Definite Sequence Research Articles

Conformation impact in the deformation of DNA TATA-box

The ability to undergo specific deformation in response to conformational changes of some sites of the macromolecule is the key element of DNA genetic activity regulation in biological cells. The deformation of the definite sequences in DNA chain provides an accurate reading of genetic information and the process of protein synthesis passing. The model based on the analysis of conformational changes of the TATA nucleotide sequence in DNA double helix is developed. In addition to elastic components (bending, twisting), the presented model includes the conformational rearrangements of the TATA-box. Obtained form, value, and energy of DNA cite deformation allow to offer the probable mechanism of recognition of key DNA sequences and makes it possible to explain the high accuracy of the processes of reproducing of genetic information in biological cells. The formulated physical mechanism of DNA deformation can be one of the main principles of genetic information realization.

Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses.

The 5′UTR part of coronavirus genomes plays key roles in the viral replication cycle and translation of viral mRNAs. The first 75–80 nt, also called the leader sequence, are identical for genomic mRNA and subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5′UTR segment and the nonstructural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5′UTR RNA segment and the NSP1 protein have been done for several coronaviruses, with special attention to the betacoronaviruses. The conclusions are: (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein, indicating a coevolution between the 5′UTR and NSP1 in betacoronaviruses. Experimental mutational data on 5′UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support these conclusions and show that some conserved key residues in the amino-terminal half of the NSP1 protein are essential for evasion to the inhibitory effect of NSP1 on translation.

Study on the influence of stacking pattern on mechanical behaviour of banana/snake grass fibers hybrid epoxy composite

The present work analyses the effect of staking order on the mechanical behaviour of a hybrid polymer composites. The composites were prepared by arranging the banana and snake grass fibers in a definite sequence within the epoxy-based polymer matrix. For achieving a better composite materials’ interaction characteristic, banana as well as snake grass fibers had been cleaned with NaOH alkaline solution. By utilizing a digitalized universal testing machine, the tensile, compressive and flexural characteristics of the hybrid composite samples with the pre-determined stacking orders were assessed. The results revealed that the stacking sequence strongly influenced the mechanical characteristics of the hybrid composites. The banana fibers at the ends and in alternative laminates had resulted in the maximization of mechanical strengths including tensile, compressive and flexural characteristics. Specifically, the augmentation in tension, compressive as well as flexural values had been recorded as 14.25%, 11.76%, and 20.6%, correspondingly for the composite material with banana fibers at the ends.

Fuzzy c-Means Clusterization and ANN- MLP Prediction of Malign Breast Cancer in a Cohort of Patients

Abstract A model based on to cluster and predict the presence of malign breast cancer. The algorithms are applied to an open dataset of 569 patients that have either benign or malign breast cancer. First the article presents a detailed data description that is followed by a correlation matrix analysis and a regression analysis to verify the select the best variables for the clustering analysis and the predictive model. The clusterization is realized with the fuzzy c-Means algorithms. The prediction is performed by the Artificial Neural Network (ANN) Multilayer Perceptron (MLP) algorithm showing the best performance in comparison with the results of other machine learning algorithms. The use of all the tools in a definite sequence is the model proposed in this work providing an auto consistent approach to automatize the risk calculus with a good efficiency. The proposed approach can be applied for other typologies of cancers.

Determination of Age by Studying Radiological Fusion of Shoulder Joint in Relation to Birth Certificates in 16-20 Years Age Group

Age estimation of an individual is of medicolegal importance. Age becomes an important criteria for voting, driving licence, marriage, in civil cases e.g. to get government jobs and pensions. In criminal cases, the judgment is based on the opinion about age given by the forensic experts. Ossification centres appear in a fairly definite sequence at a particular age group and fuses at a particular age group from which an age of the individual can be determined. Materials and methods: 60 subjects were randomly selected from various schools, from neighbourhood as well as the cases attending the OPD of General Medicine Department of Madras Medical College, Chennai – 3. Conclusion :None of the cases in the age group of 16 – 17 yrs among males showed fusion of the secondary ossification centre of the shoulder joint. 30.76% and 28.57% of the cases showed fusion of the secondary ossification centre of the shoulder joint among males in the age group of 17 – 18yrs and 18 – 19 yrs respectively. 30%, 40%, 50% of the cases showed fusion of the secondary ossification centre of the shoulder joint among females in the age group of 16 – 17 yrs, 17 – 18 yrs, 18 – 19 yrs respectively. In the present study, it is observed that the mean age at which the secondary ossification centre of the shoulder joint fuses is 18 – 19 yrs in both boys and girls. In the present study, the fusion of the secondary ossification centre of the shoulder joint occurred one year later among females in comparison to ages mentioned in various standard literatures.It is due to the racial, economic, hereditary and hormonal factors.

Conditional positive definiteness in operator theory

In this paper we extensively investigate the class of conditionally positive definite operators, namely operators generating conditionally positive definite sequences. This class itself contains subnormal operators, $2$-and $3$-isometries, complete hyperc

Herglotz's theorem for Jacobi-Dunkl positive definite sequences

Abstract In this work, we introduce the notion of Jacobi-Dunkl positive definite sequences using the properties of the discrete Jacobi-Dunkl translation. Then, we establish the analogous of Herglotz’s theorem to characterize these sequences.

P0809 - Real life applicability of VI-RADS score for bladder cancer staging: Challenges of cut-offs definition and MRI sequences weighting

P0809 - Real life applicability of VI-RADS score for bladder cancer staging: Challenges of cut-offs definition and MRI sequences weighting

Improvement of Pilot Symbol Orthogonal Sequences in 2×2 to 4×4 MIMO Wireless Communication Systems with Channel State Estimation

AbstractMIMO wireless communication systems with channel state estimation, in which 2 to 4 transmit-receive antenna pairs are employed, are simulated. The channel estimation is fulfilled by the orthogonal pilot signal approach, where the Walsh Hadamard-ordered sequences are commonly used for piloting. The signal is modulated by applying the quaternary phase shift keying method. Maximum 250 000 packets are transmitted through flat-fading Rayleigh channels, to which white Gaussian noise is added. Based on simulating 10 subcases of the frame length and number of pilot symbols per frame, it is ascertained that pilot symbol orthogonal sequences in 2×2 to 4×4 MIMO systems can be improved by substituting Walsh functions with partially unsymmetrical binary functions constituting the eight known orthogonal bases. The benefit is that the bit-error rate is substantially decreased, especially for 2×2 MIMO systems. Considering three cases of the pilot signal de-orthogonalization caused by two indefinite and definite pilot sequence symbol errors, the relative decrement varies from 0.123 % to 14.7 %. However, the decrement becomes less significant as the number of transmit-receive antenna pairs is increased.

New open clusters found by manual mining of data based on Gaia DR2

The physical nature of a series of 20 new open clusters is confirmed employing existing data on putative star members, mainly from the second Gaia Data Release (DR2). The clusters were discovered as overdensities of stars by visual inspection of either photographic DSS plates or proper motion plots of random source fields. The reported objects are not present in the most comprehensive or recent catalogs of stellar clusters and associations. For all of them, clumps of comoving stars are revealed in the proper motion space. The parallaxes of the clumped stars are compatible with the real existence of open clusters over narrow ranges of distances. Surface density calculations, free of most noise from non-member sources, allow differentiating a cluster core and an extended cluster corona in some instances. Color-magnitude diagrams generally show a definite main sequence that allows confirmation of the physical existence of the clusters and some of their characteristics. Two of the new clusters seem to form a double system with a common origin. Several of the new clusters challenge the claim of near completeness of the known OC population in the distance range from 1.0 to 1.8 kpc from the Sun (Kharchenko et al.).

Cataloguing experimentally confirmed 80.7\xa0kb-long ACKR1 haplotypes from the 1000 Genomes Project database

BackgroundClinically effective and safe genotyping relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project recorded individual genotypes across 26 different populations and, using computerized genotype phasing, reported haplotype data. In contrast, we identified long reference sequences by analyzing the homozygous genomic regions in this online database, a concept that has rarely been reported since next generation sequencing data became available.Study design and methodsPhased genotype data for a 80.6 kb region of chromosome 1 was downloaded for all 2,504 unrelated individuals of the 1000 Genome Project Phase 3 cohort. The data was centered on the ACKR1 gene and bordered by the CADM3 and FCER1A genes. Individuals with heterozygosity at a single site or with complete homozygosity allowed unambiguous assignment of an ACKR1 haplotype. A computer algorithm was developed for extracting these haplotypes from the 1000 Genome Project in an automated fashion. A manual analysis validated the data extracted by the algorithm.ResultsWe confirmed 902 ACKR1 haplotypes of varying lengths, the longest at 80,584 nucleotides and shortest at 1,901 nucleotides. The combined length of haplotype sequences comprised 19,895,388 nucleotides with a median of 16,014 nucleotides. Based on our approach, all haplotypes can be considered experimentally confirmed and not affected by the known errors of computerized genotype phasing.ConclusionsTracts of homozygosity can provide definitive reference sequences for any gene. They are particularly useful when observed in unrelated individuals of large scale sequence databases. As a proof of principle, we explored the 1000 Genomes Project database for ACKR1 gene data and mined long haplotypes. These haplotypes are useful for high throughput analysis with next generation sequencing. Our approach is scalable, using automated bioinformatics tools, and can be applied to any gene.

Myocardial gene expression in patients with myocardial infarction

Abstract Funding Acknowledgements Type of funding sources: None. Introduction. Myocardial infarction (MI) and following heart failure (HF) have various clinical scenarios. However, despite the clinical heterogeneity, the management of MI lacks effective personalized approaches. The response to ischemic injury in the infarct zone and remote myocardium has a definite spatio-temporal sequence and underlies the mechanism of adverse cardiac remodeling. Understanding its myocardial biology remains unclear due to insufficiency of heart tissue molecular and genetic analysis. Although animal models play an important role in data accumulation, they failure to reflect all the compounds of response to ischemic injury and following HF syndrome. Purpose. The purpose of the study was to investigate myocardial expression profile in the infarct zone in comparison to remote myocardium in patients with MI. Methods. The study included 4 patients with fatal MI type 1. All patients died within 48 hours of MI. The post-mortem examination was performed according to country policy. In each case, we obtained myocardial samples from the infarct zone and remote myocardium. Genome-wide gene-level expression was assessed by microarray analysis. We used transcriptome analysis software to analyze and visualize global expression patterns of genes. The analysis included normalization process. Differentially expressed genes (DEGs) were defined as gene-level fold change <-2 or >2 and adjusted P-value of <0.05. Results. We studied expression of 21448 genes. A total of 1785 DEGs, including 1692 up-regulated genes and 93 down-regulated genes in the infarct zone, were identified (Figure 1). According to the fold change, the first 10 up-regulated genes were TNFSF10 (TRAIL), SUCLA2, NAE1, PDCL3, OSBPL5, FCGR2C, SELE, CEP63, ST3GAL3, C4orf3. Fold changes for TNFSF10 (TRAIL), SUCLA2, and NAE1 were 19.83 (p = 0.049), 10.68 (p = 0.048), and 10.24 (p = 0.008), respectively. These 3 up-regulated genes were enriched in apoptotic signaling pathways, immune response, angiogenesis, inflammation, tricarboxylic acid cycle, and protein binding. Conclusions. We performed myocardial transcriptomic analysis in patients with MI. DEG analysis clearly distinguishes the infarct zone and remote myocardium. Genes overexpressed in the infarct zone included TNFSF10 (TRAIL), SUCLA2, NAE1. TNFSF10 (TRAIL) regulates vasodilation, angiogenesis, and inflammation. TNFSF10 (TRAIL) regulated effects could be both protective and harmful in ischemic heart disease. The enzyme encoded by SUCLA2 is active in tissues that require a large amount of energy, such as those of the heart, brain, and muscle. Overexpression of NAE1 causes apoptosis through deregulation of NEDD8 conjugation. It is known that the protein encoded by NAE1 binds to the beta-amyloid precursor protein, and it is thought to play a role in the pathogenesis of Alzheimer"s disease. Thus, our pilot study emphasized the potential of translational approach and identified targets to consider for precision diagnostics and therapeutics. Abstract Figure. С1: infarct zone; C2: remote myocardium

“Semiotic Canalization”: a Process Directing the Use and Interpretation of Signals in Animal Interactions?

C. S. Peirce defined the sign as a means to communicate a form or habit embodied in the object to the interpretant, thus constraining (through a sign) the behavior of an interpreter to a limited series of effects. This is part of the process of “semiotic scaffolding” in which sign relations interlock and reinforce one another, providing directionality to the process. In biological evolutionary studies canalization is defined as the adjustment of developmental pathways by natural selection to bring about a uniform result despite genetic and environmental variations. Establishing parallelism between the two concepts allows the possibility of understanding how semiotic processes introduce information from the environment resulting in canalization (and assimilation), determining “fixed” pathways to elaborate signal repertoires for particular species adapted to particular environments sensed by particular organs. This kind of sign action can produce an “encapsulation” process of the sign meaning, further affecting the meaning-making process developing in the receiver, a process affecting signal usage by animals, constraining agency of biological systems’ behavior towards a definite sequence of events or signals and providing a certain orientation of the process (“semiotic canalization”). Therefore, we can also say that signs could potentially be built by senders (i.e. by the sign-vehicle) in a sort of pre-determined way and not extracted by the receiver from a “neutral” sender. Semiotic canalization is seen as a part of a more general process of scaffolding during development, acting mainly during some information exchanges between communicating subjects, providing adaptive responses to some standard communicative situations.

Exploring DNA Diversity in Leathers:

DNA based approaches have become widespread in recent times to identify the origin of samples when its phenotypic characteristics are not distinguishable. This, in particular, applies to the leather industry wherein with an increase in duplicated embossing of grain patterns; there is a need to detect the animal origin of commercial leather articles. Thus, the characterization of molecular markers that enables rapid detection of the leather source helps us in precise species identification. The present study aims to generate definite sequences between the four major species in the Bovidae family (Buffalo, Cow, Goat, and Sheep), which are the major players in the manufacture of leather products, especially in India. Based on specific mitochondrial sequences, a specific fragment of the mitochondrial 12SrRNA gene was amplified by PCR as a marker for species-level identification. By the maximum homogeneity, from the NCBI and BOLD database, the BLAST analysis of the sequences of amplicons from unknown sources, distinguish closely related species of the subfamilies Bovinae (buffalo and Cow) and Caprinae (sheep and goat) and this 12SrRNA based PCR-BLAST analysis is a good tool to identify the origin and control the quality of leathers that are being manufactured. The present study has optimized an approach for the extraction and amplification of DNA from the finished leather, which is one of the most significant challenges because of the vigorous processes encountered during their manufacture. The findings of the study have commercial value at large scale.

ESTRO ACROP guideline for target volume delineation of skull base tumors

Background and purposeFor skull base tumors, target definition is the key to safe high-dose treatments because surrounding normal tissues are very sensitive to radiation. In the present work we established a joint ESTRO ACROP guideline for the target volume definition of skull base tumors. Material and methodsA comprehensive literature search was conducted in PubMed using various combinations of the following medical subjects headings (MeSH) and free-text words: “radiation therapy” or “stereotactic radiosurgery” or “proton therapy” or “particle beam therapy” and “skull base neoplasms” “pituitary neoplasms”, “meningioma”, “craniopharyngioma”, “chordoma”, “chondrosarcoma”, “acoustic neuroma/vestibular schwannoma”, “organs at risk”, “gross tumor volume”, “clinical tumor volume”, “planning tumor volume”, “target volume”, “target delineation”, “dose constraints”. The ACROP committee identified sixteen European experts in close interaction with the ESTRO clinical committee who analyzed and discussed the body of evidence concerning target delineation. ResultsAll experts agree that magnetic resonance (MR) images with high three-dimensional spatial accuracy and tissue-contrast definition, both T2-weighted and volumetric T1-weighted sequences, are required to improve target delineation. In detail, several key issues were identified and discussed: i) radiation techniques and immobilization, ii) imaging techniques and target delineation, and iii) technical aspects of radiation treatments including planning techniques and dose-fractionation schedules. Specific target delineation issues with regard to different skull base tumors, including pituitary adenomas, meningiomas, craniopharyngiomas, acoustic neuromas, chordomas and chondrosarcomas are presented. ConclusionsThis ESTRO ACROP guideline achieved detailed recommendations on target volume definition for skull base tumors, as well as comprehensive advice about imaging modalities and radiation techniques.

Compositional MRI of the anterior cruciate ligament of professional alpine ski racers: preliminary report on seasonal changes and load sensitivity

The purpose of this study was to investigate potential changes in the anterior cruciate ligament (ACL) structure of alpine ski racers over the course of an entire season using quantitative magnetic resonance imaging (T2* mapping). The dominant legs of three alpine ski racers were examined on a 3-T MR scanner four times at 3-month intervals. Multi-echo sequences for T2* maps, which were coregistered with high-resolution morphological sequences for reproducible definition of ACL regions of interest, were acquired. Means and standard deviations of T2* values from the central and femoral portion of the ACL were extracted and presented in a descriptive manner. T2* values were subject to seasonal changes, which were most pronounced in the ligament central region. Substantial increases (+ 41%) occurred between the measurements taken in January and April. A partial recovery of T2* (-19%) was observed in the July follow-up. The increased T2* times may reflect decreased stress tolerance and increased susceptibility for fatigue tears at the end of the competitive season. Further research in larger samples is required. The likeliness of ACL tears may depend on the precedent history of mechanical loading and vary in professional athletes over the course of the competitive season.

Pilot Symbol Error Re - Orthogonalization in 2 × 2 MIMO Systems of Wireless Communication

Abstract A 2×2 MIMO wireless communication system with channel estimation is simulated, in which two transmit, and two receive antennas are employed. The orthogonal pilot signal approach is used for the channel estimation, where the Hadamard sequences are used for piloting. Data are modulated by coherent binary phase-shift keying, whereupon an orthogonal space-time block coding subsystem encodes information symbols by using the Alamouti code. Based on the simulation, it is ascertained a possibility to decrease the bit-error rate by substituting the Hadamard sequences for the sequences having irregular structures, and constituting the eight known orthogonal bases. Considering a de-orthogonalization caused by two any pilot sequence symbol errors, the bit-error rate is decreased by almost 2.9 %. If de-orthogonalizations are caused by two repeated indefinite, and definite pilot sequence symbol errors, the decrements are almost 16 % and 10 %, respectively. Whichever sequences are used for piloting, the 2×2 MIMO system is ascertained to be resistant to the de-orthogonalization if the frame is of 128 to 256 symbols piloted with 32 to 64 symbols, respectively.

New Open Clusters Found by Manual Mining of Data Based in Gaia DR2

The physical nature of a series of 20 new open clusters is confirmed employing existing data on putative star members, mainly from second Gaia Data Release (DR2). The clusters were discovered as over-densities of stars by visual inspection of either photographic DSS plates or proper motion plots of random source fields. The reported objects are not present in the most comprehensive or recent catalogs of stellar clusters and associations. For all of them, clumps of co-moving stars are revealed in the proper motion space. The parallaxes of the clumped stars are compatible with the real existence of open clusters over narrow ranges of distances. Surface density calculations, free of most noise from non-member sources, allow in some cases differentiating a cluster core and an extended cluster corona. Color-magnitude diagrams generally show a definite main sequence that allows the confirmation of the physical existence of the clusters and some of their characteristics. Two of the new clusters seem to form a double system with a common origin. Several of the new clusters challenge the claim of near completeness of the known OC population in the distance range from 1.0 to 1.8 kpc of the Sun (Kharchenko et al. 2013).

On generalization of classical Hurwitz stability criteria for matrix polynomials

In this paper we associate a class of Hurwitz matrix polynomials with Stieltjes positive definite matrix sequences. This connection leads to an extension of two classical criteria of Hurwitz stability for real polynomials to matrix polynomials: tests for Hurwitz stability via positive definiteness of block-Hankel matrices built from matricial Markov parameters and via matricial Stieltjes continued fractions. We obtain further conditions for Hurwitz stability in terms of block-Hankel minors and quasiminors, which may be viewed as a weak version of the total positivity criterion.

Peptide Receptor Radionuclide Therapy as First-Line Systemic Treatment in Advanced Inoperable/Metastatic Neuroendocrine Tumors.

Advanced inoperable/metastatic neuroendocrine tumors (NETs) pose a therapeutic challenge with limited treatment options. Peptide receptor radionuclide therapy (PRRT), being specific in targeting the somatostatin receptors, is a promising and viable option in this setting. In this study, we intended to evaluate the role of PRRT as the first-line systemic therapy in advanced inoperable/metastatic NETs. Data of consecutive patients of advanced inoperable/metastatic NETs treated with first-line Lu-DOTATATE at our center, from September 2012 to August 2019, were collected and analyzed. Forty-five patients (median age, 50 years; range, 14-72 years) with treatment-naive advanced NETs received a median cumulative dose of 27 GBq (range, 13.3-41.3 GBq; over 2-7 cycles) Lu-DOTATATE and 1250 mg/m capecitabine from days 0 to 14 of each PRRT cycle. Three patients were lost to follow-up, 2 had nonmeasurable lesions on CT, and hence, radiological response using Response Evaluation Criteria in Solid Tumors version 1.1 could be assessed in 40 patients. Twelve of 40 patients (30%) showed a partial response, whereas stable disease was observed in 22 of 40 patients (55%). Disease progression was limited to 6 of 40 patients (15%). Treatment-related adverse effects were minimal with grade 3/4 anemia, leukopenia, neutropenia, and hepatotoxicity observed in 2%, 2%, 4%, and 4% of the patients, respectively. Median progression-free survival was 48 months (95% confidence interval, 34.7-61.3 months). Our results indicate the efficacy and safety of first-line PRRT in advanced NETs. Future randomized trials, comparing PRRT and somatostatin analogs in treatment-naive patients, are required to identify the definite sequence of treatment options for these patients.