Saliva-Based, COVID-19 RT-PCR Pooled Screening Strategy to Keep Schools Open

Background: As of March 2020, governments throughout the world implemented business closures, work from home policies, and school closures due to exponential increase of coronavirus disease 2019 (COVID-19) cases, leaving only essential workers being able to work on site. For most of the children and adolescent school closures during the first lockdown had significant physical and psychosocial consequences. Here, we describe a comprehensive Return to School program based on a behavior safety protocol combined with the use of saliva-based reverse transcriptase-polymerase chain reaction (RT-PCR) pooled screening technique to keep schools opened. Methods: The program had 2 phases: before school (safety and preparation protocols) and once at school (disease control program: saliva-based RT-PCR pooled screening protocol and contact tracing). Pooling: Aliquots of saliva from 24 individuals were pooled and 1 RT-PCR test was performed. If positive, the initial 24-pool was then retested (12 pools of 2). Individual RT-PCR tests from saliva samples from positive pools of 2 were performed to get an individual diagnosis. Results: From August 31 until December 20, 2020 (16-wk period) a total of 3 pools, and subsequent 3 individual diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease were reported (2 teachers and 1 staff). Conclusion: Until COVID-19 vaccine can be administered broadly to all-age children, saliva-based RT-PCR pooling testing is the missing piece we were searching for to keep schools opened.

Engineered cell differentiation and sexual reproduction in probiotic and mating yeasts

G protein-coupled receptors (GPCRs) enable cells to sense environmental cues and are indispensable for coordinating vital processes including quorum sensing, proliferation, and sexual reproduction. GPCRs comprise the largest class of cell surface receptors in eukaryotes, and for more than three decades the pheromone-induced mating pathway in baker's yeast Saccharomyces cerevisiae has served as a model for studying heterologous GPCRs (hGPCRs). Here we report transcriptome profiles following mating pathway activation in native and hGPCR-signaling yeast, and use a model-guided approach to correlate gene expression to morphological changes. From this we demonstrate mating between haploid cells armed with hGPCRs and endogenous biosynthesis of their cognate ligands. Furthermore, we devise a ligand-free screening strategy for hGPCR compatibility with the yeast mating pathway and enable hGPCR-signaling in the probiotic yeast Saccharomyces boulardii. Combined, our findings enable new means to study mating, hGPCR-signaling, and cell-cell communication in a model eukaryote and yeast probiotics.

Virtual-Ligand-Assisted Screening Strategy to Discover Enabling Ligands for Transition Metal Catalysis

The ligand screening process, in which an optimal ligand for a reaction of interest is identified from an enormous and diverse set of candidate molecules, is of particular importance in the development of transition metal catalysis. Conventionally, this process has been performed by experimental trial-and-error cycles, which require significant time and resources. Herein, we report a novel strategy called “virtual-ligand-assisted (VLA) screening” that enables practical in silico ligand screening based on the transition state theory. We developed a virtual ligand, PCl*3, which parameterizes both the electronic and steric effects of monodentate phosphorus(III) ligands in quantum chemical calculations, and used it to assess how these effects perturb the energy profile of a reaction. This parameter-based ligand screening approach allowed us to identify the optimal electronic and steric effects for a reaction of interest, thereby affording guiding principles for rational ligand design. The VLA screening strategy was demonstrated for the selectivity-determining step of the rhodium-catalyzed hydroformylation of a terminal olefin, and phosphorus(III) ligands with potentially high linear or branched selectivities were designed. These findings indicate that VLA screening is a promising approach for streamlining the ligand screening process.

Brief family history questionnaire to screen for Lynch syndrome in women with newly diagnosed non-serous, non-mucinous ovarian cancers

ObjectivesWhile ovarian cancer is the third most common Lynch syndrome-associated cancer in women, there is no established screening strategy to identify Lynch syndrome in this population. The objective of this study was to assess whether the 4-item brief Family History Questionnaire can be used as a screening tool to identify women with ovarian cancer at risk of Lynch syndrome.MethodsIn this prospective cohort study, participants with newly diagnosed non-serous, non-mucinous ovarian cancer completed the brief Family History Questionnaire, extended Family History Questionnaire, and had tumors assessed with immunohistochemistry for mismatch repair proteins, MLH1 methylation, and microsatellite instability testing. All underwent universal germline testing for Lynch syndrome. Performance characteristics were compared between the brief Family History Questionnaire, extended Family History Questionnaire, immunohistochemistry±MLH1 methylation, and microsatellite instability testing.ResultsOf 215 participants, 169 (79%) were evaluable with both the brief Family History Questionnaire and germline mutation status; 12 of these 169 were confirmed to have Lynch syndrome (7%). 10 of 12 patients (83%) with Lynch syndrome were correctly identified by the brief Family History Questionnaire, compared with 6 of 11 (55%) by the extended Family History Questionnaire, 11 of 13 (85%) by immunohistochemistry±MLH1 methylation, and 9 of 11 (82%) by microsatellite instability testing. The sensitivity, specificity, positive predictive values, and negative predictive values of the brief Family History Questionnaire were 83%, 65%, 15%, and 98%, respectively. A combined approach with immunohistochemistry and the brief Family History Questionnaire correctly identified all 12 patients with Lynch syndrome. The brief Family History Questionnaire was more sensitive than the extended Family History Questionnaire and took <10 min for each patient to complete.ConclusionsThe brief Family History Questionnaire alone or combined with immunohistochemistry may serve as an adequate screening strategy, especially in centers without access to universal tumor testing.

Factors associated with positive predictive value of preliminary screening in a two-step screening strategy for colorectal neoplasms in China

Background The positive predictive value (PPV) of high risk factor questionnaire (HRFQ) plus fecal immunochemical test (FIT) as preliminary screening strategy for colorectal-related neoplasia is relatively low. We aim to explore independent factors associated with PPVs of HRFQ combined FIT for selecting high risk individuals for colonoscopy. Methods A total of 6971 residents were enrolled in a community-based screening program. Participants who had positive results of HRFQ and/or FIT and subsequently received colonoscopy were involved. The associations of socio-demographic factors, lifestyle behaviors, and high risk factors of colorectal cancer with PPVs of HRFQ, FIT, and their combination were evaluated by multivariable logistic regression models. Results Among 572 involved cases, 249 (43.5%) colorectal neoplasms were detected by colonoscopy, including 71 advanced adenoma (12.4%) and 9 colorectal cancer (CRC) (1.6%). The PPVs of preliminary screening were 43.5% for total colorectal neoplasms, 14.0% for advanced neoplasm, and 1.6% for CRC. Adding positive HRFQ to FIT could improve the PPV from 3.5 to 8.0% for detecting CRC. Preliminarily screened positive individuals who were males [adjusted odds ratio (AOR): 1.95, 95% CI 1.31, 2.90; p < 0.001], elders (> 60 years) (AOR: 1.70, 95% CI 1.17, 2.46; p = 0.005), or ex-/current smokers (AOR: 3.04, 95% CI 1.31, 7.09; p = 0.10) had higher odds of PPVs of detecting colorectal neoplasms. Conclusions Combining HRFQ and FIT could largely improve PPVs for screening advanced neoplasm and CRC. Gender and age-specific FIT cut-off values as well as initiating ages for CRC screening might be recommended to improve the accuracy and effectiveness of current screening algorithm.

Discovery of EDA-Complex Photocatalyzed Reactions Using Multidimensional Image Processing: Iminophosphorane Synthesis as a Case Study

Herein, we report a multidimensional screening strategy for the discovery of EDA-complex photocatalyzed reactions using only photographic devices (webcam, cellphone) and TLC analysis. An algorithm was designed to identify automatically EDA-complex reactive mixtures in solution from digital image processing in a 96-wells microplate and by TLC-analysis. The code highlights the region of absorption of the mixture in the visible spectrum, and the quantity of the color change through grayscale values. Furthermore, the code identifies automatically the blurs on the TLC plate and classifies the mixture as colorimetric reactions, non-reactive or potentially reactive EDA mixtures. This strategy allowed us to discover and then optimize a new EDA-mediated approach for obtaining iminophosphoranes in up to 90% yield.

Modeling the Impact of Screening on the Transmission Dynamics of Human Papillomavirus with Optimal Control

In this study, a nonlinear deterministic mathematical model of Human Papillomavirus was formulated. The model is studied qualitatively using the stability theory of differential equations. The model is analyzed qualitatively for validating the existence and stability of disease ¬free and endemic equilibrium points using a basic reproduction number that governs the disease transmission. It's observed that the model exhibits a backward bifurcation and the sensitivity analysis is performed. The optimal control problem is designed by applying Pontryagin maximum principle with three control strategies viz. prevention strategy, treatment strategy, and screening strategy. Numerical results of the optimal control model reveal that a combination of prevention, screening, and treatment is the most effective strategy to wipe out the disease in the community.

Comparative Chiral Separation of Thalidomide Class of Drugs Using Polysaccharide-Type Stationary Phases with Emphasis on Elution Order and Hysteresis in Polar Organic Mode

The enantioseparation of four phthalimide derivatives (thalidomide, pomalidomide, lenalidomide and apremilast) was investigated on five different polysaccharide-type stationary phases (Chiralpak AD, Chiralpak AS, Lux Amylose-2, Chiralcel OD and Chiralcel OJ-H) using neat methanol (MeOH), ethanol (EtOH), 1-propanol (PROP), 2-propanol (IPA) and acetonitrile (ACN) as polar organic mobile phases and also in combination. Along with the separation capacity of the applied systems, our study also focuses on the elution sequences, the effect of mobile phase mixtures and the hysteresis of retention and selectivity. Although on several cases extremely high resolutions (Rs > 10) were observed for certain compounds, among the tested conditions only Chiralcel OJ-H column with MeOH was successful for baseline-separation of all investigated drugs. Chiral selector- and mobile-phase-dependent reversals of elution order were observed. Reversal of elution order and hysteresis of retention and enantioselectivity were further investigated using different eluent mixtures on Chiralpak AD, Chiralcel OD and Lux Amylose-2 column. In an IPA/MeOH mixture, enantiomer elution-order reversal was observed depending on the eluent composition. Furthermore, in eluent mixtures, enantioselectivity depends on the direction from which the composition of the eluent is approached, regardless of the eluent pair used on amylose-based columns. Using a mixture of polar alcohols not only the selectivities but the enantiomer elution order can also be fine-tuned on Chiralpak AD column, which opens up the possibility of a new type of chiral screening strategy.

SARS-CoV-2 detection in multi-sample pools in a real pandemic scenario: a screening strategy of choice for active surveillance

Background The current COVID-19 pandemic has overloaded the diagnostic capacity of laboratories by the gold standard method rRT-PCR. This disease has a high spread rate and almost a quarter of infected individuals never develop symptoms. In this scenario, active surveillance is crucial to stop the virus propagation. Methods Between July 2020 and April 2021, 11580 oropharyngeal swab samples collected in closed and semi-closed institutions were processed for SARS-CoV-2 detection in pools, implementing this strategy for the first time in Cordoba, Argentina. Five-sample pools were constituted before nucleic acid extraction and amplification by rRT-PCR. Comparative analysis of cycle threshold (Ct) values from positive pools and individual samples along with a cost-benefit report of the whole performance of the results was performed. Results From 2314 5-sample pools tested, 158 were classified as positive (6.8%), 2024 as negative (87.5%), and 132 were categorized as indeterminate (5.7%). The Ct value shift due to sample dilution showed an increase in Ct of 2.6 ±1.53 cycles for N gene and 2.6 ±1.78 for ORF1ab gene. Overall, 290 pools were disassembled and 1450 swabs were analyzed individually. This strategy allowed correctly identifying 99.8% of the samples as positive (7.6%) or negative (92.2%), avoiding the execution of 7,806 rRT-PCR reactions which represents a cost saving of 67.5%. Conclusion This study demonstrates the feasibility of pooling samples to increase the number of tests performed, helping to maximize molecular diagnostic resources and reducing the work overload of specialized personnel during active surveillance of the COVID-19 pandemic.