ABSTRACT
The present study was conducted to investigate the aqueous extracts of Azadirachta indica (AZN), Cnidoscolus angustidens (CNA), and their combination (MIX) at dosages of 0-, 0.6-, 1.2-, and 1.8- mL for their ability to reduce greenhouse gases and fermentation profiles in an in vitro study using horse feces and a nutrient-dense diet (as substrate). The quantity of greenhouse gas and fermentation profiles were determined in in vitro incubation for 48 h. Extracts of AZN, CNA, and MIX reduced total gas production of the incubated and degraded substrates in a dose-dependent and time-dependent manner. Production of CH4 was reduced (P < .05) by 4.41% to 54.54% with the incubated substrates and by 1.16% to 61.82% with the degraded substrates. However, AZN and MIX reduced (P < .05) CO by 4.43% to 12.85% with the incubated substrates and by 0.70% to 16.78% with the degraded substrates. In like manner, the plant extracts and combination reduced (P < .05) H2S production in a dose-dependent and time-dependent manner by 18.37% to 67.35% with the incubated substrates and by 8.51% to 67.23% with the degraded substrates. Extracts maintained pH within the normal range, reduced dry matter digestibility and metabolizable energy, and improved (P < .05) concentration of short chain fatty acids. Overall, aqueous extracts of AZN and CNA and their combinations had a positive effect on reducing the greenhouse gas production with no deleterious effect on fecal horses' fermentation activities.
Subject(s)
Azadirachta , Euphorbiaceae , Greenhouse Gases , Animals , Azadirachta/metabolism , Diet/veterinary , Euphorbiaceae/metabolism , Feces , Greenhouse Gases/metabolism , Horses , RumenABSTRACT
In the race against deadly diseases, multiple drugs have been developed as a treatment strategy in livestock. Each treatment is based on a specific mechanism to find a suitable drug. Antibiotics have become a fundamental part of the equine industry to treat bacterial diseases. These antibiotics have specific doses and side effects, and understanding each parameter allows veterinarians to avoid or limit the adverse effects of such drugs. Use of antibiotics causes microbial imbalance, decreased microbial diversity and richness in both cecal and fecal samples. Antibiotics reduced metabolites production such as amino acids, carbohydrates, lipids, and vitamins, increased multi-resistant microbes, and gives opportunity to pathogenic microbes such as Clostridium perfringens and Salmonella spp., to overgrow. Therefore, appropriate use of these antibiotics in equine therapy will reduce the adverse consequence of antibiotics on cecal microbiota activities.
Subject(s)
Gastrointestinal Microbiome , Animals , Anti-Bacterial Agents/adverse effects , Cecum , Clostridium perfringens , Feces , HorsesABSTRACT
A Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) method was developed to detect Zika. The primers were designed based on the NS5 region of 64 complete genomes. Lyophilized LAMP reagent was used. Initially, seven different arboviruses were tested and only Zika samples tested positive. Additionally, serial dilutions of one of Zika's RNA were compared using RT-LAMP and qRT-PCR, demonstrating that RT-LAMP is 1,000 times more sensitive. We also evaluated 300 serum samples with RT-LAMP comparing the results with standard qRT-PCR methods, and we obtained a 99.3% sensitivity, 100% specificity, 100% positive predictive value, and 99.3% negative predictive value. In conclusion, this method provides a low-cost, high-performance, viable, and reliable alternative for the rapid diagnosis of Zika in primary health-care facilities.
Se desarrolló un método de amplificación isotérmica mediada en lazo de transcriptasa inversa (RT-LAMP) para detectar Zika. Los primers se diseñaron basándose en la región NS5 de 64 genomas completos. Se usó reactivo LAMP liofilizado. Inicialmente, se probaron siete arbovirus diferentes y solo las muestras de Zika resultaron positivas. Además, las diluciones seriadas de una de los ARN de Zika se compararon mediante RT-LAMP y qRT-PCR, demostrando que RTLAMP es 1000 veces más sensible. También se evaluó 300 muestras de suero usando RT-LAMP y los resultados se compararon con los métodos de qRT-PCR estándar y obtuvimos un 99,3% (IC95%: 97,7 - 100,0) de sensibilidad, 100% (IC95%: 99,7 - 100,0) de especificidad, 100% (IC95%: 99,7 -100,0) de valor predictivo positivo y 99,3% (IC95%: 97,7 - 100,0) de valor predictivo negativo. En conclusión, este método brinda una alternativa de bajo costo, alto rendimiento, viabilidad y confiabilidad para el diagnóstico rápido de Zika en instalaciones de atención primaria de salud.
Subject(s)
Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Zika Virus/isolation & purification , Humans , Zika Virus Infection/diagnosis , Zika Virus Infection/virologyABSTRACT
RESUMEN Se desarrolló un método de amplificación isotérmica mediada en lazo de transcriptasa inversa (RT-LAMP) para detectar Zika. Los primers se diseñaron basándose en la región NS5 de 64 genomas completos. Se usó reactivo LAMP liofilizado. Inicialmente, se probaron siete arbovirus diferentes y solo las muestras de Zika resultaron positivas. Además, las diluciones seriadas de una de los ARN de Zika se compararon mediante RT-LAMP y qRT-PCR, demostrando que RTLAMP es 1000 veces más sensible. También se evaluó 300 muestras de suero usando RT-LAMP y los resultados se compararon con los métodos de qRT-PCR estándar y obtuvimos un 99,3% (IC95%: 97,7 - 100,0) de sensibilidad, 100% (IC95%: 99,7 - 100,0) de especificidad, 100% (IC95%: 99,7 -100,0) de valor predictivo positivo y 99,3% (IC95%: 97,7 - 100,0) de valor predictivo negativo. En conclusión, este método brinda una alternativa de bajo costo, alto rendimiento, viabilidad y confiabilidad para el diagnóstico rápido de Zika en instalaciones de atención primaria de salud.
ABSTRACT A Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) method was developed to detect Zika. The primers were designed based on the NS5 region of 64 complete genomes. Lyophilized LAMP reagent was used. Initially, seven different arboviruses were tested and only Zika samples tested positive. Additionally, serial dilutions of one of Zika's RNA were compared using RT-LAMP and qRT-PCR, demonstrating that RT-LAMP is 1,000 times more sensitive. We also evaluated 300 serum samples with RT-LAMP comparing the results with standard qRT-PCR methods, and we obtained a 99.3% sensitivity, 100% specificity, 100% positive predictive value, and 99.3% negative predictive value. In conclusion, this method provides a low-cost, high-performance, viable, and reliable alternative for the rapid diagnosis of Zika in primary health-care facilities.
Subject(s)
Humans , Nucleic Acid Amplification Techniques/methods , Molecular Diagnostic Techniques/methods , Zika Virus/isolation & purification , Zika Virus Infection/diagnosis , Zika Virus Infection/virologyABSTRACT
Objective To determine the use and performance of a line probe assay (LPA) compared with conventional culture and drug sensitivity testing (CDST) in patients registered with tuberculosis (TB) under routine program conditions in Peru in 2011-2013. Methods This was a descriptive, operational research, cross-sectional study of sputum specimens from patients with smear-positive pulmonary TB and mycobacterial cultures from patients with smear-negative or positive TB. Drug resistance to rifampicin and/or isoniazid detected by LPA was compared to CDST. Sensitivity, specificity, and predictive values were calculated and reliability for detecting drug resistance was assessed through kappa coefficient, with values 0.61-0.80 showing substantial correlation, and 0.81 or above showing almost-perfect correlation. Results In 2011-2013, there were 16 169 LPA tests performed, with the proportion of TB patients receiving the test increasing from 3.2% to 30.2%. In all, 2 905 LPA test results were compared to CDST. For LPA in sputum specimens, sensitivity for rifampicin was 92%; isoniazid, 94%; and MDR-TB, 88%; while specificity for rifampicin was 92%; isoniazid, 92%; and MDR-TB, 95%. For LPA in mycobacterial cultures, sensitivity for rifampicin was 95%; isoniazid, 96%; and MDR-TB, 90%; while specificity for rifampicin was 85%; isoniazid, 91%; and MDR-TB, 94%. Kappa coefficients were at 0.81 or above for all comparisons of LPA with CDST using sputum specimens and cultures, except for isoniazid in cultures, which was at 0.79. Conclusions This study suggests that LPA is a reliable and rapid screening test for drug-resistant TB and should be considered suitable for routine use and scale up in Peru.
Subject(s)
Tuberculosis , Antitubercular Agents , Cross-Sectional Studies , Humans , Microbial Sensitivity Tests , Mycobacterium tuberculosis , Peru , Reproducibility of Results , Rifampin/therapeutic use , Sputum , Tuberculosis/drug therapy , Tuberculosis, Multidrug-Resistant/diagnosisABSTRACT
Objective. To determine the use and performance of a line probe assay (LPA) compared with conventional culture and drug sensitivity testing (CDST) in patients registered with tuberculosis (TB) under routine program conditions in Peru in 2011–2013. Methods. This was a descriptive, operational research, cross-sectional study of sputum specimens from patients with smear-positive pulmonary TB and mycobacterial cultures from patients with smear-negative or positive TB. Drug resistance to rifampicin and/or isoniazid detected by LPA was compared to CDST. Sensitivity, specificity, and predictive values were calculated and reliability for detecting drug resistance was assessed through kappa coefficient, with values 0.61–0.80 showing substantial correlation, and 0.81 or above showing almost-perfect correlation. Results. In 2011–2013, there were 16 169 LPA tests performed, with the proportion of TB patients receiving the test increasing from 3.2% to 30.2%. In all, 2 905 LPA test results were compared to CDST. For LPA in sputum specimens, sensitivity for rifampicin was 92%; isoniazid, 94%; and MDR-TB, 88%; while specificity for rifampicin was 92%; isoniazid, 92%; and MDR-TB, 95%. For LPA in mycobacterial cultures, sensitivity for rifampicin was 95%; isoniazid, 96%; and MDR-TB, 90%; while specificity for rifampicin was 85%; isoniazid, 91%; and MDR-TB, 94%. Kappa coefficients were at 0.81 or above for all comparisons of LPA with CDST using sputum specimens and cultures, except for isoniazid in cultures, which was at 0.79. Conclusions. This study suggests that LPA is a reliable and rapid screening test for drug-resistant TB and should be considered suitable for routine use and scale up in Peru.
Objetivo. Definir la utilización de un ensayo con sondas en línea y evaluar su desempeño, en comparación con el método convencional de cultivo y antibiograma, en los pacientes registrados con tuberculosis en condiciones programáticas en el Perú del 2011 al 2013. Métodos. Investigación operativa descriptiva con un estudio transversal de las muestras de esputo de los pacientes con diagnóstico de tuberculosis pulmonar y baciloscopia positiva y de los cultivos de micobacterias de los pacientes con tuberculosis y baciloscopia positiva o negativa. La farmacorresistencia a la rifampicina, la isoniacida o a ambas, detectada mediante el ensayo con sondas en línea, se comparó con los resultados obtenidos por el método de cultivo y antibiograma. Se calculó la sensibilidad, la especificidad y los valores predictivos del ensayo con sondas en línea y se evaluó su fiabilidad en la detección de la farmacorresistencia mediante el coeficiente k, cuyos valores de 0,61 a 0,80 correspondían a una fuerte correlación y los valores de 0,81 o superiores reflejaban una correlación casi perfecta. Resultados. Del 2011 al 2013 se practicaron 16 169 ensayos con sondas en línea, y la proporción de pacientes con diagnóstico de tuberculosis en quienes se practicaba aumentó de 3,2% a 30,2%. En total, se compararon 2 905 resultados del ensayo molecular con el método convencional. En las muestras de esputo, el ensayo molecular ofreció una sensibilidad de 92% para la resistencia a la rifampicina, 94% a la isoniacida y 88% para la tuberculosis multirresistente; su especificidad fue 92% con respecto a la rifampicina, 92% a la isoniacida y 95% a la tuberculosis multirresistente. En los cultivos de micobacterias, el ensayo con sondas en línea mostró una sensibilidad de 95% para la resistencia a la rifampicina, 96% a la isoniacida y 90% para la tuberculosis multirresistente; la especificidad fue 85% para la rifampicina, 91% para la isoniacida y 94% para la tuberculosis multirresistente. El coeficiente k fue 0,81 o superior en todas las comparaciones del ensayo molecular con el método tradicional cuando se usaron muestras de esputo y cultivo, excepto con la isoniacida en cultivo, cuyo coeficiente fue 0,79. Conclusiones. Los resultados del presente estudio indican que el ensayo con sondas en línea constituye una prueba de detección fiable y rápida para la tuberculosis multirresistente , y se debe considerar
Subject(s)
Mycobacterium tuberculosis , Tuberculosis , Tuberculosis, Multidrug-Resistant , Molecular Probes , Molecular Probe Techniques , Operations Research , Peru , Tuberculosis, Multidrug-Resistant , Molecular Probes , Molecular Probe Techniques , Operations ResearchABSTRACT
ABSTRACT Objective To determine the use and performance of a line probe assay (LPA) compared with conventional culture and drug sensitivity testing (CDST) in patients registered with tuberculosis (TB) under routine program conditions in Peru in 2011–2013. Methods This was a descriptive, operational research, cross-sectional study of sputum specimens from patients with smear-positive pulmonary TB and mycobacterial cultures from patients with smear-negative or positive TB. Drug resistance to rifampicin and/or isoniazid detected by LPA was compared to CDST. Sensitivity, specificity, and predictive values were calculated and reliability for detecting drug resistance was assessed through kappa coefficient, with values 0.61–0.80 showing substantial correlation, and 0.81 or above showing almost-perfect correlation. Results In 2011–2013, there were 16 169 LPA tests performed, with the proportion of TB patients receiving the test increasing from 3.2% to 30.2%. In all, 2 905 LPA test results were compared to CDST. For LPA in sputum specimens, sensitivity for rifampicin was 92%; isoniazid, 94%; and MDR-TB, 88%; while specificity for rifampicin was 92%; isoniazid, 92%; and MDR-TB, 95%. For LPA in mycobacterial cultures, sensitivity for rifampicin was 95%; isoniazid, 96%; and MDR-TB, 90%; while specificity for rifampicin was 85%; isoniazid, 91%; and MDR-TB, 94%. Kappa coefficients were at 0.81 or above for all comparisons of LPA with CDST using sputum specimens and cultures, except for isoniazid in cultures, which was at 0.79. Conclusions This study suggests that LPA is a reliable and rapid screening test for drug-resistant TB and should be considered suitable for routine use and scale up in Peru.
RESUMEN Objetivo Definir la utilización de un ensayo con sondas en línea y evaluar su desempeño, en comparación con el método convencional de cultivo y antibiograma, en los pacientes registrados con tuberculosis en condiciones programáticas en el Perú del 2011 al 2013. Métodos Investigación operativa descriptiva con un estudio transversal de las muestras de esputo de los pacientes con diagnóstico de tuberculosis pulmonar y baciloscopia positiva y de los cultivos de micobacterias de los pacientes con tuberculosis y baciloscopia positiva o negativa. La farmacorresistencia a la rifampicina, la isoniacida o a ambas, detectada mediante el ensayo con sondas en línea, se comparó con los resultados obtenidos por el método de cultivo y antibiograma. Se calculó la sensibilidad, la especificidad y los valores predictivos del ensayo con sondas en línea y se evaluó su fiabilidad en la detección de la farmacorresistencia mediante el coeficiente k, cuyos valores de 0,61 a 0,80 correspondían a una fuerte correlación y los valores de 0,81 o superiores reflejaban una correlación casi perfecta. Resultados Del 2011 al 2013 se practicaron 16 169 ensayos con sondas en línea, y la proporción de pacientes con diagnóstico de tuberculosis en quienes se practicaba aumentó de 3,2% a 30,2%. En total, se compararon 2 905 resultados del ensayo molecular con el método convencional. En las muestras de esputo, el ensayo molecular ofreció una sensibilidad de 92% para la resistencia a la rifampicina, 94% a la isoniacida y 88% para la tuberculosis multirresistente; su especificidad fue 92% con respecto a la rifampicina, 92% a la isoniacida y 95% a la tuberculosis multirresistente. En los cultivos de micobacterias, el ensayo con sondas en línea mostró una sensibilidad de 95% para la resistencia a la rifampicina, 96% a la isoniacida y 90% para la tuberculosis multirresistente; la especificidad fue 85% para la rifampicina, 91% para la isoniacida y 94% para la tuberculosis multirresistente. El coeficiente k fue 0,81 o superior en todas las comparaciones del ensayo molecular con el método tradicional cuando se usaron muestras de esputo y cultivo, excepto con la isoniacida en cultivo, cuyo coeficiente fue 0,79. Conclusiones Los resultados del presente estudio indican que el ensayo con sondas en línea constituye una prueba de detección fiable y rápida para la tuberculosis multirresistente, y se debe considerar apropiada su utilización en la práctica de rutina y la ampliación de su empleo en el Perú.
Subject(s)
Tuberculosis/diagnosis , Clinical Trial , Prospecting Probe , PeruABSTRACT
Using chemical extraction to evaluate plant arsenic availability in contaminated soils is important to estimate the time frame for site cleanup during phytoremediation. It is also of great value to assess As mobility in soil and its risk in environmental contamination. In this study, four conventional chemical extraction methods (water, ammonium sulfate, ammonium phosphate, and Mehlich III) and a new root-exudate based method were used to evaluate As extractability and to correlate it with As accumulation in P. vittata growing in five As-contaminated soils under greenhouse condition. The relationship between different soil properties, and As extractability and plant As accumulation was also investigated. Arsenic extractability was 4.6%, 7.0%, 18%, 21%, and 46% for water, ammonium sulfate, organic acids, ammonium phosphate, and Mehlich III, respectively. Root exudate (organic acids) solution was suitable for assessing As bioavailability (81%) in the soils while Mehlich III (31%) overestimated the amount of As taken up by plants. Soil organic matter, P and Mg concentrations were positively correlated to plant As accumulation whereas Ca concentration was negatively correlated. Further investigation is needed on the effect of Ca and Mg on As uptake by P. vittata. Moreover, additional As contaminated soils with different properties should be tested.
Subject(s)
Arsenic/pharmacokinetics , Biodegradation, Environmental , Pteris/metabolism , Soil Pollutants/pharmacokinetics , Arsenic/chemistry , Biological Availability , Industrial Waste , Mining , Pesticides , Soil/chemistry , Soil Pollutants/chemistryABSTRACT
Clinical documentation needs to be fine-grained to truthfully represent the history, development, and treatment of a patient. But natural language, as the main information carrier, is characterized by many issues, like idiosyncratic terminology, spelling and grammar errors, and a lack of grammatical structure. Therefore coding systems, like ICD-10, have been introduced, but their use varies highly among physicians, and they are often used incompletely or incorrectly. The almost exponential growth of clinical data is yet another problem. We present a new methodology to process this data: Through combining several natural language processing methods we extract morphemes from clinical texts and map them onto concepts from SNOMED CT. We first performed a manual analysis of clinical texts received from a university hospital and evaluated the issues found in them. Based on this we implemented a prototypical system which incorporates both the OpenNLP and the MorphoSaurus natural language processing systems.
Subject(s)
Documentation , Electronic Data Processing/methods , Systematized Nomenclature of Medicine , Medical Records Systems, Computerized , Terminology as TopicABSTRACT
Quality assurance and audit issues play a major role in maintening large biomedical terminology, such as SNOMED CT. Several automatized techniques have been proposed to facilitate the identification of weak spots and suggest adequate improvements.In this study, we address a well-known issue within SNOMED CT: Albeit the wording of many free-text concept descriptions suggests a connection to other concepts, they are often not referred to in the logical concept definition.To detect such inconsistencies, we use a semantic indexing approach which maps free text onto a sequence of semantic identifiers. Applied to SNOMED CT concepts without attributes, our technique spots refinable concepts and suggests appropriate attributes, i.e., connections to other concepts. Based on a manual analysis of random samples, we estimate that approximately 18,000 refinable concepts can be found.
Subject(s)
Natural Language Processing , Subject Headings , Systematized Nomenclature of Medicine , Abstracting and Indexing/methods , SemanticsABSTRACT
Cross-language document retrieval systems require support by some kind of multilingual thesaurus for semantically indexing documents in different languages. The peculiarities of the medical sublanguage, together with the subjectivism of lexicographers' choices, complicates the thesaurus construction process. It furthermore requires a high degree of communication and interaction between the lexicographers involved. In order to detect errors, a systematic procedure is therefore necessary. We here describe a method which supports the maintenance of the multilingual medical subword repository of the MorphoSaurus system which assigns language-independent semantic identifiers to medical texts. Based on the assumption that the distribution of these semantic identifiers should be similar whenever comparing closely related texts in different languages, our approach identifies those semantic identifiers that vary most in distribution comparing language pairs. The revision of these identifiers and the lexical items related to them revealed multiple errors which were subsequently classified and fixed by the lexicographers. The overall quality improvement of the thesaurus was finally measured using the OHSUMED IR benchmark, resulting in a significant improvement of the retrieval quality for one of the languages tested.
Subject(s)
Information Storage and Retrieval , Multilingualism , Quality Control , Vocabulary, Controlled , Abstracting and Indexing , Clinical Medicine/classificationABSTRACT
The construction and maintenance of a medical thesaurus is a non-trivial task, due to the inherent complexity of a proper medical terminology. We present a methodology for transaction-based anomaly detection in the process of thesaurus maintenance. Our experiences are based on lexicographic work with the MorphoSaurus lexicons, which are the basis for a mono- and cross-lingual biomedical information retrieval system. Any "edit"or "delete" actions within these lexicons that undo an action defined earlier were defined as anomalous. We identify four types of such anomalies. We also analyzed to which extent the anomalous lexicon entries had been detected by an alternative, corpus-based approach.
Subject(s)
Vocabulary, Controlled , Methods , Quality Control , Subject HeadingsABSTRACT
Leguminosas quando consorciadas com o café e usadas como adubação verde podem contribuir fornecendo nitrogênio e proteção ao solo pela adição de matéria orgânica. O trabalho foi conduzido com o objetivo de avaliar o efeito do uso de leguminosas no sistema de produção de café, no segmento de agricultura familiar, visando promover a implantação e a manutenção dos cafezais de forma técnica e economicamente sustentável. O experimento foi conduzido no período de novembro de 2000 a abril de 2003, em delineamento experimental de blocos ao acaso em esquema de parcelas subdivididas, com quatro repetições. Os tratamentos utilizados nas parcelas foram as leguminosas (Stizolobium atterrimum, Cajanus cajan, Canavalia endiformis e Flemingia congesta) e a testemunha (sem leguminosa) e, nas subparcelas, duas doses de N (0 e 22 g de N por cova). A Flemingia congesta e a Mucuna aterrima foram as leguminosas que mais influenciaram positivamente a produtividade dos cafeeiros, independente da adubação nitrogenada. Em relação à testemunha, o aumento em produção foi de 109 por cento quando utilizou-se a Flemingia congesta e 52 por cento com a Mucuna aterrima. A Flemingia congesta foi também a leguminosa que melhor controlou as invasoras, dado o volume de fitomassa produzida e a possibilidade de 2 cortes durante um período de doze meses, evidenciando o potencial desta leguminosa na formação de novos cafezais no Acre. Por outro lado, a Canavalia ensiformis, leguminosa que é normalmente utilizada nas entrelinhas dos cafeeiros pelos cafeicultores, do Acre e de outras regiões produtoras, neste trabalho influenciou negativamente a altura das plantas, diâmetro da copa e crescimento dos cafeeiros.
Subject(s)
Coffee , Amazonian Ecosystem , Coffea , Health Consortia , FabaceaeABSTRACT
Este trabalho relata a primeira ocorrência de Stenodiplosis sorghicola (Coquillett) no Estado do Acre, Brasil, e a incidência dessa praga em diferentes genótipos de sorgo. Panículas foram coletadas dez dias após o início do florescimento e colocadas em caixas de emergência. S. sorghicola ocorreu em sorgo forrageiro e granífero, sendo a incidência maior no primeiro, no qual o genótipo 698005 foi o mais atacado. A presença de S. sorghicola, em plantios experimentais de sorgo no Acre, revela que tal inseto ocorre na regiäo, sobrevivendo, provavelmente, em outras espécies do gênero Sorghum
