Sequence Of Variables Research Articles

Open-ended molecular recording of sequential cellular events into DNA.

Genetically encoded DNA recorders noninvasively convert transient biological events into durable mutations in a cell's genome, allowing for the later reconstruction of cellular experiences by DNA sequencing. We present a DNA recorder, peCHYRON, that achieves high-information, durable, and temporally resolved multiplexed recording of multiple cellular signals in mammalian cells. In each step of recording, prime editor, a Cas9-reverse transcriptase fusion protein, inserts a variable triplet DNA sequence alongside a constant propagator sequence that deactivates the previous and activates the next step of insertion. Insertions accumulate sequentially in a unidirectional order, editing can continue indefinitely, and high information is achieved by coexpressing a variety of prime editing guide RNAs (pegRNAs), each harboring unique triplet DNA sequences. We demonstrate that the constitutive expression of pegRNA collections generates insertion patterns for the straightforward reconstruction of cell lineage relationships and that the inducible expression of specific pegRNAs results in the accurate recording of exposures to biological stimuli.

On the Non-Linearity of S-Type Variable Exponent Absolutely Summable New Difference Sequence Space

This article presents the domain of general quantum difference in Nakano sequence space. Some topological and geometric behavior, the multiplication mappings defined on it, and the spectrum of mapping ideals constructed by this space and s−numbers have been introduced. Existing results are constructed by controlling the general quantum difference and power of this new space, which is a major strength.

Design of calibration-free RF pulses for T -weighted single-slab 3D turbo-spin-echo sequences at 7T utilizing parallel transmission.

T -weighted turbo-spin-echo (TSE) sequences are a fundamental technique in brain imaging but suffer from field inhomogeneities at ultra-high fields. Several methods have been proposed to mitigate the problem, but were limited so far to nonselective three-dimensional (3D) measurements, making short acquisitions difficult to achieve when targeting very high resolution images, or needed additional calibration procedures, thus complicating their application. Slab-selective excitation pulses were designed for flexible placement utilizing the concept of k -spokes. Phase-coherent refocusing universal pulses were subsequently optimized with the Gradient Ascent Pulse Engineering algorithm and tested in vivo for improved signal homogeneity. Implemented within a 3D variable flip angle TSE sequence, these pulses led to a signal-to-noise ratio (SNR) improvement ranging from 10%to 30% compared to a two-dimensional (2D) T2w TSE sequence employing -shimmed pulses. field inhomogeneities could be mitigated and artifacts from deviations reduced. The concept of universal pulses was successfully applied. We present a pulse design method which provides a set of calibration-free universal pulses (UPs) for slab-selective excitation and phase-coherent refocusing in slab-selective TSE sequences.

Arbitrary Random Variables and Wiman’s Inequality

We study the class of random entire functions given by power series, in which the coefficients are formed as the product of an arbitrary sequence of complex numbers and two sequences of random variables. One of them is the Rademacher sequence, and the other is an arbitrary complex-valued sequence from the class of sequences of random variables, determined by a certain restriction on the growth of absolute moments of a fixed degree from the maximum of the module of each finite subset of random variables. In the paper we prove sharp Wiman–Valiron’s type inequality for such random entire functions, which for given p∈(0;1) holds with a probability p outside some set of finite logarithmic measure. We also considered another class of random entire functions given by power series with coefficients, which, as above, are pairwise products of the elements of an arbitrary sequence of complex numbers and a sequence of complex-valued random variables described above. In this case, similar new statements about not improvable inequalities are also obtained.

Single-cell Sequencing of Circulating Human Plasmablasts during Staphylococcus aureus Bacteremia.

Staphylococcus aureus is the major cause of healthcare-associated infections, including life-threatening conditions as bacteremia, endocarditis, and implant-associated infections. Despite adequate antibiotic treatment, the mortality of S. aureus bacteremia remains high. This calls for different strategies to treat this infection. In past years, sequencing of Ab repertoires from individuals previously exposed to a pathogen emerged as a successful method to discover novel therapeutic monoclonal Abs and understand circulating B cell diversity during infection. In this paper, we collected peripheral blood from 17 S. aureus bacteremia patients to study circulating plasmablast responses. Using single-cell transcriptome gene expression combined with sequencing of variable heavy and light Ig genes, we retrieved sequences from >400 plasmablasts revealing a high diversity with >300 unique variable heavy and light sequences. More than 200 variable sequences were synthesized to produce recombinant IgGs that were analyzed for binding to S. aureus whole bacterial cells. This revealed four novel monoclonal Abs that could specifically bind to the surface of S. aureus in the absence of Ig-binding surface SpA. Interestingly, three of four mAbs showed cross-reactivity with Staphylococcus epidermidis. Target identification revealed that the S. aureus-specific mAb BC153 targets wall teichoic acid, whereas cross-reactive mAbs BC019, BC020, and BC021 target lipoteichoic acid. All mAbs could induce Fc-dependent phagocytosis of staphylococci by human neutrophils. Altogether, we characterize the active B cell responses to S. aureus in infected patients and identify four functional mAbs against the S. aureus surface, of which three cross-react with S. epidermidis.

Double sequences of complex uncertain variables associated with multiplier sequences

Abstract In this article we introduce the notion of double sequences of complex uncertain variables associated with multiplier sequences. We study their different algebraic and topological properties like solidity, symmetricity, completeness etc.

On a weak law of large numbers and Lp -convergence for general random variables

In the present paper, we consider a sequence of the general random variables, which include the sequences of martingale differences, and establish the weak law of large numbers and the convergence in Lp under some weaker conditions.

CDR identification, epitope mapping and binding affinity determination of novel monoclonal antibodies generated against human apolipoprotein B-100

In-house generated mAbs to apolipoprotein B-100 (apoB-100) clones hLDL-E8, hLDL-2D8 and hLDL-F5 were extensively studied to determine their complementarity-determining regions (CDRs), binding epitopes and affinity. RT-PCR revealed that all mAbs consisted of kappa light chains and gamma heavy chains. DNA sequencing and bioinformatic analysis showed that the variable gene and protein sequences of their CDRs shared over 50 % identity with the existing databases. The 3D structures of the mAb variable fragments (Fv) with a QSQE score above 0.7 were constructed using the SWISS-MODEL platform. The structural accuracy was confirmed by Ramachandran plots, with 99 % of amino acid residues falling within acceptable regions. Thrombolytic cleavage of apoB-100 and Western blot analysis demonstrated that hLDL-E8 and hLDL-F5 specifically bind to the T3 fragment (aa 1297–3249), whereas hLDL-2D8 binds to the T4 fragment (aa 1–1297). These findings were supported with epitope-binding assays using inhibition ELISA, which indicated that hLDL-E8 binds at different epitopes from hLDL-2D8 and has some overlap with hLDL-F5. Lastly, the binding affinity of the mAbs was examined by indirect ELISA. The average affinity constants (Kaff) for mAbs hLDL-2D8, hLDL-E8 and hLDL-F5 are 1.51 ± 0.69 × 109 Mol−1, 7.25 ± 3.56 × 108 Mol−1 and 4.39 ± 2.63 × 106 Mol−1, respectively. Additionally, the behavior of the antibodies in the dose-response curve revealed that hLDL-F5 may recognize two epitopes of apoB-100 or have very low binding affinity. In contrast, hLDL-2D8 and hLDL-E8 each recognize a single epitope. These findings provide information that will be useful when selecting mAbs for both laboratory and clinical research purposes.

Comparison of B Cell Variable Region Gene Segment Characteristics in Neuro-autoantibodies.

Autoimmune pediatric neurologic diseases have variable phenotypes and presentations, making diagnosis challenging. The pathologic mechanisms are also distinct, including cell-mediated and Ab-mediated autoimmunity, paraneoplastic syndromes, and postinfectious processes. In recent years a number of studies have described the characteristics of the autoantibodies involved in a number of these diseases. Some of the described Abs use a restricted set of variable gene segments. We sought to compare the Ab characteristics of autoantibodies related to some of the more common disorders to discover whether specific Ab signatures are universally associated with neuroautoimmune diseases. We initially performed a literature review to summarize the Ab characteristics of autoantibodies related to some of the more common disorders, including N-methyl-d-aspartate receptor (NMDAR) and leucine-rich, glioma-inactivated 1 (LGI-1). Next, we performed data analysis from selected studies that sequenced Ig genes to further characterize NMDAR and LGI-1 autoantibodies including CDR3 length distribution, variable gene sequence usage, and isotype use. We found that CDR3 length of NMDAR autoantibodies was normally distributed whereas the CDR3 length distribution of LGI-1 autoantibodies was skewed, suggesting that there is no global structural restriction on types of autoantibodies that can cause encephalitis. We also found that IgG1-IgG3 were the main NMDAR autoantibody isotypes detected, while IgG4 was the major isotype used in autoantibodies from LGI-1 encephalitis. These findings are useful for our understanding of autoimmune encephalitis and will help facilitate better diagnosis and treatment of these conditions in the future.

Deconvolution of ℙ(Xt < Yt ) for stationary processes with supersmooth error distributions

This paper focuses on nonparametrically estimating the probability P ( X t < Y t ) when two strongly mixing stationary processes, X t and Y t , are observed with additional errors at discrete time points t j = j Δ (where Δ is a positive constant). This problem has practical significance in some applications where data is time-dependent random variable sequences (generated from stochastic processes) like time-dependent stress–strength reliability modelling and receiver operating characteristic (ROC) curve analysis. We extend our analysis to account for errors generated from another strongly mixing stationary processes and derive convergence rate and asymptotic normality results for the estimator under supersmooth error distributions. Through applications and simulations, we illustrate the properties of our estimator.

Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to pneumococcal vaccination

Single-cell RNA sequencing (scRNA-seq) can resolve transcriptional features from individual cells, but scRNA-seq techniques capable of resolving the variable regions of B cell receptors (BCRs) remain limited, especially from widely-used 3′-barcoded libraries. Here, we report a method that can recover paired, full-length variable region sequences of BCRs from 3′-barcoded scRNA-seq libraries. We first verify this method (B3E-seq) can produce accurate, full-length BCR sequences. We then apply this method to profile B cell responses elicited against the capsular polysaccharide of Streptococcus pneumoniae serotype 3 (ST3) by glycoconjugate vaccines in five infant rhesus macaques. We identify BCR features associated with specificity for the ST3 antigen which are present in multiple vaccinated monkeys, indicating a convergent response to vaccination. These results demonstrate the utility of our method to resolve key features of the B cell repertoire and profile antigen-specific responses elicited by vaccination.

In-silico identification of simple sequence repeat (SSR) markers and phylogenetic analysis from chloroplast genomes of the genus Bambusa

Microsatellites or simple sequence repeats (SSRs), are short DNA sequences composed of repetitive units typically 1 to 6 base pairs long. These highly variable sequences are found in both protein-coding and noncoding DNA regions and exhibit a high degree of polymorphism. In the present study, chloroplast genomes of five species of Bambusa viz. B. bambos, B. multiplex, B. teres, B. vulgaris, and B. tulda, along with three outgroup species viz. Sorghum timorense, Hordeum vulgare, and Triticum aestivum were retrieved from NCBI in FASTA and GenBank formats and screened for chloroplast SSRs (cpSSRs) using MISA Perl script. The sequence analysis of the chloroplast genomes of different species of Bambusa confirmed the presence of 144 cpSSRs. The number of cpSSRs varied among the five bamboo species, with B. vulgaris exhibiting the highest count (31) and B. multiplex showing the lowest (27). Tetranucleotides were the most observed repeats in Bambusa, followed by mono-, di- and trinucleotides. Of the 144 SSR markers identified, only 16 (11.11 %) were suitable for primer design since the remaining sequences failed to produce acceptable primer pairs. An unweighted pair-group method with an arithmetic mean (UPGMA) dendrogram was constructed to analyze the genetic relationships among the genotypes. This analysis revealed three distinct clusters among the genotypes. SSR markers were found to be informative in differentiating the species of Bambusa and were likely to find potential applications in genetic fingerprinting, population genetics, conservation, and phylogenetics.

Projected gradient descent method for cardinality-constrained portfolio optimization

Cardinality-constrained portfolio optimization aims at determining the investment weights on given assets using the historical data. This problem typically requires three constraints, namely, capital budget, long–only, and sparsity. The sparsity restraint allows investment managers to select a small number of stocks from the given assets. Most existing approaches exploit the penalty technique to handle the sparsity constraint. Therefore, they require tweaking the associated regularization parameter to obtain the desired cardinality level, which is time-consuming. This paper formulates the sparse portfolio design as a cardinality-constrained nonconvex optimization problem, where the sparsity constraint is modeled as a bounded ℓ0-norm. The projected gradient descent (PGD) method is then utilized to deal with the resultant problem. Different from existing algorithms, the suggested approach, called ℓ0-PGD, can explicitly control the cardinality level. In addition, its convergence is established. Specifically, the ℓ0-PGD guarantees that the objective function value converges, and the variable sequences converges to a local minimum. To remedy the weaknesses of gradient descent, the momentum technique is exploited to enhance the performance of the ℓ0-PGD, yielding ℓ0-PMGD. Numerical results on four real-world datasets, viz. NASDAQ 100, S&P 500, Russell 1000, and Russell 2000 exhibit the superiority of the ℓ0-PGD and ℓ0-PMGD over existing algorithms in terms of mean return and Sharpe ratio.

Population differences in putty-nosed monkey (Cercopithecus nictitans) call order.

Non-human primates generally lack the ability to learn new call structures or to substantially modify existing ones, suggesting that callers need alternative mechanisms to convey information. One way to escape the constraints of limited vocal control is by assembling calls into variable sequences, as has been documented in various animal species. Here, we were interested in the flexibility with which different calls might be assembled in a species known for its meaningful call order, putty-nosed monkeys (Cercopithecus nictitans). Since most information comes from studies conducted at Gashaka Gumti National Park (Nigeria), we tested two further populations in the Nouabalé-Ndoki National Park (Republic of the Congo) and Taï National Park (Côte d'Ivoire) in how males responded to common threats, leopards, and crowned eagles. As predicted, callers produced the same basic call types as seen elsewhere-long 'pyow', short 'pyow' ('kek'), 'hack'-but populations differed in how males assembled calls. To leopards, males from both populations started with 'pyows' and 'keks', with occasional hacks later, as already reported from Gashaka. To crowned eagle, however, Nouabalé-Ndoki males consistently initiated their responses with 'pyows', whereas neither Taï nor Gashaka males ever did, demonstrating that nonhuman primates have some control over sequence production. We discuss possible mechanisms to account for the population differences, predation pressure, and male-male competition, and address implications for linguistic theories of animal call order, notably the Urgency and Informativity Principles.

Construction of on-site DNA pre-treatment device and rapid electrochemical biosensor set for Escherichia coli detection in milk

Restaurants and cafeterias are constantly exposed to bacterial contamination. In such environments, it is highly needed the rapid bacteria detection system with simple pre-treatment device. To solve this problem, this study presented the pre-treatment device and Rapid electrochemical (REC) biosensor set for detecting Escherichia coli (E. coli) gene in milk sample. The pre-treatment device is consisted of tetraethyl orthosilicate (TEOS)-coated bead that operated with sonication method, and it can effectively remove the E. coli residues and extract E. coli DNA well. By analyzing the sequences of various foodborne pathogens, we selected the highly variable region sequences of E. coli DNA to use as the bioprobe for REC biosensor. The selected thiol-modified bioprobe was immobilized onto the fabricated biosensor electrode. For detecting the extracted E. coli gene fragment rapidly, the alternating current electrothermal flow (ACEF) technique was introduced to REC-biosensor. ACEF technique minimize the target-bioprobe binding time to 10 mins. Using the extracted E. coli DNA fragments with the pre-treatment device, the proposed REC-biosensor shows the limit of detection (LOD) in milk samples was 9.235 × 10-5 ng/μL, and the target detection accuracy was 92.5 %, with a maximal error rate up to 6.730 %. Moreover, the biosensor demonstrated high selectivity in electrochemical performance evaluation (Matrix effect = 7.425 %). The developed pre-treatment device provides simple and quick preprocessing time (within 20 min) of E. coli, and REC biosensor provides the rapid detection of E. coli (within 10 min). In conclusion, the proposed pre-treatment device and biosensor set can be easily applied to other types of bacteria, virus or germs in the near future.

Distribution of unit mass on one fractal self-similar web-type curve

In the article, we study structural, spectral, topological, metric and fractal properties of distribution of complex-valued random variable$\tau=\sum\nolimits_{n=1}^{\infty}\frac{2\varepsilon_{\tau}}{3^n}\equiv\Delta^g_{\tau_1...\tau_n...}$, where $(\tau_n)$ is a~sequence of independent random variables taking the values $0,1,\cdots,6$ with the probabilities $p_{0n}$, $p_{1n},\cdots,p_{6n}$; $\varepsilon_{6}=0$, $\varepsilon_0$, $\varepsilon_1,\cdots,\varepsilon_5$ are 6th roots of unity. We prove that the set of values of random variable $\tau$ is self-similar six petal snowflake which is a fractal curve $G$ of spider web type with dimension $\log_37$. Its outline is the Koch snowflake. We establish that $\tau$ has either a discrete or a singularly continuous distribution with respect to two-dimensional Lebesgue measure. The criterion of discreteness for the distribution is found and its point spectrum (set of atoms) is described. It is proved that the point spectrum is a countable everywhere dense set of values of the random variable $\tau$, which is the tail set of the seven-symbol representation of the points of the curve $G$. In the case of identical distribution of the random variables $\tau_n$ (namely: $p_{kn}=p_k$) we establish that the spectrum of distribution $\tau$ is a self-similar fractal and that the essential support of density is the fractal Besicovitch-Eggleston type set. The set is defined by terms digits frequencies and has the fractal dimension $\alpha_0(E)=\frac{\ln {p_0^{p_0}\cdots p_6^{p_6}}}{-\ln 7}$ with respect to the Hausdorff-Billingsley $\alpha$-measure. The measure is a probabilistic generalization of the Hausdorff $\alpha$-measure. In this case, the random variables $\tau=\Delta^g_{\tau_1\cdots\tau_n\cdots}$ and $\tau'=\Delta^g_{\tau_1'...\tau_n'...}$ defined by different probability vectors $(p_0,\cdots,p_6)$ and $(p'_0,\cdots,p'_6)$ have mutually orthogonal distributions.

Correlation between Serum Levels of Factor I, CD59, Interferon-gamma, and Interleukin-6 with the Response to Rituximab in Iraqi Patients with Rheumatoid Arthritis

Background: Rituximab is a chimeric IgG1 kappa immunoglobulin that has been genetically modified to incorporate human constant region sequences together with murine light- and heavy-chain variable region sequences. People use it to treat rheumatoid arthritis and certain malignancies. Objective: The study aimed to assess the potential association between the serum levels of Factor I, CD59, interleukins (IL)-6, and interferon-gamma (IFN)-γ and the response to Rituximab treatment in Iraqi rheumatoid arthritis patients. Methods: A cross-sectional study was conducted at the rheumatology center at Baghdad Teaching Hospital. Ninety adult patients who have been diagnosed with rheumatoid arthritis and are receiving Rituximab intravenous infusions were included. The enrolled patients were divided into a responder group (45 patients) and a non-responder group (45 patients). The response to Rituximab was assessed according to the 28-joint Disease Activity Score (DAS28). Results: The serum levels of Factor I and CD59 were significantly higher in the non-responders group in comparison to the responders group. In addition, the serum IL-6 and IFN-γ levels were significantly elevated in the non-responders group in comparison to the responders group. The estimated marker serum levels showed a strong, significant correlation with the 6-month change in DAS28. Conclusions: In Rituximab nonresponder RA patients, serum levels of Factor I, CD59, Factor H, IL-6, and IFN-γ are higher, and they have good potential to be used in the assessment of the response to Rituximab therapy.

Development of nucleic acid lateral flow immunoassay for duplex detection of Leishmania martiniquensis and Leishmania orientalis in asymptomatic patients with HIV.

Leishmaniasis, a neglected tropical disease caused by parasitic protozoa of the Leishmania genus, remains a global health concern with significant morbidity and mortality. In Thailand, the rising incidence of autochthonous leishmaniasis cases involving Leishmania (Mundinia) martiniquensis and novel Leishmania (Mundinia) orientalis underscores the critical need for accurate diagnosis and effective control strategies. This study presents a sensitive and specific nucleic acid lateral flow immunoassay (NALFIA) that integrates a duplex PCR assay with a lateral flow device (LFD) strip format. Targeting the internal transcribed spacer 1 (ITS1) region, known for its unique combination of conserved and variable sequences, this assay employs primers labeled with biotin, digoxigenin, and fluorescein isothiocyanate (FITC) markers, enabling precise species identification and differentiation of these two Leishmania species. Remarkably, the assay achieves a sensitivity that surpasses agarose gel electrophoresis, detecting as few as 10-2 parasite/μL for L. martiniquensis and 10-4 parasite/μL for L. orientalis. Notably, the assay exhibited reliable specificity, revealing no cross-amplification with other major viscerotropic Leishmania species or reference organisms. Evaluation using 62 clinical samples further confirms the effectiveness of the PCR-LFD assay, with a sensitivity of 100% for L. martiniquensis and 83.3% for L. orientalis, and an excellent agreement (κ value = 0.948) with nested PCR. This integrated assay represents a promising advancement in diagnostic tools, offering rapid and accurate results that can significantly contribute to effective disease management and control. Given the increasing relevance of these Leishmania species in current public health scenarios, this assay serves as a valuable tool for both diagnostic and research applications.

Generation of a Phage Display Chicken Single-Chain Variable Fragment Library.

Phage-displayed antibody fragment libraries can be constructed using essentially any species that is easily immunized, as long as the immunoglobulin variable region gene sequences are known. This protocol describes the procedures for the generation of a phage-displayed chicken single-chain variable fragment (scFv) library after immunization with a target antigen. Briefly, the rearranged heavy chain variable region (V H ) genes and the λ light chain variable region (V λ ) genes are amplified separately and are linked through two separate PCR steps to give the final scFv genes. The genes are then cloned into pComb3XSS to generate the phage display chicken scFv library, which can then be used for test and final library ligations.

In-Depth Analysis of GAF-Net: Comparative Fusion Approaches in Video-Based Person Re-Identification

This study provides an in-depth analysis of GAF-Net, a novel model for video-based person re-identification (Re-ID) that matches individuals across different video sequences. GAF-Net combines appearance-based features with gait-based features derived from skeletal data, offering a new approach that diverges from traditional silhouette-based methods. We thoroughly examine each module of GAF-Net and explore various fusion methods at the both score and feature levels, extending beyond initial simple concatenation. Comprehensive evaluations on the iLIDS-VID and MARS datasets demonstrate GAF-Net’s effectiveness across scenarios. GAF-Net achieves state-of-the-art 93.2% rank-1 accuracy on iLIDS-VID’s long sequences, while MARS results (86.09% mAP, 89.78% rank-1) reveal challenges with shorter, variable sequences in complex real-world settings. We demonstrate that integrating skeleton-based gait features consistently improves Re-ID performance, particularly with long, more informative sequences. This research provides crucial insights into multi-modal feature integration in Re-ID tasks, laying a foundation for the advancement of multi-modal biometric systems for diverse computer vision applications.