Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macro...Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macrophages have been poorly understood and largely overlooked. However, a recent study reported that border-associated macrophages participate in stroke-induced inflammation, although many details and the underlying mechanisms remain unclear. In this study, we performed a comprehensive single-cell analysis of mouse border-associated macrophages using sequencing data obtained from the Gene Expression Omnibus(GEO) database(GSE174574 and GSE225948). Differentially expressed genes were identified, and enrichment analysis was performed to identify the transcription profile of border-associated macrophages. CellChat analysis was conducted to determine the cell communication network of border-associated macrophages. Transcription factors were predicted using the ‘pySCENIC' tool. We found that, in response to hypoxia, borderassociated macrophages underwent dynamic transcriptional changes and participated in the regulation of inflammatory-related pathways. Notably, the tumor necrosis factor pathway was activated by border-associated macrophages following ischemic stroke. The pySCENIC analysis indicated that the activity of signal transducer and activator of transcription 3(Stat3) was obviously upregulated in stroke, suggesting that Stat3 inhibition may be a promising strategy for treating border-associated macrophages-induced neuroinflammation. Finally, we constructed an animal model to investigate the effects of border-associated macrophages depletion following a stroke. Treatment with liposomes containing clodronate significantly reduced infarct volume in the animals and improved neurological scores compared with untreated animals. Taken together, our results demonstrate comprehensive changes in border-associated macrophages following a stroke, providing a theoretical basis for targeting border-associated macrophages-induced neuroinflammation in stroke treatment.展开更多
Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality.Despite advancements in resuscitation science,our limited understanding of the cellular and molecular mecha...Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality.Despite advancements in resuscitation science,our limited understanding of the cellular and molecular mechanisms underlying post-cardiac arrest brain injury have hindered the development of effective neuroprotective strategies.Previous studies primarily focused on neuronal death,potentially overlooking the contributions of non-neuronal cells and intercellular communication to the pathophysiology of cardiac arrest-induced brain injury.To address these gaps,we hypothesized that single-cell transcriptomic analysis could uncover previously unidentified cellular subpopulations,altered cell communication networks,and novel molecular mechanisms involved in post-cardiac arrest brain injury.In this study,we performed a single-cell transcriptomic analysis of the hippocampus from pigs with ventricular fibrillation-induced cardiac arrest at 6 and 24 hours following the return of spontaneous circulation,and from sham control pigs.Sequencing results revealed changes in the proportions of different cell types,suggesting post-arrest disruption in the blood-brain barrier and infiltration of neutrophils.These results were validated through western blotting,quantitative reverse transcription-polymerase chain reaction,and immunofluorescence staining.We also identified and validated a unique subcluster of activated microglia with high expression of S100A8,which increased over time following cardiac arrest.This subcluster simultaneously exhibited significant M1/M2 polarization and expressed key functional genes related to chemokines and interleukins.Additionally,we revealed the post-cardiac arrest dysfunction of oligodendrocytes and the differentiation of oligodendrocyte precursor cells into oligodendrocytes.Cell communication analysis identified enhanced post-cardiac arrest communication between neutrophils and microglia that was mediated by neutrophil-derived resistin,driving pro-inflammatory microglial polarization.Our findings provide a comprehensive single-cell map of the post-cardiac arrest hippocampus,offering potential novel targets for neuroprotection and repair following cardiac arrest.展开更多
As an important resource in data link,time slots should be strategically allocated to enhance transmission efficiency and resist eavesdropping,especially considering the tremendous increase in the number of nodes and ...As an important resource in data link,time slots should be strategically allocated to enhance transmission efficiency and resist eavesdropping,especially considering the tremendous increase in the number of nodes and diverse communication needs.It is crucial to design control sequences with robust randomness and conflict-freeness to properly address differentiated access control in data link.In this paper,we propose a hierarchical access control scheme based on control sequences to achieve high utilization of time slots and differentiated access control.A theoretical bound of the hierarchical control sequence set is derived to characterize the constraints on the parameters of the sequence set.Moreover,two classes of optimal hierarchical control sequence sets satisfying the theoretical bound are constructed,both of which enable the scheme to achieve maximum utilization of time slots.Compared with the fixed time slot allocation scheme,our scheme reduces the symbol error rate by up to 9%,which indicates a significant improvement in anti-interference and eavesdropping capabilities.展开更多
The occurrence of severe thalassemia,an inherited blood disorder that is either blood-transfusiondependent or fatal,can be mitigated through carrier screening.Here,we aim to evaluate the effectiveness and outcomes of ...The occurrence of severe thalassemia,an inherited blood disorder that is either blood-transfusiondependent or fatal,can be mitigated through carrier screening.Here,we aim to evaluate the effectiveness and outcomes of pre-conceptional and early pregnancy screening initiatives for severe thalassemia prevention in a diverse population of 28,043 women.Using next-generation sequencing(NGS),we identify 4,226(15.07%)thalassemia carriers across 29 ethnic groups and categorize them into high-(0.75%),low-(25.86%),and unknown-risk(69.19%)groups based on their spouses'screening results.Post-screening follow-up reveals 59 fetuses with severe thalassemia exclusively in high-risk couples,underscoring the efficacy of risk classification.Among 25,053 live births over 6 months of age,two severe thalassemia infants were born to unknown-risk couples,which was attributed to incomplete screening and late NGS-based testing for a rare variant.Notably,64 rare variants are identified in 287 individuals,highlighting the genetic heterogeneity of thalassemia.We also observe that migrant flow significantly impacts carrier rates,with 93.90%of migrants to Chenzhou originating from high-prevalence regions in southern China.Our study demonstrates that NGS-based screening during pre-conception and early pregnancy is effective for severe thalassemia prevention,emphasizing the need for continuous screening efforts in areas with high and underestimated prevalence.展开更多
This study establishes and validates a method for the precise quantification of aquatic microbial loads using microbial diversity absolute quantitative sequencing.By adding synthetic spike-in DNA to water samples from...This study establishes and validates a method for the precise quantification of aquatic microbial loads using microbial diversity absolute quantitative sequencing.By adding synthetic spike-in DNA to water samples from the Dahei River prior to DNA extraction and 16S rRNA gene sequencing,it generates standard curves to convert sequencing data into absolute microbial copy numbers.The method,which is proved highly accurate(R^(2)>0.99),reveals a clear contrast between the river sites:the upstream community has not only a significantly higher total microbial load but also a completely different makeup of species compared to the downstream site.This approach effectively overcomes the limitations of relative abundance analysis,providing a powerful tool for environmental monitoring,and proposes key steps for future standardization to ensure data comparability and integration.展开更多
We are sorry for the mistakes of Affiliation,"a State Key Laboratory of Advanced Fiber Materials,Center for Advanced Low-Dimension Materials,Donghua University,Shanghai 201620,China"should be replaced by&quo...We are sorry for the mistakes of Affiliation,"a State Key Laboratory of Advanced Fiber Materials,Center for Advanced Low-Dimension Materials,Donghua University,Shanghai 201620,China"should be replaced by"a State Key Laboratory of Advanced Fiber Materials,Center for Advanced Low-Dimension Materials,College of Materials Science and Engineering,Donghua University,Shanghai 201620,China".We apologized for the inconvenience caused by this error.展开更多
The Ordos Basin is a large superimposed hydrocarbon-bearing basin in China,and further research on the sedimentary characteristics and sedimentary evolution of the sequence framework of target layers is of great theor...The Ordos Basin is a large superimposed hydrocarbon-bearing basin in China,and further research on the sedimentary characteristics and sedimentary evolution of the sequence framework of target layers is of great theoretical and practical significance for guiding oil and gas exploration.The sedimentary facies and sedimentary evolution of the high-resolution sequence framework of the Carboniferous Taiyuan Formation in the Hangjinqi area have been systematically analyzed for the first time by drilling,logging and seismic data.The results show that four types of sequence interfaces can be identified in the Taiyuan Formation:regional unconformity surfaces,scour surfaces,lithologic-lithofacies transformation surfaces and flooding surfaces.According to the sedimentary response caused by the upward and downward movements of the base level at different levels,the Taiyuan Formation can be divided into 2 long-term cycles(LSC_(1)-LSC_(2)),4 mid-term cycles(MSC_(1)-MSC4)and 7 short-term cycles(SSC_(1)-SSC7).The long-and mid-term cycles correspond to members T_(1)and T_(2)and layers T_(1)-1,T_(1-2),T_(2-1),and T_(2)-2,respectively.Long-term cycles are dominated by C_(1);mid-term cycles are dominated by C_(1)and C_(2),followed by A2;and short-term cycles are dominated by C_(1),C_(2),A1 and A2.Under the high-resolution sequence stratigraphic framework,the Hangjinqi area underwent a transformation of fan delta and tidal flat depositional systems during the Taiyuan Formation sedimentary period.In the MSC_(1)-MSC_(2)stage,owing to a large-scale paleocontinent,the fan delta sedimentary body,which was limited in scale and scope,developed only in the southeastern corner and gradually transitioned basinward to tidal flat facies.In the MSC3-MSC4 stage,as the paleocontinent continuously decreased and the sedimentary range expanded,fan-delta plain sedimentation began in the study area.Several braided distributary channels with poor connectivity developed on the fan-delta plain,and between them were floodplains and peat swamps.展开更多
Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches...Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.展开更多
The Fujian oyster(Crassostrea angulata)is an economically significant shellfish species distributed mainly along the Fujian coast,Southeast China.However,its genetic diversity and structure remain unclear.The main dis...The Fujian oyster(Crassostrea angulata)is an economically significant shellfish species distributed mainly along the Fujian coast,Southeast China.However,its genetic diversity and structure remain unclear.The main distribution area of the C.angulata is located in Fujian,South China.In total,420 C.angulata were collected from 14 natural habitats(populations)along the Fujian coast,and their genetic diversity and structure were analyzed in the mitochondrial COⅠand nuclear gene ITS2 sequences.Results reveal that all the 14 populations of C.angulata exhibited high levels of genetic diversity,with a total of 57(haplotype diversity:0.811±0.016)and 124(haplotype diversity:0.912±0.007)haplotypes revealed by COⅠand ITS2,respectively.Notably,significant intermediate level of genetic differentiations between the Ningde Zhujiang(ZJ)population(F_(ST)by COI:0.035-0.142,P<0.05;F_(ST)by ITS2:0.078-0.123,P<0.05)with other populations were observed for the first time,which is also supported by the results of molecular variance analysis(F_(CT)by COⅠ:0.105,P<0.05;F_(CT)by ITS2:0.086,P<0.05)and the clustering of the ZJ population into distinct branches in the interpopulation genetic differentiation tree.Furthermore,the evolutionary tree and haplotype network analyses do not support the formation of a clear geographical genealogical structure among these 14 populations.In addition,the population dynamics analysis suggests that the C.angulata may have undergone expansion during the third ice age of the Pleistocene.These results provide a reference for the preservation and further genetic improvement of C.angulata.展开更多
Few studies have investigated alterations in the immune cell microenvironment of the dorsal root ganglia following spinal cord injury and whether these modifications facilitate axonal regeneration.In this study,we use...Few studies have investigated alterations in the immune cell microenvironment of the dorsal root ganglia following spinal cord injury and whether these modifications facilitate axonal regeneration.In this study,we used a single-cell RNA sequencing dataset to create a comprehensive profile of the diverse cell types in the dorsal root ganglia and spinal cord of a mid-thoracic contusion injury model in cynomolgus monkeys.Cell communication analysis indicated that specific signaling events among various dorsal root ganglia cell types occur in response to spinal cord injury.Single-cell analysis using dimensionality reduction clustering identified distinct molecular signatures for nine cell types,including macrophage subpopulations,and differential gene expression profiles between dorsal root ganglia cells and spinal cord cells following spinal cord injury.The macrophage subpopulations were categorized into 11 clusters(MC0-MC10)based on differentially expressed genes,with the top 10 genes being ABCA6,RBMS3,EBF1,LAMA4,ANTXR2,LAMA2,SOX5,FOXP2,GHR,and APOD.MC0,MC1,and MC2 constituted the predominant macrophage populations.MC4,MC6,and MC9 were nearly absent in the spinal cord,but exhibited significant increases in the dorsal root ganglia post-spinal cord injury.Notably,these subpopulations possess a strong capacity for regulating axonal regeneration.The developmental progression of dorsal root ganglia macrophages after spinal cord injury was elucidated using cell trajectory and pseudo-time analyses.Genes such as EBF1(MC6 and MC9 marker),RBMS3(MC6 and MC9 marker),and ABCA6(MC6 marker)showed high expression levels in the critical pathways of macrophage function.Through ligand-receptor pair analysis,we determined that the effects of macrophages on microglia are predominantly mediated through interaction pairs(e.g.,SPP1-CD44,LAMC1-CD44,and FN1-CD44),potentially facilitating specific cellular communications within the immune microenvironment.The single-cell RNA sequencing dataset used in this study represents the first comprehensive transcriptional analysis of the dorsal root ganglia after spinal cord injury in cynomolgus monkeys,encompassing nearly all cell types within the dorsal root ganglia region.Using this dataset,we evaluated diverse subtypes of macrophages in the post-spinal cord injury dorsal root ganglia area and examined the signaling pathways that facilitate interactions among immune response-related macrophages in the dorsal root ganglia.Findings from this study provide a theoretical basis for understanding how the immune microenvironment influences the regenerative capacity of dorsal root ganglia neurons after spinal cord injury and offer novel insights into the complex processes underlying the pathobiology of spinal cord injury.展开更多
Hyperpolarization of nuclear spins is crucial for advancing nuclear magnetic resonance and quantum information technologies,as nuclear spins typically exhibit extremely low polarization at room temperature due to thei...Hyperpolarization of nuclear spins is crucial for advancing nuclear magnetic resonance and quantum information technologies,as nuclear spins typically exhibit extremely low polarization at room temperature due to their small gyromagnetic ratios.A promising approach to achieving high nuclear spin polarization is transferring the polarization of electrons to nuclear spins.The nitrogen-vacancy(NV)center in diamond has emerged as a highly effective medium for this purpose,and various hyperpolarization protocols have been developed.Among these,the pulsed polarization(PulsePol)method has been extensively studied due to its robustness against static energy shifts of the electron spin.In this work,we present a novel polarization protocol and uncover a family of magic sequences for hyperpolarizing nuclear spins,with PulsePol emerging as a special case of our general approach.Notably,we demonstrate that some of these magic sequences exhibit significantly greater robustness compared to the PulsePol protocol in the presence of finite half𝜋pulse duration of the protocol,Rabi and detuning errors.This enhanced robustness positions our protocol as a more suitable candidate for hyper-polarizing nuclear spins species with large gyromagnetic ratios and also ensures better compatibility with high-efficiency readout techniques at high magnetic fields.Additionally,the generality of our protocol allows for its direct application to other solid-state quantum systems beyond the NV center.展开更多
In industrial control systems,such as power transmission facilities and water treatment plants,Programmable Logic Controllers(PLCs)can work consistently and stably over long periods if there are no faults.Black-box id...In industrial control systems,such as power transmission facilities and water treatment plants,Programmable Logic Controllers(PLCs)can work consistently and stably over long periods if there are no faults.Black-box identification aims to automatically construct Petri net models with the help of I/O signals from PLC devices only.The main challenge is how to convert the infinitely long PLC signals into an event sequence,which is the foundation for subsequent modeling.The current algorithms are confronted with a number of challenges,including an exponential increase in the number of transitions,high time complexity,and susceptibility to noisy signals.To solve these problems,this paper proposes a new method for converting PLC signals into a transition sequence.The method is based on the principles of Boolean absorption law,which filters out noise information in the I/O signals.Then firing functions representing input–output causality are constructed from the filtered signals.Finally,the original signal sequence is traversed to generate a transition sequence.The experimental results show that these methods can rapidly identify a transition sequence.Compared to traditional methods,the proposed algorithms have polynomial time complexity.展开更多
An accurate assessment of host and pathogen gene expression during infection is critical for understanding the molecular aspects of host-pathogen interactions.Often,pathogen-derived transcripts are difficult to ascert...An accurate assessment of host and pathogen gene expression during infection is critical for understanding the molecular aspects of host-pathogen interactions.Often,pathogen-derived transcripts are difficult to ascertain at early infection stages owing to the unfavourable transcript representation compared to the host genes.In this study,we compare two sequencing techniques,RNAseq and enrichment sequencing(RenSeq and PenSeq)of cDNA,to investigate gene expression patterns in the doubled monoploid potato(DM)infected with the late blight pathogen Phytophthora infestans.Our results reveal distinct advantages of cDNA RenSeq and PenSeq over traditional RNAseq in terms of target gene representation and transcriptional quantification at early infection stages.Throughout the infection time course,cDNA enrichment sequencing enables transcriptomic analyses for more targeted host and pathogen genes.For highly expressed genes that were sampled in parallel by both cDNA enrichment and RNAseq,a high level of concordance in expression profiles is observed,indicative of at least semi-quantitative gene expression representation following enrichment.展开更多
Genotyping by target sequencing(GBTS)integrates the advantages of silicon-based technology(high stability and reliability)and genotyping by sequencing(high flexibility and cost-effectiveness).However,GBTS panels are n...Genotyping by target sequencing(GBTS)integrates the advantages of silicon-based technology(high stability and reliability)and genotyping by sequencing(high flexibility and cost-effectiveness).However,GBTS panels are not currently available in pigs.In this study,based on GBTS technology,we first developed a 50K panel,including 52,000 single-nucleotide polymorphisms(SNPs),in pigs,designated GBTS50K.A total of 6,032 individuals of Large White,Landrace,and Duroc pigs from 10 breeding farms were used to assess the newly developed GBTS50K.Our results showed that GBTS50K obtained a high genotyping ability,the SNP and individual call rates of GBTS50K were 0.997–0.998,and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993,respectively,in replicate samples.We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis,selection signature detection,genome-wide association studies(GWAS),genotyped imputation,genetic selection(GS),etc.The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding.For example,GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs.Particularly,due to the multiple SNPs(mSNPs),GBTS50K generated 100K qualified SNPs without increasing genotyping cost,and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%.Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs,and it is also helpful for developing SNP panels for other farm animals.展开更多
The Fushan Depression is one of the petroliferous depressions in the Beibuwan Basin,South China Sea.Previous studies have preliminarily explored the origin and source of crude oils in some areas of this depression.Nev...The Fushan Depression is one of the petroliferous depressions in the Beibuwan Basin,South China Sea.Previous studies have preliminarily explored the origin and source of crude oils in some areas of this depression.Nevertheless,no systematic investigations on the classification and origin of oils and hy-drocarbon migration processes have been made for the entire petroleum system in this depression,which has significantly hindered the hydrocarbon exploration in the region.A total of 32 mudstone and 58 oil samples from the Fushan Depression were analyzed to definite the detailed oil-source correlation within the sequence and sedimentary framework.The organic matter of third member of Paleogene Liushagang Formation(Els(3))source rocks,both deltaic and lacustrine mudstone,are algal-dominated with high abundance of C_(23)tricyclic terpane and C_(30)4-methylsteranes.The deltaic source rocks occur-ring in the first member(Els_(1))and second member(Els_(2))of the Paleogene Liushagang Formation are characterized by high abundance of C_(19+20)tricyclic terpane and oleanane,reflecting a more terrestrial plants contribution.While lacustrine source rocks of Els_(1)and Els_(2)display the reduced input of terrige-nous organic matter with relatively low abundance of C 19+20 tricyclic terpane and oleanane.Three types of oils were identified by their biomarker compositions in this study.Most of the oils discovered in the Huachang and Bailian Els_(1)reservoir belong to group A and were derived from lacustrine source rocks of Els_(1)and Els_(2).Group B oils are found within the Els_(1)and Els_(2)reservoirs,showing a close relation to the deltaic source rocks of Els_(1)and Els_(2),respectively.Group C oils,occurring in the Els3 reservoirs,have a good affinity with the Els3 source rocks.The spatial distribution and accumulation of different groups of oils are mainly controlled by the sedimentary facies and specific structural conditions.The Els_(2)reservoir in the Yong'an area belonging to Group B oil,are adjacent to the source kitchen and could be considered as the favorable exploration area in the future.展开更多
BACKGROUND The gastric microbiome is closely associated with gastric cancer,and single-region 16S rRNA sequencing has limitations in analyzing its characteristics,necessitating the search for a better sequencing metho...BACKGROUND The gastric microbiome is closely associated with gastric cancer,and single-region 16S rRNA sequencing has limitations in analyzing its characteristics,necessitating the search for a better sequencing method.AIM To evaluate the effectiveness of multi-region 16S rRNA gene sequencing in studying the microbiome of gastric cancer tissues.METHODS Patients with gastric cancer(n=118)who underwent surgery at Liyang People's Hospital from January 2022 to December 2024 were enrolled.Fifty-nine paraffinembedded and 59 fresh tissue samples were obtained.The ZymoBIOMICSTM microbial community standard and Escherichia coli ATCC 25922 were used as positive controls.Multi-region and single-region 16S rRNA gene sequencing were performed.Species identification,detection rates at varying microbial abundances,operational taxonomic unit(OTU)counts,and alpha diversity indices in gastric cancer tissues were compared between the two methods.RESULTS Multi-region 16S rRNA sequencing identified more species(eight species and eight genera)in the positive controls compared with single-region sequencing(one species and six genera).Detection rates at concentrations of 103,102,and 10 CFU/mg were significantly higher using multi-region sequencing(P<0.05).Multi-region sequencing also revealed significantly higher OTU counts and alpha diversity indices(Shannon,Simpson,and Chao1)in gastric cancer tissues(P<0.05).CONCLUSION Compared with single-region sequencing,multi-region 16S rRNA gene sequencing demonstrates superior species resolution and detection sensitivity,providing a more comprehensive profile of microbial diversity in gastric cancer tissues.展开更多
BACKGROUND Adenomatous polyposis confers an increased risk of developing colorectal cancer.APC and MUTYH are the major genes investigated in patients suspected of having polyposis.In addition to APC and MUTYH genes,ot...BACKGROUND Adenomatous polyposis confers an increased risk of developing colorectal cancer.APC and MUTYH are the major genes investigated in patients suspected of having polyposis.In addition to APC and MUTYH genes,other genes,such as POLE,POLD1,NTHL1,MBD4,MSH3 and MLH3,have recently been associated with polyposis phenotypes,conferring heterogeneity in terms of the clinical,etiological and heritable aspects of patients with polyposis.AIM To investigate the underlying variant landscape in patients with suspected polyposis who lack variants in the APC and MUTYH genes using whole-exome sequencing.METHODS Twenty-seven participants were included in the study and subjected to germline whole-exome sequencing.In addition,their clinical-pathological,personal,and family history data were collected.RESULTS The mean age at diagnosis was 51 years,and most participants had attenuated forms of polyposis(88.9%),with 63.0%diagnosed with a primary tumor,mostly colorectal cancer(76.5%).Among the variants identified,17 were classified as pathogenic or likely pathogenic(in 12 participants),including variants in genes involved in the Wnt/β-catenin signaling pathway,such as ST7 L,A1CF,and DKK4,and variants in DNA-repair genes,such as NTHL1,PNKP,and PMS2,as well as a variant found at the FRK gene identified in a patient with classic polyposis at age 19 and with a family history of polyps.CONCLUSION This study identified novel genes potentially associated with polyposis in patients lacking germline pathogenic variants in the APC and MUTYH genes.These findings support the use of next-generation sequencing for screening,expanding the scope of polyposis-related variants beyond these two genes.展开更多
Based on the experimental results of casting thin section,low temperature nitrogen adsorption,high pressure mercury injection,nuclear magnetic resonance T2 spectrum,contact angle and oil-water interfacial tension,the ...Based on the experimental results of casting thin section,low temperature nitrogen adsorption,high pressure mercury injection,nuclear magnetic resonance T2 spectrum,contact angle and oil-water interfacial tension,the relationship between pore throat structure and crude oil mobility characteristics of full particle sequence reservoirs in the Lower Permian Fengcheng Formation of Mahu Sag,Junggar Basin,are revealed.(1)With the decrease of reservoir particle size,the volume of pores connected by large throats and the volume of large pores show a decreasing trend,and the distribution and peak ranges of throat and pore radius shift to smaller size in an orderly manner.The upper limits of throat radius,porosity and permeability of unconventional reservoirs in Fengcheng Formation are approximately 0.7μm,8%and 0.1×10^(−3)μm^(2),respectively.(2)As the reservoir particle size decreases,the distribution and peak ranges of pores hosting retained oil and movable oil are shifted to a smaller size in an orderly manner.With the increase of driving pressure,the amount of retained and movable oil of the larger particle reservoir samples shows a more obvious trend of decreasing and increasing,respectively.(3)With the increase of throat radius,the driving pressure of reservoir with different particle levels presents three stages,namely rapid decrease,slow decrease and stabilization.The oil driving pressures of various reservoirs and the differences of them decrease with the increase of temperature and obviously decrease with the increase of throat radius.According to the above experimental analysis,it is concluded that the deep shale oil of Fengcheng Formation in Mahu Sag has great potential for production under geological conditions.展开更多
In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology bas...In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology based on the principle of high-throughput sequencing,and established a multi-locus 10 animalderived components identification method of cattle,goat,sheep,donkey,horse,chicken,duck,goose,pigeon,quail in meat and meat products.The specific loci of each species could be detected and the species could be accurately identified,including 5 loci for cattle and duck,3 loci for sheep,9 loci for chicken and horse,10 loci for goose and pigeon,6 loci for quail and 1 locus for donkey and goat,and an adulteration model was established to simulate commercially available samples.The results showed that the method established in this study had high throughput,good repeatability and accuracy,and was able to identify 10 animalderived components simultaneously with 100%repeatability accuracy.The detection limit was 0.1%(m/m)in simulated samples of chicken,duck and horse.Using the method established in this study to test commercially available samples,4 samples from 14 commercially available samples were detected to be inconsistent with the labels,of which 2 did not contain the target ingredient and 2 were adulterated with small amounts of other ingredients.展开更多
To address the discrepancies between well and seismic data in stratigraphic correlation of the Triassic Yanchang Formation in the Ordos Basin,NW China,traditional stratigraphic classification schemes,the latest 3D sei...To address the discrepancies between well and seismic data in stratigraphic correlation of the Triassic Yanchang Formation in the Ordos Basin,NW China,traditional stratigraphic classification schemes,the latest 3D seismic and drilling data,and reservoir sections are thoroughly investigated.Guided by the theory of sequence stratigraphy,the progradational sequence stratigraphic framework of the Yanchang Formation is systematically constructed to elucidate new deposition mechanisms in the depressed lacustrine basin,and it has been successfully applied to the exploration and development practices in the Qingcheng Oilfield.Key findings are obtained in three aspects.First,the seismic progradational reflections,marker tuff beds,and condensed sections of flooding surfaces in the Yanchang Formation are consistent and isochronous.Using flooding surface markers as a reference,a progradational sequence stratigraphic architecture is reconstructed for the middle-upper part of Yanchang Formation,and divided into seven clinoform units(CF1-CF7).Second,progradation predominantly occurs in semi-deep to deep lake environments,with the depositional center not always coinciding with the thickest strata.The lacustrine basin underwent an evolution of“oscillatory regression-progradational infilling-multi-phase superimposition”.Third,the case study of Qingcheng Oilfield reveals that the major pay zones consist of“isochronous but heterochronous”gravity-flow sandstone complexes.Guided by the progradational sequence stratigraphic architecture,horizontal well oil-layer penetration rates remain above 82%.The progradational sequence stratigraphic architecture and associated geological insights are more consistent with the sedimentary infilling mechanisms of large-scale continental depressed lacustrine basins and actual drilling results.The research results provide crucial theoretical and technical support for subsequent refined exploration and development of the Yanchang Formation,and are expected to offer a reference for research and production practice in similar continental lacustrine basins.展开更多
基金supported by Qingdao Key Medical and Health Discipline ProjectThe Intramural Research Program of the Affiliated Hospital of Qingdao University,No. 4910Qingdao West Coast New Area Science and Technology Project,No. 2020-55 (all to SW)。
文摘Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macrophages have been poorly understood and largely overlooked. However, a recent study reported that border-associated macrophages participate in stroke-induced inflammation, although many details and the underlying mechanisms remain unclear. In this study, we performed a comprehensive single-cell analysis of mouse border-associated macrophages using sequencing data obtained from the Gene Expression Omnibus(GEO) database(GSE174574 and GSE225948). Differentially expressed genes were identified, and enrichment analysis was performed to identify the transcription profile of border-associated macrophages. CellChat analysis was conducted to determine the cell communication network of border-associated macrophages. Transcription factors were predicted using the ‘pySCENIC' tool. We found that, in response to hypoxia, borderassociated macrophages underwent dynamic transcriptional changes and participated in the regulation of inflammatory-related pathways. Notably, the tumor necrosis factor pathway was activated by border-associated macrophages following ischemic stroke. The pySCENIC analysis indicated that the activity of signal transducer and activator of transcription 3(Stat3) was obviously upregulated in stroke, suggesting that Stat3 inhibition may be a promising strategy for treating border-associated macrophages-induced neuroinflammation. Finally, we constructed an animal model to investigate the effects of border-associated macrophages depletion following a stroke. Treatment with liposomes containing clodronate significantly reduced infarct volume in the animals and improved neurological scores compared with untreated animals. Taken together, our results demonstrate comprehensive changes in border-associated macrophages following a stroke, providing a theoretical basis for targeting border-associated macrophages-induced neuroinflammation in stroke treatment.
基金supported by the National Science Foundation of China,Nos.82325031(to FX),82030059(to YC),82102290(to YG),U23A20485(to YC)Noncommunicable Chronic Diseases-National Science and Technology Major Project,No.2023ZD0505504(to FX),2023ZD0505500(to YC)the Key R&D Program of Shandong Province,No.2022ZLGX03(to YC).
文摘Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality.Despite advancements in resuscitation science,our limited understanding of the cellular and molecular mechanisms underlying post-cardiac arrest brain injury have hindered the development of effective neuroprotective strategies.Previous studies primarily focused on neuronal death,potentially overlooking the contributions of non-neuronal cells and intercellular communication to the pathophysiology of cardiac arrest-induced brain injury.To address these gaps,we hypothesized that single-cell transcriptomic analysis could uncover previously unidentified cellular subpopulations,altered cell communication networks,and novel molecular mechanisms involved in post-cardiac arrest brain injury.In this study,we performed a single-cell transcriptomic analysis of the hippocampus from pigs with ventricular fibrillation-induced cardiac arrest at 6 and 24 hours following the return of spontaneous circulation,and from sham control pigs.Sequencing results revealed changes in the proportions of different cell types,suggesting post-arrest disruption in the blood-brain barrier and infiltration of neutrophils.These results were validated through western blotting,quantitative reverse transcription-polymerase chain reaction,and immunofluorescence staining.We also identified and validated a unique subcluster of activated microglia with high expression of S100A8,which increased over time following cardiac arrest.This subcluster simultaneously exhibited significant M1/M2 polarization and expressed key functional genes related to chemokines and interleukins.Additionally,we revealed the post-cardiac arrest dysfunction of oligodendrocytes and the differentiation of oligodendrocyte precursor cells into oligodendrocytes.Cell communication analysis identified enhanced post-cardiac arrest communication between neutrophils and microglia that was mediated by neutrophil-derived resistin,driving pro-inflammatory microglial polarization.Our findings provide a comprehensive single-cell map of the post-cardiac arrest hippocampus,offering potential novel targets for neuroprotection and repair following cardiac arrest.
基金supported by the National Science Foundation of China(No.62171387)the Science and Technology Program of Sichuan Province(No.2024NSFSC0468)the China Postdoctoral Science Foundation(No.2019M663475).
文摘As an important resource in data link,time slots should be strategically allocated to enhance transmission efficiency and resist eavesdropping,especially considering the tremendous increase in the number of nodes and diverse communication needs.It is crucial to design control sequences with robust randomness and conflict-freeness to properly address differentiated access control in data link.In this paper,we propose a hierarchical access control scheme based on control sequences to achieve high utilization of time slots and differentiated access control.A theoretical bound of the hierarchical control sequence set is derived to characterize the constraints on the parameters of the sequence set.Moreover,two classes of optimal hierarchical control sequence sets satisfying the theoretical bound are constructed,both of which enable the scheme to achieve maximum utilization of time slots.Compared with the fixed time slot allocation scheme,our scheme reduces the symbol error rate by up to 9%,which indicates a significant improvement in anti-interference and eavesdropping capabilities.
基金supported by the National Natural Science Foundation of China(81760037)Yunling Scholar Project of Yunnan Province(YNWR-YLXZ-2019-0005)+1 种基金Hunan Provincial Innovation Platform and Talent Program(2018SK4004)Hunan Provincial Natural Science Foundation(2019JJ80048).
文摘The occurrence of severe thalassemia,an inherited blood disorder that is either blood-transfusiondependent or fatal,can be mitigated through carrier screening.Here,we aim to evaluate the effectiveness and outcomes of pre-conceptional and early pregnancy screening initiatives for severe thalassemia prevention in a diverse population of 28,043 women.Using next-generation sequencing(NGS),we identify 4,226(15.07%)thalassemia carriers across 29 ethnic groups and categorize them into high-(0.75%),low-(25.86%),and unknown-risk(69.19%)groups based on their spouses'screening results.Post-screening follow-up reveals 59 fetuses with severe thalassemia exclusively in high-risk couples,underscoring the efficacy of risk classification.Among 25,053 live births over 6 months of age,two severe thalassemia infants were born to unknown-risk couples,which was attributed to incomplete screening and late NGS-based testing for a rare variant.Notably,64 rare variants are identified in 287 individuals,highlighting the genetic heterogeneity of thalassemia.We also observe that migrant flow significantly impacts carrier rates,with 93.90%of migrants to Chenzhou originating from high-prevalence regions in southern China.Our study demonstrates that NGS-based screening during pre-conception and early pregnancy is effective for severe thalassemia prevention,emphasizing the need for continuous screening efforts in areas with high and underestimated prevalence.
基金supported by the National Natural Science Foundation of China(Grant No.32160172)the Key Science-Technology Project of Inner Mongolia(2023KYPT0010)+1 种基金the Natural Science Foundation of Inner Mongolia Autonomous Region of China(Grant No.2025QN03006)the 2023 Inner Mongolia Public Institution High-level Talent Introduction Scientific Research Support Project.
文摘This study establishes and validates a method for the precise quantification of aquatic microbial loads using microbial diversity absolute quantitative sequencing.By adding synthetic spike-in DNA to water samples from the Dahei River prior to DNA extraction and 16S rRNA gene sequencing,it generates standard curves to convert sequencing data into absolute microbial copy numbers.The method,which is proved highly accurate(R^(2)>0.99),reveals a clear contrast between the river sites:the upstream community has not only a significantly higher total microbial load but also a completely different makeup of species compared to the downstream site.This approach effectively overcomes the limitations of relative abundance analysis,providing a powerful tool for environmental monitoring,and proposes key steps for future standardization to ensure data comparability and integration.
文摘We are sorry for the mistakes of Affiliation,"a State Key Laboratory of Advanced Fiber Materials,Center for Advanced Low-Dimension Materials,Donghua University,Shanghai 201620,China"should be replaced by"a State Key Laboratory of Advanced Fiber Materials,Center for Advanced Low-Dimension Materials,College of Materials Science and Engineering,Donghua University,Shanghai 201620,China".We apologized for the inconvenience caused by this error.
基金supported by the Fundamental Research Funds for the Liaoning Universities(Grant No.LJ202410166012).
文摘The Ordos Basin is a large superimposed hydrocarbon-bearing basin in China,and further research on the sedimentary characteristics and sedimentary evolution of the sequence framework of target layers is of great theoretical and practical significance for guiding oil and gas exploration.The sedimentary facies and sedimentary evolution of the high-resolution sequence framework of the Carboniferous Taiyuan Formation in the Hangjinqi area have been systematically analyzed for the first time by drilling,logging and seismic data.The results show that four types of sequence interfaces can be identified in the Taiyuan Formation:regional unconformity surfaces,scour surfaces,lithologic-lithofacies transformation surfaces and flooding surfaces.According to the sedimentary response caused by the upward and downward movements of the base level at different levels,the Taiyuan Formation can be divided into 2 long-term cycles(LSC_(1)-LSC_(2)),4 mid-term cycles(MSC_(1)-MSC4)and 7 short-term cycles(SSC_(1)-SSC7).The long-and mid-term cycles correspond to members T_(1)and T_(2)and layers T_(1)-1,T_(1-2),T_(2-1),and T_(2)-2,respectively.Long-term cycles are dominated by C_(1);mid-term cycles are dominated by C_(1)and C_(2),followed by A2;and short-term cycles are dominated by C_(1),C_(2),A1 and A2.Under the high-resolution sequence stratigraphic framework,the Hangjinqi area underwent a transformation of fan delta and tidal flat depositional systems during the Taiyuan Formation sedimentary period.In the MSC_(1)-MSC_(2)stage,owing to a large-scale paleocontinent,the fan delta sedimentary body,which was limited in scale and scope,developed only in the southeastern corner and gradually transitioned basinward to tidal flat facies.In the MSC3-MSC4 stage,as the paleocontinent continuously decreased and the sedimentary range expanded,fan-delta plain sedimentation began in the study area.Several braided distributary channels with poor connectivity developed on the fan-delta plain,and between them were floodplains and peat swamps.
文摘Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.
基金Supported by the National Natural Science Foundation of China(No.32172979)the Natural Science Foundation of Fujian Province(No.2021J05159)the 2023 Special Program for Promoting High-Quality Development of Marine and Fishery Industry in Fujian Province(No.PJHYF-L-2023-2)。
文摘The Fujian oyster(Crassostrea angulata)is an economically significant shellfish species distributed mainly along the Fujian coast,Southeast China.However,its genetic diversity and structure remain unclear.The main distribution area of the C.angulata is located in Fujian,South China.In total,420 C.angulata were collected from 14 natural habitats(populations)along the Fujian coast,and their genetic diversity and structure were analyzed in the mitochondrial COⅠand nuclear gene ITS2 sequences.Results reveal that all the 14 populations of C.angulata exhibited high levels of genetic diversity,with a total of 57(haplotype diversity:0.811±0.016)and 124(haplotype diversity:0.912±0.007)haplotypes revealed by COⅠand ITS2,respectively.Notably,significant intermediate level of genetic differentiations between the Ningde Zhujiang(ZJ)population(F_(ST)by COI:0.035-0.142,P<0.05;F_(ST)by ITS2:0.078-0.123,P<0.05)with other populations were observed for the first time,which is also supported by the results of molecular variance analysis(F_(CT)by COⅠ:0.105,P<0.05;F_(CT)by ITS2:0.086,P<0.05)and the clustering of the ZJ population into distinct branches in the interpopulation genetic differentiation tree.Furthermore,the evolutionary tree and haplotype network analyses do not support the formation of a clear geographical genealogical structure among these 14 populations.In addition,the population dynamics analysis suggests that the C.angulata may have undergone expansion during the third ice age of the Pleistocene.These results provide a reference for the preservation and further genetic improvement of C.angulata.
基金supported by the Tianjin Key Medical Discipline(Specialty)Construct Project,No.TJYXZDXK-027A(to SF)the National Key Research andDevelopment Project of Stem Cell and Transformation Research,No.2019YFA0112100(to SF)+2 种基金Tianjin Natural Science Foundation’s Youth Project for DiverseInvestments,No.21JCQNJC01300(to BF)the National Natural Science Foundation of China(Youth Program),No.82102563(to BF)Tianjin Major Science andTechnology Special Projects and Engineering Projects,No.21ZXJBSY00080(to YR).
文摘Few studies have investigated alterations in the immune cell microenvironment of the dorsal root ganglia following spinal cord injury and whether these modifications facilitate axonal regeneration.In this study,we used a single-cell RNA sequencing dataset to create a comprehensive profile of the diverse cell types in the dorsal root ganglia and spinal cord of a mid-thoracic contusion injury model in cynomolgus monkeys.Cell communication analysis indicated that specific signaling events among various dorsal root ganglia cell types occur in response to spinal cord injury.Single-cell analysis using dimensionality reduction clustering identified distinct molecular signatures for nine cell types,including macrophage subpopulations,and differential gene expression profiles between dorsal root ganglia cells and spinal cord cells following spinal cord injury.The macrophage subpopulations were categorized into 11 clusters(MC0-MC10)based on differentially expressed genes,with the top 10 genes being ABCA6,RBMS3,EBF1,LAMA4,ANTXR2,LAMA2,SOX5,FOXP2,GHR,and APOD.MC0,MC1,and MC2 constituted the predominant macrophage populations.MC4,MC6,and MC9 were nearly absent in the spinal cord,but exhibited significant increases in the dorsal root ganglia post-spinal cord injury.Notably,these subpopulations possess a strong capacity for regulating axonal regeneration.The developmental progression of dorsal root ganglia macrophages after spinal cord injury was elucidated using cell trajectory and pseudo-time analyses.Genes such as EBF1(MC6 and MC9 marker),RBMS3(MC6 and MC9 marker),and ABCA6(MC6 marker)showed high expression levels in the critical pathways of macrophage function.Through ligand-receptor pair analysis,we determined that the effects of macrophages on microglia are predominantly mediated through interaction pairs(e.g.,SPP1-CD44,LAMC1-CD44,and FN1-CD44),potentially facilitating specific cellular communications within the immune microenvironment.The single-cell RNA sequencing dataset used in this study represents the first comprehensive transcriptional analysis of the dorsal root ganglia after spinal cord injury in cynomolgus monkeys,encompassing nearly all cell types within the dorsal root ganglia region.Using this dataset,we evaluated diverse subtypes of macrophages in the post-spinal cord injury dorsal root ganglia area and examined the signaling pathways that facilitate interactions among immune response-related macrophages in the dorsal root ganglia.Findings from this study provide a theoretical basis for understanding how the immune microenvironment influences the regenerative capacity of dorsal root ganglia neurons after spinal cord injury and offer novel insights into the complex processes underlying the pathobiology of spinal cord injury.
基金supported by the National Natural Science Foundation of China (Grant Nos.12475012,62461160263 for P.W.,and 62276171 for H.L.)Quantum Science and Technology-National Science and Technology Major Project of China (Project No.2023ZD0300600 for P.W.)+3 种基金Guangdong Provincial Quantum Science Strategic Initiative (Grant Nos.GDZX240-3009 and GDZX2303005 for P.W.)Guangdong Basic and Applied Basic Research Foundation (Grant No.2024-A1515011938 for H.L.)Shenzhen Fundamental ResearchGeneral Project (Grant No.JCYJ20240813141503005 for H.L.)the Talents Introduction Foundation of Beijing Normal University (Grant No.310432106 for P.W.)。
文摘Hyperpolarization of nuclear spins is crucial for advancing nuclear magnetic resonance and quantum information technologies,as nuclear spins typically exhibit extremely low polarization at room temperature due to their small gyromagnetic ratios.A promising approach to achieving high nuclear spin polarization is transferring the polarization of electrons to nuclear spins.The nitrogen-vacancy(NV)center in diamond has emerged as a highly effective medium for this purpose,and various hyperpolarization protocols have been developed.Among these,the pulsed polarization(PulsePol)method has been extensively studied due to its robustness against static energy shifts of the electron spin.In this work,we present a novel polarization protocol and uncover a family of magic sequences for hyperpolarizing nuclear spins,with PulsePol emerging as a special case of our general approach.Notably,we demonstrate that some of these magic sequences exhibit significantly greater robustness compared to the PulsePol protocol in the presence of finite half𝜋pulse duration of the protocol,Rabi and detuning errors.This enhanced robustness positions our protocol as a more suitable candidate for hyper-polarizing nuclear spins species with large gyromagnetic ratios and also ensures better compatibility with high-efficiency readout techniques at high magnetic fields.Additionally,the generality of our protocol allows for its direct application to other solid-state quantum systems beyond the NV center.
基金supported by the Science and Technology Planning Project of Fujian Province,China,under Grant No.2024H0014(2024H01010100).
文摘In industrial control systems,such as power transmission facilities and water treatment plants,Programmable Logic Controllers(PLCs)can work consistently and stably over long periods if there are no faults.Black-box identification aims to automatically construct Petri net models with the help of I/O signals from PLC devices only.The main challenge is how to convert the infinitely long PLC signals into an event sequence,which is the foundation for subsequent modeling.The current algorithms are confronted with a number of challenges,including an exponential increase in the number of transitions,high time complexity,and susceptibility to noisy signals.To solve these problems,this paper proposes a new method for converting PLC signals into a transition sequence.The method is based on the principles of Boolean absorption law,which filters out noise information in the I/O signals.Then firing functions representing input–output causality are constructed from the filtered signals.Finally,the original signal sequence is traversed to generate a transition sequence.The experimental results show that these methods can rapidly identify a transition sequence.Compared to traditional methods,the proposed algorithms have polynomial time complexity.
基金supported by the Rural & Environment Science & Analytical Services (RESAS) Division of the Scottish Government through project JHI-B1-1the Biotechnology and Biological Sciences Research Council (BBSRC) through awards BB/ S015663/1+2 种基金BB/X009068/1Research Leaders 2025 fellowship funded by European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement no. 754380the Research/Scientific Computing teams at The James Hutton Institute and NIAB for providing computational resources and technical support for the “UK’s Crop Diversity Bioinformatics HPC” (BBSRC grant BB/ S019669/1)。
文摘An accurate assessment of host and pathogen gene expression during infection is critical for understanding the molecular aspects of host-pathogen interactions.Often,pathogen-derived transcripts are difficult to ascertain at early infection stages owing to the unfavourable transcript representation compared to the host genes.In this study,we compare two sequencing techniques,RNAseq and enrichment sequencing(RenSeq and PenSeq)of cDNA,to investigate gene expression patterns in the doubled monoploid potato(DM)infected with the late blight pathogen Phytophthora infestans.Our results reveal distinct advantages of cDNA RenSeq and PenSeq over traditional RNAseq in terms of target gene representation and transcriptional quantification at early infection stages.Throughout the infection time course,cDNA enrichment sequencing enables transcriptomic analyses for more targeted host and pathogen genes.For highly expressed genes that were sampled in parallel by both cDNA enrichment and RNAseq,a high level of concordance in expression profiles is observed,indicative of at least semi-quantitative gene expression representation following enrichment.
基金supported by the grants from the Key R&D Program of Shandong Province,China(2022LZGC003)the China Agriculture Research System of MOF and MARA(CARS-35)+1 种基金the National Key Research and Development Project of China(2019YFE0106800)the 2115 Talent Development Program of China Agricultural University。
文摘Genotyping by target sequencing(GBTS)integrates the advantages of silicon-based technology(high stability and reliability)and genotyping by sequencing(high flexibility and cost-effectiveness).However,GBTS panels are not currently available in pigs.In this study,based on GBTS technology,we first developed a 50K panel,including 52,000 single-nucleotide polymorphisms(SNPs),in pigs,designated GBTS50K.A total of 6,032 individuals of Large White,Landrace,and Duroc pigs from 10 breeding farms were used to assess the newly developed GBTS50K.Our results showed that GBTS50K obtained a high genotyping ability,the SNP and individual call rates of GBTS50K were 0.997–0.998,and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993,respectively,in replicate samples.We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis,selection signature detection,genome-wide association studies(GWAS),genotyped imputation,genetic selection(GS),etc.The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding.For example,GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs.Particularly,due to the multiple SNPs(mSNPs),GBTS50K generated 100K qualified SNPs without increasing genotyping cost,and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%.Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs,and it is also helpful for developing SNP panels for other farm animals.
基金funded by the South Oil Exploration and Development Company of PetroChina(2021-HNYJ-010).
文摘The Fushan Depression is one of the petroliferous depressions in the Beibuwan Basin,South China Sea.Previous studies have preliminarily explored the origin and source of crude oils in some areas of this depression.Nevertheless,no systematic investigations on the classification and origin of oils and hy-drocarbon migration processes have been made for the entire petroleum system in this depression,which has significantly hindered the hydrocarbon exploration in the region.A total of 32 mudstone and 58 oil samples from the Fushan Depression were analyzed to definite the detailed oil-source correlation within the sequence and sedimentary framework.The organic matter of third member of Paleogene Liushagang Formation(Els(3))source rocks,both deltaic and lacustrine mudstone,are algal-dominated with high abundance of C_(23)tricyclic terpane and C_(30)4-methylsteranes.The deltaic source rocks occur-ring in the first member(Els_(1))and second member(Els_(2))of the Paleogene Liushagang Formation are characterized by high abundance of C_(19+20)tricyclic terpane and oleanane,reflecting a more terrestrial plants contribution.While lacustrine source rocks of Els_(1)and Els_(2)display the reduced input of terrige-nous organic matter with relatively low abundance of C 19+20 tricyclic terpane and oleanane.Three types of oils were identified by their biomarker compositions in this study.Most of the oils discovered in the Huachang and Bailian Els_(1)reservoir belong to group A and were derived from lacustrine source rocks of Els_(1)and Els_(2).Group B oils are found within the Els_(1)and Els_(2)reservoirs,showing a close relation to the deltaic source rocks of Els_(1)and Els_(2),respectively.Group C oils,occurring in the Els3 reservoirs,have a good affinity with the Els3 source rocks.The spatial distribution and accumulation of different groups of oils are mainly controlled by the sedimentary facies and specific structural conditions.The Els_(2)reservoir in the Yong'an area belonging to Group B oil,are adjacent to the source kitchen and could be considered as the favorable exploration area in the future.
基金Supported by Liyang People's Hospital Technology Project,No.2021YJKT0013。
文摘BACKGROUND The gastric microbiome is closely associated with gastric cancer,and single-region 16S rRNA sequencing has limitations in analyzing its characteristics,necessitating the search for a better sequencing method.AIM To evaluate the effectiveness of multi-region 16S rRNA gene sequencing in studying the microbiome of gastric cancer tissues.METHODS Patients with gastric cancer(n=118)who underwent surgery at Liyang People's Hospital from January 2022 to December 2024 were enrolled.Fifty-nine paraffinembedded and 59 fresh tissue samples were obtained.The ZymoBIOMICSTM microbial community standard and Escherichia coli ATCC 25922 were used as positive controls.Multi-region and single-region 16S rRNA gene sequencing were performed.Species identification,detection rates at varying microbial abundances,operational taxonomic unit(OTU)counts,and alpha diversity indices in gastric cancer tissues were compared between the two methods.RESULTS Multi-region 16S rRNA sequencing identified more species(eight species and eight genera)in the positive controls compared with single-region sequencing(one species and six genera).Detection rates at concentrations of 103,102,and 10 CFU/mg were significantly higher using multi-region sequencing(P<0.05).Multi-region sequencing also revealed significantly higher OTU counts and alpha diversity indices(Shannon,Simpson,and Chao1)in gastric cancer tissues(P<0.05).CONCLUSION Compared with single-region sequencing,multi-region 16S rRNA gene sequencing demonstrates superior species resolution and detection sensitivity,providing a more comprehensive profile of microbial diversity in gastric cancer tissues.
基金Supported by the National Oncology Care Support Program,No.25000.056766/2015-64.
文摘BACKGROUND Adenomatous polyposis confers an increased risk of developing colorectal cancer.APC and MUTYH are the major genes investigated in patients suspected of having polyposis.In addition to APC and MUTYH genes,other genes,such as POLE,POLD1,NTHL1,MBD4,MSH3 and MLH3,have recently been associated with polyposis phenotypes,conferring heterogeneity in terms of the clinical,etiological and heritable aspects of patients with polyposis.AIM To investigate the underlying variant landscape in patients with suspected polyposis who lack variants in the APC and MUTYH genes using whole-exome sequencing.METHODS Twenty-seven participants were included in the study and subjected to germline whole-exome sequencing.In addition,their clinical-pathological,personal,and family history data were collected.RESULTS The mean age at diagnosis was 51 years,and most participants had attenuated forms of polyposis(88.9%),with 63.0%diagnosed with a primary tumor,mostly colorectal cancer(76.5%).Among the variants identified,17 were classified as pathogenic or likely pathogenic(in 12 participants),including variants in genes involved in the Wnt/β-catenin signaling pathway,such as ST7 L,A1CF,and DKK4,and variants in DNA-repair genes,such as NTHL1,PNKP,and PMS2,as well as a variant found at the FRK gene identified in a patient with classic polyposis at age 19 and with a family history of polyps.CONCLUSION This study identified novel genes potentially associated with polyposis in patients lacking germline pathogenic variants in the APC and MUTYH genes.These findings support the use of next-generation sequencing for screening,expanding the scope of polyposis-related variants beyond these two genes.
基金Supported by Leading Talent Program of Autonomous Region(2022TSYCLJ0070)PetroChina Prospective and Basic Technological Project(2021DJ0108)Natural Science Foundation for Outstanding Young People in Shandong Province(ZR2022YQ30).
文摘Based on the experimental results of casting thin section,low temperature nitrogen adsorption,high pressure mercury injection,nuclear magnetic resonance T2 spectrum,contact angle and oil-water interfacial tension,the relationship between pore throat structure and crude oil mobility characteristics of full particle sequence reservoirs in the Lower Permian Fengcheng Formation of Mahu Sag,Junggar Basin,are revealed.(1)With the decrease of reservoir particle size,the volume of pores connected by large throats and the volume of large pores show a decreasing trend,and the distribution and peak ranges of throat and pore radius shift to smaller size in an orderly manner.The upper limits of throat radius,porosity and permeability of unconventional reservoirs in Fengcheng Formation are approximately 0.7μm,8%and 0.1×10^(−3)μm^(2),respectively.(2)As the reservoir particle size decreases,the distribution and peak ranges of pores hosting retained oil and movable oil are shifted to a smaller size in an orderly manner.With the increase of driving pressure,the amount of retained and movable oil of the larger particle reservoir samples shows a more obvious trend of decreasing and increasing,respectively.(3)With the increase of throat radius,the driving pressure of reservoir with different particle levels presents three stages,namely rapid decrease,slow decrease and stabilization.The oil driving pressures of various reservoirs and the differences of them decrease with the increase of temperature and obviously decrease with the increase of throat radius.According to the above experimental analysis,it is concluded that the deep shale oil of Fengcheng Formation in Mahu Sag has great potential for production under geological conditions.
基金financially supported by National Key R&D Program(2021YFF0701905)。
文摘In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology based on the principle of high-throughput sequencing,and established a multi-locus 10 animalderived components identification method of cattle,goat,sheep,donkey,horse,chicken,duck,goose,pigeon,quail in meat and meat products.The specific loci of each species could be detected and the species could be accurately identified,including 5 loci for cattle and duck,3 loci for sheep,9 loci for chicken and horse,10 loci for goose and pigeon,6 loci for quail and 1 locus for donkey and goat,and an adulteration model was established to simulate commercially available samples.The results showed that the method established in this study had high throughput,good repeatability and accuracy,and was able to identify 10 animalderived components simultaneously with 100%repeatability accuracy.The detection limit was 0.1%(m/m)in simulated samples of chicken,duck and horse.Using the method established in this study to test commercially available samples,4 samples from 14 commercially available samples were detected to be inconsistent with the labels,of which 2 did not contain the target ingredient and 2 were adulterated with small amounts of other ingredients.
基金Supported by the National Science and Technology Major Project(2017ZX05001)CNPC Technology Project(2023YQX20111).
文摘To address the discrepancies between well and seismic data in stratigraphic correlation of the Triassic Yanchang Formation in the Ordos Basin,NW China,traditional stratigraphic classification schemes,the latest 3D seismic and drilling data,and reservoir sections are thoroughly investigated.Guided by the theory of sequence stratigraphy,the progradational sequence stratigraphic framework of the Yanchang Formation is systematically constructed to elucidate new deposition mechanisms in the depressed lacustrine basin,and it has been successfully applied to the exploration and development practices in the Qingcheng Oilfield.Key findings are obtained in three aspects.First,the seismic progradational reflections,marker tuff beds,and condensed sections of flooding surfaces in the Yanchang Formation are consistent and isochronous.Using flooding surface markers as a reference,a progradational sequence stratigraphic architecture is reconstructed for the middle-upper part of Yanchang Formation,and divided into seven clinoform units(CF1-CF7).Second,progradation predominantly occurs in semi-deep to deep lake environments,with the depositional center not always coinciding with the thickest strata.The lacustrine basin underwent an evolution of“oscillatory regression-progradational infilling-multi-phase superimposition”.Third,the case study of Qingcheng Oilfield reveals that the major pay zones consist of“isochronous but heterochronous”gravity-flow sandstone complexes.Guided by the progradational sequence stratigraphic architecture,horizontal well oil-layer penetration rates remain above 82%.The progradational sequence stratigraphic architecture and associated geological insights are more consistent with the sedimentary infilling mechanisms of large-scale continental depressed lacustrine basins and actual drilling results.The research results provide crucial theoretical and technical support for subsequent refined exploration and development of the Yanchang Formation,and are expected to offer a reference for research and production practice in similar continental lacustrine basins.
