Bring barcoding to the bedside.
A 240-bed regional hospital shares best practices for implementing a patient safety initiative that targets point-of-care barcode technology.
Biomedical Technology↗
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Results for “barcode”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
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Barcode identification for transfusion safety.
PURPOSE OF REVIEW: Errors related to blood transfusion in hospitals may produce catastrophic consequences. This review addresses potential solutions to prevent patient misidentification including the use of new technology, such as barcoding. RECENT FINDINGS: A small number of studies using new technology for the transfusion process in hospitals have shown promising results in preventing errors. The studies demonstrated improved transfusion safety and staff preference for new technology such as bedside handheld scanners to carry out pretransfusion bedside checking. They also highlighted the need for considerable efforts in the training of staff in the new procedures before their successful implementation. SUMMARY: Improvements in hospital transfusion safety are a top priority for transfusion medicine, and will depend on a combined approach including a better understanding of the causes of errors, a reduction in the complexity of routine procedures taking advantage of new technology, improved staff training, and regular monitoring of practice. The use of new technology to improve the safety of transfusion is very promising. Further development of the systems is needed to enable staff to carry out bedside transfusion procedures quickly and accurately, and to increase their functionality to justify the cost of their wider implementation.
Blood Transfusion↗
Biological identifications through DNA barcodes.
Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
Animals↗
Hardcopy image barcodes via block-error diffusion.
Error diffusion halftoning is a popular method of producing frequency modulated (FM) halftones for printing and display. FM halftoning fixes the dot size (e.g., to one pixel in conventional error diffusion) and varies the dot frequency according to the intensity of the original grayscale image. We generalize error diffusion to produce FM halftones with user-controlled dot size and shape by using block quantization and block filtering. As a key application, we show how block-error diffusion may be applied to embed information in hardcopy using dot shape modulation. We enable the encoding and subsequent decoding of information embedded in the hardcopy version of continuous-tone base images. The encoding-decoding process is modeled by robust data transmission through a noisy print-scan channel that is explicitly modeled. We refer to the encoded printed version as an image barcode due to its high information capacity that differentiates it from common hardcopy watermarks. The encoding/halftoning strategy is based on a modified version of block-error diffusion. Encoder stability, image quality versus information capacity tradeoffs, and decoding issues with and without explicit knowledge of the base image are discussed.
Algorithms↗
Barcoding generalist predators by polymerase chain reaction: carabids and spiders.
Identification of arthropod predators is challenging when closely related species are found at a given locality. Identification of the immature stages is especially problematic, because distinguishing morphological features are difficult to use or have not been described. We used polymerase chain reaction (PCR) to distinguish closely related carabids and spiders, and to match eggs and larvae (or nymphs) with identified adult parents. Within the Carabidae, we amplified species-specific mitochondrial cytochrome oxidase I (COI) fragments for three species each in the genera Poecilus and Harpalus, and two each in Chlaenius and Bembidion. Within the Araneae, we amplified species-specific COI fragments for two Hibana species (Anyphaenidae), Pardosa milvina and Rabidosa rabida (Lycosidae), Frontinella communis and Grammonota texana (Linyphiidae), and Cheiracanthium inclusum (Miturgidae). We are able to correctly identify all immature stages tested--eggs, larvae (or nymphs) and pupae--by comparison of the amplified fragments with those of the adults. Using COI markers as species identifiers is a tenet of the Barcode of Life initiative, an international consortium to provide a molecular identifier for every animal species.
Animals↗
Lessons from leeches: a call for DNA barcoding in the lab.
Many evolution of development labs study organisms that must be periodically collected from the wild. Whenever this is the case, there is the risk that different field collections will recover genetically different strains or cryptic species. Ignoring this potential for genetic variation may introduce an uncontrolled source of experimental variability, leading to confusion or misinterpretation of the results. Leeches in the genus Helobdella have been a workhorse of annelid developmental biology for 30 years. Nearly all early Helobdella research was based on a single isolate, but in recent years isolates from multiple field collections and multiple sites across the country have been used. To assess the genetic distinctness of different isolates, we obtained specimens from most Helobdella laboratory cultures currently or recently in use and from some of their source field sites. From these samples, we sequenced part of the mitochondrial gene cytochrome oxidase I (COI). Sequence divergences and phylogenetic analyses reveal that, collectively, the Helobdella development community has worked on five distinct species from two major clades. Morphologically similar isolates that were thought to represent the same species (H. robusta) actually represent three species, two of which coexist at the same locality. Another isolate represents part of a species complex (the "H. triserialis" complex), and yet another is an invasive species (H. europaea). We caution researchers similarly working on multiple wild-collected isolates to preserve voucher specimens and to obtain from these a molecular "barcode," such as a COI gene sequence, to reveal genetic variation in animals used for research.
Animals↗
Nematode molecular diagnostics: from bands to barcodes.
Nematodes are considered among the most difficult animals to identify. DNA-based diagnostic methods have already gained acceptance in applications ranging from quarantine determinations to assessments of biodiversity. Researchers are currently in an information-gathering mode, with intensive efforts applied to accumulating nucleotide sequence of 18S and 28S ribosomal genes, internally transcribed spacer regions, and mitochondrial genes. Important linkages with collateral data such as digitized images, video clips and specimen voucher web pages are being established on GenBank and NemATOL, the nematode-specific Tree of Life database. The growing DNA taxonomy of nematodes has lead to their use in testing specific short sequences of DNA as a "barcode" for the identification of all nematode species.
Animals↗
An in vivo barcoded CRISPR-Cas9 screen identifies Ncoa4-mediated ferritinophagy as a dependence in Tet2-deficient hematopoiesis.
TET2 is among the most commonly mutated genes in both clonal hematopoiesis and myeloid malignancies; thus, the ability to identify selective dependencies in TET2-deficient cells has broad translational significance. Here, we identify regulators of Tet2 knockout (KO) hematopoietic stem and progenitor cell (HSPC) expansion using an in vivo CRISPR-Cas9 KO screen, in which nucleotide barcoding enabled large-scale clonal tracing of Tet2-deficient HSPCs in a physiologic setting. Our screen identified candidate genes, including Ncoa4, that are selectively required for Tet2 KO clonal outgrowth compared with wild type. Ncoa4 targets ferritin for lysosomal degradation (ferritinophagy), maintaining intracellular iron homeostasis by releasing labile iron in response to cellular demands. In Tet2-deficient HSPCs, increased mitochondrial adenosine triphosphate production correlates with increased cellular iron requirements and, in turn, promotes Ncoa4-dependent ferritinophagy. Restricting iron availability reduces Tet2 KO stem cell numbers, revealing a dependency in TET2-mutated myeloid neoplasms.
CRISPR-Cas Systems↗
The approximability of the String Barcoding problem.
The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given strings represent a set of known viruses, while the substrings can be used as probes for an hybridization experiment via microarray. Eventually, one aims at the classification of new strings (unknown viruses) through the result of the hybridization experiment. In this paper we show that SBC is as hard to approximate as Set Cover. Furthermore, we show that the constrained version of SBC (with probes of bounded length) is also hard to approximate. These negative results are tight.
Journal Article↗
Short-read genome skimming enables molecular barcoding of old myxomycete collections.
This study evaluates the effectiveness of Illumina-based genome skimming for barcoding myxomycete herbarium collections ranging from 29 to 91 years in age. We successfully retrieved partial sequences of the standard marker gene (nucSSU) in all cases, as well as additional markers (mtSSU, EF1a, and COI) for certain collections. Altogether, 28 genes were recognized in the studied material. In a 33-year-old specimen of Lindbladia tubulina, the assembly reached an N50 of 4.19 kb, enabling the recovery of extended functional loci. The input genomic DNA quantity emerges as the primary determinant of sequencing success. Samples with high DNA yields provide representative amounts of contigs coming confirmedly (matching sequences in the NCBI nucleotide database) or potentially (no-hit fraction) from myxomycetes, regardless of specimen age. In addition to target DNA, we revealed distinct signals of both anthropogenic contamination (human DNA and skin microflora) and natural substrate inhabitants, including oribatid mites and bacteria from dead wood, soil, and grass litter. Thus, even in old collections, metagenomic data still carry information regarding the substrate upon which the myxomycete developed. The results demonstrate that short-read genome skimming may help to integrate historical type material of myxomycetes into contemporary phylogenetic research. This method overcomes the length-dependent limitations of traditional Sanger sequencing, thus providing a roadmap for the future of museomics in myxomycetology.
Amoebozoa↗
A comprehensive, barcoded system for the management of animal information in a research facility.
The authors describe an easy-to-use barcode-based animal tracking system that has improved record keeping and data retrieval and proved instrumental in the containment of an outbreak.
Animal Welfare↗
Scanning medication barcodes improves accuracy at Lehigh Valley Hospital.
Performance improvement often means doing tasks faster, but it can also involve increasing the accuracy of a health care process and reducing error rates. At Lehigh Valley Hospital in Allentown, PA, the implementation of a wireless barcode scanning system has increased the accuracy of nurses giving medications to patients, even though it has slowed them down a bit.
Clinical Pharmacy Information Systems↗
Development of nursing care support system using PDA with wireless and barcode reader.
In this study, we developed nursing care support system using Personal Digital Assistants (PDA) with wireless and barcode reader. Our goals were to minimize the cost of deployment, to maximize the ease of operation, and to adapt to existing features and tasks of nursing care. The success of achieving these objectives was evaluated from the case study results involving system training session and trial of the system at a university hospital.
Computers, Handheld↗
An interactive histology image-barcode manual for a videodisc image library.
UNLABELLED: Cell Biology and HISTOLOGY (alias Microanatomy, alias Microscopic Anatomy) is a required course for first-year medical and dental students in most health science centers. The traditional approach used in teaching this discipline is to present photomicrographic images of structures to students in lecture using 35 mm slides of fields seen through the microscope. The students then spend many hours viewing and studying specimens of tissues using a light microscope in a laboratory setting. Students in traditional courses of histology spend an inordinate amount of time learning the component structures by attempting to find and identify them in tissue sections using a microscope, where the structure being sought is surrounded by a multitude of other structures with which they are also not familiar. With the recent availability of videodisc stored image libraries of histological samples, it is now possible to study histological principles without the use of the microscope as the primary learning tool. A videodisc entitled " HISTOLOGY: A Photographic Atlas" by S. Downing (published by Image Premastering Services Limited, Minneapolis, MN, 1991) has been incorporated into our histology course. Fifteen videodisc player stations are provided for 150 students. Images are retrieved by students using a bar code scanner attached to a videodisc player (Pioneer CLD-2400). Using this kind of image library, students can now learn basic histological structure, such as cell and tissue types, without the use of a microscope or as a tool for facilitating microscopy. The use of a videodisc library of randomly accessible images simplifies learning the basic components which all organs are composed of by presenting the learner with clear-cut examples to avoid confusion with other structures. However, videodisc players and TV monitors are still not appropriately priced for every student to own. This presents a problem in that the same images studied in class are not available to study and review outside of class. There is a need for resources for additional study outside of the institutional setting, for students to have and interact with to reinforce the learning experience in the teaching laboratory. A hard copy manual was created and is being used in our course; it incorporates photos captured from the videodisc. The images displayed in the manual are chosen to give the student one example of each histological component. Additional labeling is added to the images, and each image is accompanied by a bar code that may be used at a videodisc player with a bar code reader to retrieve the same color image from the disc displayed in larger format on a TV monitor. Each topic in the manual is accompanied by learning objectives and a statement of clinical relevance. Following the presentation of the images in each section of the manual, the students are encouraged to practice by viewing multiple examples of each structural component presented in the lesson. They can do this by using the bar-coded catalog supplied with each disc. The presentation of each topic concludes with a quiz composed of questions about images that the student can retrieve from the videodisc using barcodes in the text of the manual. Some of the images on the quiz are printed in miniature in the manual to provide the student with an opportunity for personal review at home when hardware to obtain and display images from a video disc is not available. This manual provides an answer to the dilemma faced by the learner when access to hardware is not available; reinforcement is therefore facilitated outside the teaching laboratory. This allows learning to continue outside of the classroom, using the same materials. (abstract truncated)
Computer-Assisted Instruction↗
Nanotech group's "bio-barcode" test a promising diagnostic, research tool.
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Biomedical Research↗
DNA-based barcodes, nanoparticles, and nanostructures for the ultrasensitive detection and quantification of proteins.
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Biosensing Techniques↗
A fluorophore-based bio-barcode amplification assay for proteins.
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Biological Assay↗
[Number of complaints in cashiers at workplaces with conventional cash registers and those with barcode reader equipment].
115 cash register operators of supermarkets have been studied. Postural complaints are high, compared to office workers. The results obtained by questionnaire and by a rheumatological examination revealed that most cash register operators complain about pains in the back, in the left shoulder and in the left arm. The cashiers working on laser-scanner-systems have the same complaints, but they have significantly less pains in the right arm and the right hand because the cash register is only used infrequently. It seems to be better if cashiers have to do different tasks in a supermarket because the study shows that cashiers who work at different workplaces have significantly less pains then those who work only at the cash register.
Back Pain↗