Chromosome-level genome assembly of the yellow boxfish (Ostracion cubicus) provides insights into the evolution of bone plates and ostracitoxin secretion

The Ostracion cubicus, commonly known as the yellow boxfish, is a remarkable species with a body encased in a bone plate and the ability to produce an ostracitoxin from their skin when under stress. However, the genetic basis of those effective defense traits is still largely unknown due to the lack of genomic resources. Here, we assembled the first chromosome-level genome of O. cubicus with 867.50 Mb in genome size and 34.86 Mb N50 scaffold length by HiFi and Hi-C sequencing. Twenty-five pseudo-chromosomes, numbered according to size, covered 94.13% of the total assembled sequences. A total of 23,224 protein-coding genes were predicted, with a BUSCO completeness of 98.6%. Positive selection or rapid evolution was observed in genes related to scale and bone development (acsl4a, casr, keap1a, tbx1), and up-regulation of transcription was found in the skin of boxfish (bmp1, bmp2k, bmp4, bmp7, smad5, suco, prelp, mitf), likely associated with the bone plates evolution in the yellow boxfish. An expansion of the solute carrier family 22, a cluster of genes in solute carrier (SLCs) family, transmembrane protein family (TMEMs), vesicle trafficking (SECs), ATP-binding cassette (ABCs) and apolipoproteins (APOs) were identified under positive selection, rapid evolution, or up-regulated in the skin of boxfish, likely associated with the ostracitoxin secretion in the yellow boxfish. Our study not only presents a high-quality boxfish genome but also provides insights into bone plates evolution and ostracitoxin secretion of O. cubicus

Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening

Plant virus technology, in particular virus-induced gene silencing, is a widely used reverse- and forward-genetics tool in plant functional genomics. However the potential of virus technology to express genes to induce phenotypes or to complement mutants in order to understand the function of plant genes is not well documented. Here we exploit Potato virus X as a tool for virus-induced gene complementation (VIGC). Using VIGC in tomato, we demonstrated that ectopic viral expression of LeMADS-RIN, which encodes a MADS-box transcription factor (TF), resulted in functional complementation of the non-ripening rin mutant phenotype and caused fruits to ripen. Comparative gene expression analysis indicated that LeMADS-RIN up-regulated expression of the SBP-box (SQUAMOSA promoter binding protein-like) gene LeSPL-CNR, but down-regulated the expression of LeHB-1, an HD-Zip homeobox TF gene. Our data support the hypothesis that a transcriptional network may exist among key TFs in the modulation of fruit ripening in tomato

A Simple Single-Scale Vision Transformer for Object Localization and Instance Segmentation

This work presents a simple vision transformer design as a strong baseline for object localization and instance segmentation tasks. Transformers recently demonstrate competitive performance in image classification tasks. To adopt ViT to object detection and dense prediction tasks, many works inherit the multistage design from convolutional networks and highly customized ViT architectures. Behind this design, the goal is to pursue a better trade-off between computational cost and effective aggregation of multiscale global contexts. However, existing works adopt the multistage architectural design as a black-box solution without a clear understanding of its true benefits. In this paper, we comprehensively study three architecture design choices on ViT -- spatial reduction, doubled channels, and multiscale features -- and demonstrate that a vanilla ViT architecture can fulfill this goal without handcrafting multiscale features, maintaining the original ViT design philosophy. We further complete a scaling rule to optimize our model's trade-off on accuracy and computation cost / model size. By leveraging a constant feature resolution and hidden size throughout the encoder blocks, we propose a simple and compact ViT architecture called Universal Vision Transformer (UViT) that achieves strong performance on COCO object detection and instance segmentation tasks.Comment: ECCV 2022 accepte

Substantial transition to clean household energy mix in rural China

The household energy mix has significant impacts on human health and climate, as it contributes greatly to many health- and climate-relevant air pollutants. Compared to the well-established urban energy statistical system, the rural household energy statistical system is incomplete and is often associated with high biases. Via a nationwide investigation, this study revealed high contributions to energy supply from coal and biomass fuels in the rural household energy sector, while electricity comprised ∼20%. Stacking (the use of multiple sources of energy) is significant, and the average number of energy types was 2.8 per household. Compared to 2012, the consumption of biomass and coals in 2017 decreased by 45% and 12%, respectively, while the gas consumption amount increased by 204%. Increased gas and decreased coal consumptions were mainly in cooking, while decreased biomass was in both cooking (41%) and heating (59%). The time-sharing fraction of electricity and gases (E&G) for daily cooking grew, reaching 69% in 2017, but for space heating, traditional solid fuels were still dominant, with the national average shared fraction of E&G being only 20%. The non-uniform spatial distribution and the non-linear increase in the fraction of E&G indicated challenges to achieving universal access to modern cooking energy by 2030, particularly in less-developed rural and mountainous areas. In some non-typical heating zones, the increased share of E&G for heating was significant and largely driven by income growth, but in typical heating zones, the time-sharing fraction was <5% and was not significantly increased, except in areas with policy intervention. The intervention policy not only led to dramatic increases in the clean energy fraction for heating but also accelerated the clean cooking transition. Higher income, higher education, younger age, less energy/stove stacking and smaller family size positively impacted the clean energy transition

Research on Robust Adaptive RTK Positioning of Low-Cost Smart Terminals

The performance of low-cost smart terminals is limited by the performance of their low-cost Global Navigation Satellite System (GNSS) hardware and chips, as well as by the impact of complex urban environments, which affect the positioning accuracy and stability of GNSS services. To this end, this paper proposes a robust adaptive Kalman filter for different environments that can be applied after data preprocessing. Based on the Kalman filter algorithm, a robust estimation approach is introduced into real-time kinematic (RTK) positioning to make judgments on the abnormal observation values of low-cost smart terminals, which amplifies the variance and covariance of the outlier observation equation, and reduces the impact of outliers on positioning performance. The Institute of Geodesy and Geophysics III (IGG III) function is used for regulation purposes, where prior information is modified and refreshed using the equivalent weight matrix and adaptive factors, thus reducing the impact of system model errors on system state estimation results. In addition, a robust factor is defined to adjust positioning deviation weighting between the pre- and post-test robust estimates. The experimental results show that after robust RTK positioning in the static experiments, the overall improvement in positioning accuracies of the Xiaomi 8, Huawei P40, Huawei mate40, and low-cost M8 receiver reached 29.6%, 31.3%, 32.1%, and 30.7%, respectively. Similarly, after applying the proposed robust method in the dynamic experiments, the overall positioning accuracies of the Xiaomi 8, Huawei P40, Huawei mate40, and the low-cost M8 receiver improved by 28.3%, 32.9%, 35.4%, and 26.2%, respectively. The experimental results reveal that an excellent positioning effect of a smartphone is positively correlated with robust RTK positioning performance. However, it is worth noting that when the positioning accuracy reaches a high level, such as the positioning results achieved using low-cost receivers, the robustness performance shows a relatively decreasing trend. This finding suggests that under the condition of high positioning accuracy, the sensitivity of specific positioning equipment to interference sources may increase, resulting in a decline in the effect of robust RTK positioning

Influence of Last Glacial Maximum legacies on functional diversity and community assembly of extant Chinese terrestrial vertebrates

Contemporary biodiversity patterns are shaped by not only modern climate but also factors such as past climate fluctuations. Investigating the relative degree of paleoclimate legacy could help us understand the formation of current biodiversity patterns. However, an assessment of this issue in China is lacking. Here, we investigated the phylogenetic structure and functional diversity patterns of Chinese terrestrial vertebrates. We found that Southern China harbored higher functional richness, while Northern and Western China were more phylogenetically clustered with higher functional divergence and evenness, indicating environmental filtering effects. Moreover, we found that drastic Last Glacial Maximum climate changes were positively related to phylogenetic clustering, lower functional richness, and higher functional divergence and evenness, although this effect varied among different taxonomic groups. We further found that mammal communities experiencing more drastic Last Glacial Maximum temperature changes were characterized by “faster” life-history trait values. Our findings provide new evidence of the paleoclimate change legacies influencing contemporary biodiversity patterns that will help guide national-level conservation plans

Phytochemical Characterization of Chinese Bayberry (Myrica rubra Sieb. et Zucc.) of 17 Cultivars and Their Antioxidant Properties

In order to fully understand the variations of fruit quality-related phytochemical composition in Chinese bayberry (Myrica rubra Sieb. et Zucc.), mature fruit of 17 cultivars from Zhejiang and Jiangsu provinces was used for the investigation of fruit quality attributes, including fruit color, soluble sugars, organic acids, total phenolics, flavonoids, antioxidant capacity, etc. Sucrose was the main soluble sugar, while citric acid was the main organic acid in bayberry fruit. The content of total phenolics and total flavonoids were positively correlated with 2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP) antioxidant activity and 2,2ʹ-azino-bis(3-ethylbenzothiazoline- 6-sulphonic acid) (ABTS) radical scavenging activity. Five anthocyanidins, i.e., delphinidin–hexoside (Dp–Hex), cyanidin-3–O-galactoside (C-3–Gal), cyanidin-3–O-glucoside (C-3–Glu), pelargonidin-3–O-glucoside (Pg-3–Glu) and peonidin-3-O-glucoside (Pn-3–Glu), and seven flavonols compounds, i.e., myricetin-3-O-rhamnoside (M-3–Rha), myricetin deoxyhexoside–gallate (M-DH–G), quercetin-3-O-galactoside (Q-3–Gal), quercetin-3– O-glucoside (Q-3–Glu), quercetin-3–O-rhamnoside (Q-3–Rha), kaempferol-3–O-galactoside (K-3–Gal) and kaempferol-3–O-glucoside (K-3–Glu), were identified and characterized among the cultivars. The significant differences in phytochemical compositions among cultivars reflect the diversity in bayberry germplasm, and cultivars of good flavor and/or rich in various health-promoting phytochemicals are good candidates for future genetic breeding of bayberry fruit of high quality. In conclusion, our results may provide important information for further breeding or industrial utilization of different bayberry resources

Stochastic Programming-Based Fault Diagnosis in Power Systems Under Imperfect and Incomplete Information

When a fault occurs in a section or a component of a given power system, the malfunctioning of protective relays (PRs) and circuit breakers (CBs), and the false and missing alarms, may manifestly complicate the fault diagnosis procedure. It is necessary to develop a methodologically appropriate framework for this application. As a branch of stochastic programming, the well-developed chance-constrained programming approach provides an efficient way to solve programming problems fraught with uncertainties. In this work, a novel fault diagnosis analytic model is developed with the ability of accommodating the malfunctioning of PRs and CBs, as well as the false and/or missing alarms. The genetic algorithm combined with Monte Carlo simulations are then employed to solve the optimization model. The feasibility and efficiency of the developed model and method are verified by a real fault scenario in an actual power system. In addition, it is demonstrated by simulation results that the computation speed of the developed method meets the requirements for the on-line fault diagnosis of actual power systems