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1.
Bioinformatics ; 40(6)2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38830083

ABSTRACT

MOTIVATION: Answering and solving complex problems using a large language model (LLM) given a certain domain such as biomedicine is a challenging task that requires both factual consistency and logic, and LLMs often suffer from some major limitations, such as hallucinating false or irrelevant information, or being influenced by noisy data. These issues can compromise the trustworthiness, accuracy, and compliance of LLM-generated text and insights. RESULTS: Knowledge Retrieval Augmented Generation ENgine (KRAGEN) is a new tool that combines knowledge graphs, Retrieval Augmented Generation (RAG), and advanced prompting techniques to solve complex problems with natural language. KRAGEN converts knowledge graphs into a vector database and uses RAG to retrieve relevant facts from it. KRAGEN uses advanced prompting techniques: namely graph-of-thoughts (GoT), to dynamically break down a complex problem into smaller subproblems, and proceeds to solve each subproblem by using the relevant knowledge through the RAG framework, which limits the hallucinations, and finally, consolidates the subproblems and provides a solution. KRAGEN's graph visualization allows the user to interact with and evaluate the quality of the solution's GoT structure and logic. AVAILABILITY AND IMPLEMENTATION: KRAGEN is deployed by running its custom Docker containers. KRAGEN is available as open-source from GitHub at: https://github.com/EpistasisLab/KRAGEN.


Subject(s)
Software , Natural Language Processing , Problem Solving , Algorithms , Information Storage and Retrieval/methods , Humans , Computational Biology/methods , Databases, Factual
2.
Bioinformatics ; 39(10)2023 10 03.
Article in English | MEDLINE | ID: mdl-37796839

ABSTRACT

MOTIVATION: Biomedical and healthcare domains generate vast amounts of complex data that can be challenging to analyze using machine learning tools, especially for researchers without computer science training. RESULTS: Aliro is an open-source software package designed to automate machine learning analysis through a clean web interface. By infusing the power of large language models, the user can interact with their data by seamlessly retrieving and executing code pulled from the large language model, accelerating automated discovery of new insights from data. Aliro includes a pre-trained machine learning recommendation system that can assist the user to automate the selection of machine learning algorithms and its hyperparameters and provides visualization of the evaluated model and data. AVAILABILITY AND IMPLEMENTATION: Aliro is deployed by running its custom Docker containers. Aliro is available as open-source from GitHub at: https://github.com/EpistasisLab/Aliro.


Subject(s)
Algorithms , Software , Machine Learning , Language
3.
Diagn Microbiol Infect Dis ; 103(4): 115721, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35635888

ABSTRACT

Our objectives were to evaluate the role of procalcitonin in identifying bacterial co-infections in hospitalized COVID-19 patients and quantify antibiotic prescribing during the 2020 pandemic surge. Hospitalized COVID-19 patients with both a procalcitonin test and blood or respiratory culture sent on admission were included in this retrospective study. Confirmed co-infection was determined by an infectious diseases specialist. In total, 819 patients were included; 335 (41%) had an elevated procalcitonin (>0.5 ng/mL) and of these, 42 (13%) had an initial bacterial co-infection. Positive predictive value of elevated procalcitonin for co-infection was 13% while the negative predictive value was 94%. Ninety-six percent of patients with an elevated procalcitonin received antibiotics (median 6 days of therapy), compared to 82% with low procalcitonin (median 4 days of therapy) (adjusted OR:3.3, P < 0.001). We observed elevated initial procalcitonin in many COVID patients without concurrent bacterial co-infections which potentially contributed to antibiotic over-prescribing.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Procalcitonin , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/diagnosis , Bacterial Infections/drug therapy , Biomarkers , COVID-19/complications , Calcitonin , Calcitonin Gene-Related Peptide , Coinfection/epidemiology , Humans , Procalcitonin/analysis , Retrospective Studies
6.
Transfus Apher Sci ; 58(4): 439-441, 2019 Aug.
Article in English | MEDLINE | ID: mdl-31307834

ABSTRACT

Babesiosis is a tick-borne infectious disease caused by the protozoa Babesia but transplacental, and transfusion transmission may occur. While most infections are asymptomatic, rarely, it can present with a severe, life-threatening illness. Treatment is primarily with antibiotics, but red cell exchange (RCE) has been used in more severe cases which are characterized by high-grade parasitemia, evidence of severe hemolysis and or multi-organ failure. A threshold parasite level of 10% has arbitrarily been applied as an indication for RCE; however, this threshold is not evidence-based. We report on three cases of severe babesiosis in which we considered the use of RCE on the basis of a parasite level greater than 10%, but the procedure was not performed. We deferred RCE on account of the good clinical state of the patient and the absence of end-organ failure. All patients were followed daily until discharge. Two of these patients had been splenectomized, and each received a single unit of red blood cells during the hospitalization. The third patient had a long history of refractory lymphoma and was pancytopenic requiring multiple transfusions during the years before the diagnosis of babesiosis. She had transfusion-transmitted babesiosis from a red blood cell transfused 46 days prior to diagnosis. All three patients responded well to antibiotics, and none expired. This small case series suggests that requests for RCE solely on the basis of an arbitrary level of parasitemia should be questioned and the clinical state and evidence of end-organ failure considered in the decision to perform RCE.


Subject(s)
Anti-Bacterial Agents/administration & dosage , Babesiosis/drug therapy , Parasitemia/drug therapy , Adult , Aged, 80 and over , Babesiosis/blood , Erythrocyte Transfusion , Female , Humans , Male , Middle Aged , Parasitemia/blood , Retrospective Studies
7.
Braz J Infect Dis ; 22(5): 387-391, 2018.
Article in English | MEDLINE | ID: mdl-30389350

ABSTRACT

OBJECTIVES: To determine the factors associated with Mycobacterium tuberculosis complex-positive blood culture. METHODS: Case-control study. Sociodemographic, clinical and laboratory data were collected from 2000 to 2015. RESULTS: We reviewed medical records of 533 patients with culture-proven tuberculosis, of whom 27.2% (145/533) had blood culture available. Patients with mycobacteremia presented more frequently with abdominal tuberculosis, body mass index <18kg/m2, and had lower hemoglobin and albumin levels. No differences were observed regarding HIV status. CONCLUSIONS: Few studies have reported on the characteristics associated with Mycobacterium tuberculosis complex bacteremia, especially among Human Immunodeficiency Virus-negative patients. Out of 145 tuberculosis-infected patients with blood culture results available, 21 turned out positive. Anemia, hypoalbuminemia, and a body mass index<18kg/m2 were associated with mycobacteremia.


Subject(s)
Bacteremia/microbiology , HIV Infections/microbiology , Mycobacterium tuberculosis/isolation & purification , Tuberculosis/microbiology , Adult , Bacteremia/blood , Blood Culture , Female , HIV Infections/blood , Humans , Male , Mexico , Middle Aged , Reference Values , Retrospective Studies , Statistics, Nonparametric , Tertiary Care Centers , Tuberculosis/blood
8.
Braz. j. infect. dis ; 22(5): 387-391, Sept.-Oct. 2018. tab
Article in English | LILACS | ID: biblio-974236

ABSTRACT

ABSTRACT Objectives: To determine the factors associated with Mycobacterium tuberculosis complex-positive blood culture. Methods: Case-control study. Sociodemographic, clinical and laboratory data were collected from 2000 to 2015. Results: We reviewed medical records of 533 patients with culture-proven tuberculosis, of whom 27.2% (145/533) had blood culture available. Patients with mycobacteremia presented more frequently with abdominal tuberculosis, body mass index <18 kg/m2, and had lower hemoglobin and albumin levels. No differences were observed regarding HIV status. Conclusions: Few studies have reported on the characteristics associated with Mycobacterium tuberculosis complex bacteremia, especially among Human Immunodeficiency Virus-negative patients. Out of 145 tuberculosis-infected patients with blood culture results available, 21 turned out positive. Anemia, hypoalbuminemia, and a body mass index < 18 kg/m2 were associated with mycobacteremia.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Tuberculosis/microbiology , HIV Infections/microbiology , Bacteremia/microbiology , Mycobacterium tuberculosis/isolation & purification , Reference Values , Tuberculosis/blood , HIV Infections/blood , Retrospective Studies , Bacteremia/blood , Statistics, Nonparametric , Tertiary Care Centers , Blood Culture , Mexico
9.
IDCases ; 11: 73, 2018.
Article in English | MEDLINE | ID: mdl-29619326

ABSTRACT

Despite the dramatic decrease in invasive pneumococcal disease since the widespread use of the first pneumococcal vaccine, invasive and resistant disease still occurs. We present a case of ceftriaxone-resistant pneumococcal meningitis suggesting that continued vigilance is warranted for empiric treatment of meningitis when Streptococcus pneumoniae is a concern.

11.
J Surg Case Rep ; 2017(4): rjx072, 2017 Apr.
Article in English | MEDLINE | ID: mdl-28458877

ABSTRACT

Splenic abscess as a complication of laparoscopic sleeve gastrectomy (LSG) is rare. There have only been six cases in the literature. In most of these cases, the classic predisposing factors for developing splenic abscess were absent, leading to the hypothesis that transient bacteraemia caused by mucosal disruption during the surgical procedure and splenic ischaemia may play a role. These patients usually present in the late post-operative period with abdominal pain, fever and leucocytosis. The preferred treatment is intravenous antibiotics and percutaneous drainage or splenectomy. We report a case of splenic abscess caused by Streptococcus anginosus that occurred 20 days after LSG in a 45-year-old woman without immunosuppressive conditions. The patient was successfully treated with antibiotic therapy and percutaneous drainage.

12.
BMC Infect Dis ; 16(1): 657, 2016 11 08.
Article in English | MEDLINE | ID: mdl-27825312

ABSTRACT

BACKGROUND: Human tuberculosis caused by Mycobacterium bovis is believed to be frequent in developing countries. Transmission is usually through ingestion of unpasteurized dairy products, although airborne contagion is possible. Disease caused by M. tuberculosis or M. bovis is clinically indistinguishable from each other. The aim of this study was to determine the factors associated with M. bovis disease. METHODS: Retrospective analysis of all culture-positive cases of M. bovis and M. tuberculosis from 2000 to 2015, in a Mexican tertiary-care centre. Sociodemographic, clinical, and radiographic data from medical records were compared. Disease site was classified as pulmonary, extrapulmonary, or pulmonary and extrapulmonary, based on cultures. RESULTS: We evaluated 533 cases, 372 (69.7 %) of which were caused by M. tuberculosis and 161 (30.2 %) by M. bovis. Characteristics associated with M. bovis disease were: younger age (aOR 0.97, 95 % CI 0.95-0.98), glucocorticoid use (aOR 2.27, 95 % CI 1.42-3.63), and extrapulmonary disease (aOR 1.80, 95 % CI 1.21-2.69). M. tuberculosis was associated with lower socioeconomic status (aOR 0.52, 95 % CI 0.28-0.97). When we analysed only pulmonary cases, younger age (aOR 0.97, 95 % CI 0.96-0.99), glucocorticoid use (aOR 2.41, 95 % CI 1.30-4.46), and smoking (aOR 1.94, CI 95 % 1.15-3.27) were associated with M. bovis. Both groups showed similar proportions of direct microscopy smear results (respiratory samples) and chest X-ray cavitations. CONCLUSIONS: Younger age, glucocorticoid use, and extrapulmonary disease were associated with M. bovis as the causative agent of tuberculosis in a group of patients from a tertiary care centre in a country where bovine tuberculosis is endemic. Further studies must be conducted in the general population to determine pathogen-specific associated factors and outcomes.


Subject(s)
Mycobacterium bovis/pathogenicity , Mycobacterium tuberculosis/pathogenicity , Tuberculosis/microbiology , Adult , Animals , Female , Glucocorticoids/therapeutic use , Humans , Male , Mexico/epidemiology , Middle Aged , Retrospective Studies , Socioeconomic Factors , Tertiary Care Centers , Tuberculosis/epidemiology , Tuberculosis/etiology , Tuberculosis, Pulmonary/epidemiology , Tuberculosis, Pulmonary/etiology , Tuberculosis, Pulmonary/microbiology
13.
Salud Publica Mex ; 58(3): 366-70, 2016 Jun.
Article in English | MEDLINE | ID: mdl-27598934

ABSTRACT

OBJECTIVE: To describe the seroprevalence and associated factors for brucellosis among dairy farm workers. MATERIALS AND METHODS: We performed a secondary analysis of a data set and sera from a previous cross-sectional study in a dairy farm. Sera were tested for Brucella spp. antibodies by the slide agglutination test. Seropositivity was defined as a titer ≥1:40; recent infection was titers ≥1:160. RESULTS: We tested 331 human sera. Seroprevalence of brucellosis was 18.1% (60/331; 95% CI 14.1-22.7); 13.3% of them (8/60; 95% CI 5.9 24.5) corresponded to recent infection. Highexposure occupation (calf caretaker; OR 3.3; 95%CI 1.1 - 9.7), daily hours in contact with cows (OR 1.1; 95%CI 1.03 - 1.2), and living on-site (OR 2.2; 95% CI 1.1 - 4.4) remained independently associated with seropositivity. CONCLUSIONS: We found a high seroprevalence of brucellosis among dairy farm workers, as well as a significant association among those with prolonged and close contact with cattle.


Subject(s)
Brucellosis/epidemiology , Dairying , Occupational Diseases/epidemiology , Abattoirs , Adult , Agglutination Tests , Animals , Antibodies, Bacterial/blood , Brucellosis/diagnosis , Cattle , Cross-Sectional Studies , Endemic Diseases , Female , Humans , Male , Mexico/epidemiology , Middle Aged , Occupational Diseases/diagnosis , Seroepidemiologic Studies , Zoonoses/epidemiology
14.
Salud pública Méx ; 58(3): 366-370, may.-jun. 2016. tab
Article in English | LILACS | ID: lil-793027

ABSTRACT

Abstract: Objective: To describe the seroprevalence and associated factors for brucellosis among dairy farm workers. Materials and methods: We performed a secondary analysis of a data set and sera from a previous cross-sectional study in a dairy farm. Sera were tested for Brucella spp. antibodies by the slide agglutination test. Seropositivity was defined as a titer ≥1:40; recent infection was titers ≥1:160. Results: We tested 331 human sera. Seroprevalence of brucellosis was 18.1% (60/331; 95% CI 14.1-22.7); 13.3% of them (8/60; 95% CI 5.9 24.5) corresponded to recent infection. Highexposure occupation (calf caretaker; OR 3.3; 95%CI 1.1 - 9.7), daily hours in contact with cows (OR 1.1; 95%CI 1.03 - 1.2), and living on-site (OR 2.2; 95% CI 1.1 - 4.4) remained independently associated with seropositivity. Conclusions: We found a high seroprevalence of brucellosis among dairy farm workers, as well as a significant association among those with prolonged and close contact with cattle.


Resumen: Objetivos: Describir la seroprevalencia y factores asociados con la brucelosis en los trabajadores de una cuenca lechera. Material y métodos: Se realizó un análisis secundario de datos y sueros obtenidos en una cuenca lechera. Se buscaron anticuerpos contra Brucella spp. en los sueros por medio de la prueba de aglutinación en placa. Se definió seropositividad a partir de un título ≥1:40, e infección reciente con títulos ≥1:160. Resultados: Se analizaron 331 sueros humanos. La seroprevalencia de brucelosis fue de 18.1% (60/331; IC 95% 14.1-22.7); el 13.3% (8/60; IC 95% 5.9 24.5) correspondieron a infección reciente. Alta exposición (becerrero; RM 3.3; IC 95% 1.1 - 9.7), horas diarias en contacto con vacas (RM 1.1; IC 95% 1.03 - 1.2), y vivir en el establo (RM 2.2; IC 95% 1.1 - 4.4) estuvieron asociadas independientemente con seropositividad. Conclusiones: Se encontró alta seroprevalencia de brucelosis en trabajadores de una cuenca lechera, y asociación en aquellos con contacto cercano y prolongado con vacas.


Subject(s)
Humans , Animals , Male , Female , Adult , Middle Aged , Brucellosis/epidemiology , Dairying , Occupational Diseases/epidemiology , Brucellosis/diagnosis , Agglutination Tests , Cattle , Zoonoses/epidemiology , Seroepidemiologic Studies , Cross-Sectional Studies , Abattoirs , Endemic Diseases , Mexico/epidemiology , Antibodies, Bacterial/blood , Occupational Diseases/diagnosis
15.
Horm Metab Res ; 12(10): 529-36, 1980 Oct.
Article in English | MEDLINE | ID: mdl-7439877

ABSTRACT

We studied the kinetic behavior of triiodothyronine (T3) and thyroxine (T4) in two groups of 10 sheep. One was used as the control group (I) and the other consisted of sheep with acute renal failure (A.R.F.) induced by an iv. injection of mercuric dichloride. Five sheep of each group were injected with 125IT3 and the remaining five with 125IT4, later taking periodical extractions throughout the first 96 hours. The radioactive contaminants in the plasma were eliminated by extracting the hormones through immunoextraction. The mathematical calculation of the kinetics was based on the open two-compartment model. The A.R.F. caused a decrease in the disposition constant of the slow phase in the T3 kinetics, while at the same time prolonging the plasma half-life of the phase. The steady state distribution volume increases and the distribution constant K21 decreases in the group suffering from renal insufficiency. As regards the T4, all the kinetic parameters were altered with the exception of the distribution volumes, the most significant changes being the shortening of the plasma half-life in the end phases, the rise of the elimination constant K13 and the increase in the plasma clearance and thyroxine turnover rates. The analysis of the peripheral conversion rate revealed with a great amount of variation, that there is evidence of the conversion of T4 to T3 in the healthy group while this phenomenon remains undetected in the sick animals.


Subject(s)
Acute Kidney Injury/physiopathology , Thyroxine/metabolism , Triiodothyronine/metabolism , Animals , Female , Kinetics , Sheep
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