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关键词： Protein identification   Peptide identification   Biochemistry   Peptides and proteins   Biological databases  

关键词： RNA-seq   Small RNA-seq   Unique molecular identifier   UMI   PCR duplicates   PCR cycle   Starting material   Sequencing depth   Transcriptome   Ribognome  

摘要： Background: RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules. Results: We have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species in both RNA-seq and small RNA-seq libraries generated from mouse testis. Our approach yields high-quality data while allowing unique tagging of all molecules in high-depth libraries. Conclusions: Using simulated and real datasets, we demonstrate that our methods increase the reproducibility of RNA-seq and small RNA-seq data. Notably, we find that the amount of starting material and sequencing depth, but not the number of PCR cycles, determine PCR duplicate frequency. Finally, we show that computational removal of PCR duplicates based only on their mapping coordinates introduces substantial bias into data analysis.

关键词： Algorithms   Applied mathematics   Astronomical instruments   Astronomical sciences   Astronomy   Autosomal recessive diseases   Biology and life sciences   Body mass index   Body weight   Catalogs   Celestial objects   Clinical genetics   Computer and information sciences   Computer applications   Cystic fibrosis   Danish people   Database and informatics methods   Developmental biology   Disease registries   Engineering and technology   Equipment   Ethnicities   European people   Fibrosis   Galaxies   Genetic diseases   Health informatics   Mathematics   Medicine and health sciences   Optical equipment   People and places   Physical sciences   Physiological parameters   Physiology   Population groupings   Pulmonology   Research and analysis methods   Research Article   Simulation and modeling   Telescopes  

摘要： Patient registry data are commonly collected as annual snapshots that need to be amalgamated to understand the longitudinal progress of each patient. However, patient identifiers can either change or may not be available for legal reasons when longitudinal data are collated from patients living in different countries. Here, we apply astronomical statistical matching techniques to link individual patient records that can be used where identifiers are absent or to validate uncertain identifiers. We adopt a Bayesian model framework used for probabilistically linking records in astronomy. We adapt this and validate it across blinded, annually collected data. This is a high-quality (Danish) sub-set of data held in the European Cystic Fibrosis Society Patient Registry (ECFSPR). Our initial experiments achieved a precision of 0.990 at a recall value of 0.987. However, detailed investigation of the discrepancies uncovered typing errors in 27 of the identifiers in the original Danish sub-set. After fixing these errors to create a new gold standard our algorithm correctly linked individual records across years achieving a precision of 0.997 at a recall value of 0.987 without recourse to identifiers. Our Bayesian framework provides the probability of whether a pair of records belong to the same patient. Unlike other record linkage approaches, our algorithm can also use physical models, such as body mass index curves, as prior information for record linkage. We have shown our framework can create longitudinal samples where none existed and validate pre-existing patient identifiers. We have demonstrated that in this specific case this automated approach is better than the existing identifiers.

关键词： 数字对象唯一标识符   DOI  

摘要： 数字对象唯一标识符（digital object identifier,DOI）是对包括互联网信息在内的数字信息进行标识的一种工具。在传统的出版物中,书刊、磁带、光盘都有国际标准编号（ISBN、ISSN、ISCN）及其条形码,作为出版物的唯一标识。这些标识使出版物得到有效的管理,便于读者查找和利用。而网上的文档一旦变更了网址便无从追索。数字信息标注DOI如同出版物的条形码,是一个永久和唯一的标识号。

关键词： GENE amplification   POLYMERASE chain reaction   COMPUTER-assisted drug design   GENETIC algorithms   COMBINATORIAL optimization   COMPUTATIONAL biology  

摘要： Motivation: Unique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon-based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments. Results: Based on the total number of DNA fragments and the distribution of allele frequencies, we present a model for the determination of the minimum UMI length required to prevent UMI collisions and reduce allelic distortion. We also introduce a user-friendly software tool called AmpUMI to assist in the design and the analysis of UMI-based amplicon sequencing studies. AmpUMI provides quality control metrics on frequency and quality of UMIs, and trims and deduplicates amplicon sequences with user specified parameters for use in downstream analysis.

关键词： 条形码   编码规则   平行线   标识符   简称   条码  

摘要： 众所周知，现在我们常见的条形码是将宽度不等的多个黑条（简称条）和白条（简称空），按照一定的编码规则排列成的平行线图案，用以表达一组信息的图形标识符，也可统称为条码。

关键词： 期刊   编辑工作   规范   数字  

摘要： DOI是＂Digital Object Indentifier＂的缩写,中文名是＂数字对象标识符＂,是一种包括字母和数字组合的针对数字内容或对象的唯一标识符,其主要作用是实现引文互联。

关键词： multicast   universal identifier network   SPT   central   controllable   secure  

摘要： With the rapid increase of network users and services, the breadth and depth of Internet have greatly changed. The mismatch between current network requirements and original network architecture design has spurred the evolution or revolution of Internet to remedy this gap. Lots of research projects on future network architecture have been launched, in which Universal Identifier Network (UIN) architecture that is based on the identifier/location separation, access/core separation and control/forwarding separation can provide better mobility, security and reliability. On the other hand, the demand of group communication has increased due to the fine-grained network services and successive booming of new applications such as IoT (Internet of Things). Most of current multicast schemes are based on the open group model with open group membership (multicast only care the multicast group state, not the group member) and open access to send/receive multicast data, which are beneficial to multicast routing for its simplification. However, the open group membership makes the group member management difficult to be realized, and open access may result in lots of security vulnerabilities such as Denial of service (DoS), eavesdropping and masquerading, which make deployment more difficult. Therefore, in this paper we propose a Central-Controllable and Secure Multicast (CCSM) system based on the UIN architecture, and redesign the multicast service procedures including registration, join/leave, multicast routing construction and update with objective to achieve better mobility support, security, scalability and controllable. More specifically, we design a new group management scheme to perform the multicast members join/leave with authentication and a central-controllable multicast routing scheme to provide a secure way to set up multicast entries on routers. The CCSM inherits the characteristics of UIN in terms of mobility and security, and it can provide the centralized multicas

关键词： Low Earth Orbit Satellites   Ground Station   Space Traffic Control   Space Situational Awareness   Flight Testing   Telescopes   Laser Diodes   Photovoltaic Cells   Los Alamos National Laboratories   Albedo  

摘要： Space object identification is vital for operating spacecraft, space traffic control, and space situational awareness, but initial determination, maintenance, and recovery of identity are all difficult, expensive, and error prone, especially for small objects like CubeSats. Attaching a beacon or license plate with a unique identification number to a space object before launch would greatly simplify the task, but radio beacons are power hungry and can cause interference. This Paper describes a new concept for a satellite license plate: the extremely low resource optical identifier. The extremely low resource optical identifier is a milliwatt-scale self-powered autonomous optical beacon that can be attached to any space object to transmit a persistent identification signal to ground stations. A system appropriate for a low-Earth-orbit CubeSat or other small space object can fit in a package with the area of a postage stamp and a few millimeters thick;and it requires no power, data, or control from the host object. The concept has been validated with ground tests, and the first flight-test unit is scheduled for launch in 2018. The unique identification number of a low-Earth-orbit satellite can be determined unambiguously in a single orbital pass over a low-cost ground station.

关键词： Diet Therapy   National Government