Reference-agnostic representation and visualization of pan-genomes

BackgroundThe pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.ResultsHere we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations.ConclusionsThe PGV software can be installed via conda or downloaded from https://github.com/ucrbioinfo/PGV . The companion PGV browser at http://pgv.cs.ucr.edu can be tested using example bed tracks available from the GitHub page

Explicit Visual Prompts for Visual Object Tracking

How to effectively exploit spatio-temporal information is crucial to capture target appearance changes in visual tracking. However, most deep learning-based trackers mainly focus on designing a complicated appearance model or template updating strategy, while lacking the exploitation of context between consecutive frames and thus entailing the \textit{when-and-how-to-update} dilemma. To address these issues, we propose a novel explicit visual prompts framework for visual tracking, dubbed \textbf{EVPTrack}. Specifically, we utilize spatio-temporal tokens to propagate information between consecutive frames without focusing on updating templates. As a result, we cannot only alleviate the challenge of \textit{when-to-update}, but also avoid the hyper-parameters associated with updating strategies. Then, we utilize the spatio-temporal tokens to generate explicit visual prompts that facilitate inference in the current frame. The prompts are fed into a transformer encoder together with the image tokens without additional processing. Consequently, the efficiency of our model is improved by avoiding \textit{how-to-update}. In addition, we consider multi-scale information as explicit visual prompts, providing multiscale template features to enhance the EVPTrack's ability to handle target scale changes. Extensive experimental results on six benchmarks (i.e., LaSOT, LaSOT\rm $_{ext}$, GOT-10k, UAV123, TrackingNet, and TNL2K.) validate that our EVPTrack can achieve competitive performance at a real-time speed by effectively exploiting both spatio-temporal and multi-scale information. Code and models are available at https://github.com/GXNU-ZhongLab/EVPTrack

Empirical noise performance of prototype active pixel arrays employing polycrystalline silicon thin- film transistors

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/162751/2/mp14321.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162751/1/mp14321_am.pd

Secure Mobile Agent from Leakage-Resilient Proxy Signatures

A mobile agent can sign a message in a remote server on behalf of a customer without exposing its secret key; it can be used not only to search for special products or services, but also to make a contract with a remote server. Hence a mobile agent system can be used for electronic commerce as an important key technology. In order to realize such a system, Lee et al. showed that a secure mobile agent can be constructed using proxy signatures. Intuitively, a proxy signature permits an entity (delegator) to delegate its signing right to another entity (proxy) to sign some specified messages on behalf of the delegator. However, the proxy signatures are often used in scenarios where the signing is done in an insecure environment, for example, the remote server of a mobile agent system. In such setting, an adversary could launch side-channel attacks to exploit some leakage information about the proxy key or even other secret states. The proxy signatures which are secure in the traditional security models obviously cannot provide such security. Based on this consideration, in this paper, we design a leakage-resilient proxy signature scheme for the secure mobile agent systems

Endophyte-mediated enhancement of salt resistance in Arachis hypogaea L. by regulation of osmotic stress and plant defense-related genes

IntroductionSoil salinization poses a significant environmental challenge affecting plant growth and agricultural sustainability. This study explores the potential of salt-tolerant endophytes to mitigate the adverse effects of soil salinization, emphasizing their impact on the development and resistance of Arachis hypogaea L. (peanuts).MethodsThe diversity of culturable plant endophytic bacteria associated with Miscanthus lutarioriparius was investigated. The study focused on the effects of Bacillus tequilensis, Staphylococcus epidermidis, and Bacillus siamensis on the development and germination of A. hypogaea seeds in pots subjected to high NaCl concentrations (200 mM L−1).ResultsUnder elevated NaCl concentrations, the inoculation of endophytes significantly (p < 0.05) enhanced seedling germination and increased the activities of enzymes such as Superoxide dismutase, catalase, and polyphenol oxidase, while reducing malondialdehyde and peroxidase levels. Additionally, endophyte inoculation resulted in increased root surface area, plant height, biomass contents, and leaf surface area of peanuts under NaCl stress. Transcriptome data revealed an augmented defense and resistance response induced by the applied endophyte (B. tequilensis, S. epidermidis, and B. siamensis) strain, including upregulation of abiotic stress related mechanisms such as fat metabolism, hormones, and glycosyl inositol phosphorylceramide (Na+ receptor). Na+ receptor under salt stress gate Ca2+ influx channels in plants. Notably, the synthesis of secondary metabolites, especially genes related to terpene and phenylpropanoid pathways, was highly regulated.ConclusionThe inoculated endophytes played a possible role in enhancing salt tolerance in peanuts. Future investigations should explore protein–protein interactions between plants and endophytes to unravel the mechanisms underlying endophyte-mediated salt resistance in plants

Biological functions of endophytic bacteria in Robinia pseudoacacia ‘Hongsen’

IntroductionEndophytes and their host plants have co-evolved for a very long time. This relationship has led to the general recognition of endophytes as a particular class of microbial resources. R. pseudoacacia ‘Hongsen’ is drought- and barren-resistant species that can be grown in both the north and south of China, efficiently addresses the ecological issues caused by China’s ‘southern eucalyptus and northern poplar. Up to date, cultured-dependent studies are available for the R. pseudoacacia nitrogen-fixing and other endophytes. Therefore, the present research studied the R. pseudoacacia ‘Hongsen,’ microbiome in detail by high-throughput sequencing and culture dependant.MethodsThis study examined microbial species and functional diversity in Robinia pseudoacacia ‘Hongsen’ using culture-dependent (isolation) and culture-independent techniques.ResultsA total of 210 isolates were isolated from R. pseudoacacia ‘Hongsen.’ These isolates were clustered into 16 groups by the In Situ PCR (IS-PCR) fingerprinting patterns. 16S rRNA gene sequence analysis of the representative strain of each group revealed that these groups belonged to 16 species of 8 genera, demonstrating the diversity of endophytes in R. pseudoacacia ‘Hongsen’. ’Bacillus is the most prevalent genus among all the endophytic bacteria. High-throughput sequencing of endophytic bacteria from R. pseudoacacia ‘Hongsen’ of the plant and the rhizosphere soil bacteria showed that the bacterial populations of soil near the root, leaf, and rhizosphere differed significantly. The microbial abundance decreased in the endophytes as compared to the rhizosphere. We observed a similar community structure of roots and leaves. With and without root nodules, Mesorhizobium sp. was significantly different in R. pseudoacacia ‘Hongsen’ plant.DiscussionIt was predicted that R. pseudoacacia ‘Hongsen’ plant endophytic bacteria would play a significant role in the metabolic process, such as carbohydrate metabolism, amino acid metabolism, membrane transport, and energy metabolism

Rare Copy Number Variants Identify Novel Genes in Sporadic Total Anomalous Pulmonary Vein Connection

Total anomalous pulmonary venous connection (TAPVC) is a rare congenital heart anomaly. Several genes have been associated TAPVC but the mechanisms remain elusive. To search novel CNVs and candidate genes, we screened a cohort of 78 TAPVC cases and 100 healthy controls for rare copy number variants (CNVs) using whole exome sequencing (WES). Then we identified pathogenic CNVs by statistical comparisons between case and control groups. After that, we identified altogether eight pathogenic CNVs of seven candidate genes (PCSK7, RRP7A, SERHL, TARP, TTN, SERHL2, and NBPF3). All these seven genes have not been described previously to be related to TAPVC. After network analysis of these candidate genes and 27 known pathogenic genes derived from the literature and publicly database, PCSK7 and TTN were the most important genes for TAPVC than other genes. Our study provides novel candidate genes potentially related to this rare congenital birth defect (CHD) which should be further fundamentally researched and discloses the possible molecular pathogenesis of TAPVC

The genome of cowpea (Vigna unguiculata [L.] Walp.)

[EN] Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presentedS

The lncRNA MALAT1 rs619586 G Variant Confers Decreased Susceptibility to Recurrent Miscarriage

Cardiovascula disease and recurrent miscarriage have shared risk factors, and some cardiovascular disease-related candidate genes have been confirmed to be associated with recurrent miscarriage. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA (lncRNA) that is considered to be associated with susceptibility to cardiovascular disease. However, whether lncRNA MALAT1 polymorphisms are related to recurrent miscarriage susceptibility is unclear. We genotyped three lncRNA MALAT1 polymorphisms (rs591291, rs619586, and rs3200401) in 284 patients and 392 controls using TaqMan methods. Logistic regression was used to evaluate the odds ratios (ORs) and 95% confidence intervals (CIs) adjusted for age. Our results showed that the rs619586 G variant had protective effects against recurrent miscarriage (AG vs. AA: adjusted OR = 0.670, 95% CI = 0.457–0.982, p = 0.040; GG vs. AA: adjusted OR = 0.278, 95% CI = 0.079–0.975, p = 0.046; GG/AG vs. AA adjusted OR = 0.621, 95% CI = 0.429–0.900, p = 0.012). In a combined analyses of protective genotypes, with regard to the three single nucleotide polymorphisms (SNPs), we found that individuals with two or three protective genotypes exhibited a significantly lower risk of recurrent miscarriage than those with no or only one protective genotype (adjusted OR = 0.369, 95% CI = 0.199–0.684, p = 0.002). Moreover, the decrease in recurrent miscarriage risk with two or three protective genotypes was most pronounced in women less than 35 years of age (OR = 0.290, 95% CI = 0.142–0.589, p < 0.001) and in women with 2–3 miscarriages (adjusted OR = 0.270, 95% CI = 0.126–0.580, p < 0.001). In conclusion, our study suggests that the rs619586 G variant may have potential protective effects conferring a decreased risk of recurrent miscarriage in the southern Chinese population