Admixture mapping analysis reveals differential genetic ancestry associated with Chagas disease susceptibility in the Colombian population.

Chagas disease is an infection caused by the parasite Trypanosoma cruzi, endemic in Latino America. Leveraging the three-way admixture between Native American (AMR), European (EUR) and African (AFR) populations in Latin Americans, we aimed to better understand the genetic basis of Chagas disease by performing an admixture mapping study in a Colombian population. A two-stage study was conducted, and subjects were classified as seropositive and seronegative for T. cruzi. In stage 1, global and local ancestries were estimated using reference data from the 1000 Genomes Project (1KGP), and local ancestry associations were performed by logistic regression models. The AMR ancestry showed a protective association with Chagas disease within the major histocompatibility complex region [Odds ratio (OR) = 0.74, 95% confidence interval (CI) = 0.66-0.83, lowest P-value = 4.53 × 10-8]. The fine mapping assessment on imputed genotypes combining data from stage 1 and 2 from an independent Colombian cohort, revealed nominally associated variants in high linkage disequilibrium with the top signal (rs2032134, OR = 0.93, 95% CI = 0.90-0.97, P-value = 3.54 × 10-4) in the previously associated locus. To assess ancestry-specific adaptive signals, a selective sweep scan in an AMR reference population from 1KGP together with an in silico functional analysis highlighted the Tripartite Motif family and the human leukocyte antigen genes, with crucial role in the immune response against pathogens. Furthermore, these analyses emphasized the macrophages, neutrophils and eosinophils, as key players in the defense against T. cruzi. This first admixture mapping study in Chagas disease provided novel insights underlying the host immune response in the pathogenesis of this neglected disease.

Artificial Intelligence Techniques for Automatic Detection of Peri-implant Marginal Bone Remodeling in Intraoral Radiographs.

Peri-implantitis can cause marginal bone remodeling around implants. The aim is to develop an automatic image processing approach based on two artificial intelligence (AI) techniques in intraoral (periapical and bitewing) radiographs to assist dentists in determining bone loss. The first is a deep learning (DL) object-detector (YOLOv3) to roughly identify (no exact localization is required) two objects: prosthesis (crown) and implant (screw). The second is an image understanding-based (IU) process to fine-tune lines on screw edges and to identify significant points (intensity bone changes, intersections between screw and crown). Distances between these points are used to compute bone loss. A total of 2920 radiographs were used for training (50%) and testing (50%) the DL process. The mAP@0.5 metric is used for performance evaluation of DL considering periapical/bitewing and screws/crowns in upper and lower jaws, with scores ranging from 0.537 to 0.898 (sufficient because DL only needs an approximation). The IU performance is assessed with 50% of the testing radiographs through the t test statistical method, obtaining p values of 0.0106 (line fitting) and 0.0213 (significant point detection). The IU performance is satisfactory, as these values are in accordance with the statistical average/standard deviation in pixels for line fitting (2.75/1.01) and for significant point detection (2.63/1.28) according to the expert criteria of dentists, who establish the ground-truth lines and significant points. In conclusion, AI methods have good prospects for automatic bone loss detection in intraoral radiographs to assist dental specialists in diagnosing peri-implantitis.

Filter pruning for convolutional neural networks in semantic image segmentation.

The remarkable performance of Convolutional Neural Networks (CNNs) has increased their use in real-time systems and devices with limited resources. Hence, compacting these networks while preserving accuracy has become necessary, leading to multiple compression methods. However, the majority require intensive iterative procedures and do not delve into the influence of the used data. To overcome these issues, this paper presents several contributions, framed in the context of explainable Artificial Intelligence (xAI): (a) two filter pruning methods for CNNs, which remove the less significant convolutional kernels; (b) a fine-tuning strategy to recover generalization; (c) a layer pruning approach for U-Net; and (d) an explanation of the relationship between performance and the used data. Filter and feature maps information are used in the pruning process: Principal Component Analysis (PCA) is combined with a next-convolution influence-metric, while the latter and the mean standard deviation are used in an importance score distribution-based method. The developed strategies are generic, and therefore applicable to different models. Experiments demonstrating their effectiveness are conducted over distinct CNNs and datasets, focusing mainly on semantic segmentation (using U-Net, DeepLabv3+, SegNet, and VGG-16 as highly representative models). Pruned U-Net on agricultural benchmarks achieves 98.7% parameters and 97.5% FLOPs drop, with a 0.35% gain in accuracy. DeepLabv3+ and SegNet on CamVid reach 46.5% and 72.4% parameters reduction and a 51.9% and 83.6% FLOPs drop respectively, with almost no decrease in accuracy. VGG-16 on CIFAR-10 obtains up to 86.5% parameter and 82.2% FLOPs decrease with a 0.78% accuracy gain.

Transforming growth factor beta 1 (TGFbeta1) gene polymorphisms and Chagas disease susceptibility in Peruvian and Colombian patients.

Susceptibility to Chagas disease infections and its clinical manifestations may be influenced by host genetic factors. Among cytokines, the multifunctional transforming growth factor beta 1 (TGFbeta1), plays a major role in the establishment and pathogenesis of Trypanosoma cruzi infection, the etiological agent of Chagas disease. Several single-nucleotide polymorphisms (SNP) in the TGFbeta1 gene that may affect cytokine production have been described. We investigated, by PCR methods, five SNP in the TGFbeta1 gene of known or suggested functional significance (-988 C/A; -800 G/A; -509 C/T; 10 T/C and 263 C/T) in 347 seropositive (asymptomatic, n=175; cardiomyopathic, n=172) and 279 seronegative unrelated individuals from a Peruvian and a Colombian population where T. cruzi is highly endemic. We found a significant difference in the distribution of the TGFbeta1 10T and 10C alleles between patients and healthy controls in both cohorts, analyzed independently and combined. The frequency of the high TGFbeta1 producer genotype 10 C/C was increased in the patients groups of both populations. Our data suggests that TGFbeta1 genetic polymorphisms at codon 10 may be involved in a differential susceptibility to T. cruzi infection in these South American samples.

Assessment of Fatty liver syndrome and its predisposing factors in a dairy herd from Venezuela.

The present on-farm research evaluated the occurrence of fatty liver syndrome and its predisposing risk factors for multiparous dairy cows from a commercial herd in Venezuela. Liver biopsy samples were collected at 35 days (d) prepartum (Holstein, n = 14; Holstein × Carora crossbred, n = 17) as well as 1 to 7 d (Holstein, n = 8; Holstein × Carora crossbred, n = 11) and 28 to 35 d (Holstein, n = 6; Holstein × Carora crossbred, n = 14) postpartum in order to analyse hepatic triacylglycerols (TAG, % wet basis) and glycogen concentrations. At postpartum, an occurrence of 72.0% for severe fatty liver along with 73.5% of subclinical ketosis (SCK) was found. The multiple regression model that best explained the association between milk production in the previous lactation (MYP) and TAG at first week postpartum was as follows: TAG, % = -11.2 + 3.16 (prepartum body condition) + 0.0009176 (MYP) (R(²) = 0.36, P < 0.05). Logistic regression indicated that Holstein × Carora crossbred cows tended to have 27% higher relative risk than Holstein to experience SCK, whereas prepartum liver TAG greater than 3% tended to be associated with a higher relative risk for SCK compared to cows with TAG ≤3%.

HLA-Matched Donor-Recipient Combinations and Kidney Transplant Probabilities in a Specific Colombian Population / Compatibilidad HLA donante-receptor y probabilidades de trasplante renal en una población colombiana / Compatibilidade HLA doador-receptor e probabilidades de transplante renal em uma população colombiana

Introduction: In Colombia, despite the fact that kidney transplants are the most common type of transplant surgery, a great number of transplanted patients do not achieve the desired Human Leucocyte Antigen (HLA) compatibility. HLA compatibility plays an important role in graft survival; patients with matched-HLA have a lower chance of graft-versus-host disease and graft rejection. Objective: To determine the probability of finding an HLA-matched donor-recipient pairs according to HLA−A, −B and −DRB1 frequencies in a specific Colombian population. Materials and methods: The study included a total of 484 unrelated individuals (61 donors and 423 recipients) from the HLA registry. HLA alleles were determined by polymerase chain reaction sequence with specific indicators. Results: HLA-A*02, -A*24, -B*35 and -DRB1*04 alleles showed the highest minimum allele frequency (>10%). In addition, HLA-A*24-B*35-DRB1*04 was the most frequent extended haplotype in both donors and recipients (7.38% and 6.76%, respectively). Our experimental evidence showed that the maximum chance of finding at least one HLA allele-matched kidney is 20.3% for a patient with the most frequent extended haplotype, whereas for patients with rare or non-common haplotypes this probability is rather unlikely. Discussion: In terms of probability, the chance of finding an HLA matched kidney donor/recipients in our region is low. This is due, at least in part, to the higher number of alleles and a the lower donation rate. Therefore, to define the HLA profile of a population is important for establishing transplantation programs and alternative strategies in the kidney donation and allocation processes.

Introducción: en Colombia, el trasplante renal es el más común, sin embargo, un gran número de personas trasplantadas no tiene la compatibilidad HLA deseada. Esta compatibilidad es importante en la supervivencia del trasplante; pacientes con HLA-compatible tienen un menor chance de rechazo o desarrollo de la enfermedad injerto frente a hospedero. Objetivo: determinar la probabilidad de encontrar compatibilidad HLA receptor-donante acorde con las frecuencias en población colombiana de HLA−A, −B y −DRB1. Materiales y métodos: el estudio incluyó 484 individuos no relacionados (61 donantes y 423 receptores) con registro de HLA. Los alelos HLA fueron determinados por reacción en cadena de la polimerasa con iniciadores específicos. Resultados: los alelos HLA-A*02, -A*24, -B*35 y -DRB1*04 tuvieron la frecuencia alélica mínima más alta (>10%). El alelo extendido HLA-A*24-B*35-DRB1*04 fue el más frecuente, en donantes y receptores (7,38% y 6,76%, respectivamente). Nuestro análisis mostró que el máximo chance de encontrar un riñón con un alelo HLA compatible es de 20,3% para un paciente con el haplotipo extendido más frecuente, mientras para pacientes con haplotipos raros o no comunes esta probabilidad es mínima. Conclusión: en términos de probabilidad, el chance de encontrar en nuestra región, un riñón con compatibilidad HLA entre donante/receptor es baja. Por lo menos, en parte, es debido al alto número de alelos y a la baja tasa de donación. Por lo tanto, determinar el perfil de HLA de una población es importante para establecer programas de trasplante y estrategias alternativas en donación de riñones y procesos de asignación.

Introdução: Na Colômbia, o transplante renal é o mais comum, no entanto, um grande número de pessoas transplantadas não tem a compatibilidade HLA desejada. Esta compatibilidade é importante na supervivência do transplante; pacientes com HLA-compatível têm uma menor chance de rejeição ou desenvolvimento da enfermidade enxerto versus hospedeiro. Objetivo: determinar a probabilidade de encontrar compatibilidade HLA receptor-doador conforme às frequências em população colombiana de HLA-A, -B e -DRB1. Materiais e métodos: O estudo incluiu 484 indivíduos não relacionados (61 doadores e 423 receptores) com registro de HLA. Os alelos HLA-A*02, -A*24, -B*35 e -DRB1*04 tiveram a frequência alélica mínima mais alta (>10%). Resultados: O alelo estendido HLA-A*24-B*35-DRB1*04 foi o mais frequente, em doadores e receptores (7,38% e 6,76%, respectivamente). Nossa análise mostrou que a máxima chance de encontrar um rim com um alelo HLA compatível é de 20,3% para um paciente com o haplótipo estendido mais frequente, enquanto para pacientes com haplótipos raros ou não comuns esta probabilidade é mínima. Conclusões: em termos de probabilidade, a chance de encontrar em nossa região, um rim com compatibilidade HLA entre doador/receptor é baixa. Pelo menos em parte, é devido ao alto número de alelos e à baixa taxa de doação. Pelo tanto, determinar o perfil de HLA de uma população é importante para estabelecer programas de transplante e estratégias alternativas em doação de rins e processos de atribuição.

International study to evaluate PCR methods for detection of Trypanosoma cruzi DNA in blood samples from Chagas disease patients.

BACKGROUND: A century after its discovery, Chagas disease still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The purpose of this study was to evaluate the performance of PCR methods in detection of Trypanosoma cruzi DNA by an external quality evaluation. METHODOLOGY/FINDINGS: An international collaborative study was launched by expert PCR laboratories from 16 countries. Currently used strategies were challenged against serial dilutions of purified DNA from stocks representing T. cruzi discrete typing units (DTU) I, IV and VI (set A), human blood spiked with parasite cells (set B) and Guanidine Hidrochloride-EDTA blood samples from 32 seropositive and 10 seronegative patients from Southern Cone countries (set C). Forty eight PCR tests were reported for set A and 44 for sets B and C; 28 targeted minicircle DNA (kDNA), 13 satellite DNA (Sat-DNA) and the remainder low copy number sequences. In set A, commercial master mixes and Sat-DNA Real Time PCR showed better specificity, but kDNA-PCR was more sensitive to detect DTU I DNA. In set B, commercial DNA extraction kits presented better specificity than solvent extraction protocols. Sat-DNA PCR tests had higher specificity, with sensitivities of 0.05-0.5 parasites/mL whereas specific kDNA tests detected 5.10(-3) par/mL. Sixteen specific and coherent methods had a Good Performance in both sets A and B (10 fg/µl of DNA from all stocks, 5 par/mL spiked blood). The median values of sensitivities, specificities and accuracies obtained in testing the Set C samples with the 16 tests determined to be good performing by analyzing Sets A and B samples varied considerably. Out of them, four methods depicted the best performing parameters in all three sets of samples, detecting at least 10 fg/µl for each DNA stock, 0.5 par/mL and a sensitivity between 83.3-94.4%, specificity of 85-95%, accuracy of 86.8-89.5% and kappa index of 0.7-0.8 compared to consensus PCR reports of the 16 good performing tests and 63-69%, 100%, 71.4-76.2% and 0.4-0.5, respectively compared to serodiagnosis. Method LbD2 used solvent extraction followed by Sybr-Green based Real time PCR targeted to Sat-DNA; method LbD3 used solvent DNA extraction followed by conventional PCR targeted to Sat-DNA. The third method (LbF1) used glass fiber column based DNA extraction followed by TaqMan Real Time PCR targeted to Sat-DNA (cruzi 1/cruzi 2 and cruzi 3 TaqMan probe) and the fourth method (LbQ) used solvent DNA extraction followed by conventional hot-start PCR targeted to kDNA (primer pairs 121/122). These four methods were further evaluated at the coordinating laboratory in a subset of human blood samples, confirming the performance obtained by the participating laboratories. CONCLUSION/SIGNIFICANCE: This study represents a first crucial step towards international validation of PCR procedures for detection of T. cruzi in human blood samples.

Role of the IFNG +874T/A polymorphism in Chagas disease in a Colombian population.

Genetic susceptibility to Trypanosoma cruzi infection and the development of cardiomyopathy is complex, heterogeneous, and likely involves several genes. Previous studies have implicated cytokine and chemokine genes in susceptibility to Chagas disease. Here we investigated the association between the interferon-gamma gene (IFNG) +874T/A polymorphism and Chagas disease, focusing on susceptibility and severity. This study included 236 chagasic patients (asymptomatic, n=116; cardiomyopathic, n=120) and 282 healthy controls from a Colombian population where T. cruzi is highly endemic. Individuals were genotyped for functional single nucleotide polymorphism (SNP; rs2430561; A/T) of the IFNG gene by amplification refractory mutational system PCR (ARMS-PCR). Moreover, clinical manifestations of Chagas in patients were analyzed. We found a significant difference in the distribution of the IFNG +874 "A" allele between patients and healthy controls (P=0.003; OR=1.46, 95% CI, 1.13-1.89). The frequency of the IFNG +874 genotype A/A, which is associated with reduced production of interferon-gamma, was increased in the patients relative to controls (38.1% vs. 26.6%). We compared the frequencies of IFNG alleles and genotypes between asymptomatic patients and those with chagasic cardiomyopathy and found no significant difference. Our data suggest that the IFNG +874T/A genetic polymorphism may be involved in susceptibility but not in the progression of Chagas disease in this Colombian population.

Enfermedad de Chagas agudo: transmisión oral de Trypanosoma cruzi como una vía de transmisión re-emergente

La forma clínica más común de la enfermedad de Chagas en Colombia es la cardiomiopatía chagásica crónica. Sin embargo, recientemente se han presentado nueve brotes de Chagas agudo (EChA) de probable transmisión oral en áreas de baja endemia con escasa presencia de vectores domiciliados. Estos brotes han presentado altas tasas de morbilidad y mortalidad. La transmisión oral de Trypanosoma cruzi ocurre por ingestión de alimentos contaminados con heces de insectos vectores o secreciones de reservorios silvestres contaminadas. Se considera un brote de transmisión oral cuando se detecta más de un caso agudo de enfermedad febril, sin vía de inoculación aparente, asociado con ingesta de alimentos sospechosos. El diagnóstico se hace por la detección del parásito en sangre u otros fluidos biológicos, en los primeros días de presentación del síndrome febril.

The most common clinical form of Chagas disease in Colombia is the chronic Chagas cardiomyopathy. However, recently nine outbreaks of acute Chagas disease by probable oral transmission have been described in low endemic areas with scarce presence of domiciliated vectors. These outbreaks have had high rates of morbidity and mortality. The oral transmission of Trypanosoma cruzi occurs by the ingestion of contaminated food with feces of vectors or secretions of wild reservoirs. An oral transmission outbreak is considered when more than one individual shows an acute febrile illness without an inoculation route, and associated with suspected food intake. The diagnosis is made by detection of parasite in blood or other biological fluids, in the early days of presentation of febrile syndrome.

Association of the macrophage migration inhibitory factor -173G/C polymorphism with Chagas disease.

Our aim was to evaluate the association of functional polymorphism of macrophage migration inhibitory factor (MIF) gene with Chagas disease. Our study includes two independent cohorts: 240 chagasic patients and 199 controls from Colombia; and 74 chagasic patients and 85 controls from Peru. The single nucleotide polymorphism (SNP) -173 G/C of MIF gene was determined using a polymerase chain reaction (PCR) system with pre-developed TaqMan assay. We observed a statistically significant difference in the distribution of -173*C allele of MIF gene between patients and controls in the Colombian cohort (OR = 1.6, 95% CI = 1.12-2.18, p = 0.006). Similar association was found in the Peruvian cohort (OR = 2.4, 95% CI = 1.31-4.38, p = 0.003). A meta-analysis of the Colombian and Peruvian cohorts demonstrated that the -173 C allele confers a risk effect in chagasic patients (pooled OR = 1.75, 95% CI = 1.30-2.33, p = 0.0002). In addition, a gene dose of the MIF -173 C allele was observed (pooled OR = 4.01, 95% CI = 1.25-12.85, p = 0.004). Our results suggest that the MIF -173G/C polymorphism confers susceptibility to Chagas disease in the populations under study.

ELISA en el diagnóstico de cisticercosis / ELISA in the diagnosis of cysticercosis

Se describe el desarrollo y la aplicación del inmunoensayo enzimatico (ELISA) en suero y líquido cefalorraquídeo de pacientes con cisticercosis e individuos normalez. En 35 pacientes con Cisticercosis el 92% presentó anticuerpos en suero. En 31% de los LCR se demostraron anticuerpos. El ELISA demostró ser un método más sensible que la hemaglutinación indirecta para el diagnóstico de cisticercosis en suero

Cisticercosis: estudio de 80 casos / Cysticercosis: a study of 80 cases

Se estudiaron 80 pacientes con cisticercosis, entre octubre de 1981 y junio de 1985. El 97.5% tenían neurocisticercosis. Las manifestaciones clínicas más frecuentes fueron síndrome convulsivo (65%), cefalea (40%) e hipertensión endocraneana (18.8%). La edad promedio fue de 31.7 años. El 56% mostraron anticuerpos en suero por hemaglutinación indirecta. Por ELISA el 89%, tuvieron anticuerpos contra cisticerco. La escanografía mostró quistes, calcificaciones e hidrocefalia. La neurocisticercosis es la más frecuente de las parasitosis del sistema nervioso central y la disponibilidad de tratamiento médico efectivo hace imperativo su diagnóstico temprano