Data treatment methods for real-time colorimetric loop-mediated isothermal amplification reactions.

With the SARS-CoV-2 pandemic and the need for affordable and rapid mass testing, colorimetric isothermal amplification reactions such as Loop-Mediated Isothermal Amplification (LAMP) are quickly rising in importance. The technique generates data that is similar to quantitative Polymerase Chain Reaction (qPCR), but instead of an endpoint color visualization, it is possible to construct a signal over a time curve. As the number of works using time-course analysis of isothermal reactions increases, there is a need to analyze data and standardize their related treatments quantitatively. Here, we take a step forward toward this goal by evaluating different available data treatments (curve models) for amplification curves, which allows for a cycle threshold-like parameter extraction. In this study, we uncover evidence of a double sigmoid equation as the most adequate model to describe amplification data from our remote diagnostics system and discuss possibilities for similar setups. We also demonstrate the use of multimodal Gompertz regression models. Thus, this work provides advances toward standardized and unbiased data reporting of Reverse Transcription (RT) LAMP reactions, which may facilitate and quicken assay interpretation, potentially enabling the application of machine learning techniques for further optimization and classification.

Descending Necrotizing Mediastinitis by Streptococcus anginosus and Prevotella buccae in an Intensive Care Unit Patient: A Case Report.

Necrotizing infections of deep neck spaces are a group of life-threatening infectious diseases acquired through trauma or as a descending infection from an odontogenic source. The isolation of pathogens is unusual because of the anaerobic nature of the infection; however, one way to achieve this is through the use of automated microbiological methods like matrix-assisted laser desorption/ionization and time-of-flight (MALDI-TOF) following standard microbiology protocols for analyzing samples from potential anaerobic infections. We present a case of a patient without risk factors for descending necrotizing mediastinitis with isolation of Streptococcus anginosus and Prevotella​​​​​​​ buccae managed at the intensive care unit with a multidisciplinary team. We present our approach and how we successfully treat this complicated infection.

Hilab System Device in an Oncological Hospital: A New Clinical Approach for Point of Care CBC Test, Supported by the Internet of Things and Machine Learning.

The complete blood count (CBC) is a highly requested test that is generally restricted to centralized laboratories, which are limited by high cost, being maintenance-demanding, and requiring costly equipment. The Hilab System (HS) is a small, handheld hematological platform that uses microscopy and chromatography techniques, combined with machine learning (ML) and artificial intelligence (AI), to perform a CBC test. This platform uses ML and AI techniques to add higher accuracy and reliability to the results besides allowing for faster reporting. For clinical and flagging capability evaluation of the handheld device, the study analyzed 550 blood samples of patients from a reference institution for oncological diseases. The clinical analysis encompassed the data comparison between the Hilab System and a conventional hematological analyzer (Sysmex XE-2100) for all CBC analytes. The flagging capability study compared the microscopic findings from the Hilab System and the standard blood smear evaluation method. The study also assessed the sample collection source (venous or capillary) influences. The Pearson correlation, Student t-test, Bland-Altman, and Passing-Bablok plot of analytes were calculated and are shown. Data from both methodologies were similar (p > 0.05; r ≥ 0.9 for most parameters) for all CBC analytes and flagging parameters. Venous and capillary samples did not differ statistically (p > 0.05). The study indicates that the Hilab System provides humanized blood collection associated with fast and accurate data, essential features for patient wellbeing and quick physician decision making.

Clinical Validation of a Colorimetric Loop-Mediated Isothermal Amplification Using a Portable Device for the Rapid Detection of SARS-CoV-2.

Quick and reliable mass testing of infected people is an effective tool for the contingency of SARS-CoV-2. During the COVID-19 pandemic, Point-of-Care (POC) tests using Loop-Mediated Isothermal Amplification (LAMP) arose as a useful diagnostic tool. LAMP tests are a robust and fast alternative to Polymerase Chain Reaction (PCR), and their isothermal property allows easy incorporation into POC platforms. The main drawback of using colorimetric LAMP is the reported short-term stability of the pre-mixed reagents, as well as the relatively high rate of false-positive results. Also, low-magnitude amplification can produce a subtle color change, making it difficult to discern a positive reaction. This paper presents Hilab Molecular, a portable device that uses the Internet of Things and Artificial Intelligence to pre-analyze colorimetric data. In addition, we established manufacturing procedures to increase the stability of colorimetric RT-LAMP tests. We show that ready-to-use reactions can be stored for up to 120 days at -20 °C. Furthermore, we validated both the Hilab Molecular device and the Hilab RT-LAMP test for SARS-CoV-2 using 581 patient samples without any purification steps. We achieved a sensitivity of 92.93% and specificity of 99.42% (samples with CT ≤ 30) when compared to RT-qPCR.

Enhancing a SARS-CoV-2 nucleocapsid antigen test sensitivity with cost efficient strategy through a cotton intermembrane insertion.

Lateral flow antigen tests have been widely used in the Covid-19 pandemic, allowing faster diagnostic test results and preventing further viral spread through isolation of infected individuals. Accomplishment of this screening must be performed with tests that show satisfactory sensitivity in order to successfully detect the target protein and avoid false negatives. The aim of this study was to create a lateral flow test that could detect SARS-CoV-2 nucleocapsid protein in low concentrations that were comparable to the limits of detection claimed by existing tests from the market. To do so, several adjustments were necessary during research and development of the prototypes until they were consistent with these criteria. The proposed alternatives of increasing the test line antibody concentration and addition of an intermembrane between the conjugate pad and the nitrocellulose membrane were able to increase the sensitivity four-fold and generate a new rapid test prototype called "lateral flow intermembrane immunoassay test" (LFIIT). This prototype showed an adequate limit of detection (2.0 ng mL-1) while maintaining affordability and simplicity in manufacturing processes.

Development of an optimized colorimetric RT-LAMP for SARS-CoV-2 assay with enhanced procedure controls for remote diagnostics.

The coronavirus pandemic accentuated the need for molecular diagnostic tests. A technique highly used to this end is the Polymerase Chain Reaction (PCR)-a sensitive and specific technique commonly used as the gold standard for molecular diagnostics. However, it demands highly trained personnel and high-maintenance equipment and is relatively time-consuming. An alternative is the Loop-Mediated Isothermal Amplification (LAMP) technique, which doesn't need sample purification or expensive equipment, and is similar to PCR when compared in sensitivity and specificity. In this paper, we developed an optimized colorimetric Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) Point-of-Care test using a portable device to diagnose COVID-19. Variables such as concentration of primers, magnesium sulfate, betaine, hydrochloride guanidine, Bst, and temperature of the reactions were tested. We also created a pipetting quality control system-using a combination of dyes-to avoid false negatives due to a lack of samples added to the reaction test tube. Mineral oil was incorporated in the composition of the RT-LAMP reactions to avoid evaporation when a heating lid isn't available. The final RT-LAMP test is tenfold more sensitive when compared to the WarmStart Colorimetric Master mix from New England Biolabs with a sensitivity of 5 copies per µL.

Hilab system, a new point-of-care hematology analyzer supported by the Internet of Things and Artificial Intelligence.

The complete blood count (CBC) is one of the most requested tests by physicians. CBC tests, most realized in conventional hematological analyzers, are restricted to centralized laboratories due to frequent maintenance, large devices, and expensive costs required. On the other hand, most handheld CBC devices commercially available show high prices and are not liable to calibration or control procedures, which results in poor quality compared to standard hematology instruments. The Hilab system is a small-handed hematological platform that uses microscopy and chromatography techniques for blood cells and hematimetric parameters analysis through artificial intelligence, machine learning, and deep learning techniques. For clinical evaluation of the handheld CBC device, 450 blood samples were analyzed. The samples encompassed normal (82%) and pathological conditions (18%), such as thalassemias (2.2%), anemias (6.6%), and infections (9.2%). For all analytes, accuracy, precision, method comparison, and flagging capabilities of the Hilab System, were compared with the Sysmex XE-2100 (Sysmex, Japan) results. The sample source (venous and capillary) influences were also evaluated. Pearson correlation, Student t test, bias, and the Bland-Altman plot of each blood count analyte were calculated and shown. The significance level was set at p ≤ 0.05. For clinical evaluation, Hilab System and the Sysmex XE-2100 showed a strong correlation (r ≥ 0.9) for most evaluated parameters. In the precision study, analytes showed CV inside the limits established according to European Federation of Clinical Chemistry and Laboratory Medicine guidelines. The flagging capabilities of the Hilab system, compared to the manual microscopy technique, presented high sensibility, specificity, and accuracy. Venous and capillary samples (p > 0.05) do not differ statistically. Considering the need for point-of-care CBCs, the study indicated that the Hilab system provides fast, accurate, low cost, and robust analysis for reliable clinical use.

"We All Get Raped": Sexual Violence Against Latin American Women in Migratory Transit in Mexico.

The article addresses some forms of sexual violence suffered by Latin American women during migratory transit through Mexico. In-depth, semi-structured, qualitative-phenomenological interviews were conducted with 10 women in different stages of major transmigration states. The findings demonstrate the ubiquity of sexual violence during the migration. Five themes were identified: (a) The migration dimension of "being a woman"; (b) Recognition of contextual factors associated with the migratory process: "Intermediaries, road, shelters and sisterhood"; (c) The costs of migration: Abuse, discrimination, and persecution: "Criminal groups, physical violence, and "La Bestia"; (d) Triggers and supports: "Escape and future expectations"; and (e) God as a support.

Educação de tempo integral: da carência à proteção / Full-time education: from lack to protection / Educación de tiempo integral: de la carencia a la protección

A noção de periculosidade da infância pobre vem sendo construída, desde as políticas higienistas do início do século passado, figurando a escola, muitas vezes, como solução para a desigualdade social. Tratou-se de pesquisa qualitativo-descritiva, a partir de entrevistas individuais com trabalhadores de um Núcleo de Educação de Tempo Integral, acerca das crianças e adolescentes em situação de risco e vulnerabilidade social, a partir da teoria das Representações Sociais. Os discursos dos entrevistados descrevem as crianças e adolescentes como vítimas tanto da rua como de suas próprias famílias, percebidas como perigosas e negligentes. Emerge a imagem de uma escola que não apenas instrui e ensina, mas cuida e protege os alunos de uma realidade dura e cruel, alunos cujas famílias não apresentam condições adequadas de exercer o cuidado necessário. Concluindo, tal proteção é descrita como importante para a defesa da sociedade, pois as crianças e adolescentes pobres aparecem não como estando em risco social, mas como sendo o próprio risco.

The notion of dangerousness of poor childhood has been constructed, since the hygienist policies of the beginning of the last century, with school as often a solution to social inequality. This was a qualitative-descriptive research, based on individual interviews with workers of a Center for Full-time Education for children and adolescents at risk and social vulnerability, based on the theory of Social Representations. The interviewees' speeches describe children and adolescents as victims of both, the street and their own families, perceived as dangerous and negligent. Emerges the image of a school that not only instructs and teaches but takes care of and protects students from a harsh and cruel reality, students whose families do not have adequate conditions to exercise the necessary care. Thus, such protection is described as important for the defense of society, since poor children and adolescents appear not as being at social risk, but as the risk themselves.

La noción de peligrosidad de la infancia pobre se ha construido a partir de las políticas higienistas del siglo pasado en los cuales se ubica la escuela, a menudo, como una solución a la desigualdad social. Este fue un estudio cualitativo-descriptivo, a partir de entrevistas individuales con los empleados de un Núcleo de Educación de tiempo integral, sobre los niños y adolescentes en situación de riesgo y vulnerabilidad social, a partir de la teoría de las representaciones sociales. Los discursos de los encuestados describen los niños y adolescentes como víctimas tanto de la calle como de sus propias familias, percibidas como peligrosas y negligentes. Emerge la imagen de una escuela que no sólo instruye y enseña, pero cuida y protege a los estudiantes de una realidad dura y cruel, alumnos cuyas familias no presentan condiciones adecuadas de ejercer el cuidado necesario. En conclusión, esta protección es descrita como importante para la defensa de la sociedad, porque los niños y adolescentes pobres no configuran como personas en situación de riesgo social, mas como sendo ellos el propio riesgo.

Implementation of rapid diagnostics assays for detection of histoplasmosis and cryptococcosis in central american people living with HIV.

OBJECTIVES: Histoplasmosis and cryptococcosis are important public health problems in people living with HIV (PLHIV) in Central America. Conventional laboratory assays, based on microscopy and culture, are not optimal for the diagnosis of either disease. However, antigen (Ag) assays are rapid and highly accurate for the diagnosis of these infections. METHODS: Laboratory surveillance of PLHIV was carried out in four hospitals in Panama, Honduras and Nicaragua, between 2015 and 2019. Detection of Histoplasma antigens in urine was performed by enzyme immunoassay (EIA), and Cryptococcus antigen detection in sera and cerebrospinal fluid specimens was performed by lateral flow assay (LFA). RESULTS: A total of 4,453 PLHIV with clinical suspicion of histoplasmosis (n = 1,343) or cryptococcosis (n = 3,110; 2,721 sera and 389 CSF) were tested. Of 1,343 patients suspected of having histoplasmosis, 269 (20%) were Histoplasma Ag positive. Of 3,110 patients tested using the Cryptococcus Ag assay, 329 (11%) were positive. Honduras reported the highest positivity rates (32% for Histoplasma Ag, and 16% for Cryptococcus Ag); Panama reported the largest number of patients testing positive using the Histoplasma Ag assay (n = 201); and Nicaragua reported the largest number of patients testing positive using the Cryptococcus Ag assay (n = 170). CONCLUSION: Here, we show how the implementation of rapid diagnostics assays impacted case detection and was useful for the care of people with advanced HIV. Rapid and accurate diagnosis could reduce mortality associated with histoplasmosis and cryptococcosis in PLHIV.

Geographic Distribution and Incidence of Melioidosis, Panama1.

Melioidosis is an infection caused by Burkholderia pseudomallei. Most cases occur in Southeast Asia and northern Australia; <100 cases have been reported in the Americas. We conducted a retrospective study and identified 12 melioidosis cases in Panama during 2007-2017, suggesting possible endemicity and increased need for surveillance.

Emerging Multidrug-Resistant Candida duobushaemulonii Infections in Panama Hospitals: Importance of Laboratory Surveillance and Accurate Identification.

Candida duobushaemulonii, a yeast closely related to Candida auris, is thought to cause infections in rare cases and is often misidentified. In October 2016, the Panamanian Ministry of Health implemented laboratory surveillance for C. auris Suspected C. auris isolates were forwarded to the national reference laboratory for identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry and antifungal susceptibility testing. Between November 2016 and May 2017, 17 of 36 (47%) isolates suspected to be C. auris were identified as C. duobushaemulonii. These 17 isolates were obtained from 14 patients at six hospitals. Ten patients, including three children, had bloodstream infections, and MICs for fluconazole, voriconazole, and amphotericin B were elevated. No resistance to echinocandins was observed. C. duobushaemulonii causes more invasive infections than previously appreciated and poses a substantial problem, given its resistance to multiple antifungals. Expanded laboratory surveillance is an important step in the detection and control of such emerging pathogens.

Isolation of Candida auris from 9 patients in Central America: Importance of accurate diagnosis and susceptibility testing.

Candida auris is an emerging multidrug-resistant (MDR) fungus associated with invasive infections and high mortality. This report describes 9 patients from whom C. auris was isolated at a hospital in Panama City, Panama, the first such cases in Central America, and highlights the challenges of accurate identification and methods for susceptibility testing.

Gender in the allocation of organs in kidney transplants: meta-analysis.

UNLABELLED: OBJECTIVE To analyze whether gender influence survival results of kidney transplant grafts and patients.METHODS Systematic review with meta-analysis of cohort studies available on Medline (PubMed), LILACS, CENTRAL, and Embase databases, including manual searching and in the grey literature. The selection of studies and the collection of data were conducted twice by independent reviewers, and disagreements were settled by a third reviewer. Graft and patient survival rates were evaluated as effectiveness measurements. Meta-analysis was conducted with the Review Manager® 5.2 software, through the application of a random effects model. Recipient, donor, and donor-recipient gender comparisons were evaluated. RESULTS: Twenty-nine studies involving 765,753 patients were included. Regarding graft survival, those from male donors were observed to have longer survival rates as compared to the ones from female donors, only regarding a 10-year follow-up period. Comparison between recipient genders was not found to have significant differences on any evaluated follow-up periods. In the evaluation between donor-recipient genders, male donor-male recipient transplants were favored in a statistically significant way. No statistically significant differences were observed in regards to patient survival for gender comparisons in all follow-up periods evaluated.CONCLUSIONS The quantitative analysis of the studies suggests that donor or recipient genders, when evaluated isolatedly, do not influence patient or graft survival rates. However, the combination between donor-recipient genders may be a determining factor for graft survival.

Gender in the allocation of organs in kidney transplants: meta-analysis / Gênero na alocação de órgãos no transplante renal: metanálise

OBJECTIVE To analyze whether gender influence survival results of kidney transplant grafts and patients.METHODS Systematic review with meta-analysis of cohort studies available on Medline (PubMed), LILACS, CENTRAL, and Embase databases, including manual searching and in the grey literature. The selection of studies and the collection of data were conducted twice by independent reviewers, and disagreements were settled by a third reviewer. Graft and patient survival rates were evaluated as effectiveness measurements. Meta-analysis was conducted with the Review Manager® 5.2 software, through the application of a random effects model. Recipient, donor, and donor-recipient gender comparisons were evaluated.RESULTS : Twenty-nine studies involving 765,753 patients were included. Regarding graft survival, those from male donors were observed to have longer survival rates as compared to the ones from female donors, only regarding a 10-year follow-up period. Comparison between recipient genders was not found to have significant differences on any evaluated follow-up periods. In the evaluation between donor-recipient genders, male donor-male recipient transplants were favored in a statistically significant way. No statistically significant differences were observed in regards to patient survival for gender comparisons in all follow-up periods evaluated.CONCLUSIONS The quantitative analysis of the studies suggests that donor or recipient genders, when evaluated isolatedly, do not influence patient or graft survival rates. However, the combination between donor-recipient genders may be a determining factor for graft survival.

OBJETIVO Analisar se o gênero influencia os resultados da sobrevida do enxerto e do paciente no transplante renal.MÉTODOS Revisão sistemática com metanálise de estudos de coorte disponíveis nas bases de dados Medline (PubMed), Lilacs, Central e Embase, incluindo busca manual e na literatura cinzenta. A seleção dos estudos e a coleta dos dados foram realizadas em duplicata por revisores independentes e as discordâncias foram resolvidas por um terceiro revisor. A sobrevida do enxerto e do paciente foram avaliadas como medidas de efetividade. A metanálise foi conduzida no softwareReview Manager® 5.2, aplicando o modelo de efeitos aleatórios. Foram avaliadas as comparações entre gênero de receptor, doador e doador-receptor.RESULTADOS Foram incluídos 29 estudos envolvendo 765.753 pacientes. Em relação à sobrevida do enxerto, aqueles provenientes de doadores masculinos apresentaram maior sobrevida quando comparado com aqueles de doadores femininos, somente no tempo de acompanhamento de 10 anos. A comparação entre gênero de receptor não apresentou diferença significativa em nenhum tempo de acompanhamento avaliado. Na avaliação entre gênero de doador-receptor houve favorecimento estatisticamente significante para doador masculino-receptor masculino. Não houve diferença, estatisticamente significante, na sobrevida do paciente para as comparações entre gênero em todos os períodos de acompanhamento avaliados.CONCLUSÕES A análise quantitativa dos estudos sugere que o gênero do doador ou do receptor, avaliado isoladamente, não influencia na sobrevida do enxerto e paciente. Contudo, a combinação entre gênero de doador-receptor pode ser fator determinante para a sobrevida do enxerto.