Design and direct assembly of synthesized uracil-containing non-clonal DNA fragments into vectors by USER^TM cloning

This protocol describes how to order and directly assemble uracil-containing non-clonal DNA fragments by uracil excision based cloning (USER cloning). The protocol was generated with the goal of making synthesized non-clonal DNA fragments directly compatible with USER(TM) cloning. The protocol is highly efficient and would be compatible with uracil-containing non-clonal DNA fragments obtained from any synthesizing company. The protocol drastically reduces time and handling between receiving the synthesized DNA fragments and transforming with vector and DNA fragment(s)

Effects of Antiretroviral Therapy and Depressive Symptoms on All-Cause Mortality Among HIV-Infected Women

Abstract Depression affects up to 30% of human immunodeficiency virus (HIV)-infected individuals. We estimated joint effects of antiretroviral therapy (ART) initiation and depressive symptoms on time to death using a joint marginal structural model and data from a cohort of HIV-infected women from the Women's Interagency HIV Study (conducted in the United States) from 1998–2011. Among 848 women contributing 6,721 years of follow-up, 194 participants died during follow-up, resulting in a crude mortality rate of 2.9 per 100 women-years. Cumulative mortality curves indicated greatest mortality for women who reported depressive symptoms and had not initiated ART. The hazard ratio for depressive symptoms was 3.38 (95% confidence interval (CI): 2.15, 5.33) and for ART was 0.47 (95% CI: 0.31, 0.70). Using a reference category of women without depressive symptoms who had initiated ART, the hazard ratio for women with depressive symptoms who had initiated ART was 3.60 (95% CI: 2.02, 6.43). For women without depressive symptoms who had not started ART, the hazard ratio was 2.36 (95% CI: 1.16, 4.81). Among women reporting depressive symptoms who had not started ART, the hazard ratio was 7.47 (95% CI: 3.91, 14.3). We found a protective effect of ART initiation on mortality, as well as a harmful effect of depressive symptoms, in a cohort of HIV-infected women

The water lily genome and the early evolution of flowering plants

Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1–3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.Supplementary Tables: This file contains Supplementary Tables 1-21.National Natural Science Foundation of China, the open funds of the State Key Laboratory of Crop Genetics and Germplasm Enhancement (ZW201909) and State Key Laboratory of Tree Genetics and Breeding, the Fujian provincial government in China, the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement and the Special Research Fund of Ghent University.http://www.nature.com/naturecommunicationsam2021BiochemistryGeneticsMicrobiology and Plant Patholog

Joint Kinematics and Sealing Capacity Assessment of Ductile Iron Pipes under Abrupt Transverse Ground Movements

Joint kinematic behaviour, i.e., joint rotation and axial translation, can partially help pipelines to accommodate abrupt ground movements, and cause leaking if joint service limit is exceeded, even without any structural failure. Kinematic behaviour of bell-spigot jointed ductile iron (DI) pipes and its influence on joint sealing capacity under abrupt transverse ground movements are investigated in this study. Firstly, a beam-on-spring finite element analysis on joint kinematics of DI pipes is conducted, in which different fault-pipe crossing positions are implemented. Based on simulated results, a modified joint kinematic solution incorporating pipe deflection and joint shear force under different fault-pipe crossing positions is proposed. Then, a Monte Carlo simulation (MCS)-based reliability assessment procedure for joint sealing capacity is developed. Sensitivity analysis is subsequently conducted to investigate the effects of uncertainties associated with initial axial translation, soil properties, and crossing positions on the joint sealing capacity, and the effects of different deterministic solutions are compared. The proposed method allows engineers to effectively evaluate how the joint sealing capacity of DI pipes changes with consideration of uncertainties when abrupt transverse ground movements are encountered.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Context Information Refinement for Few-Shot Object Detection in Remote Sensing Images

Recently, few-shot object detection based on fine-tuning has attracted much attention in the field of computer vision. However, due to the scarcity of samples in novel categories, obtaining positive anchors for novel categories is difficult, which implicitly introduces the foreground–background imbalance problem. It is difficult to identify foreground objects from complex backgrounds due to various object sizes and cluttered backgrounds. In this article, we propose a novel context information refinement few-shot detector (CIR-FSD) for remote sensing images. In particular, we design a context information refinement (CIR) module to extract discriminant context features. This module uses dilated convolutions and dense connections to capture rich context information from different receptive fields and then uses a binary map as the supervision label to refine the context information. In addition, we improve the region proposal network (RPN). Concretely, the RPN is fine-tuned on novel categories, and the constraint of non-maximum suppression (NMS) is relaxed, which can obtain more positive anchors for novel categories. Experiments on two remote sensing public datasets show the effectiveness of our detector

Calculation of effective explosive volume of premixed methane-air gas under unconstraint conditions

The leakage volume of natural gas is an important factor affecting the consequences of pipeline leakage and explosion. Restricted by the ratio of methane and air concentration, not all of the leakage gas will explode. Therefore, a calculation model for the explosive peak overpressure of premixed methane-air gas was established under unconstraint conditions. The relationship between the volume of premixed methane-air gas and the peak overpressure was simulated and analyzed with the Fluent software, and the calculation model was verified. Moreover, the law between the effective explosive volume of methane and the peak overpressure was obtained, and a method for calculating the effective volume was proposed. The results show that the propagation time of the explosion peak overpressure obtained by the numerical simulation model is consistent with the experimental results, and the attenuation law of the explosion peak overpressure is consistent with that as indicated by the existing research. Additionally, the effective volume of methane involved in the explosion is about 0.11 to 0.12 times the actual volume of the premixed gas, and the precision is high in the case the actual premixed gas volume is large. Hence, the results can provide a theoretical basis for the simulation and prediction of natural gas explosion, the consequence evaluation and the configuration of protection resources

Context Information Refinement for Few-Shot Object Detection in Remote Sensing Images

Recently, few-shot object detection based on fine-tuning has attracted much attention in the field of computer vision. However, due to the scarcity of samples in novel categories, obtaining positive anchors for novel categories is difficult, which implicitly introduces the foreground–background imbalance problem. It is difficult to identify foreground objects from complex backgrounds due to various object sizes and cluttered backgrounds. In this article, we propose a novel context information refinement few-shot detector (CIR-FSD) for remote sensing images. In particular, we design a context information refinement (CIR) module to extract discriminant context features. This module uses dilated convolutions and dense connections to capture rich context information from different receptive fields and then uses a binary map as the supervision label to refine the context information. In addition, we improve the region proposal network (RPN). Concretely, the RPN is fine-tuned on novel categories, and the constraint of non-maximum suppression (NMS) is relaxed, which can obtain more positive anchors for novel categories. Experiments on two remote sensing public datasets show the effectiveness of our detector