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1.
Open Forum Infect Dis ; 11(8): ofae416, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39100532

RESUMO

Background: Adherence to anti-tuberculosis treatment (ATT) in Brazil remains a challenge in achieving the goals set by the World Health Organization (WHO). Patients who are lost to follow-up during treatment pose a significant public health problem. This study aimed to investigate the factors associated with unfavorable ATT outcomes among those undergoing retreatment in Brazil. Methods: We conducted an observational study of patients aged ≥18 years with tuberculosis (TB) reported to the Brazilian National Notifiable Disease Information System between 2015 and 2022. Clinical and epidemiologic variables were compared between the study groups (new cases and retreatment). Regression models identified variables associated with unfavorable outcomes. Results: Among 743 823 reported TB cases in the study period, 555 632 cases were eligible, consisting of 462 061 new cases and 93 571 undergoing retreatments (44 642 recurrent and 48 929 retreatments after loss to follow-up [RLTFU]). RLTFU (odds ratio [OR], 3.96 [95% confidence interval {CI}, 3.83-4.1]) was a significant risk factor for any type of unfavorable ATT. Furthermore, RLTFU (OR, 4.93 [95% CI, 4.76-5.11]) was the main risk factor for subsequent LTFU. For death, aside from advanced age, living with HIV (OR, 6.28 [95% CI, 6.03-6.54]) was the top risk factor. Conclusions: Retreatment is a substantial risk factor for unfavorable ATT outcomes, especially after LTFU. The rates of treatment success in RLTFU are distant from the WHO End TB Strategy targets throughout Brazil. These findings underscore the need for targeted interventions to improve treatment adherence and outcomes in persons who experience RLTFU.

2.
ACS Chem Biol ; 19(9): 2002-2011, 2024 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-39207862

RESUMO

Aminoglycosides are essential antibiotics used to treat severe infections caused mainly by Gram-negative bacteria. Gentamicin is an aminoglycoside and, despite its toxicity, is clinically used to treat several pulmonary and urinary infections. The commercial form of gentamicin is a mixture of five compounds with minor differences in the methylation of one of their aminosugars. In the case of two compounds, gentamicin C2 and C2a, the only difference is the stereochemistry of the methyl group attached to C-6'. GenB2 is the enzyme responsible for this epimerization and is one of the four PLP-dependent enzymes encoded by the gentamicin biosynthetic gene cluster. Herein, we have determined the structure of GenB2 in its holo form in complex with PMP and also in the ternary complex with gentamicin X2 and G418, two substrate analogues. Based on the structural analysis, we were able to identify the structural basis for the catalytic mechanism of this enzyme, which was also studied by site-directed mutagenesis. Unprecedently, GenB2 is a PLP-dependent enzyme from fold I, which is able to catalyze an epimerization but with a mechanism distinct from that of fold III PLP-dependent epimerases using a cysteine residue near the N-terminus. The substitution of this cysteine residue for serine or alanine completely abolished the epimerase function of the enzyme, confirming its involvement. This study not only contributes to the understanding of the enzymology of gentamicin biosynthesis but also provides valuable details for exploring the enzymatic production of new aminoglycoside derivatives.


Assuntos
Gentamicinas , Gentamicinas/metabolismo , Gentamicinas/biossíntese , Gentamicinas/química , Antibacterianos/química , Antibacterianos/biossíntese , Antibacterianos/metabolismo , Racemases e Epimerases/metabolismo , Racemases e Epimerases/genética , Racemases e Epimerases/química , Modelos Moleculares , Cristalografia por Raios X , Mutagênese Sítio-Dirigida , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética
3.
Lancet Reg Health Am ; 36: 100804, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38912329

RESUMO

Background: Since 2014, Brazil has gradually implemented the Xpert MTB/RIF (Xpert) test to enhance early tuberculosis (TB) and drug-resistant (DR-TB) detection and control, yet its nationwide impact remains underexplored. Our study conducts an intervention time-series analysis (ITSA) to evaluate how the Xpert's implementation has improved TB and DR-TB detection nationwide. Methods: 1,061,776 cases from Brazil's National TB Registry (2011-2022) were reviewed and ITSA (2011-2019) was used to gauge the impact of the Xpert's adoption on TB and DR-TB notification. Granger Causality and dynamic regression modelling determined if incorporating Xpert testing as an external regressor enhanced forecasting accuracy for Brazil's future TB trends. Findings: Xpert implementation resulted in a 9.7% increase in TB notification and substantial improvements in DR-TB (63.6%) and drug-susceptible TB (92.1%) detection compared to expected notifications if it had not been implemented. Xpert testing counts also presented a time-dependent relationship with DR-TB detection post-implementation, and improved predictions in forecasting models, which depicted a potential increase in TB and DR-TB detection in the next six years. Interpretation: This study underscores the critical role of Xpert's adoption in boosting TB and DR-TB detection in Brazil, reinforcing the case for its widespread use in disease control. Improvements in prediction accuracy resulting from integrating Xpert data are crucial for allocating resources and reducing the incidence of TB. By acknowledging Xpert's role in both disease control and improving predictions, we advocate for its expanded use and further research into advanced molecular diagnostics for effective TB and DR-TB control. Funding: FIOCRUZ.

4.
Phys Rev E ; 109(3-1): 034303, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38632720

RESUMO

Graphs have become widely used to represent and study social, biological, and technological systems. Statistical methods to analyze empirical graphs were proposed based on the graph's spectral density. However, their running time is cubic in the number of vertices, precluding direct application to large instances. Thus, efficient algorithms to calculate the spectral density become necessary. For sparse graphs, the cavity method can efficiently approximate the spectral density of locally treelike undirected and directed graphs. However, it does not apply to most empirical graphs because they have heterogeneous structures. Thus, we propose methods for undirected and directed graphs with heterogeneous structures using a new vertex's neighborhood definition and the cavity approach. Our methods' time and space complexities are O(|E|h_{max}^{3}t) and O(|E|h_{max}^{2}t), respectively, where |E| is the number of edges, h_{max} is the size of the largest local neighborhood of a vertex, and t is the number of iterations required for convergence. We demonstrate the practical efficacy by estimating the spectral density of simulated and real-world undirected and directed graphs.

5.
J Leukoc Biol ; 116(2): 398-408, 2024 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-38527801

RESUMO

Eosinophil sombrero vesicles are large tubular carriers resident in the cytoplasm of human eosinophils, identifiable by transmission electron microscopy, and important for immune mediator transport. Increased formation of sombrero vesicles occurs in activated eosinophils in vitro and in vivo. In tissue sites of eosinophilic cytolytic inflammation, extracellular eosinophil sombrero vesicles are noted, but their frequency and significance in eosinophil-associated diseases remain unclear. Here, we performed comprehensive quantitative transmission electron microscopy analyses and electron tomography to investigate the numbers, density, integrity, and 3-dimensional structure of eosinophil sombrero vesicles in different biopsy tissues from 5 prototypic eosinophil-associated diseases (eosinophilic chronic rhinosinusitis/nasal sinuses, ulcerative colitis/intestines, hypereosinophilic syndrome/skin, dermatitis/skin, and schistosomiasis/rectum). The morphology of extracellular eosinophil sombrero vesicles was also compared with that of cytoplasmic eosinophil sombrero vesicles, isolated by subcellular fractionation from peripheral blood eosinophils. We demonstrated that (i) eosinophil cytolysis, releasing intact sombrero vesicles and membrane-bound granules, is a consistent event in all eosinophil-associated diseases; (ii) eosinophil sombrero vesicles persist intact even after complete disintegration of all cell organelles, except granules (late cytolysis); (iii) the eosinophil sombrero vesicle population, composed of elongated, curved, and typical sombreros, and the eosinophil sombrero vesicle 3-dimensional architecture, diameter, and density remain unchanged in the extracellular matrix; (iv) free eosinophil sombrero vesicles closely associate with extracellular granules; and (v) free eosinophil sombrero vesicles also associate with externalized chromatin during eosinophil ETosis. Remarkably, eosinophil sombrero vesicles appeared on the surface of other cells, such as plasma cells. Thus, eosinophil cytolysis/ETosis can secrete intact sombrero vesicles, alongside granules, in inflamed tissues of eosinophil-associated diseases, potentially serving as propagators of eosinophil immune responses after cell death.


Assuntos
Degranulação Celular , Eosinófilos , Vesículas Extracelulares , Humanos , Eosinófilos/imunologia , Eosinófilos/patologia , Vesículas Extracelulares/imunologia , Vesículas Extracelulares/metabolismo , Masculino , Eosinofilia/imunologia , Eosinofilia/patologia , Síndrome Hipereosinofílica/patologia , Síndrome Hipereosinofílica/imunologia
6.
RNA Biol ; 21(1): 1-12, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38528797

RESUMO

The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy. This framework employs a combination of k-mer one-hot, k-mer dictionary, and feature extraction techniques for input representation. Extracted features, when embedded into the deep network, enable optimal utilization of spatial and sequential nuances of ncRNA sequences. Using benchmark datasets and real-world RNA samples from bacterial organisms, we evaluated the performance of BioDeepFuse. Results exhibited high accuracy in ncRNA classification, underscoring the robustness of our tool in addressing complex ncRNA sequence data challenges. The effective melding of CNN or BiLSTM with external features heralds promising directions for future research, particularly in refining ncRNA classifiers and deepening insights into ncRNAs in cellular processes and disease manifestations. In addition to its original application in the context of bacterial organisms, the methodologies and techniques integrated into our framework can potentially render BioDeepFuse effective in various and broader domains.


Assuntos
Aprendizado Profundo , RNA não Traduzido/genética , Algoritmos , RNA , Redes Neurais de Computação
7.
BMC Surg ; 23(1): 361, 2023 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-38012603

RESUMO

PURPOSE: Introducing new surgical techniques in a developing country can be challenging. Inguinal hernias in children are a common surgical problem, and open repair is the standard surgical approach. Laparoscopic repair has gained popularity in developed countries because of similar results. This study aimed to determine the outcomes following the introduction of laparoscopic repairs in Guatemala. METHODS: This retrospective analysis of prospectively collected data from all patients under 18 years who underwent laparoscopic repair at Corpus Christi Hospital in Patzun, Guatemala, from September 5th to September 8th, 2022. RESULTS: A total of 14 patients were included in the study. A board-certified pediatric surgeon and a Guatemalan physician performed all cases. The mean patient age was 7.6 years; 7 boys and 7 girls. All patients were interviewed at 7 days, 30 days, and 6 months. There were no postoperative infections, pain requiring re-evaluation, gonadal atrophy, or hernia recurrence. CONCLUSION: Under controlled circumstances with limited but proper equipment and disposables, laparoscopic inguinal hernia repairs can be introduced and performed in a developing country with a risk complication profile comparable to that in developed countries. This study provides promising evidence of laparoscopic repair feasibility and safety where surgical resources are limited.


Assuntos
Hérnia Inguinal , Laparoscopia , Masculino , Feminino , Humanos , Criança , Adolescente , Hérnia Inguinal/cirurgia , Estudos Retrospectivos , Guatemala , Herniorrafia/métodos , Laparoscopia/métodos , Recidiva , Resultado do Tratamento
8.
J Pediatr ; 259: 113487, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37201683

RESUMO

OBJECTIVE: To analyze laboratory testing results from pediatric patients newly diagnosed with celiac disease to determine the usefulness of each test derived from recommended guidelines. METHODS: Serological testing at the time of diagnosis from patients enrolled in our celiac disease registry from January 2018 through December 2021 was reviewed. The incidence of abnormal laboratory results, routinely obtained as per the recommendations of Snyder et al and our institution's Celiac Care Index, was assessed. Rates of abnormal laboratory values and estimated costs associated with these screening measures were analyzed. RESULTS: Our data demonstrated abnormalities in all serological testing obtained at celiac diagnosis. Hemoglobin, alanine aminotransferase, ferritin, iron, and vitamin D screening were found to be abnormal with notable frequency. Only 7% of patients had an abnormal thyroid-stimulating hormone and <0.1% had an abnormal free T4. Nonresponse to hepatitis B vaccination was prominent, with 69% of patients considered nonimmune. Screening protocols as currently outlined in our Celiac Care Index resulted in an estimated cost of approximately $320 000 during our study. CONCLUSIONS: Review of screening laboratory results at our center reveals that abnormal values for several recommended measures are uncommon. Thyroid screening was infrequently abnormal and the usefulness of screening for hepatitis B at diagnosis is uncertain. Similarly, our data suggest that iron deficiency screening may be condensed effectively into hemoglobin and ferritin testing, eliminating the need for initial iron studies. Decreasing baseline screening measures could safely decrease the burden of testing on patients and overall healthcare expenditures.


Assuntos
Doença Celíaca , Humanos , Criança , Doença Celíaca/diagnóstico , Doença Celíaca/epidemiologia , Doença Celíaca/complicações , Ferro , Programas de Rastreamento , Ferritinas , Hemoglobinas
9.
Front Pediatr ; 11: 877550, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36950175

RESUMO

During a 2-year period, eight cases of a distinct illness were seen among 1,424 neonates admitted to a newly established neonatal care unit in southern Haiti. The newborns presented with a picture of sepsis with shock, vomiting, hypotonia, lethargy, and abdominal distention. Five cases proved fatal and another case left the hospital against advice in extremis with little chance of survival. In each case, the illness was associated with a history of ingestion of teas that included castor oil, known as lok in Haitian Creole. The presumptive cause of the illness was established by the presence of a dark, oily substance in drainage from the nares and nasogastric tubes and by subsequent admission on direct questioning of the caregivers, who said that the infants had been given large amounts of lok. The castor oil tea had been given to three infants in the immediate neonatal period where its use is attributed to encouraging the passage of meconium. The five remaining infants were between 15 and 30 days of life when they were given lok shortly before admission to the neonatal unit for treatment of an undefined illness. All of them were term infants with no identified risks at birth. As nasogastric tubes are not routinely placed in sick neonates, and the parents did not volunteer information about lok administration, the practice may be more widespread than that recorded here. Although our data are confined to observations in Haiti, the use of traditional medicines is a globally widespread phenomenon. Attention must be drawn to the potential toxicity of such preparations and means found to ban their use in neonates.

10.
Menopause ; 29(12): 1375-1380, 2022 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-36449932

RESUMO

OBJECTIVE: The objective of this study is to assess whether the presence of breast arterial calcifications (BACs) found on routine mammography is prospectively associated with the development of cardiovascular disease (CVD) events after 10 years of follow-up. METHODS: Women presenting for screening mammography were enrolled in this prospective cohort. Baseline data were collected including history of CVD and CVD risk factors. Mammograms were assessed for the presence or absence of BAC. Participants completed questionnaires 10 years after baseline that assessed the development of CVD (coronary artery disease [CAD] and stroke) and CVD risk factors. RESULTS: Of the 1,995 participants who enrolled at baseline, complete 10-year follow-up data were available for 1,039; of those, 114 (11.0%) were BAC-positive and 925 (89.0%) were BAC-negative at baseline. After controlling for age, BAC-positive women were more likely to develop CAD (odds ratio, 3.14; 95% confidence interval, 1.86-5.27; P < 0.001) compared with BAC-negative women after 10 years of follow-up. After controlling for age, BAC-positive women were more likely to have had a stroke (odds ratio, 5.10; 95% CI, 1.82-14.30) compared with BAC-negative women after 10 years. CONCLUSIONS: The presence of BAC on routine screening mammography was associated with a significantly increased risk of developing CAD and stroke after 10 years of follow-up. Additional large prospective, population-based studies are needed to confirm BAC as a predictor of future CVD events and its utility in stratifying a woman's risk of CVD.


Assuntos
Neoplasias da Mama , Doenças Cardiovasculares , Doença da Artéria Coronariana , Acidente Vascular Cerebral , Feminino , Humanos , Mamografia , Estudos Prospectivos , Doença da Artéria Coronariana/diagnóstico por imagem , Doença da Artéria Coronariana/epidemiologia , Detecção Precoce de Câncer , Neoplasias da Mama/diagnóstico por imagem , Neoplasias da Mama/epidemiologia , Acidente Vascular Cerebral/epidemiologia
11.
Menopause ; 29(12): 1365-1374, 2022 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-36219813

RESUMO

OBJECTIVE: The aim of this study was to examine the association between common menopausal symptoms (MS) and long-term cardiovascular disease (CVD) and all-cause mortality. METHODS: In an observational cohort of 80,278 postmenopausal women with no known CVD at baseline from the Women's Health Initiative, we assessed individual MS severity (mild vs none; moderate/severe vs none) for night sweats, hot flashes, waking up several times at night, joint pain or stiffness, headaches or migraines, vaginal or genital dryness, heart racing or skipping beats, breast tenderness, dizziness, tremors (shakes), feeling tired, forgetfulness, mood swings, restless or fidgety, and difficulty concentrating. Outcomes included total CVD events (primary) and all-cause mortality (secondary). Associations between specific MS, their severity, and outcomes were assessed during a median of 8.2 years of follow-up. All results were multivariable adjusted, and individual associations were Bonferroni corrected to adjust for multiple comparisons. A machine learning approach (least absolute shrinkage and selection operator) was used to select the most parsimonious set of MS most predictive of CVD and all-cause mortality. RESULTS: The severity of night sweats, waking up several times at night, joint pain or stiffness, heart racing or skipping beats, dizziness, feeling tired, forgetfulness, mood swings, restless or fidgety, and difficulty concentrating were each significantly associated with total CVD. The largest hazard ratio (HR) for total CVD was found for moderate or severe heart racing or skipping beats (HR, 1.55; 95% confidence interval [CI], 1.29-1.86). The individual severities of heart racing or skipping beats, dizziness, tremors (shakes), feeling tired, forgetfulness, mood swings, restless or fidgety, and difficulty concentrating were associated with increased all-cause mortality. Moderate or severe dizziness had the largest HR (1.58; 95% CI, 1.24-2.01). Multiple symptom modeling via least absolute shrinkage and selection operator selected dizziness, heart racing, feeling tired, and joint pain as most predictive of CVD, whereas dizziness, tremors, and feeling tired were most predictive of all-cause mortality. CONCLUSION: Among postmenopausal women with no known CVD at baseline, the severity of specific individual MS was significantly associated with incident CVD and mortality. Consideration of severe MS may enhance sex-specific CVD risk predication in future cohorts, but caution should be applied as severe MS could also indicate other health conditions.


Assuntos
Doenças Cardiovasculares , Masculino , Feminino , Humanos , Pós-Menopausa , Tontura , Tremor , Saúde da Mulher , Artralgia , Fatores de Risco
12.
J Am Acad Orthop Surg ; 30(22): e1474-e1482, 2022 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-36084330

RESUMO

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (COVID-19) pandemic has continued to generate notable disruption in elective total hip arthroplasty (THA) and total knee arthroplasty (TKA). The purpose of this study was to determine whether there is any difference in patient characteristics, revenue, and clinical outcomes in patients undergoing THA and TKA after the start of the pandemic. METHODS: We reviewed a consecutive series of 26,493 patients undergoing primary and revision THA and TKA by 48 surgeons in a single arthroplasty practice. We compared demographics, comorbidities, outcomes, and surgeon revenue from THA and TKA procedures from March 2020 to February 2021 with a prepandemic group undergoing a procedure from March 2019 to February 2020. RESULTS: There was a 20% decline in the volume of all cases in the pandemic group ( 11,688 versus 14,664 , P < 0.001). The postpandemic cohort had shorter length of stay (1.58 versus 1.70 days, P = 0.007), had higher rates of home discharge (98% versus 91%, P < 0.001), and were more likely to have their procedure done at an outpatient facility (21% versus 7%, P < 0.001). Even among patients older than 65 years, more pandemic patients underwent a procedure as an outpatient (19% versus 7%, P < 0.001), with no difference in complications or readmissions. Total surgeon charges and payments declined by 17.6% and 16.3%, respectively, during the pandemic ( P = 0.010). CONCLUSION: Although the COVID-19 pandemic resulted in a notable reduction in surgical volume and revenue loss for our practice, we found a marked shift of arthroplasty patients to outpatient facilities with increased rates of home discharge without compromising patient safety.


Assuntos
Artroplastia de Quadril , Artroplastia do Joelho , COVID-19 , Humanos , Artroplastia do Joelho/efeitos adversos , Pandemias , Readmissão do Paciente , Tempo de Internação , Complicações Pós-Operatórias/etiologia , Artroplastia de Quadril/efeitos adversos , Estudos Retrospectivos
13.
Front Immunol ; 13: 938691, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35874692

RESUMO

Eosinophilic diseases, also termed eosinophil-associated diseases (EADs), are characterized by eosinophil-rich inflammatory infiltrates and extensive eosinophil degranulation with clinically relevant organ pathology. Recent evidence shows that eosinophil cytolytic degranulation, that is, the release of intact, membrane-delimited granules that arises from the eosinophil cytolysis, occurs mainly through ETosis, meaning death with a cytolytic profile and extrusion of nucleus-originated DNA extracellular traps (ETs). The ultrastructural features of eosinophil ETosis (EETosis) have been studied mostly in vitro after stimulation, but are still poorly understood in vivo. Here, we investigated in detail, by transmission electron microscopy (TEM), the ultrastructure of EETosis in selected human EADs affecting several tissues and organ systems. Biopsies of patients diagnosed with eosinophilic chronic rhinosinusitis/ECRS (frontal sinus), ulcerative colitis/UC (intestine), and hypereosinophilic syndrome/HES (skin) were processed for conventional TEM. First, we found that a large proportion of tissue-infiltrated eosinophils in all diseases (~45-65% of all eosinophils) were undergoing cytolysis with release of free extracellular granules (FEGs). Second, we compared the morphology of tissue inflammatory eosinophils with that shown by in vitro ETosis-stimulated eosinophils. By applying single-cell imaging analysis, we sought typical early and late EETosis events: chromatin decondensation; nuclear delobulation and rounding; expanded nuclear area; nuclear envelope alterations and disruption; and extracellular decondensed chromatin spread as ETs. We detected that 53% (ECRS), 37% (UC), and 82% (HES) of all tissue cytolytic eosinophils had ultrastructural features of ETosis in different degrees. Eosinophils in early ETosis significantly increased their nuclear area compared to non-cytolytic eosinophils due to excessive chromatin decondensation and expansion observed before nuclear envelope disruption. ETosis led not only to the deposition of intact granules, but also to the release of eosinophil sombrero vesicles (EoSVs) and Charcot-Leyden crystals (CLCs). Free intact EoSVs and CLCs were associated with FEGs and extracellular DNA nets. Interestingly, not all cytolytic eosinophils in the same microenvironment exhibited ultrastructure of ETosis, thus indicating that different populations of eosinophils might be selectively activated into this pathway. Altogether, our findings captured an ultrastructural signature of EETosis in vivo in prototypic EADs highlighting the importance of this event as a form of eosinophil degranulation and release of inflammatory markers (EoSVs and CLCs).


Assuntos
Eosinófilos , Síndrome Hipereosinofílica , Cromatina/metabolismo , DNA/metabolismo , Eosinófilos/metabolismo , Humanos , Síndrome Hipereosinofílica/patologia , Microscopia Eletrônica de Transmissão
14.
Brief Bioinform ; 23(4)2022 07 18.
Artigo em Inglês | MEDLINE | ID: mdl-35753697

RESUMO

Recent technological advances have led to an exponential expansion of biological sequence data and extraction of meaningful information through Machine Learning (ML) algorithms. This knowledge has improved the understanding of mechanisms related to several fatal diseases, e.g. Cancer and coronavirus disease 2019, helping to develop innovative solutions, such as CRISPR-based gene editing, coronavirus vaccine and precision medicine. These advances benefit our society and economy, directly impacting people's lives in various areas, such as health care, drug discovery, forensic analysis and food processing. Nevertheless, ML-based approaches to biological data require representative, quantitative and informative features. Many ML algorithms can handle only numerical data, and therefore sequences need to be translated into a numerical feature vector. This process, known as feature extraction, is a fundamental step for developing high-quality ML-based models in bioinformatics, by allowing the feature engineering stage, with design and selection of suitable features. Feature engineering, ML algorithm selection and hyperparameter tuning are often manual and time-consuming processes, requiring extensive domain knowledge. To deal with this problem, we present a new package: BioAutoML. BioAutoML automatically runs an end-to-end ML pipeline, extracting numerical and informative features from biological sequence databases, using the MathFeature package, and automating the feature selection, ML algorithm(s) recommendation and tuning of the selected algorithm(s) hyperparameters, using Automated ML (AutoML). BioAutoML has two components, divided into four modules: (1) automated feature engineering (feature extraction and selection modules) and (2) Metalearning (algorithm recommendation and hyper-parameter tuning modules). We experimentally evaluate BioAutoML in two different scenarios: (i) prediction of the three main classes of noncoding RNAs (ncRNAs) and (ii) prediction of the eight categories of ncRNAs in bacteria, including housekeeping and regulatory types. To assess BioAutoML predictive performance, it is experimentally compared with two other AutoML tools (RECIPE and TPOT). According to the experimental results, BioAutoML can accelerate new studies, reducing the cost of feature engineering processing and either keeping or improving predictive performance. BioAutoML is freely available at https://github.com/Bonidia/BioAutoML.


Assuntos
Vacinas contra COVID-19 , COVID-19 , Algoritmos , Bactérias/genética , Humanos , Aprendizado de Máquina
15.
Artigo em Inglês | MEDLINE | ID: mdl-35528706

RESUMO

Background: An obesity epidemic has been documented among adult Latinos/as in Latin America and the United States (US); however, little is known about obesity among Latinos/as with HIV (PWH). Moreover, Latinos/as PWH in the US may have different weight trajectories than those in Latin America due to the cultural and environmental contexts. We assessed weight and body mass index (BMI) trajectories among PWH initiating antiretroviral therapy (ART) across 5 countries in Latin America and the Caribbean and the US. Methods: ART-naÿve PWH ≥18 years old, enrolled in Brazil, Honduras, Mexico, Peru, and Haiti (sites within CCA-SAnet) and the US (NA-ACCORD) starting ART between 2000 and 2017, with at least one weight measured after ART initiation were included. Participants were classified according to site/ethnicity as: Latinos/as in US, non-Latinos/as in US, Haitians, and Latinos/as in Latin America. Generalized least squares models were used to assess trends in weight and BMI. Models estimating probabilities of becoming overweight/obese (BMI ≥25 kg/m2) and of becoming obese (BMI ≥30 kg/m2) post ART initiation for males and females were fit using generalized estimating equations with a logit link and an independence working correlation structure. Findings: Among 59,207 PWH, 9% were Latinos/as from Latin America, 9% Latinos/as from the US, 68% non-Latinos/as from the US and 14% were Haitian. At ART initiation, 29% were overweight and 14% were obese. Post-ART weight and BMI increases were steeper for Latinos/as in Latin America compared with other sites/ethnicities; however, BMI at 3-years post ART remained lower compared to Latinos/as and non-Latinos/as in the US. Among females, at 3-years post ART initiation the greatest adjusted probability of obesity was found among non-Latinas in the US (15·2%) and lowest among Latinas in Latin America (8.6%). Among males, while starting with a lower BMI, Latinos in Latin America had the greatest adjusted probability of becoming overweight or obese 3-years post-ART initiation. Interpretation: In the Americas, PWH gain substantial weight after ART initiation. Despite environmental and cultural differences, PWH in Latin America, Haiti and Latinos and non-Latinos in the US share similar BMI trajectories on ART and high probabilities of becoming overweight and obese over time. Multicohort studies are needed to better understand the burden of other metabolic syndrome components in PWH across different countries.

16.
Artigo em Inglês | MEDLINE | ID: mdl-35602655

RESUMO

Background: Clinical outcomes are rarely studied in virologically suppressed people living with HIV (PWH) and incomplete CD4 recovery. To explore whether time living with severe immunosuppression predict clinical outcomes better than baseline or time updated CD4, we estimated the association between cumulative percentage of time with CD4 <200 cells/µL during viral suppression (VS) (%tCD4<200), and mortality and comorbidities during 2000-2019. Methods: In a retrospective cohort analysis, we followed PWH initiating ART in Latin America from first VS (HIV-RNA<200 copies/µL) to death, virological failure or loss to follow-up. We fit Cox models to estimate risk of death and/or AIDS-defining and serious non-AIDS-defining events (ADE and SNADE -cancer, cardiovascular, liver, and renal diseases) by %tCD4<200 (continuous variable). We predicted survival probabilities for each event and calculated risks of hypothetical cases of different %tCD4<200. Findings: In 8,369 patients with 34·9 months of follow-up (median, IQR: 16·7, 69·1), 4,274 (51%) started ART with CD4<200 cells/µL. Median %tCD4<200 was 0% (IQR: 0, 15%). We identified 195 (2·3%) deaths and 584 (7·2%) patients with ADE/SNADE. For an increased %tCD4<200 of 15% (e.g., 15% vs. 0%), the adjusted relative hazard (aHR) of death was 1·27 (95% confidence interval [CI]: 1·19 - 1·35), of ADE/SNADE was 1·13 (95%CI: 1·09 - 1·17), of SNADE was 0·96 (95%CI: 0·89 - 1·02) and of death/ADE/SNADE was 1·11 (95%CI: 1·07 - 1·14). Estimates were similar after adjusting for time updated CD4 count. Interpretation: In virologically suppressed PWH, increased time living with severe immunosuppression had an increased risk of death and ADE/SNADE in this Latin American cohort, independently of time updated CD4 count. Funding: This work was supported by the NIH-funded Caribbean, Central and South America network for HIV epidemiology (CCASAnet, U01AI069923), a member cohort of the International Epidemiologic Databases to Evaluate AIDS (leDEA). This award is funded by the following institutes: Eunice Kennedy Shriver National Institute Of Child Health & Human Development (NICHD), National Cancer Institute (NCI), National Institute Of Allergy And Infectious Diseases (NIAID), National Institute Of Mental Health (NIMH), the National Heart, Lung, and Blood Institute (NHLBI), the National Institute on Alcohol Abuse and Alcoholism (NIAAA), the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), and the Fogarty International Center (FIC). Specific funding was provided from the Fogarty International Center (FIC) for lead author, Yanink Caro-Vega, for the Fogarty-IeDEA Mentorship Program (FIMP).

17.
Front Cell Dev Biol ; 10: 836755, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35386204

RESUMO

Mitochondria are multifunctional organelles of which ultrastructure is tightly linked to cell physiology. Accumulating evidence shows that mitochondrial remodeling has an impact on immune responses, but our current understanding of the mitochondrial architecture, interactions, and morphological changes in immune cells, mainly in eosinophils, is still poorly known. Here, we applied transmission electron microscopy (TEM), single-cell imaging analysis, and electron tomography, a technique that provides three-dimensional (3D) views at high resolution, to investigate mitochondrial dynamics in mouse eosinophils developing in cultures as well as in the context of inflammatory diseases characterized by recruitment and activation of these cells (mouse models of asthma, H1N1 influenza A virus (IAV) infection, and schistosomiasis mansoni). First, quantitative analyses showed that the mitochondrial area decrease 70% during eosinophil development (from undifferentiated precursor cells to mature eosinophils). Mitophagy, a consistent process revealed by TEM in immature but not in mature eosinophils, is likely operating in mitochondrial clearance during eosinophilopoiesis. Events of mitochondria interaction (inter-organelle membrane contacts) were also detected and quantitated within developing eosinophils and included mitochondria-endoplasmic reticulum, mitochondria-mitochondria, and mitochondria-secretory granules, all of them significantly higher in numbers in immature compared to mature cells. Moreover, single-mitochondrion analyses revealed that as the eosinophil matures, mitochondria cristae significantly increase in number and reshape to lamellar morphology. Eosinophils did not change (asthma) or reduced (IAV and Schistosoma infections) their mitochondrial mass in response to inflammatory diseases. However, asthma and schistosomiasis, but not IAV infection, induced amplification of both cristae numbers and volume in individual mitochondria. Mitochondrial cristae remodeling occurred in all inflammatory conditions with the proportions of mitochondria containing only lamellar or tubular, or mixed cristae (an ultrastructural aspect seen just in tissue eosinophils) depending on the tissue/disease microenvironment. The ability of mitochondria to interact with granules, mainly mobilized ones, was remarkably captured by TEM in eosinophils participating in all inflammatory diseases. Altogether, we demonstrate that the processes of eosinophilopoiesis and inflammation-induced activation interfere with the mitochondrial dynamics within mouse eosinophils leading to cristae remodeling and inter-organelle contacts. The understanding of how mitochondrial dynamics contribute to eosinophil immune functions is an open interesting field to be explored.

19.
J Arthroplasty ; 37(9): 1763-1770, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35390457

RESUMO

BACKGROUND: Multimodal analgesia has become the standard of care for pain management following total knee arthroplasty (TKA). Cannabidiol (CBD) is increasingly utilized in the postoperative period. The purpose of this study was to analyze the analgesic benefits of topical CBD following primary TKA. METHODS: In this randomized double-blinded placebo-controlled trial, 80 patients undergoing primary unilateral TKA applied topical CBD (CBD; n = 19), essential oil (EO; n = 21), CBD and essential oil (CBD + EO; n = 21), or placebo (PLA; n = 19) thrice daily around the knee for two weeks postoperatively. This supplemented a standardized multimodal analgesic protocol. Outcomes included visual analog scale (VAS) pain and numeric rating scale (NRS) sleep scores (collected on postoperative day [POD] 0, 1, 2, 7, 14, 42), and cumulative postoperative opioid use (42 days). RESULTS: Demographic characteristics were similar among the four cohorts. Preoperative VAS and NRS scores were similar among groups. The CBD cohort had a higher mean VAS pain score on POD 2 compared to the EO cohort (CBD: 69.9 ± 19.3 versus. EO: 51.0 ± 18.2; P = .013). No statistically significant differences existed for VAS scores at other times, and no statistically significant differences were observed for postoperative NRS sleep scores or postoperative opioid use at any time point. CONCLUSION: Utilization of topical CBD in supplement to multimodal analgesia did not reduce pain or opioid consumption, or improve sleep scores following TKA. These results suggest that the local effects of topical CBD are not beneficial for providing additional pain relief after TKA.


Assuntos
Artroplastia do Joelho , Canabidiol , Óleos Voláteis , Transtornos Relacionados ao Uso de Opioides , Analgésicos Opioides/uso terapêutico , Anestésicos Locais , Artroplastia do Joelho/efeitos adversos , Artroplastia do Joelho/métodos , Canabidiol/uso terapêutico , Método Duplo-Cego , Humanos , Óleos Voláteis/uso terapêutico , Dor Pós-Operatória/tratamento farmacológico , Dor Pós-Operatória/etiologia , Dor Pós-Operatória/prevenção & controle , Estudos Prospectivos
20.
J Pediatr Orthop ; 42(3): 131-137, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-35138296

RESUMO

INTRODUCTION: Early-onset scoliosis (EOS) is a spinal deformity that occurs in patients 9 years of age or younger. Severe deformity may result in thoracic insufficiency, respiratory failure, and premature death. The purpose of this study is to describe the modern-day natural history of mortality in patients with EOS. METHODS: The multicenter Pediatric Spine Study Group database was queried for all patients with EOS who are deceased, without exclusion. Demographics, underlying diagnoses, EOS etiology, operative and nonoperative treatments or observation, complications, and date of death were retrieved. Descriptive statistics and survival analysis with Kaplan-Meier curves were performed. RESULTS: There were 130/8009 patients identified as deceased for a registry mortality rate of 16 per 1000 patients. The mean age at death was 10.6 years (range: 1.0 to 30.2 y) and the most common EOS etiology was neuromuscular (73/130, 56.2%; P<0.001). Deceased patients were more likely be treated operatively than nonoperatively or observed (P<0.001). The mean age of death for patients treated operatively (12.3 y) was older than those treated nonoperatively (7.0 y) or observed (6.3 y) (P<0.001) despite a larger deformity and similar index visit body mass index and ventilation requirements. Kaplan-Meier analysis confirmed an increased survival time in patients with a history of any spine operation compared with patients without a history of spine operation (P<0.0001). Operatively treated patients experienced a median of 3.0 complications from diagnosis to death. Overall, cardiopulmonary related complications were the most common (129/271, 47.6%; P<0.001), followed by implant-related (57/271, 21.0%) and wound-related (26/271, 9.6%). The primary cause of death was identified for 78/130 (60.0%) patients, of which 57/78 (73.1%) were cardiopulmonary related. CONCLUSIONS: This study represents the largest collection of EOS mortality to date, providing surgeons with a modern-day examination of the effects of surgical intervention to better council patients and families. Both fatal and nonfatal complications in children with EOS are most likely to involve the cardiopulmonary system. LEVEL OF EVIDENCE: Level IV-therapeutic.


Assuntos
Escoliose , Criança , Humanos , Próteses e Implantes , Sistema de Registros , Estudos Retrospectivos , Escoliose/cirurgia , Coluna Vertebral
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