Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms.

Control measures are being introduced globally to reduce the prevalence of antibiotic resistance (ABR) in bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in bacterial species with the potential to be key opportunistic human pathogens, such as Escherichia coli, on South American farms. Working with 30 dairy cattle farms and 40 pig farms across two provinces in central-eastern Argentina, we report a comprehensive genomic analysis of third-generation cephalosporin-resistant (3GC-R) E. coli, which were recovered from 34.8% (cattle) and 47.8% (pigs) of samples from fecally contaminated sites. Phylogenetic analysis revealed substantial diversity suggestive of long-term horizontal and vertical transmission of 3GC-R mechanisms. CTX-M-15 and CTX-M-2 were more often produced by isolates from dairy farms, while CTX-M-8 and CMY-2 and co-carriage of amoxicillin/clavulanate resistance and florfenicol resistance were more common in isolates from pig farms. This suggests different selective pressures for antibiotic use in these two animal types. We identified the ß-lactamase gene blaROB, which has previously only been reported in the family Pasteurellaceae, in 3GC-R E. coli. blaROB was found alongside a novel florfenicol resistance gene, ydhC, also mobilized from a pig pathogen as part of a new composite transposon. As the first comprehensive genomic survey of 3GC-R E. coli in Argentina, these data set a baseline from which to measure the effects of interventions aimed at reducing on-farm ABR and provide an opportunity to investigate the zoonotic transmission of resistant bacteria in this region. IMPORTANCE: Little is known about the ecology of critically important antibiotic resistance among bacteria with the potential to be opportunistic human pathogens (e.g., Escherichia coli) on South American farms. By studying 70 pig and dairy cattle farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli and 3GC-R plasmids were diverse, suggestive of long-term circulation in this region. We identified the de novo mobilization of the resistance gene blaROB from pig pathogens into E. coli on a novel mobile genetic element, which shows the importance of surveying poorly studied regions for antibiotic resistance that might impact human health.

The multiple-stimulus-without-replacement preference assessment tool and its predictive validity.

This study demonstrates the use of two web-based programs, one to identify video preferences and the other to assess their reinforcing effects. We used the Multiple-Stimulus-Without-Replacement Preference Assessment Tool (MSWO PAT) to identify the video preference hierarchies of seven participants, ages 4-11 years old. We then used a customized reinforcer assessment program that arranged a concurrent-chains preparation with programmed conjugate schedules of reinforcement. Button presses emitted by participants modulated the quality (volume and opacity) of selected videos on a moment-to-moment basis, allowing us to identify the reinforcing effects of the videos in little time. The results showed that the preference assessment had predictive value for five of seven participants. We discuss the MSWO PAT, parameters that may affect the identification of preferences and the use of conjugate schedules to identify reinforcers.

GITR and TIGIT immunotherapy provokes divergent multicellular responses in the tumor microenvironment of gastrointestinal cancers.

BACKGROUND: Understanding the mechanistic effects of novel immunotherapy agents is critical to improving their successful clinical translation. These effects need to be studied in preclinical models that maintain the heterogenous tumor microenvironment (TME) and dysfunctional cell states found in a patient's tumor. We investigated immunotherapy perturbations targeting co-stimulatory molecule GITR and co-inhibitory immune checkpoint TIGIT in a patient-derived ex vivo system that maintains the TME in its near-native state. Leveraging single-cell genomics, we identified cell type-specific transcriptional reprogramming in response to immunotherapy perturbations. METHODS: We generated ex vivo tumor slice cultures from fresh surgical resections of gastric and colon cancer and treated them with GITR agonist or TIGIT antagonist antibodies. We applied paired single-cell RNA and TCR sequencing to the original surgical resections, control, and treated ex vivo tumor slice cultures. We additionally confirmed target expression using multiplex immunofluorescence and validated our findings with RNA in situ hybridization. RESULTS: We confirmed that tumor slice cultures maintained the cell types, transcriptional cell states and proportions of the original surgical resection. The GITR agonist was limited to increasing effector gene expression only in cytotoxic CD8 T cells. Dysfunctional exhausted CD8 T cells did not respond to GITR agonist. In contrast, the TIGIT antagonist increased TCR signaling and activated both cytotoxic and dysfunctional CD8 T cells. This included cells corresponding to TCR clonotypes with features indicative of potential tumor antigen reactivity. The TIGIT antagonist also activated T follicular helper-like cells and dendritic cells, and reduced markers of immunosuppression in regulatory T cells. CONCLUSIONS: We identified novel cellular mechanisms of action of GITR and TIGIT immunotherapy in the patients' TME. Unlike the GITR agonist that generated a limited transcriptional response, TIGIT antagonist orchestrated a multicellular response involving CD8 T cells, T follicular helper-like cells, dendritic cells, and regulatory T cells. Our experimental strategy combining single-cell genomics with preclinical models can successfully identify mechanisms of action of novel immunotherapy agents. Understanding the cellular and transcriptional mechanisms of response or resistance will aid in prioritization of targets and their clinical translation.

Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer.

In this proof-of-concept study, we developed a single-cell method that provides genotypes of somatic alterations found in coding regions of messenger RNAs and integrates these transcript-based variants with their matching cell transcriptomes. We used nanopore adaptive sampling on single-cell complementary DNA libraries to validate coding variants in target gene transcripts, and short-read sequencing to characterize cell types harboring the mutations. CRISPR edits for 16 targets were identified using a cancer cell line, and known variants in the cell line were validated using a 352-gene panel. Variants in primary cancer samples were validated using target gene panels ranging from 161 to 529 genes. A gene rearrangement was also identified in one patient, with the rearrangement occurring in two distinct tumor sites.

Sex Differences in Immune Cell Infiltration and Hematuria in SCI-Induced Hemorrhagic Cystitis.

Rats manifest a condition called hemorrhagic cystitis after spinal cord injury (SCI). The mechanism of this condition is unknown, but it is more severe in male rats than in female rats. We assessed the role of sex regarding hemorrhagic cystitis and pathological chronic changes in the bladder. We analyzed the urine of male and female Sprague-Dawley and Fischer 344 rats after experimental spinal cord contusion, including unstained microscopic inspections of the urine, differential white blood cell counts colored by the Wright stain, and total leukocyte counts using fluorescent nuclear stains. We examined bladder histological changes in acute and chronic phases of SCI, using principal component analysis (PCA) and clustered heatmaps of Pearson correlation coefficients to interpret how measured variables correlated with each other. Male rats showed a distinct pattern of macroscopic hematuria after spinal cord injury. They had higher numbers of red blood cells with significantly more leukocytes and neutrophils than female rats, particularly hypersegmented neutrophils. The histological examination of the bladders revealed a distinct line of apoptotic umbrella cells and disrupted bladder vessels early after SCI and progressive pathological changes in multiple bladder layers in the chronic phase. Multivariate analyses indicated immune cell infiltration in the bladder, especially hypersegmented neutrophils, that correlated with red blood cell counts in male rats. Our study highlights a hitherto unreported sex difference of hematuria and pathological changes in males and females' bladders after SCI, suggesting an important role of immune cell infiltration, especially neutrophils, in SCI-induced hemorrhagic cystitis.

Validation of a new strategy for the identification of SARS-CoV-2 variants by sequencing the spike gene by Sanger.

INTRODUCTION: The emergence of multiple variants of SARS-CoV-2 during the COVID-19 pandemic is of great world concern. Until now, their analysis has mainly focused on next-generation sequencing. However, this technique is expensive and requires sophisticated equipment, long processing times, and highly qualified technical personnel with experience in bioinformatics. To contribute to the analysis of variants of interest and variants of concern, increase the diagnostic capacity, and process samples to carry out genomic surveillance, we propose a quick and easy methodology to apply, based on Sanger sequencing of 3 gene fragments that code for protein spike. METHODS: Fifteen positive samples for SARS-CoV-2 with a cycle threshold below 25 were sequenced by Sanger and next-generation sequencing methodologies. The data obtained were analyzed on the Nextstrain and PANGO Lineages platforms. RESULTS: Both methodologies allowed the identification of the variants of interest reported by the WHO. Two samples were identified as Alpha, 3 Gamma, one Delta, 3 Mu, one Omicron, and 5 strains were close to the initial Wuhan-Hu-1 virus isolate. According to in silico analysis, key mutations can also be detected to identify and classify other variants not evaluated in the study. CONCLUSION: The different SARS-CoV-2 lineages of interest and concern are classified quickly, agilely, and reliably with the Sanger sequencing methodology.

Validación de una nueva estrategia para la identificación de variantes de SARS-CoV-2 mediante secuenciación del gen espiga por Sanger / Validation of a new strategy for the identification of SARS-CoV-2 variants by sequencing the spike gene by Sanger

Introducción: La aparición de múltiples variantes del SARS-CoV-2 durante la pandemia de COVID-19 es motivo de gran preocupación mundial. Hasta el momento, su análisis se ha centrado principalmente en la secuenciación de nueva generación. Sin embargo, esta técnica es costosa y requiere equipos sofisticados, largos tiempos de procesamiento y personal técnico altamente cualificado con experiencia en bioinformática. Para contribuir al análisis de variantes de interés y de preocupación, aumentar la capacidad diagnóstica y procesar muestras para realizar vigilancia genómica, proponemos una metodología rápida y fácil de aplicar, basada en la secuenciación Sanger de 3 fragmentos del gen que codifica para la proteína espiga. Métodos: Se secuenciaron 15 muestras positivas para SARS-CoV-2 con un valor de umbral de ciclo inferior a 25 por metodologías Sanger y secuenciación de nueva generación. Los datos obtenidos fueron analizados en las plataformas Nextstrain y PANGO Lineages. Resultados: Ambas metodologías permitieron identificar las variantes de interés reportadas por la OMS. Se identificaron 2 muestras como alfa, 3 gamma, una delta, tres mu, una ómicron y 5 cepas cercanas al aislado inicial del virus Wuhan-Hu-1. Según el análisis in silico, también se pueden detectar mutaciones clave para identificar y clasificar otras variantes no evaluadas en el estudio. Conclusión: Los diferentes linajes de interés y preocupación de SARS-CoV-2 se clasifican de forma rápida, ágil y fiable con la metodología de secuenciación de Sanger.(AU)

Introduction: The emergence of multiple variants of SARS-CoV-2 during the COVID-19 pandemic is of great world concern. Until now, their analysis has mainly focused on next-generation sequencing. However, this technique is expensive and requires sophisticated equipment, long processing times, and highly qualified technical personnel with experience in bioinformatics. To contribute to the analysis of variants of interest and variants of concern, increase the diagnostic capacity, and process samples to carry out genomic surveillance, we propose a quick and easy methodology to apply, based on Sanger sequencing of 3 gene fragments that code for protein spike. Methods: Fifteen positive samples for SARS-CoV-2 with a cycle threshold below 25 were sequenced by Sanger and next-generation sequencing methodologies. The data obtained were analyzed on the Nextstrain and PANGO Lineages platforms. Results: Both methodologies allowed the identification of the variants of interest reported by the WHO. Two samples were identified as Alpha, 3 Gamma, one Delta, 3 Mu, one Omicron, and 5 strains were close to the initial Wuhan-Hu-1 virus isolate. According to in silico analysis, key mutations can also be detected to identify and classify other variants not evaluated in the study. Conclusion: The different SARS-CoV-2 lineages of interest and concern are classified quickly, agilely, and reliably with the Sanger sequencing methodology.(AU)

Fuzzy Control Application to an Irrigation System of Hydroponic Crops under Greenhouse: Case Cultivation of Strawberries (Fragaria Vesca).

Hydroponics refers to a modern set of agricultural techniques that do not require the use of natural soil for plant germination and development. These types of crops use artificial irrigation systems that, together with fuzzy control methods, allow plants to be provided with the exact amount of nutrients for optimal growth. The diffuse control begins with the sensorization of the agricultural variables that intervene in the hydroponic ecosystem, such as the environmental temperature, electrical conductivity of the nutrient solution and the temperature, humidity, and pH of the substrate. Based on this knowledge, these variables can be controlled to be within the ranges required for optimal plant growth, reducing the risk of a negative impact on the crop. This research takes, as a case study, the application of fuzzy control methods to hydroponic strawberry crops (Fragaria vesca). It is shown that, under this scheme, a greater foliage of the plants and a larger size of the fruits are obtained in comparison with natural cultivation systems in which irrigation and fertilization are carried out by default, without considering the alterations in the aforementioned variables. It is concluded that the combination of modern agricultural techniques such as hydroponics and diffuse control allow us to improve the quality of the crops and the optimization of the required resources.

GITR and TIGIT immunotherapy provokes divergent multi-cellular responses in the tumor microenvironment of gastrointestinal cancers.

Understanding the cellular mechanisms of novel immunotherapy agents in the human tumor microenvironment (TME) is critical to their clinical success. We examined GITR and TIGIT immunotherapy in gastric and colon cancer patients using ex vivo slice tumor slice cultures derived from cancer surgical resections. This primary culture system maintains the original TME in a near-native state. We applied paired single-cell RNA and TCR sequencing to identify cell type specific transcriptional reprogramming. The GITR agonist was limited to increasing effector gene expression only in cytotoxic CD8 T cells. The TIGIT antagonist increased TCR signaling and activated both cytotoxic and dysfunctional CD8 T cells, including clonotypes indicative of potential tumor antigen reactivity. The TIGIT antagonist also activated T follicular helper-like cells and dendritic cells, and reduced markers of immunosuppression in regulatory T cells. Overall, we identified cellular mechanisms of action of these two immunotherapy targets in the patients' TME.

Neutralizing Antibodies as Predictors of Vaccine Breakthrough Infection in Healthcare Workers Vaccinated with or without a Heterologous Booster Dose: A Cohort Study during the Third COVID-19 Wave in Peru.

We evaluated neutralizing antibody (NAbs) levels as a protective factor against vaccine breakthrough infection (VBI) in healthcare workers (HCWs) during the third COVID-19 wave in Peru. This retrospective cohort study employed the information from a private laboratory in Lima (Peru) of HCW who received only two BBIBP-CorV vaccines or (additionally) a heterologous booster with BNT162b2. We evaluated the association between the VBI and the levels of NAbs at 21, 90, 180, and 210 days after the BBIBP-CorV second dose. NAbs were calculated with the cPass™ SARS-CoV-2 Neutralization Antibody Detection kit (surrogate virus neutralization test (sVNT)) and the Elecsys® anti-SARS-CoV-2 S Test. Of the 435 HCW evaluated, 31.72% had an infection previous to vaccination, 68.28% received a booster dose, and 23.21% had a VBI during the third wave. The variables associated with a lower risk of VBI were male sex (aRR: 0.43) and those who had (180 days after BBIBP-CorV inoculation) NAbs levels ≥ 60% (aRR: 0.58) and ≥90% (aRR: 0.59) on cPass™, and ≥500 with Elecsys® (aRR: 0.58). HCW whose NAbs persisted at higher levels six months after the BBIBP-CorV showed a lower risk of suffering from a VBI during the third COVID-19 wave.

[Validation of a new strategy for the identification of SARS-CoV-2 variants by sequencing the spike gene by Sanger]. / Validación de una nueva estrategia para la identificación de variantes de SARS-CoV-2 mediante secuenciación del gen espiga por Sanger.

Introduction: The emergence of multiple variants of SARS-CoV-2 during the COVID-19 pandemic is of great world concern. Until now, their analysis has mainly focused on next-generation sequencing. However, this technique is expensive and requires sophisticated equipment, long processing times, and highly qualified technical personnel with experience in bioinformatics. To contribute to the analysis of variants of interest and variants of concern, increase the diagnostic capacity, and process samples to carry out genomic surveillance, we propose a quick and easy methodology to apply, based on Sanger sequencing of 3 gene fragments that code for protein spike. Methods: Fifteen positive samples for SARS-CoV-2 with a cycle threshold below 25 were sequenced by Sanger and next-generation sequencing methodologies. The data obtained were analyzed on the Nextstrain and PANGO Lineages platforms. Results: Both methodologies allowed the identification of the variants of interest reported by the WHO. Two samples were identified as Alpha, 3 Gamma, one Delta, 3 Mu, one Omicron, and 5 strains were close to the initial Wuhan-Hu-1 virus isolate. According to in silico analysis, key mutations can also be detected to identify and classify other variants not evaluated in the study. Conclusion: The different SARS-CoV-2 lineages of interest and concern are classified quickly, agilely, and reliably with the Sanger sequencing methodology.

Species Differences in Blood Lymphocyte Responses After Spinal Cord Injury.

People with spinal cord injury (SCI) get recurrent infections, such as urinary tract infections (UTIs) and pneumonias, that cause mortality and worsen neurological recovery. Over the past decades, researchers have proposed that post-SCI lymphopenia and decreased lymphocyte function increase susceptibility to infections and worsen neurological outcome in humans, leading to a condition called SCI-induced immune depression syndrome (SCI-IDS). In this review, we explore how SCI affects blood lymphocyte homeostasis and function in humans and rodents. Understanding how SCI affects blood lymphocytes will help the management of recurrent infections in spinal cord injured people and shed light on the clinical translation of findings in animal models to humans.

Análisis de tesis médicas de pregrado en una universidad de Perú, 2011-2020: publicación en revistas indizadas y factores asociados / Analysis of undergraduate medical theses at a Peruvian university, 2011-2020: publication in indexed journals and associated factors

Los factores cuantitativos asociados a la publicación de tesis médicas en el pregrado no han sido lo suficientemente estudiados. Por ello, la investigación describió las tasas de publicación, así como la asociación con las características de las tesis, del asesor y del tesista. Se accedió, de manera virtual, a las tesis médicas de pregrado de la Universidad Nacional de San Agustín de Arequipa, Perú, durante el período 2011-2020. Mediante el análisis de regresión logística múltiple, se evaluó la asociación entre la publicación de la tesis en revistas indizadas (Scopus) y la experiencia previa en publicación en revistas indizadas en Scopus del asesor y del tesista, la unidad de análisis, el tamaño de muestra, diseño de estudio, número de páginas, aprobación por el comité de ética de investigación y el sexo del tesista. De 884 tesis solo 12 (1,5 por ciento) se publicaron; lo que constituye el 1,23 por ciento de las tesis publicadas anualmente, con tendencia constante. La experiencia previa en publicación del asesor se asoció con la colocación de las tesis en revistas indizadas (OR = 8,97 [1,70-42,98]; p = 0,005) y en revistas indizadas a Scopus (OR = 14,64 [1,24-336,11]; p = 0,037). Presentar la aprobación del comité de ética de la institución se asoció con publicar la tesis en revistas indizadas a Scopus (OR = 12,45 [1,06-285,94]; p = 0,050). La publicación de tesis médicas de pregrado en esta universidad es baja y constante. Se asoció con tener un asesor de tesis con experiencia previa en publicaciones en revistas indizadas a Scopus y a tener aprobación por comité de ética. Urge implementar estrategias para aumentar la publicación de tesis(AU)

Quantitative factors associated with the publication of undergraduate medical theses have not been sufficiently studied. Therefore, the research described publication rates, as well as the association with thesis, advisor, and thesis writer characteristics. Undergraduate medical theses from the Universidad Nacional de San Agustín de Arequipa, Peru, during the period 2011-2020 were accessed virtually. Multiple logistic regression analysis was used to evaluate the association between thesis publication in indexed journals (Scopus) and the previous publication experience in indexed journals in Scopus of the advisor and the thesis author, the unit of analysis, sample size, study design, number of pages, approval by the research ethics committee and the gender of the thesis author. Out of 884 theses only 12 (1.5percent) were published; this constitutes 1.23percent of the theses published annually, with a constant trend. The previous publication experience of the advisor was associated with the placement of theses in indexed journals (OR = 8.97 [1.70-42.98]; p = 0.005) and in journals indexed to Scopus (OR = 14.64 [1.24-336.11]; p = 0.037). Presenting the approval of the institution's ethics committee was associated with publishing the thesis in journals indexed to Scopus (OR = 12.45 [1.06-285.94]; p = 0.050). Publication of undergraduate medical theses at this university is low and consistent. It was associated with having a thesis advisor with previous experience in publishing in Scopus-indexed journals and having approval by an ethics committee. There is an urgent need to implement strategies to increase thesis publication(AU)

CHL1-Deficient and Wild-Type Male Mice do Not Differ in Locomotor Recovery from Spinal Cord Injury.

CHL1 is a close homolog of L1, a cell adhesion molecule that plays major roles in neural and tumor cell functions. We had found that young adult female mice deficient in CHL1 recovered better than their wild-type female littermates after thoracic Spinal Cord Injury (SCI). This observation was surprising, because CHL1 increases neurite outgrowth in vitro. Injury of adult mouse central and peripheral nervous systems upregulate CHL1 expression in neurons and astrocytes, consistent with CHL1's pro-active, homophilic interaction between CHL1 surface molecules in wild-type mice. After SCI, CHL1 expression was observed to increase in the glial scar, areas of axonal regrowth and remodeling of neural circuits. These observations were made only in females, and we therefore sought to analyze SCI in CHL1-deficient male mice. We now show that CHL1-deficient males did not recover better or worse than their male wild-type littermates. Primary and secondary lesion volumes were similar in the two genotypes, as seen in female mice which were studied in parallel with male mice. Assessment of peripheral leukocytes showed a significant increase in numbers of blood neutrophils at 24 h after SCI in males, but not in females. Lymphocyte numbers in mutant males increased slightly, but numbers of lymphocytes or monocytes did not differ significantly between males or females. These results indicate that CHL1-deficient males and females differ in the number of neutrophils but not lymphocytes or monocytes, suggesting that the difference between males and females is unlikely due to differences in leukocytes.

Validación de una técnica de PCR dúplex usando el gen E y RNasa P para el diagnóstico de SARS-CoV-2 / Validation of a duplex PCR technique using the gen E and RNase P for the diagnosis of SARS-CoV-2

Introducción: El estándar de diagnóstico para SARS-CoV-2 es la reacción en cadena de la polimerasa (PCR). La Organización Mundial de la Salud recomendó el protocolo de Charité-Berlín para el diagnóstico de COVID-19; esta metodología implica tres PCR, limitando la capacidad de procesamiento y retrasando los resultados. Con el fin de reducir estas limitaciones, se validó una PCR dúplex para la detección del gen E y RNasa P. Métodos: Se comparó el límite de detección, sensibilidad y especificidad de la técnica de PCR dúplex (gen E más RNasa P), comparada contra el estándar monoplex (gen E), en muestras de ARN de un aislado de SARS-CoV-2 y de 88 especímenes clínicos, con resultados previamente conocidos. Se determinó la repetibilidad y reproducibilidad de los valores de ciclos umbrales (cycle threshold [Ct]), en dos laboratorios independientes de la Facultad de Medicina de la Universidad de Antioquia, usando reactivos y equipos diferentes. Resultados: No hay diferencias significativas (p = 0,84) en los resultados de Ct entre ambas estrategias. Al utilizar como referencia el gen E amplificado en monoplex, el análisis de concordancia demostró fuerte similitud entre las dos estrategias, con un coeficiente kappa de Cohen de 0,89, una sensibilidad del 90%, y una especificidad del 87%. Conclusión: La PCR dúplex no afecta la sensibilidad y especificidad informadas por el protocolo Charité, Berlín, siendo una herramienta útil para el cribado de SARS-CoV-2 en muestras clínicas.(AU)

Introduction: Reverse transcriptase - polymerase chain reaction (RT-PCR) is the standard technique for SARS-CoV-2 diagnosis. The World Health Organization recommends the Charité-Berlin protocol for COVID-19 diagnosis, which requires triple PCR, limiting the process capability of laboratories and delaying the results. In order to reduce these limitations, a duplex PCR is validated for the detection of the E and RNase P genes. Methods: We compared the limit of detection, sensitivity and specificity of the duplex PCR technique (E gene and RNase P) against the monoplex standard (E gene) in RNA samples from a SARS-CoV-2 isolate and 88 clinical specimens with previously known results. The repeatability and reproducibility of the threshold cycle values (Ct) were determined in two independent laboratories of the Faculty of Medicine of the Universidad de Antioquia, using different reagents and real time instruments. Results: There were no significant differences in the Ct results between both techniques (p = 0.84). Using the monoplex PCR of E gene as a reference, the interrater reliability analysis showed similarity between the two techniques, with a kappa coefficient of 0.89, the sensitivity and the specificity of duplex PCR were 90% and 87%, respectively. Conclusions: Duplex PCR does not affect the sensitivity and specificity reported by the Charité, Berlin protocol, being a useful tool for SARS-CoV-2 screening in clinical samples.(AU)

Validation of a duplex PCR technique using the gen E and RNase P for the diagnosis of SARS-CoV-2.

INTRODUCTION: Reverse transcriptase - polymerase chain reaction (RT-PCR) is the standard technique for SARS-CoV-2 diagnosis. The World Health Organization recommends the Charité-Berlin protocol for COVID-19 diagnosis, which requires triple PCR, limiting the process capability of laboratories and delaying the results. In order to reduce these limitations, a duplex PCR is validated for the detection of the E and ribonuclease P genes. METHODS: We compared the limit of detection, sensitivity and specificity of the duplex PCR technique (E gene and Rnasa P) against the monoplex standard (E gene) in RNA samples from a SARS-CoV-2 isolate and 88 clinical specimens with previously known results. The repeatability and reproducibility of the threshold cycle values ​​(Ct) were determined in two independent laboratories of the Faculty of Medicine of the Universidad de Antioquia, using different reagents and real time instruments. RESULTS: There were no significant differences in the Ct results between both techniques (P = .84). Using the monoplex PCR of E gene as a reference, the interrater reliability analysis showed similarity between the two techniques, with a kappa coefficient of 0.89, the sensitivity and the specificity of duplex PCR were 90% and 87%, respectively. CONCLUSIONS: Duplex PCR does not affect the sensitivity and specificity reported by the Charité, Berlin protocol, being a useful tool for SARS-CoV-2 screening in clinical samples.

Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62.

Autophagy is a housekeeping mechanism tasked with eliminating misfolded proteins and damaged organelles to maintain cellular homeostasis. Autophagy deficiency results in increased oxidative stress, DNA damage and chronic cellular injury. Among the core genes in the autophagy machinery, ATG7 is required for autophagy initiation and autophagosome formation. Based on the analysis of an extended pedigree of familial cholangiocarcinoma, we determined that all affected family members had a novel germline mutation (c.2000C>T p.Arg659* (p.R659*)) in ATG7. Somatic deletions of ATG7 were identified in the tumors of affected individuals. We applied linked-read sequencing to one tumor sample and demonstrated that the ATG7 somatic deletion and germline mutation were located on distinct alleles, resulting in two hits to ATG7. From a parallel population genetic study, we identified a germline polymorphism of ATG7 (c.1591C>G p.Asp522Glu (p.D522E)) associated with increased risk of cholangiocarcinoma. To characterize the impact of these germline ATG7 variants on autophagy activity, we developed an ATG7-null cell line derived from the human bile duct. The mutant p.R659* ATG7 protein lacked the ability to lipidate its LC3 substrate, leading to complete loss of autophagy and increased p62 levels. Our findings indicate that germline ATG7 variants have the potential to impact autophagy function with implications for cholangiocarcinoma development.

Nomophobia and Its Associated Factors in Peruvian Medical Students.

Nomophobia is the discomfort caused by not being in contact with a cell phone. Few studies have addressed nomophobia in university students. The study aimed to evaluate nomophobia and its associated factors in Peruvian medical students. We conducted an analytical cross-sectional study on Peruvian medical students between June 2020 and March 2021, using an online survey disseminated through social networks. We analyzed 3139 responses (females: 61.1%, median age: 22 years): 25.7% presented moderate nomophobia and 7.4% severe nomophobia. In the adjusted model, the nomophobia score was lower in students ≥24 years (ß: −4.1, 95% CI: −7.2 to −1.0) and was higher in those who had a mobile internet data plan (ß: 2.9, 0.8 to 5.0), used the cell phone >4 h (ß: 4.5, 2.3 to 6.7), used a smartphone mainly for education (ß: 2.5, 0.2 to 4.8), social networks (ß: 8.2, 5.8 to 10.6) and entertainment (ß: 3.3, 0.5 to 6.1), and those who presented possible anxious (ß: 6.6, 4.3 to 8.9) or depressive (ß: 19.5, 5.2 to 9.6) symptomatology. In conclusion, nomophobia in university students is a frequent and emerging problem, present mainly at younger ages and associated with symptoms of anxiety or depression. Implementing evaluation and early intervention strategies would favor the mental health of university students.