The Power of Using Novel Nanopore Sequencing Technology for Diagnosis, Genomic and Pathological Studies of Covid-19

The novel coronavirus disease 2019 (COVID‐19), originally identified in December 2019 Wuhan, China, has propagated to worldwide pandemic, causing many cases of death and morbidity. Since the development of COVID-19 vaccines is still under experimental stages without public access, different types of testing and detection ensuring rapid and accurate results are urgently required to prevent delaying isolation of infected patients. The traditional diagnostic and analytical methods of COVID-19 relied heavily on nucleic acid and antibody-antigen methods but are subject to assembly bias, restricted by reading length, showed some false positive/negative results and had a long turnaround time. Hence, three styles of nanopore sequencing techniques as complementary tools for COVID-19 diagnosis and analysis are introduced. The long-read nanopore sequencing technology has been adopted in metagenomic and pathological studies of virosphere including SARS-CoV-2 recently by either metagenomically, directly or indirectly sequencing the viral genomic RNA of SARS-CoV-2 in real-time to detect infected specimens for early isolation and treatment, to investigate the transmission and evolutionary routes of SARS-CoV-2 as well as its pathogenicity and epidemiology. In this article, the Nanopore-Based Metagenomic Sequencing, Direct RNA Nanopore Sequencing (DRS), and Nanopore Targeted Sequencing (NTS) become the main focus of the novel COVID-19 detecting analytical methods in sequencing platforms, which are discussed in comparison with other traditional and popular diagnostic methods. Finally, different types of nanopore sequencing platforms that are developed by Oxford Nanopore Technologies (ONT) due to various purposes and demands in viral genomic research are briefly discussed

A long short-temory relation network for real-time prediction of patient-specific ventilator parameters

Accurate prediction of patient-specific ventilator parameters is crucial for optimizing patient-ventilator interaction. Current approaches encounter difficulties in concurrently observing long-term, time-series dependencies and capturing complex, significant features that influence the ventilator treatment process, thereby hindering the achievement of accurate prediction of ventilator parameters. To address these challenges, we propose a novel approach called the long short-term memory relation network (LSTMRnet). Our approach uses a long, short-term memory bank to store rich information and an important feature selection step to extract relevant features related to respiratory parameters. This information is obtained from the prior knowledge of the follow up model. We also concatenate the embeddings of both information types to maintain the joint learning of spatio-temporal features. Our LSTMRnet effectively preserves both time-series and complex spatial-critical feature information, enabling an accurate prediction of ventilator parameters. We extensively validate our approach using the publicly available medical information mart for intensive care (MIMIC-III) dataset and achieve superior results, which can be potentially utilized for ventilator treatment (i.e., sleep apnea-hypopnea syndrome ventilator treatment and intensive care units ventilator treatment

Global systematic review with meta-analysis shows that warming effects on terrestrial plant biomass allocation are influenced by precipitation and mycorrhizal association

Biomass allocation in plants is fundamental for understanding and predicting terrestrial carbon storage. Yet, our knowledge regarding warming effects on root: shoot ratio (R/S) remains limited. Here, we present a meta-analysis encompassing more than 300 studies and including angiosperms and gymnosperms as well as different biomes (cropland, desert, forest, grassland, tundra, and wetland). The meta-analysis shows that average warming of 2.50 °C (median = 2 °C) significantly increases biomass allocation to roots with a mean increase of 8.1% in R/S. Two factors associate significantly with this response to warming: mean annual precipitation and the type of mycorrhizal fungi associated with plants. Warming-induced allocation to roots is greater in drier habitats when compared to shoots (+15.1% in R/S), while lower in wetter habitats (+4.9% in R/S). This R/S pattern is more frequent in plants associated with arbuscular mycorrhizal fungi, compared to ectomycorrhizal fungi. These results show that precipitation variability and mycorrhizal association can affect terrestrial carbon dynamics by influencing biomass allocation strategies in a warmer world, suggesting that climate change could influence belowground C sequestration

Permo-Triassic detrital records of South China and implications for the Indosinian events in East Asia

This work was supported by the National Natural Science Foundation of China (Grant No. 41602105, 41672106 and 41530966) and China Postdoctoral Science Foundation (Grant No. 2016M590655), the Fundamental Research Funds for the Central Universities, Ocean University of China. Peter Cawood acknowledges support from the Australian Research Council grant FL160100168.Provenance analyses of Lower to Middle Triassic strata from the Greater Youjiang Basin along with the Permian strata of Hainan Island, provide a record of the collisional assembly of the South China Craton and Indochina Block and their incorporation into Asia. Detrital zircons from Lower and Middle Triassic samples show similar overall age spectra ranging from Archean to Triassic with major age groups at 300–250 Ma, 480–420 Ma, and 1200–900 Ma, as well as at 400–300 Ma in one Triassic sample. Permian siltstones from Hainan Island, to the southeast of the Greater Youjiang Basin, record different age spectra with major age groups at 400–300 Ma and 530–420 Ma and subordinate components at 1200–900 Ma and 1900–1700 Ma. These age data in combination with available paleocurrent data and regional geological relations suggest that Precambrian detrital zircons were derived from the Precambrian basement or recycled from the overlying early Paleozoic sedimentary rocks that contain Precambrian detritus. Early Paleozoic detrital zircons were derived from igneous rocks in the South China Craton. Devonian-Triassic detrital zircons in the Triassic strata were likely sourced from coeval magmatic activity related to closure of Paleo-Tethys branch ocean that lay to the southwest, whereas 400–300 Ma detrital zircons in the Permian siltstones of Hainan Island were likely derived from a Paleozoic magmatic arc source that extended along the eastern-southeastern margin of China from Hainan Island to Japan in response to subduction of the Paleo-Pacific oceanic crust. Detrital zircon, trace element, and sandstone modal data for Permo-Triassic strata from the Greater Youjiang Basin indicate that the basin evolved from a trailing-edge passive margin setting to a peripheral foreland basin during closure of the Paleo-Tethys Ocean and collision between Indochina and South China. The initiation time of the foreland basin decreases from southeast to southwest across the basin, probably reflecting oblique collision. In contrast, the Permian strata on Hainan Island record a provenance history distinct from the Greater Youjiang Basin, which is related to late Paleozoic to Mesozoic subduction of the Paleo-Pacific Plate beneath South China.PostprintPeer reviewe

A meaningful exploration of ofatumumab in refractory NMOSD: a case report

ObjectiveTo report the case of a patient with refractory neuromyelitis optica spectrum disorder (NMOSD), who, despite showing poor response or intolerance to multiple immunosuppressants, was successfully treated with Ofatumumab.Case presentationA 42-year-old female was diagnosed with NMOSD in the first episode of the disease. Despite treatment with intravenous methylprednisolone, immunoglobulin, rituximab and immunoadsorption, together with oral steroids, azathioprine, mycophenolate mofetil and tacrolimus, she underwent various adverse events, such as abnormal liver function, repeated infections, fever, rashes, hemorrhagic shock, etc., and experienced five relapses over the ensuing four years. Finally, clinicians decided to initiate Ofatumumab to control the disease. The patient received 9 doses of Ofatumumab over the next 10 months at customized intervals. Her symptoms were stable and there was no recurrence or any adverse events.ConclusionOfatumumab might serve as an effective and safe alternative for NMOSD patients who are resistant to other current immunotherapies

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Prediction of the Water Inrush Risk from an Overlying Separation Layer in the Thick Overburden of a Thick Coal Seam

With the expansion of coal mining westward in China, water inrush from seam roofs has become a prominent safety problem during mining. The roof rock of the coal seam in the Shilawusu coal mine has the characteristics of a double-layer structure, and the overlying separation space formed in the mining process of the coal seam poses a risk of water inrush. To ensure the safety of coal mine production, considering the geological and hydrogeological data of the mining area, the core recovery rate, lithologic assemblage index, key aquifer thickness, hydrostatic head and lithologic structure index of the Zhidan Formation are selected as evaluation indexes. The index weights are calculated based on the attribute hierarchical model and coefficient of variation methods, and subjective and objective preference coefficients are introduced to determine the ranking of comprehensive indexes. The catastrophe progression method is improved, and a zoning prediction model for water inrush risk is established by the improved catastrophe progression method. The results show that only a tiny part of the mining area is in danger, and most areas are in the safe and transition zones. The model realizes the prediction of the risk of water inrush from the overlying separation layer in the study area and provides a theoretical basis for the prevention and control of water inrush from the overlying separation layer in coal mining

Comparison of Submillimeter Spot Ablation of Copper and Nickel by Multipulse Picosecond and Femtosecond Laser

The current transmission and reflection laser ablation micropropulsion modes have the problem of a complex working medium supply system in engineering. Therefore, we propose large-spot laser ablation with a one-dimensional supply mode. In order to verify this ablation mode, a multipulse ablation experiment of submillimeter-scale light spots was carried out on the surface of pretreated copper and nickel under the atmosphere using an ultrafast laser with a pulse width of 290 fs and 10 ps. The results show that femtosecond laser multipulse ablation (FLMA) leads to the grain refinement of copper, the crater quality of the two metals under FLMA is better, and picosecond laser multipulse ablation (PLMA) causes the crater of nickel to form a dense remelting bulge that affects laser absorption; both metals have obvious heat-affected zones after FLMA and PLMA, the heat-affected zones of nickel are 5–10% larger than those of copper, and the ablation depth of copper is deeper. Under the same conditions, the ablation mass of copper is smaller than that of nickel, and the specific impulse performance of laser ablation micropropulsion is better

Ultralarge interlayer distance and C,N-codoping enable superior sodium storage capabilities of MoS2 nanoonions

Sodium-ion batteries have emerged as a desired alternative to lithium-ion batteries (LIBs) on account of their low cost, good safety, and large reserves of sodium in the earth's crust. The sodium storage capabilities of batteries significatnly depend on the structure and composition of electrode materials. Herein, a new type of C,N-codoped MoS nanoonions with ultralarge interlayer spacing of 1.16 nm has been successfully fabricated by vapor phase sulfuration of the as-prepared PPy-PMo precursor at an optimized vulcanization temperature. More importantly, the delicate internal nanostructure has been directly observed via electron tomography (ET) technique and 3D reconstruction. Thanks to the structure and composition merits, the resulting anode materials of C/N-MoS-800 delivers remarkable sodium storage properties. The reversible capacity retains 617.7 mA h g at 100 mA g after 200 cycles. The electrochemical kinetic analysis and density functional theory (DFT) calculations further comfirm that the expanded interlayer distance and C,N-codoping of MoS nanosheets promote the superior Na intercalation/deintercalation kinetics. In turn, the resulted pseudocapacitance-dominated electrochemical behavior also enables the superior rate capability