225 research outputs found
Reagents and swab tests during the COVID-19 Pandemic: An optimized supply chain management with UAVs
No full textIn this paper, we develop a supply chain optimization model for the preparation, provision, transportation, and execution of swab tests during COVID-19 pandemic. The proposed approach is based on a multi-tiered network consisting of manufacturing companies of reagents, processing laboratories (where the swab kits are prepared and some swab tests are analyzed), landing stations for UAVs and test centers. As innovations in the supply chain, the sharing of reagents between processing laboratories and the use of UAVs, using 5G technology, are contemplated in the management of the COVID-19 Pandemic. To obtain the optimal solutions of the underlying optimization problem, we provide a variational formulation problem for which results of existence and uniqueness will be provided. Finally, some numerical simulations are examined to validate the effectiveness of our approach
Surge and swab pressure: A transient approach to running expandable assemblies
No full textShell is working on mono-diameter drilling (MOD). A MOD well, or MOD well section, has a (nearly) constant diameter over several sections. This is achieved by deploying expandable liners: a liner is lowered into position and is expanded by pulling an over-sized cone through it. This plasticly deforms the pipe, increasing its inner diameter to that of the previous section. MOD eliminates many of the constraints of conventional well design. Greater depths may be reached and zonal isolation may be performed without paying the penalty of reduced production rates.While lowering an expandable assembly (expandable liner and expansion tools) into a well, caution is required. Displacement of the drilling mud causes a pressure drop due to fluid friction and acceleration. The running speed of the assembly into the well is limited by the surge (overpressure) or swab (underpressure) pressure. Pressure must remain within a predefined window to ensure well control.The current understanding of the mechanisms governing surge/swab pressure, as well as the models used to predict it, are deemed insufficient. The effect of unorthodox MOD conditions is unknown. This study is conducted to overcome these obstacles.Firstly, a model is programmed so that transient surge and swab pressures, induced by assembly movement, may be predicted. The drilling mud’s velocity and pressure are described by the water hammer equations, which are solved using the interpolated method of characteristics. One dimensional (1D), unsteady and nonuniform flow of a slightly compressible fluid in a conduit with linearly elastic walls is considered. The annular pressure drop for flow with a moving inner pipe is solved considering both laminar and turbulent flow of a Herschel-Bulkley fluid. Flow over the expansion tools is solved separately and is considered 1D and incompressible.Secondly, the model is validated. The model is first validated under conventional conditions using field measurements presented in literature and performs better than existing models. The validity of the model while dealing with extremely small clearances, as found in MOD applications, is investigated through a full-scale experiment on Shell’s test rig. The surge and swab pressures are generally predictable. Some discrepancies between predictions and measurements are observed and are attributed to the relatively large uncertainty in clearance size and shape, which results from imperfect pipes. The surge/swab pressure’s sensitivity to the size and shape of the pipes means that predictions should be treated with care. The effect of local annular flow restriction over the expansion tools is investigated too. The tools are found to cause acceleration induced transient pressures not predicted by the model. This implies that the 1D and/or incompressible assumption at the interface does not describe the flow adequately.Thirdly, the effect of MOD well design at true well depths and assembly lengths is investigated through a case study. The surge pressure is significant. The pressure drop generated in the narrow annulus between assembly and wellbore is too high to allow significant flow. Instead, all drilling mud is displaced upwards through the drillstring. Swabbing occurs behind the assembly. Circulation while tripping in expandable assemblies is therefore impossible. At these depth and length scales, the effect of fluid compression and borehole expansion becomes significant, causing steady state models to become increasingly inaccurate with depth
Large-scale SNP genotyping with canine buccal swab DNA
No full textThe dog is an attractive model for genetic studies of complex disease. With drafts of the canine genome complete, a large number of single-nucleotide polymorphisms (SNPs) that are potentially useful for gene-mapping studies and empirical estimations of canine diversity and linkage disequilibrium (LD) are now available. Unfortunately, most canine SNPs remain uncharacterized, and the amount and quality of DNA available from population-based samples are limited. We assessed how these real-world challenges influence automated SNP genotyping methods such as Illumina's GoldenGate assay. We examined 384 SNPs on canine chromosome 9 and successfully genotyped a minimum of 217 and a maximum of 275 SNPs using buccal swab samples for 181 dogs (86 beagles, 76 border collies, and 15 Australian shepherds). Call rates per SNP and sample averaged 97%, with reproducibility within and between analyses averaging 98%. The majority of these SNPs were polymorphic across all 3 breeds. We observed extensive LD, albeit less than reported for surveys using fewer dogs, consistent between breeds. Analyses of population substructure indicated that beagles are distinct from border collies and Australian shepherds. These results demonstrate the suitability of amplified canine buccal samples for high-throughput multiplex genotyping and confirm extensive LD in the dog
Detection of Human Bocaviruses 1 to 4 from Nasopharyngeal Swab Samples Collected from Patients with Respiratory Tract Infections
No full textHuman bocaviruses (HBoV) 1, 2, 3, and 4 were detected in 132 (15.5%), 5 (0.6%), 3 (0.4%) and 5 (0.6%) of 850 nasopharyngeal swab samples collected from children with respiratory tract infections, respectively. Out of the 145 HBoV1-4-positive samples, 62 (42.8%) were co-detected with other respiratory viruses
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Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 infection
No full textThe ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing has led to issues in scaling diagnostic lab efforts and in securing basic supplies for collection and processing of samples. This has motivated efforts by the scientific community to establish improved protocols that are more scalable, less resource intensive, and less expensive. One such developmental effort has resulted in an assay called “Swab-Seq”, so named because it was originally developed to work with dry nasal swab samples. The existing gold standard test consists of RNA extracted from a nasopharyngeal (NP) swab that is subjected to quantitative reverse transcription polymerase chain reaction (qRT-PCR). Swab-Seq adapts this method to a next-generation sequencing readout. By pairing this modification with extraction-free sampling techniques, Swab-Seq achieves high scalability, low cost per sample, and a reasonable turnaround time. We evaluated the effectiveness of this assay in a community surveillance setting by testing samples collected from both symptomatic and asymptomatic individuals using the traditional NP swab. In addition, we evaluated extraction-free sampling techniques (both saliva and saline mouth gargle samples). We found the assay to be as clinically sensitive as the qRT-PCR assay, adaptable to multiple sample types, and able to easily accommodate hundreds of samples at a time. We thus provide independent validation of Swab-Seq and extend its utility regarding sample type and sample stability. Assays of this type greatly expand the possibility of routine, noninvasive, repeated testing of asymptomatic individuals suitable for current and potential future needs. © 2022, The Author(s).Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]
Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples
No full textAttenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with machine learning-based partial least squares discriminant analysis (PLS-DA) was applied to study if severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be detected from nasopharyngeal swab samples originally collected for polymerase chain reaction (PCR) analysis. Our retrospective study included 558 positive and 558 negative samples collected from Northern Finland. Overall, we found moderate diagnostic performance for ATR-FTIR when PCR analysis was used as the gold standard: the average area under the receiver operating characteristics curve (AUROC) was 0.67–0.68 (min. 0.65, max. 0.69) with 20, 10 and 5 k-fold cross validations. Mean accuracy, sensitivity and specificity was 0.62–0.63 (min. 0.60, max. 0.65), 0.61 (min. 0.58, max. 0.65) and 0.64 (min. 0.59, max. 0.67) with 20, 10 and 5 k-fold cross validations. As a conclusion, our study with relatively large sample set clearly indicate that measured ATR-FTIR spectrum contains specific information for SARS-CoV-2 infection (P < 0.001 for AUROC in label permutation test). However, the diagnostic performance of ATR-FTIR remained only moderate, potentially due to low concentration of viral particles in the transport medium. Further studies are needed before ATR-FTIR can be recommended for fast screening of SARS-CoV-2 from nasopharyngeal swab samples
A randomised controlled study of mouth swab testing versus same day blood tests for HIV infection in young people attending a community drug service.
No full textAuthor(s) Pre Print Version OnlyINTRODUCTION AND AIMS: This study was designed to determine whether providing an oral swab test in the community for blood borne virus testing leads to an increase in subsequent attendance for sexually transmitted infection (STI) screening at the STI clinic compared with making appointments for young people to attend the clinic for same day HIV testing and STI screening. DESIGN AND METHODS: Participants were randomised into either the oral swab test group or the blood test group of the trial if eligible. RESULTS: All the 27 participants in the oral swab test group were tested for HIV and hepatitis C compared with five for HIV and two for hepatitis C in the blood test group (P < 0.001). Only two of the 27 participants in the blood test group were tested for hepatitis B compared with 25 in the oral swab test group (P < 0.001). Nine participants in the oral swab test group attended the STI clinic for STI screening compared with three in the blood test group (P = 0.09). DISCUSSION AND CONCLUSIONS: An oral swab test in the community for blood borne virus testing leads to an increase in the number of young high-risk people tested for blood borne infections and is associated with a trend towards higher rates of subsequent attendance for STI screening
Utility of a buccal swab point-of-care test for the IFNL4 genotype in the era of direct acting antivirals for hepatitis C virus
No full textCopyright: \ua9 2023 Sy et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.BACKGROUND: The CC genotype of the IFNL4 gene is known to be associated with increased Hepatitis C (HCV) cure rates with interferon-based therapy and may contribute to cure with direct acting antivirals. The Genedrive\uae IFNL4 is a CE marked Point of Care (PoC) molecular diagnostic test, designed for in vitro diagnostic use to provide rapid, real-time detection of IFNL4 genotype status for SNP rs12979860. METHODS: 120 Participants were consented to a substudy comparing IFNL4 genotyping results from a buccal swab analysed on the Genedrive\uae platform with results generated using the Affymetix UK Biobank array considered to be the gold standard. RESULTS: Buccal swabs were taken from 120 participants for PoC IFNL4 testing and a whole blood sample for genetic sequencing. Whole blood genotyping vs. buccal swab PoC testing identified 40 (33%), 65 (54%), and 15 (13%) had CC, CT and TT IFNL4 genotype respectively. The Buccal swab PoC identified 38 (32%) CC, 64 (53%) CT and 18 (15%) TT IFNL4 genotype respectively. The sensitivity and specificity of the buccal swab test to detect CC vs non-CC was 90% (95% CI 76-97%) and 98% (95% CI 91-100%) respectively. CONCLUSIONS: The buccal swab test was better at correctly identifying non-CC genotypes than CC genotypes. The high specificity of the Genedrive\uae assay prevents CT/TT genotypes being mistaken for CC, and could avoid patients being identified as potentially \u27good responders\u27 to interferon-based therapy
A comparison of the efficacy of different swab types in the absorption and elution of spermatozoa
No full textThesis (M.S.F.S.) PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at [email protected]. Thank you.Swabs are an integral part of any forensic science “toolkit”. They can be used to gather many types of evidence at crime scenes, in the lab, or even in the hospital or morgue. Cotton swabs have been the traditional choice for most forensic laboratories, and for sexual assault kits. They have been the obvious choice for decades as cotton swabs were really the only option and they were and still are relatively inexpensive and easy to obtain. In the past dozen years or so, new synthetic fibers have been incorporated into novel swab designs. Fiber swabs can be made of polyester or rayon, polyurethane foam swabs can be round, narrow, oval or arrow shaped; swabs can also be flocked, or sprayed with strands of material such as nylon. The effectiveness of any type of swab used to collect biological material is based on three characteristics: the ability to pick up the material for which they are designed, the ability to hold that material until processed and then the ability to release as much of that material as possible to be analyzed in the lab.
In this study, the efficacy of four different commercially available swabs to collect, store and release spermatozoa was evaluated. Puritan Cotton fiber swabs, Fisher Polyester fiber swabs, Fisher polyurethane swabs, and Copan nylon flocked swabs were all compared for their ability to pick-up and elute cells from solid surfaces. The surfaces included three types of commonly found tile: a smooth glossy ceramic tile, a rough non-porous ceramic tile, and a smooth semi-porous quarry tile. In general, polyester fiber swabs outperformed both the polyurethane foam and the nylon flocked swab when used on all three surfaces (P < 0.05). Polyester swabs were not significantly different from the cotton fiber swabs even though the average number of cells picked-up and eluted was higher overall.
Swabs used to collect postcoital samples were also compared. Volunteer couples were given a variety of swabs to use after intercourse. The result of the comparison for the same four swab types when used as postcoital swabs was different from the results of the tile study. After estimating the number of cells collected and released from each swab, a comparison was made within each couple. Nylon flocked swabs yielded the highest level of cellular material overall and foam swabs recovered the least. This study demonstrates the need for further research into different swab types and in what capacities they are to be used in forensic science.2031-01-0
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