Novel technique for cost reduction in mutation testing

Aimed at the problem of expensive costs in mutation testing which has hampered its wide use,a technique of introducing a test case selection into the process of mutation testing is proposed.For each mutant,a fixed number of test cases are selected to constrain the maximum allowable executions so as to reduce useless work.Test case selection largely depends on the degree of mutation.The mutation distance is an index describing the semantic difference between the original program and the mutated program.It represents the percentage of effective test cases in a test set,so it can be used to guide the selection of test cases.The bigger the mutation distance is,the easier it is that the mutant will be killed,so the corresponding number of effective test cases for this mutant is greater.Experimental results suggest that the technique can remarkably reduce execution costs without a significant loss of test effectiveness.

Genetic mutation of Tas2r104/Tas2r105/Tas2r114 cluster leads to a loss of taste perception to denatonium benzoate and cucurbitacin B

Background:Bitter taste receptors(Tas2rs)are generally considered to sense various bitter compounds to escape the intake of toxic substances.Bitter taste receptors have been found to widely express in extraoral tissues and have important physiological functions outside the gustatory system in vivo.Methods:To investigate the physiological functions of the bitter taste receptor cluster Tas2r106/Tas2r104/Tas2r105/Tas2r114 in lingual and extraoral tissues,multiple Tas2rs mutant mice and Gnat3 were produced using CRISPR/Cas9 gene-editing technique.A mixture containing Cas9 and sgRNA mRNAs for Tas2rs and Gnat3 gene was microinjected into the cytoplasm of the zygotes.Then,T7EN1 assays and sequencing were used to screen genetic mutation at the target sites in founder mice.Quantitative real-time polymerase chain reaction(qRT-PCR)and immunostaining were used to study the expression level of taste signaling cascade and bitter taste receptor in taste buds.Perception to taste substance was also studied using twobottle preference tests.Results:We successfully produced several Tas2rs and Gnat3 mutant mice using the CRISPR/Cas9 technique.Immunostaining results showed that the expression of GNAT3 and PLCB2 was not altered in Tas2rs mutant mice.But qRT-PCR results revealed the changed expression profile of m Tas2rs gene in taste buds of these mutant mice.With two-bottle preference tests,these mutant mice eliminate responses to cycloheximide due to genetic mutation of Tas2r105.In addition,these mutant mice showed a loss of taste perception to quinine dihydrochloride,denatonium benzoate,and cucurbitacin B(CuB).Gnat3-mediated taste receptor and its signal pathway contribute to CuB perception.Conclusions:These findings implied that these mutant mice would be a valuable means to understand the biological functions of TAS2Rs in extraoral tissues and investigate bitter compound-induced responses mediated by these TAS2Rs in many extraoral tissues.

Study on MCM Interconnect Test Generation Based on Ant Algorithm with Mutation Operator

A novel multi-chip module(MCM) interconnect test generation scheme based on ant algorithm(AA) with mutation operator was presented.By combing the characteristics of MCM interconnect test generation,the pheromone updating rule and state transition rule of AA is designed.Using mutation operator,this scheme overcomes ordinary AA’s defects of slow convergence speed,easy to get stagnate,and low ability of full search.The international standard MCM benchmark circuit provided by the MCNC group was used to verify the approach.The results of simulation experiments,which compare to the results of standard ant algorithm,genetic algorithm(GA) and other deterministic interconnecting algorithms,show that the proposed scheme can achieve high fault coverage,compact test set and short CPU time,that it is a newer optimized method deserving research.

Towards Semantic Mutation Testing of Aspect-Oriented Programs

Aspect-oriented programs have received much attention from software testing researchers. Various testing techniques and approaches have been proposed to tackle issues and challenges when testing aspect-oriented programs including traditional mutation testing. In traditional mutation testing of aspect-oriented programs, mutants are generated by making small changes to the syntax of the aspect-oriented language. Recently, a new approach known as semantic mutation testing has been proposed. This approach mutates the semantics of the language in which the program is written. The mutants generated misunderstandings of the language which are different classes of faults. Aspect-oriented programming presents itself with different properties that can be further explored with respect to semantic mutation testing. This paper describes various possible scenarios that semantic mutation testing strategy might have particular value in testing aspect-oriented programs.

Temperature Variation and Mutation Analysis over the Past 59 Years in Shenyang

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.

Relationship between Mutation of IR in the mtr System of Neisseria Gonorrhoeae and Multiple Antibiotic Resistance

To study the relationship between mutation of the inverted repeat sequence （IR） in the multiple transferable resistant system （mtr） of Neisseria gonorrhoeae （NG） and its multiple antibiotic resistance, minimal inhibitory concentrations （MICs） for the clinically isolated strains were tested by agar-dilution-method. The mtr system＇s IR gene of NG was sequenced after amplification by polymerase chain reaction （PCR）. Either two susceptive or five penicillin-resistant strains had no base mutation in IR gene, while all of the 13 strains with multiple-antibiotic-resistance had a singlebase deletion （A/T）. The result suggests that a single-base deletion of the thirteen-base IR sequence in mtr system of NG might result in multiple antibiotic resistance but is not associated with single antibiotic resistance.

Mutation Analysis of STR Locus on 23 Autosomes in Hainan Population

[Objective] To analyze the mutation signature and regularity of STR locus on 23 autosomes in paternity testing cases in Hainan. [Methods] A total of 2715 paternity testing cases accepted by the Forensic Medical Identification Centre of our hospital from 2017 to 2020 derived from counties and cities in Hainan Province were collected, the cases containing gene mutations were selected, the mutation rate and details of each locus were counted, and the mutation regu-larity of 23 STR loci was analyzed. [Results] Of the 2715 cases identified as “support”, 1487 were triplet cases and 1640 were dyad cases, totaling 4614 meioses;There were 50 gene mutation events (including 17 triplet mutations and 33 dyad mutations), with an average mutation rate of 0.0047% and a cumulative mutation rate of 1.0837%. A total of 19 of the 23 STR loci were mutated, with a mutation rate of 0.1301% at the D12S391 locus and 0.0217% at five loci, TPOX, D1S1656, D2S441, D22S1045, and PentaD, while no muta-tion events were found at four loci, D19S433, TH01, D13S317, and D7S820. Of the 50 mutation events, 47 were one-step mutations, 1 was two-step, and 2 were three-step. There were 35 paternal mutations (13 triplets and 22 dyads), 6 maternal mutations (4 triplets and 2 dyads), and 9 indeterminate pater-nal/maternal mutations, with a paternal to maternal mutation ratio of 5.83:1. [Conclusion] The mutation rate of D12S391 locus is the highest, and the muta-tion rate of TPOX, D1S1656, D2S441, D22S1045 and PentaD loci is the lowest in Hainan population, and paternal mutations are more than maternal muta-tions. In the paternity test, if 1 - 3 STR loci do not conform to the genetic law, especially when the mutant locus is homozygous or the next of kin is identi-fied, it is necessary to use other kits to review and increase the number of loci or use the second-generation sequencing technology to confirm, carefully de-termine the mutation and ensure the accuracy of the identification conclusion.

Establishment and application of a multiplex genetic mutation-detection method of lung cancer based on MassARRAY platform

Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena i PLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on Mass ARRAY mass spectrometry platform.Methods: We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a Lung Carta^(TM) kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencing EGFR and KRAS genes in 100 lung cancer cases.Results: The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with Lung Carta^(TM) kit. However, an FGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively.Conclusions: The proposed Mass ARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues.

ACE gene missense mutation in a case with early-onset, rapid progressing dementia

The population of early-onset Alzheimer's disease(EOAD)accounts for 1%-2%of the total population of Alzheimer's disease,and genetic mutations are more common in EOAD.The first symptom of the patient in the present case report was the decline in memories of recent events,and the disease progressed rapidly in the following 2 years.Genetic testing has revealed the presence of genetic mutations(c.A479G,p.N160S)of ACE,which causes the 160th codon of the ACE protein to change from aspartic acid to serine,and at the same time genotype of apolipoprotein E(APOE)is ε3/ε4.We think that this patient carries the mutation type of the sensitive gene ACE and the risk gene APOE of Alzheimer's disease,and this is the reason why the disease progressed rapidly.Moreover,we discussed ACE genetic mutation's meaning in EOAD progression.

New real-time-PCR method to identify single point mutations in hepatitis C virus

AIM To develop a fast, low-cost diagnostic strategy to identify single point mutations in highly variable genomes such as hepatitis C virus(HCV).METHODS In patients with HCV infection, resistance-associated amino acid substitutions within the viral quasispecies prior to therapy can confer decreased susceptibility to direct-acting antiviral agents and lead to treatment failure and virological relapse. One such naturally occurring mutation is the Q80 K substitution in the HCV-NS3 protease gene, which confers resistance to PI inhibitors, particularly simeprevir. Low-cost, highly sensitive techniques enabling routine detection of these single point mutations would be useful to identify patients at a risk of treatment failure. Light Cycler methods, based on real-time PCR with sequencespecific probe hybridization, have been implemented in most diagnostic laboratories. However, this technique cannot identify single point mutations in highly variable genetic environments, such as the HCV genome. To circumvent this problem, we developed a new method to homogenize all nucleotides present in a region except the point mutation of interest. RESULTS Using nucleotide-specific probes Q, K, and R substitutions at position 80 were clearly identified at a sensitivity of 10%(mutations present at a frequency of at least 10% were detected). The technique was successfully applied to identify the Q80 K substitution in 240 HCV G1 serum samples, with performance comparable to that of direct Sanger sequencing, the current standard procedure for this purpose. The new method was then validated in a Catalonian population of 202 HCV G1-infected individuals. Q80 K was detected in 14.6% of G1 a patients and 0% of G1 b in our setting. CONCLUSION A fast, low-cost diagnostic strategy based on real-time PCR and fluorescence resonance energy transfer probe melting curve analysis has been successfully developed to identify single point mutations in highly variable genomes such as hepatitis C virus. This technique can be adapted to detect any single point mutation in highly variable genomes.

A Novel Gene Mutation of Runx2 in Cleidocranial Dysplasia

Haploinsufficiency of the runt-related transcription factor 2（Runx2） gene is widely known to be responsible for cleidocranial dysplasia（CCD）. To date, more than 190 mutations in Runx2 gene have been reported to be related to CCD. In this study, a novel mutation of Runx2 gene was observed in a female with CCD. Genomic DNA was extracted from peripheral venous blood of the proband and eleven members of her family. Genetic testing on these twelve people identified a novel missense mutation（c.895 T〉C, Y299 H） in exon 5 of the RUNX2 gene in the proband. This mutation results in an amino acid change at codon 895（P.Tyr 299 His.） from a tryptophan codon（TAT） to a histidine codon（CAT）. Our finding may further extend the known mutation spectrum of the RUNX2 gene, and facilitate prenatal genetic diagnosis of CCD in the future.

Novel Metrics for Mutation Analysis

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.

Novel mutation of SPG4 gene in a Chinese family with hereditary spastic paraplegia:A case report

BACKGROUND Hereditary spastic paraplegia(HSP)is a group of neurogenetic diseases of the corticospinal tract,accompanied by distinct spasticity and weakness of the lower extremities.Mutations in the spastic paraplegia type 4(SPG4)gene,encoding the spastin protein,are the major cause of the disease.This study reported a Chinese family with HSP caused by a novel mutation of the SPG4 gene.CASE SUMMARY A 44-year-old male was admitted to our hospital for long-term right lower limb weakness,leg stiffness,and unstable walking.His symptoms gradually worsened,while no obvious muscle atrophy in the lower limbs was found.Neurological examinations revealed that the muscle strength of the lower limbs was normal,and knee reflex hyperreflexia and bilateral positive Babinski signs were detected.Members of his family also had the same symptoms.Using mutation analysis,a novel heterozygous duplication mutation,c.1053dupA,p.(Gln352Thrfs*15),was identified in the SPG4 gene in this family.CONCLUSION A Chinese family with HSP had a novel mutation of the SPG4 gene,which is autosomal dominant and inherited as pure HSP.The age of onset,sex distribution,and clinical manifestations of all existing living patients in this family were analyzed.The findings may extend the current knowledge on the existing mutations in the SPG4 gene.

基于M-K法与SPI指数的泰安降水量分析

对泰安气象站1984—2016年的实测降水量资料采用线性趋势、累积距平法、M-K突变检验法、SPI指数进行研究分析,发现泰安多年平均降水量呈微小减少的趋势,平均降水量减少的速度约为10.9 mm/10 a。将M-K突变检验法和累积距平法相结合,得出1989、2002、2011年为研究区间的降水量突变年份。另外,分析不同时间尺度的SPI,得出1个月尺度的SPI的正负波动范围较大,随着时间尺度延长,SPI发生干旱的持续时间增长,旱涝变化趋于稳定。对降水量突变点的检验和不同时间尺度的SPI演变分析有助于更好地认识干旱现象,提高防旱抗旱意识,为泰安的降水量预测、水资源管理提供科学参考。

Implementation of Hybrid Particle Swarm Optimization for Optimized Regression Testing

Software test case optimization improves the efficiency of the software by proper structure and reduces the fault in the software.The existing research applies various optimization methods such as Genetic Algorithm,Crow Search Algorithm,Ant Colony Optimization,etc.,for test case optimization.The existing methods have limitations of lower efficiency in fault diagnosis,higher computa-tional time,and high memory requirement.The existing methods have lower effi-ciency in software test case optimization when the number of test cases is high.This research proposes the Tournament Winner Genetic Algorithm(TW-GA)method to improve the efficiency of software test case optimization.Hospital Information System(HIS)software was used to evaluate TW-GA model perfor-mance in test case optimization.The tournament Winner in the proposed method selects the instances with the best fitness values and increases the exploitation of the search to find the optimal solution.The TW-GA method has higher exploita-tion that helps to find the mutant and equivalent mutation that significantly increases fault diagnosis in the software.The TW-GA method discards the infor-mation with a lower fitness value that reduces the computational time and mem-ory requirement.The TW-GA method requires 5.47 s and the MOCSFO method requires 30 s for software test case optimization.

基于Daikon与C++Test的自动测试用例集约简工具生成

程序似然不变量是程序中隐含的属性,可以应用于程序验证、软件测试技术、逆向工程等领域。针对自动化测试工具C++Test产生的测试用例集,利用程序不变量分析工具Daikon判断这些测试用例是否改变了当前的不变量;并将两种工具结合生产一种自动化测试用例集约简工具CDRT(C++Test And Daikon Reduction Testing),从而达到约简测试用例集的效果,再通过变异测试工具INSURE++对简化后的测试用例集进行评估。实验结果表明,CDRT工具能有效地约简测试用例集。

MC/DC Test Data Generation Algorithm Based on Whale Genetic Algorithm

The automatic generation of test data is a key step in realizing automated testing.Most automated testing tools for unit testing only provide test case execution drivers and cannot generate test data that meets coverage requirements.This paper presents an improved Whale Genetic Algorithm for generating test data re-quired for unit testing MC/DC coverage.The proposed algorithm introduces an elite retention strategy to avoid the genetic algorithm from falling into iterative degradation.At the same time,the mutation threshold of the whale algorithm is introduced to balance the global exploration and local search capabilities of the genetic al-gorithm.The threshold is dynamically adjusted according to the diversity and evolution stage of current popu-lation,which positively guides the evolution of the population.Finally,an improved crossover strategy is pro-posed to accelerate the convergence of the algorithm.The improved whale genetic algorithm is compared with genetic algorithm,whale algorithm and particle swarm algorithm on two benchmark programs.The results show that the proposed algorithm is faster for test data generation than comparison methods and can provide better coverage with fewer evaluations,and has great advantages in generating test data.

2+0 CYP21A2 deletion carrier—a limitation of the genetic testing and counseling:A case report

BACKGROUND CYP21A2 gene mutations may all cause reduction or loss of 21-hydroxylase activity,leading to development of congenital adrenal hyperplasia(CAH)with different clinical phenotypes.For families with CAH children,genetic testing of the parents and genetic counseling are recommended to assess the risk of recurrence.CASE SUMMARY We report a case of CAH with a high suspicion before delivery.The risk of the child suffering from CAH during the pregnancy had been underestimated due to the deviation of genetic counseling and genetic testing results.Our report confirmed a CYP21A2 homozygous deletion in this case,CYP21A2 heterozygous deletion in the mother,and a rare 2+0 CYP21A2 deletion in the father.CONCLUSION It is important to analyze the distribution of CYP21A2 gene in the two alleles of parents of children with CAH.

A Fault-Based Testing Approach in Safety Critical Medical Systems

The advent of technology has opened unprecedented opportunities in health care delivery system as the demand for intelligent and knowledge-based systems has increased as modern medical practices become more knowledge-intensive. As a result of this, there is greater need to investigate the pervasiveness of software faults in Safety critical medical systems for proper diagnosis. The sheer volume of code in these systems creates significant concerns about the quality of the software. The rate of untimely deaths nowadays is alarming partly due to the medical device used to carry out the diagnosis process. A safety-critical medical (SCM) system is a complex system in which the malfunctioning of software could result in death, injury of the patient or damage to the environment. The malfunctioning of the software could be as a result of the inadequacy in software testing due to test suit problem or oracle problem. Testing a SCM system poses great challenges to software testers. One of these challenges is the need to generate a limited number of test cases of a given regression test suite in a manner that does not compromise its defect detection ability. This paper presents a novel five-stage fault-based testing procedure for SCM, a model-based approach to generate test cases for differential diagnosis of Tuberculosis. We used Prime Path Coverage and Edge-Pair Coverage as coverage criteria to ensure maximum coverage to identify feasible paths. We analyzed the proposed testing procedure with the help of three metrics consisting of Fault Detection Density, Fault Detection Effectiveness and Mutation Adequacy Score. We evaluated the effectiveness of our testing procedure by running the suggested test cases on a sample historical data of tuberculosis patients. The experimental results show that our developed testing procedure has some advantages such as creating mutant graphs and Fuzzy Cognitive Map Engine while resolving the problem of eliminating infeasible test cases for effective decision making.

Uncertainty following an inconclusive result from the BRCA1/2 genetic test:A review about psychological outcomes

BACKGROUND An inconclusive result from BRCA1/2 genetic testing indicates that a genetic variant of uncertain significance is detected.This case constitutes the majority of genetic test results,but studies specifically addressing the psychological adjustment of people with inconclusive results are scarce.AIM To examine psychological outcomes of receiving an uninformative BRCA1/2 test result.METHODS PubMed,PsychInfo,and Cochrane Central Register of Controlled Trials were screened for studies focusing on distress,anxiety,and depression levels in individuals with inconclusive genetic test results.This review is based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses method.RESULTS Studies on psychological outcomes of inconclusive BRCA1/2 focused on general and specific distress,anxiety,and depression.Overall,they produced mixed results.These inconsistent findings are probably due to the uncertainty caused by this type of result,that may also influence the decisions of individuals about surveillance and prophylactic options,reducing their compliance.In addition,this review highlights specific risk and protective factors that affect psychological adjustment in individuals with an inconclusive genetic testing result.CONCLUSION Individuals with inconclusive genetic test results need specific educational programs and support to better understand the meaning of their results in order to be able to make decisions about surveillance and prophylactic options.