Rapid detection of Ebolavirus using isothermal recombinase-aided amplification.

Ebolavirus disease (EVD) is an often-lethal disease caused by the genus Ebolavirus (EBOV). Although vaccines are being developed and recently used, outbreak control still relies on a combination of various factors, including rapid identification of EVD cases. This allows rapid patient isolation and control measure implementation. Ebolavirus diagnosis is performed in treatment centers or reference laboratories, which usually takes a few hours to days to confirm the outbreak or deliver a clear result. A fast and field-deployable molecular detection method, such as the isothermal amplification recombinase-aided amplification (RAA), could significantly reduce sample-to-result time. In this study, a RT-RAA assay was evaluated for EBOV detection. Various primer and probe combinations were screened; analytical sensitivity and cross-specificity were tested. A total of 40 archived samples from the 2014 to 2016 Ebola outbreak in West Africa were tested with both the reference method real-time RT-PCR and the established RT-RAA assay. The assay could detect down to 22.6 molecular copies per microliter. No other pathogens were detected with the Ebolavirus RT-RAA assay. Testing 40 samples yield clinical sensitivity and specificity of 100% each. This rapid isothermal RT-RAA assay can replace the previous RT-RPA and continue to offer rapid EBOV diagnostics.

A new lineage nomenclature to aid genomic surveillance of dengue virus.

Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here we propose adding two sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present an assignment tool to show that the proposed lineages are useful for regional, national and sub-national discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.

Fully automated deep learning models with smartphone applicability for prediction of pain using the Feline Grimace Scale.

This study used deep neural networks and machine learning models to predict facial landmark positions and pain scores using the Feline Grimace Scale© (FGS). A total of 3447 face images of cats were annotated with 37 landmarks. Convolutional neural networks (CNN) were trained and selected according to size, prediction time, predictive performance (normalized root mean squared error, NRMSE) and suitability for smartphone technology. Geometric descriptors (n = 35) were computed. XGBoost models were trained and selected according to predictive performance (accuracy; mean square error, MSE). For prediction of facial landmarks, the best CNN model had NRMSE of 16.76% (ShuffleNetV2). For prediction of FGS scores, the best XGBoost model had accuracy of 95.5% and MSE of 0.0096. Models showed excellent predictive performance and accuracy to discriminate painful and non-painful cats. This technology can now be used for the development of an automated, smartphone application for acute pain assessment in cats.

Unusual coordination mode for 1,3-diphosphete ligands towards a Cr-Cr quintuple bond complex.

The reaction of LCr5̲CrL (L = N2C25H29, 1) with the phosphaalkynes R-C≡P (R = tBu, Me, Ad) yields the neutral dimerisation compounds [L2Cr2(µ,η1:η1:η2:η2-P2C2R2)] (R = tBu (2), Me (3)) and the tetrahedrane complex [L2Cr2(µ,η2:η2-PCAd)] (4). The 1,3-diphosphete ligands in complexes 2 and 3 are the first to possess this structural feature spanned over a metal-metal multiple bond, while the slightly bigger adamantyl phosphaalkyne remains a monomer in 4 with a side-on coordination mode.

Multimodal Biomarkers That Predict the Presence of Gleason Pattern 4: Potential Impact for Active Surveillance.

PURPOSE: Latent grade group ≥2 prostate cancer can impact the performance of active surveillance protocols. To date, molecular biomarkers for active surveillance have relied solely on RNA or protein. We trained and independently validated multimodal (mRNA abundance, DNA methylation, and/or DNA copy number) biomarkers that more accurately separate grade group 1 from grade group ≥2 cancers. MATERIALS AND METHODS: Low- and intermediate-risk prostate cancer patients were assigned to training (n=333) and validation (n=202) cohorts. We profiled the abundance of 342 mRNAs, 100 DNA copy number alteration loci, and 14 hypermethylation sites at 2 locations per tumor. Using the training cohort with cross-validation, we evaluated methods for training classifiers of pathological grade group ≥2 in centrally reviewed radical prostatectomies. We trained 2 distinct classifiers, PRONTO-e and PRONTO-m, and validated them in an independent radical prostatectomy cohort. RESULTS: PRONTO-e comprises 353 mRNA and copy number alteration features. PRONTO-m includes 94 clinical, mRNAs, copy number alterations, and methylation features at 14 and 12 loci, respectively. In independent validation, PRONTO-e and PRONTO-m predicted grade group ≥2 with respective true-positive rates of 0.81 and 0.76, and false-positive rates of 0.43 and 0.26. Both classifiers were resistant to sampling error and identified more upgrading cases than a well-validated presurgical risk calculator, CAPRA (Cancer of the Prostate Risk Assessment; P < .001). CONCLUSIONS: Two grade group classifiers with superior accuracy were developed by incorporating RNA and DNA features and validated in an independent cohort. Upon further validation in biopsy samples, classifiers with these performance characteristics could refine selection of men for active surveillance, extending their treatment-free survival and intervals between surveillance.

Instrumental procedures to assess the extensibility of pounded yam and relationship with sensory stretchability and consumer preferences.

BACKGROUND: Stretchability is the most important sensory textural attribute considered by consumers of pounded yam. It is important both for the processor during pounding and for the consumer during consumption to measure this attribute while screening large populations of yam genotypes intended for advanced breeding and eventual adoption. Texture determined by sensory evaluation and consumer perception is time consuming and expensive. It can be instrumentally mimicked by texture analyzer, thereby providing an efficient alternative screening tool. RESULTS: Two instrumental methods (uniaxial extensibility and lubricated squeezing flow) were applied to assess the extensional properties of pounded yam. In order to evaluate the accuracy, repeatability and discrimination of the methods, six yam genotypes with contrasting extensional properties, previously evaluated by 13 panellists in terms of stretchability and moldability and by 99 participants randomly selected in terms of overall liking, were used. Both methods allowed the discrimination of different genotypes as a function of extensional properties. Principal components showed that the genotypes were grouped within separate components associated with specific sensory attributes and their related instrumental texture parameters. Moreover, significant correlations were found between uniaxial extensibility textural attributes, bi-extensional viscosity and consumer overall liking. However, the sensory attributes were not significantly correlated with instrumental data and consumer overall liking. CONCLUSION: Bi-extensional viscosity and uniaxial extensibility attributes can be used to discriminate and screen yam genotypes for their stretchability characteristics. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Craniofacial Bones and Teeth in Spacefarers: Systematic Review and Meta-analysis.

INTRODUCTION: Estimating the risk of dental problems in long-duration space missions to the Moon and Mars is critical for avoiding dental emergencies in an environment that does not support proper treatment. Previous risk estimates were constructed based on the experience in short-duration space missions and isolated environments on Earth. However, previous estimates did not account for potential changes in dental structures due to space travel, even though bone loss is a known problem for long-duration spaceflights. The objective of this study was to systematically analyze the changes in hard tissues of the craniofacial complex during spaceflights. METHODS: Comprehensive search of Medline, Embase, Scopus, the NASA Technical Report Server, and other sources identified 1,585 potentially relevant studies. After screening, 32 articles that presented quantitative data for skull in humans (6/32) and for calvariae, mandible, and lower incisors in rats (20/32) and mice (6/32) were selected. RESULTS: Skull bone mineral density showed a significant increase in spacefaring humans. In spacefaring rodents, calvariae bone volume to tissue volume (BV/TV) demonstrated a trend toward increasing that did not reach statistical significance, while in mandibles, there was a significant decrease in BV/TV. Dentin thickness and incisor volume of rodent incisors were not significantly different between spaceflight and ground controls. DISCUSSION: Our study demonstrates significant knowledge gaps regarding many structures of the craniofacial complex such as the maxilla, molar, premolar, and canine teeth, as well as small sample sizes for the studies of mandible and incisors. Understanding the effects of microgravity on craniofacial structures is important for estimating risks during long-duration spaceflight and for formulating proper protocols to prevent dental emergencies. KNOWLEDGE TRANSFER STATEMENT: Avoiding dental emergencies in long-duration spaceflights is critical since this environment does not support proper treatment. Prior risk estimates did not account for changes in dental structures due to space travel. We reviewed and synthesized the literature for changes in craniofacial complex associated with spaceflight. The results of our study will help clinicians and scientists to better prepare to mitigate potential oral health issues in space travelers on long-duration missions.

General Versus Locoregional Anesthesia in TEVAR: An NSQIP Analysis.

BACKGROUND: Thoracic Endovascular Aortic Repair (TEVAR) is a minimally invasive surgery for repairing thoracic aneurysms and dissections. This study aims to compare postoperative outcomes of TEVAR performed under general versus locoregional anesthesia. METHODS: Utilizing the 2008-2019 American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database, patients older than the age of 18 years who received TEVAR, were identified using the following current procedural terminology codes: 33,880, 33,881, 33,883, 33,884, or 33,886. Patients who underwent concomitant procedures, those with both thoracoabdominal and abdominal aortic pathologies, and trauma cases were excluded. Standard descriptive statistics, in addition to χ2, Fisher's exact test, and Mann-Whitney U-tests were used to compare patient baseline characteristics and postoperative outcomes between general and locoregional anesthesia groups as appropriate. Univariable and multivariable logistic regression analyses were performed to assess independent predictors of hospital length of stay (LOS) greater than 7 days. RESULTS: Of the 1,028 patients included in the study, 86.5% received general anesthesia, and 13.5% received locoregional anesthesia, such as local anesthesia with monitored anesthesia care or regional anesthesia. No significant differences were found between patients receiving locoregional versus general anesthesia in mortality (3.6% vs. 7.9%, respectively, P = 0.071) and morbidity (18.7% and 24.8%, respectively, P = 0.121) within 30 days post-TEVAR, including any wound, pulmonary, thromboembolic, renal, septic, and cardiac arrest complications. Patients who received general anesthesia had significantly higher median LOS compared to those who received locoregional anesthesia [5 days (interquartile range (IQR): 3-10) versus 4 days (IQR: 2-7), P = 0.002], with 34.3% of the general anesthesia group having an LOS greater than 7 days compared to 21.6% of locoregional anesthesia group, P = 0.003. On multivariable logistic regression analysis, general anesthesia was found to be an independent predictor of prolonged LOS greater than 7 days (odds ratio (OR): 1.72, 95% confidence interval (CI): 1.05-2.81, P = 0.031). CONCLUSIONS: Locoregional anesthesia results in significantly lower postoperative hospital LOS with similar postoperative mortality and morbidity compared to general anesthesia in patients undergoing TEVAR.

Can ventral TAPP achieve favorable outcomes in minimally invasive ventral hernia repair? A systematic review and meta-analysis.

PURPOSE: The concept of the transabdominal preperitoneal (TAPP) was transferred from the inguinal hernia repair to be adopted in minimally invasive ventral hernia repair (VHR) and since then it has been gaining popularity. However, there are minimal data supporting the ventral TAPP (vTAPP) technique which may lead to reticence in the adoption of this approach. The aim of this meta-analysis was to evaluate the outcomes of patients who received minimally invasive vTAPP for VHR. STUDY DESIGN: A systematic search was performed of PubMed, Science Direct, Google Scholar and Cochrane Library until July 2022. We selected studies that compared the vTAPP technique with any of other minimally invasive techniques. A meta-analysis was done for the outcomes of perioperative characteristics and postoperative parameters. RESULTS: A total of 9 studies (1429 patients) were identified. vTAPP was associated with considerable benefit when compared to IPOM. vTAPP was less painful (MD = - 1.01; 95% CI [- 1.39, - 0.64], p < 0.00001), of reduced average cost (MD = - 457.10; 95% CI [- 457.27, - 456.92], p < 0.00001) and decreased SSI (OR = 0.29; 95% [0.09, 0.96], p = 0.04). On the other hand, the vTAPP approach consumed less operative time (MD: - 31.01, 95% CI [- 33.50, - 28.51]), p < 0.00001) and shorter hospital stay than the e-TEP approach. CONCLUSION: vTAPP appears to be safe and effective procedure for VHR, superior or similar to other minimally invasive techniques for perioperative characteristics and short-term outcomes.

Study of the mineral contents of Matricaria pubescens and Brocchia cinerea from Algeria.

Two species of plants commonly used for mainly their therapeutic values and available in some herbalists shops, namely: Brocchia cinerea and Matricaria pubescens that both belong to asteraceae family, and encountered mainly in the Algerian desert, have drawn attention in the scope of assessing their mineral contents, in fact minerals play an important role in the plant homeostasis and metabolism, on the other hand they may influence the health conditions mainly due to toxicity, and also the benefits that the plant consumer could have, the current study aimed to assess the contents of Al, Cd, Cr, Cu, Fe, Hg, Ni, Pb, Zn, As, Na, K, Mg, P, S and SI, beside comparing the obtained results to other similar studies, the aerial parts of the plants are collected from several sites then mineralized and analyzed using ICP-AES and AAS, high levels of Na, K and Mg have been noted, on the other hands levels of metals were noted to be overall marginal, except for Al and Hg for the sample of Brocchia cinerea from El oued, the levels of As also seemed to be high in all the samples, inversely to the levels of S and P which seemed lower than those noted for other plants in paralleled studies, while that similar results were found for Zn, Fe, the chemical and geologic features of the soils may be the influencing factor. Additionally the current study may put first milestone for the establishment of national guidelines regarding the mineral contents of medicinal plants.

Testing spatial working memory in pigs using an automated T-maze.

Pigs are an important large animal model for translational clinical research but underutilized in behavioral neuroscience. This is due, in part, to a lack of rigorous neurocognitive assessments for pigs. Here, we developed a new automated T-maze for pigs that takes advantage of their natural tendency to alternate. The T-maze has obvious cross-species value having served as a foundation for cognitive theories across species. The maze (17' × 13') was constructed typically and automated with flanking corridors, guillotine doors, cameras, and reward dispensers. We ran nine pigs in (1) a simple alternation task and (2) a delayed spatial alternation task. Our assessment focused on the delayed spatial alternation task which forced pigs to wait for random delays (5, 60, 120, and 240 s) and burdened spatial working memory. We also looked at self-paced trial latencies, error types, and coordinate-based video tracking. We found pigs naturally alternated but performance declined steeply across delays (R2 = 0.84). Self-paced delays had no effect on performance suggestive of an active interference model of working memory. Positional and head direction data could differentiate subsequent turns on short but not long delays. Performance levels were stable over weeks in diverse strains and sexes, and thus provide a benchmark for future neurocognitive assessments in pigs.

Plasmodium infection is associated with cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein.

Sero-surveillance can monitor and project disease burden and risk. However, SARS-CoV-2 antibody test results can produce false positive results, limiting their efficacy as a sero-surveillance tool. False positive SARS-CoV-2 antibody results are associated with malaria exposure, and understanding this association is essential to interpret sero-surveillance results from malaria-endemic countries. Here, pre-pandemic samples from eight malaria endemic and non-endemic countries and four continents were tested by ELISA to measure SARS-CoV-2 Spike S1 subunit reactivity. Individuals with acute malaria infection generated substantial SARS-CoV-2 reactivity. Cross-reactivity was not associated with reactivity to other human coronaviruses or other SARS-CoV-2 proteins, as measured by peptide and protein arrays. ELISAs with deglycosylated and desialated Spike S1 subunits revealed that cross-reactive antibodies target sialic acid on N-linked glycans of the Spike protein. The functional activity of cross-reactive antibodies measured by neutralization assays showed that cross-reactive antibodies did not neutralize SARS-CoV-2 in vitro. Since routine use of glycosylated or sialated assays could result in false positive SARS-CoV-2 antibody results in malaria endemic regions, which could overestimate exposure and population-level immunity, we explored methods to increase specificity by reducing cross-reactivity. Overestimating population-level exposure to SARS-CoV-2 could lead to underestimates of risk of continued COVID-19 transmission in sub-Saharan Africa.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Expected Bayesian estimation for exponential model based on simple step stress with Type-I hybrid censored data.

The procedure of selecting the values of hyper-parameters for prior distributions in Bayesian estimate has produced many problems and has drawn the attention of many authors, therefore the expected Bayesian (E-Bayesian) estimation method to overcome these problems. These approaches are used based on the step-stress acceleration model under the Exponential Type-I hybrid censored data in this study. The values of the distribution parameters are derived. To compare the E-Bayesian estimates to the other estimates, a comparative study was conducted using the simulation research. Four different loss functions are used to generate the Bayesian and E-Bayesian estimators. In addition, three alternative hyper-parameter distributions were used in E-Bayesian estimation. Finally, a real-world data example is examined for demonstration and comparative purposes.

Differential expression of metallothionein and p21 in gastric cancer and some precursor lesions.

OBJECTIVE: Gastric cancer (GC) is a heterogeneous disease with molecular diversity between and within tumors; therefore, searching for altered genes within this cancer is mandatory to reach the proper individualized targeted therapy. Expressions of Metallothionein (MT) and p21 are not uniform in various types of cancers and their predictive value in GC is controversial. This study aimed to assess the role of MT and p21 in intestinal-type GC and some of its precursor lesions. MATERIALS AND METHODS: Immunohistochemical staining for MT and p21 was applied on paraffin blocks belonging to 30 GCs and 51 benign gastric lesions/precancerous lesions [33 chronic gastritis and 18 chronic gastritis with gastric intestinal metaplasia (GIM)]; 27 of them were associated with H. pylori infection. RESULTS: MT expression was dramatically increased while p21 expression was dramatically decreased from chronic gastritis to GIM to GC. In precancerous lesions, H. pylori-positive cases had significantly higher MT expression and lower p21 expression compared to H. pylori-negative cases. In GCs, decreased expression of both MT and p21 was associated with high-grade and advanced-stage cancers. CONCLUSIONS: Both MT and p21 may have a role in the development and progression of GC, and both proteins may be useful for selecting targeted therapy for GC patients.

Regeneration potential of bone marrow derived mesenchymal stem cells and platelet rich plasma (PRP) on irradiation-induced damage of submandibular salivary gland in albino rats.

Radiation-induced damage to salivary glands (SG) is a consequence of radiotherapy for head and neck cancers. Recovery of the irradiated SG has been studied using various regenerative approaches. This study aims to compare the regenerative potentials of platelet-rich plasma (PRP) and bone marrow mononuclear cells (BMMCs) on irradiated rat submandibular salivary glands (SMD). 32 healthy male albino rats were irradiated with a single dose of 6 Gy then classified into four groups. Group A received no treatment while the other 3 groups were injected 24 h post-radiation with a single dose of either; BMMCs (Group B), PRP (Group C), or BMMCs suspended in PRP (Group D). SMD regeneration was assessed in terms of histological changes and TGF- ß1 gene expression. The results showed that compared to the untreated group all groups showed successful regeneration with group D showing the best results. A statistically significant increase in the surface area of acini and TGF- ß1 gene expression was observed in group D, followed by group C, then B. Our results prove that using PRP and BMMCs could be promising in decreasing irradiation side effects on SG. Moreover, combining PRP and BMMCs gives better effects compared to each therapy alone.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks. One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.

Field performance of three Ebola rapid diagnostic tests used during the 2018-20 outbreak in the eastern Democratic Republic of the Congo: a retrospective, multicentre observational study.

BACKGROUND: The Democratic Republic of the Congo has confronted 13 outbreaks of Ebola virus disease since 1976. Rapid diagnostic tests (RDTs) detecting viral antigens have been developed to circumvent difficulties encountered with RT-PCR for diagnosis in remote low-resource settings, but there is still uncertainty about their performance characteristics and usability during outbreaks. We aimed to assess the field performance of three antigen detection RDTs compared with the gold-standard Cepheid GeneXpert Ebola assay results. METHODS: We conducted a retrospective, multicentre observational study using complete and de-identified databases of five mobile laboratories (managed by the Institut National de Recherche Biomédicale) to assess the performance of three Ebola virus disease RDTs (QuickNavi-Ebola, OraQuick Ebola Rapid Antigen Test, and Coris EBOLA Ag K-SeT rapid test) run on blood samples of patients with suspected Ebola virus disease in direct comparison with the Cepheid GeneXpert Ebola assay reference test during the 2018-20 outbreak in the eastern Democratic Republic of the Congo. We estimated the sensitivity and specificity of each test through generalised linear mixed models against the GeneXpert Ebola assay reference test and corrected for cycle threshold value and random site effects. FINDINGS: 719 (7·9%) of 9157 samples had a positive GeneXpert Ebola assay result. The QuickNavi-Ebola RDT had a sensitivity of 87·4% (95% CI 63·6-96·8) around the mean cycle threshold value and a specificity of 99·6% (99·3-99·8). The OraQuick Ebola Rapid Antigen Test had a sensitivity of 57·4% (95% CI 38·8-75·8) and specificity of 98·3% (97·5-99·0), and the Coris EBOLA Ag K-SeT rapid test had a sensitivity of 38·9% (23·0-63·6) against the GeneXpert Ebola assay reference and specificity of 97·4% (85·3-99·6). The QuickNavi-Ebola RDT showed a robust performance with good sensitivity, particularly with increasing viral loads (ie, low cycle threshold values), and specificity. INTERPRETATION: The three RDTs evaluated did not achieve the desired sensitivity and specificity of the WHO target product profile. Although the RDTs cannot triage and rule out Ebola virus infection among clinical suspects, they can still help to sort people with suspected Ebola virus disease into high-risk and low-risk groups while waiting for GeneXpert Ebola assay reference testing. FUNDING: None. TRANSLATION: For the French translation of the abstract see Supplementary Materials section.