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What can we learn from quality assurance badges in open-source software?

Science China(Information Sciences) 2024年第4期67卷 146-163页

作者： feng LI yiling LOU Xin TAN Zhenpeng CHEN Jinhao DONG Yang LI Xuanzhi WANG Dan HAO Lu ZHANG MoE Key Lab of HCST School of Computer SciencePeking University Department of Computer Science Purdue University School of Computer Science & Engineering Beihang University(BUAA) Department of Computer Science University College London(UCL)

In the development of open-source software(OSS), many developers use badges to give an overview of the software and share some key features/metrics conveniently. Among various badges, quality assurance(QA) badges make up a large proportion and are the most prevalent because QA is of vital importance in software development, and ineffective QA may lead to anomalies or defects. In this paper, we focus on QA badges in open-source projects, which present quality assurance information directly and instantly,and aim to produce some interesting findings and provide practical implications. We collect and analyze 100000 projects written in popular programming languages from GitHub and conduct a comprehensive empirical study both inside and outside QA badges. Inside QA badges, we build a category classification for all QA badges based on the properties they focus on, which shows the types of QA badges developers use. Then,we analyze the frequency of the properties that QA badges focus on, and property combinations, too, which present their use status. We find that QA badges focus on various properties while developers give different preferences to different properties. The use status also differs between different programming languages. For example, projects written in C focus on Security to a great extent. Our findings also provide implications for developers and badge providers. Outside QA badges, we conduct a correlation analysis between QA badges and some software metrics that have potential relationships with code quality, contribution quality, and popularity. We find that QA badges have statistically significant correlations with various software metrics.

关键词： quality assurance badge open-source software code quality empirical study

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Oryzalexin S biosynthesis:a cross-stitched disappearing pathway

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aBIOTECH 2023年第1期4卷 1-7页

作者： Le Zhao Richard Oyagbenro yiling feng Meimei Xu Reuben J.Peters Roy J.Carver Department of Biochemistry Biophysics and Molecular BiologyIowa State UniversityAmesIA50011USA

Rice produces many diterpenoid phytoalexins and,reflecting the importance of these natural products in this important cereal crop plant,its genome contains three biosynthetic gene clusters(BGCs)for such metabolism.The chromosome 4 BGC(c4BGC)is largely associated with momilactone production,in part due to the presence of the initiating syn-copalyl diphosphate(CPP)synthase gene(OsCPS4).Oryzalexin S is also derived from syn-CPP.However,the relevant subsequently acting syn-stemarene synthase gene(OsKSL8)is not located in the c4BGC.Production of oryzalexin S further requires hydroxylation at carbons 2 and 19(C2 and C19),presumably catalyzed by cytochrome P450(CYP)monooxygenases.Here it is reported the closely related CYP99A2 and CYP99A3,whose genes are also found in the c4BGC catalyze the necessary C19-hydroxylation,while the closely related CYP71Z21 and CYP71Z22,whose genes are found in the recently reported chromosome 7 BGC(c7BGC),catalyze subsequent hydroxylation at C2α.Thus,oryzalexin S biosynthesis utilizes two distinct BGCs,in a pathway cross-stitched together by OsKSL8.Notably,in contrast to the widely conserved c4BGC,the c7BGC is subspecies(ssp.)specific,being prevalent in ssp.japonica and only rarely found in the other major ssp.indica.Moreover,while the closely related syn-stemodene synthase OsKSL11 was originally considered to be distinct from OsKSL8,it has now been reported to be a ssp.indica derived allele at the same genetic loci.Intriguingly,more detailed analysis indicates that OsKSL8(j)is being replaced by OsKSL11(OsKSL8i),suggesting introgression from ssp.indica to(sub)tropical japonica,with concurrent disappearance of oryzalexin S production.

关键词： Biosynthetic gene clusters Phytoalexins Diterpenoids Rice evolution

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灵长类特异基因在男性生殖系统中的作用探究

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中国科学：生命科学 2024年第1期54卷 94-102页

作者：周大鹏李阔阔田世雄周怡伶张锋贺小进刘春雨复旦大学附属妇产科医院遗传工程国家重点实验室生殖与发育研究院上海200011 复旦大学人类表型组研究院代谢与整合生物学研究院上海200438 安徽医科大学第一附属医院国家卫生健康委配子及生殖道异常研究重点实验室合肥230022 上海交通大学医学院附属国际和平妇幼保健院上海200030

男性不育是一类多因素的复杂疾病.作为导致男性不育的重要因素,弱畸精子症越来越受到人们的关注并且被发现与遗传因素有关.随着高通量测序技术的不断发展,多个弱畸精子症的致病基因被揭示.其中,对于在人和小鼠中进化保守的致病基因,利... 详细信息

男性不育是一类多因素的复杂疾病.作为导致男性不育的重要因素,弱畸精子症越来越受到人们的关注并且被发现与遗传因素有关.随着高通量测序技术的不断发展,多个弱畸精子症的致病基因被揭示.其中,对于在人和小鼠中进化保守的致病基因,利用传统的基因编辑小鼠模型即可完成表型或致病机理的探究.然而,随着研究的进行,人们陆续发现了与生殖疾病相关的一类灵长类特异基因(primate specific genes, PSGs),即存在人类基因组中、在灵长类和小鼠进化分支产生后出现的基因.对于此类基因,小鼠不再是疾病研究的理想模型,新的动物模型以及研究系统的探索尤为必要.本文在总结前期利用小鼠模型开展弱畸精子症遗传致病机理以及干预探究的基础上,重点介绍了新近发现的灵长类特异基因在男性生殖系统中的作用及研究系统构建.相关论述不仅为遗传咨询和临床诊断提供理论指导,也将为睾丸组织中富集的灵长类特异基因在生殖系统中的功能探索提供新的研究思路.

关键词：男性不育弱畸精子症 PSGs 新型研究系统

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容器育苗对不同柿砧木生长发育的影响

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北方园艺 2024年第12期 11-20页

作者：冯伊玲吕中一龙海涛杨勇关长飞西北农林科技大学园艺学院陕西杨凌712100

以9种柿砧木为试材,采用5种不同比例的基质处理,研究了不同基质配方对植株生长发育和光合特性的影响,以期为柿砧木容器育苗最佳基质配方及最适砧木品种提供参考依据。结果表明:不同基质配方对柿砧木生长发育存在显著影响,柿砧木容器育... 详细信息

以9种柿砧木为试材,采用5种不同比例的基质处理,研究了不同基质配方对植株生长发育和光合特性的影响,以期为柿砧木容器育苗最佳基质配方及最适砧木品种提供参考依据。结果表明:不同基质配方对柿砧木生长发育存在显著影响,柿砧木容器育苗最佳基质配方为T1(园土∶营养基质=1∶2);‘圃砧2号’‘圃砧3号’‘圃砧4号’‘圃砧5号’‘圃砧7号’及‘实生-482’的综合评价值均超过50%,是可推广的优良砧木品种。

关键词：柿砧木基质生长发育容器

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A cationic amphiphilic tetraphenylethylene derivative with hydrochromic sensitive property:Applications in anti-counterfeiting ink and rewritable paper

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Chinese Chemical Letters 2022年第11期33卷 4838-4841页

作者： Qian Xu Ziyu Qin yiling Bei Shengyu feng Xing-Dong Xu National Engineering Research Center for Colloidal Materials Key Laboratory of Special Functional Aggregated Materials of Ministry of EducationShandong Key Laboratory of Advanced Silicone Materials and TechnologySchool of Chemistry and Chemical EngineeringShandong UniversityJi'nan 250100China

Since the discovery of aggregation induced emission(AIE)phenomenon,various stimuli-responsive materials have been rapidly developed,but there are still great challenges in the application of ink printing due to the bad water solubility.In this research,a new cationic amphiphilic TPE-functionalized pyridine salt(TPE-OTs)was designed,which shows good water solubility and hydrochromic properties.The optical properties of the compound have been studied,which is equipped with the typical AIEE characteristics and TICT effect.The compound can self-assemble to form aggregates with a particle size of about 30 nm in water.What is more,the compound is responsive to the environmental humidity,whose fluorescent color changes from green to yellow as the humidity gradually increased.Based on this characteristic,we applied it to the fluorescent anti-counterfeiting ink,realizing the protection and encryption of information.

关键词： Aggregation induced emission Amphiphilic compounds Hydrochromic responsive Tetraphenylethylene Green fluorescent ink

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基于动态时间规整的气温日值数据二次插补

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大气科学学报 2024年第3期47卷 476-485页

作者：周笑天张茜茹郭庆燕陈益玲周雪松李长军冯勇张平山东省气象防灾减灾重点实验室山东济南250031 山东省气象数据中心山东济南250031 福建省气象信息中心福建福州350001

气温作为研究气候演变最基础的物理量,其日值序列的完整性和准确性对于气候分析与评估工作有着重要意义。近些年随着大量无人值守地面加密自动气象站的布设,不断出现随机站点和随机长度这种双随机特点的气象资料序列缺失,给气候分析和... 详细信息

气温作为研究气候演变最基础的物理量,其日值序列的完整性和准确性对于气候分析与评估工作有着重要意义。近些年随着大量无人值守地面加密自动气象站的布设,不断出现随机站点和随机长度这种双随机特点的气象资料序列缺失,给气候分析和业务应用造成了不小的障碍。针对现有气象数据插补方案的不足,提出了一种全新的基于动态时间规整(dynamic time warping,DTW)的气温日值数据二次插补方法。该方法采用了一种实时的插补策略,主要技术内容包括:1)利用一元线性回归方程将原始气温观测时间序列分解出拟合直线和残差曲线,并将二者重构组成新的气温序列;2)给出了气温插补区的定义和插补条件;3)提出了利用动态时间规整方法计算站点间距离的新模式。利用山东省2021年的气温实况数据对该方法进行了双随机检验,检验结果表明:该方法可以满足日平均气温、日最高气温和日最低气温数据的插补需求;在插补流程中采用DTW距离测度和二次插补的组合方法,其插补效果优于目前常见的基于站点地理临近关系的组合方法;该方法对地形有一定的敏感性,平原或丘陵地区的插补效果要优于山地地区。

关键词：气温日值动态时间规整重构二次插补

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6~10岁注意缺陷多动障碍男童的执行功能发展特点

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中国健康心理学杂志 2024年第3期32卷 339-345页

作者：宋以玲朱飞龙任园春范碧瑶杨莉王芳丰雷姚方远北京师范大学体育与运动学院北京100875 清华大学体育部北京大学精神卫生研究所北京市海淀区万泉小学首都医科大学附属安定医院

目的:探讨不同年龄段、不同亚型注意缺陷多动障碍(ADHD)男童的核心执行功能(抑制控制、工作记忆、认知灵活性)发展特点。方法:从北京市某三甲医院招募17名ADHD男童、北京市某公立小学1~4年级学生中筛查出48名ADHD男童。其中6~8岁41人,9... 详细信息

目的:探讨不同年龄段、不同亚型注意缺陷多动障碍(ADHD)男童的核心执行功能(抑制控制、工作记忆、认知灵活性)发展特点。方法:从北京市某三甲医院招募17名ADHD男童、北京市某公立小学1~4年级学生中筛查出48名ADHD男童。其中6~8岁41人,9~10岁24人,ADHD-PI型48人,ADHD-C型17人,募集年龄相差不超过半岁的正常发育男童65名为正常对照,分别采用Stroop色词测验(SCWT)、Rey复杂图形测验(ROCFT)、连线测验(TMT)评估被试儿童的抑制控制、工作记忆和认知灵活性。结果:整体分析显示,6~10岁ADHD男童的SCWT、ROCFT、TMT测试结果均显著差于正常男童(P<0.05);不同年龄段分析显示,6~8岁ADHD男童在核心执行功能任务中的测试结果均差于正常男童(P<0.05);9~10岁ADHD男童仅SCWT和ROCFT的测试结果差于正常男童(P<0.05);不同亚型分析显示,ADHD-PI和ADHD-C型在核心执行功能任务中的测试结果均显著差于正常男童(P<0.05);且与ADHD-PI型相比,ADHD-C型的SCWT测试结果更差(P<0.05)。结论:6~10岁ADHD男童存在核心执行功能缺陷,且低年龄段ADHD男童的核心执行功能损害范围更广;ADHD-C型的抑制控制缺陷重于ADHD-PI型。

关键词：注意缺陷多动障碍执行功能抑制控制工作记忆认知灵活性

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The roles of phosphate in shaping the structure and dynamics of Antarctic soil microbiomes

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Advances in Polar Science 2023年第1期34卷 28-44页

作者： TAN Jiankang CAO Huansheng LIU Li QIN yiling LIU feng John CAVA YIN Xiaofei SHEN Jihong WANG Nengfei Department of Ecology and Environment of Lishui Nanjing 200200China Division of Natural and Applied Sciences Duke Kunshan UniversitySuzhou 215316China The First Institute of Oceanography Ministry of Natural ResourcesQingdao 266061China Center for Fundamental and Applied Microbiomics Biodesign InstituteArizona State UniversityTempeAZ 85287USA School of Chemistry and Chemical Engineering Linyi UniversityLinyi 276000China

One major consequence of global warming in the Antarctic region is increased ice-free zones.Subsequent colonization of these ice-free areas by penguins alters their biogeochemistry,with one prominent example being elevation of inorganic phosphate concentrations around feces depositions.The complex soil biochemistry in the region makes it difficult to define the causal factors of these changes using common research approaches.Here,we addressed the effects of phosphate alone on microbiome structure and dynamics over time by adding external phosphate to selected soils in the Antarctic region.We then analyzed the soil bacterial community composition and diversity using 16S rRNA amplicon sequencing and compared these data with phosphate levels.Parallel geochemical analysis revealed changes in nine soil geochemical factors upon phosphate addition,all of which were relevant to microbiome structure,with soil pH showing the highest correlation.Links between geochemical factors and composition were identified,as were interactions between bacterial taxa.Additionally,Sphingobacteriia,Sphingobacteriales and Chitinophagaceae were found to be more abundant in phosphate-treated soils.Co-occurrence network analysis revealed significantly increased levels of associations in all major network properties over time after phosphate supplementation.Therefore,we conclude phosphate addition has diverse effects on Antarctic soil microbiomes.

关键词： phosphate Antarctic microbiome composition network geochemical factors ice-free zone

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Clinical evaluation of 4D dynamic dose for thoracic tumor stereotactic body radiation therapy with variable parameters

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Radiation Medicine and Protection 2023年第3期4卷 150-158页

作者： yiling Zeng Yu Chang Sheng Zhang Jun Han Hongyuan Liu feng Xiao Bo Pang Bin Hu Junping Cheng Hong Quan Zhiyong Yang Department of Medical Physics School of Physics and TechnologyWuhan UniversityWuhan 430072China Cancer Center Union HospitalTongji Medical CollegeUniversity of Science and TechnologyWuhan 430022China

Objective:To evaluate the dose uncertainty in stereotactic body radiation therapy induced by respiratory motion using a 4D dynamic dose(4DDD)reconstruction method.Methods:A retrospective analysis was conducted on five lung cancer patients who received static intensitymodulated radiation therapy.The 4DDD was constructed using beam delivery log files,four-dimensional computed tomography(4DCT)scans,and treatment plans.To evaluate the impact of respiratory motion,4DDD calculations were performed with 10 starting phases for each field.A total of 270 field doses were simulated and calculated.The differences between the cumulative volume histogram in whole-course treatment and the field doses'gamma passing rate(GPR)were compared.The correlations between plan complexity metrics and the dose deviation caused by respiratory motion were evaluated independently.The phase distributions of 398 subfields were calculated and evaluated for the influence of dose rate and breathing frequency.Results:The GPRs of all fields were different among various starting phases,with the highest range from 62.20% to 76.87% for 2 mm/3%GPR.The deviation of mean point dose was(5.42±5.21)%,and the deviation in the mean dose and D98% within the internal gross tumor volume were(0.97±0.71)% and(0.77±0.53)%,respectively.There was a significant correlation between the beam aperture-to-volume(BA2V)ratio and the average 2 mm/2%GPR(R?0.601,P<0.01).Lower dose rates led to a more homogeneous distribution of phases among subfields(t?44.100,P<0.001).Conclusions:Different beam starting phases had a limited impact on the overall treatment evaluation.However,the respiratory motion could be observed to induce dose deviations using the 4DDD reconstruction model,particularly for fields with small BA2V.

关键词： 4D dynamic dose Interplay effect Stereotactic body radiation therapy Beam starting phase Plan complexity

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The role of intraoperative electron radiotherapy in centrally located hepatocellular carcinomas treated with narrow-margin (<1 cm) hepatectomy: a prospective, phase 2 study

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Hepatobiliary Surgery and Nutrition 2022年第4期11卷 515-529,I0004页

作者： Liming Wang Yunhe Liu Weiqi Rong Fan Wu Weibo Yu Kan Liu Shengtao Lin yiling Zheng Kai Zhang Tana Siqin Changcheng Tao Mei Liu Bo Chen Qinfu feng Jianxiong Wu Department of Hepatobiliary Surgery National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina Department of Head and Neck Surgical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina Department of Pathology and Laboratory Medicine David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCAUSA Department of Diagnostic Radiology National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina Department of Surgical Oncology Fujian Provincial Hospital/Shengli Clinical Medical College of Fujian Medical UniversityFuzhouChina Laboratory of Cell and Molecular Biology&State Key Laboratory of Molecular Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina Department of Radiation Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina

Background: Postoperative radiotherapy (RT) is known to play an important role in the treatment of hepatocellular carcinomas (HCCs), but the specific role of intraoperative electron radiotherapy (IOERT) in HCCs remains unclear. The aim of this study was to investigate the safety and efficacy of IOERT in centrally located HCCs treated with narrow-margin (<1 cm) hepatectomy. Methods: This was a single-center, phase 2, prospective non-randomized controlled study, including 268 patients with centrally located HCCs who underwent narrow-margin hepatectomy. The patients were subsequently allocated to the IOERT group (n=59) or to the control group (n=65). The primary outcome of the study was to compare recurrence-free survival (RFS) between the IOERT group and the control group, and the secondary outcome was to compare overall survival (OS) rate between the two groups. Results: Of 268 patients enrolled, a total of 124 were included in the study: 59 in IOERT group, 65 in control group. The 1-, 2-, 3-year RFS rates were 79.3%, 62.1% and 45.8% for patients in the IOERT group, and 47.6%, 28.6%, and 22.9% for patients in the control group, respectively (P=0.025). The 1-, 2-, and 3-year OS rates were 100.0%, 94.9%, and 83.7% for patients in the IOERT group, and 92.3%, 87.5%, and 79.4% for patients in the control group, respectively (P=0.314). Subgroup analysis of MVI (+) patients revealed that RFS and OS are significantly prolonged in the IOERT subgroup as compared to the control, whereas there was no significant difference of RFS and OS between the two groups in MVI (−) patients. Conclusions: IOERT for centrally located HCCs with concurrent narrow-margin hepatectomy was feasible and safe. Statistically better RFS rate was observed in the IOERT group compared to the control group. Subgroup analysis revealed that IOERT was more beneficial for postoperative survival of HCC patients with MVI. Trial Registration: ChiCTR-TRC-12002802;www.***.int/ictrp.

关键词： Hepatocellular carcinoma(HCC) intraoperative electron radiotherapy(IOERT) microvascular invasion(MVI) relapse survival overall survival(OS)

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