The static and predictable characteristics of cyber systems give attackers an asymmetric advantage in gathering useful information and launching attacks.To reverse this asymmetric advantage,a new defense idea,called M...The static and predictable characteristics of cyber systems give attackers an asymmetric advantage in gathering useful information and launching attacks.To reverse this asymmetric advantage,a new defense idea,called Moving Target Defense(MTD),has been proposed to provide additional selectable measures to complement traditional defense.However,MTD is unable to defeat the sophisticated attacker with fingerprint tracking ability.To overcome this limitation,we go one step beyond and show that the combination of MTD and Deception-based Cyber Defense(DCD)can achieve higher performance than either of them.In particular,we first introduce and formalize a novel attacker model named Scan and Foothold Attack(SFA)based on cyber kill chain.Afterwards,we develop probabilistic models for SFA defenses to provide a deeper analysis of the theoretical effect under different defense strategies.These models quantify attack success probability and the probability that the attacker will be deceived under various conditions,such as the size of address space,and the number of hosts,attack analysis time.Finally,the experimental results show that the actual defense effect of each strategy almost perfectly follows its probabilistic model.Also,the defense strategy of combining address mutation and fingerprint camouflage can achieve a better defense effect than the single address mutation.展开更多
●AIM:To identify disease-causative mutations in families with congenital cataract.●METHODS:Two Chinese families with autosomaldominant congenital cataract(ADCC)were recruited and underwent comprehensive eye examinat...●AIM:To identify disease-causative mutations in families with congenital cataract.●METHODS:Two Chinese families with autosomaldominant congenital cataract(ADCC)were recruited and underwent comprehensive eye examinations.Gene panel next-generation sequencing of common pathogenic genes of congenital cataract was performed in the proband of each family.Sanger sequencing was used to valid the candidate gene mutations and sequence the other family members for co-segregation analysis.The effect of sequence changes on protein structure and function was predicted through bioinformatics analysis.Major intrinsic protein(MIP)-wildtype and MIP-G29R plasmids were constructed and microinjected into zebrafish single-cell stage embryos.Zebrafish embryonic lens phenotypes were screened using confocal microscopy.●RESULTS:A novel heterozygous mutation(c.85G>A;p.G29R)in the MIP gene was identified in the proband of one family.A known heterozygous mutation(c.97C>T;p.R33C;rs864309693)in MIP was found in the proband of another family.In-silico prediction indicated that the novel mutation might affect the MIP protein function.Zebrafish embryonic lens was uniformly transparent in both wild-type PCS2+MIP and mutant PCS2+MIP.●CONCLUSION:Two missense mutations in the MIP gene in Chinese cataract families are identified,and one of which is novel.These findings expand the genetic spectrum of MIP mutations associated with cataracts.The functional studies suggest that the novel MIP mutation might not be a gain-of-function but a loss-of-function mutation.展开更多
Due to the depletion of conventional energy reserves,there has been a global shift towards non-conventional energy sources.Shale oil and gas have emerged as key alternatives.These resources have dense and heterogeneou...Due to the depletion of conventional energy reserves,there has been a global shift towards non-conventional energy sources.Shale oil and gas have emerged as key alternatives.These resources have dense and heterogeneous reservoirs,which require hydraulic fracturing to extract.This process depends on identifying optimal fracturing layers,also known as‘sweet spots’.However,there is currently no uniform standard for locating these sweet spots.This paper presents a new model for evaluating fracturability that aims to address the current gap in the field.The model utilizes a hierarchical analysis approach and a mutation model,and is distinct in its use of original logging data to generate a fracturability evaluation map.Using this paper’s shale fracturing sweet spot evaluation method based on a two-step mutation model,four wells in different blocks of Fuling and Nanchuan Districts in China were validated,and the results showed that the proportion of high-yielding wells on the sweet spot line could reach 97.6%,while the proportion of low-producing wells was only 78.67%.Meanwhile,the evaluation results of the model were compared with the microseismic data,and the matching results were consistent.展开更多
Background:A central challenge in cancer research is to create models that bridge the gap between the molecular level on which interventions can be designed and the cellular and tissue levels on which the disease phen...Background:A central challenge in cancer research is to create models that bridge the gap between the molecular level on which interventions can be designed and the cellular and tissue levels on which the disease phenotypes are manifested.This study was undertaken to construct such a model from functional annotations and explore its use when integrated with large-scale cancer genomics data.Methods:We created a map that connects genes to cancer hallmarks via signaling pathways.We projected gene mutation and focal copy number data from various cancer types onto this map.We performed statistical analyses to uncover mutually exclusive and co-occurring oncogenic aberrations within this topology.Results:Our analysis showed that although the genetic fingerprint of tumor types could be very different,there were less variations at the level of hallmarks,consistent with the idea that different genetic alterations have similar functional outcomes.Additionally,we showed how the multilevel map could help to clarify the role of infrequently mutated genes,and we demonstrated that mutually exclusive gene mutations were more prevalent in pathways,whereas many co-occurring gene mutations were associated with hallmark characteristics.Conclusions:Overlaying this map with gene mutation and focal copy number data from various cancer types makes it possible to investigate the similarities and differences between tumor samples systematically at the levels of not only genes but also pathways and hallmarks.展开更多
We revisit the multi-allelic mutation-fitness balance problem especially when fitnesses are multiplicative. Using ideas arising from quasi-stationary distributions, we analyze the qualitative differences between the f...We revisit the multi-allelic mutation-fitness balance problem especially when fitnesses are multiplicative. Using ideas arising from quasi-stationary distributions, we analyze the qualitative differences between the fitness-first and mutation-first models, under various schemes of the mutation pattern. We give some stochastic domination relations between the equilibrium states resulting from these models.展开更多
PIK3R5 is the regulatory subunit of Phosphoinositide 3-kinase γ (PI3Kγ) that is responsible for phosphory-lating membrane lipids to activate the AKT pathway. PIK3R5 binds Gβγ and facilitates the interaction with p...PIK3R5 is the regulatory subunit of Phosphoinositide 3-kinase γ (PI3Kγ) that is responsible for phosphory-lating membrane lipids to activate the AKT pathway. PIK3R5 binds Gβγ and facilitates the interaction with p110γ catalytic subunit (PIK3CG) during PI3Kγ activation. The identification of PIK3R5 P629S mutation in AOA2 patients indicated a potential defect in the AKT pathway resulting from impaired PIK3R5 interaction with Gβγ and PIK3CG, defective AKT pathway can result in cerebellar cell death causing neurological symptoms. Our in silico macromolecular docking of the wild type and mutant PIK3R5 protein models with ligand revealed an energy requirement to maintain the mutant complexes compared to no energy required to maintain the wild type complexes, in addition, the mutant structures were loose compared to rigid wild type structures, such structural changes may impair the molecular function of the PIK3R5 and hence affect the AKT pathway.展开更多
The presenilin genes(PSEN1 and PSEN2)are mainly responsible for causing early-onset familial Alzheimer’s disease,harboring~300 causative mutations,and representing~90%of all mutations associated with a very aggressiv...The presenilin genes(PSEN1 and PSEN2)are mainly responsible for causing early-onset familial Alzheimer’s disease,harboring~300 causative mutations,and representing~90%of all mutations associated with a very aggressive disease form.Presenilin 1 is the catalytic core of theγ-secretase complex that conducts the intramembranous proteolytic excision of multiple transmembrane proteins like the amyloid precursor protein,Notch-1,N-and E-cadherin,LRP,Syndecan,Delta,Jagged,CD44,ErbB4,and Nectin1a.Presenilin 1 plays an essential role in neural progenitor maintenance,neurogenesis,neurite outgrowth,synaptic function,neuronal function,myelination,and plasticity.Therefore,an imbalance caused by mutations in presenilin 1/γ-secretase might cause aberrant signaling,synaptic dysfunction,memory impairment,and increased Aβ42/Aβ40 ratio,contributing to neurodegeneration during the initial stages of Alzheimer’s disease pathogenesis.This review focuses on the neuronal differentiation dysregulation mediated by PSEN1 mutations in Alzheimer’s disease.Furthermore,we emphasize the importance of Alzheimer’s disease-induced pluripotent stem cells models in analyzing PSEN1 mutations implication over the early stages of the Alzheimer’s disease pathogenesis throughout neuronal differentiation impairment.展开更多
BACKGROUND Preoperative knowledge of mutational status of gastrointestinal stromal tumors(GISTs)is essential to guide the individualized precision therapy.AIM To develop a combined model that integrates clinical and c...BACKGROUND Preoperative knowledge of mutational status of gastrointestinal stromal tumors(GISTs)is essential to guide the individualized precision therapy.AIM To develop a combined model that integrates clinical and contrast-enhanced computed tomography(CE-CT)features to predict gastric GISTs with specific genetic mutations,namely KIT exon 11 mutations or KIT exon 11 codons 557-558 deletions.METHODS A total of 231 GIST patients with definitive genetic phenotypes were divided into a training dataset and a validation dataset in a 7:3 ratio.The models were constructed using selected clinical features,conventional CT features,and radiomics features extracted from abdominal CE-CT images.Three models were developed:ModelCT sign,modelCT sign+rad,and model CTsign+rad+clinic.The diagnostic performance of these models was evaluated using receiver operating characteristic(ROC)curve analysis and the Delong test.RESULTS The ROC analyses revealed that in the training cohort,the area under the curve(AUC)values for model_(CT sign),model_(CT sign+rad),and modelCT_(sign+rad+clinic)for predicting KIT exon 11 mutation were 0.743,0.818,and 0.915,respectively.In the validation cohort,the AUC values for the same models were 0.670,0.781,and 0.811,respectively.For predicting KIT exon 11 codons 557-558 deletions,the AUC values in the training cohort were 0.667,0.842,and 0.720 for model_(CT sign),model_(CT sign+rad),and modelCT_(sign+rad+clinic),respectively.In the validation cohort,the AUC values for the same models were 0.610,0.782,and 0.795,respectively.Based on the decision curve analysis,it was determined that the model_(CT sign+rad+clinic)had clinical significance and utility.CONCLUSION Our findings demonstrate that the combined modelCT_(sign+rad+clinic)effectively distinguishes GISTs with KIT exon 11 mutation and KIT exon 11 codons 557-558 deletions.This combined model has the potential to be valuable in assessing the genotype of GISTs.展开更多
目的构建基于铜死亡相关的铁死亡基因的预后模型,评估其在肝癌患者中的预测能力,并探讨与免疫功能和肿瘤突变负荷的关系。方法使用TCGA(The Cancer Genome Atlas)数据库分析370例肝癌患者的与铜死亡相关的铁死亡基因和生存数据,并将数...目的构建基于铜死亡相关的铁死亡基因的预后模型,评估其在肝癌患者中的预测能力,并探讨与免疫功能和肿瘤突变负荷的关系。方法使用TCGA(The Cancer Genome Atlas)数据库分析370例肝癌患者的与铜死亡相关的铁死亡基因和生存数据,并将数据集随机分为训练组和测试组。通过Lasso回归和Cox模型的构建,筛选出与铜死亡相关的铁死亡基因进行风险模型构建。进行单因素和多因素Cox回归分析来验证风险模型对肝癌预后影响的独立性,并分析风险模型与免疫功能和肿瘤突变负荷的关系。结果在多变量Cox回归数据中选择EIF2S1、G6PD、NRAS这3个与铜死亡相关的铁死亡基因,训练组中EIF2S1、G6PD、NRAS与生存期独立相关(P均<0.05),以该3个基因构建风险模型。Kaplan-Meier分析结果显示,与低风险组比较,高风险组患者的生存期较短(P<0.05),生存率较低(P<0.05)。单因素Cox回归分析显示,铜死亡相关的铁死亡基因构建的风险模型中HR为1.734,95%CI为1.494~2.034,P<0.001。多因素Cox回归分析显示,铜死亡相关的铁死亡基因构建的风险模型中HR为1.661,95%CI为1.397~1.976,P<0.001。ROC曲线分析显示,风险模型预测肝癌患者第1,3,5年生存期的曲线下面积(AUC)分别为0.760,0.663和0.636。运用该风险模型进行Kaplan-Meier生存曲线分析显示,与早期肝癌患者相比,晚期肝癌患者生存期更短(P<0.05),生存率更低(P<0.05)。在高风险组和低风险组中,TypeⅡIFN Response、Parainflammation、APC co-stimulation、CCR、Check-point和MHC classⅠ这6个免疫功能的表达存在统计学差异(P均<0.05)。高肿瘤突变负荷组的肝癌患者生存期明显低于低肿瘤突变负荷组的患者(P<0.05)。结论基于与铜死亡相关的铁死亡基因的风险模型能够有效区分肝癌患者的预后,且铜死亡相关的铁死亡基因与免疫功能和肿瘤突变负荷密切相关。展开更多
基金supported by the National Key Research and Development Program of China(No.2016YFB0800601)the Key Program of NSFC-Tongyong Union Foundation(No.U1636209)+1 种基金the National Natural Science Foundation of China(61602358)the Key Research and Development Programs of Shaanxi(No.2019ZDLGY13-04,No.2019ZDLGY13-07)。
文摘The static and predictable characteristics of cyber systems give attackers an asymmetric advantage in gathering useful information and launching attacks.To reverse this asymmetric advantage,a new defense idea,called Moving Target Defense(MTD),has been proposed to provide additional selectable measures to complement traditional defense.However,MTD is unable to defeat the sophisticated attacker with fingerprint tracking ability.To overcome this limitation,we go one step beyond and show that the combination of MTD and Deception-based Cyber Defense(DCD)can achieve higher performance than either of them.In particular,we first introduce and formalize a novel attacker model named Scan and Foothold Attack(SFA)based on cyber kill chain.Afterwards,we develop probabilistic models for SFA defenses to provide a deeper analysis of the theoretical effect under different defense strategies.These models quantify attack success probability and the probability that the attacker will be deceived under various conditions,such as the size of address space,and the number of hosts,attack analysis time.Finally,the experimental results show that the actual defense effect of each strategy almost perfectly follows its probabilistic model.Also,the defense strategy of combining address mutation and fingerprint camouflage can achieve a better defense effect than the single address mutation.
基金Supported by the Science,Technology and Innovation Commission of Shenzhen Municipality(No.GJHZ20220913142618036,No.JCYJ20210324113610029).
文摘●AIM:To identify disease-causative mutations in families with congenital cataract.●METHODS:Two Chinese families with autosomaldominant congenital cataract(ADCC)were recruited and underwent comprehensive eye examinations.Gene panel next-generation sequencing of common pathogenic genes of congenital cataract was performed in the proband of each family.Sanger sequencing was used to valid the candidate gene mutations and sequence the other family members for co-segregation analysis.The effect of sequence changes on protein structure and function was predicted through bioinformatics analysis.Major intrinsic protein(MIP)-wildtype and MIP-G29R plasmids were constructed and microinjected into zebrafish single-cell stage embryos.Zebrafish embryonic lens phenotypes were screened using confocal microscopy.●RESULTS:A novel heterozygous mutation(c.85G>A;p.G29R)in the MIP gene was identified in the proband of one family.A known heterozygous mutation(c.97C>T;p.R33C;rs864309693)in MIP was found in the proband of another family.In-silico prediction indicated that the novel mutation might affect the MIP protein function.Zebrafish embryonic lens was uniformly transparent in both wild-type PCS2+MIP and mutant PCS2+MIP.●CONCLUSION:Two missense mutations in the MIP gene in Chinese cataract families are identified,and one of which is novel.These findings expand the genetic spectrum of MIP mutations associated with cataracts.The functional studies suggest that the novel MIP mutation might not be a gain-of-function but a loss-of-function mutation.
基金This work was supported by the National Science and Technology Major Project during the 13th Five-Year Plan under Grant Number 2016ZX05060004.
文摘Due to the depletion of conventional energy reserves,there has been a global shift towards non-conventional energy sources.Shale oil and gas have emerged as key alternatives.These resources have dense and heterogeneous reservoirs,which require hydraulic fracturing to extract.This process depends on identifying optimal fracturing layers,also known as‘sweet spots’.However,there is currently no uniform standard for locating these sweet spots.This paper presents a new model for evaluating fracturability that aims to address the current gap in the field.The model utilizes a hierarchical analysis approach and a mutation model,and is distinct in its use of original logging data to generate a fracturability evaluation map.Using this paper’s shale fracturing sweet spot evaluation method based on a two-step mutation model,four wells in different blocks of Fuling and Nanchuan Districts in China were validated,and the results showed that the proportion of high-yielding wells on the sweet spot line could reach 97.6%,while the proportion of low-producing wells was only 78.67%.Meanwhile,the evaluation results of the model were compared with the microseismic data,and the matching results were consistent.
基金supported in part by the National Cancer Institute (U24CA143835 to IS and TAK)the Netherlands Organization for Scientific Research-The Cancer System Biology Center(to LFAW and TB)
文摘Background:A central challenge in cancer research is to create models that bridge the gap between the molecular level on which interventions can be designed and the cellular and tissue levels on which the disease phenotypes are manifested.This study was undertaken to construct such a model from functional annotations and explore its use when integrated with large-scale cancer genomics data.Methods:We created a map that connects genes to cancer hallmarks via signaling pathways.We projected gene mutation and focal copy number data from various cancer types onto this map.We performed statistical analyses to uncover mutually exclusive and co-occurring oncogenic aberrations within this topology.Results:Our analysis showed that although the genetic fingerprint of tumor types could be very different,there were less variations at the level of hallmarks,consistent with the idea that different genetic alterations have similar functional outcomes.Additionally,we showed how the multilevel map could help to clarify the role of infrequently mutated genes,and we demonstrated that mutually exclusive gene mutations were more prevalent in pathways,whereas many co-occurring gene mutations were associated with hallmark characteristics.Conclusions:Overlaying this map with gene mutation and focal copy number data from various cancer types makes it possible to investigate the similarities and differences between tumor samples systematically at the levels of not only genes but also pathways and hallmarks.
文摘We revisit the multi-allelic mutation-fitness balance problem especially when fitnesses are multiplicative. Using ideas arising from quasi-stationary distributions, we analyze the qualitative differences between the fitness-first and mutation-first models, under various schemes of the mutation pattern. We give some stochastic domination relations between the equilibrium states resulting from these models.
文摘PIK3R5 is the regulatory subunit of Phosphoinositide 3-kinase γ (PI3Kγ) that is responsible for phosphory-lating membrane lipids to activate the AKT pathway. PIK3R5 binds Gβγ and facilitates the interaction with p110γ catalytic subunit (PIK3CG) during PI3Kγ activation. The identification of PIK3R5 P629S mutation in AOA2 patients indicated a potential defect in the AKT pathway resulting from impaired PIK3R5 interaction with Gβγ and PIK3CG, defective AKT pathway can result in cerebellar cell death causing neurological symptoms. Our in silico macromolecular docking of the wild type and mutant PIK3R5 protein models with ligand revealed an energy requirement to maintain the mutant complexes compared to no energy required to maintain the wild type complexes, in addition, the mutant structures were loose compared to rigid wild type structures, such structural changes may impair the molecular function of the PIK3R5 and hence affect the AKT pathway.
基金supported by the Consejo Nacional de Ciencia y Tecnología Scholarship 711893(to MAH)and 711874(to EER)。
文摘The presenilin genes(PSEN1 and PSEN2)are mainly responsible for causing early-onset familial Alzheimer’s disease,harboring~300 causative mutations,and representing~90%of all mutations associated with a very aggressive disease form.Presenilin 1 is the catalytic core of theγ-secretase complex that conducts the intramembranous proteolytic excision of multiple transmembrane proteins like the amyloid precursor protein,Notch-1,N-and E-cadherin,LRP,Syndecan,Delta,Jagged,CD44,ErbB4,and Nectin1a.Presenilin 1 plays an essential role in neural progenitor maintenance,neurogenesis,neurite outgrowth,synaptic function,neuronal function,myelination,and plasticity.Therefore,an imbalance caused by mutations in presenilin 1/γ-secretase might cause aberrant signaling,synaptic dysfunction,memory impairment,and increased Aβ42/Aβ40 ratio,contributing to neurodegeneration during the initial stages of Alzheimer’s disease pathogenesis.This review focuses on the neuronal differentiation dysregulation mediated by PSEN1 mutations in Alzheimer’s disease.Furthermore,we emphasize the importance of Alzheimer’s disease-induced pluripotent stem cells models in analyzing PSEN1 mutations implication over the early stages of the Alzheimer’s disease pathogenesis throughout neuronal differentiation impairment.
基金Supported by the National Natural Science Foundation of China Program Grant,No.82203108China Postdoctoral Science Foundation,No.2022M722275+1 种基金Beijing Bethune Charitable Foundation,No.WCJZL202105Beijing Xisike Clinical Oncology Research Foundation,No.Y-zai2021/zd-0185。
文摘BACKGROUND Preoperative knowledge of mutational status of gastrointestinal stromal tumors(GISTs)is essential to guide the individualized precision therapy.AIM To develop a combined model that integrates clinical and contrast-enhanced computed tomography(CE-CT)features to predict gastric GISTs with specific genetic mutations,namely KIT exon 11 mutations or KIT exon 11 codons 557-558 deletions.METHODS A total of 231 GIST patients with definitive genetic phenotypes were divided into a training dataset and a validation dataset in a 7:3 ratio.The models were constructed using selected clinical features,conventional CT features,and radiomics features extracted from abdominal CE-CT images.Three models were developed:ModelCT sign,modelCT sign+rad,and model CTsign+rad+clinic.The diagnostic performance of these models was evaluated using receiver operating characteristic(ROC)curve analysis and the Delong test.RESULTS The ROC analyses revealed that in the training cohort,the area under the curve(AUC)values for model_(CT sign),model_(CT sign+rad),and modelCT_(sign+rad+clinic)for predicting KIT exon 11 mutation were 0.743,0.818,and 0.915,respectively.In the validation cohort,the AUC values for the same models were 0.670,0.781,and 0.811,respectively.For predicting KIT exon 11 codons 557-558 deletions,the AUC values in the training cohort were 0.667,0.842,and 0.720 for model_(CT sign),model_(CT sign+rad),and modelCT_(sign+rad+clinic),respectively.In the validation cohort,the AUC values for the same models were 0.610,0.782,and 0.795,respectively.Based on the decision curve analysis,it was determined that the model_(CT sign+rad+clinic)had clinical significance and utility.CONCLUSION Our findings demonstrate that the combined modelCT_(sign+rad+clinic)effectively distinguishes GISTs with KIT exon 11 mutation and KIT exon 11 codons 557-558 deletions.This combined model has the potential to be valuable in assessing the genotype of GISTs.
