Pig pangenome graph reveals functional features of non‑reference sequences

Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in animals.This constraint is particularly pronounced for non-reference sequences(NRSs),which have not been extensively studied.Results In this study,we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb.Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome.Furthermore,we observed that NRSs were rarely found within coding sequences,while NRS insertions were enriched in immune-related Gene Ontology terms.Notably,our investigation also unveiled a close association between novel genes and the immune capacity of pigs.We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs,and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X.Additionally,we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in South-ern Chinese pigs.Conclusions Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.

An approach for determination of lateral limit angle in kinematic planar sliding analysis for rock slopes

Planar sliding is one of the frequently observed types of failure in rock slopes.Kinematic analysis is a classic and widely used method to examine the potential failure modes in rock masses.The accuracy of planar sliding kinematic analysis is significantly influenced by the value assigned to the lateral limit angleγlim.However,the assignment ofγlim is currently used generally based on an empirical criterion.This study aims to propose an approach for determining the value ofγlim in deterministic and probabilistic kinematic planar sliding analysis.A new perspective is presented to reveal thatγlim essentially influences the probability of forming a potential planar sliding block.The procedure to calculate this probability is introduced using the block theory method.It is found that the probability is correlated with the number of discontinuity sets presented in rock masses.Thus,different values ofγlim for rock masses with different sets of discontinuities are recommended in both probabilistic and deterministic planar sliding kinematic analyses;whereas a fixed value ofγlim is commonly assigned to different types of rock masses in traditional method.Finally,an engineering case was used to compare the proposed and traditional kinematic analysis methods.The error rates of the traditional method vary from 45%to 119%,while that of the proposed method ranges between 1%and 17%.Therefore,it is likely that the proposed method is superior to the traditional one.

A simple atomization approach enables monolayer dispersion of nano graphenes in cementitious composites with excellent strength gains

Carbon nano additives(CNAs)are critical to achieving the unique properties of functionalized composites,however,controlling the dispersion of CNAs in material matrix is always a challenging task.In this study,a simple atomization approach was successfully developed to promote the dispersion efficiency of graphene nanoplatelets(GNPs)in cement composites.This atomization approach can be integrated with the direct,indirect and combined ultrasonic stirrings in a homemade automatic stirring-atomization device.Mechanical and microstructure tests were performed on hardened cement pastes blended with GNPs in different stirring and mixing approaches.Results show that the direct ultrasonic stirrings enabled more homogeneous dispersions of GNP particles with a smaller size for a longer duration.The atomized droplets with the mean size of~100μm largely mitigated GNPs’agglomerations.Monolayer GNPs were observed in the cement matrix with the strength gain by up to 54%,and the total porosity decrease by 21%in 0.3 wt%GNPs dosage.The greatly enhanced dispersion efficiency of GNPs in cement also raised the cement hydration.This work provides an effective and manpower saving technique toward dispersing CNAs in engineering materials with great industrialization prospects.

Design and optimization of a greener sinomenine hydrochloride preparation process considering variations among different batches of the medicinal herb

The current methods used to industrially produce sinomenine hydrochloride involve several issues,including high solvent toxicity,long process flow,and low atomic utilization efficiency,and the greenness scores of the processes are below 65 points.To solve these problems,a new process using anisole as the extractant was proposed.Anisole exhibits high selectivity for sinomenine and can be connected to the subsequent water-washing steps.After alkalization of the medicinal material,heating extraction,water washing,and acidification crystallization were carried out.The process was modeled and optimized.The design space was constructed.The recommended operating ranges for the critical process parameters were 3.0–4.0 h for alkalization time,60.0–80.0℃ for extraction temperature,2.0–3.0(volume ratio)for washing solution amount,and 2.0–2.4 mol·L^(-1) for hydrochloric acid concentration.The new process shows good robustness because different batches of medicinal materials did not greatly impact crystal purity or sinomenine transfer rate.The sinomenine transfer rate was about 20%higher than that of industrial processes.The greenness score increased to 90 points since the novel process proposed in this research solves the problems of long process flow,high solvent toxicity,and poor atomic economy,better aligning with the concept of green chemistry.

Metabolic reprogramming: a new option for the treatment of spinal cord injury

Spinal cord injuries impose a notably economic burden on society,mainly because of the severe after-effects they cause.Despite the ongoing development of various therapies for spinal cord injuries,their effectiveness remains unsatisfactory.However,a deeper understanding of metabolism has opened up a new therapeutic opportunity in the form of metabolic reprogramming.In this review,we explore the metabolic changes that occur during spinal cord injuries,their consequences,and the therapeutic tools available for metabolic reprogramming.Normal spinal cord metabolism is characterized by independent cellular metabolism and intercellular metabolic coupling.However,spinal cord injury results in metabolic disorders that include disturbances in glucose metabolism,lipid metabolism,and mitochondrial dysfunction.These metabolic disturbances lead to corresponding pathological changes,including the failure of axonal regeneration,the accumulation of scarring,and the activation of microglia.To rescue spinal cord injury at the metabolic level,potential metabolic reprogramming approaches have emerged,including replenishing metabolic substrates,reconstituting metabolic couplings,and targeting mitochondrial therapies to alter cell fate.The available evidence suggests that metabolic reprogramming holds great promise as a next-generation approach for the treatment of spinal cord injury.To further advance the metabolic treatment of the spinal cord injury,future efforts should focus on a deeper understanding of neurometabolism,the development of more advanced metabolomics technologies,and the design of highly effective metabolic interventions.

Effects of surface chlorine atoms on charge distribution and reaction barriers for photocatalytic CO_(2)reduction

Photocatalytic CO_(2)reduction to produce high value-added carbon-based fuel has been proposed as a promising approach to mitigate global warming issues.However,the conversion efficiency and product selectivity are still low due to the sluggish dynamics of transfer processes involved in proton-assisted multi-electron reactions.Lowering the formation energy barriers of intermediate products is an effective method to enhance the selectivity and productivity of final products.In this study,we aim to regulate the surface electronic structure of Bi_(2)WO_(6)by doping surface chlorine atoms to achieve effective photocatalytic CO_(2)reduction.Surface Cl atoms can enhance the absorption ability of light,affect its energy band structure and promote charge separation.Combined with DFT calculations,it is revealed that surface Cl atoms can not only change the surface charge distribution which affects the competitive adsorption of H_(2)O and CO_(2),but also lower the formation energy barrier of intermediate products to generate more intermediate*COOH,thus facilitating CO production.Overall,this study demonstrates a promising surface halogenation strategy to enhance the photocatalytic CO_(2)reduction activity of a layered structure Bi-based catalyst.

The First Reported Case of Co-Infection with Neisseria Meningitidis and Bordetella Pertussis in the Cerebrospinal Fluid Specimen of a Normal Four-Year-Old Child

Pertussis is an acute and highly contagious respiratory disease caused by Bordetella pertussis(B.pertussis),which occurs in people of all ages and is most dangerous for young children,especially infants.The introduction of whole-cell pertussis vaccines(wPVs)in the 1950s dramatically reduced the incidence of pertussis worldwide[1].However,over the past two decades,many studies have reported the resurgence of pertussis in different countries[2].Epidemiological surveillance in Hubei Province over the last 3 years revealed a clear increasing trend in the incidence of pertussis during the coronavirus disease 2019(COVID-19)epidemic.

A novel mouse model of calcific aortic valve stenosis

Background:Calcific aortic valve stenosis(CAVS)is one of the most challenging heart diseases in clinical with rapidly increasing prevalence.However,study of the mecha-nism and treatment of CAVS is hampered by the lack of suitable,robust and efficient models that develop hemodynamically significant stenosis and typical calcium deposi-tion.Here,we aim to establish a mouse model to mimic the development and features of CAVS.Methods:The model was established via aortic valve wire injury(AVWI)combined with vitamin D subcutaneous injected in wild type C57/BL6 mice.Serial transthoracic echocardiography was applied to evaluate aortic jet peak velocity and mean gradi-ent.Histopathological specimens were collected and examined in respect of valve thickening,calcium deposition,collagen accumulation,osteogenic differentiation and inflammation.Results:Serial transthoracic echocardiography revealed that aortic jet peak velocity and mean gradient increased from 7 days post model establishment in a time depend-ent manner and tended to be stable at 28 days.Compared with the sham group,sim-ple AVWI or the vitamin D group,the hybrid model group showed typical pathological features of CAVS,including hemodynamic alterations,increased aortic valve thicken-ing,calcium deposition,collagen accumulation at 28 days.In addition,osteogenic dif-ferentiation,fibrosis and inflammation,which play critical roles in the development of CAVS,were observed in the hybrid model.Conclusions:We established a novel mouse model of CAVS that could be induced efficiently,robustly and economically,and without genetic intervention.It provides a fast track to explore the underlying mechanisms of CAVS and to identify more effec-tive pharmacological targets.

Surplus energy utilization of spent lithium-ion batteries for high-profit organolithiums

It is challenging to efficiently and economically recycle many lithium-ion batteries(LIBs)because of the low valuation of commodity metals and materials,such as LiFePO_(4).There are millions of tons of spent LIBs where the barrier to recycling is economical,and to make recycling more feasible,it is required that the value of the processed recycled material exceeds the value of raw commodity materials.The presented research illustrates improved profitability and economics for recycling spent LIBs by utilizing the surplus energy in lithiated graphite to drive the preparation of organolithiums to add value to the recycled lithium materials.This study methodology demonstrates that the surplus energy of lithiated graphite obtained from spent LIBs can be utilized to prepare high-value organolithiums,thereby significantly improving the economic profitability of LIB recycling.Organolithiums(R-O-Li and R-Li)were prepared using alkyl alcohol(R-OH)and alkyl bromide(R-Br)as substrates,where R includes varying hindered alkyl hydrocarbons.The organolithiums extracted from per kilogram of recycled LIBs can increase the economic value between$29.5 and$226.5 kg^(−1) cell.The value of the organolithiums is at least 5.4 times the total theoretical value of spent materials,improving the profitability of recycling LIBs over traditional pyrometallurgical($0.86 kg^(−1) cell),hydrometallurgical($1.00 kg^(−1) cell),and physical direct recycling methods($5.40 kg^(−1) cell).

Design and optimization of purification process of sinomenine hydrochloride

Sinomenine hydrochloride is generally produced from Caulis Sinomenii. At present, the purification process in industrial production suffers from large amount of solid waste, high solvent toxicity, and low sinomenine hydrochloride yield. In this study, a new purification process for sinomenine hydrochloride was proposed by using the extract obtained from acid extraction of Caulis Sinomenii as the starting material.The process included the following steps: alkalization, extraction, water washing, acid–water stripping,drying, and crystallization. 1-Heptanol was used as the extractant. The distribution coefficients of sinomenine and sinomenine hydrochloride in 1-heptanol–water system were 27.4 and 0.0167, respectively.The dissociation constants of sinomenine hydrochloride were 8.27 and 11.24, respectively. Process parameters of the new purification process were optimized with experimental design. The extractant1-heptanol and sinomenine hydrochloride in the crystallization mother solution can be recycled in the new process. The purity of the obtained sinomenine hydrochloride crystals exceeded 85%, and the yield was about 70%. Compared with current industrial processes, safer extractant, less solid waste, and higher sinomenine hydrochloride yield can be achieved using the new purification process of sinomenine hydrochloride provided in this study.

Efficient, continuous oxidation of durene to pyromellitic dianhydride mediated by a V-Ti-P ternary catalyst: The remarkable doping effect

Continuous preparation of pyromellitic dianhydride(PMDA) from durene has been studied using a fixedbed reactor. The reaction was performed using a phosphorus-vanadium-titanium ternary catalyst.Relatively high selectivity and yield of PMDA was obtained. The in-situ characterization was combined with theoretical calculation to reveal the reaction mechanisms, and the remarkable doping effect was discussed.

Benidipine-loaded nanoflower-likemagnesium silicate improves bone regeneration

Regeneration and reconstruction of bone tissue is always a challenge for clinicians due to the uncertainty of bone repair materials in terms of long-term and efficient effects on osteoblasts.Here,we propose a novel strategy combining benidipine,an antihypertensive drug and nanoparticles to synergistically promote the healing of bone defects.Loose and porous benidipine-loaded magnesium silicate nanoparticles were prepared and validated for their biosafety.The nanoparticles were efficiently taken up by preosteoblasts and uniformly distributed around the nucleus.After internalization into cells,the nanosystem is degraded by lysosomes,and the effect of promoting osteogenic differentiation is reflected by the continuous release of benidipine,silicon and magnesium ions.Our results clearly evaluated that the nanoflower-like magnesium silicate delivering benidipine tends to be more appropriate for the bone regeneration in preosteoblasts,indicating that it might be a potential approach in guiding bone repair in clinical applications.

Experience of Overseas Countryside Development and Construction of “Beautiful Countryside” in Zhejiang

Countryside development paths and phase characters of typical developed countries and regions were analyzed,such as the East Asian Model(Japan and South Korea),and Western European Model(Germany and the Netherlands).The former is based on the big gap between urban and rural development,and the latter is based on the balanced development of urban and rural areas,both of them achieved the world’s leading level of countryside construction.In Zhejiang Province,"China’s Beautiful Countryside"represented by Anji,and"Zhejiang Green Agricultural Product Base"represented by Xianju emerged in the county level.Motivation mechanisms for countryside development in China and abroad were analyzed,including industrial system,infrastructure,ecological environment,and local culture.

Seasonal variation of the shape and location of the Luzon cold eddy

Using observational data from multiple satellites,we studied seasonal variations of the shape and location of the Luzon cold eddy(LCE)northwest of Luzon Island.The shape and location of the LCE have obvious seasonal variations.The LCE occurs,develops,and disappears from December to April of the next year.During this period,the shape of the LCE changed from a flat ellipse to a circular ellipse,and the change in shape can be reflected by the increase of the ellipticity of the LCE from 0.16 to 0.82.The latitude of center location of the LCE changes from 17.4°N to 19°N,and the change in latitude can reach 1.6°.Further study showed that seasonal variation of the northeast monsoon intensity leads to the change in the shape and location of the LCE.The seasonal variation of the LCE shape can significantly alter the spatial distribution of the thermal front and chlorophyll a northwest of the Luzon Island by geostrophic advection.

Allelic functional variation of FimH among Salmonella enterica subspecies

Salmonella enterica has a wide diversity,with numerous serovars belonging to six different subspecies with dynamic animal-host tropism.The FimH protein is the adhesin mediating binding to various cells,and slight amino acid discrepancy significantly affects the adherence capacities.To date,the general function of FimH variability across dif-ferent subspecies of Salmonella enterica has not been addressed.To investigate the biological functions of FimH among the six Salmonella enterica subspecies,the present study performed several assays to determine biofilm for-mation,Caenorhabditis elegans killing,and intestinal porcine enterocyte cell IPEC-J2 adhesion by using various FimH allele mutants.In general,allelic mutations in both the lectin and pilin domains of FimH could cause changes in bind-ing affnity,such as the N79S mutation.We also observed that the N79S variation in Salmonella Dublin increased the adhesive ability of IPEC-J2 cells.Moreover,a new amino acid substitution,T260M,within the pilin domain in one subspecies llb strain beneficial to binding to cells was highlighted in this study,even though the biofilm-forming and Caenorhabditis elegans-killing abilities exhibited no significant differences in variants.Combined with point muta-tions being a natural tendency due to positive selection in harsh environments,we speculate that allelic variation T26oM probably contributes to pathoadaptive evolution in Salmonella enterica subspecies llb.

Single-cell RNA sequencing reveals the dynamics of hepatic non-parenchymal cells in autoprotection against acetaminophen-induced hepatotoxicity

Gaining a better understanding of autoprotection against drug-induced liver injury(DILI)may provide new strategies for its prevention and therapy.However,little is known about the underlying mechanisms of this phenomenon.We used single-cell RNA sequencing to characterize the dynamics and functions of hepatic non-parenchymal cells(NPCs)in autoprotection against DILI,using acetaminophen(APAP)as a model drug.Autoprotection was modeled through pretreatment with a mildly hepatotoxic dose of APAP in mice,followed by a higher dose in a secondary challenge.NPC subsets and dynamic changes were identified in the APAP(hepatotoxicity-sensitive)and APAP-resistant(hepatotoxicity-resistant)groups.A chemokine(C-C motif)ligand 2^(+)endothelial cell subset almost disappeared in the APAP-resistant group,and an R-spondin 3^(+)endothelial cell subset promoted hepatocyte proliferation and played an important role in APAP autoprotection.Moreover,the dendritic cell subset DC-3 may protect the liver from APAP hepatotoxicity by inducing low reactivity and suppressing the autoimmune response and occurrence of inflammation.DC-3 cells also promoted angiogenesis through crosstalk with endothelial cells via vascular endothelial growth factor-associated ligand-receptor pairs and facilitated liver tissue repair in the APAP-resistant group.In addition,the natural killer cell subsets NK-3 and NK-4 and the Sca-1^(-)CD62L^(+)natural killer T cell subset may promote autoprotection through interferon-γ-dependent pathways.Furthermore,macrophage and neutrophil subpopulations with anti-inflammatory phenotypes promoted tolerance to APAP hepatotoxicity.Overall,this study reveals the dynamics of NPCs in the resistance to APAP hepatotoxicity and provides novel insights into the mechanism of autoprotection against DILI at a high resolution.

High-throughput transcriptional profiling of perturbations by Panax ginseng saponins and Panax notoginseng saponins using TCM-seq

Panax ginseng(PG)and Panax notoginseng(PN)are highly valuable Chinese medicines(CM).Although both CMs have similar active constituents,their clinical applications are clearly different.Over the past decade,RNA sequencing(RNA-seq)analysis has been employed to investigate the molecular mechanisms of extracts or monomers.However,owing to the limited number of samples in standard RNA-seq,few studies have systematically compared the effects of PG and PN spanning multiple conditions at the transcriptomic level.Here,we developed an approach that simultaneously profiles transcriptome changes for multiplexed samples using RNA-seq(TCM-seq),a high-throughput,low-cost workflow to molecularly evaluate CM perturbations.A species-mixing experiment was conducted to illustrate the accuracy of sample multiplexing in TCM-seq.Transcriptomes from repeated samples were used to verify the robustness of TCM-seq.We then focused on the primary active components,Panax notoginseng saponins(PNS)and Panax ginseng saponins(PGS)extracted from PN and PG,respectively.We also characterized the transcriptome changes of 10 cell lines,treated with four different doses of PNS and PGS,using TCM-seq to compare the differences in their perturbing effects on genes,functional pathways,gene modules,and molecular networks.The results of transcriptional data analysis showed that the transcriptional patterns of various cell lines were significantly distinct.PGS exhibited a stronger regulatory effect on genes involved in cardiovascular disease,whereas PNS resulted in a greater coagulation effect on vascular endothelial cells.This study proposes a paradigm to comprehensively explore the differences in mechanisms of action between CMs based on transcriptome readouts.

Scalable Electrophysiology of Millimeter-Scale Animals with Electrode Devices

Millimeter-scale animals such as Caenorhabditis elegans,Drosophila larvae,zebrafish,and bees serve as powerful model organisms in the fields of neurobiology and neuroethology.Various methods exist for recording large-scale electrophysiological signals from these animals.Existing approaches often lack,however,real-time,uninterrupted investigations due to their rigid constructs,geometric constraints,and mechanical mismatch in integration with soft organisms.The recent research establishes the foundations for 3-dimensional flexible bioelectronic interfaces that incorporate microfabricated components and nanoelectronic function with adjustable mechanical properties and multidimensional variability,offering unique capabilities for chronic,stable interrogation and stimulation of millimeter-scale animals and miniature tissue constructs.This review summarizes the most advanced technologies for electrophysiological studies,based on methods of 3-dimensional flexible bioelectronics.A concluding section addresses the challenges of these devices in achieving freestanding,robust,and multifunctional biointerfaces.

A Polyvinyl Alcohol/Acrylamide Hydrogel with Enhanced Mechanical Properties Promotes Full-Thickness Skin Defect Healing by Regulating Immunomodulation and Angiogenesis Through Paracrine Secretion

Hydrogel-based tissue-engineered skin has attracted increased attention due to its potential to restore the structural integrity and functionality of skin.However,the mechanical properties of hydrogel scaffolds and natural skin are substantially different.Here,we developed a polyvinyl alcohol(PVA)/acrylamide based interpenetrating network(IPN)hydrogel that was surface modified with polydopamine(PDA)and termed Dopa-gel.The Dopa-gel exhibited mechanical properties similar to native skin tissue and a superior ability to modulate paracrine functions.Furthermore,a tough scaffold with tensile resistance was fabricated using this hydrogel by three-dimensional printing.The results showed that the interpenetration of PVA,alginate,and polyacrylamide networks notably enhanced the mechanical properties of the hydrogel.Surface modification with PDA endowed the hydrogels with increased secretion of immunomodulatory and proangiogenic factors.In an in vivo model,Dopa-gel treatment accelerated wound closure,increased vascularization,and promoted a shift in macrophages from a proinflammatory M1 phenotype to a prohealing and anti-inflammatory M2 phenotype within the wound area.Mechanistically,the focal adhesion kinase(FAK)/extracellular signal-related kinase(ERK)signaling pathway may mediate the promotion of skin defect healing by increasing paracrine secretion via the Dopa-gel.Additionally,proangiogenic factors can be induced through Rho-associated kinase-2(ROCK-2)/vascular endothelial growth factor(VEGF)-mediated paracrine secretion under tensile stress conditions.Taken together,these findings suggest that the multifunctional Dopa-gel,which has good mechanical properties similar to those of native skin tissue and enhanced immunomodulatory and angiogenic properties,is a promising scaffold for skin tissue regeneration.

Differentially private SGD with random features

In the realm of large-scale machine learning,it is crucial to explore methods for reducing computational complexity and memory demands while maintaining generalization performance.Additionally,since the collected data may contain some sensitive information,it is also of great significance to study privacy-preserving machine learning algorithms.This paper focuses on the performance of the differentially private stochastic gradient descent(SGD)algorithm based on random features.To begin,the algorithm maps the original data into a lowdimensional space,thereby avoiding the traditional kernel method for large-scale data storage requirement.Subsequently,the algorithm iteratively optimizes parameters using the stochastic gradient descent approach.Lastly,the output perturbation mechanism is employed to introduce random noise,ensuring algorithmic privacy.We prove that the proposed algorithm satisfies the differential privacy while achieving fast convergence rates under some mild conditions.