Search

Bat boxes can be employed to provide short-term mitigation for the loss of trees with bat roost potential. Traditionally bat box utilisation (by long-tailed bats) has been difficult to confirm in NZ, partly due to a lack of published survey techniques to confirm bat box utilisation when bats are not present at the time of sampling. While environmental deoxyribonucleic acid (eDNA) has been widely applied as a biomonitoring tool, it has not been used previously in the context of bat box surveys in New Zealand. Here we present a method for collecting eDNA from bat boxes using swabs and test the efficacy of eDNA in validating bat box utilisation as confirmation of roosting. Bat boxes were deployed by the Hamilton City Council as part of the bat mitigation strategy for the Southern Links Project in southern Hamilton. The eDNA method confirmed a total of 25 boxes out of the 73 (34%) included in this study were being utilised by long-tailed bats. The results indicate that eDNA can be applied with confidence to demonstrate box use, even at very low and infrequent occupancy rates. [ABSTRACT FROM AUTHOR]

Zoonotic sporotrichosis caused by Sporothrix brasiliensis is an emerging mycosis in Latin America. One of the problems to quickly treat infected animals and break the transmission chain is associated with the time-consuming gold-standard diagnosis method (culture). We aimed to evaluate a species-specific polymerase chain reaction (PCR) for the diagnosis of sporotrichosis caused by S. brasiliensis using non-invasive samples. We performed a retrospective cross-sectional study using samples collected with swabs from humans and cats with clinical suspicion of sporotrichosis. Deoxyribonucleic acid (DNA) was extracted using a commercial kit, and a species-specific PCR for S. brasiliensis detection was performed. One hundred ten samples were included. PCR showed a good concordance with culture (86% of agreement) for human and cat samples (Kappa coefficient = 0.722, and 0.727, respectively). In conclusion, our data shows that this adapted PCR using non-invasive samples can be applied to sporotrichosis diagnosis, being a good alternative mainly in regions with a lack of mycologists to identify the fungus in culture, contributing to the control of this emergent zoonosis. [ABSTRACT FROM AUTHOR]

ABSTRACT Background Fish is a possible source of foodborne infections with Salmonella and Escherichia coli. This study was conducted to identify Salmonella and E. coli along the fish value chain in Bahir Dar City, Ethiopia. Methods A cross‐sectional study was undertaken with purposive sampling. A total of 121 specimens comprising fresh fish, retailing fish, filleted and cooked fish, swabs, and water samples were collected. Both culture based and molecular methods were used for detection. Results E. coli isolated from 41 (33.88%) and Salmonella from 6 (4.96%) specimen. The highest E. coli isolation rate was from retailing fish 16 (80%), whereas the highest Salmonella isolation rate from filleted tissue 2 (20%). At restaurants, 12 (30%) samples were positive for E. coli and 3 (7.50%) for Salmonella. All 41 E. coli isolates were resistant to amoxicillin/clavulanate, whereas no resistance was shown for gentamicin and amikacin. Two thirds of Salmonella isolate and 95.12% of E. coli were detected as they develop multidrug resistance. The highest rate of resistance was recorded for ceftazidime against all (n = 6) isolates of Salmonella species. From a total of 10 E. coli isolates tested by PCR, 4 were positive for hemolysin A1 and/or eae virulence genes. Conclusions The study detects the potential biological hazards along the value chain. Hygiene of fish handlers and their working environment and proper fish cooking are highly valuable. One health campaign should be carried out on drug resistance, contamination of the lake, and fish safety.

The dual recovery of DNA samples and fingerprints from touched objects and surfaces is highly desirable for many criminal investigations as it provides greater probative value, particularly compared to relying solely on DNA evidence, which may be present due to secondary transfer or unresolvable due to a high number of contributors. Despite this, DNA sampling is generally given priority over fingerprint examination to minimize contamination even though the mechanical action of DNA sampling is generally thought to obliterate fingerprint residues. This study aimed to strengthen decision-making around sequencing fingerprints and DNA examinations by assessing whether any fingerprint ridge details remained after first sampling for DNA and whether DNA-free fingerprint brushes and powders were fit for purpose. The results demonstrated that DNA sampling and powder fingerprint development are not necessarily a zero-sum game. High-quality fingerprints were developed using DNA-free consumables without any contamination, and DNA sampling using tapelifts was shown to leave sufficient latent material to develop a fingerprint suitable for comparison whilst also generating a high-quality DNA profile. This represents valuable insight for informing evidence-based decision-making by forensic examiners for the optimal strategy for sequential examination and collection of critical fingerprint and DNA evidence. [ABSTRACT FROM AUTHOR]

Clinical swabs with suspected viral infection are usually transported in virus transport medium (VMT). During epidemics/pandemics, tampons without VTM would be more suitable for saving space and cost. This study was conducted to verify the applicability of throat swabs without VTM in the diagnosis/screening of enteroviral infections by polymerase chain reaction (PCR) in a volunteer study group. Three different swab types were used in 40 volunteers: swabs with two different tips (cotton- or synthetic-tipped) without VTM and standard synthetic tips with VTM. The swabs were processed immediately or after 12 days of storage at either -80°C or +4°C. The molecular analysis included viral RNA extraction, and combination of reverse transcriptase PCR and nested PCR. Enteroviral RNA was detected in 15% (6/40) of the studied volunteers. When processed immediately, the results for all three swab types were compatible. Swabs without VTM may be used for collection of clinical samples in the diagnosis of suspected enteroviral infections or as potential screening tools for enteroviruses. [ABSTRACT FROM AUTHOR]

This paper presents data-driven modeling and a results analysis. Group method data handling (GMDH), multivariable regression (MVR), artificial neuron network (ANN), and new proposed GMDH-featured ANN machine learning algorithms were implemented to model a field telemetry equivalent mud circulating density (ECD) dataset based on surface and subsurface drilling parameters. Unlike the standard GMDH-ANN model, the proposed GMDH-featured ANN utilizes a fully connected network. Based on the considered eighteen experimental modeling designs, all the GMDH regression results showed higher R-squared and minimum mean-square error values than the multivariable regression results. In addition, out of the considered eight experimental designs, the GMDH-ANN model predicts about 37.5% of the experiments correctly, while both algorithms have shown similar results for the remaining experiments. However, further testing with diverse datasets is necessary for better evaluation. [ABSTRACT FROM AUTHOR]

Copyright of Iraqi Journal of Chemical & Petroleum Engineering is the property of Republic of Iraq Ministry of Higher Education & Scientific Research (MOHESR) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Background Lameness is defined as altered or abnormal gait due to dysfunction of the locomotor system, and is a health issue of feedlot cattle, having major economic, labour, and welfare implications. Digital dermatitis (DD—a lesion of the plantar surface of the foot) and foot rot (FR—affects the interdigital cleft) are common infectious causes of lameness in feedlots. These hoof lesions can occur alone or in combination (DD + FR) in the same hoof. A total of 208 hoof swabs were collected from three commercial feedlots located in southern Alberta. Every lesion sample was matched with a corresponding control skin sample taken from a healthy contralateral foot. Control skin samples were also collected from cattle with no lesion on any feet. Bacterial communities of three types of hoof lesions (DD, DD + FR, FR) and healthy skin were profiled using 16S amplicon sequencing. Results Alpha diversity analysis revealed a lower bacterial diversity on DD and FR lesions compared to control skin. Beta diversity analysis showed that bacterial communities of DD, FR, and DD + FR lesions were distinct from those of the control skin. While the impact of feedlot was minimal, lesion type contributed to 22% of the variation observed among bacterial communities (PERMANOVA-R = 0.22, P

Mediterranean spotted fever (MSF) has been diagnosed clinically in the Crimean Peninsula since the 1930s. We describe the recent illness of an elderly patient from Crimea who had developed a classic triad of MSF symptoms consisting of fever, maculopapular rash, and eschar. Clinical diagnosis of rickettsiosis was confirmed using real-time PCR and sequencing of 4 Rickettsia protein genes. The strain causing clinical illness was characterized as Rickettsia conorii subspecies conorii Malish 7. This report corroborates the utility of eschar swab material as a source of DNA for PCR-based diagnostics that enables timely patient treatment and management.

Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions and to test whether our past observations linking SARS-CoV-2 abundance to Rothia sp. in hospitals also hold in a residential setting, we performed a detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences (to assess the bacterial community at each location), and to the Cq value of the contemporaneous clinical test. Our results showed that the highest SARS-CoV-2 load in this setting is on touched surfaces, such as light switches and faucets, but a detectable signal was present in many untouched surfaces (e.g., floors) that may be more relevant in settings, such as schools where mask-wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g., touching a light switch) or indirectly (e.g., by droplets or aerosols settling). We found the highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g., in schools, where students did not touch the light switches and also wore masks such that they had no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.

Background: Lameness is defined as altered or abnormal gait due to dysfunction of the locomotor system, and is a health issue of feedlot cattle, having major economic, labour, and welfare implications. Digital dermatitis (DD—a lesion of the plantar surface of the foot) and foot rot (FR—affects the interdigital cleft) are common infectious causes of lameness in feedlots. These hoof lesions can occur alone or in combination (DD + FR) in the same hoof. A total of 208 hoof swabs were collected from three commercial feedlots located in southern Alberta. Every lesion sample was matched with a corresponding control skin sample taken from a healthy contralateral foot. Control skin samples were also collected from cattle with no lesion on any feet. Bacterial communities of three types of hoof lesions (DD, DD + FR, FR) and healthy skin were profiled using 16S amplicon sequencing. Results: Alpha diversity analysis revealed a lower bacterial diversity on DD and FR lesions compared to control skin. Beta diversity analysis showed that bacterial communities of DD, FR, and DD + FR lesions were distinct from those of the control skin. While the impact of feedlot was minimal, lesion type contributed to 22% of the variation observed among bacterial communities (PERMANOVA-R = 0.22, P < 0.01). Compared to the corresponding control skin, there were 11, 12, and 3 differentially abundant (DA) bacterial genera in DD, DD + FR, and FR lesions, respectively. Conclusions: The bacterial community description of a DD + FR lesion is a novel finding. Not only did lesions lead to altered bacterial communities when compared to healthy skin, but the composition of those communities also differed depending on the hoof lesion. The 16S amplicon sequencing of surface swabs has significant value as a research tool in separating different hoof lesions and can provide additional insights to the polybacterial etiology of DD and FR in feedlot cattle. [ABSTRACT FROM AUTHOR]

In this study, we aimed to compare uterine microbial profiles in postpartum dairy cows, determined by bacteriological culture and next-generation sequencing, using three uterine sampling techniques (swab, cytobrush, and lavage) and induced phases of the estrous cycle (estrus and diestrus). Fifteen healthy postpartum dairy cows at 53 ± 5 days postpartum were enrolled in the study. Uterine samples were collected during a fixed-time artificial insemination protocol. Viable bacteria were aerobically cultured from part of each sample, and bacterial isolates were identified through Sanger sequencing of the 16S rRNA gene. Total genomic DNA was extracted from the remainder of undiluted samples to quantify bacterial load using 16S rRNA qPCR and characterize the microbiome by metagenomic sequencing of the V1–V3 region of the 16S rRNA gene. Microbial profiles and composition were analyzed using the Shannon-Weaver diversity index and principal component analysis, respectively. Out of 87 samples, 88 % (77/87) were culture positive. The proportion of culture-positive uterine samples did not differ between sampling techniques (P = 0.39) or estrous cycle phases (P = 0.99). However, swab, cytobrush, and lavage techniques yielded 1.5, 9 and 9 times greater bacterial loads (P < 0.01), respectively, during diestrus than estrus phase. Moreover, during diestrus phase, the cytobrush method yielded 3 and 6 times more bacteria (P < 0.01) than both the lavage and swab methods. The most abundant bacterial genera identified from both bacteriological culture and metagenomic sequencing were Bacillus and Enterococcus, regardless of sampling technique or phases of the estrous cycle. Bacterial genera in moderate to low abundance through metagenomic sequencing included Streptococcus , Oscillospiraceae, and Lachnospiraceae. Notably, the uterine microbial profiles and composition, determined by metagenomic sequencing, did not differ by sampling techniques (P = 0.55 and P = 0.60, respectively) or estrous cycle phases (P = 0.34 and P = 0.17, respectively). In conclusion, our results suggest that any of the sampling techniques can be reliably used to study the uterine microbiome of healthy cows at random phases of the estrous cycle. However, it is important to consider potential differences in bacterial yield as a confounding factor. • Sampling methods do not affect uterine microbial composition and diversity in healthy postpartum cows. • Induced phases of the estrous cycle do not influence the microbial composition of the uterus in healthy postpartum cows. • A higher bacterial load is observed during diestrus, regardless of the sampling method. • Uterine cytobrush method consistently yields a higher bacterial load. [ABSTRACT FROM AUTHOR]

The cycle‐threshold‐value (CT‐value) is a quantitative value of the polymerase chain reaction (PCR), which represents the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS CoV 2). The CT‐value can be used to indicate the viral load in swabs of the airways. The collection of a specimen is the only part of the testing process, which is performed manually and carries, therefore, a high potential for increasing measurement variability. The comparison of different PCR results is often difficult since the exact swabbing technique of each test and how do swabs relate in a direct comparison is unknown. For these reasons, the infection course in a patient can be hard infer even after multiple swabs. As the Omicron variant spread from 06/2022 to 08/2022, all common modalities of the upper airway swabs (nasopharyngeal, oropharyngeal, combined naso‐oropharyngeal, nasal orifice swabs as well as swabs of the buccal mucosa), which were performed on patients with a suspected infection with SARS CoV 2. RT‐PCR was used for SARS CoV 2 RNA detection and the sample comparison was based on the CT‐values obtained. Viral loads can vary significantly depending on the swab sites of the upper airways. For the maximum clinical sensitivity, a combined naso‐oropharyngeal swab should be considered. In case a single point and single sample measurement is the norm, a nasopharyngeal swab can deliver the highest viral load at the presumed beginning of the infection. Furthermore, the findings of this study can be valuable to correctly interpret results of different PCR with different sampling techniques. [ABSTRACT FROM AUTHOR]

The axial movement of pipe in and out of the well generates positive (surge) and negative (swab) pressures that will impact the well pressure. When the swab and surge effects cause well pressures outside the allowable operational limits, wellbore instability (well collapse/well fracture), kick, and induced drill string sticking issues will occur. The problems increase the operational and nonproductive time-related costs. Consequently, the drilling budget rises significantly. It is therefore, imperative to predict the differential pressures in order to mitigate the problems. Even though several models have been developed in the past, models work for the considered experimental setup and conditions. In this paper, a simple analytical model was derived for eccentric/concentric annuli. The fluid rheological behaviors were assumed to be described by power law and yielded power-law. The model is derived based on a steady state condition, and the effects of tripping speed, the power-law fluids, the yield-power-law fluids rheological parameters, and well geometries are considered. The model is compared with experimental data from the literature and with the existing model. Parametric sensitivity studies have been conducted. Results show that the model prediction exhibited quite good performance, with an average percentile error deviation of 9.9% and 6.2% for the power-law and yield-power-law fluids, respectively. However, more testing is required to determine the model's limitations and application. [ABSTRACT FROM AUTHOR]

To characterize COVID-19 epidemiology, numerous population-based studies have been undertaken to model the risk of SARS-CoV-2 infection. Less is known about what may drive the probability to undergo testing. Understanding how much testing is driven by contextual or individual conditions is important to delineate the role of individual behavior and to shape public health interventions and resource allocation. In the Val Venosta/Vinschgau district (South Tyrol, Italy), we conducted a population-representative longitudinal study on 697 individuals susceptible to first infection who completed 4,512 repeated online questionnaires at four-week intervals between September 2020 and May 2021. Mixed-effects logistic regression models were fitted to investigate associations of self-reported SARS-CoV-2 testing with individual characteristics (social, demographic, and biological) and contextual determinants. Testing was associated with month of reporting, reflecting the timing of both the pandemic intensity and public health interventions, COVID-19-related symptoms (odds ratio, OR:8.26; 95% confidence interval, CI:6.04–11.31), contacts with infected individuals within home (OR:7.47, 95%CI:3.81–14.62) or outside home (OR:9.87, 95%CI:5.78–16.85), and being retired (OR:0.50, 95%CI:0.34–0.73). Symptoms and next within- and outside-home contacts were the leading determinants of swab testing predisposition in the most acute phase of the pandemics. Testing was not associated with age, sex, education, comorbidities, or lifestyle factors. In the study area, contextual determinants reflecting the course of the pandemic were predominant compared to individual sociodemographic characteristics in explaining the SARS-CoV-2 probability of testing. Decision makers should evaluate whether the intended target groups were correctly prioritized by the testing campaign. [ABSTRACT FROM AUTHOR]

Copyright of Nursing Journal / Sestrinski Glasnik is the property of Croatian Nurses Association and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Surge and swab pressures are frequently produced during various stages of well construction, including casing running and tripping operations. Managing downhole pressure within the mud window is crucial for mitigating the risks associated with drilling operations including wellbore failure, lost circulation, kicks, and well control issues. The primary objectives of this study are to emphasize the theoretical foundation of surge and swab pressures, forecast the optimum pipe and casing tripping speeds, as well as identify the changes in surge and swab pressures (i.e., equivalent circulating density-ECD) for both open-ended and close-ended drill strings. To achieve these goals, a steady state surge and swab model was used to simulate a case study in the Rumaila oil field, located in Southern Iraq, by utilizing landmark-well plan software. The results of this study support the evidence that the string trip speed plays a substantial role in controlling the swab and surge pressures. It was found that pulling out the 5" drill string from the 12 1/4" open hole section drilled with a 9.51 ppg water-based mud at a speed of 10 sec/stand resulted in a swab ECD below the formation pore pressure against all formations, thus resulting in a kick. Moreover, it was found that the annular clearance had a significant impact on the surge and swab ECD whereas the surge ECD at the bit was bigger than that obtained at the previous hole casing shoe. For example, in our case study pulling speeds ranging from 10-190 sec/stand for the 9 5/8" casing could cause the swab ECD to be below the formation pore pressure gradient at total depth (TD), which is 9.23 ppg. While it was safe to run the same casing through the same interval within 55-190 sec/stand. Furthermore, the results emphasized high trip speeds ranging between 10-30 sec/stand, where for close-ended drill strings, greater surge ECD was observed compared to the open-ended ones. The surge ECD of a 5" close-ended drill string at 30 sec/stand (60 m/min) at bit was 9.92 ppg, while an open-ended string at the same speed was 9.9 ppg.

Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with coronavirus disease 2019 (COVID-19) and inform appropriate infection mitigation responses. Research groups have reported detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2-positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative PCR (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over 7 days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle [Cq]) can be correlated with surface viral load using only one linear regression model per material category. The same experiment was performed with untreated viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods. IMPORTANCE Environmental monitoring is an important tool for public health surveillance, particularly in settings with low rates of diagnostic testing. Time between sampling public environments, such as hospitals or schools, and notifying stakeholders of the results should be minimal, allowing decisions to be made toward containing outbreaks of coronavirus disease 2019 (COVID-19). The Safer At School Early Alert program (SASEA) (https://saseasystem.org/), a large-scale environmental monitoring effort in elementary school and child care settings, has processed >13,000 surface samples for SARS-CoV-2, detecting viral signals from 574 samples. However, consecutive detection events necessitated the present study to establish appropriate response practices around persistent viral signals on classroom surfaces. Other research groups and clinical labs developing environmental monitoring methods may need to establish their own correlation between RT-qPCR results and viral load, but this work provides evidence justifying simplified experimental designs, like reduced testing materials and the use of heat-inactivated viral particles.

BackgroundDetermining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a synthetic swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, synthetic, and foam) and one clinical-grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients including COVID-19+ patients. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent.ResultsCompared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2-4× higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved synthetic (SYN) swab. The limit of detection (LoD) of SARS-CoV-2 from floor samples collected using the consumer-grade plastic (CGp) or research-grade plastic The Microsetta Initiative (TMI) swabs was similar or better than the SYN swab, further suggesting that swab type does not impact RNA recovery as measured by the abundance of SARS-CoV-2. The LoD for TMI was between 0 and 362.5 viral particles, while SYN and CGp were both between 725 and 1450 particles. Lastly microbiome analyses (16S rRNA gene sequencing) of paired samples (nasal and floor from same patient room) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type, but instead driven by the patient and sample type.ConclusionsCompared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer-grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity and lack of antibiotics in these samples makes it possible to perform concomitant microbiome analyses. Video abstract.

Background: Cardiac implantable electronic device (CIED) procedures can be associated with serious complications, including infection with significant mortality and morbidity, necessitating removal of the device and prolonged hospitalization. One potential pathophysiological mechanism is pocket contamination at the time of device implantation. Therefore, steps taken to prevent contamination at this stage can potentially reduce CIED infections.The barrier dressing, an adhesive material applied to the skin, has the potential to reduce the colonization of the surgical site with host flora that can predispose to infection. There are a limited number of randomized prospective studies on barrier dressing use during various surgeries, but it has never been systematically studied in CIED implantation. Objectives: Do Barrier Dressings Reduce Cardiac Implantable Device Infection? (BARRIER-PROTECT trial; NCT04591366) is a single-centre, prospective, double-armed, single-blinded, randomized controlled trial designed to evaluate the use of an intra-operative adhesive barrier dressing to reduce the risk of end-of-procedure pocket swab positivity. We hypothesize that adhesive draping during implant procedures will reduce the risk of contamination from the skin flora. Also, we aim to investigate if the end-of-procedure pocket swab culture positivity can be used as a potential surrogate marker of CIED infection. Methods and Design: Patients undergoing a second or later procedure on the same device pocket (pulse generator change, lead/pocket revision or upgrade) will be enrolled. Eligible and consenting patients will be equally randomized to the use of barrier dressing or not using an automated web-based system. Patients, but not the operator, will be blinded to the arm. The person performing the pocket swabs will also be blinded. The primary endpoint is the end-of-procedure pocket swab culture positivity. The main secondary endpoint is the CIED infection rate. Discussion: This is the first randomized controlled trial to assess the effectiveness of using a barrier adhesive draping on reducing the end-of-procedure pocket swab culture positivity. In this study, we are exploring a low-cost intervention that may significantly reduce CIED infection. Also, having a valid surrogate marker for CIED infection at the time of implant will facilitate design of future clinical trials.

Simple Summary: The enormous demand for swabs for clinical use that has characterised recent years, together with the need to develop effective, eco-friendly, and low-cost strategies for their production, has driven nanotechnological research to the development of new manufacturing processes. In this context, electrospinning represents a promising solution as it guarantees broad control in terms of fibre size and porosity and good scalability of the production process. In this study, this technique was chosen for the fabrication of biodegradable polymeric membranes to be used for the manufacture of swab tips. The electrospun mats thus obtained were characterised, and the prototype swab thus assembled was investigated in its uptake and release properties. Furthermore, the use of this prototype for the collection of bacteriological samples was preliminarily evaluated. The in vitro tests revealed a good potential, comparable to those of commercial foam swabs adopted as the reference standard and hopefully replaceable by the manufactured prototype. In recent years, the enormous demand for swabs for clinical use has promoted their relevance and, consequently, brought the environmental issues due to their single use and lack of biodegradability to the attention of the healthcare industry. Swabs consist of a stick that facilitates their easy handling and manoeuvrability even in complex districts and an absorbent tip designed to uptake and release biological samples. In this study, we focused on the fabrication of an innovative biodegradable poly(vinyl alcohol) (PVA) nanofiber swab tip using the electrospinning technique. The innovative swab tip obtained showed comparable uptake and release capacity of protein and bacterial species (Pseudomonas aeruginosa and Staphylococcus aureus) with those of the commercial foam-type swab. In this way, the obtained swab can be attractive and suitable to fit into this panorama due to its low-cost process, easy scalability, and good uptake and release capabilities. [ABSTRACT FROM AUTHOR]

Saliva is a largely unexplored liquid biopsy that can be readily obtained noninvasively. Not dissimilar to blood plasma or serum, it contains a vast array of bioconstituents that may be associated with the absence or presence of a disease condition. Given its ease of access, the use of saliva is potentially ideal in a point-of-care screening or diagnostic test. Herein, we developed a swab "dip" test in saliva obtained from consenting patients participating in a lung cancer-screening programme being undertaken in north-west England. A total of 998 saliva samples (31 designated as lung-cancer positive and 17 as prostate-cancer positive) were taken in the order in which they entered the clinic (i.e., there was no selection of participants) during the course of this prospective screening programme. Samples (sterile Copan blue rayon swabs dipped in saliva) were analysed using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. In addition to unsupervised classification on resultant infrared (IR) spectra using principal component analysis (PCA), a range of feature selection/extraction algorithms were tested. Following preprocessing, the data were split between training (70% of samples, 22 lung-cancer positive versus 664 other) and test (30% of samples, 9 lung-cancer positive versus 284 other) sets. The training set was used for model construction and the test set was used for validation. The best model was the PCA-quadratic discriminant analysis (QDA) algorithm. This PCA-QDA model was built using 8 PCs (90.4% of explained variance) and resulted in 93% accuracy for training and 91% for testing, with clinical sensitivity at 100% and specificity at 91%. Additionally, for prostate cancer patients amongst the male cohort (n = 585), following preprocessing, the data were split between training (70% of samples, 12 prostate-cancer positive versus 399 other) and test (30% of samples, 5 prostate-cancer positive versus 171 other) sets. A PCA-QDA model, again the best model, was built using 5 PCs (84.2% of explained variance) and resulted in 97% accuracy for training and 93% for testing, with clinical sensitivity at 100% and specificity at 92%. These results point to a powerful new approach towards the capability to screen large cohorts of individuals in primary care settings for underlying malignant disease. [ABSTRACT FROM AUTHOR]

Background: Burns rank among the most prevalent and severe types of injuries. Severe thermal damage patients need to receive expert care right away in order to reduce their risk of morbidity and death. Despite rigorous treatment with topical and parenteral antibiotics, sepsis and burn wound infection cause 50% to 60% of fatalities in burn patients. Aim: To investigate the burn wound bacteriological pattern in patients who come to a tertiary care facility. Materials and Methods: A total of 112 swab culture samples and 56 blood culture samples were obtained for this prospective observational study, which included 56 patients admitted to the burns ward at Government General Hospital. The samples were processed at the laboratory of the institution, government general hospital. Results: 15 samples (28.3%) and 38 samples (71.7%) of the 56 swab culture isolates were gram positive and gram negative, respectively. The major organism identified from 16 (28.50%) of the study's second-week culture samples was the gram-negative bacterium Klebsiella. Conclusion: This study focuses on the microbiological etiology, and microbial analysis of burn wounds, with a particular emphasis on the methodologies for culturing and surveillance of burn wound infections. [ABSTRACT FROM AUTHOR]

The origin of surgical site and biomaterial-associated infection is still elusive. Micro-organisms contaminating the wound may come from the air in the operating theatre, the surgical team or the skin of the patient. The skin of patients is disinfected prior to surgery, but bacteria deeper in the skin (e.g. in sweat glands or sebaceous glands) may not be reached. A preliminary cohort study was performed to study the origin of surgical site and biomaterial-associated infection between May 2020 and February 2021. In order to investigate whether cutaneous microbiota colonize the wound when released from the skin upon cutting, aerobic and anaerobic bacteria were isolated, quantified and identified from the skin of 99 patients undergoing trauma surgery, before and after skin disinfection, from knife blades and from the wound directly after the first cut. Ninety-nine percent of the patients were culture-positive before disinfection with chlorhexidine. Of these, 40% were still culture-positive after disinfection. Of these, 54% had a positive culture of the wound after cutting the skin. Twenty percent of the patients with a negative culture after disinfection had a positive wound culture after cutting the skin. Staphylococcus epidermidis and Cutibacterium acnes were the most commonly cultured bacterial species. In 9% of cases, more than 100 bacterial colonies were cultured from the wound; this may cause biomaterial-associated infection. Bacteria residing in the skin and not eradicated by disinfection may enter the surgical wound upon cutting, resulting in contamination which may cause biomaterial-associated infection. [ABSTRACT FROM AUTHOR]

Drilling operations are the major cost factor for the oil industry. Appropriately designed operations are essential for successful drilling. Optimized drilling operations also enhance drilling performance and reduce drilling costs. This is achieved by increasing the bit life (minimizing premature bit wear), drilling more quickly, which reduces drilling time, and also reducing tripping operations. This paper is presented in two parts. The first part compares the parametric physics-based swab and surge simulation results obtained from the Bingham plastic, power law, and Robertson–Stiff models. The aim is to show how the model's predictions deviate from each other. Two 80:20 oil/water ratio (OWR) oil-based drilling fluids and two 90:10 OWR oil-based drilling fluids, 1.96 sg and 2.0 sg, were considered in vertical and deviated wells. Analysis of the simulation results revealed that the deviations depend on the drilling fluid's physical and rheological parameters as well as the well trajectory. Moreover, the model's predictions were inconsistent. Data-driven machine learning (ML) modeling is the focus of the second section. Data-driven modeling was performed using both software-generated datasets and field datasets. The results show that the random forest regressor (RF), artificial neural network (ANN), long short-term memory (LSTM), LightGBM, XGBoost, and multivariate regression models predicted the training and test datasets with higher R-squared and minimum mean square error values. Deploying the ML model in real-time applications and the planning phase would lead to potential applications of artificial intelligence for well planning and optimization processes. [ABSTRACT FROM AUTHOR]

Copyright of Iraqi Journal of Chemical & Petroleum Engineering is the property of Republic of Iraq Ministry of Higher Education & Scientific Research (MOHESR) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Nasal swabs and saliva samples are being considered alternatives to nasopharyngeal swabs (NPSs) for detecting severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2); however, few studies have compared the usefulness of nasal swabs, NPSs, and saliva samples for detecting SARS-CoV-2 and other respiratory virus infections. We compared the positivity rates and concentrations of viruses detected in nasal swabs, NPSs, and saliva samples using cycle threshold (Ct) values from real-time PCR tests for respiratory viruses. Methods: In total, 236 samples (48 five-rub and 10 10-rub nasal swabs, 96 NPSs collected using two different products, 48 saliva swabs, and 34 undiluted saliva samples) from 48 patients (34 patients with SARS-CoV-2 and 14 with other respiratory virus infections) and 40 samples from eight healthy controls were obtained. The PCR positivity and Ct values were compared using Allplex Respiratory Panels 1/2/3 and Allplex SARS-CoV-2 real-time PCR. Results: NPSs showed the lowest Ct values (indicating the highest virus concentrations); however, nasal and saliva samples yielded positive results for SARS-CoV-2 and other respiratory viruses. The median Ct value for SARS-CoV-2 E gene PCR using nasal swab samples collected with 10 rubs was significantly different from that obtained using nasal swabs collected with five rubs (Ct=24.3 vs. 28.9; P =0.002), but not from that obtained using NPSs. Conclusions: Our results confirm that the NPS is the best sample type for detecting respiratory viruses, but nasal swabs and saliva samples can be alternatives to NPSs. Vigorously and sufficiently rubbed nasal swabs can provide SARS-CoV-2 concentrations similar to those obtained with NPSs. [ABSTRACT FROM AUTHOR]

Abstract Background COVID-19 pandemic is not yet over, and it has been generating lots of plastic wastes that become a big concern. To catch the virus, for example, no matter via antigen or PCR test, swab is generally used for sampling. Unfortunately, the swab tip is commonly made of plastics, and thus it can be a potential source of microplastics. This study aims to propose and optimise several Raman imaging to identify the microplastic fibres released from different COVID-19 test swabs. Results The results show that Raman imaging can effectively identify and visualise the microplastic fibres released from the swabs. In the meantime, on the surface of the fibres, additives such as titanium oxide particles are also captured for some brands of swabs. To increase the result certainty, scanning electron microscope (SEM) is first employed to get the morphology of the released microplastic fibres, along with Energy-dispersive X-ray spectroscopy (EDS) to confirm the presence of titanium element. Then, Raman imaging is advanced to identify and visualise the microplastics and titanium oxide particles, from different characteristic peaks in the scanning spectrum matrix. To further increase the imaging certainty, these images can be merged and cross-checked using algorithms, or the raw data from the scanning spectrum matrix can be analysed and decoded via chemometrics, such as principal component analysis (PCA). Beyond the advantages, the disadvantages of the confocal Raman imaging (affected by focal height) and algorithms (non-supervised calculation) are also discussed and intentionally corrected. In brief, the imaging analysis (particularly the combined SEM with Raman) is recommended to avoid the possible result bias that might be generated from the single spectrum analysis at a selective but random position. Conclusions Overall, the results indicate that Raman imaging can be a useful tool to detect microplastics. The results also send us a strong warning that, if we worry about the potential microplastics contamination, we should be cautious to select the suitable COVID-19 testing kits.

Tujuan: Mengetahui angka dan jenis bakteri udara, lantai, dan meja berdasarkan pewarnaan Gram di laboratorium Mikroskopik Fakultas Kedokteran Universitas Tanjungpura. Metode: Penelitian ini menggunakan metode settling plate, selama 15 menit dengan media agar darah untuk sampel bakteri udara. Sampel lantai dan meja diambil menggunakan swab lidi kapas steril dengan cairan buffer phospate, kemudian digores pada media agar darah. Semua media sampel diinkubasi pada suhu 36℃ selama 24 jam, kemudian dilakukan penghitungan koloni serta pewarnaan Gram untuk melihat variasi jenis bakterinya. Hasil: Angka bakteri udara tertinggi adalah 208,33 CFU/m3, dan yang paling rendah 52,08 CFU/m3. Dari pewarnaan Gram, bentuk morfologi bakteri udara yaitu kokkus Gram positif dan negatif, serta basil Gram negatif. Sedangkan angka bakteri swab permukaan lantai dan meja yang paling tinggi adalah 200 CFU/m2, terendah adalah 18 CFU/m2. Morfologi bakteri permukaan lantai dan meja yang paling banyak yaitu diplobasil Gram negatif. Kesimpulan: Rata – rata angka bakteri udara laboratorium Mikroskopik adalah 52,08 CFU/m3, dan masih memenuhi standar nilai batas yang ditetapkan. Rata-rata angka bakteri swab permukaan adalah 64 CFU/m2 yang cukup tinggi, melebihi standar nilai batas permukaan dinding dan lantai ruang perawatan yang ditetapkan oleh Kepmenkes. Kata kunci: Angka Bakteri; Laboratorium; CFU; Settling Plate; Swab

Background. Tuberculosis is one of the world's health problems, with larger mortality rate than HIV/AIDS. In order to control this disease, a new and inexpensive diagnostic method is needed. Oral samples, such as buccal mucosa epithelium, can be an alternative specimen, other than sputum, in the diagnosis of tuberculosis. Purpose. This study aimed to analyze the presence of Mycobacterium tuberculosis on buccal swabbing of tuberculosis patients. Method. Study was conducted on 18 new pulmonary tuberculosis patients in TB DOTS unit of Dr. Soetomo General Hospital. Each subject was swabbed on the buccal mucosa of the oral cavity for subsequent examination of PCR, AFB, and culture to detect Mycobacterium tuberculosis in the oral cavity. Result. The results showed that Mycobacterium tuberculosis was detected from 2 study subjects (11%) using PCR, whereas in AFB and culture examination methods no Mycobacterium tuberculosis was detected on buccal mucosa of the oral cavity. Conclusion. This study showed that Mycobacterium tuberculosis was detected on buccal mucosa swab of tuberculosis patients based on PCR technique, but this method is less suitable in diagnosis of pulmonary tuberculosis.

This paper presents data-driven modeling and a results analysis. Group method data handling (GMDH), multivariable regression (MVR), artificial neuron network (ANN), and new proposed GMDH-featured ANN machine learning algorithms were implemented to model a field telemetry equivalent mud circulating density (ECD) dataset based on surface and subsurface drilling parameters. Unlike the standard GMDH-ANN model, the proposed GMDH-featured ANN utilizes a fully connected network. Based on the considered eighteen experimental modeling designs, all the GMDH regression results showed higher R-squared and minimum mean-square error values than the multivariable regression results. In addition, out of the considered eight experimental designs, the GMDH-ANN model predicts about 37.5% of the experiments correctly, while both algorithms have shown similar results for the remaining experiments. However, further testing with diverse datasets is necessary for better evaluation.

Accurate quantification of infectious contaminants on environmental surfaces, particularly infectious viruses, is essential for contact transmission risk assessment; however, difficulties in recovering viruses from surfaces using swabs complicates this quantification process. Herein, we identified the factors that significantly affected virus recovery rates and developed an ideal swab method that yielded the highest rate of virus recovery. We comprehensively analyzed the effects of swab type (cotton/polyester), swab water content (wet/dry conditions), surface material, and surface area on the rates of viral RNA and infectious virus recovery.The virus recovery rate was significantly lower than the viral RNA recovery rate (P 0.8) with the target surface area. The maximum surface area where the virus recovery rate was ≥10% (MSA-10%) was identified as the maximum quantifiable area. For influenza virus recovery, MSA-10% on polyvinyl chloride (PVC) sheet, PVC leather, stainless steel, silicone, glass, and polycarbonate surfaces was 66.7, 193, 60.2, 144, 105, and 15.6 cm2, respectively. For feline calicivirus recovery, MSA-10% on PVC sheet, PVC leather, stainless steel, silicone, glass, and polycarbonate surfaces was 210, 111, 2120, 250, 322, and 180 cm2, respectively.The most accurate and ideal method for quantifying infectious viruses on environmental surfaces with the highest recovery rates meets three specifications: “wet conditions,” “the use of cotton swabs,” and “a target surface area of approximately 10 cm2.

Introduction. MicroRNA (miR) 155 has been implicated in the regulation of innate and adaptive immunity as well as antiviral responses, but its role during respiratory syncytial virus (RSV) infections is not known. The objective of this study was to investigate the expression of miR-155 using pharyngeal swabs and peripheral blood in infants with RSV infection and uninfected controls. Methods. A prospective age-matched study was conducted in primary care in Torino from 1 August 2018 to 31 January 2020. We enrolled 66 subjects, 29 of them patients with RSV infection and 37 age-matched uninfected controls, and collected pharyngeal swabs and peripheral blood in order to assess miR-155 expression with real-time stem–loop–TaqMan real-time PCR. Results. The data show that there is no correlation between pharyngeal swabs and peripheral blood with respect to miR-155 expression. The 1/ΔCq miR-155 expression levels in throat swabs in RSV bronchiolitis patients and healthy controls were 0.19 ± 0.11 and 0.21 ± 0.09, respectively, and were not significantly different between healthy controls and bronchiolitis (p = 0.8414). In the peripheral blood, miR-155 levels were higher than those of healthy control subjects: 0.1 ± 0.013 and 0.09 ± 0.0007, respectively; p = 0.0002. Discussion. Our data provide evidence that miR-155 expression is higher in peripheral blood during RSV infection but not in swabs. This difference in the timing of sample recruitment could explain the differences obtained in the results; miR-155 activation is probably only assessable in the very early stages of infection in the swab and remains visible for longer in the blood. New investigations are needed in order to clarify whether the miR-155 expression in swabs can be influenced by different stages of virus disease of infants. [ABSTRACT FROM AUTHOR]

There is an increasing need for inexpensive and rapid screening tests in point-of-care clinical oncology settings. Herein, we develop a swab "dip" test in saliva obtained from consenting patients participating in a lung-cancer-screening programme being undertaken in North West England. In a pilot study, a total of 211 saliva samples (n = 170 benign, 41 designated cancer-positive) were randomly taken during the course of this prospective lung-cancer-screening programme. The samples (sterile Copan blue rayon swabs dipped in saliva) were analysed using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. An exploratory analysis using principal component analysis (PCA,) with or without linear discriminant analysis (LDA), was then undertaken. Three pairwise comparisons were undertaken including: (1) benign vs. cancer following swab analysis; (2) benign vs. cancer following swab analysis with the subtraction of dry swab spectra; and (3) benign vs. cancer following swab analysis with the subtraction of wet swab spectra. Consistent and remarkably similar patterns of clustering for the benign control vs. cancer categories, irrespective of whether the swab plus saliva sample was analysed or whether there was a subtraction of wet or dry swab spectra, was observed. In each case, MANOVA demonstrated that this segregation of categories is highly significant. A k-NN (using three nearest neighbours) machine-learning algorithm also showed that the specificity (90%) and sensitivity (75%) are consistent for each pairwise comparison. In detailed analyses, the swab as a substrate did not alter the level of spectral discrimination between benign control vs. cancer saliva samples. These results demonstrate a novel swab "dip" test using saliva as a biofluid that is highly applicable to be rolled out into a larger lung-cancer-screening programme. [ABSTRACT FROM AUTHOR]

Background: Menstrual cups (MCs) are increasingly used to collect cervicovaginal secretions to characterise vaginal mucosal immunology, in conjunction with high vaginal swabs (HVS) for metataxonomics, particularly in HIV transmission studies. We hypothesised that both methods of collecting bacterial biomass are equivalent for 16S rRNA gene sequencing. Material and Methods: Cervicovaginal fluid (CVF) samples from 16 pregnant women with HIV-1 (PWWH) were included to represent the major vaginal bacterial community state types (CST I-V). Women underwent sampling during the second trimester by liquid amies HVS followed by a MC (Soft disc™) and samples were stored at -80°C. Bacterial cell pellets obtained from swab elution and MC (500 µL, 1 in 10 dilution) were resuspended in 120 µL PBS for DNA extraction. Bacterial 16S rRNA gene sequencing was performed using V1-V2 primers and were analysed using MOTHUR. Paired total DNA, bacterial load, amplicon read counts, diversity matrices and bacterial taxa were compared by sampling method using MicrobiomeAnalyst, SPSS and R. Results: The total DNA eluted from one aliquot of diluted CVF from an MC was similar to that of a HVS (993ng and 609ng, p=0.18); the mean bacterial loads were also comparable for both methods (MC: 8.0 log10 16S rRNA gene copies versus HVS: 7.9 log10 16S rRNA gene copies, p=0.27). The mean number of sequence reads generated from MC samples was lower than from HVS (MC: 12730; HVS:14830, p=0.05). The a-diversity metrices were similar for both techniques; MC Species Observed: 41 (range 12-96) versus HVS: 47 (range 16-96), p=0.15; MC Inverse Simpson Index: 1.98 (range 1.0-4.0) versus HVS: 0.48 (range 1.0-4.4), p=0.22). The three most abundant species observed were: Lactobacillus iners, Lactobacillus crispatus and Gardnerella vaginalis. Hierarchical clustering of relative abundance data showed that samples obtained using different techniques in an individual clustered in the same CST group. Conclusion: These data demonstrate that despite sampling slightly different areas of the lower genital tract, there was no difference in bacterial load or composition between methods. Both are suitable for characterisation of vaginal microbiota in PWWH. The MC offers advantages, including a higher volume of sample available for DNA extraction and complimentary assays. [ABSTRACT FROM AUTHOR]

Background: COVID-19 pandemic is not yet over, and it has been generating lots of plastic wastes that become a big concern. To catch the virus, for example, no matter via antigen or PCR test, swab is generally used for sampling. Unfortunately, the swab tip is commonly made of plastics, and thus it can be a potential source of microplastics. This study aims to propose and optimise several Raman imaging to identify the microplastic fibres released from different COVID-19 test swabs. Results: The results show that Raman imaging can effectively identify and visualise the microplastic fibres released from the swabs. In the meantime, on the surface of the fibres, additives such as titanium oxide particles are also captured for some brands of swabs. To increase the result certainty, scanning electron microscope (SEM) is first employed to get the morphology of the released microplastic fibres, along with Energy-dispersive X-ray spectroscopy (EDS) to confirm the presence of titanium element. Then, Raman imaging is advanced to identify and visualise the microplastics and titanium oxide particles, from different characteristic peaks in the scanning spectrum matrix. To further increase the imaging certainty, these images can be merged and cross-checked using algorithms, or the raw data from the scanning spectrum matrix can be analysed and decoded via chemometrics, such as principal component analysis (PCA). Beyond the advantages, the disadvantages of the confocal Raman imaging (affected by focal height) and algorithms (non-supervised calculation) are also discussed and intentionally corrected. In brief, the imaging analysis (particularly the combined SEM with Raman) is recommended to avoid the possible result bias that might be generated from the single spectrum analysis at a selective but random position. Conclusions: Overall, the results indicate that Raman imaging can be a useful tool to detect microplastics. The results also send us a strong warning that, if we worry about the potential microplastics contamination, we should be cautious to select the suitable COVID-19 testing kits. [ABSTRACT FROM AUTHOR]

IntroductionThe porcine reproductive and respiratory syndrome virus (PRRSV) continues to challenge swine production in the US and most parts of the world. Effective PRRSV surveillance in swine herds can be challenging, especially because the virus can persist and sustain a very low prevalence. Although weaning-age pigs are a strategic subpopulation in the surveillance of PRRSV in breeding herds, very few sample types have been validated and characterized for surveillance of this subpopulation. The objectives of this study, therefore, were to compare PRRSV RNA detection rates in serum, oral swabs (OS), nasal swabs (NS), ear-vein blood swabs (ES), and family oral fluids (FOF) obtained from weaning-age pigs and to assess the effect of litter-level pooling on the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of PRRSV RNA.MethodsThree eligible PRRSV-positive herds in the Midwestern USA were selected for this study. 666 pigs across 55 litters were sampled for serum, NS, ES, OS, and FOF. RT-qPCR tests were done on these samples individually and on the litter-level pools of the swabs. Litter-level pools of each swab sample type were made by combining equal volumes of each swab taken from the pigs within a litter.ResultsNinety-six piglets distributed across 22 litters were positive by PRRSV RT-qPCR on serum, 80 piglets distributed across 15 litters were positive on ES, 80 piglets distributed across 17 litters were positive on OS, and 72 piglets distributed across 14 litters were positive on NS. Cohen's kappa analyses showed near-perfect agreement between all paired ES, OS, NS, and serum comparisons (). The serum RT-qPCR cycle threshold values (Ct) strongly predicted PRRSV detection in swab samples. There was a ≥ 95% probability of PRRSV detection in ES-, OS-, and NS pools when the proportion of positive swab samples was ≥ 23%, ≥ 27%, and ≥ 26%, respectively.DiscussionES, NS, and OS can be used as surveillance samples for detecting PRRSV RNA by RT-qPCR in weaning-age pigs. The minimum number of piglets to be sampled by serum, ES, OS, and NS to be 95% confident of detecting ≥ 1 infected piglet when PRRSV prevalence is ≥ 10% is 30, 36, 36, and 40, respectively.

Cervicovaginal bacteria cause inflammation which in turn increases HIV risk. Profiling the cervicovaginal microbiome, therefore, is instrumental for vaccine development. We show that the microbiome profile captured by cervicovaginal lavage is comparable to samples obtained by vaginal swabs. Thus, lavage may serve as a sampling strategy in NHP vaccine studies.

BackgroundMenstrual cups (MCs) are increasingly used to collect cervicovaginal secretions to characterise vaginal mucosal immunology, in conjunction with high vaginal swabs (HVS) for metataxonomics, particularly in HIV transmission studies. We hypothesised that both methods of collecting bacterial biomass are equivalent for 16S rRNA gene sequencing.Material and MethodsCervicovaginal fluid (CVF) samples from 16 pregnant women with HIV-1 (PWWH) were included to represent the major vaginal bacterial community state types (CST I-V). Women underwent sampling during the second trimester by liquid amies HVS followed by a MC (Soft disc™) and samples were stored at -80°C. Bacterial cell pellets obtained from swab elution and MC (500 µL, 1 in 10 dilution) were resuspended in 120 µL PBS for DNA extraction. Bacterial 16S rRNA gene sequencing was performed using V1-V2 primers and were analysed using MOTHUR. Paired total DNA, bacterial load, amplicon read counts, diversity matrices and bacterial taxa were compared by sampling method using MicrobiomeAnalyst, SPSS and R.ResultsThe total DNA eluted from one aliquot of diluted CVF from an MC was similar to that of a HVS (993ng and 609ng, p=0.18); the mean bacterial loads were also comparable for both methods (MC: 8.0 log10 16S rRNA gene copies versus HVS: 7.9 log10 16S rRNA gene copies, p=0.27). The mean number of sequence reads generated from MC samples was lower than from HVS (MC: 12730; HVS:14830, p=0.05). The α-diversity metrices were similar for both techniques; MC Species Observed: 41 (range 12-96) versus HVS: 47 (range 16-96), p=0.15; MC Inverse Simpson Index: 1.98 (range 1.0-4.0) versus HVS: 0.48 (range 1.0-4.4), p=0.22). The three most abundant species observed were: Lactobacillus iners, Lactobacillus crispatus and Gardnerella vaginalis. Hierarchical clustering of relative abundance data showed that samples obtained using different techniques in an individual clustered in the same CST group.ConclusionThese data demonstrate that despite sampling slightly different areas of the lower genital tract, there was no difference in bacterial load or composition between methods. Both are suitable for characterisation of vaginal microbiota in PWWH. The MC offers advantages, including a higher volume of sample available for DNA extraction and complimentary assays.

Nasopharyngeal swabs (NPS) are considered the gold standard for SARS-CoV-2 testing but are technically challenging to perform and associated with discomfort. Alternative specimens for viral testing, such as oropharyngeal swabs (OPS) and nasal swabs, may be preferable, but strong evidence regarding their diagnostic sensitivity for SARS-CoV-2 testing is still missing. We conducted a head-to-head prospective study to compare the sensitivity of NPS, OPS and nasal swabs specimens for SARS-CoV-2 molecular testing. Adults with an initial positive SARS-CoV-2 test were invited to participate. All participants had OPS, NPS and nasal swab performed by an otorhinolaryngologist. We included 51 confirmed SARS-CoV-2-positive participants in the study. The sensitivity was highest for OPS at 94.1% (95% CI, 87 to 100%) compared to NPS at 92.5% (95% CI, 85 to 99%) (p = 1.00) and lowest for nasal swabs at 82.4% (95% CI, 72 to 93%) (p = 0.07). Combined OPS/NPS was detected in 100% of cases, while the combined OPS/nasal swab increased the sensitivity significantly to 96.1% (95% CI, 90 to 100%) compared to that of the nasal swab alone (p = 0.03). The mean Ct value for NPS was 24.98 compared to 26.63 for OPS (p = 0.084) and 30.60 for nasal swab (p = 0.002). OPS achieved a sensitivity comparable to NPS and should be considered an equivalent alternative for SARS-CoV-2 testing. [ABSTRACT FROM AUTHOR]

Cytokines in wound fluid are used as surrogates for wound healing in clinical research. The current methods used to collect and process wound fluid are noninvasive but not optimal. The aim of this prospective study was to evaluate a method (NovaSwab) by which wound fluid is collected by a surface swab and eluted in a physiological buffer for subsequent cytokine analysis. Wound fluid from 12 patients with leg ulcers was assessed by NovaSwab at the start (Day 0) and at the end of a 23‐h collection period of wound fluid retained by foam oblates beneath an occlusive film dressing (Day 1). GM‐CSF, IL‐1α, IL‐1β, IL‐6, IL‐8, PDGF‐AA, TNF‐α and VEGF levels were measured by multiplex and electrochemiluminescence assays. IL‐1α (2.4×), IL‐1β (2.0×) and IL‐8 (1.8×) levels increased from Day 0 to Day 1 as detected by NovaSwab, indicating local production of these polypeptides in the wounds. On Day 1, the NovaSwab method yielded higher levels of IL‐1α (4.0×), IL‐1β (2.7×) and IL‐6 (2.7×), and 35% lower levels of VEGF than those in wound fluid accumulated for 23 h in foam oblates (on average, 5 ml of wound fluid). In vitro experiments showed that the investigated cytokines in cell‐free wound fluid were recovered in a quantitative manner by the NovaSwab method. We conclude that the method presented here is a promising research tool to study the kinetics of soluble cytokines over the course of wound healing. More studies are needed to determine the interobserver variation and reproducibility of the NovaSwab method. [ABSTRACT FROM AUTHOR]

Background/Aim: Cervical cancer is the fourth most common type of cancer in women worldwide and it is a major cause of cancer-related deaths in developing countries. Despite the marked reduction observed in the rates of the disease as a result of screening programs, it is necessary to develop robust biomarkers that can detect the neoplastic progression early in HPV-related cervical lesions. Materials and Methods: We performed comparative mRNA sequencing from exfoliative cervical cytology samples from nine Korean women using the Illumina NovaSeq6000 platform. Each pathological tissue was matched to the corresponding cytological sample. The pathologic diagnosis was scrutinized with ancillary immunohistochemistry and was considered a confirmative (endpoint) diagnosis. The pathological diagnoses consisted of three cases of chronic cervicitis, 2 high-grade squamous intraepithelial lesions (HSILs), 2 squamous cell carcinomas in situ (CIS), and 2 invasive squamous cell carcinomas (SQCCs), respectively. Using bioinformatic analyses, differentially expressed genes (DEGs; fold change ≥1.5; p<0.05) were applied for Gene Ontology (GO), Gene Set Enrichment Analysis (GSEA), and protein-protein interaction (PPI) networks. Results: From a total of 55,882 genes, 438 DEGs were pinpointed; 282 genes were up-regulated and 156 genes down-regulated. These transcriptomic profiles were clearly divided into neoplastic (HSIL, CIS, and SQCC; ≥HSILs) and non-neoplastic lesions. The up-regulated DEGs were HIF-1a, EDN1, PIK3R3, PPP1CA and AKR1C1. GO, GSEA, and PPI network analyses showed marked associations with metabolism, proteolysis, or proteoglycan process pathways in cervical carcinogenesis. Conclusion: The transcriptomic analysis using exfoliative cervical cells was more likely representative of its corresponding histopathological diagnosis, thus emphasizing its potential utility in clinical practice. This study provides comprehensive transcriptomic network analyses for robust biomarkers that might present a high potential risk of progression to cancer in the exfoliative cervical cytology; our findings support their clinical utility for improved cervical cancer screening. [ABSTRACT FROM AUTHOR]

Biofilm formation in wounds contributes greatly to the lack of healing and increased healthcare expenditures. Antimicrobial efficacy is decreased significantly in the presence of biofilms, which can, in turn, promote the development of antibiotic resistance. Antibiofilm strategies to prevent the formation and persistence of biofilm in wounds would consequently decrease the incidence of chronic wounds and improve wound healing. The use of preclinical biofilm models to assess the antibiofilm efficacy of wound dressings is a prerequisite to identifying new technologies that can improve outcomes in hardto- heal wounds. Improvements to preclinical approaches (in vitro and in vivo) to biofilm models are needed. Living tissue (ex vivo) derived from pig and human skin donors is a developing approach that translates the research to the clinic, including the native microenvironment of the biofilm. [ABSTRACT FROM AUTHOR]

Background: We compared four combinations of nasopharyngeal swabs and transport media for their ability to transfer and recover viruses under different storage conditions. Methods: Each swab was immersed in culture supernatants of influenza A virus (IAV), respiratory syncytial virus, and adenovirus, placed in transport medium, and stored at -20°C, +4°C, +20 to 25°C, and +37°C for 5 days. On each day, virus culture and real-time PCR were performed for each virus. Results: All samples under different storage conditions showed positive results up to 5 days using both virus culture and real-time PCR. Real-time PCR showed that samples stored at -20°C, 4°C, and 20 - 25°C were within two cycle thresholds (Cts) up to 5 days, but IAV at 37°C showed that viral titer decreased after 3 days. Conclusions: Our results indicate that these swab and transport media maintained the stability of the above viruses for 5 days at room temperature, refrigerated, and frozen storage conditions. [ABSTRACT FROM AUTHOR]

• Cell quantification in saliva did not improve the positive predictive value of congenital CMV infection diagnosis. • Using thresholds to determine viral load in infected newborns did not improve positive predictive value but reduced sensitivity. • Saliva screening on day 2 or 3 had better PPV (38.7 %) than at birth (23.8 %). • Symptomatology at birth was not significantly associated with viral load in saliva swabs at birth. • Occurrence of sequelae was associated with higher viral load in saliva swabs at birth. Early diagnosis of congenital CMV infection (cCMVI) allows for early intervention and follow-up to detect delayed hearing loss. While CMV PCR in urine is the gold standard for cCMVI diagnosis, saliva testing is often performed. Our aim was to determine (i) if swab saliva sampling needed standardization, (ii) if a threshold value in "virus copies per million cells (Mc)" in saliva samples could improve clinical specificity, and (iii) to establish a correlation between viral load in saliva and symptomatology/outcome of cCMVI. In our institution, universal newborn screening is performed on saliva swabs at delivery or until day 3 of life. If positive, CMV PCR in urine is done within 2 weeks to confirm or exclude cCMVI. Cell quantification showed that saliva swab sampling was well performed as 95.4 % samples had more than 100 cells/10 µL. There was a good correlation between saliva viral load in copies/mL and in copies/Mc (Pearson's r = 0.96, p < 0.0001). However, threshold values, established to determine a viral load level at which we could confidently identify infected newborns, did not improve positive predictive value (21.8 % for copies/mL and 21 % for copies/Mc vs 25.4 % without threshold) but instead reduced sensitivity (88 % and 85% vs 100 % without threshold). Samples collected on day 2 or 3 had better positive predictive value (38.7 %) compared to those collected on day 1 (23.8 %). Symptomatology at birth was not significantly associated with viral load in saliva at diagnosis. However, sequelae occurrence was associated with viral load in saliva (copies/Mc). Our results confirm that saliva swab is a suitable sample for universal neonatal screening. However, identifying newborns that will develop sequelae remains an issue in the management of cCMVI. [ABSTRACT FROM AUTHOR]

The axial movement of pipe in and out of the well generates positive (surge) and negative (swab) pressures that will impact the well pressure. When the swab and surge effects cause well pressures outside the allowable operational limits, wellbore instability (well collapse/well fracture), kick, and induced drill string sticking issues will occur. The problems increase the operational and nonproductive time-related costs. Consequently, the drilling budget rises significantly. It is therefore, imperative to predict the differential pressures in order to mitigate the problems. Even though several models have been developed in the past, models work for the considered experimental setup and conditions. In this paper, a simple analytical model was derived for eccentric/concentric annuli. The fluid rheological behaviors were assumed to be described by power law and yielded power-law. The model is derived based on a steady state condition, and the effects of tripping speed, the power-law fluids, the yield-power-law fluids rheological parameters, and well geometries are considered. The model is compared with experimental data from the literature and with the existing model. Parametric sensitivity studies have been conducted. Results show that the model prediction exhibited quite good performance, with an average percentile error deviation of 9.9% and 6.2% for the power-law and yield-power-law fluids, respectively. However, more testing is required to determine the model’s limitations and application.