MLC or HDD in sequential orders. Hercules organizes the metadata for the mapping of the physical locations of the reference blocks and the delta data of the original blocks, intelligently identifies hot/cold data and performs the data migration between MLC and disk for performance improvements. To validate our findings, we implemented Hercules and made evaluation to show that Hercules can effectively improve the data access speed and reduce the response time, compared with the Flashcache storage structure, and in particular, with Hercules, we can achieve 10% performance improvement over the system in absence of hot delta data caching.

Local and global theories of relativity in flat and curved spacetimes

Special and general theories of relativity consist in describing both local and global phenomena - the first in flat, and the second in curved spacetime. In the paper it is shown that each of these two classes of relativistic effects, local and global, is universal and is the subject of a separate theory. First, descriptions in local frames of reference, related by the local Lorentz transformations, form the local theory of relativity, or local relativity (LR). The locality principle allows to apply LR to non-inertial local frames, and the equivalence principle to the local frames in gravitational field. Secondly, descriptions in global frames of reference, constructed from local frames coexisting on a common hypersurface of simultaneity, form the global theory of relativity, or global relativity (GlR). LR and GlR are based on physical coordinates and complement each other, the special and general theories of relativity were hybrids of these two theories. LR and GlR describe the local and global properties of gravity, separating the field effects from the effects of motion by different methods, such as bimetric formalism, where one metric describes geometry of the global frames, and other describes spacetime geometry. It is shown that GlR leads to a picture of collapse with formation of frozars, and also leads to a cutoff of the loop integrals of quantum fields at the Planck length. In GlR, cosmological models are built on hypersurfaces of simultaneity, where both stretching and the Doppler effect contribute to redshifts, and aberration is also taken into account. Predicted an initial violetshift removing the double redshift paradox, and this leads to the slowing time cosmology consistent with observational data.

TZ-MRAS: A Remote Attestation Scheme for the Mobile Terminal Based on ARM TrustZone

With the widespread use of mobile embedded devices in the Internet of Things, mobile office, and edge computing, security issues are becoming more and more serious. Remote attestation, one of the mobile security solutions, is a process of verifying the identity and integrity status of the remote computing device, through which the challenger determines whether the platform is trusted by discovering an unknown fingerprint. The remote attestation on the mobile terminal faces many security challenges presently because there is a lack of trusted roots, devices are heterogeneous, and hardware resources are strictly limited. To ARM’s mobile platform, we propose a mobile remote attestation scheme based on ARM TrustZone (TZ-MRAS), which uses the highest security authority of TrustZone to implement trusted attestation service. Compared with the existing mobile remote attestation scheme, it has the advantages of wide application, easy deployment, and low cost. To defend against the time-of-check-to-time-of-use (TOC-TOU) attack, we propose a probe-based dynamic integrity measurement model, ProbeIMA, which can dynamically detect unknown fingerprints that generate during kernel and process execution. Finally, according to the characteristics of the improved dynamic measurement model, that is, the ProbeIMA will expand the scale of the measurement dataset, an optimized stored measurement log construction algorithm based on the locality principle (LPSML) is proposed, which has the advantages of shortening the length of the authentication path and improving the verification efficiency of the platform configuration. As a proof of concept, we implemented a prototype for each service and made experimental evaluations. The experimental results show the proposed scheme has higher security and efficiency than some existing schemes.

A Novel Coordinate Rotation Digital Computer Method for Energy and Latency Saving by Trigonometric Operations Spatial Locality Principle

In this work, we propose an approximate and energy-efficient CORDIC method, based on a trigonometric function spatial locality principle derived from benchmarks profiling. Successive sine/cosine computation requests cover more than 50% when the absolute phase difference is at most ten degrees. Consequently, this property suggests an optimized circuit implementation, both iterative or a succession of microrotation modules, where the last CORDIC requires fewer iterations, reducing the latency and the total energy budget at the same precision of two separate and independent instances. Thus, this simple design strategy allows significant area and energy dissipation in general-purpose VLSI architectures, but it introduces also dramatically optimizations in applicationspecific embedded systems used in the area of signal processing and radio frequency communication. In this contribution, we introduce a method, the hardware overhead and the energy budget per single cycle. Simulation results show the total energy saving in considered benchmarks is 40% in pipelined and iterative general purposes CORDIC. Furthermore, our application-specific systems (fast Fourier transform and digital oscillators for radiofrequency down conversions) show remarkable cycle savings when the successive sine/cosine computation requests are more than 70%. Finally, in this work, we extend the proposed approach to whichever phase difference less than 26.56° , as a variable for the second CORDIC number of angle rotations.