REVIEW | doi:10.20944/preprints202102.0496.v1
Subject: Medicine & Pharmacology, Allergology Keywords: non-coding; leukemia; B-cell; RNA-sequencing; small RNA-sequencing
Online: 22 February 2021 (16:33:30 CET)
Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell Acute Lymphoblastic Leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.
ARTICLE | doi:10.20944/preprints202301.0039.v1
Subject: Biology, Other Keywords: somatic point mutations; non-coding RNA; biomarker discovery; driver genes; non-coding RNAs prioritization; health data analytics
Online: 4 January 2023 (02:22:00 CET)
Previous studies demonstrate the critical importance of non-coding RNAs interfacing with chromatin-modifying machinery resulting in promoter-enhancer-based gene regulation and raise the possibility that many other enhancer-like RNAs may operate via similar mechanisms. Critically, more than 80% of the disease-linked variations identified in genome-wide studies are located in the non-coding regions of genomes, especially non-coding RNA, suggesting non-coding RNAs are relevant to disease. Thus, a critical path forward for understanding non-coding RNAs' role, especially long non-coding RNAs, is to understand the genomic regions' transcriptional regulation, especially non-coding regions. Here, we developed a user-friendly R package called SomaGene for studying and identifying enhancer-like non-coding RNAs with enriched somatic mutations in the cancer genome. SomaGene accepts different genomic variants (whole genome/exome somatic point mutations, structural variations, copy number variations) to identify those RNAs that significantly mutated in diseases (e.g., cancer). It then uses multiple publicly available genomics and epigenetics datasets including ENCODE epigenomics annotations, FANTOM5 tissue-specific expression profiles, disease-associated genome-wide association SNPs, and tissue-specific eQTL pairs to identify those RNAs with potentially enhancer function. SomaGene, as a powerful R package, can provide the opportunity to cancer scientists to study the roles of non-coding RNAs in different cancer genomes.
ARTICLE | doi:10.20944/preprints201802.0009.v1
Subject: Keywords: Cache Coding, Source Coding, Absorbing Markov Chain
Online: 1 February 2018 (16:45:19 CET)
Network coding approaches typically consider an unrestricted recoding of coded packets in the relay nodes for increased performance. However, this can expose the system to pollution attacks that cannot be detected during transmission, until the receivers attempt to recover the data. To prevent these attacks while allowing for the benefits of coding in mesh networks, the Cache Coding was proposed. This protocol only allows recoding at the relays when the relay has received enough packets to decode an entire generation of packets. At that point, the relay node recodes and signs the recoded packets with its own private key allowing for the system to detect and minimize the effect of pollution attacks and make relays accountable for changes on the data. This paper analyzes the delay performance of Cache Coding to understand the security-performance trade-off of this scheme. We introduce an analytical model for the case of two relays in an erasure channel relying on an Absorbing Markov Chain and a approximate model to estimate the performance in terms of the number of transmissions before successfully decoding at the receiver. We confirm our analysis using simulation results. We show that Cache Coding can overcome security issues of unrestricted recoding with only a moderate decrease in system performance.
ARTICLE | doi:10.20944/preprints201811.0086.v1
Online: 5 November 2018 (06:51:04 CET)
Objective: This paper aims to build an Effort Estimation Model for design, coding and testing Web Applications Based Fuzzy and Practical Models, which will help in optimizing the efforts in software development. Methods/Analysis: Soft computing approach is adopted and applied in the effort estimation and then compared with practical efforts in the development process with interpreting the historical data available for the existing functionalities. Findings: The effort estimation model presented in this paper focuses on the first level estimates published by Project Managers and the second level estimates presented by Project Leaders or Developers for any new requirement or enhancement for a web application built on 3-tier architecture using Microsoft technologies. The model considers the classification of each task as either Low or Medium or High complexity. These tasks pertain to the lowest level parts in bottom-up estimation. Efforts are estimated for designing, coding and unit testing of these tasks and the efforts are summed up to get the effort estimation for the higher level which is a feature to be implemented. Novelty/Improvement: The paper also discusses about the application of the effort estimation model by taking a new requirement as a case study. The first level estimates calculated using the effort estimation model has a variance of about 25% when compared with the actual effort. This variance is very much acceptable considering the fact that the first level estimates can be tolerable up to 35%. The proposed effort estimation tool would help the project managers to efficiently control the project, manage the resources effectively, and improve the software development process and also trade off analyses among schedule, performance, quality and functionality. Fuzzy logic is used to verify the claims made in efforts estimation. It is proposed a new relation between the number of data and efforts value membership for actual data. And converts it into crisp value in the range [0…1] which helps to classify the complexity of the task and subtask in the design, coding and testing phases.
TECHNICAL NOTE | doi:10.20944/preprints202211.0241.v1
Subject: Earth Sciences, Environmental Sciences Keywords: Google Earth Engine; R coding; GIS, Restoration, Decision-Making
Online: 14 November 2022 (06:29:30 CET)
Land degradation and climate change are among the main threats to the sustainability of ecosystems worldwide. Therefore, the restoration of degraded landscapes is essential to maintain the functionality of ecosystems, especially those with greater social, economic and environmental vulnerability. Nevertheless, policy-makers are frequently challenged by deciding on where to prioritize restoration actions, which usually includes to deal with multiple and complex needs under an always short budget. If these decisions are not taken based on proper data and processes, restoration implementation can easily fail. To help decision-makers taking informed decisions on where to implement restoration activities, we have developed a semiautomatic geospatial platform to prioritize areas for restoration activities based on ecological, social and economic variables. This platform takes advantage of the potential to integrate R coding, Google Earth Engine cloud computing and GIS visualization services to generate an interactive geospatial decision-maker tool for restoration. Here, we present a prototype version called "RePlant alpha" which was tested with data from the Central Zone of Chile. This exercise proved that integrating R and GEE was feasible, and that the analysis, with at least six indicators and for a specific region was also feasible to implement even from a personal computer. Therefore, the use of a virtual machine in the cloud with a large number of indicators over large areas is both possible and practical.
ARTICLE | doi:10.20944/preprints202108.0319.v1
Online: 16 August 2021 (10:56:10 CEST)
Climate risk is one of the confronting factors in Indian agriculture. To overcome this distrust, a large number of sensors can be installed in the fields,The extensive IoT platform can process the data sent by these sensors.The Data stream can be processed in real-timeusing Fuzzylogic, to offer smart solution. Network coding can enhance throughput and security. Thus reducing human interaction and improve efficiency.
ARTICLE | doi:10.20944/preprints202108.0262.v1
Subject: Engineering, Other Keywords: IoT; Smart Farming; sensor data; agricultural; Fuzzy logic; Network coding
Online: 11 August 2021 (14:09:12 CEST)
Climate risk is one of the confronting factors in Indian agriculture. To overcome this distrust, a large number of sensors can be installed in the fields,The extensive IoT platform can process the data sent by these sensors.The Data stream can be processed in real-timeusing Fuzzylogic, to offer smart solution. Network coding can enhance throughput and security. Thus reducing human interaction and improve efficiency.
ARTICLE | doi:10.20944/preprints201903.0041.v1
Online: 4 March 2019 (10:37:46 CET)
Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3'UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs xrRNAs within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3'UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs
ARTICLE | doi:10.20944/preprints202205.0336.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Long non-coding RNA; Prostate androgen-regulated transcript 1; miR-204-3p; insulin-like growth factor binding protein 2
Online: 24 May 2022 (11:57:26 CEST)
Lung cancer is a common malignant tumor of the lung and the leading cause of cancer mortality worldwide. Non-small-cell lung cancer (NSCLC) accounts for 80%–85% of lung cancer, 40% of NSCLCs will have spread beyond the lungs by the time it is diagnosed. Long non-coding RNA (LncRNA) prostate androgen-regulated transcript 1 (PART-1) was reported that promote the development of several cancers. In the current study, we conducted experiments to investigate the role of PART-1 in the proliferation, invasion, and migration of NSCLC. The expression level of the PART-1 gene increased significantly in the NSCLC cell lines, including A549, H1229, H1650, H1975, and PC9. Knocking down of PART-1 inhibited the proliferation, invasion, and migration of A549 cells, moreover, decreased the tumor proliferation in nude mice. We confirmed that PART-1 targeted miR-204-3p directly, and miR-204-3p targeted the insulin-like growth factor binding protein 2 (IGFBP-2) directly. Furthermore, we discovered that PART-1 involved the NSCLC progression by regulating the miR-204-3p-targeted IGFBP-2 pathway. LncRNA PART-1 might be a target for treating NSCLC, and a warning sign of diagnosis of early lung cancer.
ARTICLE | doi:10.20944/preprints201805.0234.v1
Subject: Biology, Other Keywords: non-coding RNA; telomerase RNA; secondary structure; synteny; homology search; yeast
Online: 16 May 2018 (11:58:28 CEST)
The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina still remain without annotated telomerase RNA.
COMMUNICATION | doi:10.20944/preprints202004.0533.v1
Online: 30 April 2020 (14:04:40 CEST)
The Standard Genetic Code (SGC) exists in every organism known on Earth. SGC evolution via early unique codon assignment, then later wobble, yields coding resembling the near-universal code. Below, later wobble also creates an optimal route to accurate codon assignment. This assignment time matches a previous mean time for ordered codes, exhibiting ≥ 90% of SGC order. Accurate evolution is also accessible, sufficiently frequent to appear in populations of 103 to 104 codes. SGC-like coding capacity, code order and assignments therefore arise together, in one attainable evolutionary intermediate. Examples, which plausibly resemble coding at evolutionary domain separation, are characterized.
ARTICLE | doi:10.20944/preprints202011.0423.v1
Subject: Biology, Anatomy & Morphology Keywords: RY coding; multispecies coalescent; phylogenomics; raptors; waterbirds; landbirds
Online: 16 November 2020 (13:57:46 CET)
The phylogeny of Neoaves, the largest clade of extant birds, has remained unclear despite intense study. The difficulty associated with resolving the early branches in Neoaves is likely driven by the rapid radiation of this group. However, conflicts among studies may be exacerbated by the hypothesis that relationships are sensitive to the data type analyzed. For example, analyses of coding exons typically yield trees that place Strisores (nightjars and allies) sister to the remaining Neoaves, while analyses of non-coding data typically yield trees where Mirandornites (flamingos and grebes) is the sister of the remaining Neoaves. Our understanding of data type effects is hampered by the fact that previous analyses have used different taxa, loci, and types of non-coding data. Herein, we provide strong corroboration of the data type effects hypothesis for Neoaves by comparing trees based on coding and non-coding data derived from the same taxa and gene regions. A simple analytical method known to minimize biases due to base composition (coding nucleotides as purines and pyrimidines) resulted in coding exon data with increased congruence to the non-coding topology using concatenated analyses. These results improve our understanding of the resolution of neoavian phylogeny and point to a challenge - data type effects - that is likely to be an important factor in phylogenetic analyses of birds (and many other taxonomic groups). Using our results, we provide a summary phylogeny that identifies well-corroborated relationships and highlights specific nodes where future efforts should focus.
REVIEW | doi:10.20944/preprints202209.0204.v1
Subject: Life Sciences, Genetics Keywords: Alzheimer’s disease; inflammation; non-coding RNAs; exosomes vesicles
Online: 14 September 2022 (09:20:29 CEST)
Alzheimer´s Disease (AD) has currently no effective treatment; however, preventive measures can significantly delay the progress/onset of the disease. Thus, accurate and early prediction of risk is an important strategy to alleviate the AD burden. Neuroinflammation is a major factor prompting the onset of the disease. Inflammation exerts its toxic effect via multiple mechanisms. Amongst others, it is affecting gene expression via modulation of non-coding RNAs (ncRNAs), such as miRNAs. Recent evidence supports that inflammation can also affect long non-coding RNAs (lncRNAs) expression. While the association between miRNAs and inflammation in AD has been extensively studied, the role of lncRNAs in neurodegenerative diseases has been less explored. In this review, we focus on lncRNAs and inflammation in the context of AD. Furthermore, since plasma-isolated extracellular vesicles (EVs) are increasingly recognized as an effective monitoring strategy of brain pathologies, we have focused on the studies reporting dysregulated lncRNAs in EVs isolated from AD patients and controls. The revised literature shows a positive association between pro-inflammatory lncRNAs and AD. However, the reports evaluating lncRNAs alterations in EVs isolated from plasma of patients and controls, although still limited confirm the value of specific lncRNAs associated with AD as reliable biomarkers. This is an emerging field that will open new avenues to improve risk prediction, patients’ stratification and may lead to the discovery of potential novel therapeutic targets for AD
ARTICLE | doi:10.20944/preprints202212.0040.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: hash embedding; deep learning; attribute information; entity coding
Online: 2 December 2022 (04:23:37 CET)
Most machine learning and deep learning algorithms can only use low-dimensional data as input, but the data that must be processed in practical applications is diverse and irregular. There are two main problems with big dynamic data. (1) The size of the embedding table grows linearly with the vocabulary size, resulting in massive memory consumption. (2) For different newly added vocabularies. To solve these two problems, this paper proposes a novel embedding algorithm that can learn attribute associations with entities based on deep and hash algorithms. Taking movie data as an example, the encoding method and the specific flow of the algorithm are presented in detail, and the effect of dynamic reuse of data models is realized. Compared with the four existing embedding algorithms which can fuse entity attribute information, the deep hash embedding algorithm proposed in this paper has obvious optimization of time and space complexity.
REVIEW | doi:10.20944/preprints202106.0145.v1
Subject: Life Sciences, Molecular Biology Keywords: Repetitive element; Transposable element; Non-coding RNA; ncRNA; Functional element; Bioinformatics
Online: 4 June 2021 (15:33:17 CEST)
With a large number of annotated non-coding RNAs (ncRNAs), repetitive sequences are found to constitute functional components (termed as repetitive elements) in ncRNAs that perform specific biological functions. Bioinformatics analysis is a powerful tool for improving our understanding of the role of repetitive elements in ncRNAs. This chapter summarizes recent findings that reveal the role of repetitive elements in ncRNAs. Furthermore, relevant bioinformatics approaches are systematically reviewed, which promises to provide valuable resources for studying the functional impact of repetitive elements on ncRNAs.
ARTICLE | doi:10.20944/preprints201705.0214.v1
Subject: Earth Sciences, Geoinformatics Keywords: multi-spectral analysis; remote sensing images; sparse coding; generalized aggregation; scene recognition
Online: 30 May 2017 (08:54:08 CEST)
Satellite scene classification is challenging because of the high variability inherent in satellite data. Although rapid progress in remote sensing techniques has been witnessed in recent years, the resolution of the available satellite images remains limited compared with the general images acquired using a common camera. On the other hand, a satellite image usually has a greater number of spectral bands than a general image, thereby permitting the multi-spectral analysis of different land materials and promoting low-resolution satellite scene recognition. This study advocates multi-spectral analysis and explores the middle-level statistics of spectral information for satellite scene representation instead of using spatial analysis. This approach is widely utilized in general image and natural scene classification and achieved promising recognition performance for different applications. The proposed multi-spectral analysis firstly learns the multi-spectral prototypes (codebook) for representing any pixel-wise spectral data, and then based on the learned codebook, a sparse coded spectral vector can be obtained with machine learning techniques. Furthermore, in order to combine the set of coded spectral vectors in a satellite scene image, we propose a hybrid aggregation (pooling) approach, instead of conventional averaging and max pooling, which includes the benefits of the two existing methods but avoids extremely noisy coded values. Experiments on three satellite datasets validated that the performance of our proposed approach is much more accurate than even the deep learning framework for spatial analysis.
ARTICLE | doi:10.20944/preprints201711.0050.v1
Online: 8 November 2017 (03:24:52 CET)
Vibrotactile displays have been reported effective in enhancing awareness of flight attitude for pilots and releasing other heavily loaded sensory channels. Although some work have been done on vibrotactile coding of flight altitude, there is lack of a systematic investigation into coding methods with combination of multiple coding parameters. In this paper, seven coding methods with combinations of multiple coding parameters (location, rhythm, intensity, and mode) were systematically studied to cue flight attitude for pilots with a vibrotactile vest. We conducted two psychophysical experiments in a static tactile sensory environment in which the attitude commands in the form of vibrotactile feedback are presented randomly, and quantitatively evaluated the effectiveness of the vest according to the users’ recognition accuracy, reaction time and information transfer rate. The results show that vibrotactile vest is effective to cue attitude information. The preferred coding method with combinations of location, rhythm and mode allowed users to perform with lowest reaction time and highest recognition accuracy and yield about 255 bits/min of information transfer rate. Overall, the presented work provides valuable insights and guidance for the design of haptic displays for vibrotactile aids for the pilots.
HYPOTHESIS | doi:10.20944/preprints202210.0371.v1
Subject: Life Sciences, Molecular Biology Keywords: Evolution, Information Evolution; Information Laws; Coding Information; System Information; Species; Stasis
Online: 25 October 2022 (02:04:56 CEST)
Others have proposed that living systems are characterized by the possession of a kind of information unique to them. This information, variously called semantic, symbolic, or coding information conveys meaning from senders to recipients, most commonly among genome and other cellular components, different cells, organisms, etc., enabling all biological functions. Unlike other kinds of information, it is only indirectly quantifiable and does not increase by copying. Here, the term system information is used to encompass the entire package of coding information enabling all organisms of a species to complete their life cycles through possession of its copy (Crkvenjakov and Heng 2021). System information grows in a nonreductive evolution only during speciation proper by the acquisition of novel functions by daughter species. Contemporary science agrees that species are units of evolution but has failed to recognize and parse the importance of phases of speciation and stasis for evolution. Confinement of system information change to speciation only explains for the first time why there are species and why their number increases nearly exponentially throughout evolution. More importantly, here we define that evolution as a process operating on a planetary scale, while chance based, is non-random mathematically since it obeys the Laws of Information which dictate the behavior of System information in organisms. Growth and persistence of system information on the non-degenerative portion of Tree of Life follow the law of conservation, which states that its growth is as parsimonious (minimal) as possible and the persistence of parental system information the maximal possible in each unit speciation step. This formulation is a restatement of Loewnstain's (1999) principle of information economy and our lock-in law (Crkvenjakov and Drmanac 2007). The principle holds that since, on chance assumption, the system information change cost is directly proportional to time, more costly pathways of achieving the same new functional goal will be, almost without exception, competed out by the less costly ones. As a corollary of the conservation law, the speciation law states that speciation follows the most economical way of growth of system information while conserving the existing one, which is horizontal information transfer by molecular sex (uptake of exogenous nucleic acid into the progeny genome) by exchange among two parents from maximally possible divergent lineages. The speciation law dictates that molecular sex mode be used since it is the most parsimonious one. The molecular sex cost in information bits is zero to the recipient, which is not the case with the generally accepted mode of vertical accumulation of information bits in a population gene pool within a lineage.
BRIEF REPORT | doi:10.20944/preprints202004.0009.v5
Online: 7 July 2020 (18:09:21 CEST)
The world is facing a major health crisis, the global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus, for which no approved antiviral agents or vaccines are currently available. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available via Addgene. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.
ARTICLE | doi:10.20944/preprints201903.0157.v1
Subject: Life Sciences, Molecular Biology Keywords: long non-coding RNA; hESC; cardiomyocyte; RNA-seq
Online: 15 March 2019 (02:11:52 CET)
Long non-coding RNAs (lncRNAs) have been found to be involved in many biological processes, including the regulation of cell differentiation, but a complete characterization of lncRNA is still lacking. Additionally, there is evidence that lncRNAs interact with ribosomes, raising questions about their functions in cells. Here, we used a developmentally staged protocol to induce cardiogenic commitment of hESCs and then investigated the differential association of lncRNAs with polysomes. Our results identified lncRNAs in both the ribosome-free and polysome-bound fractions during cardiogenesis and showed a very well-defined temporal lncRNA association with polysomes. Clustering of lncRNAs was performed according to the gene expression patterns during the five timepoints analyzed. In addition, differential lncRNA recruitment to polysomes was observed when comparing the differentially expressed lncRNAs in the ribosome-free and polysome-bound fractions or when calculating the polysome-bound vs ribosome-free ratio. The association of lncRNAs with polysomes could represent an additional cytoplasmic role of lncRNAs, e.g., in translational regulation of mRNA expression.
ARTICLE | doi:10.20944/preprints201812.0209.v2
Subject: Mathematics & Computer Science, Probability And Statistics Keywords: neural population coding; mutual information; Kullback-Leibler divergence; Rényi divergence; Chernoff divergence; approximation; discrete variables
Online: 7 March 2019 (07:36:24 CET)
Although Shannon mutual information has been widely used, its effective calculation is often difficult for many practical problems, including those in neural population coding. Asymptotic formulas based on Fisher information sometimes provide accurate approximations to the mutual information but this approach is restricted to continuous variables because the calculation of Fisher information requires derivatives with respect to the encoded variables. In this paper, we consider information-theoretic bounds and approximations of the mutual information based on Kullback--Leibler divergence and Rényi divergence. We propose several information metrics to approximate Shannon mutual information in the context of neural population coding. While our asymptotic formulas all work for discrete variables, one of them has consistent performance and high accuracy regardless of whether the encoded variables are discrete or continuous. We performed numerical simulations and confirmed that our approximation formulas were highly accurate for approximating the mutual information between the stimuli and the responses of a large neural population. These approximation formulas may potentially bring convenience to the applications of information theory to many practical and theoretical problems.
REVIEW | doi:10.20944/preprints201809.0004.v1
Subject: Life Sciences, Virology Keywords: gammaherpesviruses, long non-coding RNAs, RNA structure and function, viral pathogenesis
Online: 1 September 2018 (17:36:48 CEST)
Advances in next-generation sequencing have facilitated the discovery of a multitude of long non-coding RNAs (lncRNAs) with pleiotropic functions in cellular processes, disease and viral pathogenesis. It came as no surprise when viruses were also revealed to transcribe their own lncRNAs. Among them, gammaherpesviruses, one of the three subfamilies of the Herpesviridae, code their largest number. These structurally and functionally intricate non-coding (nc) transcripts modulate cellular and viral gene expression to maintain viral latency or prompt lytic reactivation. The lncRNAs allow the virus to escape cytosolic surveillance, sequester and re-localize essential cellular factors and modulate the cell cycle and proliferation. Some viral lncRNAs act as “messenger molecules”, transferring information about viral infection to neighboring cells. This broad range of lncRNA functions is achieved through lncRNA structure-mediated interactions with effector molecules of viral and host origin, including other RNAs, proteins and DNAs. In this review, we discuss examples of gammaherpesvirus-encoded lncRNAs, emphasize their unique structural attributes, and link them to viral life cycle, pathogenesis and disease progression. We will address their potential as novel targets for drug discovery and propose future directions to explore lncRNA structure and function relationship.
ARTICLE | doi:10.20944/preprints202104.0037.v1
Subject: Arts & Humanities, Anthropology & Ethnography Keywords: Urban morphology; Transitional morphologies; Assemblage; Urban coding; Adaptive city; Permutation; Parametric Design
Online: 1 April 2021 (17:46:19 CEST)
Grounded on urban morphology studies, the research tries to overcome the analysis of the permanents elements of the city seeking for a transitional paradigm in urban morphology, aiming at grasping the dynamics in urban evolution and providing operative tools for urban regeneration design in an adaptive approach. A combination of four actions of urban analysis is here suggested to highlight urban dynamics: a. Sorting the transitional steps of urban morphologies (within rapid market processes), b. Underlining rules and Processes characterizing urban coding in transition, c. Mapping urban assemblages in the adaptive city and d. Reading and representing urban permutation phenomenon. The results of this multifaced and multidimensional set of analytical tools allow to outline a new design thinking paradigm moving towards a parametric approach to urban design of cities in transition broadening the extent of urban regeneration process and supporting urban policies in the framework community based approach.
ARTICLE | doi:10.20944/preprints202211.0537.v2
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: Backpropagation-free Network, Information Theory, Maximal Coding Rate Reduction
Online: 29 November 2022 (08:13:27 CET)
We propose a forward-only multi-layer encoding-decoding framework based on the principle of Maximal Coding Rate Reduction (MCR$^2$), an information-theoretic metric that measures a statistical distance between two sets of feature vectors up to the second moment. The encoder directly transforms data vectors themselves via gradient ascent to maximize the MCR$^2$ distance between different classes in the feature space, resulting in class-wise mutually orthogonal subspace representations. The decoder follows a process symmetric to the encoder, and transforms the subspace feature vectors via gradient descent to minimize the MCR$^2$ distance between the reconstructed data and the original data. We show that the encoder transforms data to linear discriminative representations without breaking the higher-order manifolds, and the decoder reconstructs the data with high fidelity.
REVIEW | doi:10.20944/preprints202109.0253.v1
Subject: Biology, Other Keywords: Mycobacteria; Mycobacterium tuberculosis; non-coding RNA; RNA-seq; transcriptome
Online: 15 September 2021 (11:00:59 CEST)
A definitive transcriptome atlas for the non-coding expressed elements of pathogenic mycobacteria does not exist. Incomplete lists of non-coding transcripts can be obtained for some of the reference genomes (e.g. Mycobacterium tuberculosis H37Rv) but to what extent these transcripts have homologues in closely related species or even strains is not clear. This has implications for the analysis of transcriptomic data; non-coding parts of the transcriptome are often ignored in the absence of formal, reliable annotation. Here, we review the state of our knowledge of non-coding RNAs in pathogenic mycobacteria, emphasising the disparities in the information included in commonly used databases. We then proceed to review ways of combining computational solutions for predicting the non- coding transcriptome with experiments that can help refine and confirm these predictions.
Subject: Engineering, Automotive Engineering Keywords: data transmission; erasure communication channel; adaptive coding; satellite formation
Online: 3 November 2020 (12:39:08 CET)
The paper deals with the navigation data exchange between two satellites moving in a swarm. It is focused on reduction of the inter-satellite demanded communication channel capacity taking into account dynamics of the satellites relative motion and possible erasing in the channel the navigation data. The feedback control law is designed ensuring regulation of the relative satellites motion. The adaptive binary coding/decoding procedure for the satellites navigation data transmission over the limited capacity communication channel is proposed and studied for the cases of ideal and erasure channels. Dependence of the regulation time on the data transmission rate is numerically evaluated. Results of the numerical study of the closed-loop system performance and accuracy of the data transmission algorithm on the communication channel bitrate and erasure probability are obtained based on the extensive simulations. These results provide dependence of the required load of the communication channel on the desired quality of the regulation process. It is shown that both data transmission error and regulation time depend inversely proportional on the communication rate, and that for the significantly high data transmission rate erasure of data in the channel with probability up to 0.3 does not make an effect on the regulation time.
REVIEW | doi:10.20944/preprints201804.0051.v1
Subject: Medicine & Pharmacology, Cardiology Keywords: atherosclerosis; cardiovascular disease; chaos theory; non-coding RNAs; Alu-elements; NF-κB; miRNA; miRNA sponges
Online: 4 April 2018 (06:36:55 CEST)
Atherosclerosis (ATH) and Coronary Artery Disease (CAD) are chronic inflammatory diseases with an important genetic background which derive from the cumulative effect of multiple common risk alleles, most of them located in genomic non-coding regions. These complex diseases behave as non-linear dynamical systems that show a high dependence on their initial conditions, so that long-term predictions of disease progression are unreliable. One likely possibility is that the non-linear nature of ATH could be dependent on non-linear correlations in the structure of the human genome. In this review we show how Chaos theory analysis highlighted genomic regions that shared specific structural constraints that could have a role in ATH progression. These regions were shown to be enriched in repetitive sequences of the Alu family, genomic parasites which colonized the human genome, which show a particular secondary structure and have been involved in the regulation of gene expression. We also review the impact of Alu elements on the mechanisms that regulate gene expression, especially highlighting the molecular mechanisms by which the Alu elements could alter the inflammatory homeostasis. We devise especial attention to their relationship with the lncRNA ANRIL, the strongest risk factor for ATH, their role as miRNA sponges, and their ability to interfere with the regulatory circuitry of the NF-kB response. We aim to characterize ATH as a non-linear dynamic system in which small initial alterations in the expression of a number of repetitive elements are somehow amplified to reach phenotypic significance.
ARTICLE | doi:10.20944/preprints202204.0088.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: Lossy/ lossless compression; Huffman coding; real-time PPG measurement; heart rate estimate, Message Queueing Telemetry Transport (MQTT); healthcare system
Online: 11 April 2022 (04:21:00 CEST)
Nowadays, wearable devices for human health monitoring are increasingly become popular and widely used. Typically, the wearable device is small size and operates with batteries. Therefore, the wearable device acquires bio-signals and transfers to smartphones or personal computers (PC) via WiFi/ Bluetooth for processing data. To reduce power consumption is one of the most important challenges of designing wearable devices. To solve this problem, the proposed signal quality valuation (SQV) method can be select the high-quality signal and reduce the transfer time to other devices. In this paper, the proposed SQV and data compression method rely on real-time PPG signals analysis to retain important information of PPG signal, improve performance and power consumption of PPG devices. Besides, we also proposed Heuristic rules for heart rate (HR) estimation with compression data. The experimental results show that the highest compression ratio (CR) is 387.8 with BIDMC Physionet database (sampling frequencies of 125 Hz) and HR error as 1.43 bpm for averaging absolute error (avAE), the standard deviation absolute error (sdAE as 0.4) and relative error mean (avRE as 0.019). The proposed real-time PPG measurement system (sampling frequency as 100/ 200/ 400 Hz) reduce power consumption and open the new structure for healthcare application systems
REVIEW | doi:10.20944/preprints202206.0046.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Acute myeloid leukemia; Pediatric; Epigenetics; DNA methylation; Histone modification; Non-coding RNAs; Therapy
Online: 3 June 2022 (10:59:28 CEST)
Acute myeloid leukemia (AML) is a hematological malignancy that is the culmination of genetic and epigenetic alterations in the hematopoietic progenitor cells, leading to uncontrolled proliferation at the expense of normal hematopoiesis and bone marrow exhaustion. Although the outcomes for pediatric AML have improved in recent decades, at least one third of children still have relapses. Recent studies have notably highlighted the important role of dysregulated epi-genetic mechanisms in myeloid leukemogenesis. Epigenetic modifications are frequently reversible compared to genetic alterations, thus providing opportunities for targeted epigenetic therapy. In this review, we summarize the landscape of epigenetic alterations and the progress to date in epigenetic targeted therapy, and focus on the future role of epigenetic abnormalities in predicting relapse and the precision therapy in pediatric AML.
ARTICLE | doi:10.20944/preprints201901.0308.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: encryption space ratio; entropy coding; H.264/AVC; internet of multimedia things; lightweight cipher; selective encryption
Online: 30 January 2019 (10:09:35 CET)
Within an Internet of Multimedia Things, the risk of disclosing streamed video content, such as arising from video surveillance, is of heightened concern. This leads to the encryption of that content. To reduce the overhead and lack of flexibility arising from full encryption of the content, a good number of selective-encryption algorithms have been proposed in the last decade. Some of them have limitations, in terms of significant delay due to computational cost, or excess memory utilization, or, despite being energy efficient, do not provide a satisfactory level of confidentiality, due to their simplicity. To address such issues, this paper presents a lightweight selective encryption scheme, in which encoder syntax elements are encrypted with the innovative EXPer (EXtended Permutation with exclusive OR). The selected syntax elements are taken from the final stage of video encoding that is during entropy coding. As a diagnostic tool, the Encryption Space Ratio measures encoding complexity of the video relative to the level of encryption so as to judge the success of the encryption process, according to entropy coder. A detailed comparative analysis of EXPer with state-of-the-art algorithms confirms that the EXPer provides significant confidentiality with a small computational cost and negligible encryption bitrate overhead. Thus, the results demonstrate that the proposed security scheme is a suitable choice for constrained devices in an Internet of Multimedia Things environment.
ARTICLE | doi:10.20944/preprints201802.0099.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: Random Linear Network Coding; Mobile Cellular Networks; 4G Long-Term Evolution (LTE); 5G New Radio (NR); Mobile video delivery
Online: 14 February 2018 (13:38:12 CET)
Exponential increase in mobile video delivery will continue with the demand for higher resolution, multi-view and large-scale multicast video services. Novel fifth generation (5G) 3GPP New Radio (NR) standard will bring a number of new opportunities for optimizing video delivery across both 5G core and radio access network. One of the promising approaches for video quality adaptation, throughput enhancement and erasure protection is the use of packet-level random linear network coding (RLNC). In this work, we discuss the integration of RLNC into the 5G NR standard, building upon the ideas and opportunities identified in 4G LTE. We explicitly identify and discuss in detail novel 5G NR features that provide support for RLNC-based video delivery in 5G, thus pointing out to the promising avenues for future research.
ARTICLE | doi:10.20944/preprints202212.0431.v1
Subject: Life Sciences, Immunology Keywords: transcriptomics; COVID-19; tuberculosis; progression; non-coding RNA; hub proteins
Online: 23 December 2022 (01:24:48 CET)
The pandemic of COVID-19 ravaged most countries and made the healthcare system go for a toss. The impact of the disease is different in each patient and it progresses differently. Based on the severity, the COVID-19 infection is stratified into three main categories- mild, moderate, and severe. In this study, we performed a transcriptomic study of different stages and studied the progression of the disease. The study was based on an Indian population of 28 COVID-19 patients, which were classified into different groups. Our analysis has shown that as the disease progresses, the genes involved in the degranulation of the neutrophils and galactose metabolism increase. Furthermore, we identified the hub proteins in each stage. TB is one of the comorbidities of COVID-19 and a comparative study was done to identify the preserved module of genes in both. Enrichment analysis showed that the members of this module are significantly involved in translation and ribosome synthesis.
ARTICLE | doi:10.20944/preprints202206.0331.v1
Subject: Mathematics & Computer Science, General Mathematics Keywords: Alien Tiles; Coding Theory; Lights Out; Recreational Mathematics; Abstract Algebra
Online: 24 June 2022 (05:13:05 CEST)
The switching game Lights Out and its variants were studied extensively as recreational mathematics problems. The game board of the ordinary Lights Out is a rectangular grid of lights, where each light is either on or off. By clicking a light, the clicked light and its adjacent rectilinear neighbors are toggled. Given an arbitrary initial configuration of lights, the final mission is to “solve” this game by switching off all the lights. Most studies on Lights Out and its variants focused on the solvability of given games or the number of solvable games, but when the game is viewed in a coding-theoretical perspective, more interesting questions with special meanings in coding theory will naturally pop up, such as finding the minimal number of lit lights among all solvable games except the solved game, or finding the minimal number of lit lights that the player can achieve from a given unsolvable game, etc. However, these problems are usually hard to be solved in general in terms of algorithmic complexity. This study considers a natural extension of the Lights Out game, which enlarges the toggle pattern in a way that all the lights in the same row and those in the same column of the clicked light are toggled. This variant of Lights Out is a two-state version of a switching game called Alien Tiles. In this paper, we investigate the properties of the two-state Alien Tiles, and discuss several coding-theoretical problems about this game. Then, we apply this game as an error correction code and investigate its optimality. We also give a brief overview on algorithmic complexity and coding theory for readers who are not familiar with these topics. The purpose of this paper is to propose ways of playing switching games in a think-outside-the-box manner, which benefit the recreational mathematics community.
REVIEW | doi:10.20944/preprints202010.0159.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Thyroid carcinoma; non-coding RNA; radioactive iodine; drug resistance; prognosis
Online: 7 October 2020 (14:28:40 CEST)
Thyroid cancer is the most prevalent malignancy of the endocrine system and the ninth most common cancer globally. Despite the advances in the management of thyroid cancer, there are critical issues with the diagnosis and treatment of thyroid cancer that result in the poor overall survival of undifferentiated and metastatic thyroid cancer patients. Recent studies have revealed the role of different non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) that are dysregulated during thyroid cancer development or the acquisition of resistance to therapeutics, and may play key roles in treatment failure and poor prognosis of the thyroid cancer patients. Here, we systematically review the emerging roles and molecular mechanisms of ncRNAs that regulate thyroid tumorigenesis and drug response. We then propose the potential clinical implications of ncRNAs as novel diagnostic and prognostic biomarkers for thyroid cancer.
Subject: Life Sciences, Genetics Keywords: mucosal melanoma; dogs; transcriptome sequencing; long non-coding RNAs (lncRNAs)
Online: 3 May 2019 (13:59:22 CEST)
Mucosal melanomas (MM) are rare aggressive cancers in humans and one of the most common forms of oral cancers in dogs. Similar biological and histological features are shared between MM in both species making dogs a powerful model for comparative oncology studies of melanomas. Although exome sequencing recently identified recurrent coding mutations in canine MM, little is known about changes in non-coding gene expression and more particularly in canine long non-coding RNAs (lncRNAs), which are commonly dysregulated in human cancers. Here, we sampled a large cohort (n= 52) of canine normal/tumor oral MM from three predisposed breeds (poodles, Labrador retrievers and golden retrievers) and used deep transcriptome sequencing to identify more than 400 differentially expressed (DE) lncRNAs. We further prioritized candidate lncRNAs by comparative genomic analysis to pinpoint 26 dog-human conserved DE lncRNAs, including SOX21-AS, ZEB2-AS and CASC15 lncRNAs. Using unsupervised co-expression networks analysis with coding genes, we inferred potential functions of DE lncRNAs suggesting associations with cancer-related genes, cell cycle and carbohydrate metabolism GO terms. Finally, we exploited our multi-breed design to identify DE lncRNAs per breed. This study provides a unique transcriptomic resource for studying oral melanoma in dogs and highlights lncRNAs that may potentially be diagnostic or therapeutic targets for human and veterinary medicine.
ARTICLE | doi:10.20944/preprints201810.0206.v1
Subject: Behavioral Sciences, Behavioral Neuroscience Keywords: human psychophysics; apparent motion; temporal integration; cat; retina; neural coding; Hassenstein-Reichardt detector; model analysis
Online: 10 October 2018 (06:31:03 CEST)
Under optimal conditions, just 3–6 ms of visual stimulation suffices for humans to see motion. Motion perception on this time scale implies that the visual system under these conditions reliably encodes, transmits, and processes neural signals with near-millisecond precision. Motivated by in vitro evidence for high temporal precision of motion signals in the primate retina, we investigated how neuronal and perceptual limits of motion encoding relate. Specifically, we examined the correspondence between the time scale at which cat retinal ganglion cells in vivo represent motion information and temporal thresholds for human motion discrimination. The time scale for motion encoding by ganglion cells ranged from 4.6–91 ms, depended nonlinearly on temporal frequency but not on contrast. Human psychophysics revealed that minimal stimulus durations required for perceiving motion direction were similarly brief, 5.6–65 ms, similarly depended on temporal frequency but, above ~10%, not on contrast. Notably, physiological and psychophysical measurements corresponded closely throughout (r = 0.99), despite more than a 20-fold variation in both human thresholds and optimal time scales for motion encoding in the retina. These results demonstrate that neural circuits for motion vision in cortex can maintain and make use of the high temporal fidelity of the retinal output signals.
ARTICLE | doi:10.20944/preprints202110.0281.v1
Subject: Biology, Animal Sciences & Zoology Keywords: selective pressures; mitochondrial protein-coding genes; subterranean voles; adaptations; subterranean lifestyle.
Online: 19 October 2021 (15:01:42 CEST)
The current study evaluates the selection signals in the evolution of mitochondrial DNA of voles, subfamily Arvicolinae, during the colonization of subterranean environments. The comparative sequence analysis of mitochondrial protein-coding genes of eight subterranean vole species (Prometheomys schaposchnikowi, three species of the genus Ellobius: E. talpinus, E. fuscocapillus and E. lutescens, two species of the genus Terricola: T. subterraneus and T. daghestanicus, Lasiopodomys mandarinus and Hyperacrius fertilis) and their closest aboveground relatives using codon-substitution models was applied. The highest number of selection signatures was detected in genes ATP8 and CYTB. The relaxation of selection was observed in most mtDNA protein-coding genes. In mole voles (genus Ellobius) the signatures of adaptive evolution of mitochondrial genes related to subterranean niche were most pronounced. The number of selection signatures was found to be independent of the evolutionary age of the lineage but fits the degree of specialization to the subterranean niche. The common trends of selective pressures were observed among the evolutionary ancient and highly specialized subterranean rodent families and phylogenetically young lineages of voles. It suggests that the signatures of adaptations in individual mitochondrial protein-coding genes associated with the colonization of the subterranean niche may appear within a rather short evolutionary timespan.
ARTICLE | doi:10.20944/preprints202108.0138.v2
Subject: Materials Science, Nanotechnology Keywords: inorganic nanoparticles; in silico; optimization; theranostic; therapeutic; diagnostic; computation; coding; Python
Online: 7 September 2021 (11:57:23 CEST)
Inorganic nanoparticles are utilized for therapeutic, diagnostic, or in combination, theranostic purposes. The latter involves simultaneous sensing, imaging, or tracking of drug delivery. Furthermore, these nanoparticles can differ in their morphologies, which affect outcomes such as the effectiveness of hyperthermia, induction, drug loading, circulation time by escaping the body's immune system, imaging modality clarity, and biosensing. However, design of these theranostics is limited by the lack of a method to predict their therapeutic efficacy. Herein, we report a simple and novel computational approach via algebraic and geometric calculations of surface area (SA) to volume (V) ratios (SA:V) which can help predict the efficacy of the inorganic nanoparticles of the investigated morphologies. The approach comprises a coding platform for the program and uses Python 3 on a Windows 10 operating system. Analyses of 29 polyhedral morphologies that inorganic nanoparticles could assume ex silico showed that only particular concave and convex morphologies in this size regime are more productive over the standard sizes as well as a few noted in literature for baseline comparison. Our results provide a method that can aid in predicting the efficacy of inorganic nanoparticles with certain morphology giving rise to their fundamental basis and eventual implementation ex silico.
Subject: Engineering, Other Keywords: error-correction coding, polar codes, convolutional codes, list decoding, sequential decoding
Online: 11 May 2021 (10:42:11 CEST)
Polar coding gives rise to the first explicit family of codes that provably achieve capacity with efficient encoding and decoding for a wide range of channels. Recently, Arikan presented a new polar coding scheme, which he called polarization-adjusted convolutional (PAC) codes. At short blocklengths, such codes offer a dramatic improvement in performance as compared to CRC-aided list decoding of conventional polar codes. PAC codes are based primarily upon the following main ideas: replacing CRC codes with convolutional precoding (under appropriate rate profiling) and replacing list decoding by sequential decoding. Simulation results show that PAC codes, resulting from the combination of these ideas, are close to finite-length lower bounds on the performance of any code under ML decoding. One of our main goals in this paper is to answer the following question: is sequential decoding essential for the superior performance of PAC codes? We show that similar performance can be achieved using list decoding when the list size $L$ is moderately large (say, $L \geq 128$). List decoding has distinct advantages over sequential decoding in certain scenarios, such as low-SNR regimes or situations where the worst-case complexity/latency is the primary constraint. Another objective is to provide some insights into the remarkable performance of PAC codes. We first observe that both sequential decoding and list decoding of PAC codes closely match ML decoding thereof. We then estimate the number of low weight codewords in PAC codes, and use these estimates to approximate the union bound on their performance. These results indicate that PAC codes are superior to both polar codes and Reed-Muller codes. We also consider random time-varying convolutional precoding for PAC codes, and observe that this scheme achieves the same superior performance with constraint length as low as $\nu = 2$.
REVIEW | doi:10.20944/preprints201801.0232.v1
Subject: Biology, Other Keywords: small non-coding RNAs; gene regulation; archaea; stress response; regulatory networks
Online: 25 January 2018 (03:57:55 CET)
Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing, and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3’ UTR, 5’ UTR, CDS-binding). These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved, and how sRNAs integrate with complex regulatory networks.
CONCEPT PAPER | doi:10.20944/preprints202007.0454.v1
Subject: Life Sciences, Genetics Keywords: gene evolution; gene formation; long non-coding RNA genes; pseudogenes; USP18; GGT5
Online: 20 July 2020 (04:39:41 CEST)
A small phylogenetically conserved sequence of 11,231 bp termed FAM247 is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or mice genomes, the long non-coding RNA genes and pseudogenes the most recent as they appear to be present only in the human genome. We propose that the conserved sequence provides a nucleation site for new gene development at evolutionary conserved chromosomal loci where the FAM247 sequences reside. The FAM247 sequence also carries information in its open reading frames that provides protein exon amino acid sequences; one exon plays an integral role in immune system regulation, specifically, the function of ubiquitin specific protease (USP18) in the regulation of interferon. An analysis of this multifaceted sequence and the genesis of genes that contain it are presented.
ARTICLE | doi:10.20944/preprints201901.0153.v1
Subject: Physical Sciences, Applied Physics Keywords: interfaces; quantum communications; quantum entanglement; quantum image processing; quantum teleportation; superdense coding
Online: 16 January 2019 (07:20:45 CET)
During the last 25 years the scientific community has coexisted with the most fascinating protocol due to Quantum Physics: quantum teleportation (QTele), which would have been impossible if quantum entanglement, so questioned by Einstein, did not exist. In this work, a complete architecture for the teleportation of Computational Basis States (CBS) is presented. Such CBS will represent each of the possible 24 classical bits commonly used to encode every pixel of a 3-color-channel-image (red-green-blue, or cyan-yellow-magenta). For this purpose, a couple of interfaces: classical-to-quantum (Cl2Qu) and quantum-to-classical (Qu2Cl) are presented with two versions of the teleportation protocol: standard and simplified.
ARTICLE | doi:10.20944/preprints201810.0118.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: bandelet; medical imaging; quadtree decomposition; SPIHT coder; video coding; video quality measure
Online: 7 October 2018 (10:26:18 CEST)
The operations of digitization, transmission and storage of medical data, particularly images require increasingly effective encoding methods not only in terms of compression ratio and flow of information but also in terms of visual quality. At first, there was DCT (discrete cosine transform) then DWT (discrete wavelet transform) and their associated standards in terms of coding and image compression. After that, the 2nd generation wavelets seeks to be positioned and confronted to the image and video coding methods currently used. It is in this context that we suggested a method combining bandelets and SPIHT (set partitioning in hierarchical trees) algorithm. There are two main reasons for our approach: the first lies in the nature of the bandelet transform to take advantage by capturing the geometrical complexity of the image structure. The second reason stems in the suitability of encoding the bandelet coefficients by the SPIHT encoder. Quality measurements shows that in some cases (for low bit rates) the performances of the proposed coding compete with the well-established ones and opens up new application prospects in the field of medical imaging.
REVIEW | doi:10.20944/preprints202101.0057.v1
Subject: Biology, Anatomy & Morphology Keywords: Genetic coding; free energy transduction; non-equilibrium thermodynamics; transition-state stabilization; conformational change; aminoacyl-tRNA synthetases; emergent phenomena
Online: 4 January 2021 (16:21:16 CET)
Bioenergetics, genetic coding, and catalysis are all difficult to imagine emerging without pre-existing historical context. That context is often posed as a “Chicken and Egg” problem; its resolution is concisely described by de Grasse Tyson: “the egg was laid by a bird that was not a chicken”. The concision and generality of that answer furnish no details—only an appropriate framework from which to examine detailed paradigms that might illuminate paradoxes underlying these three life-defining biomolecular processes. We examine experimental aspects here of five examples that all conform to the same paradigm. The paradox in each example is resolved by coupling if, and only if, conditions for two related transitions between levels. One drives, and each restricts fluxes through, or “gates” the other. That reciprocally-coupled gating, in which two gated processes constrain one another, maps onto the formal structure of “strange loops”. That mapping may help unite the axiomatic foundations of genetics, bioenergetics, and catalysis. As a physical analog for Gödel’s logic, biomolecular strange-loops provide a natural metaphor around which to organize these data, linking biology to the physics of information, free energy, and the second law of thermodynamics.
REVIEW | doi:10.20944/preprints202108.0426.v1
Subject: Life Sciences, Microbiology Keywords: Polyhydroxyalkanoates; mcl-PHA; scl-PHA; Post-transcriptional regulation; Riboregulation; Small non-coding RNAs
Online: 23 August 2021 (10:43:23 CEST)
The large production of non-degradable petrol-based plastics has become a major global issue due to its environmental pollution. Biopolymers produced by microorganisms such as polyhydroxyalkanoates (PHAs) are gaining potential as a sustainable alternative, but the high cost associated to their industrial production has been a limiting factor. Post-transcriptional regulation is a key step to control gene expression in changing environments and has been reported to play a major role in numerous cellular processes. However, limited reports are available concerning the regulation of PHA accumulation in bacteria, and many essential regulatory factors still need to be identified. Here, we review studies where the synthesis of PHA has been reported to be regulated at the post-transcriptional level, and we analyze the RNA-mediated networks involved. Finally, we discuss the forthcoming research on riboregulation, synthetic and metabolic engineering which could lead to improved strategies for PHAs synthesis in industrial production, thereby reducing the costs currently associated with this procedure.
Subject: Physical Sciences, Acoustics Keywords: Single-pixel; spectroscopy; near-infrared; DMD; multiplexing; spectral coding; sub-millisecond; compressive measurement
Online: 31 July 2021 (15:10:23 CEST)
In this contribution, we present a high-speed multiplex grating spectrometer based on a spectral coding approach that is founded on principles of compressive sensing. The spectrometer employs a single-pixel InGaAs detector to measure the signals encoded by an amplitude spatial light modulator (digital micromirror device, DMD). This approach leads to a speed advantage and multiplex sensitivity advantage atypical for standard dispersive systems. Exploiting the 18.2 kHz pattern rate of the DMD, we demonstrate 4.2 ms acquisition times for full spectra with a bandwidth of 450 nm (5250 cm-1 – 4300 cm-1; 1.9 µm – 2.33 µm). Due to the programmability of the DMD, spectral regions of interest can be chosen freely, thus reducing acquisition times further, down to the sub-millisecond regime. The adjustable resolving power of the system accessed by means of computer simulations is discussed, quantified for different measurement modes, and verified by comparison with a state-of-the-art Fourier-transform infrared spectrometer. We show measurements of characteristic polymer absorption bands in different operation regimes of the spectrometer. The theoretical multiplex advantage of 8 was experimentally verified by comparison of the noise behavior of the spectral coding approach and a standard line-scan approach.
ARTICLE | doi:10.20944/preprints202002.0460.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: digital metamaterial; liquid crystal (LC); coding particle; beam steering; RCS reduction; beam shaping
Online: 29 February 2020 (09:32:31 CET)
This paper presents a multifunctional reflective digital metasurface of arbitrary base based on voltage tunable liquid crystal (LC). The reflective digital metamaterial can be multiplexed for different desirable functions by properly biasing the LC for different code patterns. Simulation results of three significant functions, beam steering with a steering elevation angle 27° at 75 GHz, RCS reduction of at least 15dB along the incident direction, and beam shaping with different beam shapes have been presented to prove the concept.
ARTICLE | doi:10.20944/preprints201810.0185.v1
Subject: Biology, Animal Sciences & Zoology Keywords: long non-coding RNA; bovine mammary gland; linseed/safflower oil; lipid metabolism; fatty acid synthesis; cis-regulation
Online: 9 October 2018 (10:53:39 CEST)
This study aimed to characterize the long non-coding RNA (lncRNA) expression in the bovine mammary gland and to infer their functions in dietary response to 5% linseed oil (LSO) or 5% safflower oil (SFO). Twelve cows (six per treatment) in mid lactation were fed a control diet for 28 days followed by a treatment period (control diet supplemented with 5% LSO or 5% SFO) of 28 days. Mammary gland biopsies were collected from each animal on day-14 (D-14, control period), D+7 (early treatment period) and D+28 (late treatment period) and were subjected to RNA-Sequencing and subsequent bioinformatics analyses. Functional enrichment of lncRNA was performed via potential cis regulated target genes located within 50 Kb flanking regions of lncRNAs and having expression correlation of >0.7 with mRNAs. A total of 4955 lncRNAs (325 known and 4630 novel) were identified which potentially cis targeted 59 and 494 genes in LSO and SFO treatments, respectively. Enrichments of cis target genes of lncRNAs indicated potential roles of lncRNAs in immune function, nucleic acid metabolism and cell membrane organization processes as well as involvement in Notch, cAMP and TGF-β signaling pathways. Thirty-two and 21 lncRNAs were differentially expressed (DE) in LSO and SFO treatments, respectively. Six genes (KCNF1, STARD13, BCL6, NXPE2, HHIPL2 and MMD) were identified as potential cis target genes of six DE lncRNAs. In conclusion, this study indicated potential roles for lncRNAs in mammary gland immune functions and development and provided potential candidate genes and pathways via which lncRNAs can function in diet responses.
ARTICLE | doi:10.20944/preprints202110.0315.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: Code construction; minimum code distance; noise immunity; coding efficiency; theoretically achievable boundary; correction codes
Online: 21 October 2021 (15:08:02 CEST)
The digital representation of various signals allows, at the subsequent stages of their transmission, to apply correction codes that provide protection against possible errors arising from the action of interference in the communication channel. At the same time, it is important that, with the required correcting ability, these codes have the maximum possible speed. The article presents the results of calculations for linear codes, showing their really achievable limiting capabilities.
ARTICLE | doi:10.20944/preprints202104.0217.v1
Subject: Life Sciences, Biochemistry Keywords: full-length coding region sequence; HIV-1; Korean subclade B; sequence length; hemophilia; evolution
Online: 7 April 2021 (17:26:03 CEST)
We aimed to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among pa-tients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB) was performed. Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Overall, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Phylogenetic analysis indicated that within KSB, two FLs from plasma donors O and P comprised two clusters together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis for the KSB of HIV-1 revealed 91 signature nucleotide residues (1.05%). In total, 48 and 43 signature nucleotides originated from clusters O and P, respectively. Only six positions contained 100% specific nucleotide(s) in clusters O and P. Additionally, in-depth FL analysis over 30 years indicates that the KSB FL significantly increased over time before combined antiretroviral therapy (cART) and decreased with cART. The increase occurred due to a significant increase in env and nef genes, originating in the variable regions of both genes. The increase in the sequence length of HIV-1 over time suggests that it has an evolutionary direction.
ARTICLE | doi:10.20944/preprints202102.0575.v1
Subject: Life Sciences, Biochemistry Keywords: full-length coding region sequence; HIV-1; Korean subclade B; sequence length; hemophilia; evolution
Online: 25 February 2021 (10:31:36 CET)
The objective of this study is to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) in an outbreak of HIV-1 infection among patients with hemophilia and local controls identified as infected with the Korean subclade B of HIV-1 (KSB). Genes amplified by overlapping RT-PCR or nested PCR were subjected to direct sequencing. In total, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Non-KSB sequences were retrieved from the Los Alamos National Laboratory HIV Database. Phylogenetic analysis indicated that within KSB, 2 FLs from plasma donors O and P comprised two clusters together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis for the KSB of HIV-1 revealed signature nucleotide residues at 1.05%, compared with local controls. Additionally, in-depth FLs sequence analysis over 30 years in KSB indicates that the KSB FL significantly increases over time before combined antiretroviral therapy (cART) and decreases on cART. Furthermore, the increase in FLs over time significantly occurred in the subtypes B, C and G, but, there was no increase in the subtypes D, A, and F1. Consequently, subtypes F1 and D had the shortest sequence length. Our analysis was extended to compare HIV-1 with HIV-2 and SIVs. Essentially, the longer the sequence length (SIVsm > HIV-2 > SIVcpz > HIV-1), the longer the survival period. The increase in the length of the HIV-1 sequence over time suggests that it might be an evolutionary direction toward attenuated pathogenicity.
REVIEW | doi:10.20944/preprints201810.0500.v3
Subject: Chemistry, Other Keywords: DNA repair; long non-coding RNA; microRNA; DNA damage; double-strand breaks; NHEJ; HR
Online: 26 October 2018 (10:22:45 CEST)
DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer. Eukaryotes have evolved two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ) to repair DSBs. Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated. This review summarizes recent discoveries on the identification of non-coding RNAs and RNA-mediated regulation of DSB repair
COMMUNICATION | doi:10.20944/preprints201808.0534.v1
Subject: Life Sciences, Genetics Keywords: long non coding RNA, whole exome sequencing, protein interaction, congenital pouch colon, microscale thermophoresis
Online: 30 August 2018 (15:30:35 CEST)
Congenital Pouch Colon (CPC) is a rare anorectal anomaly common to North Western India specifically Rajasthan. Despite efforts to understand the clinical genetic makeup of CPC, no attempt on identifying non-coding RNAs was done. We have earlier reported CPC's rare variants from whole exome sequencing across 18 affected samples in a total of 64 subjects. A Smith-Waterman algorithm was used to infer a couple of lncRNAs from WES samples of CPC with predictions from the Noncode database. Further screening and quantification using PCR, we ascertained interactions using Micro Scale Thermophoresis (MST). We report the role of lnc-EPB41-1-1 shown to be promiscuously interacting with KIF13A substantiating their role in regulation.
ARTICLE | doi:10.20944/preprints202109.0503.v1
Subject: Biology, Animal Sciences & Zoology Keywords: mitogenome; transmembrane proteins; substitution matrix; JTT matrix; molecular evolution; partitioned models; mixture models; RY coding; cyto-nuclear discordance
Online: 29 September 2021 (16:57:38 CEST)
Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acids exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution dataset for transmembrane helices from a variety of sampled set of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.
ARTICLE | doi:10.20944/preprints202105.0176.v1
Subject: Keywords: Video Steganography, Least Significant Bit (LSB) Coding, Double key Encryption, Decryption, Password Verification, Signature Verification
Online: 10 May 2021 (11:21:29 CEST)
In today’s digital media data communication over the internet increasing day by day. Therefore the data security becomes the most important issue over the internet. With the increase of data transmission, the number of intruders also increases. That’s the reason it is needed to transmit the data over the internet very securely. Steganography is a popular method in this field. This method hides the secret data with a cover medium in a way so that the intruders cannot predict the existence of the data. Here a steganography method is proposed which uses a video file as a cover medium. This method has five main steps. First, convert the video file into video frames. Then a particular frame is selected for embedded the secret data. Second, the Least Significant Bit (LSB) Coding technique is used with the double key security technique. Third, an 8 characters password verification process. Fourth, reverse the encrypted video. Fifth, signature verification process to verify the encryption and decryption process. These five steps are followed by both the encrypting and decrypting processes.
ARTICLE | doi:10.20944/preprints201902.0153.v1
Subject: Behavioral Sciences, Behavioral Neuroscience Keywords: Temporal processing of information, surprisal, temporal coupling; sparse coding, Shannon information, time-dimension in the brain
Online: 18 February 2019 (10:08:19 CET)
Perception and motor interaction with physical surroundings can be analyzed by the changes in probability laws governing two possible outcomes of neuronal activity, namely the presence or absence of spikes (binary states). Perception and motor interaction with physical environment are accounted partly by the reduction in entropy within the probability distributions of binary states of neurons in distributed neural circuits, given the knowledge about the characteristics of stimuli in physical surroundings. This reduction in the total entropy of multiple pairs of circuits in networks, by an amount equal to the increase of mutual information among them, occurs as sensory information is processed successively from lower to higher cortical areas or between different areas at the same hierarchical level but belonging to different networks. The increase in mutual information is partly accounted by temporal coupling as well as synaptic connections as proposed by Bahmer and Gupta . We propose that robust increases in mutual information, measuring the association between the characteristics of sensory inputs and neural circuits connectivity patterns, are partly responsible for perception and successful motor interactions with physical surroundings. It is also argued that perception from a sensory input is the result of networking of many circuits to a common circuit that primarily processes the given sensory input.
ARTICLE | doi:10.20944/preprints202103.0642.v1
Subject: Engineering, Automotive Engineering Keywords: NB-IoT; DVB-S2(X); High-Throughput Satellite; Optical Feeder Link; Over-the-air updates; Time-Packing; Decode-and-Forward; Scintillation; Beam-Wander; Convolutional Coding
Online: 25 March 2021 (16:15:48 CET)
The verticals of 5G, such as the automotive, smart grid and smart cities sectors, will bring lots of new sensors and IoT devices requiring Internet connectivity. Most of these machine-type terminals will be sparsely distributed, covering a very large geographical area and, from time to time, will have to update their software, firmware and/or other relevant data. Given this situation, one viable solution to implement the “Over-the-Air” update of these IoT terminals can be with the aid of GEO satellite systems. However, due to the ultra-dense radio frequency reuse that contemporary High-Throughput Satellite (HTS) systems implement in the access link to serve the IoT terminals, the use of a time-packed Free Space Optical (FSO) link represents a practical solution to avoid the bottleneck that the satellite gateway experiences in the feeder link. The performance of both Detect-and-Forward and Decode-and-Forward relaying strategies are studied, assuming that the single-carrier M-PAM symbols that are transmitted on the optical feeder link are mapped into M-QAM symbols that modulate the multiple subcarriers of the OFDM-based radio access link. In addition, the benefits of encapsulating the NB-IoT frames into DVB-S2(X) satellite frames is also analyzed in detail. The effects of the impairments introduced in both optical feeder and radio access links are characterized in detail, and the end-to-end error correction capabilities of the Modulation and Coding Schemes (MCS) defined in the contemporary releases of the NB-IoT and DVB-S2(X) standards are studied for different working regimes.
REVIEW | doi:10.20944/preprints202011.0209.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: physical unclonable functions; secret key agreement; private authentication; coding for secrecy and privacy; polar codes; nested codes
Online: 5 November 2020 (10:39:44 CET)
We address security and privacy problems for digital devices and biometrics from an information-theoretic optimality perspective, where a secret key is generated for authentication, identification, message encryption/decryption, or secure computations. A physical unclonable function (PUF) is a promising solution for local security in digital devices and this review gives the most relevant summary for information theorists, coding theorists, and signal processing community members who are interested in optimal PUF constructions. Low-complexity signal processing methods such as transform coding that are developed to make the information-theoretic analysis tractable are discussed. The optimal trade-offs between the secret-key, privacy-leakage, and storage rates for multiple PUF measurements are given. Proposed optimal code constructions that jointly design the vector quantizer and error-correction code parameters are listed. These constructions include modern and algebraic codes such as polar codes and convolutional codes, both of which can achieve small block-error probabilities at short block lengths, corresponding to a small number of PUF circuits. Open problems in the PUF literature from a signal processing, information theory, coding theory, and hardware complexity perspectives and their combinations are listed to stimulate further advancements in the research on local privacy and security.
ARTICLE | doi:10.20944/preprints202108.0375.v1
Subject: Social Sciences, Political Science Keywords: availability; cipher coding; clogged water; honeycomb tori; maintainability; mutually independent Hamiltonian paths (MIHP); interference; privacy; reliability; wicked problems
Online: 18 August 2021 (11:22:39 CEST)
Holistic information integrity for managing wicked problems, developing equity is getting attention. Artifitial intelligence based topologies, dual sensor-information nodes, are prototyped to offer more availability, reliability, maintainability for operating healthy urbanism. Bipartite spider-webs, cube-connected cycles are aimed in ‘the radial-ring urban-building skeleton’ and ‘wetlands and sparsely populated areas’, respectively. Furthermore, honeycomb tori, mathematical HT(m), m≥2, for tasks related to wireless communications, are found having two mutually independent Hamiltonian paths (MIHP). This parallelism creates dual cipher-coding, supports logistic privacy, and help prevent information loss, electromagnetic interference, unexpected changes caused by such as clogged water.
REVIEW | doi:10.20944/preprints202002.0279.v1
Subject: Mathematics & Computer Science, Other Keywords: Content distribution networks; Peer-to-peer computing; Random Linear network coding; File sharing; rarest-piece issue; information thoery
Online: 19 February 2020 (11:42:27 CET)
Peer-to-peer (P2P) content distribution or file sharing system aims to facilitate the dissemination of large files over unreliable networks. Network coding is a new transmission technique that has captured the interest of researchers because of its ability to increase throughput and robustness of the network, and decrease the download time. In this survey paper, we extensively summarize, assess, compare, and classify the most recently used techniques to improve P2P content distribution systems performance using network coding. To the best of our knowledge, this survey is the first comprehensive survey that specifically focuses on the performance of network coding based P2P file sharing systems.
ARTICLE | doi:10.20944/preprints201910.0302.v1
Subject: Biology, Animal Sciences & Zoology Keywords: phylogenomics; protein structure; secondary structure; relative solvent accessibility CAT model; non-stationary models; RY coding; metazoan phylogeny; ctenophora; porifera
Online: 27 October 2019 (11:00:50 CET)
Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in part, the poor-fit of the models used to analyze heterogeneous datasets. Some of the heterogeneity may reflect the different patterns of selection on proteins based on their structures. To test that hypothesis, we developed a pipeline to divide phylogenomic protein datasets into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had distinct signals for the topology of the deepest branches in the metazoan tree. The most striking difference in phylogenetic signal reflected relative solvent accessibility; analyses of exposed sites (on the surface of proteins) yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge-ctenophore clade. These differences in phylogenetic signal were not ameliorated when we repeated our analyses using the CAT model, a mixture model that is often used for analyses of protein datasets. In fact, the heterogeneous CAT model resulted in several rearrangements that are unlikely to represent evolutionary history. However, analyses conducted after recoding amino acids to limit the impact of deviations from compositional stationarity increased the congruence in the estimates of phylogeny for exposed and buried sites; after recoding amino acids both trees supported placement of ctenophores sister to all other animals. These results provide striking evidence that it is necessary to achieve a better understanding of the constraints due to protein structure to improve phylogenetic estimation.
REVIEW | doi:10.20944/preprints202007.0744.v1
Subject: Life Sciences, Biochemistry Keywords: long non-coding RNA (lncRNA); RNA polymerase II (RNAPII) transcription; gene regulation; tandem transcriptional interference (tTI); antisense transcription; DNA processing
Online: 31 July 2020 (10:47:08 CEST)
RNA polymerase II (RNAPII) frequently transcribes non-protein coding DNA sequences in eukaryotic genomes into long non-coding RNA (lncRNA). Here, we focus on the impact of the act of lncRNA transcription on nearby functional DNA units. Distinct molecular mechanisms linked to the position of lncRNA relative to the coding gene illustrate how non-coding transcription controls gene expression. We review the biological significance of the act of lncRNA transcription on DNA processing, highlighting common themes, such as mediating cellular responses to environmental changes. This review presents the background in chromatin signaling to appreciate examples in different organisms where we can interpret functions of non-coding DNA through the act of RNAPII transcription.
ARTICLE | doi:10.20944/preprints201906.0259.v1
Subject: Life Sciences, Molecular Biology Keywords: long non-coding RNA; cell type specific; alternative splicing; functional enrichment; RNA-binding proteins; protein binding lncRNA sponges; secondary RNA structure; cancer
Online: 26 June 2019 (05:23:29 CEST)
Background: Recent developments in our understanding of the interactions between long non-coding RNA (lncRNA) and cellular components have improved treatment approaches for various human diseases including cancer, vascular diseases, and neurological diseases. Although investigation of specific lncRNAs revealed their role in the metabolism of cellular RNA, our understanding of their contribution to post-transcriptional regulation is relatively limited. In this study, we explore the role of lncRNAs in modulating alternative splicing and their impact on downstream protein-RNA interaction networks. Results: Analysis of alternative splicing events across 39 lncRNA wildtype and knockout RNA-sequencing datasets from three human cell lines: HeLa (Cervical Cancer), K562 (Myeloid Leukemia), and U87 (Glioblastoma), resulted in high confidence (fdr < 0.01) identification of 4432 skipped exon events and 2474 retained intron events, implicating 759 genes to be impacted at post-transcriptional level due to the loss of lncRNAs. We observed that a majority of the alternatively spliced genes in a lncRNA knockout were specific to the cell type, in agreement with the finding that genes affected by alternative splicing also displayed enriched functions in a cell type specific manner. To understand the mechanism behind this cell-type specific alternative splicing patterns, we analyzed RNA binding protein (RBP)-RNA interaction profiles across the spliced regions. Conclusions: Despite limited RBP binding data across cell lines, alternatively spliced events detected in lncRNA perturbation experiments were associated with RBPs binding in proximal intron-exon junctions, in a cell type specific manner. The cellular functions affected by alternative splicing were also affected in a cell type specific manner. Based on the RBP binding profiles in HeLa and K562 cells, we hypothesize that several lncRNAs are likely to exhibit a sponge effect in disease contexts, resulting in the functional disruption of RBPs due to altered titration of the RBPs from their target loci. We propose that such lncRNA sponges can extensively rewire the post-transcriptional gene regulatory networks by altering the protein-RNA interaction landscape in a cell-type specific manner.
ARTICLE | doi:10.20944/preprints202002.0077.v1
Subject: Life Sciences, Biophysics Keywords: special relativity; efficient coding hypothesis; temporal order judgement; circular vection; vestibulo-ocular reflex; time perception; Lorentz transformation; accelerated reference frame; equivalence principle; optimization of perception
Online: 6 February 2020 (03:08:56 CET)
An event occurring within a stationary environment, in the direction toward which an observer self-rotates, is perceived to precede a simultaneous event, in the direction away from which she moves. When self-rotation results from angular acceleration in the dark, perception of space is also distorted, such that the subjective straight-ahead shifts in the opposite direction to motion and temporal event promotion. A reference frameshift theory, based on the special theory of relativity, is proposed to explain these findings. Here, a hyperbolic tangent transformation of objective angular velocity constrains subjective self-rotation velocity within finite bounds, consistent with it being a limited perceptual resource. Identifying this subjective variable with vestibular nystagmus slow-phase angular velocity, the asymptotic perceived self-rotation velocity is estimated at ~200 °⁄s. When included in the Lorentz transformations of the new formalism, this value predicts experimental simultaneity distortion. Hypothetically, the hyperbolic tangent objective-to-subjective transfer function would maximize the differential entropy of the percept, and thereby also the stimulus/percept mutual information, if angular velocities of body rotation encountered in naturalistic environmental interaction have a logistic probability density distribution of scale 100 °⁄s, a proposed experimental test of the scheme.