A monster into the heart: an unusual presentation of cardiac leiomyosarcoma.

BACKGROUND: Malignant primary cardiac tumors are infrequent and can lead to an unfavorable prognosis if not identified and treated promptly. Early detection and prompt treatment of malignant primary cardiac tumors are crucial for a better prognosis. This article presents a case of primary cardiac leiomyosarcoma and reviews the literature on this topic. CASE PRESENTATION: Female patient that developed recurrent pericardial effusion and hemodynamic instability caused by a cardiac tumor, later identified as leiomyosarcoma. Multidisciplinary treatment was administered to the patient. CONCLUSIONS: The initial approach to this type of pathology should include multimodality imaging to establish a prompt diagnosis leading to complete standard treatment, to minimize risks to the patient's heart function which may include resection with complete margins of the neoplasm, otherwise the prognosis may be poor.

Dual U-Net-Based Conditional Generative Adversarial Network for Blood Vessel Segmentation with Reduced Cerebral MR Training Volumes.

Segmenting vessels in brain images is a critical step for many medical interventions and diagnoses of illnesses. Recent advances in artificial intelligence provide better models, achieving a human-like level of expertise in many tasks. In this paper, we present a new approach to segment Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) images, relying on fewer training samples than state-of-the-art methods. We propose a conditional generative adversarial network with an adapted generator based on a concatenated U-Net with a residual U-Net architecture (UUr-cGAN) to carry out blood vessel segmentation in TOF-MRA images, relying on data augmentation to diminish the drawback of having few volumes at disposal for training the model, while preventing overfitting by using regularization techniques. The proposed model achieves 89.52% precision and 87.23% in Dice score on average from the cross-validated experiment for brain blood vessel segmentation tasks, which is similar to other state-of-the-art methods while using considerably fewer training samples. UUr-cGAN extracts important features from small datasets while preventing overfitting compared to other CNN-based methods and still achieve a relatively good performance in image segmentation tasks such as brain blood vessels from TOF-MRA.

Prodigiosin Modulates the Immune Response and Could Promote a Stable Atherosclerotic Lession in C57bl/6 Ldlr-/- Mice.

Atherosclerosis is a chronic inflammatory disease, whose progression and stability are modulated, among other factors, by an innate and adaptive immune response. Prodiginines are bacterial secondary metabolites with antiproliferative and immunomodulatory activities; however, their effect on the progression or vulnerability of atheromatous plaque has not been evaluated. This study assessed the therapeutic potential of prodigiosin and undecylprodigiosin on inflammatory marker expression and atherosclerosis. An in vitro and in vivo study was carried out. Migration, low-density lipoprotein (LDL) uptake and angiogenesis assays were performed on cell types involved in the pathophysiology of atherosclerosis. In addition, male LDL receptor null (Ldlr-/-) C57BL/6J mice were treated with prodigiosin or undecylprodigiosin for 28 days. Morphometric analysis of atherosclerotic plaques, gene expression of atherogenic factors in the aortic sinus and serum cytokine quantification were performed. The treatments applied had slight effects on the in vitro tests performed, highlighting the inhibitory effect on the migration of SMCs (smooth muscle cells). On the other hand, although no significant difference in atherosclerotic plaque progression was observed, gene expression of IL-4 and chemokine (C-C motif) ligand 2 (Ccl2) was downregulated. In addition, 50 µg/Kg/day of both treatments was sufficient to inhibit circulating tumor necrosis factor alpha (TNF-α), interleukin-2 (IL-2) and interferon-gamma (IFN-γ) in serum. These results suggested that prodigiosin and undecylprodigiosin modulated inflammatory markers and could have an impact in reducing atherosclerotic plaque vulnerability.

Propolis Reduces the Expression of Autophagy-Related Proteins in Chondrocytes under Interleukin-1ß Stimulus.

BACKGROUND: Osteoarthritis (OA) is a progressive and multifactorial disease that is associated with aging. A number of changes occur in aged cartilage, such as increased oxidative stress, decreased markers of healthy cartilage, and alterations in the autophagy pathway. Propolis extracts contain a mixture of polyphenols and it has been proved that they have high antioxidant capacity and could regulate the autophagic pathway. Our objective was to evaluate the effect of ethanolic extract of propolis (EEP) on chondrocytes that were stimulated with IL-1ß. METHODS: Rabbit chondrocytes were isolated and stimulated with IL-1ß and treated with EEP. We evaluated cell viability, nitric oxide production, healthy cartilage, and OA markers, and the expression of three proteins associated with the autophagy pathway LC3, ATG5, and AKT1. RESULTS: The EEP treatment reduces the expression of LC3, ATG5, and AKT1, reduces the production of nitric oxide, increases the expression of healthy markers, and reduces OA markers. CONCLUSIONS: These results suggest that treatment with EEP in chondrocytes that were stimulated with IL-1ß has beneficial effects, such as a decrease in the expression of proteins associated with autophagy, MMP13, and production of nitric oxide, and also increased collagen II.

Bacterial Community Profile of the Gut Microbiota Differs between Hypercholesterolemic Subjects and Controls.

The role of gut microbiota in the development of metabolic illnesses has been abundantly demonstrated. Recent studies suggest that gut microbiota alterations may also be related to the development of hypercholesterolemia. Therefore, we aimed to assess differences in the gut bacterial community profiles between hypercholesterolemic subjects and controls. Thirty cases diagnosed with hypercholesterolemia and 27 normocholesterolemic controls were included. A fasting whole blood sample was obtained to determine the lipid profile. In parallel, stool samples were collected and total DNA was isolated to assess the bacterial community profiles by denaturing gradient gel electrophoresis (DGGE). In addition, the Richness, Shannon-Weaver, and Simpson indexes were used to evaluate the richness and diversity of bacterial communities. As expected, serum concentrations of total cholesterol, triglycerides, and LDL-cholesterol were significantly higher in the cases compared with controls. Moreover, DGGE analysis showed a lower richness and diversity of bacterial communities in hypercholesterolemic subjects. In conclusion, our results showed differences in the profiles of bacterial communities between hypercholesterolemic subjects and controls, suggesting a possible role of the gut microbiota in the development of hypercholesterolemia.

Polyphenols from Chilean Propolis and Pinocembrin Reduce MMP-9 Gene Expression and Activity in Activated Macrophages.

Polyphenols from diverse sources have shown anti-inflammatory activity. In the context of atherosclerosis, macrophages play important roles including matrix metalloproteinases synthesis involved in degradation of matrix extracellular components affecting the atherosclerotic plaque stability. We prepared a propolis extract and pinocembrin in ethanol solution. Propolis extract was chemically characterized using LC-MS. The effect of treatments on gene expression and proteolytic activity was measured in vitro using murine macrophages activated with LPS. Cellular toxicity associated with both treatments and the vehicle was determined using MTT and apoptosis/necrosis detection assays. MMP-9 gene expression and proteolytic activity were measured using qPCR and zymography, respectively. Thirty-two compounds were identified in the propolis extract, including pinocembrin among its major components. Treatment with either ethanolic extract of propolis or pinocembrin inhibits MMP-9 gene expression in a dose-dependent manner. Similarly, an inhibitory effect was observed in proteolytic activity. However, the effect showed by ethanolic extract of propolis was higher than the effect of pinocembrin, suggesting that MMP-9 inhibition results from a joint contribution between the components of the extract. These data suggest a potential role of polyphenols from Chilean propolis in the control of extracellular matrix degradation in atherosclerotic plaques.

HMGCR rs17671591 SNP Determines Lower Plasma LDL-C after Atorvastatin Therapy in Chilean Individuals.

Lipid-lowering response to statin therapy shows large interindividual variability. At a genome-wide significance level, single nucleotide polymorphisms (SNPs) in PCSK9 and HMGCR have been implicated in this differential response. However, the influence of these variants is uncertain in the Chilean population. Hence, we aimed to evaluate the contribution of PCSK9 rs7552841 and HMGCR rs17671591 SNPs as genetic determinants of atorvastatin response in Chilean hypercholesterolaemic individuals. One hundred and one hypercholesterolaemic patients received atorvastatin 10 mg/day for 4 weeks. Plasma lipid profile (TC, HDL-C, LDL-C and TG) was determined before and after statin treatment, and SNPs were identified by allelic discrimination using TaqMan(®) SNP Genotyping Assays. Adjusted univariate and multivariate analyses' models were used for statistical analyses, and a p-value <0.05 was considered significant. From baseline (week 0) to the study end-point (week 4), significant reductions were observed in plasma TC, LDL-C and TG (p < 0.001), while HDL-C levels were increased (p < 0.001). Multivariate analysis showed no association between lipid levels and atorvastatin therapy for the PCSK9 variant. However, the HMGCR rs17671591 T allele contributed to basal HDL-C concentration variability along with a higher increase in this lipid fraction after statin medication. In addition, this allele determined greater plasma LDL-C reductions after therapy with atorvastatin. Our data suggest that the HMGCR rs17671591 polymorphism can constitute a genetic marker of lower plasma LDL-C and enhanced HDL-C concentration after atorvastatin therapy in the Chilean population.

ERK1/2 and HIF1α Are Involved in Antiangiogenic Effect of Polyphenols-Enriched Fraction from Chilean Propolis.

Propolis has been shown to modulate the angiogenesis in both in vitro and in vivo models. Thus, we aimed to evaluate the antiangiogenic properties of an ethanolic extract of Chilean propolis (EEP) and Pinocembrin (Pn). Migration, formation of capillary-like structures of endothelial cells, and sprouting from rat aortic rings were used to assess the antiangiogenic properties of EEP or Pn. In addition, microRNAs and VEGFA mRNA expression were studied by qPCR. ERK1/2 phosphorylation and HIF1α stabilization were assessed by western blot. EEP or Pn attenuated the migration, the capillary-like tube formation, and the sprouting in the in vitro assays. In addition, the activation of HIF1α and ERK1/2 and the VEGFA mRNA expression was significantly inhibited in a dose-dependent manner. In summary, these results suggest that HIF1α and ERK1/2 phosphorylation could be involved in the antiangiogenic effect of Chilean propolis, but more studies are needed to corroborate these findings.

Identification of microRNAs involved in the modulation of pro-angiogenic factors in atherosclerosis by a polyphenol-rich extract from propolis.

New vessel formation plays a critical role in the progression and vulnerability of atherosclerotic lesions. It has been shown that polyphenols from propolis attenuate the progression of atherosclerosis and also exert inhibitory effects on angiogenic factors. However, the mechanisms underlying these effects are not completely understood. Thus, this study aimed to identify microRNAs (miRNAs) involved in the modulation of pro-angiogenic factors in the atherosclerotic plaques of LDL receptor gene knockout mice treated with a polyphenol-rich extract of Chilean propolis. The progression of the atherosclerotic lesions was significantly attenuated in treated mice compared with control mice. Using microarray analysis and a bioinformatic approach, we identified 29 differentially expressed miRNAs. Many of these miRNAs were involved in biological processes associated with angiogenesis, such as the cell cycle, cell migration, cell growth and proliferation. Among them, three miRNAs (miR-181a, miR-106a and miR-20b) were over-expressed and inversely related to the expression of Vegfa (vascular endothelial growth factor A) and Hif1a (hypoxia inducible factor 1 alpha). In addition, VEGF-A protein expression was attenuated in histological sections obtained from the aortic sinuses of treated mice. VEGFA is a key pro-angiogenic factor in atherosclerotic plaques, and Hif1a, which is expressed in the necrotic nucleus of the atheroma, is its main inducer. We found a correlation between the over-expression of miR-181a, miR-106a and miR-20b and their target genes, Hif1a and Vegfa, which is consistent with attenuation of the atherosclerotic lesion. In conclusion, our data analysis provides evidence that the anti-angiogenic effects of polyphenols from Chilean propolis can be modulated by miRNAs, in particular miR-181a, miR-106a and miR-20b.

Chemical and botanical characterization of Chilean propolis and biological activity on cariogenic bacteria Streptococcus mutans and Streptococcus sobrinus.

Propolis is a non-toxic natural substance with multiple pharmacological properties including anti-cancer, antioxidant, fungicidal, antibacterial, antiviral, and anti-inflammatory among others. The aim of this study was to determine the chemical and botanical characterization of Chilean propolis samples and to evaluate their biological activity against the cariogenic bacteria Streptococcus mutans and Streptococcus sobrinus. Twenty propolis samples were obtained from beekeeping producers from the central and southern regions of Chile. The botanical profile was determined by palynological analysis. Total phenolic contents were determined using colorimetric assays. Reverse phase HPLC and HPLC-MS were used to determine the chemical composition. The minimum inhibitory concentration (MIC) was determined on S. mutans and S. sobrinus. All propolis samples were dominated by structures from native plant species. The characterization by HPLC/MS, evidenced the presence of quercetin, myricetin, kaempferol, rutine, pinocembrin, coumaric acid, caffeic acid and caffeic acid phenethyl ester, that have already been described in these propolis with conventional HPLC. Although all propolis samples inhibited the mutans streptococci growth, it was observed a wide spectrum of action (MIC 0.90 to 8.22 µg mL(-1)). Given that results it becomes increasingly evident the need of standardization procedures, where we combine both the determination of botanical and the chemical characterization of the extracts. Research conducted to date, describes a promising effectiveness of propolis in the prevention of caries and other diseases of the oral cavity, making it necessary to develop studies to identify and understand the therapeutic targets or mechanisms of molecular action of the various compounds present on them.

Modulation of immune function by polyphenols: possible contribution of epigenetic factors.

Several biological activities have been described for polyphenolic compounds, including a modulator effect on the immune system. The effects of these biologically active compounds on the immune system are associated to processes as differentiation and activation of immune cells. Among the mechanisms associated to immune regulation are epigenetic modifications as DNA methylation of regulatory sequences, histone modifications and posttranscriptional repression by microRNAs that influences the gene expression of key players involved in the immune response. Considering that polyphenols are able to regulate the immune function and has been also demonstrated an effect on epigenetic mechanisms, it is possible to hypothesize that there exists a mediator role of epigenetic mechanisms in the modulation of the immune response by polyphenols.

Chemical and botanical characterization of Chilean propolis and biological activity on cariogenic bacteria Streptococcus mutans and Streptococcus sobrinus

Propolis is a non-toxic natural substance with multiple pharmacological properties including anticancer, antioxidant, fungicidal, antibacterial, antiviral, and anti-inflammatory among others. The aim of this study was to determine the chemical and botanical characterization of Chilean propolis samples and to evaluate their biological activity against the cariogenic bacteria Streptococcus mutans and Streptococcus sobrinus. Twenty propolis samples were obtained from beekeeping producers from the central and southern regions of Chile. The botanical profile was determined by palynological analysis. Total phenolic contents were determined using colorimetric assays. Reverse phase HPLC and HPLC-MS were used to determine the chemical composition. The minimum inhibitory concentration (MIC) was determined on S. mutans and S. sobrinus. All propolis samples were dominated by structures from native plant species. The characterization by HPLC/MS, evidenced the presence of quercetin, myricetin, kaempferol, rutine, pinocembrin, coumaric acid, caffeic acid and caffeic acid phenethyl ester, that have already been described in these propolis with conventional HPLC. Although all propolis samples inhibited the mutans streptococci growth, it was observed a wide spectrum of action (MIC 0.90 to 8.22 µgmL-1). Given that results it becomes increasingly evident the need of standardization procedures, where we combine both the determination of botanical and the chemical characterization of the extracts. Research conducted to date, describes a promising effectiveness of propolis in the prevention of caries and other diseases of the oral cavity, making it necessary to develop studies to identify and understand the therapeutic targets or mechanisms of molecular action of the various compounds present on them.

Identification of pharmacogenetic predictors of lipid-lowering response to atorvastatin in Chilean subjects with hypercholesterolemia.

BACKGROUND: Statins are normally the first-line therapy for hypercholesterolemia (HC); however, the lipid-lowering response shows high interindividual variation. We investigated the effect of four polymorphisms in CYP3A4, CYP3A5 and ABCB1 genes on response to atorvastatin and CYP3A4 activity in Chilean subjects with HC. METHODS: A total of 142 hypercholesterolemic individuals underwent atorvastatin therapy (10mg/day/1month). Serum lipid levels before and after treatment were measured. Genetic variants in CYP3A4 (-290A>G, rs2740574), CYP3A5 (6986A>G, rs776746) and ABCB1 (2677G>A/T, rs2032582 and 3435C>T, rs1045642) were analyzed by PCR-RFLP. CYP3A4 enzyme activity in urine samples was assessed through determination of 6ß-hydroxycortisol/cortisol free ratio (6ßOHC/FC). RESULTS: After 4weeks of therapy, a significant reduction in total cholesterol (TC) and LDL-c was observed (P<0.001). The G allele for -290A>G polymorphism was related to higher percentage of variation in TC and LDL-c (P<0.001). Moreover, same allele was associated with higher HDL-c variation (P=0.017). In addition, CYP3A4 enzyme activity was lower in subjects carrying this polymorphism (P=0.009). No differences were observed for CYP3A5 and ABCB1 variants. CONCLUSION: Our results suggest that presence of G allele for -290A>G polymorphism determines a better response to atorvastatin, being also associated with lower CYP3A4 activity in vivo, causing an increased atorvastatin activity.

Frequency of common variants in genes involved in lipid-lowering response to statins in Chilean subjects with hypercholesterolemia / Frecuencia de polimorfismos en genes relacionados a la respuesta terapéutica a estatinas en individuos chilenos con hipercolesterolemia

Interindividual differences in activity and expression of the metabolizing enzymes cytochrome P450 (CYP) 3A4 and 3A5 and the multidrug efflux pump P-glycoprotein (P-gp, encoded by ABCB1 gene) contribute considerably to lipid-lowering efficacy of statin treatment in subjects with hypercholesterolemia. Variability in the activity of CYP3A4, CYP3A5 and P-gp could be considered to result from genetic polymorphisms encoding their genes. However, the available data indicate that the frequencies of ABCB1, CYP3A4 and CYP3A5 gene polymorphisms differ significantly across populations. Thus, the aim of the present study was to determine the allelic frequency of three common variants of these genes in Chilean individuals with primary hypercholesterolemia (HC) and controls. A total of 135 unrelated patients (44 +/- 7 years old) with diagnosis of hypercholesterolemia (Total cholesterol 240 mg/dL) and 120 normolipidemic healthy controls (40 +/- 10 years old; total cholesterol 200 mg/dL) were included in this study. The 3435C>T (MDR1), -290A>G (CYP3A4) and 6986A>G (CYP3A5) gene polymorphisms were analyzed by PCR-RFLP. The genotype distribution for 3435C>T variant of ABCB1 in HC patients (CC: 49 percent, CT: 37 percent, TT: 14 percent) and controls (CC: 41 percent, CT: 48 percent, TT: 11 percent) was comparable (P=0.186). Similarly, the genotype distribution for -290A>G polymorphism of CYP3A4 in HC subjects (AA: 73 percent, AG: 27 percent, GG: 0 percent) and controls (AA: 71 percent, AG: 29 percent, GG: 0 percent) was equivalent (P = 0.863). Finally, the genotype distribution for 6986A>G variant of CYP3A5 in HC individuals (AA: 4 percent, AG: 41 percent, GG: 55 percent) and controls (AA: 4 percent, AG: 47 percent, GG: 49 percent) was similar (P=0.594). The allelic frequencies of 3435C>T (ABCB1), -290A>G (CYP3A4) and 6986A>G (CYP3A5) polymorphisms are similar between Chilean HC patients and controls, and comparable to frequencies found in Asian populations.

Polimorfismos de los genes CYP3A4, CYP3A5 y ABCB1 se han asociado a variaciones en la respuesta a fármacos hipolipemiantes, como las estatinas; principales medicamentos utilizados para disminuir los niveles plasmáticos de colesterol (CT). Sin embargo, la frecuencia de estas variantes genéticas puede variar entre las poblaciones. Así, el objetivo de este trabajo fue evaluar la frecuencia de tres polimorfismos de los genes CYP3A4, CYP3A5 y ABCB1, relacionados previamente a la respuesta a estatinas, en individuos chilenos hipercolesterolémicos (HC) y controles. Se analizaron 135 sujetos con diagnóstico de hipercolesterolemia primaria (CT 240 mg/dL) y 120 controles (CT 200 mg/dL) pertenecientes a la Región de La Araucanía (Chile). La genotipificación de las variantes genéticas se efectuó mediante la técnica de reacción en cadena de la polimerasa seguido de restricción enzimática (PCR-RFLP). La distribución de genotipos para la variante 3435C>T del gen ABCB1 en los individuos HC (CC: 49 por ciento, CT: 37 por ciento, TT: 14 por ciento) y controles (CC: 41 por ciento, CT: 48 por ciento, TT: 11 por ciento) fue semejante (P = 0,186). De forma similar, la distribución de genotipos para el polimorfismo -290A>G del gen CYP3A4 en los pacientes HC (AA: 73 por ciento, AG: 27 por ciento, GG: 0 por ciento) y controles (AA: 71 por ciento, AG: 29 por ciento, GG: 0 por ciento) fue equivalente (P = 0,863). Del mismo modo, la distribución de genotipos para la variante 6986A>G del gen CYP3A5 en el grupo HC (AA: 4 por ciento, AG: 41 por ciento, GG: 55 por ciento) y grupo control (AA: 4 por ciento, AG: 47 por ciento, GG: 49 por ciento) fue similar (P = 0,594). En resumen, nuestro estudio demuestra que las frecuencias de los polimorfismos 3435C>T (ABCB1), -290A>G (CYP3A4) y 6986A>G (CYP3A5) no difieren entre individuos HC y controles, y son comparables a las frecuencias encontradas en poblaciones asiáticas. Su efecto sobre el tratamiento con estatinas en la población chilena debe ser...

Efecto del propóleos chileno sobre el metabolismo de glucosa en ratones diabéticos / Effect of chilean propolis on glucose metabolism in diabetic mice

En el presente estudio se evaluó el efecto del propóleos sobre el metabolismo de la glucosa en ratones C57/BL-6 con diabetes mellitus tipo 2 inducida por dieta alta en grasa. Se midieron los cambios en las concentraciones séricas de lípidos, glucosa e insulina, y el efecto sobre la captación de 2-deoxi-[2,6-3H]-D-glucosa, síntesis de [14C]-glicógeno y descarboxilación de [U-14C]-D-glucosa inducida por insulina en músculo aislado. Los resultados muestran que en ratones diabéticos, el tratamiento con propóleos (150 mg/kg/día) reduce los niveles de insulina e índice HOMA (P<0.05). También disminuyó la obesidad abdominal de estos animales (P<0.05). Por otro lado, no modificó las concentraciones plasmáticas de glucosa, colesterol total y triglicéridos. Se observó también que la captación de 2-deoxi-[2,6-3H]-D-glucosa, síntesis de [14C]-glicógeno y descarboxilación de [U-14C]-D-glucosa inducida por insulina en músculo sóleo de ratones tratados con propóleos fue significativamente superior al grupo control (P<0.05). En resumen, nuestros datos confirman que el propóleos es capaz de modular el metabolismo de glucosa en ratones C57/BL-6 con diabetes mellitus tipo 2 inducida por dieta alta en grasa. Los datos obtenidos constituyen un importante antecedente que avala el posible uso del propóleos como fuente de polifenoles con actividad antidiabetogénica.

In the current study, we investigated the effect of propolis on diabetic mice undergoing propolis treatment (150 mg/kg/day) for a 6 week period. We also evaluated serum lipids, glucose, insulin levels and the effect on glucose uptake of 2-deoxy-D-[2,6-3H] glucose, [14C]-glycogen synthesis and [U-14C]-D-glucose decarboxylation induced by insulin in muscle tissue. Our results show that treatment with propolis (150 mg/kg/day) reduced insulin and HOMA index (P<0.05). Propolis also lowered abdominal obesity (P<0.05). No effects over serum glucose, total cholesterol and triglycerides levels were observed. We also observed that uptake of 2-deoxy-D-[2,6-3H] glucose, [14C]-glycogen synthesis and [U-14C]-D-glucose decarboxylation induced by insulin in soleus muscle of mice treated with propolis were significantly greater than control group (P<0.05). In summary, our data establishes that propolis modulates glucose metabolism. This result constitutes important data indicating that propolis can be used as a polyphenols source with antidiabetogenic activity.

PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids.

SUMMARY: PubDNA Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features (i) searching for papers mentioning one or more specific sequences of nucleic acids and (ii) retrieving the genetic sequences appearing in different articles. These additional query capabilities are provided by a searchable index that we created by using the full text of the 176 672 papers available at PubMed Central at the time of writing and the sequences of nucleic acids appearing in them. To automatically extract the genetic sequences occurring in each paper, we used an original method we have developed. The database is updated monthly by automatically connecting to the PubMed Central FTP site to retrieve and index new manuscripts. Users can query the database via the web interface provided. AVAILABILITY: PubDNA Finder can be freely accessed at http://servet.dia.fi.upm.es:8080/pubdnafinder

A method for automatically extracting infectious disease-related primers and probes from the literature.

BACKGROUND: Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1) convert each document into a tree of paper sections, (2) detect the candidate sequences using a set of finite state machine-based recognizers, (3) refine problem sequences using a rule-based expert system, and (4) annotate the extracted sequences with their related organism/gene information. RESULTS: We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name. CONCLUSIONS: We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch.

Polimorfismo SNP-43 del gen de calpaína-10 en individuos con enfermedad coronaria y controles / SNP43 polymorphism of Calpain-10 gene in Southern Chilean subjects with coronary artery disease and controls

Resumen: La Diabetes mellitus tipo 2 (DMT2) es un reconocido factor de riesgo cardiovascular que ha mostrado asociación con aterosclerosis subclínica; lo cual podría ser explicado por la presencia de una base genética común entre ambas patologías. Varios polimorfismos del gen de calpaína-10 (CAPNIO) han sido asociados con insulino resistencia y DMT2, sin embargo, existe escasa evidencia de su relación con enfermedad coronaria. El objetivo del presente estudio fue evaluar la posible asociación de la variante SNP-43 de CAPNIO con el desarrollo de enfermedad coronaria en individuos del sur de Chile. Métodos: Fueron incluidos en este estudio, 218 pacientes adultos no relacionados con enfermedad arterial coronaria (EAC) confirmada mediante angiografía (estenosis >70 por ciento) y 194 individuos controles. La variante genética UCSNP-43 fue estudiada por PCR-RFLP. Resultados: No se observaron diferencias significativas entre las frecuencias genotípicas de la variante UCSNP-43 en pacientes con EAC (GG: 51.4 por ciento; GA: 42.7 por ciento; AA: 5.9 por ciento) y controles (GG: 59.6 por ciento; GA: 35.1 por ciento; AA: 5.2 por ciento, p=0.228). Similarmente, no hubo diferencias significativas entre las frecuencias alélicas entre pacientes con EAC y controles (p=0.200). La Odds Ratio fue de 1.17 (I.C 95 por ciento: 0.50-2.72), confirmando la ausencia reasociación. Conclusión: Nuestros datos sugieren que la variante UCSNP-43 del gen CAPNIO no está asociada a la presencia de enfermedad arterial coronaria en la población investigada.

Background: Diabetes mellitus type 2 (DMT2) is a well know cardiovascular risk factor and has been related to subclinic atherosclerosis, which might be explained by the presence of a common genetic basis in both diseases. Several polymorphisms of the cal-pain-10 gene (CAPNIO) have been associated with insulin resistance and DMT; nevertheless, there is insufficient evidence about their relation with coronary artery disease (CAD). Thus, in the present study we investigated the possible association between the SNP-43 variant of CAPNIO and the presence of CAD in Chilean subjects. Methods: A total of 218 unrelated patients with diagnosis of CAD confirmed by angiography (33-74 years old) and 194 healthy controls (30 - 68 years old) were included in this study. The SNP43 variant of the CAPNIO gene was evaluated by PCR-RFLP. Results: The genotype distribution for SNP43 variant of CAPNIO gene in CAD patients (GG: 51.4 percent; GA: 42.7 percent; AA: 5.9 percent) and controls (GG: 59.6 percent; GA: 35.1 percent; AA: 5.2 percent) was similar (P=0.228). Similarly, the allelic frequency was no different (P = 0.200). The OR for CAD related to AA homozygous genotype was 1.17 (95 percent C.I. = 0.50 - 2.72), confirming the absence of association. Conclusion: These findings suggest that the SNP43 polymorphism of the CAPNIO gene is not associated to CAD in the studied individuals.

Asociación del polimorfismo rs2241766 del gen de la adiponectina y enfermedad arterial coronaria en individuos del sur de Chile / Association between single nucleotide polymorphism of adiponectin gene and coronary artery disease in Southern Chilean subjects

La adiponectina, hormona peptídica secretada por los adipocitos, actúa inhibiendo la formación de la placa ateromatosa en casi todas sus etapas, ya sea modulando la respuesta inflamatoria, inhibiendo la expresión de moléculas de adhesión, la activación de monocitos, la formación de células espumosas y la migración y proliferación de células de músculo liso. En el presente estudio, fue evaluada la frecuencia del polimorfismo 45TMJ (rs2241766) del gen que codifica para la hormona adiponectina (ADIPOQ), junto con su posible contribución al desarrollo de enfermedad coronaria en individuos del sur de Chile. Métodos: Fueron evaluados 416 individuos adultos (30 a 68 años); 200 casos confirmados por angiografía y 216 controles. La genotipificación del polimorfismo 451>G del gen ADIPOQ se realizó mediante la técnica de PCR-RFLP. Resultados: El análisis de los resultados demuestra que la presencia del alelo G del polimorfismo 45T>G del gen ADIPOQ duplica el riesgo de padecer enfermedad coronaria en la población estudiada (OR= 2.06; I.C.95 por ciento: 1.36-3.14). Conclusión: Nuestros datos revelaron la existencia de una interesante asociación entre el polimorfismo 45T>G del gen ADIPOQ y enfermedad arterial coronaria en los sujetos analizados. Es importante destacar, que este hallazgo constituye el primer antecedente en población chilena.

Background: Adiponectin, encoded by ADIPOQ gene, is a hormone secreted by adipocytes that acts inhibiting the atheromatous plaque formation, modulating the inflammatory response and inhibiting the expression of adhesion molecules with subsequent inhibition of adhesion and macrophage activation, foam cells formation and migration and proliferation of smooth muscle cells. Aim: to evaluate the possible association between the rs2241766 polymorphism of the ADIPOQ gene with coronary artery disease (CAD) in Southern Chilean subjects. Methods: We evaluated 416 unrelated individuals (38 -68 years old); 200 with CAD confirmed by angiography and 216 control individuals from Temuco city (Chile). The rs2241766 polymorphism (45T>G) of ADIPOQ gene was determined by PCR-RFLP. Results: CAD patients exhibited a high frequency of G allele when compared to controls (17 percent vs. 9 percent; p<0.001). The OR for CAD associated to G allele was 2.06 (95 percent CI: 1.36 - 3.14) confirming the association observed. Conclusion: Our data show that the rs2241766 ADIPOQ gene polymorphism contributed to CAD risk in the studied population.

Polimorfismos genéticos de APOA5 se asocian a hipertrigliceridemia e hiperglicemia en individuos chilenos con enfermedad coronaria y controles / Genetic polymorphisms of APOA5 are associated with hypertriglyceridemia and hyperglycemia in Chilean subjects with coronary artery disease and controls

Introducción: Diversas variantes genéticas han sido relacionadas al desarrollo de enfermedad coronaria y/o sus factores de riesgo; entre ellas, los polimorfismos S19W y -1131T>C del gen que codifica para la apolipoproteína A5 (APOA5). Así, el objetivo del presente estudio fue investigar la posible asociación entre las variantes S19W y -1131T>C del gen APOA5 y enfermedad coronaria en individuos chilenos. Métodos: Se evaluaron 425 sujetos adultos, no relacionados; 209 pacientes con enfermedad coronaria (EC) comprobada por angiografía (estenosis→ 70 por ciento), con edades entre 33 y 74 años, y 216 individuos controles (30 a 68 años). La genotipificación de los polimorfismos S19Wy -1131T>C del gen APOA5 fue realizada mediante la técnica de PCR-RFLP Resultados: La distribución de los genotipos para el polimorfismo S19W del gen APOA5 en el grupo casos (SS: 80 por ciento, SW: 19 por ciento y WW: 1 por ciento) y en el grupo control (SS: 82 por ciento, SW: 17 por ciento y WW: 1 por ciento) fue semejante (p=NS). La distribución genotípica para el polimorfismo -1131T>C en pacientes con EC (TT: 56 por ciento, TC: 37 por ciento, y CC: 7 por ciento) y controles (TT: 63 por ciento, TC: 30 por ciento y CC: 7 por ciento) fue similar (p=NS). Las ORs relacionadas a los alelos mutados 19W (1.12; I.C.95 por ciento, 0.72- 1.74, p=NS)y-1131C (1.19; I.C.95 por ciento,, 0.87- 1.63, p=NS), confirman la ausencia de asociación. Por otro lado, las concentraciones de triglicéridos y glucosa en ayunas fueron significativamente más elevadas en los sujetos portadores de los alelos 19Wy -1131C, tanto en casos como en controles (p<0.05). Conclusión: La asociación observada entre las variantes genéticas de APOA5 y las altas concentraciones séricas de triglicéridos y glucosa, en ambos grupos, sugiere que estos polimorfismos podrían contribuir al desarrollo de la dislipidemia diabética; un reconocido factor de riesgo para enfermedad arterial coronaria.

Background: Several genetic variants have been linked to the development of coronary heart disease and/or their risk factors, including the S19Wand-1131T> C polymorphisms of the gene that encodes apolipoprotein A5 (APOA5). Thus, the objective of this study was to investigate the possible association between S19W and -1131T>C genetic variants ofAPOA5 and coronary disease in Chilean individuals. Methods: We evaluated 425 not related subjects; 209 patients with coronary artery disease (CAD) confirmed by angiography (stenosis→ 70 percent,), aged between 33 and 74 years, and 216 control individuals (30 to 68 years). The genotyping of S19W and -1131T>C polymorphisms of APOA5 gene was evaluated by PCR-RFLP. Results: The genotype distribution of S19W polymorphism of APOA5 gene in CAD patients (SS: 80 percent,, SW: 19 percent, WW: 1 percent>) and controls (SS: 82 percent,, SW: 17 percent, WW: 1 percent>) was similar (p = NS). In the same way the genotype distribution of-1131T>C genetic variant in CAD subjects (TT: 56 percent,, TC: 37 percent,, and CC: 7 percent>) and controls (TT: 63 percent,, TC: 30 percent, and CC: 7 percent) was equivalent (p = NS). The Odds ratios related to the mutant alleles 19W (1.12, 95 percent, Cl, 0.72 - 1.74, p = NS) and -1131C (1.19, 95 percent, Cl, 0.87 -1.63, p = NS) confirms the absence of association. On the other hand, the triglycerides and fasting glucose concentrations were significantly higher in subjects carrying the alleles 19W and -1131C, in both groups, CAD patients and controls (p <0.05). Conclusion: The observed association between genetic variants of APOA5 and higher serum levels of triglycerides and glucose, in both groups, suggesting that these polymorphisms could be contribute to the development of diabetic dyslipidemia, a known risk factor for coronary artery disease.