Concatenated Form Research Articles

A multimodal graph neural network framework for cancer molecular subtype classification

BackgroundThe recent development of high-throughput sequencing has created a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating multi-omics data has been proven to be effective for building more precise classification models. Most current multi-omics integrative models use either an early fusion in the form of concatenation or late fusion with a separate feature extractor for each omic, which are mainly based on deep neural networks. Due to the nature of biological systems, graphs are a better structural representation of bio-medical data. Although few graph neural network (GNN) based multi-omics integrative methods have been proposed, they suffer from three common disadvantages. One is most of them use only one type of connection, either inter-omics or intra-omic connection; second, they only consider one kind of GNN layer, either graph convolution network (GCN) or graph attention network (GAT); and third, most of these methods have not been tested on a more complex classification task, such as cancer molecular subtypes.ResultsIn this study, we propose a novel end-to-end multi-omics GNN framework for accurate and robust cancer subtype classification. The proposed model utilizes multi-omics data in the form of heterogeneous multi-layer graphs, which combine both inter-omics and intra-omic connections from established biological knowledge. The proposed model incorporates learned graph features and global genome features for accurate classification. We tested the proposed model on the Cancer Genome Atlas (TCGA) Pan-cancer dataset and TCGA breast invasive carcinoma (BRCA) dataset for molecular subtype and cancer subtype classification, respectively. The proposed model shows superior performance compared to four current state-of-the-art baseline models in terms of accuracy, F1 score, precision, and recall. The comparative analysis of GAT-based models and GCN-based models reveals that GAT-based models are preferred for smaller graphs with less information and GCN-based models are preferred for larger graphs with extra information.

Coupled coordinated time-series evolution of cultural and educational attributes in tourist attractions based on transfer matrix modeling

Abstract In this paper, the transfer matrix model was first applied, and the eigenvalues of the matrix were calculated to clarify the cultural nature of tourist attractions. The concatenated form is introduced into the transfer matrix, successfully calculating the matrix’s matching function. The coupled coordinated time-series evolution was then used to derive the comprehensive evaluation index of tourist attractions and cultural and educational properties, and the weights of the indexes’ correlation and difference were analyzed to derive the index entropy value. Finally, the original data are processed by the dimensionless standard, the degree of coupling coordination is evaluated with the help of the coupling concept, and the relative level of coupling is dealt with after the matrix transfer. The analysis found that the highest coupling degree of cultural and educational attributes of tourist attractions in 10 years is 0.7. Therefore, the integration and development of cultural and educational attributes of tourist attractions is the inherent requirement and inevitable result of cultural construction and tourism development and must adhere to the principle of coordinated development of promoting tourism with culture and manifesting culture with tourism.

Extended Connectivity Fingerprints as a Chemical Reaction Representation for Enantioselective Organophosphorus-Catalyzed Asymmetric Reaction Prediction.

Predicting the outcomes of organic reactions using data-driven approaches aids in the acceleration of research. In laboratory-scale experiments, only a small number of reaction data can be accessed for machine learning model construction, where reaction representations play a pivotal role in the success of model construction. Nevertheless, representation comparison for a small data set is not adequate. Herein, focusing on the enantioselectivity of phosphoric-acid-catalyzed reactions, various two-dimensional and three-dimensional reaction representations (descriptors) were compared. Overall, the concatenated form of the extended connectivity fingerprints showed the best predictive capability for the two types of data sets: high-throughput experimental data and manually collected literature data sets. Furthermore, highlighting the substructure contribution to the prediction outcome was shown to be informative for guiding catalyst development.

THE CROWN OF SONNETS: PROBLEMS OF GENESIS AND GENRE FORMATION

The established, yet unconfirmed, viewpoint states that the crown of sonnets originated in the 13th century, although the first known instances of this genre form belong to the 16th century. These works differ from the modern (canonical) crown by the unregulated number of texts and the absence of the master sonnet. The thematic and stylistic variety of the Baroque crowns suggests that certain sonnet crown sequences did exist before the 16th century, albeit they are still undiscovered. In the absence of relevant texts, the study of the formal poetic preconditions required for the emergence of the crown of sonnets could clarify the time of the appearance of this supertextual form. Two factors determine the structure of the crown: the cohesion of adjacent texts and the ring-like organization of the supertextual unit. The first refers to the repetition of the last verse of the preceding text at the beginning of the following one. This poetic technique originates from the Provençal troubadours, who created a specific form of chained stanzas (coblas capfinidas); the Galician-Portuguese poets discovered another form of strophic concatenation (leixaprén). The second factor is the repetition of the first verse of the initial text at the end of the last one. Despite the verbatim coincidence, these verses are not semantically equal to each other, since the last verse, enriched by the previous context, acquires new semantic characteristics. One of the first poetic forms that combines the beginning and end of the text was the rondel, created in the 15th century. The examination of medieval poetic genres from the point of view of their crown-forming potential led to the conclusion that only the sonnet form meets the requirements for a poetic crown. The studied material suggests that, despite the common opinion, the non-canonical crown of sonnets could not appear in the 13th century, as the entire complex of formal poetic conditions for the emergence of this genre form developed at the end of the 15th century.

Genetic diversity and phylogeography of European Roe Deer, Capreolus capreolus, in Iran as inferred from mtDNA genes (Mammalia: Cervidae)

We examined the genetic diversity and phlogeographic characters of European Roe Deer populations across its distribution range in Iran. Mitochondrial DNA from 46 samples were sequenced for 1138 bp of cytochrome b and 1020 bp of ND2 genes and analysed alongside the retrieved sequences from GenBank in a concatenated form. The results demonstrated a relatively low nucleotide diversity and high haplotype diversity in the Roe Deer populations of Iran. Two distinct clusters of Roe Deer populations, in the northern and in the western/northwestern part of the country, were recognised based on phylogenetic trees, haplotype network analyses, and Bayesian structuring tests. The presence of some individuals of the western/northwestern regions in the clade of the northern population can be assumed as evidence for occasional gene flow between these two regions. Furthermore, the samples from both populations of Iran were clustered with samples from European countries. It seems this species probably entered Iran from Europe through northern Iran, and then spread to the western/northwestern regions of the country over time.

Some Results on Images of a Class of λ-Constacyclic Codes Over Finite Fields

In this paper, we show that any λ-constacyclic code over F qm is a λ-constacyclic code over F q under some special maps. Moreover, we show that the images of these λ_constacyclic codes can be put into the concatenated form.

LoWVR: Low Overhead Watermark based Vehicle Revocation Scheme in VANET

Background and Objective: The inter-vehicle communication is a potential issue for improving road safety, detecting traffic accidents, etc. in vehicular ad hoc network. The communication among the vehicles in VANET must be protected from the dissemination of message by unauthorized vehicles and the alteration of the message by misbehaving vehicles. Methods: In this paper, a low overhead digital watermark based vehicle revocation scheme is proposed. The sender vehicle generates a message and a random number after observing an event. It generates a deformed version of the generated message and message digest, and concatenates them. The watermark bits are generated by the sender vehicle from its unique identification and the random number. The sender vehicle embeds the watermark bits in the concatenated form of the message digest and deformed version of the generated message, and broadcasts the embedded message for its neighbours. The neighbour vehicles extract the required information from the received embedded message to verify the authentication of the sender vehicle and to identify whether the sender vehicle is an alteration attacker. It revokes unauthentic vehicles and vehicles that are identified as alteration attacker from vehicular ad-hoc network without any dependency on the trusted third party. The cracking probability and cracking time are used to measure the robustness of the scheme. The cracking probability and cracking time are measured to set the design guideline regarding the size of the watermark. The qualitative performance of the scheme is measured in terms of storage, communication and computation overhead. The significant reduction of all such overheads is observed by comparing the qualitative performance of the proposed scheme with two existing schemes. Conclusion and Results: Thus, the proposed scheme is a low overhead solution of securing vehicular ad hoc network. Performance of the scheme is also studied quantitatively in terms of the time of verifying vehicle authentication at the receiving end, delay in message dissemination at the sending end and delay in message reception at the receiving end. The quantitative performance is also compared with two of the existing schemes.

Polar Intermetallics Pr5 Co2 Ge3 and Pr7 Co2 Ge4 with Planar Hydrocarbon-Like Metal Clusters.

Planar hydrocarbon-like metal clusters may foster new insights linking organic molecules with conjugated π-π bonding interactions and inorganic structures in terms of their bonding characteristics. However, such clusters are uncommon in polar intermetallics. Herein, we report two polar intermetallic phases, Pr5 Co2 Ge3 and Pr7 Co2 Ge4 , both of which feature such planar metal clusters, namely, ethylene-like [Co2 Ge4 ] clusters plus the concatenated forms and polyacene-like [Co2 Ge2 ]n ribbons in Pr5 Co2 Ge3 , and 1,2,4,5-tetramethylbenzene-like [Co4 Ge6 ] cluster in Pr7 Co2 Ge4 . Just as in the related planar organic structures, these metal-metalloid species are dominated by covalent bonding interactions. Both compounds magnetically order at low temperature with net ferromagnetic components: Pr5 Co2 Ge3 through a series of transitions below 150 K and Pr7 Co2 Ge4 through a single ferromagnetic transition at 19 K. Spin-polarized electronic structure calculations for Pr7 Co2 Ge4 reveal strong spin-orbit coupling within Pr and considerable magnetic contributions from Co atoms. This work suggests that similar structural chemistry can emerge for other rare-earth/late-transition-metal/main-group systems.

State-of-the-art space mission telecommand receivers

Since their dawning, space communications have been among the strongest driving applications for the development of error correcting codes. Indeed, space-to-Earth telemetry (TM) links have extensively exploited advanced coding schemes, from convolutional codes to Reed-Solomon codes (also in concatenated form) and, more recently, from turbo codes to low-density parity-check (LDPC) codes. The efficiency of these schemes has been extensively proved in several papers and reports. The situation is a bit different for Earth-to-space telecommand (TC) links. Space TCs must reliably convey control information as well as software patches from Earth control centers to scientific payload instruments and engineering equipment onboard (O/B) spacecraft. The success of a mission may be compromised because of an error corrupting a TC message: a detected error causing no execution or, even worse, an undetected error causing a wrong execution. This imposes strict constraints on the maximum acceptable detected and undetected error rates.

Complete genome sequence and analysis of blackcurrant leaf chlorosis associated virus, a new member of the genus Idaeovirus.

Blackcurrant leaf chlorosis associated virus (BCLCaV) was isolated from symptomatic blackcurrants (Ribes nigrum cv. Baldwin). The virus has a genome organization similar to that of raspberry bushy dwarf virus (RBDV), the type member of the genus Idaeovirus. The RNA-1of this virus encodes the replicase complex (ORF1, Mr 197 kDa), while RNA-2 encodes a putative movement protein (ORF2a, Mr 38.8 kDa) and the putative coat protein (ORF2b, Mr 30 kDa). A concatenated form of BCLCaV RNA-2 was detected by next-generation sequencing and confirmed by RT-PCR. BCLCaV is a new member of the genus Idaeovirus.

Concatenation in Kālidāsa and Other Sanskrit Poets

Concatenation, that is, the linking of successive verses of a poem by the repetition of the same or similar words, has been discussed by several scholars in relation to Vedic and Prakrit poetry, but other than a ground-breaking article published by W. Schubring in 1955, it has been insufficiently studied in classical Sanskrit kāvya. This article argues that a particular form of concatenation, involving long-distance word repetition across as many as five or even ten verses, is characteristic of the works of Kālidāsa in particular but also of Sanskrit poets in general. Like Schubring’s article, this one focuses on the Meghadūta, but uses a broader definition of scope of concatenation.

Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology.

Integration of human papillomavirus (HPV) DNA into the host genome can be a driver mutation in cervical carcinoma. Identification of HPV integration at base resolution has been a longstanding technical challenge, largely due to sensitivity masking by HPV in episomes or concatenated forms. The aim was to enhance the understanding of the precise localization of HPV integration sites using an innovative strategy. Using HPV capture technology combined with next generation sequencing, HPV prevalence and the exact integration sites of the HPV DNA in 47 primary cervical cancer samples and 2 cell lines were investigated. A total of 117 unique HPV integration sites were identified, including HPV16 (n = 101), HPV18 (n = 7), and HPV58 (n = 9). We observed that the HPV16 integration sites were broadly located across the whole viral genome. In addition, either single or multiple integration events could occur frequently for HPV16, ranging from 1 to 19 per sample. The viral integration sites were distributed across almost all the chromosomes, except chromosome 22. All the cervical cancer cases harboring more than four HPV16 integration sites showed clinical diagnosis of stage III carcinoma. A significant enrichment of overlapping nucleotides shared between the human genome and HPV genome at integration breakpoints was observed, indicating that it may play an important role in the HPV integration process. The results expand on knowledge from previous findings on HPV16 and HPV18 integration sites and allow a better understanding of the molecular basis of the pathogenesis of cervical carcinoma.

HPV integration detection in CaSki and SiHa using detection of integrated papillomavirus sequences and restriction-site PCR

Human Papillomavirus (HPV) infection is the primary cause of cervical neoplasia. HPV DNA is integrated into the human genome in the majority of cervical cancers. The nature of integration may differ with integration incorporating a single copy of HPV or occurring in concatenated form. Our understanding of HPV tumorigenesis is largely based on studies using characterised cell lines with defined integration sites; these cell lines provide an invaluable standard for validation of diagnostic assays. Cell lines also further understanding of integration mechanisms in clinical samples. The objective of this study was to explore integration assays and to investigate integration events in cell lines where HPV is integrated in concatenated form. Restriction site PCR and detection of integrated papillomavirus sequences were performed on DNA from SiHa and CaSki. A novel integration site on Xq27.3 and HPV genome rearrangements were detected in CaSki DNA. However, where integration was previously detected by FISH in CaSki, and reported to be integrated in concatenated form, integration was not detected by DIPS or RS-PCR. The data presented illustrate that HPV copy number can hinder integration detection; this needs consideration when interpreting results from tests applied to clinical samples.

Structure, property, and design of nonbinary regular cycle codes

In this paper, we study nonbinary regular LDPC cycle codes whose parity check matrix H has fixed column weight j = 2 and fixed row weight d. Through graph analysis, we show that the parity check matrix H of a regular cycle code can be put into an equivalent structure in the form of concatenation of row-permuted block-diagonal matrices if d is even, or, if d is odd and the code's associated graph contains at least one spanning subgraph that consists of disjoint edges. This equivalent structure of H enables: i) parallel processing in lineartime encoding; ii) considerable resource reduction on the code storage for encoding and decoding; and iii) parallel processing in sequential belief-propagation decoding, which increases the throughput without compromising performance or complexity. On the code's structure design, we propose a novel design methodology based on the equivalent structure of H. Finally, we present various numerical results on the code performance and the decoding complexity.

On Cyclic $q$-ary Images in Concatenated Form

This paper shows that q-ary images of some cyclic codes can be put into concatenated form in the sense of Jensen (1985). This description utilizes an isomorphism between the GF(q)-algebras GF(q) [z] / (z <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nm</sup> - 1) and GF (q )[x, y] / (x <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> - 1, y <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sup> - x). We also describe an element of the constacyclic outer code, which is of great help in determining one of its generator polynomials.

Headhood in Yorùbá nominal compounds

The lexical status of a class of composite words known as the nominal compounds in Yorùbá, is the focus of this article. The different semantic relations associated with the constituents of Yorùbá compounds as well as their varying deep structures reveal that in locating nominal compound heads, efforts should be made to describe the percolation effects on the concatenated forms. The notion of x-bar syntax of Williams (1981a & 1981b), among others, was supported by semantic relatedness of forms in compounds for the analysis. This work essentially points to the fact that Yorùbá compounds cannot be said to exhibit a similar realization of headedness in their different tokens. Thus, Williams' (1981b:252) Right Hand Head Rule (RHHR) is found to not be a universal phenomenon. Condition is plausible anywhere in Yorùbá because Yorùbá is among those exceptional languages whose morphological heads are on the left hand for those that are headed, just as they are in the syntax of the language. We still find that some are double headed, while some are headless. As Yorùbá nominal compounds cannot be said to exhibit uniformity in their headedness, they cannot be explained using a monolithic approach of either syntax or morphology. The phenomenon of word headedness in the language can best be explained along the interface axis of morpho-syntax and semantic.

Tradeoff functions for constrained systems with unconstrained positions

We introduce a new method for analyzing and constructing combined modulation and error-correcting codes (ECCs), in particular codes that utilize some form of reverse concatenation and whose ECC decoding scheme requires easy access to soft information. We expand the work of Immink and Wijngaarden and also of Campello, Marcus, New, and Wilson, in which certain bit positions in the modulation code are deliberately left unconstrained for the ECC parity bits, in the sense that such positions can take on either bit value without violating the constraint. Our method of analysis involves creating a single graph that incorporates information on these unconstrained positions directly into the constraint graph without any assumptions of periodicity or sets of unconstrained positions, and is thus completely general. We establish several properties of the tradeoff function that relates the density of unconstrained positions to the maximum code rate. In particular, the tradeoff function is shown to be concave and continuous. Algorithms for computing lower and upper bounds for this function are presented. We also show how to compute the maximum possible density of unconstrained positions and give explicit values for the runlength-limited (RLL(d,k)) and maximum-transition-run (MTR(j,k)) constraints.

Pivotal role of the non-hr origin of DNA replication in the genesis of defective interfering baculoviruses.

The generation of deletion mutants, including defective interfering viruses, upon serial passage of Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) in insect cell culture has been studied. Sequences containing the non-homologous region origin of DNA replication (non-hr ori) became hypermolar in intracellular viral DNA within 10 passages in Se301 insect cells, concurrent with a dramatic drop in budded virus and polyhedron production. These predominant non-hr ori-containing sequences accumulated in larger concatenated forms and were generated de novo as demonstrated by their appearance and accumulation upon infection with a genetically homogeneous bacterial clone of SeMNPV (bacmid). Sequences were identified at the junctions of the non-hr ori units within the concatemers, which may be potentially involved in recombination events. Deletion of the SeMNPV non-hr ori using RecE/RecT-mediated homologous ET recombination in Escherichia coli resulted in a recombinant bacmid with strongly enhanced stability of virus and polyhedron production upon serial passage in insect cells. This suggests that the accumulation of non-hr oris upon passage is due to the replication advantage of these sequences. The non-hr ori deletion mutant SeMNPV bacmid can be exploited as a stable eukaryotic heterologous protein expression vector in insect cells.

A novel subblock partition scheme for partial transmit sequence OFDM

In general, there has been a trade-off between performance of peak-to-average power ratio (PAPR) reduction and computational complexity in partial transmit sequence (PTS) orthogonal frequency division multiplexing (OFDM). In this paper, a novel subblock partition scheme (SPS) for PTS OFDM is proposed and analyzed. In this scheme, signals assigned randomly in partial subbands are duplicated and concatenated repetitively to generate each subblock. The proposed scheme, therefore, has a form of concatenation of pseudo-random and interleaved SPS. As results of simulations, the proposed scheme shows almost same PAPR reduction performance as compared to the conventional pseudo-random SPS which has been known to have the best performance. However, computational complexity can be reduced extensively. Hence, the proposed scheme may be considered to be more suitable than the conventional ones for application in high speed transmission systems such as digital terrestrial broadcasting.

AbiQ, an abortive infection mechanism from Lactococcus lactis.

Lactococcus lactis W-37 is highly resistant to phage infection. The cryptic plasmids from this strain were coelectroporated, along with the shuttle vector pSA3, into the plasmid-free host L. lactis LM0230. In addition to pSA3, erythromycin- and phage-resistant isolates carried pSRQ900, an 11-kb plasmid from L. lactis W-37. This plasmid made the host bacteria highly resistant (efficiency of plaquing <10(-8)) to c2- and 936-like phages. pSRQ900 did not confer any resistance to phages of the P335 species. Adsorption, cell survival, and endonucleolytic activity assays showed that pSRQ900 encodes an abortive infection mechanism. The phage resistance mechanism is limited to a 2.2-kb EcoRV/BclI fragment. Sequence analysis of this fragment revealed a complete open reading frame (abiQ), which encodes a putative protein of 183 amino acids. A frameshift mutation within abiQ completely abolished the resistant phenotype. The predicted peptide has a high content of positively charged residues (pI = 10.5) and is, in all likelihood, a cytosolic protein. AbiQ has no homology to known or deduced proteins in the databases. DNA replication assays showed that phage c21 (c2-like) and phage p2 (936-like) can still replicate in cells harboring AbiQ. However, phage DNA accumulated in its concatenated form in the infected AbiQ+ cells, whereas the AbiQ- cells contained processed (mature) phage DNA in addition to the concatenated form. The production of the major capsid protein of phage c21 was not hindered in the cells harboring AbiQ.