A duplex real-time reverse transcriptase polymerase chain reaction assay for detecting western equine and eastern equine encephalitis viruses

In order to establish an accurate, ready-to-use assay for simultaneous detection of Eastern equine encephalitis virus (EEEV) and Western equine encephalitis virus (WEEV), we developed one duplex TaqMan real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay, which can be used in human and vector surveillance. First, we selected the primers and FAM-labeled TaqMan-probe specific for WEEV from the consensus sequence of NSP3 and the primers and HEX-labeled TaqMan-probe specific for EEEV from the consensus sequence of E3, respectively. Then we constructed and optimized the duplex real-time RT-PCR assay by adjusting the concentrations of primers and probes. Using a series of dilutions of transcripts containing target genes as template, we showed that the sensitivity of the assay reached 1 copy/reaction for EEEV and WEEV, and the performance was linear within the range of at least 10(6 )transcript copies. Moreover, we evaluated the specificity of the duplex system using other encephalitis virus RNA as template, and found no cross-reactivity. Compared with virus isolation, the gold standard, the duplex real time RT-PCR assay we developed was 10-fold more sensitive for both WEEV and EEEV detection

A dynamic programming approach for generalized nearly isotonic optimization

Shape restricted statistical estimation problems have been extensively studied, with many important practical applications in signal processing, bioinformatics, and machine learning. In this paper, we propose and study a generalized nearly isotonic optimization (GNIO) model, which recovers, as special cases, many classic problems in shape constrained statistical regression, such as isotonic regression, nearly isotonic regression and unimodal regression problems. We develop an efficient and easy-to-implement dynamic programming algorithm for solving the proposed model whose recursion nature is carefully uncovered and exploited. For special $\ell_2$-GNIO problems, implementation details and the optimal ${\cal O}(n)$ running time analysis of our algorithm are discussed. Numerical experiments, including the comparison between our approach and the powerful commercial solver Gurobi for solving $\ell_1$-GNIO and $\ell_2$-GNIO problems, on both simulated and real data sets are presented to demonstrate the high efficiency and robustness of our proposed algorithm in solving large scale GNIO problems

Nonconvex optimization for optimum retrieval of the transmission matrix of a multimode fiber

Transmission matrix (TM) allows light control through complex media such as multimode fibers (MMFs), gaining great attention in areas like biophotonics over the past decade. The measurement of a complex-valued TM is highly desired as it supports full modulation of the light field, yet demanding as the holographic setup is usually entailed. Efforts have been taken to retrieve a TM directly from intensity measurements with several representative phase retrieval algorithms, which still see limitations like slow or suboptimum recovery, especially under noisy environment. Here, a modified non-convex optimization approach is proposed. Through numerical evaluations, it shows that the nonconvex method offers an optimum efficiency of focusing with less running time or sampling rate. The comparative test under different signal-to-noise levels further indicates its improved robustness for TM retrieval. Experimentally, the optimum retrieval of the TM of a MMF is collectively validated by multiple groups of single-spot and multi-spot focusing demonstrations. Focus scanning on the working plane of the MMF is also conducted where our method achieves 93.6% efficiency of the gold standard holography method when the sampling rate is 8. Based on the recovered TM, image transmission through the MMF with high fidelity can be realized via another phase retrieval. Thanks to parallel operation and GPU acceleration, the nonconvex approach can retrieve an 8685$\times$1024 TM (sampling rate=8) with 42.3 s on a regular computer. In brief, the proposed method provides optimum efficiency and fast implementation for TM retrieval, which will facilitate wide applications in deep-tissue optical imaging, manipulation and treatment

Image Augmentation-Based Food Recognition with Convolutional Neural Networks

Image retrieval for food ingredients is important work, tremendously tiring, uninteresting, and expensive. Computer vision systems have extraordinary advancements in image retrieval with CNNs skills. But it is not feasible for small-size food datasets using convolutional neural networks directly. In this study, a novel image retrieval approach is presented for small and medium-scale food datasets, which both augments images utilizing image transformation techniques to enlarge the size of datasets, and promotes the average accuracy of food recognition with state-of-the-art deep learning technologies. First, typical image transformation techniques are used to augment food images. Then transfer learning technology based on deep learning is applied to extract image features. Finally, a food recognition algorithm is leveraged on extracted deep-feature vectors. The presented image-retrieval architecture is analyzed based on a small-scale food dataset which is composed of forty-one categories of food ingredients and one hundred pictures for each category. Extensive experimental results demonstrate the advantages of image-augmentation architecture for small and medium datasets using deep learning. The novel approach combines image augmentation, ResNet feature vectors, and SMO classification, and shows its superiority for food detection of small/medium-scale datasets with comprehensive experiments

Association between salivary microbiota and renal function in renal transplant patients during the perioperative period

IntroductionRenal transplantation is an effective treatment for the end stage renal disease (ESRD). However, how salivary microbiota changes during perioperative period of renal transplant recipients (RTRs) has not been elucidated.MethodsFive healthy controls and 11 RTRs who had good recovery were enrolled. Saliva samples were collected before surgery and at 1, 3, 7, and 14 days after surgery. 16S rRNA gene sequencing was performed.ResultsThere was no significant difference in the composition of salivary microbiota between ESRD patients and healthy controls. The salivary microbiota of RTRs showed higher operational taxonomic units (OTUs) amount and greater alpha and beta diversity than those of ESRD patients and healthy controls, but gradually stabilized over time. At the phylum level, the relative abundance of Actinobacteria, Tenericutes and Spirochaetes was about ten times different from ESRD patients or healthy controls for RTRs overall in time. The relative abundance of Bacteroidetes, Fusobacteria, Patescibacteria, Leptotrichiaceae and Streptococcaceae was correlated with serum creatinine (Scr) after renal transplantation.DiscussionIn short, salivary microbiota community altered in the perioperative period of renal transplantation and certain species of salivary microbiota had the potential to be a biomarker of postoperative recovery

Mitochondrial stress response and myogenic differentiation

Regeneration and repair are prerequisites for maintaining effective function of skeletal muscle under high energy demands, and myogenic differentiation is one of the key steps in the regeneration and repair process. A striking feature of the process of myogenic differentiation is the alteration of mitochondria in number and function. Mitochondrial dysfunction can activate a number of transcriptional, translational and post-translational programmes and pathways to maintain cellular homeostasis under different types and degrees of stress, either through its own signaling or through constant signaling interactions with the nucleus and cytoplasm, a process known as the mitochondrial stress responses (MSRs). It is now believed that mitochondrial dysfunction is closely associated with a variety of muscle diseases caused by reduced levels of myogenic differentiation, suggesting the possibility that MSRs are involved in messaging during myogenic differentiation. Also, MSRs may be involved in myogenesis by promoting bioenergetic remodeling and assisting myoblast survival during myogenic differentiation. In this review, we will take MSRs as an entry point to explore its concrete regulatory mechanisms during myogenic differentiation, with a perspective to provide a theoretical basis for the treatment and repair of related muscle diseases

A new 3-arylbenzofuran derivative EIE-2 reestablishes Treg-dependent tolerance in rheumatoid arthritis by targeting on Syk induced mTOR and PKCθ imbalance

IntroductionDysfunctional self-tolerance is thought to play a crucial role in the onset of rheumatoid arthritis (RA) pathogenesis. Poorly functioning regulatory T cells (Tregs) lead to extreme situations where self-tolerance is robustly disrupted. However, there are many uncertainties regarding its immunosuppressive pathways, especially concerning therapeutic drugs that are still in their infancy. Therefore, deciphering potential targets and developing novel drugs to ameliorate functional Tregs deficiency appears to be an efficient therapeutic approach for controlling RA.MethodsThe therapeutic effects of EIE-2, a novel 3-arylbenzofuran derivative, were evaluated in collagen-induced arthritis (CIA) rats and carrageenan-induced paw edema mice in vivo, as well as in LPS-, PMA- or TNF-α-stimulated human CD4+ T cells (Jurkat), human synovial sarcoma cells (SW982) and primary isolated lymphocytes in vitro. The role of Syk in Treg-dependent tolerance and the mechanism of EIE-2 were explored using western blotting, quantitative reverse transcription PCR (qRT-PCR) and flow cytometry. Potential mechanistic targets were further validated through siRNA knockdown and molecular docking analysis.ResultsEIE-2 significantly ameliorated arthritic symptoms and pathological damage in CIA rats by reducing pro-inflammatory cytokines and increasing anti-inflammatory factors in synovium and serum, and exhibited similar therapeutic effects in carrageenan-induced pedal edema mice. Moreover, EIE-2 potently suppressed the inflammatory responses in human synoviocyte SW982 cells, primary isolated lymphocytes and CD4+ Jurkat cells. Its therapeutic potential was associated with upregulation of Tregs during the active phase and downregulation during the inactive phase of RA. Mechanistically, EIE-2 modulated the PKCθ/mTOR ratio via Syk targeting, thereby restoring homeostasis in Tregs.DiscussionEIE-2 is a potential therapeutic candidate for RA. The underlying mechanism may involve its targeting on Syk to upregulate the PKCθ/mTOR ratio during the active phase of RA and downregulate the PKCθ/mTOR ratio during the inactive phase of RA, ultimately promoting Treg-dependent tolerance restoration

Prognostic risk factors analysis of low-grade gastric intraepithelial neoplasia—a single-center follow-up study

ObjectiveLow-grade gastric intraepithelial neoplasia (LGIN), as a precancerous lesion of gastric cancer, is of great significance in the prevention and treatment of gastric cancer. In this study, we investigated the risk factors associated with LGIN through the follow-up of LGIN patients, and provided a reliable basis for the clinical management of LGIN patients and the formulation of individualized clinical diagnosis and treatment strategies.MethodsA total of 283 patients, newly diagnosed with LGIN, were enrolled in the study. The regression of LGIN among these patients was assessed by comparing their gastroscopic and pathological findings before and after a rigorous follow-up period. The cohort was then stratified into a progressive group and a non-progressive group. Univariate analysis and multivariate logistic regression analysis were employed to investigate the potential risk factors contributing to the progression of LGIN in these patients.ResultsAmong 283 LGIN patients, 8.1% demonstrated lesion progression. Notably, five cases progressed to adenocarcinoma, resulting in an overall cancer incidence rate of 1.8%. Various factors, including age, gender, family history of gastrointestinal tumors, history of alcohol consumption, preference for pickled foods, preference for strong tea, H. pylori infection, lesion location, and endoscopic lesion manifestation, were found to be correlated with the progression of LGIN (p < 0.05). Multifactorial logistic regression analysis further elucidated that a history of alcohol consumption (p = 0.022, OR = 3.224, 95% CI: 1.183–8.782), a family history of gastrointestinal tumors (p = 0.029, OR = 3.526, 95% CI: 1.136–10.947), combined with H. pylori infection (p = 0.024, OR = 4.220, 95% CI: 1.205–14.783), lesion location in the cardia/gastric fundus (p = 0.004, OR = 6.838, 95% CI: 1.874–24.958), and endoscopic manifestation of an ulcerated indurated type (p = 0.023, OR = 5.073, 95% CI: 1.245–20.667) emerged as significant risk factors for lesion progression in LGIN patients.ConclusionLGIN patients with a history of alcohol consumption, a family history of gastrointestinal tumors, a combination of H. pylori infection, and lesions located in the cardia/gastric fundus versus lesions endoscopically presenting as ulcerated depressions are more likely to progress to cancer. These risk factors provide a reliable basis for the clinical management of LGIN patients and the development of individualized clinical treatment strategies