Swarm intelligence for optimizing the parameters of multiple sequence aligners

Rubio-Largo, Á., Vanneschi, L., Castelli, M., & Vega-Rodríguez, M. A. (2018). Swarm intelligence for optimizing the parameters of multiple sequence aligners. Swarm and Evolutionary Computation. DOI: 10.1016/j.swevo.2018.04.003Different aligner heuristics can be found in the literature to solve the Multiple Sequence Alignment problem. These aligners rely on the parameter configuration proposed by their authors (also known as default parameter configuration), that tried to obtain good results (alignments with high accuracy and conservation) for any input set of unaligned sequences. However, the default parameter configuration is not always the best parameter configuration for every input set; namely, depending on the biological characteristics of the input set, one may be able to find a better parameter configuration that outputs a more accurate and conservative alignment. This work's main contributions include: to study the input set's biological characteristics and to then apply the best parameter configuration found depending on those characteristics. The framework uses a pre-computed file to take the best parameter configuration found for a dataset with similar biological characteristics. In order to create this file, we use a Particle Swarm Optimization (PSO) algorithm, that is, an algorithm based on swarm intelligence. To test the effectiveness of the characteristic-based framework, we employ five well-known aligners: Clustal W, DIALIGN-TX, Kalign2, MAFFT, and MUSCLE. The results of these aligners see clear improvements when using the proposed characteristic-based framework.authorsversionpublishe

Multiobjective characteristic-based framework for very-large multiple sequence alignment

Rubio-Largo, Á., Vanneschi, L., Castelli, M., & Vega-Rodríguez, M. A. (2018). Multiobjective characteristic-based framework for very-large multiple sequence alignment. Applied Soft Computing Journal, 69, 719-736. [Advanced online publication on 27 June 2017]DOI: 10.1016/j.asoc.2017.06.022In the literature, we can find several heuristics for solving the multiple sequence alignment problem. The vast majority of them makes use of flags in order to modify certain alignment parameters; however, if no flags are used, the aligner will run with the default parameter configuration, which, often, is not the optimal one. In this work, we propose a framework that, depending on the biological characteristics of the input dataset, runs the aligner with the best parameter configuration found for another dataset that has similar biological characteristics, improving the accuracy and conservation of the obtained alignment. To train the framework, we use three well-known multiobjective evolutionary algorithms: NSGA-II, IBEA, and MOEA/D. Then, we perform a comparative study between several aligners proposed in the literature and the characteristic-based version of Kalign, MAFFT, and MUSCLE, when solving widely-used benchmarks (PREFAB v4.0 and SABmark v1.65) and very-large benchmarks with thousands of unaligned sequences (HomFam).authorsversionpublishe

Estado nutricional en menores de 10 años atendidos en la ESE Hospital Santa Mónica de Dosquebradas, Risaralda, Colombia, en el período de 2008-2012

Introduction: nutritional state in pediatric population is a major topic for public health; this reflects different aspects of life conditions and healthy environments for good growth and development. In Dosquebradas there are no studies in the last decade describing that situation. Objetive: for these reasons, a study assessing the nutritional state of children <10 years-old population attended at the Hospital Santa Monica, municipality Dosquebradas, Risaralda, Colombia, 2008-2012, was done. Materials and Methods: a non-longitudinal retrospective study, with a convenience sample of 34315 children, assessing the indicators Weight for Age (W/A global deficit malnutrition), Height for Age, chronic deficit malnutrition, Weight for Height and Body Mass Index, acute deficit malnutrition, in children less than 10 years-old, was done. Results: for global malnutrition a prevalence of 18.99% (18.99-19.41 95%CI) was found. For chronic malnutrition was 20.86% (20.43- 21.29 95%CI). And for acute malnutrition 25.81% (25.35-26.28 95%CI). Conclusions: present results should guide to the design of public policies that would impulse nutritional intervention policies, food safety, food availability and nutritional education in the municipality with the objective to integrally improve nutritional conditions at the children population of Dosquebradas. A considerable level of malnutrition still exist in the pediatric population of Dosquebradas attended at the Hospital Santa Mónica of Dosquebradas. MÉD.UIS. 2015;28(2):209-20.Key Words: Nutritional State. Epidemiology. Anthropometrics. Indicators of Quality of Life. Malnutrition. Public Health.Introducción: la evaluación del estado nutricional en la población pediátrica es uno de los aspectos de mayor importancia en salud pública, dado que refleja diferentes aspectos vinculados a las condiciones de vida y entornos saludables para el adecuado crecimiento y desarrollo. Sin embargo, en Dosquebradas no hay estudios en la última década que permitan conocer dicha situación. Objetivo: valorar el estado nutricional en la población menor de 10 años atendida en la ESE Hospital Santa Mónica del Municipio Dosquebradas, Risaralda, Colombia, en el período 2008 a 2012. Materiales y Métodos: se realizó un estudio retrospectivo, con una muestra por conveniencia de 34 315 niños entre 0 y 10 años, evaluando los indicadores peso para la edad, talla para la edad, desnutrición crónica, peso para la talla e índice de masa corporal, desnutrición aguda. Resultados: para la desnutrición global se halló una prevalencia de 18,99% (18,99-19,41 IC95%), para la crónica fue de 20,86% (20,43-21,29 IC95%) y para la aguda fue de 25,81% (25,35-26,28 IC95%). Conclusiones: los presentes resultados deben orientar al diseño de políticas públicas que impulsen estrategias de intervención nutricional, seguridad alimentaria, disponibilidad de alimentos y de educación nutricional en el municipio con el fin de mejorar en forma integral las condiciones nutricionales que tiene la población infantil en Dosquebradas. Existe aún un considerable nivel de desnutrición en la población infantil de Dosquebradas evaluada en el Hospital Santa Mónica de Dosquebradas. MÉD.UIS. 2015;28(2):209-20.Palabras Clave: Evaluación nutricional. Epidemiología. Antropometría. Indicadores de Calidad de Vida. Desnutrición. Salud Pública.

An outbreak of abortions, stillbirths and malformations in a Spanish sheep flock associated with a bovine viral diarrhoea virus 2-contaminated orf vaccine

Bovine viral diarrhoea virus (BVDV) is a pestivirus that affects both cattle and sheep, causing an array of clinical signs, which include abortions and malformations in the offspring. Manufacturing of modified live virus (MLV) vaccines often includes the use of bovine-derived products, which implies a risk of contamination with viable BVDV. Recently, the circulation of a specific strain of BVDV 2b among Spanish sheep flocks, associated with outbreaks of abortions and malformations, and whose origin was not determined, has been observed. On February 2018, a MLV orf vaccine was applied to a 1, 600 highly prolific sheep flock in the Northeast of Spain that included 550 pregnant ewes. In May 2018, during the lambing season, an unusual high rate (72.7%) of abortions, stillbirths, congenital malformations and neurological signs in the offspring was observed. It was estimated that about 1, 000 lambs were lost. Three 1- to 3-day-old affected lambs and a sealed vial of the applied vaccine were studied. Lambs showed variable degrees of central nervous system malformations and presence of pestiviral antigen in the brain. Molecular studies demonstrated the presence of exactly the same BVDV 2b in the tissues of the three lambs and in the orf vaccine, thus pointing to a pestivirus contamination in the applied vaccine as the cause of the outbreak. Interestingly, sequencing at the 5'-untranslated region-(UTR) of the contaminating virus showed a complete match with the virus described in the previously reported outbreaks in Spain, thus indicating that the same contaminated vaccine could have also played a role in those cases. This communication provides a clear example of the effects of the application of this contaminated product in a sheep flock. The information presented here can be of interest in putative future cases of suspected circulation of this or other BVDV strains in ruminants

Epithelial–Mesenchymal Transition in a Case of Metastatic Thyroid Carcinoma in a Brown Bear (Ursus arctos)

A 20-year-old male brown bear (Ursus arctos) with a 20 × 25 cm necrotic mass adjacent to the trachea was diagnosed as having an anaplastic thyroid carcinoma. Metastases were observed in the lungs and one adrenal gland and, histologically, these had anaplastic and follicular carcinoma patterns, respectively. E-cadherin labelling was observed in the adrenal mass only, while N-cadherin immunolabelling was detected in the thyroid gland and lung masses. Thyroid-specific markers (thyroid transcription factor-1, thyroglobulin) were expressed in the adrenal gland metastasis. This case illustrates an example of a primary epithelial–mesenchymal transition (EMT) enabling metastasis to distant organ sites, followed by a mesenchymal–epithelial transition within the adrenal gland microenvironment, allowing invasion and reacquisition of thyroid epithelial cell features. EMTs help to understand the phenomenon of carcinoma cell plasticity in enabling colonization and growth of metastases

Anaplasmosis outbreak in lambs: First report causing carcass condemnation

In spring and summer 2020, six outbreaks of condemnation of jaundiced lamb carcasses were diagnosed in different farms in Aragón region, Spain. Anaplasma ovis was identified in all affected farms. Four hundred and ninety-two lambs from two affected farms were more closely examined. Clinical examination, haematologies, biochemistries, histopathology and microbiological and molecular analyses were performed. After slaughter, 34.84% of the lambs showed jaundiced carcasses and 79.64% presented splenomegaly at the abattoir. All tested lambs with icteric carcasses showed positive A. ovis PCR, although 72.72% of the unaffected lambs also tested positive. However, the bacterial load was significantly higher in the animals that showed jaundiced carcasses (Cq: 25.00 vs 26.16; p = 0.004). Moreover, all the tested lambs that showed severe anaemia were PCR positive. On the contrary, the PCR negative lambs did not show anaemia. Lambs that presented icteric carcasses displayed severe regenerative anaemia with significantly lower erythrocyte count (7.18 vs. 11.97), haematocrit (26.89 vs. 34.82) and haemoglobin (8.50 vs. 11.10) than unaffected lambs. Reticulocyte count (18.80 vs. 5.65) was also significantly increased in affected animals. This article describes a new disorder caused by Anaplasma ovis that is producing significant economic losses associated with the carcass condemnation of apparently healthy lamb

Detection of aluminium hydroxide-induced granulomas in sheep by computed tomography: A feasible approach for small ruminant lentiviruses diagnosis and research

Aluminium (Al) hydroxide use as adjuvant induces local formation of long-lasting subcutaneous granulomas in sheep. Macrophages within these granulomas have been identified as a new small ruminant lentivirus (SRLV) replication site in naturally infected animals. Diagnosis of Al hydroxide-induced granulomas in sheep is mostly based on postmortem observations but little information is available on in vivo detection. Computed tomography (CT) is used for studying these reactions in other animal species. To determine if CT could be a tool for in vivo diagnosis and research of subcutaneous Al hydroxide-induced granulomas in sheep. A retrospective survey on thoracic CT scans was performed on 46 adult sheep. Analysis included absence or presence, number and location of subcutaneous nodules. Thoracic CT scans and pathological studies were prescribed to two further sheep. Single or multiple subcutaneous nodules were detected in 26 (56.52%) sheep. One or two nodules per animal were most often observed (36.95%). Size ranged between 1.5 and 4.5 cm. Pre-contrast two-dimensional (2D) CT images showed focal or multifocal increases in subcutaneous tissue thickness. Post-contrast 2D CT images revealed hypointense areas in the centre. Histopathology indicated the presence of granulomas composed by a large number of activated macrophages, surrounding a central core of necrosis. Large intracytoplasmic Al-positive aggregates were demonstrated by lumogallion staining. CT is a useful tool to detect subcutaneous Al hydroxide-induced granulomas in vivo in sheep. CT provides a diagnostic and research tool that can be very useful in future works in Al hydroxide-induced pathology, SRLV infection, or both. © 2021 The Authors. Veterinary Medicine and Science published by John Wiley & Sons Ltd

Growth performance and clinicopathological analyses in lambs repetitively inoculated with aluminum-hydroxide containing vaccines or aluminum-hydroxide only

Aluminum (Al) hydroxide is an effective adjuvant used in sheep vaccines. However, Al-adjuvants have been implicated as potential contributors to a severe wasting syndrome in sheep— the so-called ovine autoimmune-inflammatory syndrome induced by adjuvants (ASIA syndrome). This work aimed to characterize the effects of the repetitive injection of Al-hydroxide containing products in lambs. Four flocks (Flocks 1–4; n = 21 each) kept under different conditions were studied. Three groups of seven lambs (Vaccine, Adjuvant-only, and Control) were established in each flock. Mild differences in average daily gain and fattening index were observed, indicating a reduced growth performance in Vaccine groups, likely related to short-term episodes of pyrexia and decreased daily intake. Clinical and hematological parameters remained within normal limits. Histology showed no significant differences between groups, although there was a tendency to present a higher frequency of hyperchromatic, shrunken neurons in the lumbar spinal cord in the Adjuvant-only group. Although Al-hydroxide was linked to granulomas at the injection site and behavioral changes in sheep, the results of the present experimental work indicate that injected Al-hydroxide is not enough to fully reproduce the wasting presentation of the ASIA syndrome. Other factors such as sex, breed, age, production system, diet or climate conditions could play a role

Role of age and comorbidities in mortality of patients with infective endocarditis

[Purpose]: The aim of this study was to analyse the characteristics of patients with IE in three groups of age and to assess the ability of age and the Charlson Comorbidity Index (CCI) to predict mortality. [Methods]: Prospective cohort study of all patients with IE included in the GAMES Spanish database between 2008 and 2015.Patients were stratified into three age groups:<65 years,65 to 80 years,and ≥ 80 years.The area under the receiver-operating characteristic (AUROC) curve was calculated to quantify the diagnostic accuracy of the CCI to predict mortality risk. [Results]: A total of 3120 patients with IE (1327 < 65 years;1291 65-80 years;502 ≥ 80 years) were enrolled.Fever and heart failure were the most common presentations of IE, with no differences among age groups.Patients ≥80 years who underwent surgery were significantly lower compared with other age groups (14.3%,65 years; 20.5%,65-79 years; 31.3%,≥80 years). In-hospital mortality was lower in the <65-year group (20.3%,<65 years;30.1%,65-79 years;34.7%,≥80 years;p < 0.001) as well as 1-year mortality (3.2%, <65 years; 5.5%, 65-80 years;7.6%,≥80 years; p = 0.003).Independent predictors of mortality were age ≥ 80 years (hazard ratio [HR]:2.78;95% confidence interval [CI]:2.32–3.34), CCI ≥ 3 (HR:1.62; 95% CI:1.39–1.88),and non-performed surgery (HR:1.64;95% CI:11.16–1.58).When the three age groups were compared,the AUROC curve for CCI was significantly larger for patients aged <65 years(p < 0.001) for both in-hospital and 1-year mortality. [Conclusion]: There were no differences in the clinical presentation of IE between the groups. Age ≥ 80 years, high comorbidity (measured by CCI),and non-performance of surgery were independent predictors of mortality in patients with IE.CCI could help to identify those patients with IE and surgical indication who present a lower risk of in-hospital and 1-year mortality after surgery, especially in the <65-year group

ATR-FTIR spectroscopy non-destructively detects damage-induced sour rot infection in whole tomato fruit

Main conclusion ATR-FTIR spectroscopy with subsequent multivariate analysis non-destructively identifies plant–pathogen interactions during disease progression, both directly and indirectly, through alterations in the spectral fingerprint. Plant–environment interactions are essential to understanding crop biology, optimizing crop use, and minimizing loss to ensure food security. Damage-induced pathogen infection of delicate fruit crops such as tomato (Solanum lycopersicum) are therefore important processes related to crop biology and modern horticulture. Fruit epidermis as a first barrier at the plant–environment interface, is specifically involved in environmental interactions and often shows substantial structural and functional changes in response to unfavourable conditions. Methods available to investigate such systems in their native form, however, are limited by often required and destructive sample preparation, or scarce amounts of molecular level information. To explore biochemical changes and evaluate diagnostic potential for damage-induced pathogen infection of cherry tomato (cv. Piccolo) both directly and indirectly, mid-infrared (MIR) spectroscopy was applied in combination with exploratory multivariate analysis. ATR-FTIR fingerprint spectra (1800–900 cm−1) of healthy, damaged or sour rot-infected tomato fruit were acquired and distinguished using principal component analysis and linear discriminant analysis (PCA–LDA). Main biochemical constituents of healthy tomato fruit epidermis are characterized while multivariate analysis discriminated subtle biochemical changes distinguishing healthy tomato from damaged, early or late sour rot-infected tomato indirectly based solely on changes in the fruit epidermis. Sour rot causing agent Geotrichum candidum was detected directly in vivo and characterized based on spectral features distinct from tomato fruit. Diagnostic potential for indirect pathogen detection based on tomato fruit skin was evaluated using the linear discriminant classifier (PCA–LDC). Exploratory and diagnostic analysis of ATR-FTIR spectra offers biological insights and detection potential for intact plant–pathogen systems as they are found in horticultural industries