In this paper,based on the observation data of air temperature during 1951-2009 in Shenyang,the interannual and interdecadal variation of annual average temperature,maximum and minimum temperature in Shenyang were con...In this paper,based on the observation data of air temperature during 1951-2009 in Shenyang,the interannual and interdecadal variation of annual average temperature,maximum and minimum temperature in Shenyang were conducted the statistical analysis by means of linear trend estimation and mutation detection by using Mann-Kendall method.As was demonstrated in the results,the annual average temperature,maximum and minimum temperature in Shenyang showed an upward trend,whose linear tendency rate was 0.231,0.181 and 0.218 respectively.The increment trend of annual average temperature,maximum and minimum temperature was extremely clear.The increase in minimum temperature was more significant than that in mean temperature and maximum temperature.The abrupt change point of annual mean temperature in Shenyang appeared in 1981;the abrupt change point of annual mean maximum temperature appeared in 1994;the annual mean minimum temperature underwent mutation in 1978.展开更多
A measure of the“goodness”or efficiency of the test suite is used to determine the proficiency of a test suite.The appropriateness of the test suite is determined through mutation analysis.Several Finite State Machi...A measure of the“goodness”or efficiency of the test suite is used to determine the proficiency of a test suite.The appropriateness of the test suite is determined through mutation analysis.Several Finite State Machine(FSM)mutants are produced in mutation analysis by injecting errors against hypotheses.These mutants serve as test subjects for the test suite(TS).The effectiveness of the test suite is proportional to the number of eliminated mutants.The most effective test suite is the one that removes the most significant number of mutants at the optimal time.It is difficult to determine the fault detection ratio of the system.Because it is difficult to identify the system’s potential flaws precisely.In mutation testing,the Fault Detection Ratio(FDR)metric is currently used to express the adequacy of a test suite.However,there are some issues with this metric.If both test suites have the same defect detection rate,the smaller of the two tests is preferred.The test case(TC)is affected by the same issue.The smaller two test cases with identical performance are assumed to have superior performance.Another difficulty involves time.The performance of numerous vehicles claiming to have a perfect mutant capture time is problematic.Our study developed three metrics to address these issues:FDR/|TS|,FDR/|TC|,and FDR/|Time|;In this context,most used test generation tools were examined and tested using the developed metrics.Thanks to the metrics we have developed,the research contributes to eliminating the problems related to performance measurement by integrating the missing parameters into the system.展开更多
Objective To discuss clinical diagnosis and treatment of multiple endocrine neoplasia ( MEN) 2A,and report the mutation of RET proto-oncogene in a pedigree of three patients with MEN 2A. Methods Bilateral adrenalectom...Objective To discuss clinical diagnosis and treatment of multiple endocrine neoplasia ( MEN) 2A,and report the mutation of RET proto-oncogene in a pedigree of three patients with MEN 2A. Methods Bilateral adrenalectomy was performed on two of the three展开更多
The CRISPR-Cas system has revolutionized modern life sciences,enabling groundbreaking applications ranging from functional genomics to therapeutic development.Despite its transformative potential,significant technical...The CRISPR-Cas system has revolutionized modern life sciences,enabling groundbreaking applications ranging from functional genomics to therapeutic development.Despite its transformative potential,significant technical limitations persist in current computational tools for quantifying editing efficiency-particularly concerning data processing capabilities,analytical throughput,and operational flexibility.This research presents SuperDecode,a novel computational framework designed to address these methodological constraints.The SuperDecode offers key advantages,including local processing capabilities,large-size sequencing files,batch-processing,and diversified operational functions.展开更多
BACKGROUND Colorectal cancer(CRC)remains a major global health burden due to its high incidence and mortality,with treatment efficacy often hindered by tumor hetero-geneity,drug resistance,and a complex tumor microenv...BACKGROUND Colorectal cancer(CRC)remains a major global health burden due to its high incidence and mortality,with treatment efficacy often hindered by tumor hetero-geneity,drug resistance,and a complex tumor microenvironment(TME).Lactate metabolism plays a pivotal role in reshaping the TME,promoting immune eva-sion and epithelial-mesenchymal transition,making it a promising target for novel therapeutic strategies and prognostic modeling in CRC.AIM To offer an in-depth analysis of the role of lactate metabolism in CRC,high-lighting its significance in the TME and therapeutic response.METHODS Utilizing single-cell and transcriptomic data from the Gene Expression Omnibus and The Cancer Genome Atlas,we identified key lactate metabolic activities,particularly in the monocyte/macrophage subpopulation.RESULTS Seven lactate metabolism-associated genes were significantly linked to CRC prognosis and used to construct a predictive model.This model accurately forecasts patient outcomes and reveals notable distinct patterns of immune infiltration and transcriptomic profiles mutation profiles between high-and low-risk groups.High-risk patients demonstrated elevated immune cell infiltration,increased mutation frequencies,and heightened sensitivity to specific drugs(AZD6482,tozasertib,and SB216763),providing a foundation for personalized treatment approaches.Additionally,a nomogram integrating clinical and metabolic data effectively predicted 1-,3-,and 5-year survival rates.CONCLUSION This report underscored the pivotal mechanism of lactate metabolism in CRC prognosis and suggest novel avenues for therapeutic intervention.展开更多
Background Mutations in PAX6 gene have been shown to be the genetic cause of aniridia, which is a severe panocular eye disease characterised by iris hypoplasia. However, there is no study to do genetic analysis of ani...Background Mutations in PAX6 gene have been shown to be the genetic cause of aniridia, which is a severe panocular eye disease characterised by iris hypoplasia. However, there is no study to do genetic analysis of aniridia, although there are several case reports in China. Here, we describe a mutation analysis of PAX6 in a large Chinese family with aniridia. Methods Genomic DNA from venous blood samples was prepared. Haplotype analysis was performed with two genetic markers ( D11S904 and D11S935). Fourteen exons of the PAX6 gene were amplified from genomic DNA. Polymerase chain reaction ( PCR) products of each exon were analysed by single strand conformational polymorphism (SSCP). The PCR products having an abnormal pattern were sequenced to confirm the mutation. Results Significant evidence for allele sharing in affected patients was detected suggesting that PAX6 mutation links to aniridia in this family. An extra band corresponding to exon 9 in PAX6 was found by single strand conformational polymorphism analysis in all the aniridia patients in this family, but not detected in the unaffected members. A mutation of C to T was detected by sequencing at the nucleotide 1080 that converts the Arg codon (CGA) to the termination codon (TGA). Conclusions Aniridia is caused by a nonsense mutation of PAX6 gene in the large Chinese kindred. Genetic test is important to prevent the transmission of aniridia to their offsprings in the kindred by prenatal diagnosis.展开更多
Charcot-Marie-Tooth （CMT） disease is the most common inherited peripheral neuropathic disorder. CMT is clinically and genetically heterogeneous. To date, 27 genes associated with the disease have been cloned. The pr...Charcot-Marie-Tooth （CMT） disease is the most common inherited peripheral neuropathic disorder. CMT is clinically and genetically heterogeneous. To date, 27 genes associated with the disease have been cloned. The present study carried out clinical classification according to clinical, electrophysiological and pathological features, conducted inheritance classification according to inheritance patterns, and performed mutation analysis of 13 CMT disease genes （PMP22, CX32, HSPB1, MNF2, MPZ, HSPB8, GDAP1, NFL, EGR2, SIMPLE, RAB7, LMNA, MTMR2） in 57 Chinese probands with CMT. Five cases of AD-CMT1 and 13 cases of sporadic CMT1 were diagnosed as CMT1A; five cases of X-CMT1, one case of X-CMT2 and one case of sporadic CMT1 were diagnosed as CMTXl; four cases of AD-CMT2 were diagnosed as CMT2F; one case of AD-CMT2 and one case of sporadic CMT2 were diagnosed as CMT2A2; one case of AD-CMT2 was diagnosed as CMT2L; one case of AD-CMT2 was diagnosed as CMT2J; one case of AR-CMT1 was diagnosed as CMT4A. Among the 57 CMT probands, seven genotypes were determined among 34 patients, with a detection rate of 59.6%. The results indicated that the clinical classification and inheritance classification are indispensable for selecting potential disease genes for mutation detection, and for efficient molecular diagnosis.展开更多
Background Difficulties persist in differentiating pancreatic ductal adenocarcinomas （PDAC） from pancreatic inflammatory masses （PIM）. Auxiliary diagnostic techniques which enhance the endoscopic ultrasound-guided...Background Difficulties persist in differentiating pancreatic ductal adenocarcinomas （PDAC） from pancreatic inflammatory masses （PIM）. Auxiliary diagnostic techniques which enhance the endoscopic ultrasound-guided fine-needle aspiration （EUS-FNA） diagnostic yield have been attempted, for example, K-ras mutation analysis. We aimed to evaluate the accuracy of K-ras mutation analysis combined with EUS-FNA for the differential diagnosis of PDAC and PIM by pooling data of existing trials. Methods We systematically searched the Medline, PubMed, Web of Science, Embase, and Cochrane Central Trials databases for relevant published studies. Meta-analysis was performed. Pooling was conducted in fixed-effect model or random-effect model. Results In total eight studies, with 696 cases of PDAC and 138 cases of PIM, met our inclusion criteria. The pooled sensitivity, specificity, positive likely ratio and negative likely ratio of K-ras mutation analysis combined with cytopathology for diagnosis of PDAC versus PIM were 90%, 95%, 13.45, and 0.13, respectively. Especially, among total 123 patients whose EUS-FNA results were inconclusive or negative, fifty-nine had K-ras mutations and were finally diagnosed with PDAC （48%, 59/123）. Publication bias was not present. Conclusions Combining K-ras mutation analysis with routine cytology moderately improves the ability of EUS-FNA to differentially diagnose between PDAC and PIM, especially for patients with suspected PDAC yet inconclusive EUS-FNA findings, and may prove to be a valuable supplemental method to EUS-FNA.展开更多
Newcastle disease (ND) virus is a leading threat to commercial and domestic poultry in Pakistan. The virus infects and constitutes irreversible impairment to the nervous system, damages the respiratory system, and mar...Newcastle disease (ND) virus is a leading threat to commercial and domestic poultry in Pakistan. The virus infects and constitutes irreversible impairment to the nervous system, damages the respiratory system, and marks severe gastrointestinal lesions leading to heavy mortality in short-living birds and substantial losses in layers and breeders. The continuous emergence and evolution of the virus made it inclined to evade the humoral response and indirectly the circumvention of artificial active immunization. Newcastle disease is caused by the orthoavula genus of the paramyxoviridae family and has shown high genetic diversity even in their genotypes while information regarding enzootic trends of the virus is scanty in Pakistan. A total of 40 tracheal samples of NDV were collected from different commercial broiler farms and 11 isolates of NDV were identified. In the current study, we determined the genetic diversity of the Newcastle disease virus based on the partial sequencing of the fusion protein gene available in the NCBI database. Genetic analysis showed that seven isolates belonged to class I genotype VII and four belonged to class II genotype II. Interestingly, two isolates had epidemiological connections with vaccine-like class II genotype II. Our findings, concerning the recent outbreaks of class I genotype VII and class II genotype II of NDV in vaccinated commercial flocks, suggest possible potential partial mutations in the fusion protein gene. Genetic diversity and formation of the new cleavage site in an important neutralizing protein of wild strain are linked with the potency of artificial active immunization and a major cause of vaccine failure.展开更多
AIM:To compare the differences between dideoxy sequencing/KRAS StripAssay/pyrosequencing for detection of KRAS mutation in Chinese colorectal cancer (CRC) patients.METHODS:Formalin-f ixed, paraff in-embedded (FFPE) sa...AIM:To compare the differences between dideoxy sequencing/KRAS StripAssay/pyrosequencing for detection of KRAS mutation in Chinese colorectal cancer (CRC) patients.METHODS:Formalin-f ixed, paraff in-embedded (FFPE) samples with tumor cells ≥ 50% were collected from 100 Chinese CRC patients at Beijing Cancer Hospital. After the extraction of genome DNA from FFPE samples, fragments contained codons 12 and 13 of KRAS exon 2 were amplified by polymerase chain reaction and analyzed by dideoxy sequencing, the KRAS Strip Assay and pyrosequencing. In addition, the sensitivities of the 3 methods were compared on serial dilutions (contents of mutant DNA: 100%,50%,20%, 5%,10%, 5%,1%,0%) of A549 cell line DNA (carrying the codon 12 Gly>Ser mutation) into wild-type DNA (human normal intestinal mucosa). The results of dideoxy sequencing,the KRAS StripAssay and pyrosequencing were analyzed by Chromas Software, Collector forKRAS Strip Assay and the pyrosequencing PyroMarkTM Q24 system, respectively.RESULTS: Among 100 patients, KRAS mutations were identif ied in 34%, 37% and 37% of patients by dideoxy sequencing, the KRAS StripAssay and pyrosequencing, respectively. The sensitivity was highest with the KRAS Strip Assay (1%), followed by pyrosequencing (5%), and dideoxy sequencing was lowest (15%). Six different mutation types were found in this study with 3 main mutations Gly12 Asp (GGT>GAT), Gly12 Val (GGT>GTT) and Gly13 Asp (GGC>GAC). Thirty-three patients were identifi ed to have KRAS mutations by the 3 methods, and a total of 8 patients had conflicting results between 3 methods: 4 mutations not detected by dideoxy sequencing and the KRAS StripAssay were identified by pyrosequencing; 3 mutations not detected by dideoxy sequencing and pyrosequencing were identif ied by the KRAS StripAssay; and 1 mutation not detected by pyrosequencing was conf irmed by dideoxy sequencing and the KRAS StripAssay. Among these discordant results, the results identif ied by dideoxy sequencing were consistent either with the KRAS StripAssay or with pyrosequencing, which indicated that the accuracy of dideoxy sequencing was high. CONCLUSION: Taking a worldwide view of reports and our results,dideoxy sequencing remains the most popular method because of its low cost and high accuracy.展开更多
Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality.Cases are reported in several countries in Africa,Europe,the Middle East,and Asia.Phylogenetic analyses based on the virus S (nucleocapsid)...Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality.Cases are reported in several countries in Africa,Europe,the Middle East,and Asia.Phylogenetic analyses based on the virus S (nucleocapsid),M (glycoprotein),and L (polymerase) genome segments sequences indicate distinct geographic lineages exist but their specific genetic characteristics require elucidation.In this work we collected all full length S segment sequences and generated a phylogenetic tree based on the alignment of these 62 samples.We then analyzed the alignment using entries from AAIndex,the Amino Acid Index database,to identify amino acid mutations that performed significant changes in charge,pka,hydropathy and side chain volume.Finally,we mapped these changes back to the tree and alignment to identify correlated mutations or sites that characterized a specific lineage.Based on this analysis we are able to propose a number of sites that appear to be important for virus function and which would be good candidates for experimental mutational analysis studies.展开更多
Climate change and anthropogenic activities have driven significant terrestrial water storage changes(TWSC)in the Three Rivers Source Region(TRSR),exerting profound impacts on freshwater availability across China and ...Climate change and anthropogenic activities have driven significant terrestrial water storage changes(TWSC)in the Three Rivers Source Region(TRSR),exerting profound impacts on freshwater availability across China and broader Asia.However,long-term TWSC characterization remains challenging due to limited observational data in this alpine region.Here,we integrate GRACE observations(2002-2020),ERA5-Land reanalysis,and GLDAS data to reconstruct TWSC using two methods:(1)the water balance method(PER)and(2)the component summation method(SS),applied to three input datasets(ERA5-Land,GLDAS,and their average,GLER).Comparative analysis reveals that the SS method applied to GL-ER yields the highest consistency with GRACE-derived TWSC.Using this optimal approach,we extend the analysis to 1951~2020,uncovering spatiotemporal TWSC patterns.Although annual TWSC trends appear negligible due to strong seasonality,we introduce the intra-year TWSC fluctuation(TWSCF)index to quantify cumulative variability.A significant(p<0.05)transition occurred in 1980,with TWSCF shifting from a declining trend(-0.39 mm/yr)to an increasing trend(0.56 mm/yr),primarily driven by soil moisture changes.However,Hurst exponent analysis suggests this upward trend may not persist.Drought and vegetation assessments indicate concurrent wetting and greening in the TRSR.TWSC correlates strongly with meteorological drought,acting as a reliable drought indicator while its linkage with vegetation dynamics suggests a potential contribution to greening.Our findings provide a robust framework for understanding long-term TWSC evolution and its hydrological-ecological interactions under climate change.展开更多
AIM: To analyze the metallochaperone antioxidant-1 (Atox1) gene sequence in Wilson disease patients. METHODS: Mutation analysis of the four exons of the Atox1 gene including the intron- exon boundaries was performed i...AIM: To analyze the metallochaperone antioxidant-1 (Atox1) gene sequence in Wilson disease patients. METHODS: Mutation analysis of the four exons of the Atox1 gene including the intron- exon boundaries was performed in 63 Wilson disease patients by direct sequencing. RESULTS: From 63 selected patients no mutations were identified after the entire coding region including the intron- exon boundaries of Atox1 were sequenced. One known polymorphism within the Atox1 gene (5’UTR -99 T>C) in 31 (49%) of the Wilson patients as well as one previously undescribed variation (5’UTR -68 C>T) in 2 of the Wilson patients could be detected. Statistical analyses revealed that the existence of a variation within the Atox1- gene showed a tendency towards an earlier onset of the disease. CONCLUSION: Based on the data of this study, no major role can be attributed to Atox1 in the pathophysiology or clinical variation of Wilson disease.展开更多
The speckle-type POZ protein （SPOP） is a tumor suppressor in prostate cancer （PCa）. SPOP somatic mutations have been reported in up to 15% of PCa of those of European descent. However, the genetic roles of SPOP in...The speckle-type POZ protein （SPOP） is a tumor suppressor in prostate cancer （PCa）. SPOP somatic mutations have been reported in up to 15% of PCa of those of European descent. However, the genetic roles of SPOP in African American （AA）-PCa are currently unknown. We sequenced the SPOP gene to identify somatic mutations in 49 AA prostate tumors and identified three missense mutations （p.Y87C, p.F102S, and p.G111E） in five AA prostate tumors （10%） and one synonymous variant （p.11061） in one tumor. Intriguingly, all of mutations and variants clustered in exon six, and all of the mutations altered conserved amino acids. Moreover, two mutations （p.F102S and p.G111E） have only been identified in AA-PCa to date. Quantitative real-time polymerase chain reaction analysis showed a lower level of SPOP expression in tumors carrying SPOP mutations than their matched normal prostate tissues. In addition, SPOP mutations and novel variants were detected in 5 of 27 aggressive PCa and one of 22 less aggressive PCa （P 〈 0.05）. Further studies with increased sample size are needed to validate the clinicopathological significance of these SPOP mutations in AA-PCa.展开更多
AIM： To establish the role of human T Cell Factor-4 （hTCF-4） gene exons 3-9 mutation status in association with sporadic rectal cancer with microsatellite instability （MSI）. METHODS： Microsatellite markers were ...AIM： To establish the role of human T Cell Factor-4 （hTCF-4） gene exons 3-9 mutation status in association with sporadic rectal cancer with microsatellite instability （MSI）. METHODS： Microsatellite markers were genotyped in 93 sporadic rectal cancer patients. Eleven cases were found to be high-frequency MSI （MSI-H）. Sequence analysis of the coding region of the exons 3-9 of hTCF-4 gene was carried out for the 11 MSI-H cases and 10 controls （5 microsatellite stability （MSS） cases and 5 cases with normal mucosa）. The sequencing and MSI identification were used. RESULTS： Several novel mutations and variants were revealed. In exon 4, one is a 4-position continuous alteration which caused amino acid change from Q131T and S132I （391insA, 392 G 〉 A, 393 A 〉 G and 395delC） and another nucleotide deletion （395delC） is present in MSI-H cases （5/10 and 4/10, respectively） but completely absent in the controls.CONCLUSION： Novel mutations in exon 4 of hTCF-4 gene were revealed in this study, which might be of importance in the pathogenesis of sporadic rectal cancer patients with MSI-H.展开更多
Prostate cancer is one of the major health care problems, but the molecular pathogenesis has been relatively insufficiently elucidated. Recently, whole exome sequencing of prostate cancer identified recurrent mutation...Prostate cancer is one of the major health care problems, but the molecular pathogenesis has been relatively insufficiently elucidated. Recently, whole exome sequencing of prostate cancer identified recurrent mutations involving MED12 in Caucasian patients, which finding was not reproduced in one subsequent study by Sanger sequencing. Thus, we investigated mutation status of MED12 in exons 2 and 26 by Sanger sequencing in 102 radical prostatectomy cases from Korean patients. The analysis found the mutation in none of the cases. Therefore, MED12 mutation does not appear to represent a significant molecular alteration in this cohort of patients according to the analysis by the traditional ＂gold standard.＂展开更多
Advances in technology are enabling gene mutations in papillary thyroid carcinoma(PTC)to be analyzed and clinical outcomes,such as recurrence,to be predicted.To date,the most common genetic mutation in PTC is in BRAF ...Advances in technology are enabling gene mutations in papillary thyroid carcinoma(PTC)to be analyzed and clinical outcomes,such as recurrence,to be predicted.To date,the most common genetic mutation in PTC is in BRAF kinase(BRAF).However,whether mutations in other genes coincide with those in BRAF remains to be clarified.The aim of this study was to find mutations in other genes that co-exist with mutated BRAF,and to analyze their frequency and clinical relevance in PTC.Clinical and genetic data were collected from 213 PTC patients with a total of 36,572 mutation sites in 735 genes.After matching with genes from PTC entries in a global database(NCBI Gene),69 genes with mutations in coding regions were chosen for further study.Through frequency-based analysis,we identified commonly mutated genes co-existing with mutated BRAF and,using the mutation count correlation matrix(MCCM)method,analyzed their incidence according to age and gender.We designed Chord diagrams to reveal gene relationships concerning age and gender,and found that mutations in ALK,ATM,COL1A1,MSTIR,PRKCA,and WNK1 most commonly coincide with mutated BRAF,followed by APC,AURKA,and AURKB.These findings provide further insight into the genetic profile of PTC.展开更多
The mutation is a critical element in determining the proteins’stability,becoming a core element in portraying the effects of a drug in the pharmaceutical industry.Doing wet laboratory tests to provide a better persp...The mutation is a critical element in determining the proteins’stability,becoming a core element in portraying the effects of a drug in the pharmaceutical industry.Doing wet laboratory tests to provide a better perspective on protein mutations is expensive and time-intensive since there are so many potential muta-tions,computational approaches that can reliably anticipate the consequences of amino acid mutations are critical.This work presents a robust methodology to analyze and identify the effects of mutation on a single protein structure.Initially,the context in a collection of words is determined using a knowledge graph for feature selection purposes.The proposed prediction is based on an easier and sim-pler logistic regression inferred binary classification technique.This approach can able to obtain a classification accuracy(AUC)Area Under the Curve of 87%when randomly validated against experimental energy changes.Moreover,for each cross-fold validation,the precision,recall,and F-Score are presented.These results support the validity of our strategy since it performs the vast majority of prior studies in this domain.展开更多
[Objective]The research aimed to study the variation of rainfall data from Guilin Weather Station during 1957-2007.[Method]Based on the daily rainfall data in Guilin during 1957-2007,the trend,period and mutation of p...[Objective]The research aimed to study the variation of rainfall data from Guilin Weather Station during 1957-2007.[Method]Based on the daily rainfall data in Guilin during 1957-2007,the trend,period and mutation of precipitation in Guilin in 51 years were analyzed by using the trend analysis,wavelet analysis and Mann-Kendall non-parameter statistics test method.[Result]The rainfall in Guilin in 51 years presented the rising trend.The rainfall variation was same in the first,second and third quarters of most years,except in the individual year.The rainfall in the fourth quarter had the decrease trend,and the variation was obvious in each year.It illustrated that the rainfall variation in winter was very unstable and had the decrease trend in recent years.But as a whole,the variation of total rainfall in Guilin wasn’t obvious and had the rise trend.It illustrated that the climate variation in Guilin in 51 years wasn’t obvious.The wavelet analysis showed that the rainfall variation in Guilin had 15-year big period and the small period of 2-3 years.Mann-Kendall non-parameter statistics test showed that the mutation situation of total rainfall in Guilin in 51 years wasn’t obvious.But the mutation situations in the second and third quarters were more.The variation in recent 10 years was the most obvious.Maybe it was affected by the global climate variation.[Conclusion]The research provided the theory basis for analyzing the climate variation in Guilin.展开更多
Based on data of temperature and precipitation in Huanren County from 1953 to 2010, linear trend analysis and mutation detection of temperature and precipitation sequence were carried out using linear trend, Mann-Kend...Based on data of temperature and precipitation in Huanren County from 1953 to 2010, linear trend analysis and mutation detection of temperature and precipitation sequence were carried out using linear trend, Mann-Kendall detection and dryness of the de Martonne method. The results showed that during 1953-2010, annual average temperature, annual average maximum and minimum temperature in Huanren County showed an increasing trend; annual precipitation showed a decreasing trend; there was a downward trend in annual dryness. The mutation of annu- al average temperature, annual average maximum and minimum temperature appeared in 1978, 1987 and 1982 respectively; there was no mutation of annual precipitation and dryness. On the whole, the climate of Huanren County tended to be warm and dry over the past 58 years.展开更多
基金Supported by the Infrastructure Project of China Meteorological Administration(CMA) in 2010~~
文摘In this paper,based on the observation data of air temperature during 1951-2009 in Shenyang,the interannual and interdecadal variation of annual average temperature,maximum and minimum temperature in Shenyang were conducted the statistical analysis by means of linear trend estimation and mutation detection by using Mann-Kendall method.As was demonstrated in the results,the annual average temperature,maximum and minimum temperature in Shenyang showed an upward trend,whose linear tendency rate was 0.231,0.181 and 0.218 respectively.The increment trend of annual average temperature,maximum and minimum temperature was extremely clear.The increase in minimum temperature was more significant than that in mean temperature and maximum temperature.The abrupt change point of annual mean temperature in Shenyang appeared in 1981;the abrupt change point of annual mean maximum temperature appeared in 1994;the annual mean minimum temperature underwent mutation in 1978.
文摘A measure of the“goodness”or efficiency of the test suite is used to determine the proficiency of a test suite.The appropriateness of the test suite is determined through mutation analysis.Several Finite State Machine(FSM)mutants are produced in mutation analysis by injecting errors against hypotheses.These mutants serve as test subjects for the test suite(TS).The effectiveness of the test suite is proportional to the number of eliminated mutants.The most effective test suite is the one that removes the most significant number of mutants at the optimal time.It is difficult to determine the fault detection ratio of the system.Because it is difficult to identify the system’s potential flaws precisely.In mutation testing,the Fault Detection Ratio(FDR)metric is currently used to express the adequacy of a test suite.However,there are some issues with this metric.If both test suites have the same defect detection rate,the smaller of the two tests is preferred.The test case(TC)is affected by the same issue.The smaller two test cases with identical performance are assumed to have superior performance.Another difficulty involves time.The performance of numerous vehicles claiming to have a perfect mutant capture time is problematic.Our study developed three metrics to address these issues:FDR/|TS|,FDR/|TC|,and FDR/|Time|;In this context,most used test generation tools were examined and tested using the developed metrics.Thanks to the metrics we have developed,the research contributes to eliminating the problems related to performance measurement by integrating the missing parameters into the system.
文摘Objective To discuss clinical diagnosis and treatment of multiple endocrine neoplasia ( MEN) 2A,and report the mutation of RET proto-oncogene in a pedigree of three patients with MEN 2A. Methods Bilateral adrenalectomy was performed on two of the three
文摘The CRISPR-Cas system has revolutionized modern life sciences,enabling groundbreaking applications ranging from functional genomics to therapeutic development.Despite its transformative potential,significant technical limitations persist in current computational tools for quantifying editing efficiency-particularly concerning data processing capabilities,analytical throughput,and operational flexibility.This research presents SuperDecode,a novel computational framework designed to address these methodological constraints.The SuperDecode offers key advantages,including local processing capabilities,large-size sequencing files,batch-processing,and diversified operational functions.
基金Supported by Henan Province Science and Technology Research Project,No.232102310043Henan Provincial Science and Technology Research and Development Plan Joint Fund,No.222103810047Key Scientific Research Project Plan of Colleges and Universities in Henan Province,No.22A320033.
文摘BACKGROUND Colorectal cancer(CRC)remains a major global health burden due to its high incidence and mortality,with treatment efficacy often hindered by tumor hetero-geneity,drug resistance,and a complex tumor microenvironment(TME).Lactate metabolism plays a pivotal role in reshaping the TME,promoting immune eva-sion and epithelial-mesenchymal transition,making it a promising target for novel therapeutic strategies and prognostic modeling in CRC.AIM To offer an in-depth analysis of the role of lactate metabolism in CRC,high-lighting its significance in the TME and therapeutic response.METHODS Utilizing single-cell and transcriptomic data from the Gene Expression Omnibus and The Cancer Genome Atlas,we identified key lactate metabolic activities,particularly in the monocyte/macrophage subpopulation.RESULTS Seven lactate metabolism-associated genes were significantly linked to CRC prognosis and used to construct a predictive model.This model accurately forecasts patient outcomes and reveals notable distinct patterns of immune infiltration and transcriptomic profiles mutation profiles between high-and low-risk groups.High-risk patients demonstrated elevated immune cell infiltration,increased mutation frequencies,and heightened sensitivity to specific drugs(AZD6482,tozasertib,and SB216763),providing a foundation for personalized treatment approaches.Additionally,a nomogram integrating clinical and metabolic data effectively predicted 1-,3-,and 5-year survival rates.CONCLUSION This report underscored the pivotal mechanism of lactate metabolism in CRC prognosis and suggest novel avenues for therapeutic intervention.
基金This work was suppofled by grants from the Chinese National 973 Project(2002CB510100),863 Project(2003AA205070),the Ministry of Education 211 Project and the grants from the Beijing Ministry of Science and Technology(2002—489).
文摘Background Mutations in PAX6 gene have been shown to be the genetic cause of aniridia, which is a severe panocular eye disease characterised by iris hypoplasia. However, there is no study to do genetic analysis of aniridia, although there are several case reports in China. Here, we describe a mutation analysis of PAX6 in a large Chinese family with aniridia. Methods Genomic DNA from venous blood samples was prepared. Haplotype analysis was performed with two genetic markers ( D11S904 and D11S935). Fourteen exons of the PAX6 gene were amplified from genomic DNA. Polymerase chain reaction ( PCR) products of each exon were analysed by single strand conformational polymorphism (SSCP). The PCR products having an abnormal pattern were sequenced to confirm the mutation. Results Significant evidence for allele sharing in affected patients was detected suggesting that PAX6 mutation links to aniridia in this family. An extra band corresponding to exon 9 in PAX6 was found by single strand conformational polymorphism analysis in all the aniridia patients in this family, but not detected in the unaffected members. A mutation of C to T was detected by sequencing at the nucleotide 1080 that converts the Arg codon (CGA) to the termination codon (TGA). Conclusions Aniridia is caused by a nonsense mutation of PAX6 gene in the large Chinese kindred. Genetic test is important to prevent the transmission of aniridia to their offsprings in the kindred by prenatal diagnosis.
基金the National Natural Science Foundation of China, No. 81071001, 30600200the Natural Science Foundation of Hu-nan Province, No. 2006JJ30009
文摘Charcot-Marie-Tooth （CMT） disease is the most common inherited peripheral neuropathic disorder. CMT is clinically and genetically heterogeneous. To date, 27 genes associated with the disease have been cloned. The present study carried out clinical classification according to clinical, electrophysiological and pathological features, conducted inheritance classification according to inheritance patterns, and performed mutation analysis of 13 CMT disease genes （PMP22, CX32, HSPB1, MNF2, MPZ, HSPB8, GDAP1, NFL, EGR2, SIMPLE, RAB7, LMNA, MTMR2） in 57 Chinese probands with CMT. Five cases of AD-CMT1 and 13 cases of sporadic CMT1 were diagnosed as CMT1A; five cases of X-CMT1, one case of X-CMT2 and one case of sporadic CMT1 were diagnosed as CMTXl; four cases of AD-CMT2 were diagnosed as CMT2F; one case of AD-CMT2 and one case of sporadic CMT2 were diagnosed as CMT2A2; one case of AD-CMT2 was diagnosed as CMT2L; one case of AD-CMT2 was diagnosed as CMT2J; one case of AR-CMT1 was diagnosed as CMT4A. Among the 57 CMT probands, seven genotypes were determined among 34 patients, with a detection rate of 59.6%. The results indicated that the clinical classification and inheritance classification are indispensable for selecting potential disease genes for mutation detection, and for efficient molecular diagnosis.
文摘Background Difficulties persist in differentiating pancreatic ductal adenocarcinomas （PDAC） from pancreatic inflammatory masses （PIM）. Auxiliary diagnostic techniques which enhance the endoscopic ultrasound-guided fine-needle aspiration （EUS-FNA） diagnostic yield have been attempted, for example, K-ras mutation analysis. We aimed to evaluate the accuracy of K-ras mutation analysis combined with EUS-FNA for the differential diagnosis of PDAC and PIM by pooling data of existing trials. Methods We systematically searched the Medline, PubMed, Web of Science, Embase, and Cochrane Central Trials databases for relevant published studies. Meta-analysis was performed. Pooling was conducted in fixed-effect model or random-effect model. Results In total eight studies, with 696 cases of PDAC and 138 cases of PIM, met our inclusion criteria. The pooled sensitivity, specificity, positive likely ratio and negative likely ratio of K-ras mutation analysis combined with cytopathology for diagnosis of PDAC versus PIM were 90%, 95%, 13.45, and 0.13, respectively. Especially, among total 123 patients whose EUS-FNA results were inconclusive or negative, fifty-nine had K-ras mutations and were finally diagnosed with PDAC （48%, 59/123）. Publication bias was not present. Conclusions Combining K-ras mutation analysis with routine cytology moderately improves the ability of EUS-FNA to differentially diagnose between PDAC and PIM, especially for patients with suspected PDAC yet inconclusive EUS-FNA findings, and may prove to be a valuable supplemental method to EUS-FNA.
文摘Newcastle disease (ND) virus is a leading threat to commercial and domestic poultry in Pakistan. The virus infects and constitutes irreversible impairment to the nervous system, damages the respiratory system, and marks severe gastrointestinal lesions leading to heavy mortality in short-living birds and substantial losses in layers and breeders. The continuous emergence and evolution of the virus made it inclined to evade the humoral response and indirectly the circumvention of artificial active immunization. Newcastle disease is caused by the orthoavula genus of the paramyxoviridae family and has shown high genetic diversity even in their genotypes while information regarding enzootic trends of the virus is scanty in Pakistan. A total of 40 tracheal samples of NDV were collected from different commercial broiler farms and 11 isolates of NDV were identified. In the current study, we determined the genetic diversity of the Newcastle disease virus based on the partial sequencing of the fusion protein gene available in the NCBI database. Genetic analysis showed that seven isolates belonged to class I genotype VII and four belonged to class II genotype II. Interestingly, two isolates had epidemiological connections with vaccine-like class II genotype II. Our findings, concerning the recent outbreaks of class I genotype VII and class II genotype II of NDV in vaccinated commercial flocks, suggest possible potential partial mutations in the fusion protein gene. Genetic diversity and formation of the new cleavage site in an important neutralizing protein of wild strain are linked with the potency of artificial active immunization and a major cause of vaccine failure.
文摘AIM:To compare the differences between dideoxy sequencing/KRAS StripAssay/pyrosequencing for detection of KRAS mutation in Chinese colorectal cancer (CRC) patients.METHODS:Formalin-f ixed, paraff in-embedded (FFPE) samples with tumor cells ≥ 50% were collected from 100 Chinese CRC patients at Beijing Cancer Hospital. After the extraction of genome DNA from FFPE samples, fragments contained codons 12 and 13 of KRAS exon 2 were amplified by polymerase chain reaction and analyzed by dideoxy sequencing, the KRAS Strip Assay and pyrosequencing. In addition, the sensitivities of the 3 methods were compared on serial dilutions (contents of mutant DNA: 100%,50%,20%, 5%,10%, 5%,1%,0%) of A549 cell line DNA (carrying the codon 12 Gly>Ser mutation) into wild-type DNA (human normal intestinal mucosa). The results of dideoxy sequencing,the KRAS StripAssay and pyrosequencing were analyzed by Chromas Software, Collector forKRAS Strip Assay and the pyrosequencing PyroMarkTM Q24 system, respectively.RESULTS: Among 100 patients, KRAS mutations were identif ied in 34%, 37% and 37% of patients by dideoxy sequencing, the KRAS StripAssay and pyrosequencing, respectively. The sensitivity was highest with the KRAS Strip Assay (1%), followed by pyrosequencing (5%), and dideoxy sequencing was lowest (15%). Six different mutation types were found in this study with 3 main mutations Gly12 Asp (GGT>GAT), Gly12 Val (GGT>GTT) and Gly13 Asp (GGC>GAC). Thirty-three patients were identifi ed to have KRAS mutations by the 3 methods, and a total of 8 patients had conflicting results between 3 methods: 4 mutations not detected by dideoxy sequencing and the KRAS StripAssay were identified by pyrosequencing; 3 mutations not detected by dideoxy sequencing and pyrosequencing were identif ied by the KRAS StripAssay; and 1 mutation not detected by pyrosequencing was conf irmed by dideoxy sequencing and the KRAS StripAssay. Among these discordant results, the results identif ied by dideoxy sequencing were consistent either with the KRAS StripAssay or with pyrosequencing, which indicated that the accuracy of dideoxy sequencing was high. CONCLUSION: Taking a worldwide view of reports and our results,dideoxy sequencing remains the most popular method because of its low cost and high accuracy.
文摘Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality.Cases are reported in several countries in Africa,Europe,the Middle East,and Asia.Phylogenetic analyses based on the virus S (nucleocapsid),M (glycoprotein),and L (polymerase) genome segments sequences indicate distinct geographic lineages exist but their specific genetic characteristics require elucidation.In this work we collected all full length S segment sequences and generated a phylogenetic tree based on the alignment of these 62 samples.We then analyzed the alignment using entries from AAIndex,the Amino Acid Index database,to identify amino acid mutations that performed significant changes in charge,pka,hydropathy and side chain volume.Finally,we mapped these changes back to the tree and alignment to identify correlated mutations or sites that characterized a specific lineage.Based on this analysis we are able to propose a number of sites that appear to be important for virus function and which would be good candidates for experimental mutational analysis studies.
基金funded by the Postdoctoral Research Startup Foundation of University of Jinan(Grant No.100389917).
文摘Climate change and anthropogenic activities have driven significant terrestrial water storage changes(TWSC)in the Three Rivers Source Region(TRSR),exerting profound impacts on freshwater availability across China and broader Asia.However,long-term TWSC characterization remains challenging due to limited observational data in this alpine region.Here,we integrate GRACE observations(2002-2020),ERA5-Land reanalysis,and GLDAS data to reconstruct TWSC using two methods:(1)the water balance method(PER)and(2)the component summation method(SS),applied to three input datasets(ERA5-Land,GLDAS,and their average,GLER).Comparative analysis reveals that the SS method applied to GL-ER yields the highest consistency with GRACE-derived TWSC.Using this optimal approach,we extend the analysis to 1951~2020,uncovering spatiotemporal TWSC patterns.Although annual TWSC trends appear negligible due to strong seasonality,we introduce the intra-year TWSC fluctuation(TWSCF)index to quantify cumulative variability.A significant(p<0.05)transition occurred in 1980,with TWSCF shifting from a declining trend(-0.39 mm/yr)to an increasing trend(0.56 mm/yr),primarily driven by soil moisture changes.However,Hurst exponent analysis suggests this upward trend may not persist.Drought and vegetation assessments indicate concurrent wetting and greening in the TRSR.TWSC correlates strongly with meteorological drought,acting as a reliable drought indicator while its linkage with vegetation dynamics suggests a potential contribution to greening.Our findings provide a robust framework for understanding long-term TWSC evolution and its hydrological-ecological interactions under climate change.
基金German Research Foundation DFG Junior-Grant Faculty of Medicine, University of Heidelberg
文摘AIM: To analyze the metallochaperone antioxidant-1 (Atox1) gene sequence in Wilson disease patients. METHODS: Mutation analysis of the four exons of the Atox1 gene including the intron- exon boundaries was performed in 63 Wilson disease patients by direct sequencing. RESULTS: From 63 selected patients no mutations were identified after the entire coding region including the intron- exon boundaries of Atox1 were sequenced. One known polymorphism within the Atox1 gene (5’UTR -99 T>C) in 31 (49%) of the Wilson patients as well as one previously undescribed variation (5’UTR -68 C>T) in 2 of the Wilson patients could be detected. Statistical analyses revealed that the existence of a variation within the Atox1- gene showed a tendency towards an earlier onset of the disease. CONCLUSION: Based on the data of this study, no major role can be attributed to Atox1 in the pathophysiology or clinical variation of Wilson disease.
文摘The speckle-type POZ protein （SPOP） is a tumor suppressor in prostate cancer （PCa）. SPOP somatic mutations have been reported in up to 15% of PCa of those of European descent. However, the genetic roles of SPOP in African American （AA）-PCa are currently unknown. We sequenced the SPOP gene to identify somatic mutations in 49 AA prostate tumors and identified three missense mutations （p.Y87C, p.F102S, and p.G111E） in five AA prostate tumors （10%） and one synonymous variant （p.11061） in one tumor. Intriguingly, all of mutations and variants clustered in exon six, and all of the mutations altered conserved amino acids. Moreover, two mutations （p.F102S and p.G111E） have only been identified in AA-PCa to date. Quantitative real-time polymerase chain reaction analysis showed a lower level of SPOP expression in tumors carrying SPOP mutations than their matched normal prostate tissues. In addition, SPOP mutations and novel variants were detected in 5 of 27 aggressive PCa and one of 22 less aggressive PCa （P 〈 0.05）. Further studies with increased sample size are needed to validate the clinicopathological significance of these SPOP mutations in AA-PCa.
基金the National Natural Science Foundation of China, No. 39925032
文摘AIM： To establish the role of human T Cell Factor-4 （hTCF-4） gene exons 3-9 mutation status in association with sporadic rectal cancer with microsatellite instability （MSI）. METHODS： Microsatellite markers were genotyped in 93 sporadic rectal cancer patients. Eleven cases were found to be high-frequency MSI （MSI-H）. Sequence analysis of the coding region of the exons 3-9 of hTCF-4 gene was carried out for the 11 MSI-H cases and 10 controls （5 microsatellite stability （MSS） cases and 5 cases with normal mucosa）. The sequencing and MSI identification were used. RESULTS： Several novel mutations and variants were revealed. In exon 4, one is a 4-position continuous alteration which caused amino acid change from Q131T and S132I （391insA, 392 G 〉 A, 393 A 〉 G and 395delC） and another nucleotide deletion （395delC） is present in MSI-H cases （5/10 and 4/10, respectively） but completely absent in the controls.CONCLUSION： Novel mutations in exon 4 of hTCF-4 gene were revealed in this study, which might be of importance in the pathogenesis of sporadic rectal cancer patients with MSI-H.
文摘Prostate cancer is one of the major health care problems, but the molecular pathogenesis has been relatively insufficiently elucidated. Recently, whole exome sequencing of prostate cancer identified recurrent mutations involving MED12 in Caucasian patients, which finding was not reproduced in one subsequent study by Sanger sequencing. Thus, we investigated mutation status of MED12 in exons 2 and 26 by Sanger sequencing in 102 radical prostatectomy cases from Korean patients. The analysis found the mutation in none of the cases. Therefore, MED12 mutation does not appear to represent a significant molecular alteration in this cohort of patients according to the analysis by the traditional ＂gold standard.＂
基金supported by Grant No.02-2015-015 from the Seoul National University Bundang Hospital research fund.The funders had no role in the design of the studythe collection,analyses,or interpretation of the data+1 种基金the writing of the manuscriptor the decision to publish the results.
文摘Advances in technology are enabling gene mutations in papillary thyroid carcinoma(PTC)to be analyzed and clinical outcomes,such as recurrence,to be predicted.To date,the most common genetic mutation in PTC is in BRAF kinase(BRAF).However,whether mutations in other genes coincide with those in BRAF remains to be clarified.The aim of this study was to find mutations in other genes that co-exist with mutated BRAF,and to analyze their frequency and clinical relevance in PTC.Clinical and genetic data were collected from 213 PTC patients with a total of 36,572 mutation sites in 735 genes.After matching with genes from PTC entries in a global database(NCBI Gene),69 genes with mutations in coding regions were chosen for further study.Through frequency-based analysis,we identified commonly mutated genes co-existing with mutated BRAF and,using the mutation count correlation matrix(MCCM)method,analyzed their incidence according to age and gender.We designed Chord diagrams to reveal gene relationships concerning age and gender,and found that mutations in ALK,ATM,COL1A1,MSTIR,PRKCA,and WNK1 most commonly coincide with mutated BRAF,followed by APC,AURKA,and AURKB.These findings provide further insight into the genetic profile of PTC.
文摘The mutation is a critical element in determining the proteins’stability,becoming a core element in portraying the effects of a drug in the pharmaceutical industry.Doing wet laboratory tests to provide a better perspective on protein mutations is expensive and time-intensive since there are so many potential muta-tions,computational approaches that can reliably anticipate the consequences of amino acid mutations are critical.This work presents a robust methodology to analyze and identify the effects of mutation on a single protein structure.Initially,the context in a collection of words is determined using a knowledge graph for feature selection purposes.The proposed prediction is based on an easier and sim-pler logistic regression inferred binary classification technique.This approach can able to obtain a classification accuracy(AUC)Area Under the Curve of 87%when randomly validated against experimental energy changes.Moreover,for each cross-fold validation,the precision,recall,and F-Score are presented.These results support the validity of our strategy since it performs the vast majority of prior studies in this domain.
基金Supported by Guangxi Scientific and Technological Project(Guikegong 0816006-10)Scientific Research Item of Guangxi Science and Technology Agency(Guikeneng 0801Z004)
文摘[Objective]The research aimed to study the variation of rainfall data from Guilin Weather Station during 1957-2007.[Method]Based on the daily rainfall data in Guilin during 1957-2007,the trend,period and mutation of precipitation in Guilin in 51 years were analyzed by using the trend analysis,wavelet analysis and Mann-Kendall non-parameter statistics test method.[Result]The rainfall in Guilin in 51 years presented the rising trend.The rainfall variation was same in the first,second and third quarters of most years,except in the individual year.The rainfall in the fourth quarter had the decrease trend,and the variation was obvious in each year.It illustrated that the rainfall variation in winter was very unstable and had the decrease trend in recent years.But as a whole,the variation of total rainfall in Guilin wasn’t obvious and had the rise trend.It illustrated that the climate variation in Guilin in 51 years wasn’t obvious.The wavelet analysis showed that the rainfall variation in Guilin had 15-year big period and the small period of 2-3 years.Mann-Kendall non-parameter statistics test showed that the mutation situation of total rainfall in Guilin in 51 years wasn’t obvious.But the mutation situations in the second and third quarters were more.The variation in recent 10 years was the most obvious.Maybe it was affected by the global climate variation.[Conclusion]The research provided the theory basis for analyzing the climate variation in Guilin.
基金Supported by the Project of Meteorological Bureau of Benxi City,China(BQ2010002)
文摘Based on data of temperature and precipitation in Huanren County from 1953 to 2010, linear trend analysis and mutation detection of temperature and precipitation sequence were carried out using linear trend, Mann-Kendall detection and dryness of the de Martonne method. The results showed that during 1953-2010, annual average temperature, annual average maximum and minimum temperature in Huanren County showed an increasing trend; annual precipitation showed a decreasing trend; there was a downward trend in annual dryness. The mutation of annu- al average temperature, annual average maximum and minimum temperature appeared in 1978, 1987 and 1982 respectively; there was no mutation of annual precipitation and dryness. On the whole, the climate of Huanren County tended to be warm and dry over the past 58 years.
