Learning Lessons from the COVID-19 Pandemic-A Qualitative Assessment of the Experiences of Pregnant Latinas Infected with COVID-19 and Their Perspectives on Vaccination.

OBJECTIVES: To examine the experiences of pregnant Hispanic/Latine people with COVID-19, as well as their perspectives on COVID-19 vaccination in pregnancy. METHODS: We interviewed birthing parents who received care from a teaching hospital in California and tested positive for COVID-19 during pregnancy or delivery. We analyzed transcripts using the constant comparative method for analyzing data to using a phenomological epidemiological approach. We used root cause analysis to identify consistent themes across interviews and assess relationships between social determinants of health and COVID-19 infectivity. RESULTS: We interviewed 14 women from November 2021 to June 2022. Participants reported COVID-19 adversely impacted their clinical care and well-being during pregnancy or postpartum. Impacts among Spanish-speaking participants included unexpected financial hardships, challenges navigating in-patient experiences, and difficulty securing reliable childcare. While most participants were at least partially vaccinated, participants also described doubts and concerns about the vaccine. CONCLUSIONS: Our findings suggest that Spanish-speaking Hispanic/Latine patients could benefit from receiving more information about COVID-19 in pregnancy from their healthcare providers. Leveraging familial and social networks, providing reliable information in people's preferred language, and increasing communication through trusted partners may also help combat vaccine hesitancy.

Family cash transfers in childhood and birthing persons and birth outcomes later in life.

Much literature in the US documents an intergenerational transmission of birthing person and perinatal morbidity in socioeconomically disadvantaged groups. A separate line of work indicates that family cash transfers may improve life chances of low-income families well into adulthood. By exploiting a quasi-random natural experiment of a large family cash transfer among a southeastern American Indian (AI) tribe in rural North Carolina, we examine whether a "perturbation" in socioeconomic status during childhood improves birthing person/perinatal outcomes when they become parents themselves. We acquired birth records on 6805 AI and non-AI infants born from 1995 to 2018. Regression methods to examine effect modification tested whether the birthing person's American Indian (AI) status and exposure to the family cash transfer during their childhood years corresponds with improvements in birthing person and perinatal outcomes. Findings show an increase in age at childbearing (coef: 0.15 years, 95% confidence interval [CI]: 0.05, 0.25) and a decrease in pre-pregnancy body mass index (BMI; coef: -0.42, 95% CI: -0.76, -0.09) with increased duration of cash transfer exposure during childhood. The odds of large-for-gestational age at delivery, as well as mean infant birthweight, is also reduced among AI births whose birthing person had relatively longer duration of exposure to the cash transfer. We, however, observe no relation with other birthing person/perinatal outcomes (e.g., tobacco use during pregnancy, preterm birth). In this rural AI population, cash transfers in one generation correspond with improved birthing person and infant health in the next generation.

Anxiety but not menopausal status influences the risk of long-COVID-19 syndrome in women living in Latin America.

OBJECTIVE: To study sociodemographic and clinical factors associated with the long-COVID-19 syndrome among women living in Latin American countries using undirected and directed methods. METHOD: We studied 347 patients with COVID-19 (confirmed by polymerase chain reaction) living in nine Latin American countries between May 2021 and July 2022, including 70 premenopausal, 48 perimenopausal, and 229 postmenopausal women. We compared the sociodemographic and general health information of women with (n = 164) and without (n = 183) the long-COVID-19 syndrome. They also completed the Connor-Davidson Resilience Scale, the Fear of COVID-19 Scale, the Jenkins Sleep Scale, and the Menopause Rating Scale to define the minimum set of variables for adjustment. We designed a directed acyclic graph (DAG) to identify factors related to the long-COVID-19 syndrome. Data were submitted to categorical logistic regression analyses. Results are reported as means and standard deviations or ß-coefficients and 95 % confidence intervals. RESULTS: Women with long-COVID-19 syndrome had a poor lifestyle, severe menopause symptoms, hypertension, insomnia, depression, anxiety, chronic diseases/conditions, risk of hospitalization, sleep disturbance, and low menopause-related quality of life compared to women without the syndrome. The DAG identified the following long-COVID-19 covariates: age, obesity, anxiety, depression, cancer, lifestyle, smoking, and menstrual status. A multivariable logistic model with these covariates indicated that anxiety is the only factor to be significantly associated with long-COVID-19 syndrome, whereas other covariates were confounding factors. There was no significant influence of menopausal status on the long-COVID-19 syndrome. CONCLUSION: Among factors selected by the DAG, only anxiety was significantly associated with the long-COVID-19. There was no significant influence of the menopause status on the long-COVID-19 syndrome in the studied population.

Mercury and selenium in three fish species from a dam 20 months after a mine-tailing spill in the SE Gulf of California ecoregion, Mexico.

During January 2013, a mining spill occurred in the Santa Maria mining region, releasing around 300,000 m3 of tailings on Los Remedios river, which was transported through the San Lorenzo river and finally to El Comedero (EC) dam. Twenty months later, we examined the concentrations of Hg and Se in the muscle, liver, gills, and guts of three fish species (Cyprinus carpio, Oreochromis aureus, Micropterus salmoides) captured in the EC dam to assess the performance of the cleaning operations. A high Se concentration in the liver of all species (carp, 1.2 ± 0.4; tilapia, 3.9 ± 2.1; bass, 3.5 ± 1.1 µg g-1 ww) was consistently observed, while this behavior was only found in the blue tilapia for Hg (0.15 ± 0.11 µg g-1 ww). Tilapia (benthic-detritivorous) exhibited the highest Se concentrations compared to the carp (omnivore) and the largemouth bass (piscivore). In contrast, the largemouth bass had the highest Hg levels in the muscle compared with the other fishes. Such differences could be related to the different metabolism and feeding habits among species. Compared to a tilapia study carried out three months after the mine spill during a mortality event, a decrease was evident in the liver for Se and Hg by 7.2 and 4.7 times, respectively. This reveals that cleaning operations were more efficient for Se and less for Hg, and that a prolonged period was required for the partial recovery of the element levels in fish from sites impacted by mining. Considering the Mexican consumption scenarios for each fish species, it could be concluded that there will be no non-cancer risk by exposure to Hg or Se.

Prenatal anxiety during the pandemic context is related to neurodevelopment of 6-month-old babies.

Prenatal anxiety and depression in pandemic context could introduce changes in the fetal developmental trajectories that, ultimately, could alter the adaptive behaviors of the offspring, potentially affecting, for example, general neurodevelopment. The sample consisted of 105 mother-child dyads, recruited between March and May 2020. The dyads were evaluated longitudinally, prenatally and postnatally (6 months). The Pandemic Impact Questionnaire, the State-Trait Anxiety Inventory, and the Beck-II Depression Inventory were used to assess indicators of maternal anxiety and depression, respectively. Regarding the babies, their mothers responded to Age and Stages: 3, which assesses different dimensions of early neurodevelopment, in addition to a closed questionnaire to identify sociodemographic and maternal and child health variables. A series of mediation models were tested to examine the association between prenatal psychopathology/negative experiences of the pandemic and neurodevelopment. The results indicated that the negative experiences of the pandemic were indirectly associated with the socio-individual and fine motor neurodevelopment of the offspring, through maternal anxiety symptoms, during the third trimester, which functioned as a mediator.  Conclusions: This study provides evidence on the mediating effects of maternal anxiety on infant neurodevelopment in contexts of early adversity. It is important to point out the need to implement public health policies that allow a timely evaluation of neurodevelopmental variables during early childhood, which can implement early interventions to reduce the risks associated with these deficits. What is Known: • Effects of maternal mental health have been reported, effects on child neurodevelopment, in motor, cognitive, linguistic and socio-emotional dimensions. • Contexts of early adversity have been associated with maternal mental health and offspring development. What is New: • The context of pandemic adversity caused by COVID-19 is associated with motor and socio-individual neurodevelopment, mediated by maternal prenatal anxiety.

Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells.

Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.

Development of a machine learning framework for radiation biomarker discovery and absorbed dose prediction.

Background: Molecular radiation biomarkers are an emerging tool in radiation research with applications for cancer radiotherapy, radiation risk assessment, and even human space travel. However, biomarker screening in genome-wide expression datasets using conventional tools is time-consuming and underlies analyst (human) bias. Machine Learning (ML) methods can improve the sensitivity and specificity of biomarker identification, increase analytical speed, and avoid multicollinearity and human bias. Aim: To develop a resource-efficient ML framework for radiation biomarker discovery using gene expression data from irradiated normal tissues. Further, to identify biomarker panels predicting radiation dose with tissue specificity. Methods: A strategic search in the Gene Expression Omnibus database identified a transcriptomic dataset (GSE44762) for normal tissues radiation responses (murine kidney cortex and medulla) suited for biomarker discovery using an ML approach. The dataset was pre-processed in R and separated into train and test data subsets. High computational cost of Genetic Algorithm/k-Nearest Neighbor (GA/KNN) mandated optimization and 13 ML models were tested using the caret package in R. Biomarker performance was evaluated and visualized via Principal Component Analysis (PCA) and dose regression. The novelty of ML-identified biomarker panels was evaluated by literature search. Results: Caret-based feature selection and ML methods vastly improved processing time over the GA approach. The KNN method yielded overall best performance values on train and test data and was implemented into the framework. The top-ranking genes were Cdkn1a, Gria3, Mdm2 and Plk2 in cortex, and Brf2, Ccng1, Cdkn1a, Ddit4l, and Gria3 in medulla. These candidates successfully categorized dose groups and tissues in PCA. Regression analysis showed that correlation between predicted and true dose was high with R2 of 0.97 and 0.99 for cortex and medulla, respectively. Conclusion: The caret framework is a powerful tool for radiation biomarker discovery optimizing performance with resource-efficiency for broad implementation in the field. The KNN-based approach identified Brf2, Ddit4l, and Gria3 mRNA as novel candidates that have been uncharacterized as radiation biomarkers to date. The biomarker panel showed good performance in dose and tissue separation and dose regression. Further training with larger cohorts is warranted to improve accuracy, especially for lower doses.

High Glucose Promotes Inflammation and Weakens Placental Defenses against E. coli and S. agalactiae Infection: Protective Role of Insulin and Metformin.

Placentas from gestational diabetes mellitus (GDM) patients undergo significant metabolic and immunologic adaptations due to hyperglycemia, which results in an exacerbated synthesis of proinflammatory cytokines and an increased risk for infections. Insulin or metformin are clinically indicated for the treatment of GDM; however, there is limited information about the immunomodulatory activity of these drugs in the human placenta, especially in the context of maternal infections. Our objective was to study the role of insulin and metformin in the placental inflammatory response and innate defense against common etiopathological agents of pregnancy bacterial infections, such as E. coli and S. agalactiae, in a hyperglycemic environment. Term placental explants were cultivated with glucose (10 and 50 mM), insulin (50-500 nM) or metformin (125-500 µM) for 48 h, and then they were challenged with live bacteria (1 × 105 CFU/mL). We evaluated the inflammatory cytokine secretion, beta defensins production, bacterial count and bacterial tissue invasiveness after 4-8 h of infection. Our results showed that a GDM-associated hyperglycemic environment induced an inflammatory response and a decreased beta defensins synthesis unable to restrain bacterial infection. Notably, both insulin and metformin exerted anti-inflammatory effects under hyperglycemic infectious and non-infectious scenarios. Moreover, both drugs fortified placental barrier defenses, resulting in reduced E. coli counts, as well as decreased S. agalactiae and E. coli invasiveness of placental villous trees. Remarkably, the double challenge of high glucose and infection provoked a pathogen-specific attenuated placental inflammatory response in the hyperglycemic condition, mainly denoted by reduced TNF-α and IL-6 secretion after S. agalactiae infection and by IL-1ß after E. coli infection. Altogether, these results suggest that metabolically uncontrolled GDM mothers develop diverse immune placental alterations, which may help to explain their increased vulnerability to bacterial pathogens.

Preferencias y factores que influyen en la ingesta alimentaria en universitarios mexicanenses según el sexo / Preferences and factors influencing food intake among Mexican university students according to sex

Fundamentos: El estudio tiene como objetivo describir la preferencia alimentaria de universitarios del Estado de México, México, según el sexo. Métodos: La muestra fue constituida por 270 universitarios pertenecientes al Estado de México, México. Para determinar las preferencias se utilizó el cuestionario para evaluar el comportamiento alimentario en estudiantes mexicanos del área de la salud. Se obtuvieron los resultados a partir de porcentajes y frecuencias. Resultados: Las preferencias se determinan principalmente por el sabor de los alimentos, de ahí que los alimentos dulces sean de gran agrado sobre todo en universitarias. Además, se encontró mayor consumo de carne que cualquier otro alimento consumido durante los tiempos de comida, siendo más elevado en los hombres universitarios. Conclusiones: La alimentación de la muestra universitaria es aparentemente sana, evidenciado por los factores que intervienen en la elección de alimentos, así como también aquellos alimentos que son más de su agrado. (AU)

Background: The study aims to describe the food preference of university students from the State of Mexico, Mexico, according to sex. Methods: The sample consisted of 270 university students from the State of Mexico, Mexico. The questionnaire to evaluate eating behavior in Mexican health students was used to determine preferences. Results were obtained from percentages and frequencies. Results: Preferences are determined mainly by the taste of food, hence sweet foods are very popular, especially among university students. In addition, greater consumption of meat was found than any other food consumedduring mealtimes, being higher in university men. Conclusions: The nutrition of the university sample is apparently healthy, evidenced by the factors involved in the choice of food, as well as those foods that are more to their liking. (AU)

Maternal anxiety, exposure to the COVID-19 pandemic and socioemotional development of offspring.

The COVID-19 pandemic context may predispose mothers to increased maternal psychopathology, which may be associated with offspring socioemotional development. The aim of this study is to analyze the relationships between prenatal anxiety and depression and exposure to the COVID-19 pandemic with offspring socioemotional development, controlling for postnatal anxiety and depression. A total of 105 mother-child dyads were assessed in pre- and postnatal periods. Questionnaires were used to assess the impact of the pandemic, indicators of psychopathology, and the socioemotional development of the offspring. Results suggest that negative pandemic experiences are indirectly associated with offspring socioemotional development via prenatal maternal anxiety symptomatology and after controlling for postnatal anxiety and depression. These indicators predispose to emotional deficits and increase the risks of psychopathological and neurodevelopmental disorders. It is important to adopt health policies that provide timely assessment of development in early childhood to reduce the risks associated with these deficits.

Post-COVID-19 syndrome in a sample of climacteric women living in Latin America.

OBJECTIVE: The aim of this study was to assess resilience, fear of COVID-19, sleep disorders, and menopause-related symptoms after the acute phase of COVID-19 in middle-aged women with positive reverse transcription-polymerase chain reaction and noninfected women. METHODS: This is a cross-sectional, analytical study of climacteric women from 9 Latin American countries, aged 40-64 years, attending a routine health checkup. We evaluated clinical characteristics and used the Connor-Davidson Resilience Scale, the Fear of COVID-19 Scale, the Jenkins Sleep Scale, and the Menopause Rating Scale to evaluate their health. RESULTS: A total of 1,238 women were studied, including 304 who were positive for COVID-19 reverse transcription-polymerase chain reaction. The median (interquartile range) age was 53 (12) years; years of studies, 16 (6); body mass index, 25.6 (5.1) kg/m 2 ; and time since first COVID-19 symptom, 8 (6) months. COVID-19 patients reported fatigability (18.8%), joint and muscular discomfort (14.1%), and anosmia (9.5%). They had a significantly lower resilience score (26.87 ± 8.94 vs 29.94 ± 6.65), higher Fear of COVID-19 score (17.55 ± 7.44 vs 15.61 ± 6.34), and a higher Jenkins Scale score (6.10 ± 5.70 vs 5.09 ± 5.32) compared with control women. A logistic regression model confirmed these results. There was not a significant difference in the total Menopause Rating Scale score, although the odds ratios for both severe menopausal symptoms (1.34; 95% confidence interval, 1.02-1.76) and the use of hypnotics were higher in women with COVID-19 (1.80; 95% confidence interval, 1.29-2.50) compared with those without infection. We found no decrease in studied outcomes between the initial 7 months versus those reported after 8 to 18 months since first COVID-19 symptoms. CONCLUSIONS: COVID-19 climacteric women have sleep disorders, lower resilience and higher fear of COVID-19.

Incidencia de cáncer de mama a 5 años en mujeres con lesiones premalignas / Incidence of breast cancer at 5 years in women with premalignant lesions

Resumen OBJETIVO: Determinar la incidencia acumulada de cáncer de mama a cinco años de seguimiento en pacientes con lesiones preinvasoras o premalignas de la glándula mamaria en un centro de referencia y establecer los factores de riesgo asociados. MATERIALES Y MÉTODOS: Estudio de cohorte retrospectiva efectuado en pacientes atendidas en el Hospital Ángeles Lomas entre los años 2012 a 2016 con diagnóstico, durante su tamizaje mastográfico, de alguna lesión precursora o preinvasora de cáncer de mama. El seguimiento fue a cinco años para determinar la incidencia. Las variables categóricas se expresan en frecuencias y porcentajes. Se utilizó la prueba de χ2 para diferencia de proporciones entre grupos. RESULTADOS: Se obtuvieron 3360 pacientes que acudieron al servicio de Mastología durante el tiempo establecido. Se obtuvieron 245 pacientes con lesiones premalignas pero 30 de ellas no cumplieron con el seguimiento a cinco años y se perdieron en ese tiempo estipulado de vigilancia. Al final quedaron 215 pacientes que cumplieron todos los criterios de inclusión establecidos. La incidencia acumulada global de cáncer de mama invasivo fue que a 5 años el 14.9% de las pacientes con lesiones premalignas tendrá cáncer de mama. El carcinoma lobulillar in situ fue el de mayor incidencia o progresión de cáncer invasor, con un 32.1% a los cinco años, seguido de las lesiones mucocele-like, carcinoma ductal in situ y papiloma intraductal con un 23.1, 21.1 y 17.1%, respectivamente. CONCLUSIONES: El cáncer de mama sigue siendo un problema de salud pública en México y en todo el mundo. Si bien cada vez se dispone de más y mejores programas de tamizaje, ello ha traído consigo otras problemáticas, como las lesiones premalignas o de alto riesgo de carcinogénesis, que han aumentado su incidencia.

Abstract OBJECTIVE: To determine the cumulative incidence of breast cancer at five years of follow-up in patients with preinvasive or premalignant lesions of the mammary gland in a referral canter and to establish the associated risk factors. MATERIALS AND METHODS: Retrospective cohort study carried out in patients seen at Hospital Ángeles Lomas between 2012 and 2016 with a diagnosis, during their mastographic screening, of a precursor or pre-invasive lesion of breast cancer. Categorical variables are expressed in frequencies and percentages. The χ2 test was used for difference of proportions between groups. RESULTS: We obtained 3360 patients who attended the mastology service during the established time. We obtained 245 patients with premalignant lesions but 30 of them did not comply with the five-year follow-up and were lost within the stipulated surveillance period. This left 215 patients who met all the inclusion criteria. The overall cumulative incidence of invasive breast cancer was that at 5 years 14.9% of patients with premalignant lesions will have breast cancer. Lobular carcinoma in situ had the highest incidence or progression of invasive cancer, with 32.1% at 5 years, followed by mucocele-like lesions, ductal carcinoma in situ and intraductal papilloma with 23.1, 21.1 and 17.1%, respectively. CONCLUSIONS: Breast cancer remains a public health problem in Mexico and worldwide. Although more and better screening programmes are becoming available, this has brought with it other problems, such as premalignant or high-risk carcinogenic lesions, which have increased in incidence.

Factors affecting climacteric women with SARS-CoV-2 infection: A multinational Latin America study (REDLINC XI).

OBJECTIVE: To evaluate the association between factors, especially those linked to the climacteric, and a history of COVID-19 infection. METHODS: This was an observational, cross-sectional, and analytical study in which women from ten Latin American countries, aged 40-64, who attended a routine health check-up were invited to participate. A positive history for COVID-19 was based on reverse transcription-polymerase chain reaction reports. We evaluated sociodemographic, clinical, lifestyle, anthropometric variables, and menopausal symptoms using the Menopause Rating Scale (MRS). RESULTS: A total of 1238 women were included for analysis, of whom 304 (24.6 %) had a positive history for COVID-19. The median [interquartile range: IQR] age of participants was 53 [IQR 12] years, duration of formal education was 16 [6] years, body mass index 25.6 [5.1] kg/m2, and total MRS score 10 [13]. In a logistic regression model, factors positively associated with COVID-19 included postmenopausal status and having a family history of dementia (OR: 1.53; 95 % CI: 1.13-2.07, and 2.40; 1.65-3.48, respectively), whereas negatively associated were use of menopausal hormone therapy (current or past), being a housewife, and being nulliparous (OR: 0.47; 95 % CI: 0.30-0.73; 0.72; 0.53-0.97 and 0.56; 0.34-0.92, respectively). Smoking, being sexually active, and use of hypnotics were also factors positively associated with COVID-19. CONCLUSION: Postmenopausal status and a family history of dementia were more frequent among women who had had COVID-19, and the infection was less frequent among current or past menopause hormone therapy users and in those with less physical contact.

PALB2 germline mutations in a multi-gene panel testing cohort of 1905 breast-ovarian cancer patients in Argentina.

PURPOSE: PALB2 variants have been scarcely described in Argentinian and Latin-American reports. In this study, we describe molecular and clinical characteristics of PALB2 mutations found in multi-gene panels (MP) from breast-ovarian cancer (BOC) families in different institutions from Argentina. METHODS: We retrospectively identified PALB2 pathogenic (PV) and likely pathogenic (LPV) variants from a cohort of 1905 MP results, provided by one local lab (Heritas) and SITHER (Hereditary Tumor Information System) public database. All patients met hereditary BOC clinical criteria for testing, according to current guidelines. RESULTS: The frequency of PALB2 mutations is 2.78% (53/1905). Forty-eight (90.5%) are PV and five (9.5%) are LPV. Most of the 18 different mutations (89%) are nonsense and frameshift types and 2 variants are novel. One high-rate recurrent PV (Y551*) is present in 43% (23/53) of the unrelated index cases. From the 53 affected carriers, 94% have BC diagnosis with 14% of bilateral cases. BC phenotype is mainly invasive ductal (78%) with 62% of hormone-receptor positive and 22% of triple negative tumors. Self-reported ethnic background of the cohort is West European (66%) and native Latin-American (20%) which is representative of Buenos Aires and other big urban areas of the country. CONCLUSION: This is the first report describing molecular and clinical characteristics of PALB2 carriers in Argentina. Frequency of PALB2 PV in Argentinian HBOC families is higher than in other reported populations. Y551* is a recurrent mutation that seems to be responsible for almost 50% of PALB2 cases.

TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

BACKGROUND: Transgenic animal models are crucial for the study of gene function and disease, and are widely utilized in basic biological research, agriculture and pharma industries. Since the current methods for generating transgenic animals result in the random integration of the transgene under study, the phenotype may be compromised due to disruption of known genes or regulatory regions. Unfortunately, most of the tools that predict transgene insertion sites from high-throughput data are not publicly available or not properly maintained. RESULTS: We implemented TC-hunter, Transgene-Construct hunter, an open tool that identifies transgene insertion sites and provides simple reports and visualization aids. It relies on common tools used in the analysis of high-throughput data and makes use of chimeric reads and discordant read pairs to identify and support the transgenic insertion site. To demonstrate its applicability, we applied TC-hunter to four transgenic mice samples harboring the human PPM1D gene, a model used in the study of malignant tumor development. We identified the transgenic insertion site in each sample and experimentally validated them with Touchdown-polymerase chain reaction followed by Sanger sequencing. CONCLUSIONS: TC-hunter is an accessible bioinformatics tool that can automatically identify transgene insertion sites from DNA sequencing data with high sensitivity (98%) and precision (92.45%). TC-hunter is a valuable tool that can aid in evaluating any potential phenotypic complications due to the random integration of the transgene and can be accessed at https://github.com/bcfgothenburg/SSF .

Feasibility of Specimen Self-collection in Young Children Undergoing SARS-CoV-2 Surveillance for In-Person Learning.

Importance: There is an urgent need to assess the feasibility of COVID-19 surveillance measures in educational settings. Objective: To assess whether young children can feasibly self-collect SARS-CoV-2 samples for surveillance testing over the course of an academic year. Design, Setting, and Participants: This prospective pilot cohort study was conducted from September 10, 2020, to June 10, 2021, at a K-8 school in San Mateo County, California. The research consisted of quantitative data collection efforts: (1) demographic data collected, (2) student sample self-collection error rates, and (3) student sample self-collection time durations. Students were enrolled in a hybrid learning model, a teaching model in which students were taught in person and online, with students having the option to attend virtually as needed. Data were collected under waiver of consent from students participating in weekly SARS-CoV-2 testing. Main Outcomes and Measures: Errors over time for self-collection of nasal swabs such as contaminated swabs and inadequate or shallow swabbing; time taken for sample collection. Results: Of 296 participants, 148 (50.0%) were boys and 148 (50.0%) were girls. A total of 87 participants (29.2%) identified as Asian; 2 (0.6%), Black or African American; 13 (4.4%), Hispanic/Latinx; 103 (34.6%), non-Hispanic White; 87 (29.2%), multiracial; and 6 (2.0%), other. The median school grade was fourth grade. From September 2020 to March 2021, a total of 4203 samples were obtained from 221 students on a weekly basis, while data on error rates were collected. Errors occurred in 2.7% (n = 107; 95% CI, 2.2%-3.2%) of student encounters, with the highest rate occurring on the first day of testing (20 [10.2%]). There was an overall decrease in error rates over time. From April to June 2021, a total of 2021 samples were obtained from 296 students on a weekly basis while data on encounter lengths were collected. Between April and June 2021, 193 encounters were timed. The mean duration of each encounter was 70 seconds (95% CI, 66.4-73.7 seconds). Conclusions and Relevance: Mastery of self-collected lower nasal swabs is possible for children 5 years and older. Testing duration can be condensed once students gain proficiency in testing procedures. Scalability for larger schools is possible if consideration is given to the resource-intensive nature of the testing and the setting's weather patterns.

PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data.

BACKGROUND: Processed pseudogenes (PΨgs) are disabled gene copies that are transcribed and may affect expression of paralogous genes. Moreover, their insertion in the genome can disrupt the structure or the regulatory region of a gene, affecting its expression level. These events have been identified as occurring mutations during cancer development, thus being able to identify PΨgs and their location will improve their impact on diagnostic testing, not only in cancer but also in inherited disorders. RESULTS: We have implemented PΨFinder (P-psy-finder), a tool that identifies PΨgs, annotates known ones and predicts their insertion site(s) in the genome. The tool screens alignment files and provides user-friendly summary reports and visualizations. To demonstrate its applicability, we scanned 218 DNA samples from patients screened for hereditary colorectal cancer. We detected 423 PΨgs distributed in 96% of the samples, comprising 7 different parent genes. Among these, we confirmed the well-known insertion site of the SMAD4-PΨg within the last intron of the SCAI gene in one sample. While for the ubiquitous CBX3-PΨg, present in 82.6% of the samples, we found it reversed inserted in the second intron of the C15ORF57 gene. CONCLUSIONS: PΨFinder is a tool that can automatically identify novel PΨgs from DNA sequencing data and determine their location in the genome with high sensitivity (95.92%). It generates high quality figures and tables that facilitate the interpretation of the results and can guide the experimental validation. PΨFinder is a complementary analysis to any mutational screening in the identification of disease-causing mutations within cancer and other diseases.

Comparison of online learning designs during the COVID-19 pandemic within bioinformatics courses in higher education.

MOTIVATION: Due to the worldwide COVID-19 pandemic, new strategies had to be adopted to move from classroom-based education to online education, in a very short time. The lack of time to set up these strategies, hindered a proper design of online instructions and delivery of knowledge. Bioinformatics-related training and other onsite practical education, tend to rely on extensive practice, where students and instructors have a face-to-face interaction to improve the learning outcome. For these courses to maintain their high quality when adapted as online courses, different designs need to be tested and the students' perceptions need to be heard. RESULTS: This study focuses on short bioinformatics-related courses for graduate students at the University of Gothenburg, Sweden, which were originally developed for onsite training. Once adapted as online courses, several modifications in their design were tested to obtain the best fitting learning strategy for the students. To improve the online learning experience, we propose a combination of: (i) short synchronized sessions, (ii) extended time for own and group practical work, (iii) recorded live lectures and (iv) increased opportunities for feedback in several formats. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The enigmatic RNase MRP of kinetoplastids.

The ribonucleoprotein RNase MRP is responsible for the processing of ribosomal RNA precursors. It is found in virtually all eukaryotes that have been examined. In the Euglenozoa, including the genera Euglena, Diplonema and kinetoplastids, MRP RNA and protein subunits have so far escaped detection using bioinformatic methods. However, we now demonstrate that the RNA component is widespread among the Euglenozoa and that these RNAs have secondary structures that conform to the structure of all other phylogenetic groups. In Euglena, we identified the same set of P/MRP protein subunits as in many other protists. However, we failed to identify any of these proteins in the kinetoplastids. This finding poses interesting questions regarding the structure and function of RNase MRP in these species.