Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response

The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (D500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-beta levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-beta responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.Peer reviewe

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Development of main functional modules for MVB and its application in rail transit

In this work, multi-function vehicle bus (MVB) controller-based Field Programmable Gate Array (FPGA) and MVB manager based on the real-time multitasking operating system were explored and developed. The function of the MVB controller data link layer was realised by using FPGA. The embedded real-time multitasking operating system uCOS-II was applied to the development of MVB manager’s processing data, device state management, message data and bus management function. The network consistency test was performed to validate data communication of MVB link layer control protocol and the management function of MVB manager; the equipment was shown to be compatible with each other and met the requirements of IEC61375-1

Degradation kinetics of calcium polyphosphate bioceramic: an experimental and theoretical study

In this work, the degradation kinetics of calcium polyphosphate bioceramic was studied. Liquid state31P nuclear magnetic resonance (NMR), X-ray diffraction (XRD) and scanning electron microscope (SEM) were used to characterize the product. The in vitro degradation test was carried out at 37 ºC for up to 48 hours for both the simulation solution and the extreme solution. The ion concentrations were measured and analyzed by establishing a mathematical model referring to the chemical reaction kinetics. The results indicated that the degradability of calcium polyphosphate increased with the decrease of pH value, and the sample showed a rapid loss of ion concentration within the initial period of immersion followed by a slower loss ratio. The relationship between ion concentration and the degradation time coincided with Boxlucas model

Obtaining Urban Waterlogging Depths from Video Images Using Synthetic Image Data

Reference objects in video images can be used to indicate urban waterlogging depths. The detection of reference objects is the key step to obtain waterlogging depths from video images. Object detection models with convolutional neural networks (CNNs) have been utilized to detect reference objects. These models require a large number of labeled images as the training data to ensure the applicability at a city scale. However, it is hard to collect a sufficient number of urban flooding images containing valuable reference objects, and manually labeling images is time-consuming and expensive. To solve the problem, we present a method to synthesize image data as the training data. Firstly, original images containing reference objects and original images with water surfaces are collected from open data sources, and reference objects and water surfaces are cropped from these original images. Secondly, the reference objects and water surfaces are further enriched via data augmentation techniques to ensure the diversity. Finally, the enriched reference objects and water surfaces are combined to generate a synthetic image dataset with annotations. The synthetic image dataset is further used for training an object detection model with CNN. The waterlogging depths are calculated based on the reference objects detected by the trained model. A real video dataset and an artificial image dataset are used to evaluate the effectiveness of the proposed method. The results show that the detection model trained using the synthetic image dataset can effectively detect reference objects from images, and it can achieve acceptable accuracies of waterlogging depths based on the detected reference objects. The proposed method has the potential to monitor waterlogging depths at a city scale

Research trends on airway remodeling: A bibliometrics analysis

Background: Airway remodeling is an essential pathological basis of respiratory diseases such as asthma and COPD, which is significantly related to pulmonary function and clinical symptoms. And pulmonary disease can be improved by regulating airway remodeling. This study aimed to establish a knowledge map of airway remodeling to clarify current research hotspots and future research trends. Methods: A comprehensive search was performed to analyze all relevant articles on airway remodeling using the Web of Science Core Collection Database from January 01, 2004 to June 03, 2023.2 reviewers screened the retrieved literature. Besides, the CiteSpace (6.2. R3) and VOSviewer (1.6.19) were utilized to visualize the research focus and trend regarding the effect of airway remodeling. Results: A total of 4077 articles about airway remodeling were retrieved. The United States is the country with the most published literature, underscoring the country's role in airway remodeling. In recent years, China has been the country with the fastest growth in the number of published literature, suggesting that China will play a more critical role in airway remodeling in the future. From the perspective of co-operation among countries, European co-operation was closer than Asian co-operation. The co-citation analysis showed that 98,313 citations were recorded in 3594 articles, and 25 clusters could be realized. In recent years, Burst detection shows that oxidative stress and epithelial-mesenchymal transition are hot words. Conclusions: Based on the bibliometric analysis of airway remodeling studies in the past 20 years, a multi-level knowledge structure map was drawn, it mainly includes countries, institutions, research fields, authors, journals, keywords and so on. The research directions represented by obstructive airway disease, PDGF-BB treatment of airway smooth muscle, allergen-induced airway remodeling, extracellular matrix, and non-coding RNA are the research hotspots in the field of airway remodeling. While the risk factors for airway remodeling, the application of new noninvasively assessing tools, biomarkers as well as The molecular mechanism represented by EMT and autophagy had been frontiers in recent years