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PubMed2002

Evaluating two extremity dosemeters based on LiF:Mg,Ti or LiF:Mg,Cu,P.

Evaluation of a new extremity dosemeter is presented. The dosemeter is a passive device that is easy to wear and features a permanent individual numerical ID with barcode, a watertight case, an automatic TLD reader and database management software. Two dosemeters were studied: the first consists of a 100 mg x cm(-2) 7LiF:Mg,Ti (TLD-700) chip and a 42 mg x cm(-2) cap, the other consists of a 7 mg x cm(-2) layer of 7LiF:Mg,Cu,P (TLD-700H) powder and a 5 mg x cm(-2) cap. Sensitivity, repeatability, lower limit detection, angular responses and energy responses for these dosemeters are studied and presented. The dose calculation algorithm is developed and its dosimetric performance accuracy is compared with the standard ANSI N13.32-1995, Performance Testing of Extremity Dosemeters.

Beta Particles↗

PubMedDate not supplied

Nurses' perceptions of causes of medication errors and barriers to reporting.

This study describes nurses' perceptions about medication errors and the effects of physician order entry and barcode medication administration on medication errors. A convenience sample of 61 medical-surgical nurses was surveyed. All nurses surveyed perceived that information technology decreases medication errors. However, medication errors continue to occur despite the availability of sophisticated information technology systems.

Adverse Drug Reaction Reporting Systems↗

PubMed2005

Real time emergency response monitoring and data capture for chemical and radiological incidents.

The City of New York Department of Health and Mental Hygiene (DOHMH) wanted to improve both emergency environmental monitoring and reporting for environmental incidents (e.g., bio-terrorism, accidents, etc.) and day-to-day field inspections. The data collection technique in place required responders to collect readings using commonly used mobile environmental and radiological monitoring devices (Ludlum, Ludlum 2241 Rae Systems, PPB PID, Dust Track, Q Trak, HNU 102 PID) The responders would then telephone the readings in to HQ on completion of analysis or submit the information when back in the office. This method was both slow and potentially inaccurate, impeding the ability for analysts to make critical decisions related to public safety. The solution developed by Global Bay Mobile Technologies, Inc. for DOHMH leverages a ruggedized Pocket PC device that supports wireless protocols (GPRS) Bluetooth connectivity, GPS and Barcode Scanning. With this solution, the readings from the environmental monitoring instruments and related data are captured into Global Bay's HazardPoint software and then wirelessly transmitted to a central DOHMH server for 'real-time' analysis and mapping. Data collection forms are designed and deployed through Global Bay's HazardPoint web console. The DOHMH can manage users, forms and data centrally from the HazardPoint console. Forms can be edited and pushed out to devices in a matter of minutes supporting flexibility to tailor forms to specific incidents.

Accidents↗

PubMed2006

Follow-up study of medication errors reported to the vaccine adverse event reporting system (VAERS).

BACKGROUND: A study was done to determine if the apparent medication errors found in the Vaccine Adverse Event Reporting System (VAERS) database are true errors, and if true errors are found, to determine what corrective action was taken. Furthermore, if a true error did not occur, we wanted to determine at what point the misinformation was entered into the system. METHODS: The VAERS database was searched for reports received between July 1, 2001 and June 30, 2002 which had either been classified as "error" or the word "error" appeared in the text of the report. The database was also searched for reports which indicated that the measles-mumps-rubella (MMR), diphtheria-tetanus-pertussis (DTP), diphtheria-tetanus-acellular pertussis (DTaP) or diphtheria-tetanus-pertussis-haemophilus (DTPH) vaccinations had been administered at an age outside of the usual recommendation. RESULTS: A total of 119 reports of possible errors were found. Follow-up was successful in 102 (86%) cases. Additional information obtained showed that 26 cases were actual medication errors. Seventy-six cases were not actual medication errors; 9 cases were physician decisions, 37 cases were data entry errors and 30 cases were reporter errors. CONCLUSION: The nature of the actual errors was similar to those reported previously; wrong inoculum, improper interval, wrong route of administration, and overdose. Many errors could have been prevented by more attention to detail. Remedial action usually consisted of retraining. The new requirement that all medications be barcoded, purchasing products from different manufacturers and segregation of vials may help prevent vial confusion.

Adolescent↗

PubMed2005

The taxonomic feedback loop: symbiosis of morphology and molecules.

Here, we relate the ongoing taxonomic story of a species complex of problematic, cryptic Australian freshwater shrimp (Atyidae; Caridina) to highlight the relative strength and utility of different taxonomic methods in assessing species boundaries. We used popular 'DNA barcode' gene fragments cytochrome c oxidase 1 and 16S ribosomal DNA. We then assessed the morphological attributes of these specimens and developed an identification key to complement the molecular results, and conclude that, despite occasionally strident arguments in favour of either molecular or morphological taxonomy, the two are inseparably linked and form parts of a greater whole.

Animals↗

PubMed2006

Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers.

We used ancient DNA analysis of seven museum specimens of the endangered North American ivory-billed woodpecker (Campephilus principalis) and three specimens of the species from Cuba to document their degree of differentiation and their relationships to other Campephilus woodpeckers. Analysis of these mtDNA sequences reveals that the Cuban and North American ivory bills, along with the imperial woodpecker (Campephilus imperialis) of Mexico, are a monophyletic group and are roughly equidistant genetically, suggesting each lineage may be a separate species. Application of both internal and external rate calibrations indicates that the three lineages split more than one million years ago, in the Mid-Pleistocene. We thus can exclude the hypothesis that Native Americans introduced North American ivory-billed woodpeckers to Cuba. Our sequences of all three woodpeckers also provide an important DNA barcoding resource for identification of non-invasive samples or remains of these critically endangered and charismatic woodpeckers.

Animals↗

PubMed2004

The promise of a DNA taxonomy.

Not only is the number of described species a very small proportion of the estimated extant number of taxa, but it also appears that all concepts of the extent and boundaries of 'species' fail in many cases. Using conserved molecular sequences it is possible to define and diagnose molecular operational taxonomic units (MOTU) that have a similar extent to traditional 'species'. Use of a MOTU system not only allows the rapid and effective identification of most taxa, including those not encountered before, but also allows investigation of the evolution of patterns of diversity. A MOTU approach is not without problems, particularly in the area of deciding what level of molecular difference defines a biologically relevant taxon, but has many benefits. Molecular data are extremely well suited to re-analysis and meta-analysis, and data from multiple independent studies can be readily collated and investigated by using new parameters and assumptions. Previous molecular taxonomic efforts have focused narrowly. Advances in high-throughput sequencing methodologies, however, place the idea of a universal, multi-locus molecular barcoding system in the realm of the possible.

Base Sequence↗

PubMed2005

DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers.

DNA barcoding has been successfully implemented in the identification of previously described species, and in the process has revealed several cryptic species. It has been noted that such methods could also greatly assist in the discovery and delineation of undescribed species in poorly studied groups, although to date the feasibility of such an approach has not been examined explicitly. Here, we investigate the possibility of using short mitochondrial and nuclear DNA sequences to delimit putative species in groups lacking an existing taxonomic framework. We focussed on poorly known tropical water beetles (Coleoptera: Dytiscidae, Hydrophilidae) from Madagascar and dung beetles (Scarabaeidae) in the genus Canthon from the Neotropics. Mitochondrial DNA sequence variation proved to be highly structured, with >95% of the observed variation existing between discrete sets of very closely related genotypes. Sequence variation in nuclear 28S rRNA among the same individuals was lower by at least an order of magnitude, but 16 different genotypes were found in water beetles and 12 genotypes in Canthon, differing from each other by a minimum of two base pairs. The distribution of these 28S rRNA genotypes in individuals exactly matched the distribution of mtDNA clusters, suggesting that mtDNA patterns were not misleading because of introgression. Moreover, in a few cases where sequence information was available in GenBank for morphologically defined species of Canthon, these matched some of the DNA-based clusters. These findings demonstrate that clusters of close relatives can be identified readily in the sequence variation obtained in field collected samples, and that these clusters are likely to correspond to either previously described or unknown species. The results suggest that DNA-assisted taxonomy will not require more than a short fragment of mtDNA to provide a largely accurate picture of species boundaries in these groups. Applied on a large scale, this DNA-based approach could greatly improve the rate of species discovery in the large assemblages of insects that remain undescribed.

Animals↗

PubMed2026

Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.

Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.

Metagenomics↗

PubMed2025

Multi-step genomics on single cells and live cultures in sub-nanoliter capsules.

Single-cell sequencing methods uncover natural and induced variation between cells. Many functional genomic methods, however, require multiple steps that cannot yet be scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells and large analytes while being freely accessible to media, enzymes and reagents. Capsules enable high-throughput multi-step assays combining live-cell culture with genome-wide readouts. We establish methods for barcoding CAGE DNA libraries, and apply them to measure persistence of gene expression programs in cells by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and extension to live-cell assays.

Journal Article↗

PubMed2026

Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.

Minimizing experimental noise is integral to robust data generation in single-cell omics. The current standard for avoiding batch effects during sample processing is barcode- or hashtag-assisted combining of different experimental treatments into one pool, allowing all samples to be subject to the technical protocols uniformly. The final data points for each treatment group are then computationally separated based on the original hashtag labels. Clearly, whereas hashtagging all groups and pooling them in a single well is expected to minimize batch effects, the procedure can also lead to a loss of cells that cannot be confidently decoded during the computational demultiplexing step. Here, we examine four alternate experimental designs, namely, compound, reference, chain, and confounded, that could be used instead of a single-pool approach and quantify the batch effects as well as cell loss in each case. We find a linear relationship-the percentage of cells lost is double the number of hashtags used in the experiment. We use these analyses to identify experimental designs that can successfully mitigate batch effects while minimizing multiplexing, hence the cell loss, in each well. Although a reference design offers the best overall performance, this study can help individual investigators choose particular approaches that are best suited for their biological questions.

Journal Article↗

PubMed2006

Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae.

Genes with small open reading frames (sORFs; <100 amino acids) represent an untapped source of important biology. sORFs largely escaped analysis because they were difficult to predict computationally and less likely to be targeted by genetic screens. Thus, the substantial number of sORFs and their potential importance have only recently become clear. To investigate sORF function, we undertook the first functional studies of sORFs in any system, using the model eukaryote Saccharomyces cerevisiae. Based on independent experimental approaches and computational analyses, evidence exists for 299 sORFs in the S. cerevisiae genome, representing approximately 5% of the annotated ORFs. We determined that a similar percentage of sORFs are annotated in other eukaryotes, including humans, and 184 of the S. cerevisiae sORFs exhibit similarity with ORFs in other organisms. To investigate sORF function, we constructed a collection of gene-deletion mutants of 140 newly identified sORFs, each of which contains a strain-specific "molecular barcode," bringing the total number of sORF deletion strains to 247. Phenotypic analyses of the new gene-deletion strains identified 22 sORFs required for haploid growth, growth at high temperature, growth in the presence of a nonfermentable carbon source, or growth in the presence of DNA damage and replication-arrest agents. We provide a collection of sORF deletion strains that can be integrated into the existing deletion collection as a resource for the yeast community for elucidating gene function. Moreover, our analyses of the S. cerevisiae sORFs establish that sORFs are conserved across eukaryotes and have important biological functions.

Conserved Sequence↗

PubMedDate not supplied

Brain activity during the encoding, retention, and retrieval of stimulus representations.

Studies of delayed nonmatching-to-sample (DNMS) performance following lesions of the monkey cortex have revealed a critical circuit of brain regions involved in forming memories and retaining and retrieving stimulus representations. Using event-related functional magnetic resonance imaging (fMRI), we measured brain activity in 10 healthy human participants during performance of a trial-unique visual DNMS task using novel barcode stimuli. The event-related design enabled the identification of activity during the different phases of the task (encoding, retention, and retrieval). Several brain regions identified by monkey studies as being important for successful DNMS performance showed selective activity during the different phases, including the mediodorsal thalamic nucleus (encoding), ventrolateral prefrontal cortex (retention), and perirhinal cortex (retrieval). Regions showing sustained activity within trials included the ventromedial and dorsal prefrontal cortices and occipital cortex. The present study shows the utility of investigating performance on tasks derived from animal models to assist in the identification of brain regions involved in human recognition memory.

Adult↗

PubMed2005

A procedure for setting up high-throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization.

Crystallization trials at the Division of Structural Biology in Oxford are now almost exclusively carried out using a high-throughput workflow implemented in the Oxford Protein Production Facility. Initial crystallization screening is based on nanolitre-scale sitting-drop vapour-diffusion experiments (typically 100 nl of protein plus 100 nl of reservoir solution per droplet) which use standard crystallization screening kits and 96-well crystallization plates. For 294 K crystallization trials the barcoded crystallization plates are entered into an automated storage system with a fully integrated imaging system. These plates are imaged in accordance with a pre-programmed schedule and the resulting digital data for each droplet are harvested into a laboratory information-management system (LIMS), scored by crystal recognition software and displayed for user analysis via a web-based interface. Currently, storage for trials at 277 K is not automated and for imaging the crystallization plates are fed by hand into an imaging system from which the data enter the LIMS. The workflow includes two procedures for nanolitre-scale optimization of crystallization conditions: (i) a protocol for variation of pH, reservoir dilution and protein:reservoir ratio and (ii) an additive screen. Experience based on 592 crystallization projects is reported.

Animals↗

PubMed2026

Environmental Release of Genetically Intervened Microorganisms: Towards a New Narrative.

The deliberate release of genetically engineered microorganisms for environmental applications has remained largely blocked since the early days of recombinant DNA technology, when limited ecological knowledge, lack of success stories and public apprehension shaped a culture of caution and restrictive regulation. Despite profound advances in microbial ecology, synthetic biology and genetic design, current frameworks still rely on outdated assumptions and legacy regulations that equate engineered microbes with inherent danger and demand unrealistic forms of absolute containment. This review examines how laboratory-trained microorganisms exist on a continuum with naturally evolved life, and that their risks are neither categorically different nor greater. Rather than pursuing unachievable containment, governance should shift towards traceability, stewardship and long-term monitoring through genomic barcodes, digital twins and transparent oversight. The vision moves from domination and control to care and partnership recognizing engineered microbes as live amendments capable of restoring degraded ecosystems. Achieving this transformation requires new terminology, phased field-trial frameworks, improved scaling methods, and the integration of epistemological perspectives that emphasize reciprocity and coexistence with nature. Reframing biotechnology in this way could finally unlock the capacity of engineered microorganisms to contribute responsibly and effectively to planetary repair in an era of escalating environmental crises.

Microorganisms, Genetically-Modified↗

PubMed2006

New technology for transfusion safety.

Hemovigilance programs from around the world document that the greatest risk to recipients of blood transfusion is human error, resulting in transfusion of the incorrect blood component. Errors in transfusion care have strong parallels with errors in medication administration. Errors often result from 'lapse' or 'slip' mistakes in which details of patient identification are overlooked. Three areas of transfusion are focal points for improved care: the labelling of the patient's pre-transfusion sample, the decision to transfuse and the final bedside check designed to prevent mis-transfusion. Both barcodes and radio-frequency identification technology, each ideally suited to matching alpha-numeric identifiers, are being implemented in order to improve performance sample labelling and the bedside check. The decision to transfuse should ultimately be enhanced through the use of nanotechnology sensors, computerised order entry and decision support systems. Obstacles to the deployment of new technology include resistance to change, confusion regarding the best technology, and uncertainty regarding the return-on-investment. By focusing on overall transfusion safety, deploying validated systems appropriate for both medication and blood administration, thoughtful integration of technology into bedside practice and demonstration of improved performance, the application of new technologies will improve care for patients in need of transfusion therapy.

Blood Grouping and Crossmatching↗

PubMed1996

ISBT Code 128 and code changes as part of the implementation of a national IT system for the English National Blood Service.

The implementation of PULSE within the NBS will bring considerable advantages to the Service and to hospitals. A system of dual labelling has been developed to overcome intrinsic constraints identified with the ABC Codabar system. This should not, however, impact directly on hospitals which will be able to continue to utilize the ABC Codabar system. The dual labelling system incorporates the use of the ISBT Code 128 barcode system for transfusion centre use. This must be clearly differentiated from the implementation of ISBT code 128 within the UK. This latter development would bring considerable benefit to transfusion practice, increasing the overall safety of blood transfusion. It is, however, recognized that extensive discussion with appropriate stakeholders will be necessary before any implementation date can be determined for this initiative, particularly so given the significant logistical and financial implications inherent in such a change.

Blood Banks↗

PubMed2006

Transfusion recipient identification.

Recent reports from different haemovigilance systems indicate that errors in the whole-blood transfusion chain - from initial recipient identification to final blood administration - occur with a frequency of approximately 1 in 1000 events. Although mistakes occur also within the blood transfusion service, about two-thirds of errors are associated with incorrect blood recipient identification at the patient's bedside. To prevent the potentially fatal consequences of such mistakes, specific tools have been developed, including patient identification bracelets with barcodes and/or radio frequency identification devices, mechanical or electronic locks preventing access to bags assigned to other patients, and palm computers suitable for transferring blood request and administration data from the patient's bedside to the blood transfusion service information system in real time. The effectiveness of these systems in preventing mistransfusion has been demonstrated in a number of studies.

Blood Group Incompatibility↗