Number Of Sequences Research Articles

A - 48 A Preliminary Comparison of Performance on the D-KEFS Advanced Trail Making Test across ADHD, ASD, and Math LD Clinical Groups

Abstract Objective Exploratory analyses on executive function performance between clinical groups was conducted using the Delis-Kaplan Executive Function System Advanced (D-KEFS Advanced) Trail Making Test (TMT). Our goal was to see if TMT could detect differences in the cognitive profiles of examinees diagnosed with attention-deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), and math learning disorder (MLD) clinical groups. Method Participants ages of 8 and 16, diagnosed with ADHD (N = 56), ASD (N = 27), or MLD (N = 25) completed the D-KEFS Advanced TMT. DSM5 diagnostic criteria were used for diagnosis. Additionally, participants with comorbid diagnoses across the three groups were excluded from the clinical samples. Mean Correct (with errors) Connection Time for the five conditions was captured for each clinical group, as well as error rates. Results Multiple differences were found, but only two reached significances at the p < 0.01 level. Unpaired t-test results revealed a statistically significant difference between ADHD (M = 9.34, SD = 3.16) and ASD (M = 7.00, SD = 3.16) groups in Mean Correct (with errors) Connection Time scores for TMT Number Sequencing, t(81) = 3.16, p = 0.002, 95% CI [0.87, 3.81]. Additionally, Mean Correct (with errors) Connection Time scores for TMT Switching-Distraction condition between ADHD (M = 8.41, SD = 2.51) and ASD (M = 6.48, SD = 3.04) groups was statistically significant, t(81) = 3.06, p = 0.003, 95% CI [0.67–3.19]. Conclusion Overall, these preliminary findings suggest good clinical utility; however, further research is needed to determine if performance differences can aid in the evaluation of patterns of cognitive difficulties between groups.

Genome-wide analysis of flavonoid biosynthetic genes in Musaceae (Ensete, Musella, and Musa species) reveals amplification of flavonoid 3ʹ,5ʹ-hydroxylase

Abstract Flavonoids in Musaceae are involved in pigmentation and stress responses, including cold resistance, and are a component of the healthy human diet. Identification and analysis of the sequence and copy number of flavonoid biosynthetic genes are valuable for understanding the nature and diversity of flavonoid evolution in Musaceae species. In this study, we identified 71–80 flavonoid biosynthetic genes in chromosome-scale genome sequence assemblies of Musaceae, including those of Ensete glaucum, Musella lasiocarpa, Musa beccarii, M. acuminata, M. balbisiana and M. schizocarpa, checking annotations with BLAST and determining the presence of conserved domains. The number of genes increased through segmental duplication and tandem duplication. Orthologues of both structural and regulatory genes in the flavonoid biosynthetic pathway are highly conserved across Musaceae. The flavonoid 3ʹ,5ʹ-hydroxylase gene F3ʹ5ʹH was amplified in Musaceae and ginger compared with grasses (rice, Brachypodium, Avena longiglumis, and sorghum). One group of genes from this gene family amplified near the centromere of chromosome 2 in the x = 11 Musaceae species. Flavonoid biosynthetic genes displayed few consistent responses in the yellow and red bracts of Musella lasiocarpa when subjected to low temperatures. The expression levels of MlDFR2/3 (dihydroflavonol reductase) increased while MlLAR (leucoanthocyanidin reductase) was reduced by half. Overall, the results establish the range of diversity in both sequence and copy number of flavonoid biosynthetic genes during evolution of Musaceae. The combination of allelic variants of genes, changes in their copy numbers, and variation in transcription factors with the modulation of expression under cold treatments and between genotypes with contrasting bract-colours suggests the variation may be exploited in plant breeding programmes, particularly for improvement of stress-resistance in the banana crop.

Unravelling the Molecular Identity of Bulgarian Jumping Plant Lice of the Family Aphalaridae (Hemiptera: Psylloidea).

Psyllids (Hemiptera: Psylloidea) are plant sap-sucking insects whose identification is often difficult for non-experts. Despite the rapid development of DNA barcoding techniques and their widespread use, only a limited number of sequences of psyllids are available in the public databases, and those that are available are often misidentified. Here, we provide 80 sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and cytochrome b (Cytb), for 25 species of Aphalaridae, mainly from Bulgaria. The DNA barcodes for 15 of these species are published for the first time. In cases where standard primers failed to amplify the target gene fragment, we designed new primers that can be used in future studies. The distance-based thresholds for the analysed species were between 0.0015 and 0.3415 for COI and 0.0771 and 0.4721 for Cytb, indicating that the Cytb gene has a higher interspecific divergence, compared to COI, and therefore allows for more accurate species identification. The species delimitation based on DNA barcodes is largely consistent with the differences resulting from morphological and host plant data, demonstrating that the use of DNA barcodes is suitable for successful identification of most aphalarid species studied. The phylogenetic reconstruction based on maximum likelihood and Bayesian inference analyses, while showing similar results at high taxonomic levels to previously published phylogenies, provides additional information on the placement of aphalarids at the species level. The following five species represent new records for Bulgaria: Agonoscena targionii, Aphalara affinis, Colposcenia aliena, Co. bidentata, and Craspedolepta malachitica. Craspedolepta conspersa is reported for the first time from the Czech Republic, while Agonoscena cisti is reported for the first time from Albania.

Molecular epidemiology of SARS-CoV-2 genome sentinel surveillance in commercial COVID-19 testing sites targeting asymptomatic individuals during Japan’s seventh epidemic wave

Eight peaks of coronavirus disease 2019 (COVID-19) outbreak occurred in Japan, each associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern. The National Epidemiological Surveillance of Infectious Diseases (NESID) analyzed viral genome sequences from symptomatic patients and submitted the results to GISAID. Meanwhile, commercial testing services occasionally sequence samples from asymptomatic individuals. We compared a total of 1248 SARS-CoV-2 full-genome sequences obtained from the SB Coronavirus Inspection Center Corp. (SBCVIC) during Japan’s seventh wave, which was dominated by Omicron variants, with 1764 sequences obtained in Japan from GISAID during the same period using chronological phylogenies and molecular transmission networks. The number of SBCVIC sequences was consistent with the number of cases reported by NESID. The SBCVIC detected a shift in the PANGO lineage from BA.2 to BA.5 earlier than that of GISAID. BA.2 lineages from the SBCVIC were distributed at different locations in the transmission network dominated by GISAID entries, whereas BA.5 lineages from SBCVIC and GISAID often formed distinct subclusters. Test-based sentinel surveillance of asymptomatic individuals may be a more manageable approach compared to notifiable disease surveillance; however, it may not necessarily capture all infection populations throughout Japan.

Diastereomer Characterization of PS-Modified Synthetic Oligonucleotides Using Cyclic IMS-MS.

Synthetic oligonucleotides have emerged as effective therapeutics that regulate gene expression to treat and prevent diseases. Oligonucleotide therapeutics are often modified with a substitution of a phosphorothioate (PS) linkage along the phosphodiester backbone to improve the drug performance and stability. The PS modification creates a mixture of diastereomer structures, increasing by a factor of 2n where n is the number of PS linkages. Despite recent draft guidances highlighting the importance of their characterization, analytical methods to measure the resulting diastereomers are currently lacking. Here, we present a method combining tandem mass spectrometry (MS) and tandem ion mobility spectrometry (IMS) using a cyclic IMS-MS instrument to study diastereomers in PS-modified oligonucleotides. This approach requires no enzymatic digestion as the intact oligonucleotides are directly injected into the MS instrument. Analogous to top-down proteomics, MS fragmentation of the intact oligonucleotide results in 3' and 5' fragment ends that have fewer diastereomers than their intact counterpart. Tandem IMS allows for mobility resolution of the diastereomers at the terminal ends. We tested four model oligonucleotides that differ in either the number of PS bonds or sequence to demonstrate the capability of this method to elucidate diastereomer structures on modified oligonucleotides.

On Topological Properties of Fuzzy Sequence Space through Orlicz Function

In this study, a new class of fuzzy number sequences is defined using Orlicz functions, and various useful classes with a variety of structures have been imposed. The behavior of these new classes has been examined as well as their topological properties and relationship to other fuzzy sequences.

Difference Gai Sequences of Interval numbers with respect to Orlicz Function

In this article we have introduced some classes generalized difference () Gai sequences of interval numbers with Orlicz functions M. We have studied some algebraic and topological properties of the classes of sequences like, linearity, completeness, solid, symmetric and convergence free.

Structure-aided function assignment to the transcriptomic conopeptide Am931

Implementation of the next-generation technologies for gene sequencing of venom duct transcriptome has provided a large number of peptide sequences of marine cone snails. Emerging technologies on computational platforms are now rapidly evolving for the accurate predictions of the 3D structure of the polypeptide using the primary sequence. The current report aims to integrate the information derived from these two technologies to develop the concept of structure-aided function assignment of Conus peptides. The proof of the concept was demonstrated using the transcriptomic peptide Am931 of C. amadis. The 3D structure of Am931 was computed using Density Functional Theory (DFT) and the quality of the predicted structure was confirmed using 2D NMR spectroscopy of the corresponding synthetic peptide. The computed structure of Am931 aligns with the active site motif of thioredoxins, possess catalytic disulfide conformation of (+, −)AntiRHHook and selectively modulate the N-terminal Cys3 thiol. These structural features indicate that Am931 may act as a disulfide isomerase and modulate the oxidative folding of conotoxins. Synthetic peptide Am931 provides proof-of-function by exhibiting catalytic activity on the oxidative folding of α-conotoxin ImI and improving the yield of native globular fold. The approach of integration of new technologies in the Conus peptide research may help to accelerate the discovery pipeline of new/improved conotoxin functional.

LearnMSA2: deep protein multiple alignments with large language and hidden Markov models.

For the alignment of large numbers of protein sequences, tools are predominant that decide to align two residues using only simple prior knowledge, e.g. amino acid substitution matrices, and using only part of the available data. The accuracy of state-of-the-art programs declines with decreasing sequence identity and when increasingly large numbers of sequences are aligned. Recently, transformer-based deep-learning models started to harness the vast amount of protein sequence data, resulting in powerful pretrained language models with the main purpose of generating high-dimensional numerical representations, embeddings, for individual sites that agglomerate evolutionary, structural, and biophysical information. We extend the traditional profile hidden Markov model so that it takes as inputs unaligned protein sequences and the corresponding embeddings. We fit the model with gradient descent using our existing differentiable hidden Markov layer. All sequences and their embeddings are jointly aligned to a model of the protein family. We report that our upgraded HMM-based aligner, learnMSA2, combined with the ProtT5-XL protein language model aligns on average almost 6% points more columns correctly than the best amino acid-based competitor and scales well with sequence number. The relative advantage of learnMSA2 over other programs tends to be greater when the sequence identity is lower and when the number of sequences is larger. Our results strengthen the evidence on the rich information contained in protein language models' embeddings and their potential downstream impact on the field of bioinformatics. Availability and implementation: https://github.com/Gaius-Augustus/learnMSA, PyPI and Bioconda, evaluation: https://github.com/felbecker/snakeMSA.

Convex combinations of some convergent sequences

We consider the convex combinations , of a pair of sequences of real numbers and such that , converging to , and study the location of the limit inside the intervals , for every or for sufficiently large . We also investigate the same problem for the case of two corresponding sequences converging to . Among other results, we prove some, a bit, unexpected ones. Namely, for each , we determine the exact index at which the sequence changes the monotonicity, and we also determine the type of the monotonicity. A number of interesting remarks are also presented.

Multiplicative independence in the sequence of [formula omitted]-generalized Lucas numbers

Let (Ln(k))n≥2−k be the sequence of k-generalized Lucas numbers for some fixed integer k≥2, whose first k terms are 0,…,0,2,1 and each term afterward is the sum of the preceding k terms. In this paper, we find all pairs of the k-generalized Lucas numbers that are multiplicatively dependent.

MRI susceptibility artefacts caused by orthodontic wire.

To evaluate magnetic susceptibility artefacts produced by orthodontic wires on MRI and the influence of wire properties and MRI image sequences on the magnitude of the artefact. Arch form orthodontic wires [four stainless steels (SS), one cobalt chromium (CC) alloy, 13 titanium (Ti) alloys] were embedded in a polyester phantom, and scanned using a 1.5-T superconducting magnet scanner with an eight-channel phased-array coil. All wires were scanned with T1-weighted spin echo (SE) and gradient echo (GRE) sequences according to the American Society for Testing and Materials (ASTM) F2119-07 standard. The phantom also scanned other eight sequences. Artefacts were measured using the ASTM F2119-07 definition and OsiriX software. Artefact volume was analysed according to metal composition, wire length, number of wires, wire thickness, and imaging sequence as factors. With SE/GRE, black/white artefacts volumes from all SS wires were significantly larger than those produced by CC and Ti wires (P < .01). With the GRE, the black artefacts volume was the highest with the SS wires. With the SE, the black artefacts volume was small, whereas white artefacts were noticeable. The cranio-caudal extent of the artefacts was significantly longer with SS wires (P < .01). Although a direct relationship of wire length, number of wires, and wire thickness with artefact volume was noted, these factors did not influence artefact extension in the cranio-caudal direction. Ferromagnetic/paramagnetic orthodontic wires create artefacts due to local alteration of magnetic field homogeneity. The SS-type wires produced the largest artefacts followed by CC and Ti.

Reaction Times in Modern Virology: "This is not a Drill".

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of interest BA.2.87.1 has not driven any Coronavirus disease 2019 (COVID-19) pandemic wave. Nevertheless, it has served to test the reaction times of modern virology laboratories. In this commentary, we highlight how fast the reaction has been at characterizing this sublineage, leading at an unprecedented pace to almost as many papers as the number of viral sequences.

New pathways to neurogenesis: Insights from injury-induced retinal regeneration.

The vertebrate retina is a tractable system for studying control of cell neurogenesis and cell fate specification. During embryonic development, retinal neurogenesis is under strict temporal regulation, with cell types generated in fixed but overlapping temporal intervals. The temporal sequence and relative numbers of retinal cell types generated during development are robust and show minimal experience-dependent variation. In many cold-blooded vertebrates, acute retinal injury induces a different form of neurogenesis, where Müller glia reprogram into retinal progenitor-like cells that selectively regenerate retinal neurons lost to injury. The extent to which the molecular mechanisms controlling developmental and injury-induced neurogenesis resemble one another has long been unclear. However, a recent study in zebrafish has shed new light on this question, using single-cell multiomic analysis to show that selective loss of different retinal cell types induces the formation of fate-restricted Müller glia-derived progenitors that differ both from one another and from progenitors in developing retina. Here, we discuss the broader implications of these findings, and their possible therapeutic relevance.

True random number generation based on temporal fluctuations of abalone shell coherent random lasers.

The output modes of random lasers exhibit randomness, making them a potential high-quality physical entropy source for generating random numbers. In this paper, we controlled a low-cost and easily fabricated abalone shell random laser, generating forward and backward coherent random lasers simultaneously in a single channel, resulting in highly diverse mode variations. After post-processing steps such as third-order difference calculations and exclusive-or (XOR) logic operations, we generated a random number sequence for the first time, to the best of our knowledge, based on the temporal fluctuations of biomimetic random laser coherent modes. The instantaneous generation rate reached a preliminary 40 Gbps. Moreover, the random bits satisfy requirements such as random distribution, independence, and absence of bias, successfully passing the NIST SP800-22 standard test, confirming the high quality of the random number sequence.

On the Linear Recurrence of (Generalized) Hybrid Numbers Sequences and Moment Problems

On the Linear Recurrence of (Generalized) Hybrid Numbers Sequences and Moment Problems

Pell Leonardo numbers and their matrix representations

In this study, we investigate Pell numbers and Leonardo numbers and describe a new third-order number sequence entitled Pell Leonardo numbers. We then construct some identities, including the Binet formula, generating function, exponential generating function, Catalan, Cassini, and d’Ocagne’s identities for Pell Leonardo numbers and obtain a relation between Pell Leonardo and Pell numbers. In addition, we present some summation formulas of Pell Leonardo numbers based on Pell numbers. Finally, we create a matrix formula for Pell Leonardo numbers and obtain the determinant of the matrix.

A New Notion of Convergence Defined by The Fibonacci Sequence: A Novel Framework and Its Tauberian Conditions

The Fibonacci sequence has broad applications in mathematics, where its inherent patterns and properties are utilized to solve various problems. The sequence often emerges in areas involving growth patterns, series, and recursive relationships. It is known for its connection to the golden ratio, which appears in numerous natural phenomena and mathematical constructs. In this research paper, we introduce new concepts of convergence and summability for sequences of real and complex numbers by using Fibonacci sequences, called Δ-Fibonacci statistical convergence, strong Δ-Fibonacci summability, and Δ-Fibonacci statistical summability. And, these new concepts are supported by several significant theorems, properties, and relations in the study. Furthermore, for this type of convergence, we introduce one-sided Tauberian conditions for sequences of real numbers and two-sided Tauberian conditions for sequences of complex numbers.

On a Matrix Formulation of the Sequence of Bi-Periodic Fibonacci Numbers

On a Matrix Formulation of the Sequence of Bi-Periodic Fibonacci Numbers

Resolution of Optimal Mitochondrial and Nuclear DNA Enrichment in Target-Panel Sequencing and Physiological Mitochondrial DNA Copy Number Estimation in Liver Cancer and Non-Liver Cancer Subjects.

Mitochondria generate energy to support cells. They are important organelles that engage in key biological pathways. The dysfunction of mitochondria can be linked to hepatocarcinogenesis, which has been actively explored in recent years. To investigate the mitochondrial dysfunction caused by genetic variations, target-panel sequencing is a flexible and promising strategy. However, the copy number of mitochondria generally exceeds nuclear DNA, which raises a concern that uneven target enrichment of mitochondrial DNA (mtDNA) and nuclear DNA (ncDNA) in target-panel sequencing would lead to an undesirably biased representation of them. To resolve this issue, we evaluated the optimal pooling of mtDNA probes and ncDNA probes by a series of dilutions of mtDNA probes in both genomic DNA (gDNA) and cell-free DNA (cfDNA) samples. The evaluation was based on read count, average sequencing depth and coverage of targeted regions. We determined that an mtDNA:ncDNA probe ratio of around 1:10 would offer a good balance of sequencing performance and cost effectiveness. Moreover, we estimated the median physiological mtDNA:ncDNA copy ratio as 38.1 and 2.9 in cfDNA and gDNA samples of non-liver cancer subjects, respectively, whereas they were 20.0 and 2.1 in the liver cancer patients. Taken together, this study revealed the appropriate pooling strategy of mtDNA probes and ncDNA probes in target-panel sequencing and suggested the normal range of physiological variation of the mtDNA:ncDNA copy ratio in non-liver cancer individuals. This can serve as a useful reference for future target-panel sequencing investigations of the mitochondrial genome in liver cancer.