Atmospheric rivers over eastern US affected by Pacific/North America pattern.

Atmospheric rivers (ARs) play important roles in various extreme weather events across the US. While AR features in western US have been extensively studied, there remains limited understanding of their variability in the eastern US (EUS). Using both observations and a state-of-the-art climate model, we find a significant increase (~10% dec-1) in winter AR frequency in the EUS during the past four decades. This trend is closely linked to recent changes in the Pacific/North America (PNA) teleconnection pattern, accompanied by a poleward shift of the mid-latitude jet stream. We further reveal a strong correlation (R = 0.8; P < 0.001) between interannual variations in AR occurrence and the PNA index. This linkage has been verified in various model simulations. A statistical model, built on this linkage, has proven effective in predicting the AR frequency using the PNA index at both monthly and seasonal scales. These promising results have important implications for addressing concerns related to AR-associated extreme precipitation and flooding in this region.

Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing.

BACKGROUND: The CRISPR/Cas12a and CRISPR/Cas13d systems are widely used for fundamental research and hold great potential for future clinical applications. However, the short half-life of guide RNAs (gRNAs), particularly free gRNAs without Cas nuclease binding, limits their editing efficiency and durability. RESULTS: Here, we engineer circular free gRNAs (cgRNAs) to increase their stability, and thus availability for Cas12a and Cas13d processing and loading, to boost editing. cgRNAs increases the efficiency of Cas12a-based transcription activators and genomic DNA cleavage by approximately 2.1- to 40.2-fold for single gene editing and 1.7- to 2.1-fold for multiplexed gene editing than their linear counterparts, without compromising specificity, across multiple sites and cell lines. Similarly, the RNA interference efficiency of Cas13d is increased by around 1.8-fold. In in vivo mouse liver, cgRNAs are more potent in activating gene expression and cleaving genomic DNA. CONCLUSIONS: CgRNAs enable more efficient programmable DNA and RNA editing for Cas12a and Cas13d with broad applicability for fundamental research and gene therapy.

Generation of Human Embryonic Stem Cell-Derived Lung Organoids for Modeling Infection and Replication Differences between Human Adenovirus Types 3 and 55 and Evaluating Potential Antiviral Drugs.

Human adenoviruses type 3 (HAdV-3) and type 55 (HAdV-55) are frequently encountered, highly contagious respiratory pathogens with high morbidity rate. In contrast to HAdV-3, one of the most predominant types in children, HAdV-55 is a reemergent pathogen associated with more severe community-acquired pneumonia (CAP) in adults, especially in military camps. However, the infectivity and pathogenicity differences between these viruses remain unknown as in vivo models are not available. Here, we report a novel system utilizing human embryonic stem cells-derived 3-dimensional airway organoids (hAWOs) and alveolar organoids (hALOs) to investigate these two viruses. Firstly, HAdV-55 replicated more robustly than HAdV-3. Secondly, cell tropism analysis in hAWOs and hALOs by immunofluorescence staining revealed that HAdV-55 infected more airway and alveolar stem cells (basal and AT2 cells) than HAdV-3, which may lead to impairment of self-renewal functions post-injury and the loss of cell differentiation in lungs. Additionally, the viral life cycles of HAdV-3 and -55 in organoids were also observed using Transmission Electron Microscopy. This study presents a useful pair of lung organoids for modeling infection and replication differences between respiratory pathogens, illustrating that HAdV-55 has relatively higher replication efficiency and more specific cell tropism in human lung organoids than HAdV-3, which may result in relatively higher pathogenicity and virulence of HAdV-55 in human lungs. The model system is also suitable for evaluating potential antiviral drugs, as demonstrated with cidofovir. IMPORTANCE Human adenovirus (HAdV) infections are a major threat worldwide. HAdV-3 is one of the most predominant respiratory pathogen types found in children. Many clinical studies have reported that HAdV-3 causes less severe disease. In contrast, HAdV-55, a reemergent acute respiratory disease pathogen, is associated with severe community-acquired pneumonia in adults. Currently, no ideal in vivo models are available for studying HAdVs. Therefore, the mechanism of infectivity and pathogenicity differences between human adenoviruses remain unknown. In this study, a useful pair of 3-dimensional (3D) airway organoids (hAWOs) and alveolar organoids (hALOs) were developed to serve as a model. The life cycles of HAdV-3 and HAdV-55 in these human lung organoids were documented for the first time. These 3D organoids harbor different cell types, which are similar to the ones found in humans. This allows for the study of the natural target cells for infection. The finding of differences in replication efficiency and cell tropism between HAdV-55 and -3 may provide insights into the mechanism of clinical pathogenicity differences between these two important HAdV types. Additionally, this study provides a viable and effective in vitro tool for evaluating potential anti-adenoviral treatments.

Discussion on the Main Control Effect of Geological Structures on Coal and Gas Outburst.

Coal and gas outbursts are great natural disasters in underground coal mines, seriously threatening the lives of miners and coal mine safety. The study of the relationship between coal and gas outbursts and geological structures has always been an important component of gas geological work, and it also serves as a foundation for coal mines to develop gas outburst prevention measures. This study considers groups F and E coal seams, mainly mined in the southwest wing of Likou syncline in the Pingdingshan mining area, as the research object. Based on actual outburst data, this study investigates the distribution and intensity characteristics of coal and gas outbursts and the correlation between coal and gas outbursts and geological structures using gas geological analysis methods and taking structural control as the main line. The results depict that the coal and gas outbursts in the study area have obvious district and subband characteristics. The outburst district mainly occurred in the East, and the four outburst zones, I, II, III, and IV, were the concentrated occurrence subband of coal and gas outbursts. The district and subband of coal and gas outburst are mainly controlled by and related to the geological structure. The eastern fold structure has developed more than the middle and western districts, which is why the eastern part of the coal and gas outburst is more severe than in the middle and western regions. Under the structural background of the coal and gas outburst district, the subband outburst characteristics were mainly controlled by local geological structural conditions.

Comparison of DNA targeting CRISPR editors in human cells.

BACKGROUND: Profiling and comparing the performance of current widely used DNA targeting CRISPR systems provide the basic information for the gene-editing toolkit and can be a useful resource for this field. In the current study, we made a parallel comparison between the recently reported miniature Cas12f1 (Un1Cas12f1 and AsCas12f1) and the widely used Cas12a and Cas9 nucleases in mammalian cells. RESULTS: We found that as a CRISPRa activator, Un1Cas12f1 could induce gene expression with a comparable level to that of Cas12a and Cas9, while as a DNA cleavage editor, Cas12f1 exhibited similar properties to Cas12a, like high specificity and dominantly induced deletions over insertions, but with less activity. In contrast, wild-type SpCas9 showed the highest activity, lowest specificity, and induced balanced deletions and insertions. Thus, Cas12f1 is recommended for gene-activation-based applications, Cas12a is for therapy applications, and wild-type Cas9 is for in vitro and animal investigations. CONCLUSION: The comparison provided the editing properties of the widely used DNA-targeting CRISPR systems in the gene-editing field.

Engineered Cas12a-Plus nuclease enables gene editing with enhanced activity and specificity.

BACKGROUND: The CRISPR-Cas12a (formerly Cpf1) system is a versatile gene-editing tool with properties distinct from the broadly used Cas9 system. Features such as recognition of T-rich protospacer-adjacent motif (PAM) and generation of sticky breaks, as well as amenability for multiplex editing in a single crRNA and lower off-target nuclease activity, broaden the targeting scope of available tools and enable more accurate genome editing. However, the widespread use of the nuclease for gene editing, especially in clinical applications, is hindered by insufficient activity and specificity despite previous efforts to improve the system. Currently reported Cas12a variants achieve high activity with a compromise of specificity. Here, we used structure-guided protein engineering to improve both editing efficiency and targeting accuracy of Acidaminococcus sp. Cas12a (AsCas12a) and Lachnospiraceae bacterium Cas12a (LbCas12a). RESULTS: We created new AsCas12a variant termed "AsCas12a-Plus" with increased activity (1.5~2.0-fold improvement) and specificity (reducing off-targets from 29 to 23 and specificity index increased from 92% to 94% with 33 sgRNAs), and this property was retained in multiplex editing and transcriptional activation. When used to disrupt the oncogenic BRAFV600E mutant, AsCas12a-Plus showed less off-target activity while maintaining comparable editing efficiency and BRAFV600E cancer cell killing. By introducing the corresponding substitutions into LbCas12a, we also generated LbCas12a-Plus (activity improved ~1.1-fold and off-targets decreased from 20 to 12 while specificity index increased from 78% to 89% with 15 sgRNAs), suggesting this strategy may be generally applicable across Cas12a orthologs. We compared Cas12a-Plus, other variants described in this study, and the reported enCas12a-HF, enCas12a, and Cas12a-ultra, and found that Cas12a-Plus outperformed other variants with a good balance for enhanced activity and improved specificity. CONCLUSIONS: Our discoveries provide alternative AsCas12a and LbCas12a variants with high specificity and activity, which expand the gene-editing toolbox and can be more suitable for clinical applications.

Desorption Effects and Laws of Multiscale Gas-Bearing Coal with Different Degrees of Metamorphism.

Understanding gas desorption effects and laws of coal mass under different conditions is essential for the effective exploration of gas emission in underground coal mines, prediction and prevention of coal and gas outburst, accurate detection of gas [coal methane (CBM)] content in coal seams, and prediction of CBM productivity. Using a self-developed test platform, we simulated gas adsorption and desorption and performed physical simulation tests. Based on these tests, we investigated the differences in the total amount of gas desorbed, desorption rate, and initial amount of gas desorbed by long-flame coal, coking coal, meager-lean coal, and anthracite on different scales under different gas pressures. Two methods are used for compensating gas loss, namely, the method and the power function method, as stipulated in the current Standards for Determination of Gas Content in Coal Seams in China. By combining these two methods, we analyzed the applicability of these two compensation methods in coal on different scales with varying degrees of metamorphism under gas pressures. The results demonstrated that (1) under the same gas adsorption pressure, the cumulative total amount of gas desorbed per unit mass within 90 min for the four kinds of coal samples increases with the degree of metamorphism. Changes in the cumulative amount of gas desorbed per unit mass and the desorption rate with the degree of metamorphism vary with stages. Notably, a higher adsorption pressure leads to a more obvious stage change. (2) Under the same gas adsorption pressure, the cumulative total amount of gas desorbed per unit mass and the desorption rate of coal with the same degree of metamorphism are inversely proportional to the size of the coal sample. This indicates significant scale effects. The larger the degree of metamorphism and gas adsorption pressure, the more significant are the scale effects of gas desorption. (3) For coal with the same degree of metamorphism, the higher gas adsorption pressure leads to a larger cumulative total amount of gas desorbed and a higher desorption rate throughout the desorption process and a larger proportion of the cumulative amount of gas desorbed in the initial stage. The smaller the size of the coal sample, the more obvious the pressure effects of gas desorption are. (4) For coal samples with the same degree of metamorphism, when the gas content in coal seams is kept constant, the larger the size of the coal sample, the smaller the actual gas loss is. Moreover, a higher gas content in coal seams results in a greater gas loss and a larger calculation error for gas loss. Compared with the method, the power function method reveals a smaller deviation between the calculated gas loss and the actual gas loss, which is found to be more accurate. A larger size coal sample results in higher accuracy in the calculated gas loss.

Recent Trends in the Development of Bone Regenerative Biomaterials.

The goal of a biomaterial is to support the bone tissue regeneration process at the defect site and eventually degrade in situ and get replaced with the newly generated bone tissue. Biomaterials that enhance bone regeneration have a wealth of potential clinical applications from the treatment of non-union fractures to spinal fusion. The use of bone regenerative biomaterials from bioceramics and polymeric components to support bone cell and tissue growth is a longstanding area of interest. Recently, various forms of bone repair materials such as hydrogel, nanofiber scaffolds, and 3D printing composite scaffolds are emerging. Current challenges include the engineering of biomaterials that can match both the mechanical and biological context of bone tissue matrix and support the vascularization of large tissue constructs. Biomaterials with new levels of biofunctionality that attempt to recreate nanoscale topographical, biofactor, and gene delivery cues from the extracellular environment are emerging as interesting candidate bone regenerative biomaterials. This review has been sculptured around a case-by-case basis of current research that is being undertaken in the field of bone regeneration engineering. We will highlight the current progress in the development of physicochemical properties and applications of bone defect repair materials and their perspectives in bone regeneration.

Recent Advances of Chitosan-Based Injectable Hydrogels for Bone and Dental Tissue Regeneration.

Traditional strategies of bone repair include autografts, allografts and surgical reconstructions, but they may bring about potential hazard of donor site morbidity, rejection, risk of disease transmission and repetitive surgery. Bone tissue engineering (BTE) is a multidisciplinary field that offers promising substitutes in biopharmaceutical applications, and chitosan (CS)-based bone reconstructions can be a potential candidate in regenerative tissue fields owing to its low immunogenicity, biodegradability, bioresorbable features, low-cost and economic nature. Formulations of CS-based injectable hydrogels with thermo/pH-response are advantageous in terms of their high-water imbibing capability, minimal invasiveness, porous networks, and ability to mold perfectly into an irregular defect. Additionally, CS combined with other naturally-derived or synthetic polymers and bioactive agents has proven to be an effective alternative to autologous bone and dental grafts. In this review, we will highlight the current progress in the development of preparation methods, physicochemical properties and applications of CS-based injectable hydrogels and their perspectives in bone and dental regeneration. We believe this review is intended as starting point and inspiration for future research effort to develop the next generation of tissue-engineering scaffold materials.

Upregulation of microRNA-9-5p inhibits apoptosis of chondrocytes through downregulating Tnc in mice with osteoarthritis following tibial plateau fracture.

Osteoarthritis (OA) is a common degenerative joint disease which is typically progressed with age, affecting smaller joints of hands, lower limbs, and the vertebral column. It has been reported that microRNAs could regulate the biological processes of OA. Therefore, the purpose of this study was to elucidate miR-9-5p's role in regulating cartilage remodeling of OA mice following tibial plateau fracture (TPF) through regulation of tenascin C (Tnc). Initially, we determined the expression of miR-9-5p and Tnc in mice with OA and then testified their relationship. The results displayed a high expression of Tnc, but a poor expression of miR-9-5p with high methylation in OA. Tnc was confirmed to be a target gene of miR-9-5p. Moreover, based on gain- and loss-function experiments, an increase of miR-9-5p and loss of Tnc had the potential to inhibit cell apoptosis, while facilitating cell proliferation, migration, invasion, and cartilage remodeling of mice with OA following TPF. This was further demonstrated by a higher expression of type II collagen, lower type X collagen, and protogenin expression. Subsequently, downregulation of miR-9-5p aggravated the pathological changes of mice, illustrated by an increase in the Mankin score. In conclusion, the present study proved that overexpression of miR-9-5p suppressed chondrocytes apoptosis and promoted cartilage remodeling through downregulating of Tnc in mice with OA.

An Extended Eddy-Diffusivity Mass-Flux Scheme for Unified Representation of Subgrid-Scale Turbulence and Convection.

Large-scale weather forecasting and climate models are beginning to reach horizontal resolutions of kilometers, at which common assumptions made in existing parameterization schemes of subgrid-scale turbulence and convection-such as that they adjust instantaneously to changes in resolved-scale dynamics-cease to be justifiable. Additionally, the common practice of representing boundary-layer turbulence, shallow convection, and deep convection by discontinuously different parameterizations schemes, each with its own set of parameters, has contributed to the proliferation of adjustable parameters in large-scale models. Here we lay the theoretical foundations for an extended eddy-diffusivity mass-flux (EDMF) scheme that has explicit time-dependence and memory of subgrid-scale variables and is designed to represent all subgrid-scale turbulence and convection, from boundary layer dynamics to deep convection, in a unified manner. Coherent up and downdrafts in the scheme are represented as prognostic plumes that interact with their environment and potentially with each other through entrainment and detrainment. The more isotropic turbulence in their environment is represented through diffusive fluxes, with diffusivities obtained from a turbulence kinetic energy budget that consistently partitions turbulence kinetic energy between plumes and environment. The cross-sectional area of up and downdrafts satisfies a prognostic continuity equation, which allows the plumes to cover variable and arbitrarily large fractions of a large-scale grid box and to have life cycles governed by their own internal dynamics. Relatively simple preliminary proposals for closure parameters are presented and are shown to lead to a successful simulation of shallow convection, including a time-dependent life cycle.

Administration of chlorogenic acid alleviates spinal cord injury via TLR4/NF­κB and p38 signaling pathway anti­inflammatory activity.

Chlorogenic acid, as a secondary metabolite of plants, exhibits a variety of effects including free radical scavenging, antiseptic, anti­inflammatory and anti­viral, in addition to its ability to reduce blood glucose, protect the liver and act as an anti­hyperlipidemic agent and cholagogue. The present study demonstrated that administration of chlorogenic acid alleviated spinal cord injury (SCI) via anti­inflammatory activity mediated by nuclear factor (NF)­κB and p38 signaling pathways. Wistar rats were used to structure a SCI model rat to explore the effects of administration of chlorogenic acid on SCI. The Basso, Beattie and Bresnahan test was executed for assessment of neuronal functional recovery and then spinal cord tissue wet/dry weight ratio was recorded. The present study demonstrated that chlorogenic acid increased SCI­inhibition of BBB scores and decreased SCI­induction of spinal cord wet/dry weight ratio in rats. In addition, chlorogenic acid suppressed SCI­induced inflammatory activity, inducible nitric oxide synthase activity and cyclooxygenase­2 protein expression in the SCI rat. Furthermore, chlorogenic acid suppressed Toll like receptor (TLR)­4/myeloid differentiation primary response 88 (MyD88)/NF­κB/IκB signaling pathways and downregulated p38 mitogen activated protein kinase protein expression in SCI rats. The findings suggest that administration of chlorogenic acid alleviates SCI via anti­inflammatory activity mediated by TLR4/MyD88/NF­κB and p38 signaling pathways.

Numerics and subgrid-scale modeling in large eddy simulations of stratocumulus clouds.

Stratocumulus clouds are the most common type of boundary layer cloud; their radiative effects strongly modulate climate. Large eddy simulations (LES) of stratocumulus clouds often struggle to maintain fidelity to observations because of the sharp gradients occurring at the entrainment interfacial layer at the cloud top. The challenge posed to LES by stratocumulus clouds is evident in the wide range of solutions found in the LES intercomparison based on the DYCOMS-II field campaign, where simulated liquid water paths for identical initial and boundary conditions varied by a factor of nearly 12. Here we revisit the DYCOMS-II RF01 case and show that the wide range of previous LES results can be realized in a single LES code by varying only the numerical treatment of the equations of motion and the nature of subgrid-scale (SGS) closures. The simulations that maintain the greatest fidelity to DYCOMS-II observations are identified. The results show that using weighted essentially non-oscillatory (WENO) numerics for all resolved advective terms and no explicit SGS closure consistently produces the highest-fidelity simulations. This suggests that the numerical dissipation inherent in WENO schemes functions as a high-quality, implicit SGS closure for this stratocumulus case. Conversely, using oscillatory centered difference numerical schemes for momentum advection, WENO numerics for scalars, and explicitly modeled SGS fluxes consistently produces the lowest-fidelity simulations. We attribute this to the production of anomalously large SGS fluxes near the cloud tops through the interaction of numerical error in the momentum field with the scalar SGS model.

[Allelic loss of 6q16.3 microsatellite DNA in childhood acute lymphoblastic leukemia and bioinformatics analysis].

OBJECTIVE: To locate the cluster region of loss of heterozygosity (LOH) in children with acute lymphoblastic leukemia (ALL), and explore the new tumor suppressor gene. METHODS: Allelic loss was analyzed by PCR with 15 microsatellite markers mapping on 6q16.3. The LOH was analyzed by bioinformatics. The relationship between LOH and clinical factors was further analyzed. RESULTS: The frequency of LOH at least at one loci on 6q16.3 was 32.7%. The LOH in relapsed patients was higher than those in not relapsed. The higher frequency of LOH was observed in two regions of D6S1709-D6S1028 and D6S2160-D6S1580 at 6q16.3. GRIK2 may be a candidate of tumor suppressor gene. There are 12 ESTs may carry out new anti-oncogene. Patients with 6q LOH had higher WBC counts (P < 0.01), blast cells percentage (P < 0.01), relapse rate (P < 0.05) and chromosomal aberration (P < 0.05). CONCLUSION: D6S1709-D6S1028 and D6S2160-D6S1580 are two regions of minimus deletion on 6q16.3 in which tumor suppressor gene may exist. The LOH on 6q16.3 may be a prognostic index of children with ALL.