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Grace Medalyn T Castro,1 William D Taala,1 Jefferson G Guerrero,1 Niela S Rosales,1 Rino S De Sagun,2 Rock P Cordero,3 Rolven N Ciriaco,4 Rayson G Javines4 1Nursing Department, Fakeeh College for Medical Sciences, Jeddah, Saudi Arabia; 2College of Nursing, University of Hail, Hail, Saudi Arabia; 3Nursing Department, University of Fujairah, Fujairah, United Arab Emirates; 4College of Nursing, University San Agustin, Iloilo, PhilippinesCorrespondence: William D Taala, Nursing Department, Fakeeh College for Medical Sciences, P.O. Box 2537, Jeddah, 21461, Saudi Arabia, Tel +966 532543021, Email wtaala@fcms.edu.saPurpose: The study aimed to determine nursing educators’ and students’ perspectives concerning the shift of teaching methodologies to online learning platform in nursing education during the COVID-19 pandemic.Materials and Methods: The cross-sectional study investigated nursing educators’ and students’ perspectives on online learning. Non-probability convenience sampling technique was used to recruit 120 educators and 350 students, who answered the Test of e-Learning Related Attitudes scale. The data collection was conducted from November to December 2020 in five selected colleges and universities in Saudi Arabia.Results: The findings of the study revealed that the overall mean score of the nursing educators’ perspectives on online learning based on the 4 dimensions were 4.18 with a SD of 0.57 and an overall mean score of 4.22 with a SD of 0.61 for the students. Furthermore, the perspectives of both participant groups on challenges and benefits dimensions shows that there was significant difference as supported by a p-value of < 0.001 and 0.046. However, it shows in the attitude and interest dimensions that there was no significant difference as supported by a p-value of 0.313 and 0.088, respectively.Conclusion: Nursing educators and students shows an agreement on their perspectives on online learning in terms of attitude and interest dimensions. However, they show their disagreement in terms of challenges and benefits dimensions. Unfortunately, the current COVID-19 pandemic situation could persist for several years. But modern technologies can partially solve current problems in nursing education.Keywords: COVID-19, nursing education, online learning, teaching and learning, methodologies

The emergence of COVID-19 in 2020 significantly enhanced the application of wastewater monitoring for detecting SARS-CoV-2 circulation within communities. From October 2021 to October 2022, we collected 406 wastewater samples weekly from the Córdoba Central Pipeline Network (BG-WWTP) and six specific sewer manholes from sanitary zones (SZs). Following WHO guidelines, we processed samples and detected SARS-CoV-2 RNA and variants using real-time PCR. Monitoring at the SZ level allowed for the development of a viral activity flow map, pinpointing key areas of SARS-CoV-2 circulation and tracking its temporal spread and variant evolution. Our findings demonstrate that wastewater-based surveillance acts as a sensitive indicator of viral activity, detecting imminent increases in COVID-19 cases before they become evident in clinical data. This study highlights the effectiveness of targeted wastewater monitoring at both municipal and SZ levels in identifying viral hotspots and assessing community-wide circulation. Importantly, the data shows that environmental wastewater studies provide valuable insights into virus presence, independent of clinical COVID-19 case records, and offer a robust tool for adapting to future public health challenges., Competing Interests: The authors declare there is no conflict., (© 2024 The Authors This is an Open Access article distributed under the terms of the Creative Commons Attribution Licence (CC BY 4.0), which permits copying, adaptation and redistribution, provided the original work is properly cited (http://creativecommons.org/licenses/by/4.0/).)

The study of catastrophic costs incurred by people affected by tuberculosis (TB), conducted in Colombia during the COVID-19 pandemic, provided the opportunity to implement telephone surveys for data collection. This constitutes a methodological innovation regarding the standards established by the World Health Organization (WHO) which, for this type of study, usually rely on face-to-face surveys of patients attending health facilities. The study design, objectives, and methodology were adapted from the WHO publication Tuberculosis patient cost surveys: a handbook . A total of 1065 people affected by tuberculosis were selected as study participants and, by telephone, were administered a standard questionnaire adapted to the Colombian context. This allowed the collection of structured data on the direct and indirect costs faced by TB patients and their families. Greater than 80% completeness was achieved for all variables of interest, with an average survey duration of 40 minutes and a rejection rate of 8%. The described survey method to determine the baseline for further study of catastrophic costs in Colombia was novel because of its telephone-based format, which adheres to the information standards required to allow internationally comparable estimates. It is a useful means of generating standardized results in contexts in which the ability to conduct face-to-face surveys is limited., Competing Interests: Conflictos de intereses. Ninguno declarado por los autores.

Diagnostic errors comprise the leading threat to patient safety in healthcare today. Learning how to extract the lessons from cases where diagnosis succeeds or fails is a promising approach to improve diagnostic safety going forward. We present up-to-date and authoritative guidance on how the existing approaches to conducting root cause analyses (RCA's) can be modified to study cases involving diagnosis. There are several diffierences: In cases involving diagnosis, the investigation should begin immediately after the incident, and clinicians involved in the case should be members of the RCA team. The review must include consideration of how the clinical reasoning process went astray (or succeeded), and use a human-factors perspective to consider the system-related contextual factors in the diagnostic process. We present detailed instructions for conducting RCA's of cases involving diagnosis, with advice on how to identify root causes and contributing factors and select appropriate interventions., (© 2024 the author(s), published by De Gruyter, Berlin/Boston.)

Monkeypox (Mpox) is a zoonotic disease caused by the monkeypox virus (MPXV). MPXV can be transmitted by close contact with lesions, body fluids, respiratory droplets, and contaminated materials. A new pattern of spread among sexual networks has been recently described. The present work aimed to report the epidemiological and genomic characterization of the 2022 MPXV outbreak in central Argentina. A total of 113 scabs and/or lesion swab specimens were studied. MPXV infection was confirmed in 46.0% of the studied patients, all of whom were men. Varicella-zoster virus infection was the most frequent differential diagnosis. Eight complete viral genomes were obtained by next-generation sequencing. The Argentinian sequences were grouped intermingled with other sequences from the 2022 MPXV outbreak, related to samples from the USA, Europe, and Peru. Taken together, our study provided an initial assessment of the genetic and epidemiological characteristics of the 2022 MPXV outbreak in Córdoba, Argentina., (Copyright © 2024 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.)

Raynaud's phenomenon of the nipple is a possible cause of pain and breastfeeding cessation in lactating women. However, there are still few studies on the characterization of this manifestation. Thus, we aim to develop a systematic review of the literature carried out between January 1992 and January 2024 in PubMed, Scopus, Web of Science, Virtual Health Library (VHL), and Portal de Periódicos da CAPES. Of the 438 articles, 19 met the eligibility criteria. The findings were divided by heuristic questions into two groups: "Epidemiological, pathophysiological, and clinical characterization of Raynaud's Phenomenon of the nipple" and "Treatment of Raynaud's Phenomenon of the nipple". Raynaud's phenomenon of the nipple is commonly primary, being more prevalent in the postpartum period, in women with a mean age of 32 years. The main triggers appear to be stress and temperature change. Generally, it is associated with a change in color and pain during breastfeeding. A calcium channel blocker was the most used medication with or without non-pharmacological measures.

In Argentina, circulation of hepatitis E virus (HEV) genotype 3 has been described, producing sporadic cases of acute and chronic hepatitis. Limited information is available regarding HEV infection in children, so we aimed to investigate this virus in a pediatric population from the country. Serum samples from Argentine children (0-18 years old) (n = 213) were studied for IgG anti-HEV, IgM anti-HEV and RNA-HEV: 202 samples belonged to individuals attending health-care centers for routine check-ups, and 11 samples from patients with acute hepatitis of unknown etiology. Seropositivity for IgG anti-HEV was 1.49 % (3/202). One sample from an 18-years-old female patient with acute hepatitis tested positive for IgM anti-HEV detection, negative for IgG anti-HEV and RNA-HEV, but also positive for IgM anti-EBV. The HEV prevalence was low and showed circulation among children in central Argentina., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

The goal of this study was to perform systematic review (SR) to investigate the scientific literature regarding the genotoxicity effects of fluoride exposure (FE). The search of databases used for this study was PubMed/Medline, SCOPUS and Web of Science. The quality of included studies was assessed using the EPHPP (Effective Public Health Practice Project). A total of 20 potentially relevant studies were selected for evaluating the genotoxicity induced by fluoride. Few studies have revealed that FE induces genotoxicity. A total of 14 studies demonstrated negative results whereas 6 studies did not. After reviewing the twenty studies, 1 was classified as weak, 10 were considered moderate and 9 were considered strong, according to the EPHPP. Taken together, it has been established that genotoxicity of fluoride is limited.

The rapid decline of coral reefs calls for cost-effective benthic cover data to improve reef health forecasts, policy building, management responses and evaluation. Reef monitoring has been largely based on divers' observations along transects, and secondarily on quadrat-based protocols, video and photographic records. However, the accuracy and precision of the most common sampling approaches are not yet fully understood. Here, we compared benthic cover estimates from three common sampling protocols: Reef Check (RC), Atlantic and Gulf Rapid Reef Assessment (AGRRA) and photoquadrats (PQ). The reef cover of two contrasting sites was reconstructed with ∼450 m 2 orthomosaics built with high resolution Structure-from-Motion (SfM) photogrammetry, which were used as references for comparisons among protocols. In addition, we explored sample size requirements for each protocol and provided cost-effectiveness comparisons. Our results evidenced between-reef differences in the accuracy and precision of estimates with the different protocols. The three protocols performed similarly in the reef with low macroalgal cover (<0.5%), but PQ were more accurate and precise in the reef with relatively high (∼20%) macroalgal cover. The sample size for estimating coral cover with a 20% error margin and a 0.05 significance level was lower for PQ, followed by AGRRA and RC. Considering performance, cost surrogates and equipment needs, cost-effectiveness was higher for PQ. We also discuss costs, limitations and advantages/disadvantages of SfM photogrammetry as a sampling approach for coral reef monitoring., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

We present the case of a breakthrough infection by hepatitis B virus (HBV), intending to warn about the challenge that HBV represents for transfusion safety. Virological markers for HBV infection were assayed during a blood donor screening by detection of HBsAg, anti-HBc, and viral nucleic acid (HBV DNA) by a nucleic acid test (NAT). Additionally, samples were analyzed for detection of immunoglobulin M anti-HBc, HBeAg, anti-HBe, and anti-HBs. A first-time donor repeatedly tested positive for HBV DNA by NAT and nonreactive for HBV-serological markers of infection. He stated having completed the anti-HBV vaccination schedule; thus, study of anti-Hbs resulted in reactive at protective level (18 mIU/mL). The donor denied clinical symptoms of hepatitis and remained healthy during the follow-up period. 95 days postdonation, NAT was negative, seroconversion of anti-HBc ab was detected, and a significant increase in anti-HBs concentration was measured (>1000 mIU/mL). This is the first case of HBV-breakthrough infection reported in Argentina and to our knowledge, this potential threat to transfusion safety is novel in an HBV low-endemic region with high coverage of HBV vaccination. The occurrence of breakthrough infections challenges the current protocols for the identification of HBV-infected subjects, could be a source of silent HBV transmission., (© 2024 Wiley Periodicals LLC.)

This paper presents an innovative method of constructing energy absorbers, whose primary function is to effectively transform kinetic energy into strain energy in events with high deformation rates. Hybrid specimens are proposed considering thin-walled windowed metallic tubes filled with 3D-printed hexagonal honeycombs made of PET-G and ABS thermoplastic. The patterned windows dimensions vary from 20 × 20, 20 × 30, 15 × 20 and 15 × 30 mm 2 . Although using polymers in engineering and thin-walled sections is not new, their combination has not been explored in this type of structure designed to withstand impacts. Specimens resist out-of-plane quasi-static axial loading, and test results are analyzed, demonstrating that polymer core gives the samples better performance parameters than unfilled samples regarding energy absorption ( E a ), load rate ( LR ), and structural effectiveness ( η ). An optimization procedure using specialized software was applied to evaluate experimental results, which led to identifying the optimal window geometry (16.4 × 20 mm 2 , in case) and polymer to be used (ABS). The optimized sample was constructed and tested for axial compression to validate the optimization outcomes. The results reveal that the optimal sample performed similarly to the estimated parameters, making this geometry the best choice under the test conditions.

Continental shelves encompass gently sloped seascapes that are highly productive and intensively exploited for natural resources. Islands, reefs and other emergent or quasi-emergent features punctuate these shallow (<100 m) seascapes and are well known drivers of increased biomass and biodiversity, as well as predictors of fishing and other human uses. On the other hand, relict mesoscale geomorphological features that do not represent navigation hazards, such as incised valleys (IVs), remain poorly charted. Consequently, their role in biophysical processes remains poorly assessed and sampled. Incised valleys are common within rhodolith beds (RBs), the most extensive benthic habitat along the tropical and subtropical portions of the mid and outer Brazilian shelf. Here, we report on a multi-proxy assessment carried out in a tropical-subtropical transition region (~20°S) off Eastern Brazil, contrasting physicochemical and biological variables in IVs and adjacent RBs. Valleys interfere in near bottom circulation and function as conduits for water and propagules from the slope up to the mid shelf. In addition, they provide a stable and structurally complex habitat for black corals and gorgonians that usually occur in deeper water, contrasting sharply with the algae-dominated RB. Fish richness, abundance and biomass were also higher in the IVs, with small planktivores and large-bodied, commercially important species (e.g. groupers, snappers and grunts) presenting smaller abundances or being absent from RBs. Overall, IVs are unique and vulnerable habitats that sustain diverse assemblages and important ecosystem processes. As new IVs are detected by remote sensing or bathymetric surveys, they can be incorporated into regional marine management plans as conservation targets and priority sites for detailed in situ surveys., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Castro et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The aim of this systematic review was to evaluate published papers regarding the micronucleus assay in oral mucosal cells of patients undergoing orthodontic therapy (OT). A search of the scientific literature was made in the PubMed, Scopus, and Web of Science databases for all data published until November, 2021 using the combination of the following keywords: "fixed orthodontic therapy," "genetic damage", "DNA damage," "genotoxicity", "mutagenicity", "buccal cells", "oral mucosa cells," and "micronucleus assay". The systematic review was designed according to the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) guidelines. Nine studies were retrieved. Some authors demonstrated that OT induces cytogenetic damage in oral mucosal cells. Out of the nine studies included, two were classified as strong, five as moderate, and two as weak, according to the quality assessment components of the Effective Public Health Practice Project (EPHPP). Meta-analysis data revealed no relationship between mutagenicity in oral cells and OT in different months of treatment. At one month, the SMD = 0.65 and p = 0.08; after three months of OT, the SMD = 1.21 and p = 0.07; and after six months of OT, the SMD = 0.56 and p = 0.11. In the analyzed months of OT, I2 values were >75%, indicating high heterogeneity. In summary, this review was not able to demonstrate that OT induces genetic damage in oral cells. The study is important for the protection of patients undergoing fixed OT, given that mutagenesis participates in the multi-step process of carcinogenesis.

Purpose: To verify the association between caregivers' and teachers' perceptions of the changes imposed by social isolation and the impact on students' learning., Methods: This is an analytical observational and longitudinal study, with the participation of 19 caregivers (family members) of 2nd-grade students from a public financing school and their respective teachers. The caregivers were submitted to interviews by means of the questionnaires: Abilities and Difficulties Questionnaire, Family Environment Resources Inventory and COVID-19 monitoring questionnaire that checks the behavior of schoolchildren and families. The collection took place in two moments by telephone call: the first moment (M1) was started in June 2020, and the second, (M2) in December 2020. The progress reports prepared by the regular teachers were received in January 2021., Results: A negative implication was observed in the change of routine and an impact on the parents' lives. In parents' perceptions, significant and negative issues were also present in children's mental health, such as changes in routine. Teacher evaluation reports showed a similar pattern, with the vast majority of them lacking information about learning performance., Conclusion: This study pointed out the importance of accompanying schoolchildren and families in a period of social withdrawal, in order to guide and intervene together with parents and teachers.

The rocketing number of COVID-19 cases highlighted the critical role that diagnostic tests play in medical and public health decision-making to contain and mitigate the SARS-CoV-2 pandemic. This study reports the evaluation and implementation of different tests for the molecular detection of SARS-CoV-2 in the central region of Argentina. We evaluated 3 real time RT-PCR kits (GeneFinder COVID-19 Plus RealAmp Kit, DisCoVery SARS-CoV-2 RT-PCR Detection Kit and WGene SARS-CoV-2 RT Detection), 2 nucleic acid extraction methods [MagaBio plus Virus DNA/RNA Purification Kit II (BioFlux), 35-min vs. 9-min], a pre-analytical reagent (FlashPrep®) and 2 isothermal amplification tests (Neokit Plus and ELA CHEMSTRIP®). The order according to the best performance of the 3 real-time RT-PCR kits evaluated was: DisCoVery>GeneFinderTM>WGene. The 2 RNA extraction methods showed similar good results: MagaBio plus Virus RNA Purification Kit II (BioFlux) 9-min was selected due to its faster performance. FlashPrep® reagent showed excellent results to perform direct RNA detection. Isothermal amplification assays showed acceptable sensitivity and specificity values (>80%), except in samples with Ct>30. Our data show optimal real time RT-PCR kits and alternative molecular methods for SARS-CoV-2 diagnostic. These alternative assays proved to be acceptable for their use in adverse contexts, decentralization, and different epidemiological scenarios, for rapid and accurate SARS-CoV-2 detection., (Copyright © 2023 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.)

Living species vary significantly in phenotype and genomic content. Sophisticated statistical methods linking genes with phenotypes within a species have led to breakthroughs in complex genetic diseases and genetic breeding. Despite the abundance of genomic and phenotypic data available for thousands of species, finding genotype-phenotype associations across species is challenging due to the non-independence of species data resulting from common ancestry. To address this, we present CALANGO (comparative analysis with annotation-based genomic components), a phylogeny-aware comparative genomics tool to find homologous regions and biological roles associated with quantitative phenotypes across species. In two case studies, CALANGO identified both known and previously unidentified genotype-phenotype associations. The first study revealed unknown aspects of the ecological interaction between Escherichia coli , its integrated bacteriophages, and the pathogenicity phenotype. The second identified an association between maximum height in angiosperms and the expansion of a reproductive mechanism that prevents inbreeding and increases genetic diversity, with implications for conservation biology and agriculture., Competing Interests: The authors declare no competing interests., (© 2023 The Author(s).)

Introduction: Genomic analysis of hepatitis B virus (HBV) identifies phylogenetic variants, which may lead to distinct biological and clinical behaviors. The satellite hepatitis D virus (HDV) may also influence clinical outcomes in patients with hepatitis B. The aim of this study was to investigate HBV genetic variants, including clinically relevant mutations, and HDV infection in acute and chronic hepatitis B patients in central Argentina., Methods: A total of 217 adult HBV infected patients [acute (AHB): n = 79; chronic (CHB): n = 138] were studied; 67 were HBV/human immunodeficiency virus (HIV) coinfected. Clinical and demographic data were obtained from medical records. Serological markers were determined. Molecular detection of HBV and HDV was carried out by RT-Nested PCR, followed by sequencing and phylogenetic analysis., Results: Overall, genotype (gt) F [sub-genotype (sgt) F1b] was the most frequently found. In AHB patients, the gts/sgts found were: F1b (74.7%) > A2 (13.9%) > F4 (7.6%) > C (2.5%) > A1 (1.3%). Among CHB patients: F1b (39.1%) > A2 (23.9%) > F4 (18.2%) > D (9.4%) > C and F6 (3.6% each) > A1, A3 and B2 (0.7% each). The distribution of sgt A2 and gt D was significantly different between HBV mono and HBV/HIV coinfected patients [A2: 15.9% vs. 35.7% ( p < 0.05), respectively and D: 14.6% vs. 1.8% ( p < 0.05), respectively]. Mutation frequency in basal core promoter/pre-Core (BCP/pC) region was 35.5% (77/217) [AHB: 20.3% (16/79), CHB: 44.2% (61/138)]. In the open reading frame (ORF) S, mutations associated with vaccine escape and diagnostic failure were detected in 7.8% of the sequences (17/217) [AHB: 3.8% (3/79), CHB: 10.1% (14/138)]. ORF-P amino acid substitutions associated with antiviral resistance were detected in 3.2% of the samples (7/217) [AHB: 1.3% (1/79), CHB 4.3%, (6/138)]. The anti-HDV seropositivity was 5.2% (4/77); one sample could be sequenced, belonging to gt HDV-1 associated with sgt HBV-D3., Discussion: We detected an increase in the circulation of genotype F in Central Argentina, particularly among AHB patients, suggesting transmission advantages over the other genotypes. A low rate of mutations was detected, especially those with antiviral resistance implications, which is an encouraging result. The evidence of HDV circulation in our region, reported for the first time, alerts the health system for its search and diagnosis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Castro, Sosa, Sicilia, Riberi, Moreno, Cattaneo, Debes, Barbás, Cudolá, Pisano and Ré.)

Background: Simulation is part of the training provided to nurses enrolled in the master's degree for critical care nursing programmes at our institution. Although the students are practicing nurses, many still make mistakes when performing nursing procedures related to critical care during simulation sessions, and these mistakes must be addressed during the debriefing session. The aim of the study is to compare the knowledge and skills acquired by groups of postgraduate critical care nursing students who were exposed to high-fidelity simulation (HFS) by using different debriefing structures., Methods: A quasi-experimental crossover design was utilised during the post-tests and objective structured clinical examinations (OSCEs). The students were divided into two groups: one was exposed to HFS with a 3-phase debriefing, and the other was exposed to HFS with a multiphase debriefing. Both groups involved facilitator-guided and video-assisted debriefings., Results: Overall, the post-test scores (p-value: Phase 1 = 0.001 and Phase 2 = 0.000) and post-OSCE scores (p-value: Phase 1 = 0.002 and Phase 2 = 0.002) support that the group of postgraduate students who underwent HFS with a multiphase debriefing structure gained significantly higher scores compared to the group who underwent HFS with a 3-phase debriefing structure., Conclusion: Debriefing is a critical component of successful simulation. Learning requires assessment that creates constructive criticism based on feedback and reflection. A multiphase debriefing structure, specifically the healthcare simulation after-action review, provides a significant advantage for knowledge and skills acquisition., (© 2022. The Author(s).)

Cocoa beans fermentation is a spontaneous process, essential for the generation of quality starting material for fine chocolate production. The understanding of this process has been studied by the application of high-throughput sequencing technologies, which grants a better assessment of the different microbial taxa and their genes involved in this microbial succession. The present study used shotgun metagenomics to determine the enzyme-coding genes of the microbiota found in two different groups of cocoa beans varieties during the fermentation process. The statistical evaluation of the most abundant genes in each group and time studied allowed us to identify the potential metabolic pathways involved in the success of the different microorganisms. The results showed that, albeit the distinction between the initial (0 h) microbiota of each varietal group was clear, throughout fermentation (24-144 h) this difference disappeared, indicating the existence of selection pressures. Changes in the microbiota enzyme-coding genes over time pointed to the distinct ordering of fermentation at 24-48 h (T1), 72-96 h (T2), and 120-144 h (T3). At T1, the significantly more abundant enzyme-coding genes were related to threonine metabolism and those genes related to the glycolytic pathway, explained by the abundance of sugars in the medium. At T2, the genes linked to the metabolism of ceramides and hopanoids lipids were clearly dominant, which are associated with the resistance of microbial species to extreme temperatures and pH values. In T3, genes linked to trehalose metabolism, related to the response to heat stress, dominated. The results obtained in this study provided insights into the potential functionality of microbial community succession correlated to gene function, which could improve cocoa processing practices to ensure the production of more stable quality end products., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Lima, De Castro, Solar, Vaz, Lobo, Pereira, Rodrigues, Vandenberghe, Martins Pinto, da Costa, Koblitz, Benevides, Azevedo, Uetanabaro, Soccol and Góes-Neto.)

Background: The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. To better understand the evolution of SARS-CoV-2 early in the pandemic in the Province of Cordoba, Argentina, we performed a comparative genomic analysis of SARS-CoV-2 strains detected in survivors and non-survivors of COVID-19. We also carried out an epidemiological study to find a possible association between the symptoms and comorbidities of these patients with their clinical outcomes., Results: A representative sampling was performed in different cities in the Province of Cordoba. Ten and nine complete SARS-CoV-2 genomes were obtained by next-generation sequencing of nasopharyngeal specimens from non-survivors and survivors, respectively. Phylogenetic and phylodynamic analyses revealed multiple introductions of the most common lineages in South America, including B.1, B.1.1.1, B.1.499, and N.3. Fifty-six mutations were identified, with 14% of those in common between the non-survivor and survivor groups. Specific SARS-CoV-2 mutations for survivors constituted 25% whereas for non-survivors they were 41% of the repertoire, indicating partial selectivity. The non-survivors' variants showed higher diversity in 9 genes, with a majority in Nsp3, while the survivors' variants were detected in 5 genes, with a higher incidence in the Spike protein. At least one comorbidity was present in 60% of non-survivor patients and 33% of survivors. Age 75-85 years (p = 0.018) and hospitalization (p = 0.019) were associated with non-survivor patients. Related to the most common symptoms, the prevalence of fever was similar in both groups, while dyspnea was more frequent among non-survivors and cough among survivors., Conclusions: This study describes the association of clinical characteristics with the clinical outcomes of survivors and non-survivors of COVID-19 patients, and the specific mutations found in the genome sequences of SARS-CoV-2 in each patient group. Future research on the functional characterization of novel mutations should be performed to understand the role of these variations in SARS-CoV-2 pathogenesis and COVID-19 disease outcomes. These results add new genomic data to better understand the evolution of the SARS-CoV-2 variants that spread in Argentina during the first wave of the COVID-19 pandemic., (© 2022. The Author(s).)

SARS-CoV-2 variants of concern (VOC) and interest (VOI) present mutations in reference to the original virus, being more transmissible. We implemented a rapid strategy for the screening of SARS-CoV-2 VOC/VOIs using real time RT-PCR and performed monitoring and surveillance of the variants in our region. Consecutive real-time RT-PCRs for detection of the relevant mutations/deletions present in the Spike protein in VOC/VOIs (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems) were implemented. A total of 6,640 SARS-CoV-2 RNA samples (Cts < 30) from infected individuals in Central Argentina during 2021 were analyzed using different algorithms that were gradually adapted to the changing scenarios of local variant circulation. The strategy developed allowed the early detection and the identification of VOC/VOIs that circulated through the year, with a 100% of concordance with the WGS. The analyses of the samples showed introductions of VOCs Alpha and Gamma in February and March 2021, respectively. Gamma showed an exponential increase, with a peak of detection in July (72%), being responsible of the second wave of COVID19 in Argentina. Since VOC Delta entered into the region, it increased gradually, together with VOI Lambda, replacing VOC Gamma, until being the main variant (84.9%) on November. By December, these variants were replaced by the emergent VOC Omicron in a term of 2 weeks, producing the third wave. We report a useful tool for VOC/VOI detection, capable to quickly and cost-effectively monitor currently recognized variants in resource-limited settings, which allowed to track the recent expansion of Omicron in our region, and contributed to the implementation of public health measures to control the disease spread., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Castro, Sicilia, Bolzon, Lopez, Barbás, Pisano and Ré.)

The rubber tree, Hevea brasiliensis , is a neotropical Amazonian species. Despite its high economic value and fungi associated with native individuals, in its original area in Brazil, it has been scarcely investigated and only using culture-dependent methods. Herein, we integrated in silico approaches with novel field/experimental approaches and a case study of shotgun metagenomics and small RNA metatranscriptomics of an adult individual. Scientific literature, host fungus, and DNA databases are biased to fungal taxa, and are mainly related to rubber tree diseases and in non-native ecosystems. Metabarcoding retrieved specific phyllospheric core fungal communities of all individuals, adults, plantlets, and leaves of the same plant, unravelling hierarchical structured core mycobiomes. Basidiomycotan yeast-like fungi that display the potential to produce antifungal compounds and a complex of non-invasive ectophytic parasites (Sooty Blotch and Flyspeck fungi) co-occurred in all samples, encompassing the strictest core mycobiome. The case study of the same adult tree (previously studied using culture-dependent approach) analyzed by amplicon, shotgun metagenomics, and small RNA transcriptomics revealed a high relative abundance of insect parasite-pathogens, anaerobic fungi and a high expression of Trichoderma (a fungal genus long reported as dominant in healthy wild rubber trees), respectively. Altogether, our study unravels new and intriguing information/hypotheses of the foliar mycobiome of native H. brasiliensis , which may also occur in other native Amazonian trees.

Aims: To evaluate the biological activity of extracts from cultures of marine bacteria against Toxoplasma gondii and Mycobacterium tuberculosis., Methods and Results: Ethyl acetate extracts obtained from seven marine bacteria were tested against T. gondii GFP-RH and M. tuberculosis H37Rv. The cytotoxicity on HFF-1 cells was measured by a microplate resazurin fluorescent approach, and the haemolytic activity was determined photometrically. The extracts from Bacillus sp. (INV FIR35 and INV FIR48) affected the tachyzoite viability. The extracts from Bacillus, Pseudoalteromonas, Streptomyces and Micromonospora exhibited effects on infection and proliferation processes of parasite. Bacillus sp. INV FIR48 extract showed an minimum inhibitory concentration value of 50 µg ml -1 against M. tuberculosis H37Rv. All the extracts exhibited relatively low toxicity to HFF-1 cells and the primary culture of erythrocytes, except Bacillus sp. INV FIR35, which decreased cell viability under 20%. Liquid chromatography coupled to mass spectrometry analysis of the most active bacterial extract Bacillus sp. INV FIR48 showed the presence of peptide metabolites related to surfactin., Conclusions: The extract from culture of deep-sea Bacillus sp. INV FIR48 showed anti-T. gondii and anti-tuberculosis (TB) biological activity with low cytotoxicity. In addition, peptide metabolites were detected in the extract., Significance and Impact of the Study: Toxoplasmosis and TB are among the most prevalent diseases worldwide, and the current treatment drugs exhibit side effects. This study confirm that marine bacteria are on hand sources of anti-infective natural products., (© 2021 The Society for Applied Microbiology.)

Aim: The aim of this review was to evaluate the scientific literature regarding the cytogenetic damage in oral exfoliated cells of adult patients submitted to panoramic X-ray., Materials and Methods: An extensive search of the literature was conducted on PubMed, Scopus and Web of Science databases for all studies published until April 2021 using combinations of the following keywords: "panoramic X-ray," "DNA damage," "genetic damage", "genotoxicity", "mutagenicity", cytotoxicity", "buccal cells", "oral mucosa", "tongue", "gingiva", "micronucleus assay", according to the PRISMA guidelines. All clinical studies in English language were included in the study. A total of 10 studies were identified., Results: As expected, the results regarding the cytogenetic damage induced by panoramic X-ray are conflicting. Some authors have demonstrated that panoramic X-ray induces mutagenesis in oral cells, whereas others did not. After reviewing the 10 studies, two were classified as strong, four were considered moderate, and four were considered weak, according to the quality assessment components of the Effective Public Health Practice Project (EPHPP). Meta-analysis data revealed a negative response related to mutagenicity in oral cells by panoramic X-ray., Conclusion: Taken together, this review failed to demonstrate the association between micronucleus frequency and panoramic X-ray., (Copyright © 2021 International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)

Objective: To identify patient- and provider-related factors associated with the success of multidrug-resistant tuberculosis (MDR-TB) treatment in the six municipalities of Colombia with the highest number of MDR-TB cases., Methods: Bivariate and multivariate logistic regressions were used to analyze the association between treatment success (cure or treatment completion) and characteristics of the patients and physicians, nursing professionals, and psychologists involved in their treatment. The importance of knowledge in the management of MDR-TB cases was explored through focus groups with these providers., Results: Of 128 cases of TB-MDR, 63 (49.2%) experienced treatment success. Only 52.9% of the physicians and nursing professionals had satisfactory knowledge about MDR-TB. Logistic regression showed that being HIV negative, being affiliated with the contributory health insurance scheme, being cared for by a male physician, and being cared for by nursing professionals with sufficient knowledge were associated with a successful treatment outcome ( p ≤ 0.05). Qualitative analysis showed the need for in-depth, systematic training of health personnel who care for patients with MDR-TB., Conclusions: Some characteristics of patients and healthcare providers influence treatment success in MDR-TB cases. Physicians' and nurses' knowledge about MDR-TB must be improved, and follow-up of MDR-TB patients who are living with HIV and of those affiliated with the subsidized health insurance scheme in Colombia must be strengthened, as these patients have a lower likelihood of a successful treatment outcome.

Objective: To identify patient- and provider-related factors associated with the success of multidrug-resistant tuberculosis (MDR-TB) treatment in the six municipalities of Colombia with the highest number of MDR-TB cases., Methods: Bivariate and multivariate logistic regressions were used to analyze the association between treatment success (cure or treatment completion) and characteristics of the patients and physicians, nursing professionals, and psychologists involved in their treatment. The importance of knowledge in the management of MDR-TB cases was explored through focus groups with these providers., Results: Of 128 cases of TB-MDR, 63 (49.2%) experienced treatment success. Only 52.9% of the physicians and nursing professionals had satisfactory knowledge about MDR-TB. Logistic regression showed that being HIV negative, being affiliated with the contributory health insurance scheme, being cared for by a male physician, and being cared for by nursing professionals with sufficient knowledge were associated with a successful treatment outcome ( p ≤ 0.05). Qualitative analysis showed the need for in-depth, systematic training of health personnel who care for patients with MDR-TB., Conclusions: Some characteristics of patients and healthcare providers influence treatment success in MDR-TB cases. Physicians' and nurses' knowledge about MDR-TB must be improved, and follow-up of MDR-TB patients who are living with HIV and of those affiliated with the subsidized health insurance scheme in Colombia must be strengthened, as these patients have a lower likelihood of a successful treatment outcome.

Introduction: Freshwater ecosystems provide propitious conditions for the acquisition and spread of antibiotic resistance genes (ARGs), and integrons play an important role in this process., Material and Methods: In the present study, the diversity of putative environmental integron-cassettes, as well as their potential bacterial hosts in the Velhas River (Brazil), was explored through intI-attC and 16S rRNA amplicons deep sequencing. RESULTS AND DISCUSSION: ORFs related to different biological processes were observed, from DNA integration to oxidation-reduction. ARGs-cassettes were mainly associated with class 1 mobile integrons carried by pathogenic Gammaproteobacteria, and possibly sedentary chromosomal integrons hosted by Proteobacteria and Actinobacteria. Two putative novel ARG-cassettes homologs to fosB3 and novA were detected. Regarding 16SrRNA gene analysis, taxonomic and functional profiles unveiled Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Betaproteobacteria, Alphaproteobacteria, and Actinobacteria classes were the main contributors for KEGG orthologs associated with resistance., Conclusions: Overall, these results provide new information about environmental integrons as a source of resistance determinants outside clinical settings and the bacterial community in the Velhas River.

Cocoa beans used for chocolate production are fermented seeds of Theobroma cacao obtained by a natural fermentation process. The flavors and chemical compounds produced during the fermentation process make this step one of the most important in fine chocolate production. Herein, an integrative analysis of the variation of microbial community structure, using a shotgun metagenomics approach and associated physicochemical features, was performed during fermentation of fine cocoa beans. Samples of Forastero variety (FOR) and a mixture of two hybrids (PS1319 and CCN51) (MIX) from Bahia, Brazil, were analyzed at 7 different times. In the beginning (0 h), the structures of microbial communities were very different between FOR and MIX, reflecting the original plant-associated microbiomes. The highest change in microbial community structures occurred at the first 24 h of fermentation, with a marked increase in temperature and acetic acid concentration, and pH decrease. At 24-48 h both microbial community structures were quite homogenous regarding temperature, acetic acid, succinic acid, pH, soluble proteins and total phenols. During 72-96 h, the community structure resembles an acidic and warmer environment, prevailing few acetic acid bacteria. Taxonomic richness and abundance at 72-144 h exhibited significant correlation with temperature, reducing sugars, succinic, and acetic acids. Finally, we recommend that dominant microbial species of spontaneous fine cocoa fermentations should be considered as inoculum in accordance with the farm/region and GMP to maintain a differential organoleptic feature for production of fine chocolate. In our study, a starter inoculum composed of Acetobacter pausterianus and Hanseniaspora opuntiae strains is indicated., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Understanding habitat-level variation in community structure provides an informed basis for natural resources' management. Reef fishes are a major component of tropical marine biodiversity, but their abundance and distribution are poorly assessed beyond conventional SCUBA diving depths. Based on a baited-video survey of fish assemblages in Southwestern Atlantic's most biodiverse region we show that species composition responded mainly to the two major hard-bottom megahabitats (reefs and rhodolith beds) and to the amount of light reaching the bottom. Both megahabitats encompassed typical reef fish assemblages but, unexpectedly, richness in rhodolith beds and reefs was equivalent. The dissimilar fish biomass and trophic structure in reefs and rhodolith beds indicates that these systems function based on contrasting energy pathways, such as the much lower herbivory recorded in the latter. Rhodolith beds, the dominant benthic megahabitat in the tropical Southwestern Atlantic shelf, play an underrated role as fish habitats, and it is critical that they are considered in conservation planning.

In nature, arsenic (As) and iron (Fe) biotransformation are interconnected, influencing local As mobility and toxicity. While As- or Fe-metabolizing microorganisms are widely documented, knowledge concerning their cycling genes, associated with geophysicochemical data and taxonomic distribution, remains scarce. We performed a meta-analysis to explore the distribution and environmental importance of As- and Fe-redox genes (AsRGs and FeRGs) and predict their significant correlations and hosts. The most abundant and ubiquitous AsRGs and FeRGs were arsC and ccoN, respectively. The ccoN gene had the highest frequency at pH ≥ 9.1, in which dissolved Fe(II) is scarce, possibly contributing to enhanced host survival. Fe(III) oxidation genes iro and ccoN appear to be associated with As(V) detoxification in mesophilic environments. No correlation was observed between Fe(III) reduction gene omcB and arsenate reductase genes. Cytochromes with putative roles in Fe-redox reactions were identified (including yceJ and fbcH) and were significantly correlated with As(V) reduction genes under diverse geophysicochemical conditions. The taxonomies of AsRGs and FeRGs-carrying contigs revealed great diversity, among which various, such as Chlamydea (arsC) and Firmicutes (omcB), were previously undescribed. Nearly all (98.9%) of the AsRGs and FeRGs were not carried by any plasmid sequences. This meta-analysis expands our understanding of the global environmental, taxonomic and functional microbiome involved in As- and Fe-redox transformations. Moreover, these findings should help guide studies on putative in vivo functional roles of cytochromes in Fe-redox pathways., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background/aim: Genotoxicity is the capacity of an agent to induce damage to DNA. Given the close relationship between genotoxicity and carcinogenesis, several assays have been developed for detecting genetic damage. Among them, the single-cell gel (comet) assay plays an important role for evaluating DNA damage in mammalian cells, including those of the oral cavity. The purpose of this article was to provide a critical review of the application of single-cell gel comet assay to buccal cells., Material and Methods: A search of the scientific literature was conducted of published studies available on single-cell gel comet assay and oral cells., Results: The results showed that the majority of studies were conducted on humans, whereas few were designed for use in rodents and in vitro., Conclusion: Further studies within the field are relevant for better understanding the underlying mechanisms of genotoxicity in oral cells, especially since the use of humans is quite complicated due to issues of ethics., (Copyright© 2019, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)

Background: There are no reliable estimates of hospital inpatient suicides in the United States. Understanding the rate and the methods used in suicides is important to guide prevention efforts. This study analyzed two national data sets to establish an evidence-based estimate of hospital inpatient suicides and the methods used., Methods: The study is designed as a cross-sectional analysis of data from 27 states reporting to the National Violent Death Reporting System (NVDRS) for 2014-2015, and from hospitals reporting to The Joint Commission's Sentinel Event (SE) Database from 2010 to 2017. Categorical variables and qualitative reviews of event narratives were used to identify and code suicide events occurring during hospital inpatient treatment., Results: Based on the hospital inpatient suicides reported in the NVDRS during 2014-2015, 73.9% of which occurred during psychiatric treatment, it is estimated that between 48.5 and 64.9 hospital inpatient suicides occur per year in the United States. Of these, 31.0 to 51.7 are expected to involve psychiatric inpatients. Hanging was the most common method of inpatient suicide in both the NVDRS and SE databases (71.7% and 70.3%, respectively)., Conclusion: The estimated number of hospital inpatient suicides per year in the United States ranges from 48.5 to 64.9, which is far below the widely cited figure of 1,500 per year. Analysis of inpatient suicide methods suggests that hospital prevention efforts should be primarily focused on mitigating risks associated with hanging, and additional suicide prevention efforts may be best directed toward reducing the risk of suicide immediately following discharge., (Copyright © 2018 The Joint Commission. Published by Elsevier Inc. All rights reserved.)

Sugarcane production is strongly influenced by drought, which is a limiting factor for agricultural productivity in the world. In this study, the gene expression profiles obtained by de novo assembly of the leaf transcriptome of two sugarcane cultivars that differ in their physiological response to water deficit were evaluated by the RNA-Seq method: drought-tolerant cultivar (SP81-3250) and drought-sensitive cultivar (RB855453). For this purpose, plants were grown in a greenhouse for 60 days and were then submitted to three treatments: control (-0.01 to -0.015 MPa), moderate water deficit (-0.05 to -0.055 MPa), and severe water deficit (-0.075 to -0.08 MPa). The plants were evaluated 30, 60, and 90 days after the beginning of treatment. Sequencing on an Illumina platform (RNA-Seq) generated more than one billion sequences, resulting in 177,509 and 185,153 transcripts for the tolerant and sensitive cultivar, respectively. These transcripts were aligned with sequences from Saccharum spp, Sorghum bicolor, Miscanthus giganteus, and Arabidopsis thaliana available in public databases. The differentially expressed genes detected during the prolonged period of water deficit permit to increase our understanding of the molecular patterns involved in the physiological response of the two cultivars. The tolerant cultivar differentially expressed a larger number of genes at 90 days, while in the sensitive cultivar the number of differentially expressed genes was higher in 30 days. Both cultivars perceived the lack of water, but the tolerant cultivar responded more slowly than the sensitive cultivar. The latter requires rapid activation of different water-deficit stress response mechanisms for its survival. This rapid activation of metabolic pathways in response to water stress does not appear to be the key mechanism of drought tolerance in sugarcane. There is still much to clarify on the molecular and physiological pattern of plants in response to drought.

Objective: To perform classic and molecular epidemiological surveillance of human tuberculosis caused by Mycobacterium bovis in bovine supply chains at farms with PPD positive bovines in the departments of Antioquia, Boyacá and Cundinamarca during a one-year period., Methods: Livestock farms with PPD positive bovines or buffalos were visited in the study departments according to information obtained in the "Programa Nacional de Tuberculosis bovina" (National program on bovine Tuberculosis) released by ICA (Colombian Agriculture and Livestock Institute). Data on socio-demographic information and tuberculosis risk factors associated to the occupation were collected through a survey applied to all workers at the visited farms. Sputum samples were obtained after informed consent. The sputa underwent microbiological and molecular testing to identify members of the M. tuberculosis complex., Results: Thirty-three livestock farms were visited and information of 164 workers from the bovine supply chain was collected. Staying in a PPD positive farm for more than a year, ignorance about the disease and the presence of possible vectors, like dogs and cats, were identified as possible risk factors for developing tuberculosis. No cases of tuberculosis caused by M. bovis or M. tuberculosis in workers of the visited farms were found., Conclusion: No cases of the disease caused by this zoonotic agent were documented in the departments of Antioquia, Boyacá and Cundinamarca.

Background: An understanding of how health information technology (health IT) can contribute to sentinel events is necessary to learn how to safely implement and use health IT. An analysis was conducted to explore how health IT may contribute to adverse events that result in death or severe harm to the patient., Methods: For 3,375 de-identified sentinel events voluntarily reported to The Joint Commission between January 1, 2010, and June 30, 2013, categorical and keyword queries were used to search for potential health IT-related events. Each of the identified events was reviewed on the basis of findings from root cause analyses (RCAs) to determine if health IT contributed to or caused the event, and if so, how and why. The contributing factors were classified using a composite of existing classification schemes., Results: A total of 120 health IT-related sentinel events (affecting 125 patients) were identified. More than half resulted in patient death, 30% resulted in unexpected or additional care, and 11% resulted in permanent loss of function. The three most frequently identified event types were (1) medication errors, (2) wrong-site surgery (including the wrong side, wrong procedure, and wrong patient), and (3) delays in treatment. Contributing factors were most frequently associated with the human-computer interface, workflow and communication, and clinical content-related issues., Conclusions: The classification of health IT-related contributing factors indicates that health IT-related events are primarily associated with the sociotechnical dimensions of human-computer interface, workflow and communication, and clinical content. Improved identification of health IT-related contributing factors in the context of the sociotechnical dimensions may help software developers, device manufacturers, and end users in health care organizations proactively identify vulnerabilities and hazards, ultimately reducing the risk of harm to patients.

The Sox family of transcription factors have been widely studied in the context of oligodendrocyte development. However, comparatively little is known about the role of Sox2, especially during CNS remyelination. Here we show that the expression of Sox2 occurs in oligodendrocyte progenitor cells (OPCs) in rodent models during myelination and in activated adult OPCs responding to demyelination, and is also detected in multiple sclerosis lesions. In normal adult white matter of both mice and rats, it is neither expressed by adult OPCs nor by oligodendrocytes (although it is expressed by a subpopulation of adult astrocytes). Overexpression of Sox2 in rat OPCs in vitro maintains the cells in a proliferative state and inhibits differentiation, while Sox2 knockout results in decreased OPC proliferation and survival, suggesting that Sox2 contributes to the expansion of OPCs during the recruitment phase of remyelination. Loss of function in cultured mouse OPCs also results in an impaired ability to undergo normal differentiation in response to differentiation signals, suggesting that Sox2 expression in activated OPCs also primes these cells to eventually undergo differentiation. In vivo studies on remyelination following experimental toxin-induced demyelination in mice with inducible loss of Sox2 revealed impaired remyelination, which was largely due to a profound attenuation of OPC recruitment and likely also due to impaired differentiation. Our results reveal a key role of Sox2 expression in OPCs responding to demyelination, enabling them to effectively contribute to remyelination., Significance Statement: Understanding the mechanisms of CNS remyelination is central to developing effective means by which this process can be therapeutically enhanced in chronic demyelinating diseases such as multiple sclerosis. In this study, we describe the role of Sox2, a transcription factor widely implicated in stem cell biology, in CNS myelination and remyelination. We show how Sox2 is expressed in oligodendrocyte progenitor cells (OPCs) preparing to undergo differentiation, allowing them to undergo proliferation and priming them for subsequent differentiation. Although Sox2 is unlikely to be a direct therapeutic target, these data nevertheless provide more information on how OPC differentiation is controlled and therefore enriches our understanding of this important CNS regenerative process., (Copyright © 2015 the authors 0270-6474/15/3511482-018$15.00/0.)

Background: Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed for genome-wide positive selection detection., Results: We present POTION, an open source, modular and end-to-end software for genome-scale detection of positive Darwinian selection in groups of homologous coding sequences. Our software represents a key step towards genome-scale, automated detection of positive selection, from predicted coding sequences and their homology relationships to high-quality groups of positively selected genes. POTION reduces false positives through several sophisticated sequence and group filters based on numeric, phylogenetic, quality and conservation criteria to remove spurious data and through multiple hypothesis corrections, and considerably reduces computation time thanks to a parallelized design. Our software achieved a high classification performance when used to evaluate a curated dataset of Trypanosoma brucei paralogs previously surveyed for positive selection. When used to analyze predicted groups of homologous genes of 19 strains of Mycobacterium tuberculosis as a case study we demonstrated the filters implemented in POTION to remove sources of errors that commonly inflate errors in positive selection detection. A thorough literature review found no other software similar to POTION in terms of customization, scale and automation., Conclusion: To the best of our knowledge, POTION is the first tool to allow users to construct and check hypotheses regarding the occurrence of site-based evidence of positive selection in non-curated, genome-scale data within a feasible time frame and with no human intervention after initial configuration. POTION is available at http://www.lmb.cnptia.embrapa.br/share/POTION/.

Paracoccidioidomycosis (PCM) is a systemic fungal infection, endemic in Brazil, that leads to severe morbidity and even mortality if not correctly treated. Patients may respond differently to PCM depending on the pattern of the acquired immune response developed. The onset of protective immune response is notably mediated by neutrophils (PMN) that play an important role through directly killing the fungi and also by interacting with other cell types to modulate the acquired protective immune response that may follow. In that way, this study aimed to present and compare different experimental models of PCM (intraperitoneal and subcutaneous) regarding PMN production and maturation inside femoral bone marrow and also PMN infiltration in peritoneal and subcutaneous exudates of resistant and susceptible mice. We also assessed the fungal colony forming units and the levels of soluble inflammatory mediators (LTB4, KC, IFN-γ, GM-CSF, and IL-10) inside subcutaneous air-pouches to compare the efficiency of the PMN present at this site in relation to the two main neutrophil functions: initial lysis of the invading pathogen and modulation of the acquired immune response. P. brasiliensis inoculated intraperitoneally was able to disseminate to the bone marrow of susceptible mice, causing a more marked alteration of PMN production and maturation than that observed after resistant mice infection by the same route. Subcutaneous air-pouch inoculation of P. brasiliensis elicited a controlled and limited infection that produced a PMN-rich exudate, thus favoring the study of the interaction between the fungus and the neutrophils. Susceptible mice produced higher numbers of PMN; however, these cells were less effective in killing the fungi. Inflammatory cytokines were more pronounced in resistant mice, which supports their PCM raised resistance.

Vertical transmission is the main route of HIV infection in childhood. Because of the persistence of maternal HIV antibodies, virologic assays that directly detect HIV are required to diagnose HIV infection in infants younger than 18 months of age. The sensitivity of HIV RNA/DNA assays increases as the child becomes older. These tests have specificity values greater than 95%. The aim of this study was to evaluate the performance of the COBAS Taqman HIV-1 Test, v1.0 assay (Roche) and its concordance with a Multiplex Nested-PCR. Of 341 samples processed, 15 were positive and 326 negative by both methods. Sensitivity and specificity overall values for the viral load assay were 88.2% and 100%, respectively. Our results indicate that the COBAS Taqman assay evaluated could be used as an alternative method to diagnose HIV congenital infection., (Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.)