DNA database

DNA 数据库
  • 文章类型: Journal Article
    自1995年以来,国家法医DNA数据库使用了最大数量的贡献者,和最少数量的基因座,以减少提供假引线的风险。不符合这些标准的生物痕迹的DNA谱不能加载到这些数据库中。2023年,在瑞士西部分析的15,000多个痕量DNA图谱中,约有10%未在国家一级进行比较。即使它们被认为是可解释的,主要是因为它们含有两个以上人的DNA。在这种情况下,警察部门可以要求与已知人员的DNA档案和/或其他痕迹进行本地比较,但这种情况只发生在一小部分病例中,所以DNA混合物很少被用来帮助检测潜在的序列。概率基因分型软件及其相关工具的开发使这种类型的比较的有效性能成为可能,这是基于似然比(LR)而不是共享等位基因的数量。为了突出调查和情报目的的潜在共同贡献者,本研究使用软件STRmixv2.7的混合物-混合物工具比较了瑞士DNA数据库无法搜索的235个DNA图谱.这些DNA图谱源于2021年和2022年由六个不同的警察部门收集的痕迹。警方根据表明它们来自潜在系列的信息选择了痕迹。将配置文件之间的关联与预期的调查关联进行比较,以定义这种方法的价值。在27,495对DNA图谱的配对比较中,当使用1000的LR阈值时,88对(0.3%)显示出至少一个潜在的共同贡献者。在这88对中,60人(68.2%)被警方认定为“预期”(60/88),22(25.0%)作为“可能”,六个(6.8%)为“意外”。尽管重要的是要考虑这种方法的局限性(例如,不定或错过的联想,成本/效益评估,过程中DNA混合物比较的整合),这些发现表明,非CODIS可加载的DNA混合物可以为警察机构提供有关地方和国家层面潜在系列的信息.
    Since 1995, national forensic DNA databases have used a maximum number of contributors, and a minimum number of loci to reduce the risk of providing false leads. DNA profiles of biological traces that do not meet these criteria cannot be loaded into these databases. In 2023, about 10 % of more than 15,000 trace DNA profiles analyzed in western Switzerland were not compared at the national level, even though they were considered to be interpretable, mainly because they contained the DNA from more than two persons. In this situation, police services can request local comparisons with DNA profiles of known persons and/or with other traces, but this occurs in only a small proportion of cases, so that DNA mixtures are rarely used to help detect potential series. The development of probabilistic genotyping software and its associated tools have made possible the efficient performance of this type of comparison, which is based on likelihood ratios (LR) rather than on the number of shared alleles. To highlight potential common contributors for investigation and intelligence purposes, the present study used the mixture-to-mixture tool of the software STRmix v2.7 to compare 235 DNA profiles that cannot be searched the Swiss DNA database. These DNA profiles originated from traces collected by six different police services in 2021 and 2022. Traces were selected by the police based on information that indicated that they were from potential series. Associations between profiles were compared with expected investigative associations to define the value of this approach. Among the 27,495 pairwise comparisons of DNA profiles, 88 pairs (0.3 %) showed at least one potential common contributor when using a LR threshold of 1000. Of these 88 pairs, 60 (68.2 %) were qualified by the police services as \"expected\" (60/88), 22 (25.0 %) as \"possible\", and six (6.8 %) as \"unexpected\". Although it is important to consider the limits of this approach (e.g., adventitious or missed associations, cost/benefit evaluation, integration of DNA mixture comparison in the process), these findings indicate that non CODIS loadable DNA mixtures could provide police agencies with information concerning potential series at both the local and national level.
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  • 文章类型: Journal Article
    DNA技术是从生物学证据中识别个体的金标准。该技术为全球分析提供了普遍相似的方法和方法的便利。然而,由于缺乏DNA数据库以及在犯罪现场和受害者(尤其是性侵犯的受害者)的样本收集和保存方面的空白,该技术尚未在印度充分发挥其潜力。Further,在大多数情况下,DNA结果的统计解释是不存在的。尽管DNA分析领域的最新技术和发展正在被采用和实施,几乎没有制定任何措施来改善优化样品收集和保存。本文讨论了当前的案例工作场景,这些场景突出了DNA分析领域的陷阱和模糊区域,特别是在DNA数据库方面,采样,遗传数据分析的统计方法。提出了可能的解决方案和缓解措施。
    DNA technology is the gold standard with respect to the identification of individuals from biological evidence. The technology offers the convenience of a universally similar approach and methodology for analysis across the globe. However, the technology has not realised its full potential in India due to the lack of a DNA database and lacunae in sample collection and preservation from the scene of crime and victims (especially those of sexual assault). Further, statistical interpretation of DNA results is non-existent in the majority of cases. Though the latest technologies and developments in the field of DNA analysis are being adopted and implemented,very little has been enacted practically to improve optimise sample collection and preservation. This article discusses current casework scenarios that highlight the pitfalls and ambiguous areas in the field of DNA analysis, especially with respect DNA databases, sampling, andstatistical approaches to genetic data analysis. Possible solutions and mitigation measures are suggested.
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  • 文章类型: Journal Article
    萨赫勒地区持续的恐怖袭击要求通过使用人类DNA识别技术来加强安全系统。在这种情况下,在为最具侵入性的监视和特征分析形式之一建立坚实的标准和普遍保障措施时,必须考虑公众舆论。为此,我们在布基纳法索(位于萨赫勒地区的一个国家)收集了互联网用户对使用DNA技术支持刑事调查的意见。结果显示,470名参与者中有91.7%(431)认为该技术目前是布基纳法索刑事司法系统所必需的。然而,受访者对国家法医DNA数据库的保管和管理表示担忧.在这个特定的安全设置中,这项研究的公众意见可能为领导人和政治政策制定者提供考虑遗传指纹和实施国家法医DNA数据库的线索,以支持布基纳法索的刑事调查,同时也考虑伦理影响.
    Ongoing terrorist attacks in the Sahel region call for strengthening the security system by using human DNA identification technology. In this context, public opinion must be considered when establishing solid standards and universal safeguards for one of the most invasive forms of surveillance and profiling. For this purpose, we gathered internet users\' opinions in Burkina Faso (a country located in the Sahel region) on the use of DNA technology to support criminal investigations. The results revealed that 91.7% (431) of the 470 participants believed that this technology is currently necessary for the Burkina Faso\'s criminal justice system. However, the respondents expressed concerns about the custody and management of a national forensic DNA database. In this particular security setting, the public opinion of this study may provide leaders and political policymakers with clues for considering genetic fingerprints and implementing an national forensic DNA database to support criminal investigations in Burkina Faso whilst also considering the ethical implications.
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  • 文章类型: Journal Article
    DNA损伤是导致遗传改变的关键因素,直接影响人类健康,包括发展中的疾病,如癌症和年龄相关的疾病。DNA修复机制在维护遗传完整性和预防这些疾病的发作中起着关键作用。在过去的十年里,在DNA损伤和修复方面已经取得了实质性进展和关键发现。这篇全面的综述论文巩固了研究工作,专注于DNA修复机制,计算研究方法,和相关的数据库。我们的工作对于从事计算DNA研究的科学家和研究人员来说是宝贵的资源,提供有关DNA相关蛋白质的最新见解,疾病,和尖端的方法。审查解决了关键问题,包括DNA损伤的主要类型,常见的DNA修复机制,DNA损伤和相关疾病的可靠数据库的可用性,以及参与DNA损伤和修复的酶的主要计算研究方法。
    DNA damage is a critical factor contributing to genetic alterations, directly affecting human health, including developing diseases such as cancer and age-related disorders. DNA repair mechanisms play a pivotal role in safeguarding genetic integrity and preventing the onset of these ailments. Over the past decade, substantial progress and pivotal discoveries have been achieved in DNA damage and repair. This comprehensive review paper consolidates research efforts, focusing on DNA repair mechanisms, computational research methods, and associated databases. Our work is a valuable resource for scientists and researchers engaged in computational DNA research, offering the latest insights into DNA-related proteins, diseases, and cutting-edge methodologies. The review addresses key questions, including the major types of DNA damage, common DNA repair mechanisms, the availability of reliable databases for DNA damage and associated diseases, and the predominant computational research methods for enzymes involved in DNA damage and repair.
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  • 文章类型: Journal Article
    在法医科学SA(FSSA)的三个月内,针对无可疑病例,对一种自动化的DNA图谱处理系统(称为“熄灭工作流程”)进行了试验。熄灭工作流程利用FaSTR™DNA中的神经网络读取功能进行了自动DNA谱读取,没有分析阈值。然后使用自顶向下分析在STRmix™中处理来自FaSTR™DNA的谱信息,并自动与去识别的南澳大利亚可搜索DNA数据库进行比较。计算机脚本用于生成链接报告和上传报告,并将其与在实验室内进行标准处理期间为案例获得的链接和上传进行比较。与标准工作流程相比,熄灭工作流程的结果是上传和链接都有所增加,最少的不定链接或错误上传。总的来说,概念验证研究表明,在无可疑的工作流程中,使用自动DNA谱读取和自顶向下分析来提高工作流程效率的潜力.
    An automated system of DNA profile processing (termed a \'lights-out\' workflow) was trialled for no-suspect cases over a three-month period at Forensic Science SA (FSSA). The lights-out workflow utilised automated DNA profile reading using the neural network reading feature in FaSTR™ DNA with no analytical threshold. The profile information from FaSTR™ DNA was then processed in STRmix™ using a top-down analysis and automatically compared to a de-identified South Australian searchable DNA database. Computer scripts were used to generate link reports and upload reports and these were compared to the links and uploads that were obtained for the cases during their standard processing within the laboratory. The results of the lights-out workflow was an increase in both uploads and links compared to the standard workflow, with minimal adventitious links or erroneous uploads. Overall, the proof-of-concept study shows the potential for using automated DNA profile reading and top-down analysis to improve workflow efficiency in a no-suspect workflow.
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  • 文章类型: Journal Article
    DNA混合解释是法医学中最具挑战性的问题之一。当存在多于两个贡献者或相关贡献者时,复杂的DNA混合物更难以分析。微单倍型(MHs)是最近发现并用于DNA混合物分析的多态性遗传标记。然而,MH基因分型数据的证据解释需要更多的辩论。随机人不排除(RMNE)方法分析DNA混合物,而不使用等位基因峰高数据或贡献者数量(NoC)假设。本研究旨在评估RMNE对混合MH基因分型数据的解释程度。我们根据它们的Ae值将来自1000基因组项目数据库的MH基因座分类成组。然后,我们进行了具有2-10个不相关的贡献者的DNA混合物和具有一对同胞贡献者的DNA混合物的模拟。对于每个模拟的DNA混合物,估计了三种类型的非贡献者的错误纳入比率:随机男性,贡献者的父母,和贡献者的兄弟姐妹。同时,计算贡献者和三种类型的非贡献者的RMNE概率,允许基因座不匹配。结果表明,MH数,MHAe值,NoC影响了混合物的RMNE概率和不正确的非贡献者比率。当有更多的MHs时,Ae值较高的MHs,和NoC较少的混合物,RMNE概率,错误的纳入比率下降。混合物中亲缘关系的存在使混合物解释变得复杂。作为混合物中的非贡献者和相关贡献者的贡献者\'亲属增加了对遗传标记的要求,以正确识别贡献者。当使用500个Ae值高于5的高度多态MHs时,这四种个体类型可以根据RMNE概率来区分。这项研究揭示了MH作为混合DNA解释的遗传标记以及RMNE的扩展作为指示特定个体与DNA混合物在DNA数据库搜索中的关系的参数的有希望的潜力。
    DNA mixture interpretation is one of the most challenging problems in forensics. Complex DNA mixtures are more difficult to analyze when there are more than two contributors or related contributors. Microhaplotypes (MHs) are polymorphic genetic markers recently discovered and employed in DNA mixture analysis. However, the evidentiary interpretation of the MH genotyping data needs more debate. The Random Man Not Excluded (RMNE) method analyzes DNA mixtures without using allelic peak height data or the number of contributors (NoC) assumptions. This study aimed to assess how well RMNE interpreted mixed MH genotyping data. We classified the MH loci from the 1000 Genomes Project database into groups based on their Ae values. Then we performed simulations of DNA mixtures with 2-10 unrelated contributors and DNA mixtures with a pair of sibling contributors. For each simulated DNA mixture, incorrectly included ratios were estimated for three types of non-contributors: random men, parents of contributors, and siblings of contributors. Meanwhile, RMNE probability was calculated for contributors and three types of non-contributors, allowing loci mismatch. The results showed that the MH number, the MH Ae values, and the NoC affected the RMNE probability of the mixture and the incorrectly included ratio of non-contributors. When there were more MHs, MHs with higher Ae values, and a mixture with less NoC, the RMNE probability, and the incorrectly included ratio decreased. The existence of kinship in mixtures complicated the mixture interpretation. Contributors\' relatives as non-contributors and related contributors in the mixture increased the demands on the genetic markers to identify the contributors correctly. When 500 highly polymorphic MHs with Ae values higher than 5 were used, the four individual types could be distinguished according to the RMNE probabilities. This study reveals the promising potential of MH as a genetic marker for mixed DNA interpretation and the broadening of RMNE as a parameter indicating the relationship of a specific individual with a DNA mixture in the DNA database search.
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  • 文章类型: Journal Article
    生物多样性被提议作为高生物多样性地区经济发展的可持续替代方案。特别是在生物多样性基因组学领域,低成本DNA测序的发展为学术界以外的新参与者参与基因组测序提供了机会。然而,要充分补偿非学术行为者,如当地居民对创新过程的贡献,这是很有挑战性的。阻碍更好的生物经济发展。尽管许多存储库注册了基因组数据以支持生物多样性研究,它们不利于公平分享经济利益。在这项工作中,我们提议创建亚马逊生物银行,基于社区的遗传数据库。我们使用区块链来建立一个透明和可验证的涉及基因组数据的交易日志,我们使用智能合约为所有收集的参与者实施内部货币系统,插入,process,store,并验证基因组数据。我们还使用对等解决方案,允许使用商用计算机的用户与DNA文件的存储和分发进行协作。通过结合新兴技术,AmazonBiobank在与数据协作的所有参与者之间提供充分的利益共享,知识,和计算资源。它还提供了可追溯性和可审计性,允许生物技术研究和DNA数据之间的简单关联。此外,该解决方案具有高度的可扩展性,并且不太依赖于存放在任何系统播放器中的信任。因此,亚马逊生物银行可以成为释放亚马逊雨林等丰富生态系统中生物经济潜力的重要垫脚石。
    Biodiversity is proposed as a sustainable alternative for the economic development of high-biodiversity regions. Especially in the field of biodiversity genomics, the development of low-cost DNA sequencing opens an opportunity for new actors beyond academia to engage in genomic sequencing. However, it is challenging to adequately compensate non-academic actors such as local populations for their contribution to the innovation process, preventing better bioeconomy development. Although many repositories register genomic data to support biodiversity research, they do not facilitate the fair sharing of economic benefits. In this work, we propose the creation of the Amazon Biobank, a community-based genetic database. We employed blockchain to build a transparent and verifiable log of transactions involving genomic data, and we used smart contracts to implement an internal monetary system for all participants who collect, insert, process, store, and validate genomic data. We also used peer-to-peer solutions to allow users with commodity computers to collaborate with the storage and distribution of DNA files. By combining emerging technologies, Amazon Biobank provides adequate benefit-sharing among all participants that collaborate with data, knowledge, and computational resources. It also provides traceability and auditability, allowing easy association between biotechnological research and DNA data. In addition, the solution is highly scalable and less dependent on the trust deposited in any system player. Therefore, Amazon Biobank can become an important stepping stone to unlock the potential of bioeconomy in rich ecosystems such as the Amazon Rainforest.
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  • 文章类型: Journal Article
    并非所有的区块链都是平等的,许多人无法适应大数据的所有主要特征:多样性,速度,体积和准确性。目前,公共区块链既缓慢又笨重,跟上基因组数据产生的速度可能是昂贵的。Further,公共区块链的透明和普遍可访问的性质不一定能容纳所有种类的序列数据,包括非常私人的信息。定制私人许可的区块链,然而,可以创建以最佳地适应基因组数据的所有大数据特征。Further,可以实施私人许可链,以保护其中遗传信息的隐私和安全,同时也提供给研究人员。与该私有链相关的NFT市场可以提供匿名和加密数据集的离散化销售,同时还可以激励个人通过智能合约介导的支付共享数据。私有区块链可以为客户数据的每次使用提供透明的监管链,并验证此数据未损坏。然而,即使有所有这些好处,对这项新技术的实施仍然存在一些担忧,包括道德,通常与DNA数据库相关的法律和社会影响。
    Not all blockchains are created equal, and many cannot accommodate all of the primary characteristics of big data: Variety, Velocity, Volume and Veracity. Currently, public blockchains are slow and clunky, it can be expensive to keep up with the velocity of genomic data production. Further, the transparent and universally accessible nature of public blockchain doesn\'t necessarily accommodate all of the variety of sequence data, including very private information. Bespoke private permissioned blockchains, however, can be created to optimally accommodate all of the big data features of genomic data. Further, private permissioned chains can be implemented to both protect the privacy and security of the genetic information therein, while also providing access to researchers. An NFT marketplace associated with that private chain can provide the discretized sale of anonymous and encrypted data sets while also incentivizing individuals to share their data through payments mediated by smart contracts. Private blockchains can provide a transparent chain of custody for each use of the customers\' data, and validation that this data is not corrupted. However, even with all of these benefits there remain some concerns with the implementation of this new technology including the ethical, legal and social implications typically associated with DNA databases.
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  • 文章类型: Journal Article
    常染色体STR的短串联重复序列(STR)标记用于法医脱氧核糖核酸(DNA)分型以追踪缺失,验证家庭连接,并可能将嫌疑人与犯罪现场联系起来.众所周知,法医相关的遗传标记不能预测表型。没有证据支持直接使用法医STR变异导致或指示疾病的说法。这样的例子将产生重大的道德和允许的影响。必须检查是否有必要向献血者发出警报,或者在常规样本分析期间是否发现医疗问题。在这项研究中,我们评估了法医STRs可能提供超出初步鉴定所需的细节的可能性.然而,由于理解了非编码STRs在基因调控中的作用,发现有意义的链接的概率正在上升。对于这篇评论,谷歌学者,ScienceDirect,PubMed,和谷歌搜索都被用来进行彻底的电子文献检索。如果他们链接到主题,思想,回顾性研究,观察性研究,并考虑了第一批出版物。此处介绍的案例研究强调了法医DNA分型在降低犯罪风险和提供案件确凿证据方面的关键作用。法医DNA分型的主要方法是短串联重复(STR)分型。关于STR标记对刑事司法系统的重要性的讨论是本研究的一部分。作为错误信念和与真正罪魁祸首的宝贵联系的坚定证据,DNA分型提供了可以用来起诉和惩罚罪犯的证据。它甚至可能阻止某些罪犯犯下更可怕的罪行。此外,法医专家使用DNA分型技术重新检查了以前因缺乏证据而结案的古代案件。
    Short tandem repeat (STR) markers for autosomal STR are used in forensic deoxyribonucleic acid (DNA) typing to track down the missing, verify family connections, and potentially connect suspects to crime sites. It is well acknowledged that forensically relevant genetic markers cannot predict phenotype. There is no evidence to support the claim that directly using forensic STR variations causes or indicates illness. Such an example would have significant ethical and permissible repercussions. It is essential to check the necessity to alert a blood donor or if a medical problem is identified during routine sample analysis. In this study, we assess the likelihood that forensic STRs might offer details beyond those required for primary identification. However, as the role of non-coding STRs in gene regulation is understood, the probability of discovering meaningful links is rising. For this review, Google Scholar, ScienceDirect, PubMed, and Google Search were all used to conduct a thorough electronic literature search. If they linked to the topic, thoughts, retrospective studies, observational studies, and first publications were considered. The case studies presented here highlight the critical role forensic DNA typing plays in reducing criminal risk and delivering conclusive evidence in cases. The primary method for forensic DNA typing is short tandem repeat (STR) typing. This discussion on the importance of STR markers to the criminal justice system is part of the present study. As unflinching proof of false beliefs and invaluable connections to the genuine culprits, DNA typing offers proof that may be utilised to prosecute and punish criminals. It may even deter certain offenders from committing more terrible offences. Additionally, forensic experts have used DNA typing techniques to re-examine ancient cases previously closed due to a lack of evidence.
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  • 文章类型: Journal Article
    DNA证据对于获得调查线索的重要性要求大量进行法医DNA分析的快速工作流程。因此,我们开发了自动化DNA谱分析的软件解决方案,污染检查,主要捐赠者推断,DNA数据库(DDB)的比较和报告的结论。这代表了快速DNA鉴定线(FIDL),本研究描述了它的发展,作者研究所刑事案件工作中的验证和实施。该第一实施方式涉及单一供体概况和混合物的主要贡献者。验证包括单独测试软件组件以及检查不同DDB搜索策略的性能。此外,端到端测试在三个条件下进行:(1)测试DNA案例工作实践中可能发生的场景,(2)使用三个月以前的案例数据进行测试,和(3)在案例工作生产环境中与标准案例工作实践并行进行测试。与手动工作流程一样,通过该自动化生产线检索相同的DNA数据库候选物。数据流是正确的,结果具有可重复性和鲁棒性,需要手动分析的结果被正确标记,报告的结果与预期一致。总的来说,我们发现FIDL适用于我们研究所的案例工作实践。FIDL的结果在收到痕量样品后的三个工作日内自动报告。这包括登记案件所需的时间,DNA提取,量化,聚合酶链反应和毛细管电泳。FIDL本身从输入原始CE数据到报告不到两个小时。报告的结论是五个选项之一:(1)从DDB检索到的候选,(2)没有从DDB中检索到候选人,(三)案件参照的证据价值高的,(4)结果需要专家的检查,或(5)获得的DNA量不足以产生DNA谱。在我们目前的进程中,自动报告在三个工作日内发送,并提交一份完整的报告,在确认FIDL结果后,并由报告官员签名,稍后发送。签署的报告可以包括关于例如次要贡献者的附加分析。带有首例结果的自动报告可快速提供给警察,使他们能够在收到完整的DNA报告之前对DNA结果采取行动。这条生产线能够以统一有效的方式处理大量的痕迹和案件,并在调查的早期阶段提供高价值的调查线索。
    The importance of DNA evidence for gaining investigative leads demands a fast workflow for forensic DNA profiling performed in large volumes. Therefore, we developed software solutions for automated DNA profile analysis, contamination check, major donor inference, DNA database (DDB) comparison and reporting of the conclusions. This represents the Fast DNA IDentification Line (FIDL) and this study describes its development, validation and implementation in criminal casework at the authors\' institute. This first implementation regards single donor profiles and major contributors to mixtures. The validation included testing of the software components on their own and examination of the performance of different DDB search strategies. Furthermore, end-to-end testing was performed under three conditions: (1) testing of scenarios that can occur in DNA casework practice, (2) tests using three months of previous casework data, and (3) testing in a casework production environment in parallel to standard casework practices. The same DNA database candidates were retrieved by this automated line as by the manual workflow. The data flow was correct, results were reproducible and robust, results requiring manual analysis were correctly flagged, and reported results were as expected. Overall, we found FIDL valid for use in casework practice in our institute. The results from FIDL are automatically reported within three working days from receiving the trace sample. This includes the time needed for registration of the case, DNA extraction, quantification, polymerase chain reaction and capillary electrophoresis. FIDL itself takes less than two hours from intake of the raw CE data to reporting. Reported conclusions are one of five options: (1) candidate retrieved from DDB, (2) no candidate retrieved from DDB, (3) high evidential value with regards to reference within the case, (4) results require examination of expert, or (5) insufficient amount of DNA obtained to generate a DNA profile. In our current process, the automated report is sent within three working days and a complete report, with confirmation of the FIDL results, and signed by a reporting officer is sent at a later time. The signed report may include additional analyses regarding e.g. minor contributors. The automated report with first case results is quickly available to the police enabling them to act upon the DNA results prior to receiving the full DNA report. This line enables a uniform and efficient manner of handling large numbers of traces and cases and provides high value investigative leads in the early stages of the investigation.
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