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
Previous research revealed the positive activity of matrix metalloproteinase 7(MMP7) on migration and myelin regeneration of Schwa nn cells(SCs). However, understanding of the molecular changes and biological activiti...Previous research revealed the positive activity of matrix metalloproteinase 7(MMP7) on migration and myelin regeneration of Schwa nn cells(SCs). However, understanding of the molecular changes and biological activities induced by increased amounts of MMP7 in SCs remains limited. To better understand the underlying molecular events, primary SCs were isolated from the sciatic nerve stump of newborn rats and cultured with 10 nM human MMP7 for 24 hours. The results of genetic testing were analyzed at a relatively relaxed threshold value(fold change ≥ 1.5 and P-value < 0.05). Upon MMP7 exposure, 149 genes were found to be upregulated in SCs, whereas 133 genes were downregulated. Gene Ontology analysis suggested that many differentially expressed molecules were related to cellular processes, single-organism processes, and metabolic processes. Kyoto Enrichment of Genes and Genomes pathway analysis further indicated the critical involvement of cell signaling and metabolism in MMP7-induced molecular regulation of SCs. Results of Ingenuity Pathway Analysis(IPA) also revealed that MMP7 regulates biological processes, molecular functions, cellular components, diseases and functions, biosynthesis, material metabolism, cell movement, and axon guidance. The outcomes of further analysis will deepen our comprehension of MMP7-induced biological changes in SCs. This study was approved by the Laboratory Animal Ethics Committee of Nantong University, China(approval No. 20190225-004) on February 27, 2019.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
Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocyt...Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.展开更多
Single molecular real-time(SMRT)sequencing,also called third-generation sequencing,is a novel sequencing technique capable of generating extremely long contiguous sequence reads.While conventional short-read sequencin...Single molecular real-time(SMRT)sequencing,also called third-generation sequencing,is a novel sequencing technique capable of generating extremely long contiguous sequence reads.While conventional short-read sequencing cannot evaluate the linkage of nucleotide substitutions distant from one another,SMRT sequencing can directly demonstrate linkage of nucleotide changes over a span of more than 20 kbp,and thus can be applied to directly examine the haplotypes of viruses or bacteria whose genome structures are changing in real time.In addition,an error correction method(circular consensus sequencing)has been established and repeated sequencing of a single-molecule DNA template can result in extremely high accuracy.The advantages of long read sequencing enable accurate determination of the haplotypes of individual viral clones.SMRT sequencing has been applied in various studies of viral genomes including determination of the full-length contiguous genome sequence of hepatitis C virus(HCV),targeted deep sequencing of the HCV NS5A gene,and assessment of heterogeneity among viral populations.Recently,the emergence of multi-drug resistant HCV viruses has become a significant clinical issue and has been also demonstrated using SMRT sequencing.In this review,we introduce the novel third-generation PacBio RSII/Sequel systems,compare them with conventional next-generation sequencers,and summarize previous studies in which SMRT sequencing technology has been applied for HCV genome analysis.We also refer to another long-read sequencing platform,nanopore sequencing technology,and discuss the advantages,limitations and future perspectives in using these thirdgeneration sequencers for HCV genome analysis.展开更多
Wastewater treatment using Sequencing Batch Reactor (SBR) technology is one of the state-of-the art wastewater management systems. In this technology equalization, biological treatment and secondary clarification are ...Wastewater treatment using Sequencing Batch Reactor (SBR) technology is one of the state-of-the art wastewater management systems. In this technology equalization, biological treatment and secondary clarification are performed in a single reactor in a time control sequence. SBR system is idler for the areas where the available land is limited, since it operates in less space and very cost effective even on small scales. The control of the operational parameters during the process of biological wastewater treatment is often complicated due to the dynamic change in the composition and characteristics of the raw wastewater, flow rates and other parameters influencing the complex nature of the treatment process and the process in SBR has a unique cyclic batch operation. The performance of the SBR was studied using pilot and real plant at Puducherry. The parameters considered in this study are flow, Mixed Liquor Suspended Solids (MLSS), pH, temperature, influent and effluent of Total Suspended Solids (TSS), Biochemical Oxygen Demand (BOD) and Chemical Oxygen Demand (COD). As a part of the study, the effect of constant flow and varying flow on the organic loading of the influent TSS, BOD and COD and their influence on the organic load of the effluent parameters were examined to identify the level of significance of the parameters in relation to the flow. The impact of flow on other parameters was also examined. The experimental data obtained from pilot and real plants were analyzed using multi variate statistical analyses like correlation analysis, Principal Component Analysis (PCA) and Analysis of variance (ANOVA). The statistical analysis revealed that constant flow had no significant role and the influent parameters alone had the critical role, whereas varying flow as well as the influent parameters had the significant role on the performance of SBR.展开更多
Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be...Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be low.This is primarily attributed to the intricate and insufficiently understood mechanisms of disease progression,as well as the considerable challenges associated with tumor hetero-geneity.The recent study by Tang et al provides a detailed single-cell RNA se-quencing analysis of GC across different stages,revealing dynamic changes in the tumor microenvironment and key immune responses.We aim to offer a compre-hensive interpretation of the study’s findings and propose several innovative directions for future academic research in gastric cancer.These include exploring advanced multi-omics approaches,leveraging spatial transcriptomics,integrating artificial intelligence for clinical applications,and developing novel immuno-therapy strategies.We further emphasize the importance of personalized medi-cine,early detection,and novel drug discovery techniques in improving GC treatment outcomes.展开更多
Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and...Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and p53.While p16 is a well-established surrogate for HPV in oropharyngeal cancer,our review highlights its unreliable role in HNCSCC,where positivity is instead associated with recurrence and metastasis.Similarly,p53 illustrates a dual role-wild-type as a genomic safeguard,mutated as an oncogenic driver-complicating prognostication.Methodological considerations,including the limitations of immunohistochemistry for HPV detection,underscore the need for multi-method and molecular validation in future studies.Ultraviolet radiation is posited as a key modifier of p16 function,decoupling expression from tumor suppression.To contextualize these findings,we draw parallels to glioblastoma(GBM),where subclonal evolution,p53 dysfunction,and intratumoral heterogeneity drive relapse despite aggressive multimodal therapies.GBM exemplifies how bulk-level biomarker generalizations often obscure dynamic cellular ecosystems,reinforcing the necessity of single-cell and spatial approaches.Multi-omics integration-encompassing genome,transcriptome,proteome,and tumor microenvironment mapping-coupled with single-cell RNA sequencing and spatial transcriptomics,offers a path forward for resolving subclonal dynamics in both HNCSCC and GBM.These technologies provide the resolution needed to track tumor-immunestromal co-evolution,identify therapy-resistant clones,and anticipate recurrence.We argue for a N-of-1,patient-and cell-centric paradigm that reframes biomarkers not as static surrogates but as dynamic readouts of cancer evolution across time and tissue contexts.Conceptually,we propose kinetic and microenvironmental frameworks(e.g.,“load-and-lock”barriers;dormancy and immunesynapse stabilization)as hypothesis-generating avenues to stall clonal handoffs and improve outcome prediction.Together,these perspectives argue for revised biomarker frameworks in HNCSCC and ethically inclusive,mechanism-anchored studies that bridge discovery with individualized care.By bridging insights from HNCSCC with the lessons of GBM,this review underscores the need for ethically inclusive,mechanistically informed frameworks that integrate subclonal evolution,biomarker re-interpretation,and precision-personalized hybrid models.Such an approach will be essential for advancing from one-size-fits-all strategies to individualized lifetime cancer care.展开更多
In the search for a therapeutic schedule for spinal cord injury,it is necessary to understand key genes and their corresponding regulatory networks involved in the spinal cord injury process.However,ad hoc selection a...In the search for a therapeutic schedule for spinal cord injury,it is necessary to understand key genes and their corresponding regulatory networks involved in the spinal cord injury process.However,ad hoc selection and analysis of one or two genes cannot fully reveal the complex molecular biological mechanisms of spinal cord injury.The emergence of second-generation sequencing technology(RNA sequencing)has provided a better method.In this study,RNA sequencing technology was used to analyze differentially expressed genes at different time points after spinal cord injury in rat models established by contusion of the eighth thoracic segment.The numbers of genes that changed significantly were 944,1362 and 1421 at 1,4 and 7 days after spinal cord injury respectively.After gene ontology analysis and temporal expression analysis of the differentially expressed genes,C5ar1,Socs3 and CCL6 genes were then selected and identified by real-time polymerase chain reaction and western blot assay.The mRNA expression trends of C5ar1,Socs3 and CCL6 genes were consistent with the RNA sequencing results.Further verification and analysis of C5ar1 indicate that the level of protein expression of C5ar1 was consistent with its nucleic acid level after spinal cord injury.C5ar1 was mainly expressed in neurons and astrocytes.Finally,the gene Itgb2,which may be related to C5ar1,was found by Chilibot database and literature search.Immunofluorescence histochemical results showed that the expression of Itgb2 was highly consistent with that of C5ar1.Itgb2 was expressed in astrocytes.RNA sequencing technology can screen differentially expressed genes at different time points after spinal cord injury.Through analysis and verification,genes strongly associated with spinal cord injury can be screened.This can provide experimental data for further determining the molecular mechanism of spinal cord injury,and also provide possible targets for the treatment of spinal cord injury.This study was approved ethically by the Laboratory Animal Ethics Committee of Jiangsu Province,China(approval No.2018-0306-001)on March 6,2018.展开更多
BACKGROUND Hereditary spherocytosis(HS)is a hereditary disease of hemolytic anemia that occurs due to the erythrocyte membrane defects.Dubin–Johnson syndrome(DJS),which commonly results in jaundice,is a benign heredi...BACKGROUND Hereditary spherocytosis(HS)is a hereditary disease of hemolytic anemia that occurs due to the erythrocyte membrane defects.Dubin–Johnson syndrome(DJS),which commonly results in jaundice,is a benign hereditary disorder of bilirubin clearance that occurs only rarely.The co-occurrence of HS and DJS is extremely rare.We recently diagnosed and treated a case of co-occurring HS and DJS.CASE SUMMARY A 21-year-old female patient presented to our department because of severe jaundice,severe splenomegaly,and mild anemia since birth.We eventually confirmed the diagnosis of co-occurring DJS and HS by next generation sequencing(NGS).The treatment of ursodeoxycholic acid in combination with phenobarbital successfully increased hemoglobin and reduced total bilirubin and direct bilirubin.CONCLUSION The routine application of NGS can efficiently render a definite diagnosis when inherited disorders are suspected.展开更多
This paper proposes a better modified version of a well-known Multi-Objective Evolutionary Algorithm (MOEA) known as Non-dominated Sorting Genetic Algorithm-II (NSGA-II). The proposed algorithm contains a new mutation...This paper proposes a better modified version of a well-known Multi-Objective Evolutionary Algorithm (MOEA) known as Non-dominated Sorting Genetic Algorithm-II (NSGA-II). The proposed algorithm contains a new mutation algorithm and has been applied on a bi-objective job sequencing problem. The objectives are the minimization of total weighted tardiness and the minimization of the deterioration cost. The results of the proposed algorithm have been compared with those of original NSGA-II. The comparison of the results shows that the modified NSGA-II performs better than the original NSGA-II.展开更多
Metagenomic next-generation sequencing(mNGS)is a culture-independent technique that directly extracts and sequences all nucleic acids from clinical specimens.By leveraging high-throughput sequencing and bioinformatic ...Metagenomic next-generation sequencing(mNGS)is a culture-independent technique that directly extracts and sequences all nucleic acids from clinical specimens.By leveraging high-throughput sequencing and bioinformatic analysis,it characterizes the entire microbial landscape,including bacteria,fungi,viruses,and parasites.This approach significantly broadens detection coverage,improves sensitivity,and reduces turnaround time compared with conventional diagnostic methods.Since its initial application to suspected infectious uveitis by Doan et al.in 2006,mNGS has been increasingly integrated into ophthalmic practice to facilitate pathogen identification or exclusion[1].展开更多
Background The molecular mechanisms of early-onset multigenerational diabetes remain unknown.This study aimed to investigate the clinical and genetic characteristics of early-onset diabetes involving at least two cons...Background The molecular mechanisms of early-onset multigenerational diabetes remain unknown.This study aimed to investigate the clinical and genetic characteristics of early-onset diabetes involving at least two consecutive generations.Methods From 1296 inpatients with diabetes,we selected individuals who were≤30 years of age and who were clinically suspected of having familial monogenic diabetes.Clinical data were collected from the probands and their family members.Whole-exome sequencing(WES)was used to identify possible causal variants for diabetes.Candidate pathogenic variants were verified by Sanger sequencing,assessed for cosegregation in family members,and evaluated on the basis of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology(ACMG/AMP)guidelines.Moreover,missense and synonymous variants were subjected to in silico pathogenicity prediction via MutationTaster and PolyPhen-2.RNAfold was used to predict RNA structural alterations for synonymous variants.Results Twenty-five early-onset diabetes patients with a history of familial diabetes were enrolled.Pathogenic/likely pathogenic variants(p.Gly292fs in HNF1A,p.Gly245Argfs*22 in PDX1,p.Asp329His in KCNJ11,p.Leu734Phe and p.Val606Gly in WFS1)were detected in four patients,who were diagnosed accurately and treated with reasonable hypoglycemic agents based on genetic testing results.The variants of uncertain significance(ABCC8 c.3039 G>A(p.Ser1013=Ser),MAPK8IP1 p.Gln144_Gly145insSerGln,and TBC1D4 p.Arg1249Trp)were identified in three probands.Conclusion Patients with early-onset diabetes involving at least two consecutive generations may harbor genetic variants.Genetic testing in this population enables precision diagnosis,informs individualized treatment,and facilitates genetic counseling.展开更多
Over the past decade,the therapeutic armamentarium for inflammatory bowel disease(IBD)has substantially expanded with the incorporation of multiple classes of advanced therapies.Currently,in addition to tumor necrosis...Over the past decade,the therapeutic armamentarium for inflammatory bowel disease(IBD)has substantially expanded with the incorporation of multiple classes of advanced therapies.Currently,in addition to tumor necrosis factor-α inhibitors,the therapeutic arsenal for IBD includes anti-integrin agents,interleukin(IL)-12/23p40 and IL-23p19 antibodies,Janus kinase inhibitors,and sphingosine 1-phosphate receptor modulators.Although advances in IBD pharmacotherapy have enabled disease remission and improved control of intestinal inflammation in many individuals previously considered clinically'intractable',they have also increased the complexity of decision-making related to the initial positioning and sequencing of therapies in the heterogeneous clinical presentations of IBD.Until molecular and genetic markers capable of predicting therapeutic responses become available in practice,the choice of initial and subsequent therapy in individuals with IBD is based on factors including disease severity,phenotype,risk of complications,comorbidities,extraintestinal manifestations,and the balance between efficacy,safety,convenience,and access.This review explores the factors that influence treatment decisions regarding initial therapy selection and sequencing across IBD scenarios,offering practical tips for personalizing therapy based on the safety and efficacy of advanced treatments and the individual's risk of disease-or therapy-related adverse outcomes.展开更多
Background: Androgen insensitivity syndrome(AIS), a disorder of sexual development in 46, XY individuals, is caused by loss-of-function mutations in the androgen receptor(AR) gene. A variety of tumors have been report...Background: Androgen insensitivity syndrome(AIS), a disorder of sexual development in 46, XY individuals, is caused by loss-of-function mutations in the androgen receptor(AR) gene. A variety of tumors have been reported in association with AIS, but no cases with colorectal cancer(CRC) have been described.Case presentation: Here, we present a male patient with AIS who developed multiple early-onset CRCs and his pedigree. His first cousin was diagnosed with AIS and harbored the same AR gene mutation, but with no signs of CRC. The difference in clinical management for the two patients was that testosterone treatment was given to the proband for a much longer time compared with the cousin. The CRC family history was negative, and no germline mutations in well-known CRC-related genes were identified. A single nucleotide polymorphism array revealed a microduplication on chromosome 22q11.22 that encompassed a micro RNA potentially related to CRC pathogenesis. In the proband, whole exome sequencing identified a polymorphism in an oncogene and 13 rare loss-of-function variants, of which two were in CRC-related genes and four were in genes associated with other human cancers.Conclusions: By pathway analysis, all inherited germline genetic events were connected in a unique network whose alteration in the proband, together with continuous testosterone stimulation, may have played a role in CRC pathogenesis.展开更多
Wastewater treatment is a complicated dynamic process affected by microbial, chemical and physical factors. Faults are inevitable during the operation of modified sequencing batch reactors(MSBRs) because of the uncert...Wastewater treatment is a complicated dynamic process affected by microbial, chemical and physical factors. Faults are inevitable during the operation of modified sequencing batch reactors(MSBRs) because of the uncertainty of various factors. Abnormal MSBR results require fault diagnosis to determine the cause of failure and implement appropriate measures to adjust system operations. Bayesian network(BN) is a powerful knowledge representation tool that deals explicitly with uncertainty. A BN-based approach to diagnosing wastewater treatment systems based on MSBR is developed in this study. The network is constructed using the knowledge derived from literature and elicited from experts, and it is parametrized using independent data from a pilot test.A one-year pilot study is conducted to verify the diagnostic analysis. The proposed model is reasonable, and the diagnosis results are accurate. This approach can be applied with minimal modifications to other types of wastewater treatment plants.展开更多
Viruses are a cause of significant health problem world-wide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of whic...Viruses are a cause of significant health problem world-wide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of nextgeneration sequencers(NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequenceindependent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.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 Priority Academic Program Development of Jiangsu Higher Education Institutions of China PAPD。
文摘Previous research revealed the positive activity of matrix metalloproteinase 7(MMP7) on migration and myelin regeneration of Schwa nn cells(SCs). However, understanding of the molecular changes and biological activities induced by increased amounts of MMP7 in SCs remains limited. To better understand the underlying molecular events, primary SCs were isolated from the sciatic nerve stump of newborn rats and cultured with 10 nM human MMP7 for 24 hours. The results of genetic testing were analyzed at a relatively relaxed threshold value(fold change ≥ 1.5 and P-value < 0.05). Upon MMP7 exposure, 149 genes were found to be upregulated in SCs, whereas 133 genes were downregulated. Gene Ontology analysis suggested that many differentially expressed molecules were related to cellular processes, single-organism processes, and metabolic processes. Kyoto Enrichment of Genes and Genomes pathway analysis further indicated the critical involvement of cell signaling and metabolism in MMP7-induced molecular regulation of SCs. Results of Ingenuity Pathway Analysis(IPA) also revealed that MMP7 regulates biological processes, molecular functions, cellular components, diseases and functions, biosynthesis, material metabolism, cell movement, and axon guidance. The outcomes of further analysis will deepen our comprehension of MMP7-induced biological changes in SCs. This study was approved by the Laboratory Animal Ethics Committee of Nantong University, China(approval No. 20190225-004) on February 27, 2019.
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.
基金supported by the National Natural Science Foundation of China,No.82301403(to DZ)。
文摘Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.
文摘Single molecular real-time(SMRT)sequencing,also called third-generation sequencing,is a novel sequencing technique capable of generating extremely long contiguous sequence reads.While conventional short-read sequencing cannot evaluate the linkage of nucleotide substitutions distant from one another,SMRT sequencing can directly demonstrate linkage of nucleotide changes over a span of more than 20 kbp,and thus can be applied to directly examine the haplotypes of viruses or bacteria whose genome structures are changing in real time.In addition,an error correction method(circular consensus sequencing)has been established and repeated sequencing of a single-molecule DNA template can result in extremely high accuracy.The advantages of long read sequencing enable accurate determination of the haplotypes of individual viral clones.SMRT sequencing has been applied in various studies of viral genomes including determination of the full-length contiguous genome sequence of hepatitis C virus(HCV),targeted deep sequencing of the HCV NS5A gene,and assessment of heterogeneity among viral populations.Recently,the emergence of multi-drug resistant HCV viruses has become a significant clinical issue and has been also demonstrated using SMRT sequencing.In this review,we introduce the novel third-generation PacBio RSII/Sequel systems,compare them with conventional next-generation sequencers,and summarize previous studies in which SMRT sequencing technology has been applied for HCV genome analysis.We also refer to another long-read sequencing platform,nanopore sequencing technology,and discuss the advantages,limitations and future perspectives in using these thirdgeneration sequencers for HCV genome analysis.
文摘Wastewater treatment using Sequencing Batch Reactor (SBR) technology is one of the state-of-the art wastewater management systems. In this technology equalization, biological treatment and secondary clarification are performed in a single reactor in a time control sequence. SBR system is idler for the areas where the available land is limited, since it operates in less space and very cost effective even on small scales. The control of the operational parameters during the process of biological wastewater treatment is often complicated due to the dynamic change in the composition and characteristics of the raw wastewater, flow rates and other parameters influencing the complex nature of the treatment process and the process in SBR has a unique cyclic batch operation. The performance of the SBR was studied using pilot and real plant at Puducherry. The parameters considered in this study are flow, Mixed Liquor Suspended Solids (MLSS), pH, temperature, influent and effluent of Total Suspended Solids (TSS), Biochemical Oxygen Demand (BOD) and Chemical Oxygen Demand (COD). As a part of the study, the effect of constant flow and varying flow on the organic loading of the influent TSS, BOD and COD and their influence on the organic load of the effluent parameters were examined to identify the level of significance of the parameters in relation to the flow. The impact of flow on other parameters was also examined. The experimental data obtained from pilot and real plants were analyzed using multi variate statistical analyses like correlation analysis, Principal Component Analysis (PCA) and Analysis of variance (ANOVA). The statistical analysis revealed that constant flow had no significant role and the influent parameters alone had the critical role, whereas varying flow as well as the influent parameters had the significant role on the performance of SBR.
基金Supported by Scientific Research Project of Putian University,No.2022059Special Project for Outstanding Young Talents of Putian University,No.2024072Natural Science Foundation of Fujian Province,No.2023J01160.
文摘Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be low.This is primarily attributed to the intricate and insufficiently understood mechanisms of disease progression,as well as the considerable challenges associated with tumor hetero-geneity.The recent study by Tang et al provides a detailed single-cell RNA se-quencing analysis of GC across different stages,revealing dynamic changes in the tumor microenvironment and key immune responses.We aim to offer a compre-hensive interpretation of the study’s findings and propose several innovative directions for future academic research in gastric cancer.These include exploring advanced multi-omics approaches,leveraging spatial transcriptomics,integrating artificial intelligence for clinical applications,and developing novel immuno-therapy strategies.We further emphasize the importance of personalized medi-cine,early detection,and novel drug discovery techniques in improving GC treatment outcomes.
文摘Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and p53.While p16 is a well-established surrogate for HPV in oropharyngeal cancer,our review highlights its unreliable role in HNCSCC,where positivity is instead associated with recurrence and metastasis.Similarly,p53 illustrates a dual role-wild-type as a genomic safeguard,mutated as an oncogenic driver-complicating prognostication.Methodological considerations,including the limitations of immunohistochemistry for HPV detection,underscore the need for multi-method and molecular validation in future studies.Ultraviolet radiation is posited as a key modifier of p16 function,decoupling expression from tumor suppression.To contextualize these findings,we draw parallels to glioblastoma(GBM),where subclonal evolution,p53 dysfunction,and intratumoral heterogeneity drive relapse despite aggressive multimodal therapies.GBM exemplifies how bulk-level biomarker generalizations often obscure dynamic cellular ecosystems,reinforcing the necessity of single-cell and spatial approaches.Multi-omics integration-encompassing genome,transcriptome,proteome,and tumor microenvironment mapping-coupled with single-cell RNA sequencing and spatial transcriptomics,offers a path forward for resolving subclonal dynamics in both HNCSCC and GBM.These technologies provide the resolution needed to track tumor-immunestromal co-evolution,identify therapy-resistant clones,and anticipate recurrence.We argue for a N-of-1,patient-and cell-centric paradigm that reframes biomarkers not as static surrogates but as dynamic readouts of cancer evolution across time and tissue contexts.Conceptually,we propose kinetic and microenvironmental frameworks(e.g.,“load-and-lock”barriers;dormancy and immunesynapse stabilization)as hypothesis-generating avenues to stall clonal handoffs and improve outcome prediction.Together,these perspectives argue for revised biomarker frameworks in HNCSCC and ethically inclusive,mechanism-anchored studies that bridge discovery with individualized care.By bridging insights from HNCSCC with the lessons of GBM,this review underscores the need for ethically inclusive,mechanistically informed frameworks that integrate subclonal evolution,biomarker re-interpretation,and precision-personalized hybrid models.Such an approach will be essential for advancing from one-size-fits-all strategies to individualized lifetime cancer care.
基金supported by the National Natural Science Foundation of China,No.31570983(to XDW)the Priority Academic Program Development of Jiangsu Higher Education Institutes of China
文摘In the search for a therapeutic schedule for spinal cord injury,it is necessary to understand key genes and their corresponding regulatory networks involved in the spinal cord injury process.However,ad hoc selection and analysis of one or two genes cannot fully reveal the complex molecular biological mechanisms of spinal cord injury.The emergence of second-generation sequencing technology(RNA sequencing)has provided a better method.In this study,RNA sequencing technology was used to analyze differentially expressed genes at different time points after spinal cord injury in rat models established by contusion of the eighth thoracic segment.The numbers of genes that changed significantly were 944,1362 and 1421 at 1,4 and 7 days after spinal cord injury respectively.After gene ontology analysis and temporal expression analysis of the differentially expressed genes,C5ar1,Socs3 and CCL6 genes were then selected and identified by real-time polymerase chain reaction and western blot assay.The mRNA expression trends of C5ar1,Socs3 and CCL6 genes were consistent with the RNA sequencing results.Further verification and analysis of C5ar1 indicate that the level of protein expression of C5ar1 was consistent with its nucleic acid level after spinal cord injury.C5ar1 was mainly expressed in neurons and astrocytes.Finally,the gene Itgb2,which may be related to C5ar1,was found by Chilibot database and literature search.Immunofluorescence histochemical results showed that the expression of Itgb2 was highly consistent with that of C5ar1.Itgb2 was expressed in astrocytes.RNA sequencing technology can screen differentially expressed genes at different time points after spinal cord injury.Through analysis and verification,genes strongly associated with spinal cord injury can be screened.This can provide experimental data for further determining the molecular mechanism of spinal cord injury,and also provide possible targets for the treatment of spinal cord injury.This study was approved ethically by the Laboratory Animal Ethics Committee of Jiangsu Province,China(approval No.2018-0306-001)on March 6,2018.
基金Supported by the National Science and Technology Important and Special Project of China,No.2017ZX09304024
文摘BACKGROUND Hereditary spherocytosis(HS)is a hereditary disease of hemolytic anemia that occurs due to the erythrocyte membrane defects.Dubin–Johnson syndrome(DJS),which commonly results in jaundice,is a benign hereditary disorder of bilirubin clearance that occurs only rarely.The co-occurrence of HS and DJS is extremely rare.We recently diagnosed and treated a case of co-occurring HS and DJS.CASE SUMMARY A 21-year-old female patient presented to our department because of severe jaundice,severe splenomegaly,and mild anemia since birth.We eventually confirmed the diagnosis of co-occurring DJS and HS by next generation sequencing(NGS).The treatment of ursodeoxycholic acid in combination with phenobarbital successfully increased hemoglobin and reduced total bilirubin and direct bilirubin.CONCLUSION The routine application of NGS can efficiently render a definite diagnosis when inherited disorders are suspected.
文摘This paper proposes a better modified version of a well-known Multi-Objective Evolutionary Algorithm (MOEA) known as Non-dominated Sorting Genetic Algorithm-II (NSGA-II). The proposed algorithm contains a new mutation algorithm and has been applied on a bi-objective job sequencing problem. The objectives are the minimization of total weighted tardiness and the minimization of the deterioration cost. The results of the proposed algorithm have been compared with those of original NSGA-II. The comparison of the results shows that the modified NSGA-II performs better than the original NSGA-II.
基金supported by the Beijing Hospitals Authority’s Ascent Programme(DFL20220301)Beijing Nova Program(20230484445)+2 种基金Capital Health Development Scientific Research Project Grant(SF 2022-2-2035 to Y.T.)Excellent Young Talent Innovation Project of Chinese Institutes for Medical Research(CX23YQA02)the Chinese Institute for Medical Research(CX23YQ03).
文摘Metagenomic next-generation sequencing(mNGS)is a culture-independent technique that directly extracts and sequences all nucleic acids from clinical specimens.By leveraging high-throughput sequencing and bioinformatic analysis,it characterizes the entire microbial landscape,including bacteria,fungi,viruses,and parasites.This approach significantly broadens detection coverage,improves sensitivity,and reduces turnaround time compared with conventional diagnostic methods.Since its initial application to suspected infectious uveitis by Doan et al.in 2006,mNGS has been increasingly integrated into ophthalmic practice to facilitate pathogen identification or exclusion[1].
基金supported by Diabetes Talent Research Project of China,International Medical Foundation 2019(No.2018-N-1).
文摘Background The molecular mechanisms of early-onset multigenerational diabetes remain unknown.This study aimed to investigate the clinical and genetic characteristics of early-onset diabetes involving at least two consecutive generations.Methods From 1296 inpatients with diabetes,we selected individuals who were≤30 years of age and who were clinically suspected of having familial monogenic diabetes.Clinical data were collected from the probands and their family members.Whole-exome sequencing(WES)was used to identify possible causal variants for diabetes.Candidate pathogenic variants were verified by Sanger sequencing,assessed for cosegregation in family members,and evaluated on the basis of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology(ACMG/AMP)guidelines.Moreover,missense and synonymous variants were subjected to in silico pathogenicity prediction via MutationTaster and PolyPhen-2.RNAfold was used to predict RNA structural alterations for synonymous variants.Results Twenty-five early-onset diabetes patients with a history of familial diabetes were enrolled.Pathogenic/likely pathogenic variants(p.Gly292fs in HNF1A,p.Gly245Argfs*22 in PDX1,p.Asp329His in KCNJ11,p.Leu734Phe and p.Val606Gly in WFS1)were detected in four patients,who were diagnosed accurately and treated with reasonable hypoglycemic agents based on genetic testing results.The variants of uncertain significance(ABCC8 c.3039 G>A(p.Ser1013=Ser),MAPK8IP1 p.Gln144_Gly145insSerGln,and TBC1D4 p.Arg1249Trp)were identified in three probands.Conclusion Patients with early-onset diabetes involving at least two consecutive generations may harbor genetic variants.Genetic testing in this population enables precision diagnosis,informs individualized treatment,and facilitates genetic counseling.
文摘Over the past decade,the therapeutic armamentarium for inflammatory bowel disease(IBD)has substantially expanded with the incorporation of multiple classes of advanced therapies.Currently,in addition to tumor necrosis factor-α inhibitors,the therapeutic arsenal for IBD includes anti-integrin agents,interleukin(IL)-12/23p40 and IL-23p19 antibodies,Janus kinase inhibitors,and sphingosine 1-phosphate receptor modulators.Although advances in IBD pharmacotherapy have enabled disease remission and improved control of intestinal inflammation in many individuals previously considered clinically'intractable',they have also increased the complexity of decision-making related to the initial positioning and sequencing of therapies in the heterogeneous clinical presentations of IBD.Until molecular and genetic markers capable of predicting therapeutic responses become available in practice,the choice of initial and subsequent therapy in individuals with IBD is based on factors including disease severity,phenotype,risk of complications,comorbidities,extraintestinal manifestations,and the balance between efficacy,safety,convenience,and access.This review explores the factors that influence treatment decisions regarding initial therapy selection and sequencing across IBD scenarios,offering practical tips for personalizing therapy based on the safety and efficacy of advanced treatments and the individual's risk of disease-or therapy-related adverse outcomes.
基金supported in part by funds obtained through an Italian law that allows taxpayers to allocate 0.5 percent share of their income tax contribution to a research institution of their choice
文摘Background: Androgen insensitivity syndrome(AIS), a disorder of sexual development in 46, XY individuals, is caused by loss-of-function mutations in the androgen receptor(AR) gene. A variety of tumors have been reported in association with AIS, but no cases with colorectal cancer(CRC) have been described.Case presentation: Here, we present a male patient with AIS who developed multiple early-onset CRCs and his pedigree. His first cousin was diagnosed with AIS and harbored the same AR gene mutation, but with no signs of CRC. The difference in clinical management for the two patients was that testosterone treatment was given to the proband for a much longer time compared with the cousin. The CRC family history was negative, and no germline mutations in well-known CRC-related genes were identified. A single nucleotide polymorphism array revealed a microduplication on chromosome 22q11.22 that encompassed a micro RNA potentially related to CRC pathogenesis. In the proband, whole exome sequencing identified a polymorphism in an oncogene and 13 rare loss-of-function variants, of which two were in CRC-related genes and four were in genes associated with other human cancers.Conclusions: By pathway analysis, all inherited germline genetic events were connected in a unique network whose alteration in the proband, together with continuous testosterone stimulation, may have played a role in CRC pathogenesis.
基金the Foundation of State Key Laboratory of Ocean Engineering of Shanghai Jiao Tong University(No.GKZD010071)
文摘Wastewater treatment is a complicated dynamic process affected by microbial, chemical and physical factors. Faults are inevitable during the operation of modified sequencing batch reactors(MSBRs) because of the uncertainty of various factors. Abnormal MSBR results require fault diagnosis to determine the cause of failure and implement appropriate measures to adjust system operations. Bayesian network(BN) is a powerful knowledge representation tool that deals explicitly with uncertainty. A BN-based approach to diagnosing wastewater treatment systems based on MSBR is developed in this study. The network is constructed using the knowledge derived from literature and elicited from experts, and it is parametrized using independent data from a pilot test.A one-year pilot study is conducted to verify the diagnostic analysis. The proposed model is reasonable, and the diagnosis results are accurate. This approach can be applied with minimal modifications to other types of wastewater treatment plants.
基金Supported by The author’s laboratory is supported by the Defence Research and Development Organization(DRDO),Ministry of Defence,Government of India
文摘Viruses are a cause of significant health problem world-wide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of nextgeneration sequencers(NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequenceindependent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.
