Abstract
Motivation
Although long-read sequencing technologies can produce genomes with long contiguity, they suffer from high error rates. Thus, we developed NextPolish, a tool that efficiently ...corrects sequence errors in genomes assembled with long reads. This new tool consists of two interlinked modules that are designed to score and count K-mers from high quality short reads, and to polish genome assemblies containing large numbers of base errors.
Results
When evaluated for the speed and efficiency using human and a plant (Arabidopsis thaliana) genomes, NextPolish outperformed Pilon by correcting sequence errors faster, and with a higher correction accuracy.
Availability and implementation
NextPolish is implemented in C and Python. The source code is available from https://github.com/Nextomics/NextPolish.
Supplementary information
Supplementary data are available at Bioinformatics online.
IntroductionDementia is a growing public health concern, and providing long-term care for individuals affected by this condition is challenging for their family caregivers. While researchers have ...explored various intervention options to provide psychological support for dementia caregivers, mentalising imagery therapy (MIT) has gained significant recognition as an effective programme. Despite its significance and effectiveness, there is a lack of comprehensive scoping reviews of MIT in dementia caregiving. Thus, conducting such a review can provide valuable insights into the status and outcomes of MIT, identify gaps in existing research and provide recommendations for a more effective clinical practice.Methods and analysisThis study proposes a scoping review conducted according to the Joanna Briggs Institute, Arksey and O’Malley’s methodological framework, as well as the Preferred Reporting Items for Systematic Reviews and Meta-Analyses-Scoping Review Extension. PubMed, Web of Science, Embase, Scopus, CINAHL and PsycINFO databases will be searched while grey literature will be retrieved via Google Scholar. Covidence will be used to manage the literature selection process and remove duplicate publications. Two researchers will independently screen the literature according to the inclusion criteria, with any discrepancies resolved through discussions with a third researcher. Data will be presented in a structured tabular format, with a narrative synthesis providing an overview of the findings on the identified research gaps and the effectiveness of MIT in the field of dementia caregiving.Ethics and disseminationIn a scoping review, no ethical approval is necessary. The results will be published in a peer-reviewed journal.Trial registration numberThe scoping review protocol has been registered with Open Science Framework (https://doi.org/10.17605/OSF.IO/FHRG8).
The fates of cadmium (Cd) and arsenic (As) in paddy fields are generally opposite; thus, the inconsistent transformation of Cd and As poses large challenges for their remediation. In this study, the ...impacts of zero valent iron (ZVI) and/or biochar amendments on Cd and As bioavailability were examined in pot trials with rice. Comparison with the untreated soil, both Cd and As accumulation in different rice tissues decreased significantly in the ZVI-biochar amendments and the Cd and As accumulation in rice decreased with increasing ZVI contents. In particular, the concentrations of Cd (0.15 ± 0.01 mg kg−1) and As (0.17 ± 0.01 mg kg−1) in rice grains were decreased by 93% and 61% relative to the untreated soil, respectively. A sequential extraction analysis indicated that with increasing Fe ratios in the ZVI-biochar mixtures, bioavailable Cd and As decreased, and the immobilized Cd and As increased. Furthermore, high levels of Fe, Cd, and As were detected in Fe plaque of the ZVI-biochar amendments in comparison with the single biochar or single ZVI amendments. The ZVI-biochar mixture may have a synergistic effect that simultaneously reduces Cd and As bioavailability by increasing the formation of amorphous Fe and Fe plaque for Cd and As immobilization. The single ZVI amendment significantly decreased As bioavailability, while the single biochar amendment significantly reduced the bioavailability of Cd compared with the combined amendments. Hence, using a ZVI-biochar mixture as a soil amendment could be a promising strategy for safely-utilizing Cd and As co-contaminated sites in the future.
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•The single zero valent iron amendment decreased the bioavailability of As.•The single biochar amendment reduced the bioavailability of Cd.•The ZVI-biochar amendments simultaneously reduced Cd and As bioavailability.•The Fe, Cd, and As in plaque increased significantly in the ZVI-biochar amendments.•The ZVI-biochar amendments increased the amorphous Fe oxides in soils.
Chemodynamic therapy (CDT) employs Fenton catalysts to kill cancer cells by converting intracellular hydrogen peroxide (H2O2) into hydroxyl radicals (OH•). Although many studies on H2O2 ...supplementation have been conducted to improve the therapeutic effect of CDT, few studies have focused on the application of superoxide radical (O2−•) in CDT, which may result in better efficacy. A major concern about O2−•‐mediated CDT is its tendency to induce serious oxidative damage to normal tissues, which may be addressed by using a degradable O2−• scavenger. Here, a harmless‐harmful switchable and uninterrupted laccase (LAC)‐instructed killer (HULK) is constructed, which is the first CDT agent accelerated by LAC‐instructed O2−• generation and possesses a harmless‐harmful switchable effect because of the photodegradation of the O2−• scavenger iron‐chlorin e6 (FeCe6). LAC‐instructed substrate oxidation effectively catalyzes O2−• production with the help of intracellular reduction, thereby promoting the conversion of Fe3+ to Fe2+, accelerating the generation of OH•, and inducing tumor cell apoptosis and necrosis. The introduced O2−• scavenger FeCe6 is quickly photodegraded during irradiation, while LAC‐instructed O2−• generation proceeds as before, resulting in activatable CDT. This work not only provides the first strategy for LAC‐instructed O2−• generation but also presents new insight into activatable CDT.
A harmless–harmful switchable and uninterrupted laccase (LAC)‐instructed killer (HULK) is designed as a chemodynamic therapy (CDT) agent, which is the first CDT agent accelerated by LAC‐instructed superoxide radical (O2−•) generation and possesses harmless–harmful switchable effect because of the photodegradation of O2−• scavenger Fe‐chlorin e6, showing great potential as a safe and effective CDT agent.
Oxygen plays an essential role in the photodynamic therapy (PDT) of cancer. However, hypoxia inside tumors severely attenuates the therapeutic effect of PDT. To address this issue, a novel strategy ...is reported for cutting off the oxygen consumption pathway by using sub‐50 nm dual‐drug nanoparticles (NPs) to attenuate the hypoxia‐induced resistance to PDT and to enhance PDT efficiency. Specifically, dual‐drug NPs that encapsulate photosensitizer (PS) verteporfin (VER) and oxygen‐regulator atovaquone (ATO) with sub‐50 nm diameters can penetrate deep into the interior regions of tumors and effectively deliver dual‐drug into tumor tissues. Then, ATO released from NPs efficiently reduce in advance cellular oxygen consumption by inhibition of mitochondria respiratory chain and further heighten VER to generate greater amounts of 1O2 in hypoxic tumor. As a result, accompanied with the upregulated oxygen content in tumor cells and laser irradiation, the dual‐drug NPs exhibit powerful and overall antitumor PDT effects both in vitro and in vivo, and even tumor elimination. This study presents a potential appealing clinical strategy in photodynamic eradication of tumors.
A novel strategy for reducing oxygen consumption to attenuate the hypoxia‐induced resistance to photodynamic therapy (PDT) by using sub‐50 nm dual‐drug nanoparticles (ATO/VER NPs) is described. ATO has the ability of alleviating hypoxic regions and can eliminate tumors by enhancing PDT, which provides a valuable reference for research on targeted treatment of hypoxic tumor tissues.
A systematic review of published toxicology and human intervention studies was performed to characterize potential hazards associated with consumption of green tea and its preparations. A review of ...toxicological evidence from laboratory studies revealed the liver as the target organ and hepatotoxicity as the critical effect, which was strongly associated with certain dosing conditions (e.g. bolus dose via gavage, fasting), and positively correlated with total catechin and epigallocatechingallate (EGCG) content. A review of adverse event (AE) data from 159 human intervention studies yielded findings consistent with toxicological evidence in that a limited range of concentrated, catechin-rich green tea preparations resulted in hepatic AEs in a dose-dependent manner when ingested in large bolus doses, but not when consumed as brewed tea or extracts in beverages or as part of food. Toxico- and pharmacokinetic evidence further suggests internal dose of catechins is a key determinant in the occurrence and severity of hepatotoxicity. A safe intake level of 338 mg EGCG/day for adults was derived from toxicological and human safety data for tea preparations ingested as a solid bolus dose. An Observed Safe Level (OSL) of 704 mg EGCG/day might be considered for tea preparations in beverage form based on human AE data.
•Published toxicology and human clinical studies were reviewed, and hepatotoxicity identified as the critical effect.•Feeding state, dosing condition and purity of catechins are key determinants of toxicity.•GTEs closely reflecting that of traditional infusions in composition and ingestion mode are safe.•An Observed Safe Level of 704 mg EGCG/day could be considered for GTEs consumed in beverage form.•A safe intake level of 338 mg EGCG/day for adults could be considered for GTE ingested as a concentrated solid bolus dose.
A vaccine to protect against COVID-19 is urgently needed. We aimed to assess the safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 (Ad5) vectored COVID-19 vaccine expressing ...the spike glycoprotein of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain.
We did a dose-escalation, single-centre, open-label, non-randomised, phase 1 trial of an Ad5 vectored COVID-19 vaccine in Wuhan, China. Healthy adults aged between 18 and 60 years were sequentially enrolled and allocated to one of three dose groups (5 × 1010, 1 × 1011, and 1·5 × 1011 viral particles) to receive an intramuscular injection of vaccine. The primary outcome was adverse events in the 7 days post-vaccination. Safety was assessed over 28 days post-vaccination. Specific antibodies were measured with ELISA, and the neutralising antibody responses induced by vaccination were detected with SARS-CoV-2 virus neutralisation and pseudovirus neutralisation tests. T-cell responses were assessed by enzyme-linked immunospot and flow-cytometry assays. This study is registered with ClinicalTrials.gov, NCT04313127.
Between March 16 and March 27, 2020, we screened 195 individuals for eligibility. Of them, 108 participants (51% male, 49% female; mean age 36·3 years) were recruited and received the low dose (n=36), middle dose (n=36), or high dose (n=36) of the vaccine. All enrolled participants were included in the analysis. At least one adverse reaction within the first 7 days after the vaccination was reported in 30 (83%) participants in the low dose group, 30 (83%) participants in the middle dose group, and 27 (75%) participants in the high dose group. The most common injection site adverse reaction was pain, which was reported in 58 (54%) vaccine recipients, and the most commonly reported systematic adverse reactions were fever (50 46%), fatigue (47 44%), headache (42 39%), and muscle pain (18 17%. Most adverse reactions that were reported in all dose groups were mild or moderate in severity. No serious adverse event was noted within 28 days post-vaccination. ELISA antibodies and neutralising antibodies increased significantly at day 14, and peaked 28 days post-vaccination. Specific T-cell response peaked at day 14 post-vaccination.
The Ad5 vectored COVID-19 vaccine is tolerable and immunogenic at 28 days post-vaccination. Humoral responses against SARS-CoV-2 peaked at day 28 post-vaccination in healthy adults, and rapid specific T-cell responses were noted from day 14 post-vaccination. Our findings suggest that the Ad5 vectored COVID-19 vaccine warrants further investigation.
National Key R&D Program of China, National Science and Technology Major Project, and CanSino Biologics.
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•Biochars are potential sustainable precursors for activated carbon production.•Physical activation and chemical activation are applied in the production process.•Production ...parameters affect the properties of resultant activated carbon.•Multiple applications in environmental protection and energy storage are reviewed.•Future perspectives about biochar activation and applications are highlighted.
There is a growing interest of the scientific community on production of activated carbon using biochar as potential sustainable precursors pyrolyzed from biomass wastes. Physical activation and chemical activation are the main methods applied in the activation process. These methods could have significantly beneficial effects on biochar chemical/physical properties, which make it suitable for multiple applications including water pollution treatment, CO2 capture, and energy storage. The feedstock with different compositions, pyrolysis conditions and activation parameters of biochar have significant influences on the properties of resultant activated carbon. Compared with traditional activated carbon, activated biochar appears to be a new potential cost-effective and environmentally-friendly carbon materials with great application prospect in many fields. This review not only summarizes information from the current analysis of activated biochar and their multiple applications for further optimization and understanding, but also offers new directions for development of activated biochar.
Two-dimensional materials provide extraordinary opportunities for exploring phenomena arising in atomically thin crystals. Beginning with the first isolation of graphene, mechanical exfoliation has ...been a key to provide high-quality two-dimensional materials, but despite improvements it is still limited in yield, lateral size and contamination. Here we introduce a contamination-free, one-step and universal Au-assisted mechanical exfoliation method and demonstrate its effectiveness by isolating 40 types of single-crystalline monolayers, including elemental two-dimensional crystals, metal-dichalcogenides, magnets and superconductors. Most of them are of millimeter-size and high-quality, as shown by transfer-free measurements of electron microscopy, photo spectroscopies and electrical transport. Large suspended two-dimensional crystals and heterojunctions were also prepared with high-yield. Enhanced adhesion between the crystals and the substrates enables such efficient exfoliation, for which we identify a gold-assisted exfoliation method that underpins a universal route for producing large-area monolayers and thus supports studies of fundamental properties and potential application of two-dimensional materials.
FOXM1 (forkhead box protein M1) is a critical proliferation-associated transcription factor that is widely spatiotemporally expressed during the cell cycle. It is closely involved with the processes ...of cell proliferation, self-renewal, and tumorigenesis. In most human cancers, FOXM1 is overexpressed, and this indicates a poor prognosis for cancer patients. FOXM1 maintains cancer hallmarks by regulating the expression of target genes at the transcriptional level. Due to its potential role as molecular target in cancer therapy, FOXM1 was named the Molecule of the Year in 2010. However, the mechanism of FOXM1 dysregulation remains indistinct. A comprehensive understanding of FOXM1 regulation will provide novel insight for cancer and other diseases in which FOXM1 plays a major role. Here, we summarize the transcriptional regulation, post-transcriptional regulation and post-translational modifications of FOXM1, which will provide extremely important implications for novel strategies targeting FOXM1.
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