scholarly journals cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies

mSystems ◽  
2015 ◽  
Vol 1 (1) ◽  
Author(s):  
John H. Chase ◽  
Evan Bolyen ◽  
Jai Ram Rideout ◽  
J. Gregory Caporaso
Keyword(s):  
Integrated Analysis ◽  
Sample Collection ◽  
Major Step ◽  
Global Uniqueness ◽  
Bar Codes ◽  
Sample Tracking ◽  
Sample Data ◽  
Command Line Tool ◽  
Sample Management ◽  
Scientific Results

ABSTRACT The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis, sample identifiers generated with cual-id will not need to change; thus, costly and error-prone updating of data and metadata identifiers will be avoided. Further, using cual-id will ensure that transcription errors in sample identifiers do not require the discarding of otherwise-useful samples that may have been expensive to obtain. Finally, cual-id is simple to install and use and is free for all use. No centralized infrastructure is required to ensure global uniqueness, so it is feasible for any lab to get started using these identifiers within their existing infrastructure. The number of samples in high-throughput comparative “omics” studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials, such as swabs or microcentrifuge tubes, however, so cual-id additionally generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project. By convention, we use “cual-id” to refer to the software, “CualID” to refer to the short, human-friendly identifiers, and “UUID” to refer to the globally unique identifiers. CualIDs are used by humans when they manually write or enter identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. Finally, cual-id optionally generates printable label sticker sheets containing Code 128 bar codes and CualIDs for labeling of sample collection and processing materials. IMPORTANCE The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis, sample identifiers generated with cual-id will not need to change; thus, costly and error-prone updating of data and metadata identifiers will be avoided. Further, using cual-id will ensure that transcription errors in sample identifiers do not require the discarding of otherwise-useful samples that may have been expensive to obtain. Finally, cual-id is simple to install and use and is free for all use. No centralized infrastructure is required to ensure global uniqueness, so it is feasible for any lab to get started using these identifiers within their existing infrastructure.

scholarly journals cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative -omics studies

2015 ◽  
Author(s):  
John H Chase ◽  
Evan T Bolyen ◽  
Jai Ram Rideout ◽  
J Gregory Caporaso
Keyword(s):  
High Throughput ◽  
Project Teams ◽  
Command Line ◽  
Major Step ◽  
Sample Tracking ◽  
Sample Data ◽  
Command Line Tool ◽  
Scientific Results

The number of samples in high-throughput comparative “omics” studies is increasing rapidly due to the declining experimental costs. To keep sample data and metadata manageable, and ensure the integrity of scientific results as the scale of these projects continue to increase, it is essential that we transition to better designed sample identifiers. Ideally, sample identifiers will be: globally unique across projects, project teams and institutions; be short to facilitate manual transcription; be correctable with respect to common types of transcription errors; be opaque, meaning they do not contain information about the samples; and be compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign Universally Unique Identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials such as swabs or microcentrifuge tubes however, so cual-id additionally generates human-friendly 4-12 character identifiers (CualIDs) that map to their UUIDs and are unique within a project. CualIDs are used by humans when they are manually writing or entering identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. The adoption of identifiers that are globally unique, correctable, and easily hand-written or manually entered into a computer will be a major step forward for sample tracking in comparative -omics studies within and across projects and project teams.

scholarly journals cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative -omics studies

2015 ◽  
Author(s):  
John H Chase ◽  
Evan T Bolyen ◽  
Jai Ram Rideout ◽  
J Gregory Caporaso
Keyword(s):  
High Throughput ◽  
Project Teams ◽  
Command Line ◽  
Major Step ◽  
Sample Tracking ◽  
Sample Data ◽  
Command Line Tool ◽  
Scientific Results

The number of samples in high-throughput comparative “omics” studies is increasing rapidly due to the declining experimental costs. To keep sample data and metadata manageable, and ensure the integrity of scientific results as the scale of these projects continue to increase, it is essential that we transition to better designed sample identifiers. Ideally, sample identifiers will be: globally unique across projects, project teams and institutions; be short to facilitate manual transcription; be correctable with respect to common types of transcription errors; be opaque, meaning they do not contain information about the samples; and be compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign Universally Unique Identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials such as swabs or microcentrifuge tubes however, so cual-id additionally generates human-friendly 4-12 character identifiers (CualIDs) that map to their UUIDs and are unique within a project. CualIDs are used by humans when they are manually writing or entering identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. The adoption of identifiers that are globally unique, correctable, and easily hand-written or manually entered into a computer will be a major step forward for sample tracking in comparative -omics studies within and across projects and project teams.

scholarly journals WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

2021 ◽  
Author(s):  
Pengchuan Sun ◽  
Beibei Jiao ◽  
Yongzhi Yang ◽  
Lanxing Shan ◽  
Ting Li ◽  
...  
Keyword(s):  
Detection Algorithm ◽  
Integrated Analysis ◽  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Command Line Tool ◽  
Genome Analyses ◽  
Life On Earth ◽  
User Friendly

Evidence of whole-genome duplications (WGDs) and subsequent karyotype changes has been detected in most major lineages of life on Earth. To clarify the complex resulting multiple-layered patterns of gene collinearity in genome analyses there is a need for convenient and accurate toolkits. To meet this need, we introduce here WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosomal karyotyping) that can improve detection of WGD and characterization of related events. It incorporates a more sensitive and accurate collinearity detection algorithm than previous softwares, and can accelerate WGD-related karyotype research. As a freely available toolkit at GitHub (https://github.com/SunPengChuan/wgdi), WGDI outperforms similar tools in terms of efficiency, flexibility and scalability. In an illustrative example of its application, WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.

scholarly journals PREDICT: a checklist for preventing preanalytical diagnostic errors in clinical trials

2020 ◽  
Vol 58 (4) ◽  
pp. 518-526 ◽  
Author(s):  
Giuseppe Lippi ◽  
Alexander von Meyer ◽  
Janne Cadamuro ◽  
Ana-Maria Simundic ◽  
_ _
Keyword(s):  
Clinical Trials ◽  
Clinical Chemistry ◽  
Diagnostic Testing ◽  
Diagnostic Errors ◽  
European Federation ◽  
Sample Collection ◽  
Specimen Retrieval ◽  
Sample Management ◽  
Accurate Performance ◽  
High Level

AbstractAlthough the importance of guaranteeing a high level of preanalytical quality in routine diagnostic testing has already been largely acknowledged over the past decades, minor emphasis is currently being placed on the fact that accurate performance and standardization of many preanalytical activities are also necessary prerogatives of clinical trials. Reliable evidence exists that clear indications on how to manage the different preanalytical steps are currently lacking in many clinical trials protocols, nor have detailed authoritative documents been published or endorsed on this matter to the best of our knowledge. To fill this gap, the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Working Group for Preanalytical Phase (WG-PRE) will provide here a specific checklist for preventing preanalytical diagnostic errors in clinical trials (PREDICT), especially focused on covering the most important preanalytical aspects of blood sample management in clinical studies, and thus encompassing test selection, patient preparation, sample collection, management and storage, sample transportation, as well as specimen retrieval before testing. The WG-PRE members sincerely hope that these recommendations will provide a useful contribution for increasing the success rate in clinical trials.

scholarly journals Laser Capture Microdissection (LCM) and 3D Sample Tracking Protocol

2021 ◽  
Author(s):  
Shaina Robbins ◽  
Sirisha Achanta ◽  
Rajanikanth Vadigepalli
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Laser Capture Microdissection ◽  
Image Acquisition ◽  
Heart Tissue ◽  
Right Atrial ◽  
Sample Collection ◽  
Isolation Technique ◽  
Sample Tracking ◽  
Laser Capture

Abstract This protocol demonstrates the use of Laser Capture Microdissection (LCM), a precise cell isolation technique, for acquiring single neurons from right atrial ganglionated plexus (RAGP) porcine heart tissue in sync with image acquisition to enable 3D location tracking of collected samples. Fresh frozen RAGP tissue sectioned and stained for neurons (Nissl stain) is processed through LCM for sample collection. The LCM workflow is comprised of four steps: instrument setup, slide loading and tissue inspection, microdissection and image acquisition and sample processing and storage. LCM collected samples were processed for gene expression experiments : High-throughput-qRT-PCR or Single cell RNA sequencing. Gene expression data along with 3D sample tracking was used to generate a functional map of porcine RAGP. The techniques described in this protocol can be adapted to a wide variety of sample and tissue types with minor modifications. This protocol is a part of a protocol pipeline that includes cryosectioning and staining protocols upstream and Tissue Mapper protocol, High-Throughput q-RT-PCR and RNA Seq protocols downstream.

Robotic Assistive Device for Phlebotomy

2015 ◽  
Author(s):  
Paulo Carvalho ◽  
Anurag Kesari ◽  
Sean Weaver ◽  
Patrick Flaherty ◽  
Gregory S. Fischer
Keyword(s):  
Near Infrared ◽  
Force Feedback ◽  
Point Of Care ◽  
Healthcare Delivery ◽  
The United States ◽  
Assistive Device ◽  
Sample Collection ◽  
Major Step ◽  
Proper Diagnosis

Phlebotomy is a routine task, performed over a billion times annually in the United States alone, that is essential for proper diagnosis and treatment. We designed and constructed Phlebot, a robotic assistive device that uses a novel combination of near-infrared (NIR) monocular imaging and force-feedback to guide a needle into a forearm vein for blood sample collection or intravenous catheterization. Through initial validation on phantoms, we show that our approach offers a feasible and reliable method to automate phlebotomy. We envision the device to be a first major step towards more affordable point-of-care testing and diagnostic healthcare systems. In the long term, we expect that Phlebot will expedite healthcare delivery and drastically reduce needle stick injuries, instances of hemolysis, and infections caused by blood-borne pathogens.

scholarly journals Combating drunken driving: Questioning the validity of blood alcohol concentration analysis

2016 ◽  
Author(s):  
Ursula Ehmke ◽  
Lorraine Du Toit-Prinsloo ◽  
Christelle Deysel ◽  
Joyce Jordaan ◽  
Gert Saayman
Keyword(s):  
Blood Alcohol Concentration ◽  
Alcohol Concentration ◽  
Driving Under The Influence ◽  
Chemistry Laboratory ◽  
Blood Alcohol ◽  
Sample Collection ◽  
Validity Of Results ◽  
Average Delay ◽  
Sample Management ◽  
Drunken Driving

The reliability and accuracy of blood alcohol concentration (BAC) results presented in South African courts of law in respect of possible driving under the influence (DUI) cases, have in recent years been subjected to intense scrutiny and severe criticism.  Research has shown that multiple factors may negatively impact on the reliability of results obtained from the analysis of such samples - including inappropriate or non-standardised sample management after acquisition thereof.  In particular, long delays between sample acquisition and the analysis thereof may compromise the validity of results.  Such delays may also negatively affect the outcome of both criminal and civil legal proceedings in possible DUI cases.  A retrospective descriptive study was conducted on records from the Pretoria Forensic Chemistry Laboratory (PFCL) regarding the relevant dates pertaining to blood samples from deceased persons which were received for analysis. These parameters included the date of sample acquisition at medico-legal mortuaries, delays in submission of samples to the laboratory and date of actual analysis.  In addition, the expiration dates of sample collection kits were recorded.  Our results show that numerous expired kits were utilised and that there was an average delay of approximately five months between sample acquisition and laboratory analysis thereof.  This delay period varied greatly but appears to correlate with geographical distance of the medico-legal mortuary from the PFCL.  In order to optimise and facilitate the administration of justice in both criminal and civil cases of alleged DUI, these shortcomings should be urgently addressed.  It is argued that the implementation of prescribed measures and standard operating procedures in sample management, together with other interventions such as accreditation of laboratories and improved resourcing of medico-legal and toxicology laboratories, is urgently required.

scholarly journals High spectral resolution multi-tone Spacecraft Doppler tracking software: Algorithms and implementations

2021 ◽  
Vol 38 ◽  
Author(s):  
G. Molera Calvés ◽  
S. V. Pogrebenko ◽  
J. F. Wagner ◽  
G. Cimò ◽  
L. I. Gurvits ◽  
...  
Keyword(s):  
A Priori ◽  
High Spectral Resolution ◽  
Radio Telescopes ◽  
Spacecraft Dynamics ◽  
Downlink Transmission ◽  
Software Algorithms ◽  
Initial Release ◽  
Sample Data ◽  
Scientific Results ◽  
Doppler Tracking

Abstract We present a software package for single-dish data processing of spacecraft signals observed with VLBI-equipped radio telescopes. The Spacecraft Doppler tracking (SDtracker) software allows one to obtain topocentric frequency detections with a sub-Hz precision and reconstructed and residual phases of the carrier signal of any spacecraft or landing vehicle at any location in the Solar System. These data products are estimated using the ground-based telescope’s highly stable oscillator as a reference, without requiring an a priori model of the spacecraft dynamics nor the downlink transmission carrier frequency. The software has been extensively validated in multiple observing campaigns of various deep space missions and is compatible with the raw sample data acquired by any standard VLBI radio telescope worldwide. In this paper, we report the numerical methodology of SDtracker, the technical operations for deployment and usage, and a summary of use cases and scientific results produced since its initial release.

scholarly journals The Development of Cartographical Studies and Praxis in Montenegro

2018 ◽  
Author(s):  
Gojko Nikolic ◽  
Velibor Spalevic ◽  
Zoran Susic ◽  
Mehmed Batilovic ◽  
Goran Skataric ◽  
...  
Keyword(s):  
Real Estate ◽  
Integrated Analysis ◽  
Practical Implementation ◽  
The Real Estate ◽  
University Level ◽  
Scientific Results ◽  
The University ◽  
Teaching Modules ◽  
The Impact ◽  
Advanced Computer

This paper deals with an analysis of cartographical studies, the real estate cadastre, and its practical implementation, as well as the introduction of cartography into different education modules in university-level studies in Montenegro. There is a discussion of the development, production, and creativity in the fields of cartography and real estate cadastre over time, cartographical projection, scientific results, and recent changes such as advanced computer- and satellite-based technologies, GIS, cartographical visualization, and digital cartography. The impact of these changes on cartographical studies at the University of Montenegro is considered. Particular attention is given to analyses of cartography and the cadastre in institutions, and their connection with the development of cartography teaching modules of Geography, Geodesy and Geoinformatics at the University of Montenegro. The integrated analysis also covers the results of the questionnaire and the significance of the geo-topographical and cartographical heritage of Montenegro, with the aim of carrying these out. It can be seen that the tasks solved by using maps have tended to become more complex and that the cartographical methods employed in this have been always directed towards Montenegro’s most prominent and most urgent problems, including those that appear in the area of education.

scholarly journals Early Infant Diagnosis Sample Management in Mashonaland West Province, Zimbabwe, 2017

2018 ◽  
Vol 2018 ◽  
pp. 1-7
Author(s):  
Hamufare Mugauri ◽  
Owen Mugurungi ◽  
Addmore Chadambuka ◽  
Tsitsi Juru ◽  
Notion Tafara Gombe ◽  
...  
Keyword(s):  
Standard Operating Procedure ◽  
Hiv Treatment ◽  
Reference Laboratory ◽  
Early Infant Diagnosis ◽  
Sample Collection ◽  
Effect Analysis ◽  
Sample Quality ◽  
Treatment Services ◽  
Early Infant ◽  
Sample Management

Background. In 2016, Mashonaland West Province had 7.4% (520) dried blood spot (DBS) samples for early infant diagnosis (EID) rejected by the Zimbabwe National Microbiology Reference Laboratory (NMRL). The samples were suboptimal, delaying treatment initiation for HIV-infected children. EID is the entry point to HIV treatment services in exposed infants. We determined reasons for DBS sample rejections and suggested solutions. Methods. A cause-effect analysis, modelled on Ishikawa, was used to identify factors impacting DBS sample quality. Interviewer-administered questionnaires and evaluation of sample collection process, using Standard Operating Procedure (SOP) was conducted. Rejected samples were reviewed. Epi Info™ was used to analyze findings. Results. Eleven (73.3%) facilities did not adhere to SOP and (86.7%) did not evaluate DBS sample quality before sending for testing. Delayed feedback (up to 4 weeks) from NMRL extended EID delay for 14 (93.3%) of the facilities. Of the 53 participants, 62% knew valid sample identification. Insufficient samples resulted in most rejections (77.9%). Lack of training (94.3%) and ineffective supervision (69.8%) were also cited. Conclusion. Sample rejections could have been averted through SOP adherence. Ineffective supervision, exacerbated by delayed communication of rejections, extended EID delay, disadvantaging potential ART beneficiaries. Following this study, enhanced quality control through perstage evaluations was recommended to enhance DBS sample quality.

Sign in / Sign up

Export Citation Format

Share Document