Search Results (155)

Background: Peperomia leptostachya is a herbaceous plant with significant medicinal value. To elucidate its mitochondrial genomic characteristics, this study conducted a systematic analysis. Methods: The mitochondrial genome of P. leptostachya was assembled, annotated, and subjected to comparative analysis. Results: (1) The genome exhibits significant structural peculiarities, presenting as an atypical circular structure accompanied by an independent minicircle, forming a multi-branched reticulate configuration spanning a total length of 981,249 bp. Within the mitochondrial genome of P. leptostachya, a total of 52 genes have been identified, including 35 PCGs, 14 tRNAs and 3 rRNAs. (2) A phylogenetic tree was built for 22 species based on the DNA sequences. P. leptostachya belongs to the family Piperaceae within the order Piperales and is closely related to Piper nigrum. (3) Homologous colinear blocks were detected between P. leptostachya and its close relatives, though these blocks exhibited short lengths. Additionally, blank regions were identified that showed no homology with other species. Mitochondrial genomes of P. leptostachya and two close relatives had inconsistent collinear block arrangements. The mitochondrial genome of P. leptostachya had undergone genomic rearrangement relative to closely related species. Conclusions: This study lays the foundation for research into the genetic characteristics and biological traits of P. leptostachya. Full article

Many data processing applications involve binary matrices for storing digital information. At present, there are limited results in the literature about algorithms for inverting large binary matrices. This paper contributes the following three results. First, the divide-and-conquer methods for efficiently inverting large matrices over finite fields such as Strassen’s matrix inversion often fail on singular sub-blocks, even if the original matrix is non-singular. It is proposed to combine Strassen’s method with the PLU factorization at each recursive step in order to obtain robust pivoting, which correctly inverts all non-singular matrices over any finite field. The resulting algorithm is shown to maintain the sub-cubic time complexity. Second, although there are theoretical studies on how to systematically enumerate all invertible matrices over finite fields without redundancy, no practical algorithm has been reported in the literature that is easy to understand and also suitable for enumerating large matrices. The use of Bruhat decomposition has been proposed to enumerate all invertible matrices. It leverages the linear group-theoretic structure and defines an ordered sequence of invertible matrices, so that each matrix is generated exactly once. Third, large binary matrices have about 29% probability to be invertible. In some applications, it may be desirable to repair the singular matrices by performing a small number of bit-flips. It is shown that the minimum number of bit-flips is equal to the matrix rank deficiency, i.e., the minimum Hamming distance from the general linear group. The required bit-flips are identified by pivoting during the matrix inversion, so the matrix rank can be restored. The correctness and the time complexity of the proposed algorithms were verified both theoretically and empirically. The reference implementation of these algorithms in C++ is available on Github. Full article

We investigate the multifractal geometry of irregular sets arising from weighted averages of random variables, where the weights $\left(w_n\right)$ form a positive sequence with exponential growth. Our analysis applies in particular to sequences generated by linear recurrence relations of Fibonacci type, including higher-order generalizations such as the Tetranacci sequence $\left({\mathsf{T}}_n\right)$. Using a Cantor-type construction built from alternating free and forced blocks, we show that the associated exceptional sets may attain full Hausdorff and packing dimension, independently of the precise form of the recurrence. We further develop a probabilistic interpretation of $\left({\mathsf{T}}_n\right)$ through an appropriate Markov representation that encodes its combinatorial evolution and yields sharp asymptotic behavior. Finally, given $n+1$ consecutive terms of a Fibonacci-type sequence, one may construct a polynomial $P_n\left(x\right)$ of degree at most n via Lagrange interpolation; we show that this polynomial admits an implicit recursive representation consistent with the underlying recurrence. Full article

Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and crop improvement. Using multi-region 16S rRNA sequencing, we compared the rhizosphere and endosphere bacterial communities of cultivated tomato (Solanum lycopersicum cv. Moneymaker) with six wild relatives (S. pimpinellifolium, S. huaylasense, S. peruvianum, S. chilense, S. habrochaites, and S. pennellii) spanning the main wild lineages within Solanum sect. Lycopersicon. Bacterial community structure in the rhizosphere was broadly conserved across all seven hosts, and diversity remained comparable among genotypes. Despite this overall stability, the rhizosphere microbiomes were ordered along a gradient consistent with host phylogeny, with Moneymaker clustering near S. pimpinellifolium, the four green-fruited Eriopersicon species forming a cohesive block, and S. pennellii occupying the most distinct position. Within this hierarchy, individual hosts showed specific recruitment preferences, including enrichment of Streptomycetaceae in S. pimpinellifolium, Bacillaceae in S. chilense, and contrasting patterns of nitrifiers among Eriopersicon species and S. pennellii. Differential abundance testing in the endosphere revealed consistent reductions in several bacterial families in wild accessions, alongside the enrichment of Streptomycetaceae and Rhodobiaceae in multiple wild species. Overall, our study suggests that domestication exerted a modest effect on tomato root microbiomes, while wild relatives retained microbial association traits that could be harnessed in microbiome-informed breeding to improve resilience in cultivated tomato. Full article

In hyperspectral image classification (HSIC), each pixel contains information across hundreds of contiguous spectral bands; therefore, the ability to perform long-distance modeling that stably captures and propagates these long-distance dependencies is critical. A selective structured state space model (SSM) named Mamba has shown strong capabilities for capturing cross-band long-distance dependencies and exhibits advantages in long-distance modeling. However, the inherently high spectral dimensionality, information redundancy, and spatial heterogeneity of hyperspectral images (HSI) pose challenges for Mamba in fully extracting spatial–spectral features and in maintaining computational efficiency. To address these issues, we propose S²GL-MambaResNet, a lightweight HSI classification network that tightly couples Mamba with progressive residuals to enable richer global, local, and multi-scale spatial–spectral feature extraction, thereby mitigating the negative effects of high dimensionality, redundancy, and spatial heterogeneity on long-distance modeling. To avoid fragmentation of spatial–spectral information caused by serialization and to enhance local discriminability, we design a preprocessing method applied to the features before they are input to Mamba, termed the Spatial–Spectral Gated Attention Aggregator (SS-GAA). SS-GAA uses spatial–spectral adaptive gated fusion to preserve and strengthen the continuity of the central pixel’s neighborhood and its local spatial–spectral representation. To compensate for a single global sequence network’s tendency to overlook local structures, we introduce a novel Mamba variant called the Global_Local Spatial_Spectral Mamba Encoder (GLS²ME). GLS²ME comprises a pixel-level global branch and a non-overlapping sliding-window local branch for modeling long-distance dependencies and patch-level spatial–spectral relations, respectively, jointly improving generalization stability under limited sample regimes. To ensure that spatial details and boundary integrity are maintained while capturing spectral patterns at multiple scales, we propose a multi-scale Mamba encoding scheme, the Hierarchical Spectral Mamba Encoder (HSME). HSME first extracts spectral responses via multi-scale 1D spectral convolutions, then groups spectral bands and feeds these groups into Mamba encoders to capture spectral pattern information at different scales. Finally, we design a Progressive Residual Fusion Block (PRFB) that integrates 3D residual recalibration units with Efficient Channel Attention (ECA) to fuse multi-kernel outputs within a global context. This enables ordered fusion of local multi-scale features under a global semantic context, improving information utilization efficiency while keeping computational overhead under control. Comparative experiments on four publicly available HSI datasets demonstrate that S²GL-MambaResNet achieves superior classification accuracy compared with several state-of-the-art methods, with particularly pronounced advantages under few-shot and class-imbalanced conditions. Full article

Genetic variability in terrestrial mammals is essential for understanding population and evolutionary dynamics, as well as for establishing effective strategies in conservation biology. This comprehensive review aimed to critically analyze invasive and non-invasive techniques used to assess genetic variability in wild terrestrial mammals. Using the PICO (Population, Intervention, Comparison, Outcome) format and following PRISMA guidelines, a comprehensive literature search was conducted in Web of Science, Scopus and Science Direct databases, including articles published in English from January 2015 to April 2025. Thirty-one experimental studies were selected that met specific criteria related to genetic evaluation using invasive (direct blood or tissue collection) and non-invasive (stool, hair and saliva collection) techniques. The results indicate that invasive techniques provide samples of high genetic quality, albeit with important ethical and animal welfare considerations. In contrast, non-invasive techniques offer less disruptive methods, although they present significant challenges in terms of quantity and purity of DNA obtained, potentially affecting the accuracy and confidence of genetic analysis. Detailed analysis of selected studies showed diverse patterns of heterozygosity and inbreeding coefficients between different taxonomic orders (Carnivora, Artiodactyla, Proboscidea, Primates and Rodentia). In addition, the main anthropogenic threats and current conservation strategies implemented in different species were identified. An overall genetic variability ranging from high to moderate was observed, with large species being more vulnerable to genetic reduction due to changes in habitat and human activities. Rather than a static comparison, our synthesis traces a clear methodological arc from small short tandem repeats (STR, or microsatellites) panels towards SNP-based approaches enabled by next-generation sequencing, including reduced representation (ddRAD), amplicon panels (GT-seq), and hybridisation capture tailored to degraded DNA from hair, faeces, and environmental substrates. Over 2015–2025, study designs shifted from presence/absence and coarse diversity estimates to robust inference of relatedness, assignment, effective population size, and gene flow using hundreds–thousands of SNPs and genotype-likelihood frameworks tolerant of allelic dropout and low coverage. Laboratory practice converged on multi-tube replication, synthetic blocking oligos, and capture-based enrichment; bioinformatics adopted probabilistic genotype calling, error-aware filtering, and replication-based consensus. This review provides a solid basis for optimizing genetic sampling methods, allowing for more ethical and efficient studies. Furthermore, it contributes to strengthening conservation strategies by underlining the importance of adapting the sampling method to the biological and ecological particularities of each species studied. Ultimately, these findings can significantly improve genetic conservation decision-making, benefiting the sustainability and resilience of wild land mammal populations. Full article

Xenotransplantation using pig cells, tissues or organs may be associated with the transmission of porcine zoonotic or xenozoonotic microorganisms. Porcine endogenous retroviruses (PERVs) pose a special risk for xenotransplantation as these viruses can infect human cells and are integrated in multiple copies in the genome of all pigs and, therefore, they cannot be eliminated as other viruses can. To prevent PERV transmission to the recipient, several strategies have been developed: PERV-C-free animals, siRNA and genomic editing. Another strategy is the generation of vaccines based on neutralizing antibodies in order to protect the recipient. To investigate whether a protective vaccine is feasible in the case of PERV, the recombinant transmembrane (p15E) and the surface envelope (gp70) protein of PERV were cloned, produced, purified and used to immunize rats. For the first time, an adjuvant type that is approved for human use was used. In all cases we obtained virus binding antibodies as shown in Western blot assays and neutralizing antibodies as shown in neutralization assays, indicating the potential for a protective vaccine. The epitopes recognized by the antisera against p15E were determined using overlapping peptides. Two main epitopes were found in the sequence of p15E, one in the membrane proximal external region (MPER) and one in the fusion peptide proximal region (FPPR). The epitopes correspond to epitopes determined previously when immunizing different animal species with p15E of PERV. Antibodies against these epitopes block the conformational changes in the transmembrane envelope proteins that are required for membrane fusion, thereby inhibiting infection. The epitope in the MPER is related by sequence and location to an epitope in the transmembrane envelope protein of the human immunodeficiency virus-1 (HIV-1) recognized by a broadly neutralizing antibody from infected patients. Full article

A series of PTT-b-PTMG copolyesters was synthesized via direct esterification followed by melt polycondensation using purified terephthalic acid (PTA), bio-based 1,3-propanediol (PDO), and poly(tetramethylene glycol) (PTMG) of varying molecular weights (650–3000 g/mol). The resulting materials were comprehensively characterized in terms of chemical structure, molecular weight, thermal behavior, phase morphology, crystalline architecture, and mechanical performance using a range of analytical techniques: Fourier-transform infrared spectroscopy (FTIR), ¹H-NMR, gel permeation chromatography (GPC), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), wide-angle X-ray scattering (WAXS), small-angle X-ray scattering (SAXS), dynamic mechanical thermal analysis (DMA), tensile testing, and other standard physical methods. FTIR, ¹H-NMR, and GPC data confirmed the successful incorporation of both PTT-hard and PTMG-soft segments into the copolymer backbone. As the PTMG molecular weight increased, the average sequence length of the PTT-hard segments (L_n,T) also increased, leading to higher melting (T_m) and crystallization (T_c) temperatures, albeit with a slight reduction in overall crystallinity. DMA results indicated enhanced microphase separation between hard and soft domains with increasing PTMG molecular weight. WAXS and SAXS analyses further revealed that the crystalline structure and long-range ordering were strongly dependent on the copolymer composition and block architecture. Mechanical testing showed that tensile strength at break remained relatively constant across the series, while Young’s modulus increased significantly with higher PTMG molecular weight—concurrently accompanied by a decrease in elongation at break. Furthermore, the elastic deformability and recovery behavior of PTT-b-PTMG block copolymers were evaluated through cyclic tensile testing. TGA confirmed that all copolyesters exhibited excellent thermal stability. This study demonstrates that the physical and mechanical properties of bio-based PTT-b-PTMG elastomers can be effectively tailored by adjusting the molecular weight of the PTMG-soft segment, offering valuable insights for the rational design of sustainable thermoplastic elastomers with tunable performance. Full article

Let X be a partitioned matrix and let B its equitable quotient matrix. Consider a simple, undirected, connected graph G of order n. In this paper, we employ a technique based on quotient matrices derived from block-partitioned structures to establish new spectral results for the reciprocal distance signless Laplacian matrix. In particular, we identify a sequence of graphs whose eigenvalues are all integers. Furthermore, we introduce the concept of Harary incidence energy and extend known incidence energy results to the setting of the reciprocal distance signless Laplacian matrix. Finally, we characterize the Harary incidence energy of extremal graphs by examining vertex connectivity through the generalized graph join operation. Full article

Recent analyses have revealed that orangutan alpha satellite higher-order repeat (HOR) arrays in complete centromeres are composed of three to four distinct HOR blocks, each sharing only 80–90% sequence identity, thus forming a patchwork-quilt pattern of independent HOR expansions. In contrast, using our novel HOR-detection algorithm GRhor, we analyzed the complete Y chromosome centromere in orangutan and identified a highly ordered and complex alpha satellite 58mer superHOR array, comprising 67 HOR copies, including 46 highly identical canonical copies with a remarkably low divergence of only 0.25%. Given that the largest known human alpha satellite HOR is the 34mer on the Y chromosome, this novel 58mer structure qualifies as a superHOR. The canonical 58mer HOR contains only 44 distinct monomer types, with 14 types repeated within the unit, resulting in a unique five-row cascading organization. Such complexity is not detectable using standard HOR-searching tools employed in previous studies. Additionally, we identified a second, less pronounced 45mer cascading superHOR array with 0.81% divergence. For comparative purposes, we also detected a cascading 18mer HOR in gorilla and a Willard-type 28mer HOR in chimpanzee Y centromeres. Notably, preliminary genome-wide analysis in orangutan reveals other superHORs, including 84mer and 53mer arrays in chromosome 5; a 54mer in chromosome 10; a 51mer in chromosome 14; a 53mer in chromosome 15; and a 45mer in chromosome 22. These findings underscore the power of GRMhor in revealing highly structured and species-specific HOR architectures, with potential implications for centromere evolution and primate comparative genomics. Full article

Weighted belief propagation (WBP) for the decoding of linear block codes is considered. In WBP, the Tanner graph of the code is unrolled with respect to the iterations of the belief propagation decoder. Then, weights are assigned to the edges of the resulting recurrent network and optimized offline using a training dataset. The main contribution of this paper is an adaptive WBP where the weights of the decoder are determined for each received word. Two variants of this decoder are investigated. In the parallel WBP decoders, the weights take values in a discrete set. A number of WBP decoders are run in parallel to search for the best sequence- of weights in real time. In the two-stage decoder, a small neural network is used to dynamically determine the weights of the WBP decoder for each received word. The proposed adaptive decoders demonstrate significant improvements over the static counterparts in two applications. In the first application, Bose–Chaudhuri–Hocquenghem, polar and quasi-cyclic low-density parity-check (QC-LDPC) codes are used over an additive white Gaussian noise channel. The results indicate that the adaptive WBP achieves bit error rates (BERs) up to an order of magnitude less than the BERs of the static WBP at about the same decoding complexity, depending on the code, its rate, and the signal-to-noise ratio. The second application is a concatenated code designed for a long-haul nonlinear optical fiber channel where the inner code is a QC-LDPC code and the outer code is a spatially coupled LDPC code. In this case, the inner code is decoded using an adaptive WBP, while the outer code is decoded using the sliding window decoder and static belief propagation. The results show that the adaptive WBP provides a coding gain of 0.8 dB compared to the neural normalized min-sum decoder, with about the same computational complexity and decoding latency. Full article

There are workloads that do not need the total data ordering enforced by the Transmission Control Protocol (TCP). For example, Virtual Network Computing (VNC) has a sequence of pixel-based updates in which the order of rectangles can be relaxed. However, VNC runs over the TCP and can have higher latency due to unnecessary blocking to ensure total ordering. By using Quick UDP Internet Connections (QUIC) as the underlying protocol, we are able to implement a partial order delivery approach, which can be combined with Forward Error Correction (FEC) to reduce data latency. Our earlier work on consistency fences provides a mechanism and semantic foundation for partial ordering. Our new evaluation on the Emulab testbed, with two different synthetic workloads for streaming and non-streaming updates, shows that our partial order and FEC strategy can reduce the blocking time and inter-delivery time of rectangles compared to total delivery. For one workload, partially ordered data with FEC can reduce the 99-percentile message-blocking time to 0.4 ms versus 230 ms with totally ordered data. That workload was with 0.5% packet loss, 100 ms Round-Trip Time (RTT), and 100 Mbps bandwidth. We study the impact of varying the packet-loss rate, RTT, bandwidth, and CCA and demonstrate that partial order and FEC latency improvements grow as we increase packet loss and RTT, especially with the emerging Bottleneck Bandwidth and Round-Trip propagation time (BBR) congestion control algorithm. Full article

As the most basic mechanical components, bearing troubleshooting is essential to ensure the safe and reliable operation of rotating machinery. Bearing fault diagnosis is challenging due to the scarcity of bearing fault diagnosis samples and the susceptibility of fault signals to external noise. To address these issues, a ResNet-CACNN-BiGRU-SDPA bearing fault diagnosis method based on time–frequency bi-domain and feature fusion is proposed. First, the model takes the augmented time-domain signals as inputs and reconstructs them into frequency-domain signals using FFT, which gives the signals a bi-directional time–frequency domain receptive field. Second, the long sequence time-domain signal is processed by a ResNet residual block structure, and a CACNN method is proposed to realize local feature extraction of the frequency-domain signal. Then, the extracted time–frequency domain long sequence features are fed into a two-layer BiGRU for bidirectional deep global feature mining. Finally, the long-range feature dependencies are dynamically captured by SDPA, while the global dual-domain features are spliced and passed into Softmax to obtain the model output. In order to verify the model performance, experiments were carried out on the CWRU and JNU bearing datasets, and the results showed that the method had high accuracy under both small sample size and noise perturbation conditions, which verified the model’s good fault-feature-learning capability and noise immunity performance. Full article

Satellite DNAs (satDNAs) play a crucial role in understanding chromosomal evolution and the differentiation of sex chromosomes across diverse taxa, particularly when high karyotypic diversity occurs. The Physalaemus cuvieri–Physalaemus ephippifer species complex comprises at least seven divergent lineages, each exhibiting specific karyotypic signatures. The group composed of Ph. ephippifer, Lineage 1B of ‘Ph. cuvieri’ (L1B), and a lineage resulting from their secondary contact is especially intriguing due to varying degrees of sex chromosome heteromorphism. In this study, we characterized the satellitome of Ph. ephippifer in order to identify novel satDNAs that may provide insights into chromosomal evolution, particularly concerning sex chromosomes. We identified 62 satDNAs in Ph. ephippifer, collectively accounting for approximately 10% of the genome. Notably, nine satDNA families were shared with species from distantly related clades, raising questions about their potential roles in anurans genomes. Among the seven satDNAs mapped via fluorescent in situ hybridization, PepSat3 emerged as a strong candidate for the centromeric sequence in this group. Additionally, PepSat11 and PepSat24 provided evidence supporting a translocation involving both arms of the W chromosome in Ph. ephippifer. Furthermore, a syntenic block composed of PepSat3, PcP190, and PepSat11 suggested an inversion event during the divergence of Ph. ephippifer and L1B. The variation in signal patterns of satDNAs associated with nucleolar organizer regions (NORs) highlights the complexity of NOR evolution in this species complex, which exhibits substantial diversity in this genomic region. Additionally, our findings for PepSat30-350 emphasize the importance of validating the sex-biased abundance of satDNAs. Full article

A prototype device was developed as a simple yet effective tool for the rehabilitation of individuals with upper limb paresis resulting from stroke. The primary objective of the design process was to create a portable rehabilitation device that could be remotely controlled by a therapist via a Bluetooth protocol. The device enables the execution of upper limb rehabilitation exercises and integrates essential modules for assessment, reporting, and user feedback (biofeedback). It comprises a base and three movable arms, each fitted with a container at its distal end. The central arm, positioned at the midpoint of the device’s housing, holds a storage container from which specific objects are retrieved by the user. This arm features an adjustable reach. The remaining two arms are equipped with task-specific containers mounted at their ends. The conceptual framework is based on the execution of various tasks displayed on a screen. The user retrieves objects from the central storage unit and places them into either the left or right container, as indicated. The target container is highlighted both visually on the screen and via an illuminated LED indicator. Pre-programmed sequences for object retrieval and placement are presented on the display, offering clear guidance for the correct positioning and ordering of blocks within the designated containers. The device includes 12 dedicated blocks varying in shape, colour, material, and texture. A mechatronic control system governs the container positioning and arm inclination, enabling a precise adjustment of range of movement according to the exercise’s requirements. A dedicated software system has also been developed for control and management. Functional testing of the prototype was conducted to assess the device’s effectiveness and practical applicability in rehabilitation settings. Full article