Visualizing Meta-Features in Proteomic Maps

<p>Abstract</p> <p>Background</p> <p>The steps of a high-throughput proteomics experiment include the separation, differential expression and mass spectrometry-based identification of proteins. However, the last and more challenging step is inferring the biological role of the identified proteins through their association with interaction networks, biological pathways, analysis of the effect of post-translational modifications, and other protein-related information.</p> <p>Results</p> <p>In this paper, we present an integrative visualization methodology that allows combining experimentally produced proteomic features with protein meta-features, typically coming from meta-analysis tools and databases, in synthetic Proteomic Feature Maps. Using three proteomics analysis scenarios, we show that the proposed visualization approach is effective in filtering, navigating and interacting with the proteomics data in order to address visually challenging biological questions. The novelty of our approach lies in the ease of integration of any user-defined proteomic features in easy-to-comprehend visual representations that resemble the familiar 2D-gel images, and can be adapted to the user's needs. The main capabilities of the developed VIP software, which implements the presented visualization methodology, are also highlighted and discussed.</p> <p>Conclusions</p> <p>By using this visualization and the associated VIP software, researchers can explore a complex heterogeneous proteomics dataset from different perspectives in order to address visually important biological queries and formulate new hypotheses for further investigation. VIP is freely available at <url>http://pelopas.uop.gr/~egian/VIP/index.html</url>.</p

GAMIFYING ENERGY USER PROFILES

Smartege is an educational application which aims in educating users in the basics of electrical energy consumption and production and engage them in energy saving behavior, techniques and technologies. This is accomplished through the virtual, and eventually actual, management of residential and office buildings equipped with virtual devices and renewable energy sources, with energy specifications borrowed from actual commercial devices, towards the ultimate target of transforming the buildings into net Zero Energy Buildings. Ultimately, Smartege is a gamified application targeting the behavior modification of the users. Its content development follows the persuasive model and uses cognitive learning for the educational component and game mechanics for user motivation and triggering

GAMIFYING ENERGY USER PROFILES

Smartege is an educational application which aims in educating users in the basics of electrical energy consumption and production and engage them in energy saving behavior, techniques and technologies. This is accomplished through the virtual, and eventually actual, management of residential and office buildings equipped with virtual devices and renewable energy sources, with energy specifications borrowed from actual commercial devices, towards the ultimate target of transforming the buildings into net Zero Energy Buildings. Ultimately, Smartege is a gamified application targeting the behavior modification of the users. Its content development follows the persuasive model and uses cognitive learning for the educational component and game mechanics for user motivation and triggering

Accurate Neural Network Pruning Requires Rethinking Sparse Optimization

Obtaining versions of deep neural networks that are both highly-accurate and highly-sparse is one of the main challenges in the area of model compression, and several high-performance pruning techniques have been investigated by the community. Yet, much less is known about the interaction between sparsity and the standard stochastic optimization techniques used for training sparse networks, and most existing work uses standard dense schedules and hyperparameters for training sparse networks. In this work, we examine the impact of high sparsity on model training using the standard computer vision and natural language processing sparsity benchmarks. We begin by showing that using standard dense training recipes for sparse training is suboptimal, and results in under-training. We provide new approaches for mitigating this issue for both sparse pre-training of vision models (e.g. ResNet50/ImageNet) and sparse fine-tuning of language models (e.g. BERT/GLUE), achieving state-of-the-art results in both settings in the high-sparsity regime, and providing detailed analyses for the difficulty of sparse training in both scenarios. Our work sets a new threshold in terms of the accuracies that can be achieved under high sparsity, and should inspire further research into improving sparse model training, to reach higher accuracies under high sparsity, but also to do so efficiently

Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile

In this work, molecular diversity of two hypersaline microbial mats was compared by Whole Genome Shotgun (WGS) sequencing of environmental DNA from the mats. Brava and Tebenquiche are lakes in the Salar de Atacama, Chile, where microbial communities are growing in extreme conditions, including high salinity, high solar irradiance, and high levels of toxic metals and metaloids. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. The mat from Brava was more rich and diverse, with a higher number of different taxa and with species more evenly distributed. At the phylum level, Proteobacteria, Cyanobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the most abundant, including ~75% of total sequences. At the genus level, the most abundant sequences were affilitated to anoxygenic phototropic and cyanobacterial genera. In Tebenquiche mats, Proteobacteria and Bacteroidetes covered ~70% of the sequences, and 13% of the sequences were affiliated to Salinibacter genus, thus addressing the lower diversity. Regardless of the differences at the taxonomic level, functionally the two mats were similar. Thus, similar roles could be fulfilled by different organisms. Carbon fixation through the Wood-Ljungdahl pathway was well represented in these datasets, and also in other mats from Andean lakes. In spite of presenting less taxonomic diversity, Tebenquiche mats showed increased abundance and variety of rhodopsin genes. Comparison with other metagenomes allowed identifying xantorhodopsins as hallmark genes not only from Brava and Tebenquiche mats, but also for other mats developing at high altitudes in similar environmental conditions.Fil: Kurth, Daniel German. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Elias, Dario Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. CEMIC-CONICET. Centro de Educaciones Médicas e Investigaciones Clínicas "Norberto Quirno". CEMIC-CONICET; ArgentinaFil: Rasuk, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Contreras, Emanuel. Centro de Ecología Aplicada (CEA); ChileFil: Farias, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; Argentin

Evaluación del índice de pie plano y prevalencia de trastornos músculo-esqueléticos del pie en deportistas Jóvenes: natación, remo y levantamiento de pesas

Objectives: The objective of this work was to analyze the morphology of the soles of the feet in young athletes to find the prevalence of these pathologies through the Chippaux-Smirak index. Material and Methods: Seventy-five athletes between nine and twenty years old participated in the study (56% female and 44% male), the average mass was 62.92 ± 13.46kg and the average height was 1.67 ± 0.11m. The sports considered in the study were weightlifting, swimming, and rowing. Results: The results clearly show that flatfeet in adolescents and young adults is a condition with a low prevalence level, 10.7% and 12% for the right and left foot, respectively. One of the most outstanding results found in the study is the high prevalence of cavus foot, where women are the most affected by this pathology. Furthermore, swimming presented the highest prevalence of cavus foot, 42.1% and 52.6% for the right and left foot, respectively. Conclusion: &nbsp;In conclusion, the understanding of the morphology of the soles of the feet can help to determine the foot type in these three different sports, and therefore, it can be implemented physiotherapeutic treatments or orthotics devices for overcome the musculoskeletal disorders and prevent future injures.Objetivos: El objetivo de este trabajo fue analizar la morfología de las plantas de los pies en jóvenes deportistas para encontrar la prevalencia de estas patologías a través del índice de Chippaux-Smirak. &nbsp;Material y Métodos: Setenta y cinco atletas entre nueve y veinte años de edad participaron en el estudio (56% mujeres y 44% hombres), la masa promedio fue de 62.92 ± 13.46kg y la altura promedio fue de 1.67 ± 0.11m. Los deportes considerados en el estudio fueron levantamiento de pesas, natación y remo. Resultados: Los resultados muestran claramente que los pies planos en adolescentes y adultos jóvenes son una condición con un nivel de prevalencia bajo, 10.7% y 12% para el pie derecho e izquierdo, respectivamente. Uno de los resultados más sobresalientes encontrados en el estudio es la alta prevalencia de pie cavo, donde las mujeres son las más afectadas por esta alteración. Además, natación presentó mayor prevalencia de pie cavo, 42.1% y 52.6% para el pie derecho e izquierdo, respectivamente. Conclusiones: La comprensión de la morfología de las plantas de los pies puede ayudar a determinar el tipo de pie en estos tres deportes diferentes y, por lo tanto, se pueden implementar tratamientos fisioterapéuticos o dispositivos ortopédicos para superar los trastornos músculo-esqueléticos y prevenir futuras lesiones

Coeficiente de cultura e necessidades hídricas de mudas de cajueiro anão em condições de cerradoDetermination of crop coefficient in seedlings of dwarf cashew using lysimeters groundwater constant

O objetivo do trabalho foi determinar o coeficiente de cultura (Kc) e necessidades hídricas para mudas de cajueiro anão (Anacardium occidentale L.) entre 18 a 21 meses de idade. O experimento foi conduzido na Fazenda experimental da Universidade Federal de Mato Grosso, no município de Santo Antônio de Leverger, no período de 03/09/2012 a 05/11/2012. No local, sete mudas do cultivar foram transplantadas para lisímetro de nível de lençol freático constante, das quais foram medidos a área foliar e o consumo de água em cada muda. A evapotranspiração de referência (ETo) foi estimada pelo método de Penman-Monteith-FAO, usando dados fornecidos pela estação meteorológica Padre Ricardo Remetter do INMET. A ETo variou entre 3,5 e 5,45 mmd-1, com valor médio de 4,18 mmd-1 no período. A evapotranspiração de cultura (ETc) variou entre 0,97 mm d-1 a 8 mm d-1 com valor médio de 3,17 mm d-1, no período. O coeficiente de cultura encontrado foi de 0,78 e a área foliar variou entre 0,01m² a 0,08 m², com perdas de folhas e lançamentos foliares em algumas mudas.AbstractThe objective was to determine the crop coefficient (Kc) and water needs for seedlings of dwarf cashew (Anacardium occidentale L.) 18 to 21 months of age. The experiment was conducted at the Experimental Farm of the Federal University of Mato Grosso in Santo Antônio de Leverger the period from 03/09/2012 to 05/11/2012. Onsite, seven seedlings of the cultivar studied were transplanted into soil columns of constant level of water table, which were measured leaf area and water use at each change. The reference evapotranspiration (ETo) was estimated by the Penman-Monteith-FAO method using weather station data provided by Father Ricardo Remetter INMET. The ETo ranged between 3.5 and 5.45 mmd-1 with an average value of 4.18 mmd-1 in the period. The crop evapotranspiration (ETc) ranged between 0.97 mm d-1 and 8 mm d-1 with a mean value of 3.17 mm d-1 in the period. The crop coefficient was found to be 0.78 and the leaf area ranged between 0.08 m² and 0,01m² with losses of leaves and leaf flushes in some seedlings

Pediatric thyroid nodules: predictors of malignancy

Introducción: La caracterización de los nódulos tiroideos en pediatría no ha sido aún bien comunicada. El riesgo de malignidad es mayor que en adultos por lo que requieren una evaluación exhaustiva. Objetivo: caracterizar una cohorte de pacientes pediátricos con nódulos tiroideos e identificar predictores de malignidad. Pacientes y métodos: se analizaron los hallazgos demográficos, clínicos, bioquímicos, ecográficos y citológicos de una cohorte prospectiva de 106 pacientes 2,5mU/l, nódulo sólido, márgenes irregulares, microcalcificaciones y adenopatías cervicales patológicas. Un resultado citológico Bethesda V/VI tuvo un valor predictivo (VP) positivo de 87,5% y VP negativo de 96,4%. Conclusiones: El nódulo tiroideo en pediatría es más frecuentemente maligno. La evaluación sistemática permitió identificar ciertos hallazgos clínicos, bioquímicos, ecográficos y citológicos predictores de malignidad que deben ser considerados al decidir el enfoque diagnóstico.Introduction: Published data on pediatric thyroid nodule´s characterization is scarce. With higher risk of malignancy than in adults, they require an exhaustive diagnostic work-up. Objective: To characterize a pediatric cohort with thyroid nodules to identify predictors of malignancy. Patients and methods: Demographic, clinical, biochemical, ultrasonographical and cytological data were analyzed prospectively in 106 patients 2.5mU/l, solid nodules, irregular margins, microcalcifications and pathologic adenopathies. Cytological results Bethesda V/VI showed positive and negative predictive values of 87.5% and 96.4% respectively. Conclusions: Pediatric thyroid nodules are more frequently malignant. The systematic evaluation of our cohort allowed the identification of clinical, biochemical ultrasonographical and cytological predictors of malignancy that have to be considered when deciding the diagnostic approach.Fil: Papendieck, Patricia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Gobierno de la Ciudad de Buenos Aires. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Fundación de Endocrinología Infantil. Centro de Investigaciones Endocrinológicas "Dr. César Bergada"; ArgentinaFil: Venara, Marcela Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Gobierno de la Ciudad de Buenos Aires. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Fundación de Endocrinología Infantil. Centro de Investigaciones Endocrinológicas "Dr. César Bergada"; ArgentinaFil: Elias, Eugenia. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; ArgentinaFil: Cozzani, Hugo. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; ArgentinaFil: Mateos, Fernanda. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez";; ArgentinaFil: Maglio, Silvana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; ArgentinaFil: Calcagno, María Luján. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: Gruñeiro Papendieck, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Gobierno de la Ciudad de Buenos Aires. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Fundación de Endocrinología Infantil. Centro de Investigaciones Endocrinológicas "Dr. César Bergada"; ArgentinaFil: Bergadá, Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Gobierno de la Ciudad de Buenos Aires. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Fundación de Endocrinología Infantil. Centro de Investigaciones Endocrinológicas "Dr. César Bergada"; ArgentinaFil: Chiesa, Ana Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Gobierno de la Ciudad de Buenos Aires. Centro de Investigaciones Endocrinológicas "Dr. César Bergada". Fundación de Endocrinología Infantil. Centro de Investigaciones Endocrinológicas "Dr. César Bergada"; Argentin

Eventos cardiovasculares en pacientes con lupus eritematoso sistémico y su asociación con factores de riesgo cardiovascular

Los pacientes con lupus eritematoso sistémico (LES) presentan un elevado riesgo cardiovascular, cuya etiología aún no se conoce con exactitud. Se ha postulado que podrían estar implicados tanto los factores de riesgo cardiovascular tradicionales como determinados factores relacionados a la propia enfermedad. En el presente estudio, se ha analizado a un grupo de pacientes con LES y se ha determinado la presencia de eventos cardiovasculares (EC), así como también a los factores de riesgo cardiovascular (FRCV) tradicionales y los relacionados a la enfermedad. Además, se ha estudiado la asociación de estos últimos con el desarrollo de un EC (i.e. infarto de miocardio agudo, hipertensión arterial, accidente cerebrovascular). En el total de 83 pacientes analizados, el EC más frecuente fue la hipertensión arterial (HTA) en un 41%. En relación a los FRCV tradicionales, el sedentarismo fue el hallado con más frecuencia, seguido por la obesidad. Al analizar cada EC y su asociación con los FRCV, se observó una asociación significativa entre la HTA y la dislipidemia (p = 0,001). En relación a los accidentes cerebrovasculares, se observó una asociación con la edad avanzada (p = 0,037) y la presencia de síndrome antifosfolípido (p = 0,001). La elevada frecuencia de EC en los pacientes con diagnóstico de LES pone de manifiesto la necesidad de una evaluación inicial detallada para estratificar tanto FRCV tradicionales como los no tradicionales de los pacientes con LES para permitir una mejor supervisión y así mejorar el pronóstico cardiovascular de estos pacientes