vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines.

MOTIVATION: Germline variant classification allows accurate genetic diagnosis and risk assessment. However, it is a tedious iterative process integrating information from several sources and types of evidence. It should follow gene-specific (if available) or general updated international guidelines. Thus, it is the main burden of the incorporation of next-generation sequencing into the clinical setting. RESULTS: We created the vaRiants in HC (vaRHC) R package to assist the process of variant classification in hereditary cancer by: (i) collecting information from diverse databases; (ii) assigning or denying different types of evidence according to updated American College of Molecular Genetics and Genomics/Association of Molecular Pathologist gene-specific criteria for ATM, CDH1, CHEK2, MLH1, MSH2, MSH6, PMS2, PTEN, and TP53 and general criteria for other genes; (iii) providing an automated classification of variants using a Bayesian metastructure and considering CanVIG-UK recommendations; and (iv) optionally printing the output to an .xlsx file. A validation using 659 classified variants demonstrated the robustness of vaRHC, presenting a better criteria assignment than Cancer SIGVAR, an available similar tool. AVAILABILITY AND IMPLEMENTATION: The source code can be consulted in the GitHub repository (https://github.com/emunte/vaRHC) Additionally, it will be submitted to CRAN soon.

The inhibitory effect of a non-yessotoxin-producing dinoflagellate, Lingulodinium polyedrum (Stein) Dodge, towards Vibrio vulnificus and Staphylococcus aureus.

The increased bacterial resistance to antibiotics has caused global concern, prompting the search for new compounds. Because of their abundance and diversity, marine phytoplankton are an important potential source of such compounds. Research on dinoflagellates has led to the discovery of inhibitors of bacterial growth. The marine dinoflagellate Lingulodinium polyedrum blooms in different regions of the world, including Mexico, and is also known to regulate the growth of other species in coastal waters. Here, we investigated the taxonomy of this dinoflagellate and characterized the ability of its extracts to inhibit the growth of two bacteria of medical importance (Vibrio vulnificus and Staphylococcus aureus). Taxonomic characterization was performed by PCR and gene amplification of ITS, and confirmed that the species isolated off the Pacific coast of Mexico was L. polyedrum. To prove the inhibitory effect of L. polyedrum extracts, cultures were harvested by centrifugation. Pellets from three cellular abundances were extracted with water, methanol, hexane and chloroform. The experiments on V. vulnificus showed a high growth inhibition for the four extracts, ranging from 77 to 98 %. Surprisingly, the growth inhibition was lower when the extracts originated from a higher L. polyedrum cell abundance, ranging from 0 to 34 %. For S. aureus, the growth inhibition was also high, but not statistically different for all extracts and cell abundances, ranging from 62 to 99 %. This study obtained promising results for future pharmacological applications. Our Mexican strain of L. polyedrum did not produce any detectable yessotoxins.

[Case reports of drug-induced liver injury in a reference hospital of Zulia state, Venezuela]. / Reporte de casos de lesión hepática inducida por medicamentos en un centro hospitalario de referencia del estado Zulia, Venezuela.

Drug-induced liver injury (DILI) is an important cause of morbidity and mortality worldwide, with varied geographical differences. The aim of this prospective, descriptive, cross-sectional study was to identify and characterize cases of DILI in a hospital of Zulia state, Venezuela. Thirteen patients with a presumptive diagnosis of DILI attended by the Department of Gastroenterology, Hospital Universitario, Zulia state, Venezuela, from December-2012 to December-2013 were studied. Ibuprofen (n = 3; 23.1%), acetaminophen (n = 3; 23.1), isoniazid (n = 2; 15.4%) and Herbalife products (n = 2; 15.4%) were the main drugs involved with DILI. Acetaminophen and ibuprofen showed a mixed pattern of liver injury (n = 3; 23.1%) and isoniazid presented a hepatocellular pattern (n = 2; 15.4%). The CIOMS/RUCAMS allowed the identification of possible (n = 7; 53.9%), probable (n = 4; 30.8%) and highly-probable cases (n = 2; 15.4%) of DILI. Amoxicillin/clavulanate, isoniazid, isotretinoin, methotrexate and Herbalife nutritional products were implicated as highly-probable and probable agents. The highest percentage of DILI corresponded to mild cases that recovered after the discontinuation of the agent involved (n = 9; 69.3%). The consumption of Herbalife botanical products is associated with probable causality and fatality (n = 1; 7.7%). In conclusion, the frequency of DILI cases controlled by the Department of Gastroenterology of the Hospital Universitario of Maracaibo was low, being ibuprofen, acetaminophen, isoniazid and products Herbalife the products most commonly involved. It is recommended to continue with the prospective registration of cases, with an extended follow up monitoring period and to facilitate the incorporation of other hospitals in the Zulia State and Venezuela.

Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets.

Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on a cytochrome oxidase I gene segment of all species was verified by GENBANK reference sequences. A total of 34 species from 14 families (Ariidae, Caranjidae, Centropomidae, Gerreidae, Haemulidae, Lobotidae, Lutjanidae, Malacanthidae, Mugilidae, Scianidae, Scombridae, Serranidae, Sphyraenidae, Stromateidae) were identified at the species level from 164 sequences. Additionally, three Caribbean species were molecularly identified among the analyzed samples (Mycteroperca xenarcha, Paralonchurus brasilensis and Lobotes surinamensis). Species diversity was slightly higher in the Gulf of Panama than in the Gulf of Chiriquí. For species with five or more individual sequences, genetic diversity and genetic connectivity parameters such as total number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity (π) were calculated. Overall, pelagic-migratory species showed higher values of genetic diversity than coastal and estuarine species with some exceptions. Connectivity between Gulf areas was compared using values of genetic distances and genetic differentiation (Fst). The high level of connectivity observed between the Gulf of Chiriqui and the Gulf of Montijo indicates the existence of a single stock in that area for the following species: Scomberomorus sierra, Caranx caninus and Lutjanus guttatus. The demographic history of the most common species was examined using Tajima's D values, suggesting population expansion for two snapper species, L. peru and L. argentiventris, having significant and higher values. Another important contribution from this research was the production of primers and dual-labeled probes for environmental DNA detection using qPCR for the five most abundant species (spotted rose snapper, yellow snapper, green jack, Pacific crevalle jack and the Pacific sierra fish). These markers represent a new set of tools for environmental DNA (eDNA) detection and molecular traceability of three commercially important fish species along the supply chain including landing sites and markets of the main fishery areas.

Biomarkers Predict In-Hospital Major Adverse Cardiac Events in COVID-19 Patients: A Multicenter International Study.

BACKGROUND: The COVID-19 pandemic carries a high burden of morbidity and mortality worldwide. We aimed to identify possible predictors of in-hospital major cardiovascular (CV) events in COVID-19. METHODS: We retrospectively included patients hospitalized for COVID-19 from 10 centers. Clinical, biochemical, electrocardiographic, and imaging data at admission and medications were collected. Primary endpoint was a composite of in-hospital CV death, acute heart failure (AHF), acute myocarditis, arrhythmias, acute coronary syndromes (ACS), cardiocirculatory arrest, and pulmonary embolism (PE). RESULTS: Of the 748 patients included, 141(19%) reached the set endpoint: 49 (7%) CV death, 15 (2%) acute myocarditis, 32 (4%) sustained-supraventricular or ventricular arrhythmias, 14 (2%) cardiocirculatory arrest, 8 (1%) ACS, 41 (5%) AHF, and 39 (5%) PE. Patients with CV events had higher age, body temperature, creatinine, high-sensitivity troponin, white blood cells, and platelet counts at admission and were more likely to have systemic hypertension, renal failure (creatinine ≥ 1.25 mg/dL), chronic obstructive pulmonary disease, atrial fibrillation, and cardiomyopathy. On univariate and multivariate analysis, troponin and renal failure were associated with the composite endpoint. Kaplan-Meier analysis showed a clear divergence of in-hospital composite event-free survival stratified according to median troponin value and the presence of renal failure (Log rank p < 0.001). CONCLUSIONS: Our findings, derived from a multicenter data collection study, suggest the routine use of biomarkers, such as cardiac troponin and serum creatinine, for in-hospital prediction of CV events in patients with COVID-19.

[Molecular and phenotypical typification of methicillin resistant Staphylococcus aureus (MRSA) strains in a university hospital]. / Tipificación molecular y fenotípica de Staphylococcus aureus resistentes a meticilina (SAMR) en un hospital universitario.

OBJECTIVE: To typify by molecular and phenotypical methods, MRSA strains, isolated from patients and nurses to establish their possible clonal origin. MATERIALS AND METHODS: 50 MRSA strains isolated in a teaching hospital in Maracaibo (Venezuela) were analyzed. The typification of MRSA strains was performed by means of pulsed-field gel electrophoresis (PFGE) and antibiotyping. RESULTS: In patients, 12 clusters (I-XII) and 19 antibiotypes were found; whereas in the health-care personnel, 6 clusters (I-VI) and two antbiotypes were detected. There was no statistically significative association between antibiotypes and band patterns obtained by PFGE (p>0.05). CONCLUSIONS: By means of detection of resistance markers and PFGE, it is feasible to discrimínate the nature of the clinical strains of MRSA. The obtained results show the possible nosocomial transmission of MRSA strains and their clonal spread in hospital departments, particularly at the ICU.

Preventive program based on multiple intelligences to promote oral health in disabled children from Chiclayo, Peru / Programa preventivo basado en inteligencias múltiples para promover la salud bucal en niños discapacitados de Chiclayo, Perú

Introduction: Children with physical disabilities often present deficient oral hygiene and eating habits that threaten optimal oral health. Objective: To evaluate the result of a preventive program based on multiple intelligences to pro-mote oral health care in children with physical disabilities in Chiclayo - Peru. Materials and Methods: A quasi-experimental, quan-titative, prospective and longitudinal study was carried out from the year 2020, to test a preventive intervention based on multiple intelligences (MI), comparing it with an intervention with traditional methodology, whose purpose was in both cases promote preventive oral health care in 167 boys and girls with physical disabilities from four Special Basic Education Centers (CEBES) in Chiclayo. For the pre- and post-test evaluation using a dental record of oral hygiene practices, oral hygiene index and dietary exposure to sugary carbohydrates, the Mann Whitney U test was required, with a confidence level of 95%. Results: After not very encouraging findings in the pretest for both groups, significant changes were observed in the posttest in favor of the IM-based program, for which 58% of schoolchildren registered an adequate oral hygiene index, 69.2% brushed twice to three times a day and that only 35.8% present regular exposure to carbohydrates. Statistical significance was evidenced in favor of the MI-based intervention for the three indicated variables (p= 0.000). Conclusions: The application of the IM-based program achieved better results in the significant promotion of oral hygiene practices with a favorable record of the IHO and by reducing the exposure to carbohydrates in a vulnerable population.Keywords: Health promotion; Oral health; Preventive dentistry; Health education; Children with disabilities.

Differences in Selected HIV Care Continuum Outcomes Among People Residing in Rural, Urban, and Metropolitan Areas-28 US Jurisdictions.

PURPOSE: The HIV care continuum is used to monitor success in HIV diagnosis and treatment among persons living with HIV in the United States. Significant differences exist along the HIV care continuum between subpopulations of people living with HIV; however, differences that may exist between residents of rural and nonrural areas have not been reported. METHODS: We analyzed the Centers for Disease Control and Prevention's National HIV Surveillance System data on adults and adolescents (≥13 years) with HIV diagnosed in 28 jurisdictions with complete reporting of HIV-related lab results. Lab data were used to assess linkage to care (≥1 CD4 or viral load test ≤3 months of diagnosis), retention in care (≥2 CD4 and/or viral load tests ≥3 months apart), and viral suppression (viral load <200 copies/mL) among persons living with HIV. Residence at diagnosis was grouped into rural (<50,000 population), urban (50,000-499,999 population), and metropolitan (≥500,000 population) categories for statistical comparison. Prevalence ratios and 95% CI were calculated to assess significant differences in linkage, retention, and viral suppression. FINDINGS: Although greater linkage to care was found for rural residents (84.3%) compared to urban residents (83.3%) and metropolitan residents (81.9%), significantly lower levels of retention in care and viral suppression were found for residents of rural (46.2% and 50.0%, respectively) and urban (50.2% and 47.2%) areas compared to residents of metropolitan areas (54.5% and 50.8%). CONCLUSIONS: Interventions are needed to increase retention in care and viral suppression among people with HIV in nonmetropolitan areas of the United States.

Compassionate Use of Lumacaftor/Ivacaftor in Cystic Fibrosis: Spanish Experience.

BACKGROUND: The most common cystic fibrosis (CF)-causing mutation is deltaF508 (F508del), which is present in 28% of CF Spanish patients. While the literature based on real-life studies on CF patients homozygous F508del treated with lumacaftor/ivacaftor is limited, it demonstrates the need for better strategies to prevent related adverse events (AEs) as well as the development of newer drugs. METHODS: We conducted a multicenter, retrospective, observational study to describe the effects of lumacaftor/ivacaftor treatment in real-life in Spain. 20 CF patients were included, all aged 6 and upwards and presented with ppFEV1<40%, chosen from CF units country-wide. For the purposes of the study, they were treated with lumacaftor/ivacaftor 200/125mg two tablets twice a day on a compassionate use programme throughout 2016. The primary endpoint was measured in all of the sample patients. Data were analysed from ppFEV1 at baseline and was measured every 6 months. RESULTS: The mean age was 26.65 (range of 10-45), while the mean ppFEV1 before the treatment was 32.4% and mean BMI was 19.9kg/m2. We analysed the changes in ppFEV1 and BMI from baseline during the treatment with lumacaftor/ivacaftor, but no differences were found. However, a moderate association between days of intravenous antibiotic needed and the use of lumacaftor/ivacaftor (p=0.001) was established. Indeed, under the lumacaftor/ivacaftor, patients required 5.8 days of intravenous antibiotic treatment compared to 14.9 days prior to study. Also, severe pulmonary exacerbations requiring hospitalisation were statistically fewer under lumacaftor/ivacaftor treatment (p=0.003). Finally, 75% of the sample presented with AEs, which led 35% of the subjects to discontinue the treatment. CONCLUSIONS: While treatment with lumacaftor/ivacaftor resulted in an improvement in the number of pulmonary severe exacerbations, no improvement in ppFEV1 or BMI was found.

[Vaginal colonization by genital mycoplasmas in pregnant and non-pregnant women]. / Colonización vaginal por micoplasmas genitales en mujeres embarazadas y no embarazadas.

To compare vaginal colonization by genital micoplasmas in pregnant and non pregnant women and to determine the association between pregnancy and colonization by these microorganisms, samples of exocervix an endocervix from pregnant (n = 80) and non pregnant (n = 65) women, from two health centers of Maracaibo, Zulia State, Venezuela were processed. The Mycoplasma-Lyo kit (bioMérieux laboratories) was used for the culture and identification of genital micoplasmas. In pregnant women, prevalences of 10% for M. hominis and 26.25% for Ureaplasma spp. were found; 35.38% for M. hominis and 20% for Ureaplasma spp. in non-pregnant, were obtained. Among the pregnant, Ureaplasma spp. was the most frequently isolated micoplasma, in symptomatic and asymptomatic; while in the non pregnant group, M. hominis was more common among the symptomatic patients; only one case (1.54%) was an asymptomatic carrier of Ureaplasma spp. The highest positivity percentages were obtained in primigravidas (48.71%) and during the second gestational trimester (34.21%). No statistically significant differences were found between vaginal colonization by genital micoplasmas according to age, number of pregnancy and gestational trimester; but they were found between the presented symptomatology and vaginal colonization by genital micoplasmas. Genital micoplasmas were isolated from gravid women at approximately the same recovery rate as in non-pregnant women; being M. hominis the most frequently isolated in non-pregnant women and Ureaplasma spp. in the pregnant group.