A Bayesian Approach for Clustering Constant-wise Change-point Data

Change-point models deal with ordered data sequences. Their primary goal is to infer the locations where an aspect of the data sequence changes. In this paper, we propose and implement a nonparametric Bayesian model for clustering observations based on their constant-wise change-point profiles via Gibbs sampler. Our model incorporates a Dirichlet Process on the constant-wise change-point structures to cluster observations while performing change-point estimation simultaneously. Additionally, our approach controls the number of clusters in the model, not requiring the specification of the number of clusters a priori. Our method's performance is evaluated on simulated data under various scenarios and on a publicly available single-cell copy-number dataset.Comment: 30 pages, 12 figure

DNA sequence analysis suggests that cytb-nd1 PCR-RFLP may not be applicable to sandfly species identification throughout the Mediterranean region

Molecular methods are increasingly used for both species identification of sandflies and assessment of their population structure. In general, they are based on DNA sequence analysis of targets previously amplified by PCR. However, this approach requires access to DNA sequence facilities, and in some circumstances, it is time-consuming. Though DNA sequencing provides the most reliable information, other downstream PCR applications are explored to assist in species identification. Thus, it has been recently proposed that the amplification of a DNA region encompassing partially both the cytochrome-B (cytb) and the NADH dehydrogenase 1 (nd1) genes followed by RFLP analysis with the restriction enzyme Ase I allows the rapid identification of the most prevalent species of phlebotomine sandflies in the Mediterranean region. In order to confirm the suitability of this method, we collected, processed, and molecularly analyzed a total of 155 sandflies belonging to four species including Phlebotomus ariasi, P. papatasi, P. perniciosus, and Sergentomyia minuta from different regions in Spain. This data set was completed with DNA sequences available at the GenBank for species prevalent in the Mediterranean basin and the Middle East. Additionally, DNA sequences from 13 different phlebotomine species (P. ariasi, P. balcanicus, P. caucasicus, P. chabaudi, P. chadlii, P. longicuspis, P. neglectus, P. papatasi, P. perfiliewi, P. perniciosus, P. riouxi, P. sergenti, and S. minuta), from 19 countries, were added to the data set. Overall, our molecular data revealed that this PCR-RFLP method does not provide a unique and specific profile for each phlebotomine species tested. Intraspecific variability and similar RFLP patterns were frequently observed among the species tested. Our data suggest that this method may not be applicable throughout the Mediterranean region as previously proposed. Other molecular approaches like DNA barcoding or phylogenetic analyses would allow a more precise molecular species identification.This work was supported in part by Instituto de Salud Carlos III (MPY-1248/12) grant and (PI14CIII/00016) funded by AESI. Ivonne Pamela Llanes-Acevedo was granted a student fellowship by COLCIENCIAS/COLFUTURO.S

Uso de Macromoléculas sobre la Tasa de Maduración y Desarrollo Embrionario in vitro de Ovocitos Bovinos

The effect of four supplements with macromolecules on the rate of nuclear maturation, oocyte division at 48 h and embryo development at 7 days post-fertilization was evaluated. Ovaries were collected in the slaughterhouse; oocytes with two or more layers of cells were selected and matured on TCM-99 enriched with macromolecule supplements: Polyvinylpyrrolidone (PVP), polyvinylalcohol (PVA), Bovine serum albumin (BSA), Foetal bovine serum (SFB). Oocytes were cultivated at 39 °C with 5% of CO2. Nuclear maturation was evaluated at 24 hours, classifying them as germinal vesicle, metaphase I, anaphasetelophase, metaphase II and degenerated. For the evaluation of the oocyte division and embryo development, oocytes were matured under the same conditions and fertilized with spermatozoa during 18 hours in KSOM-AA culture media, and then transferred to SOF culture media for 48 h. Significant differences on nuclear maturation (Metaphase II) were only observed between PVA and SFB (p<0.05). Furthermore, none significant differences on rate of division and embryonic development between treatments were observed. These results indicate that the macromolecule supplements provide similar conditions and requirements for the progression from metaphase I to metaphase II.Se evaluó el efecto de cuatro suplementos de macromoléculas sobre la tasa de maduración nuclear, división de ovocitos a las 48 horas y desarrollo embrionario a los siete días pos-fecundación. Se colectaron ovarios de camal, se aspiraron los folículos y se seleccionaron los ovocitos con dos o más capas de células para ser madurados en medio TCM-99 enriquecido con macromoléculas: Polivinil pirrolidona (PVP), Polivinil alcohol (PVA), Albúmina sérica bovina (BSA), Suero fetal bovino (SFB). Los ovocitos se cultivaron a 39 °C y con 5% de CO2. Se evaluó la maduración nuclear a las 24 h, calificándolos como vesícula germinal, metafase I, anafase-telofase, metafase II y degenerados. Para evaluar la división y desarrollo embrionario, otro grupo de ovocitos fueron madurados bajo las mismas condiciones y fecundados por 18 h en medio de cultivo KSOM-AA, y trasferidos al medio de cultivo SOF por 48 h. Solo hubo diferencias estadísticas en maduración nuclear (Metafase II) entre los grupos suplementados con PVA y SFB (p<0.05). Asimismo, no hubo diferencias entre tratamientos en la tasa de división y desarrollo embrionario. Los resultados indican que los suplementos de macromoléculas proporcionan condiciones y requerimientos similares para la progresión desde estadios de metafase I a metafase II

Ambipolar Pentacyclic Diamides with Interesting Electrochemical and Optoelectronic Properties

Developing organic semiconductors (OSCs) for organic thin film transistors (OTFT) and optoelectronic applications is a challenge. We developed highly crystalline pentacyclic diamides (3) and (4) which showed good OTFT and OLED potential and energy gaps of 2.60 eV and 2.54 eV. They exhibited interesting photo and eletroluminescence activity. Both compounds showed good quantum yields (0.56 for (3) and 0.6 for (4))

Infective endocarditis caused by Enterobacteriaceae:phenotypic and molecular characterization of Escherichia coli and Klebsiella pneumoniae in Rio de Janeiro, Brazil

The etiological agent for infective endocarditis (IE), a life-threatening disease, is usually gram-positive bacteria. However, gram-negative bacteria can rarely cause IE and 4% of cases are associated with morbidity and mortality. This study aimed to characterize Escherichia coli and Klebsiella pneumoniae isolates from the blood of patients with IE. The characteristics of blood isolates were compared with those of urinary isolates from patients with urinary tract infections (UTIs). The results of this study revealed that K. pneumoniae isolates from patients with IE were phylogenetically related to those from patients with UTI. Additionally, the resistance phenotype, resistance gene, virulence gene, and plasmid profiles were similar between the blood and urinary isolates. The isolates belonging to the sequence types (STs) 76, 36, 101 (K. pneumoniae), and 69 (E. coli) are reported to be associated with drug resistance. The Enterobacteriaceae isolates from patients with IE did not produce extended-spectrum β-lactamase or carbapenemase. Additionally, this study investigated the virulence phenotype, biofilm formation ability, and the ability to adhere to the epithelial cells in vitro of the isolates. The isolates from patients with IE exhibited weaker biofilm formation ability than the urinary isolates. All isolates from patients with IE could adhere to the renal epithelial cells. However, three isolates from patients with UTIs could not adhere to the epithelial cells. The closely related K. pneumoniae isolates (648, KP1, KP2, KP3, and KP4) could not form biofilms or adhere to the epithelial cells. In summary, the molecular analysis revealed that the genetic characteristics of IE-causing K. pneumoniae and E. coli were similar to those of UTI-causing isolates. These isolates belonged to the STs that are considered treatable. Genetically similar isolates did not exhibit the same virulence phenotype. Thus, these non-hypervirulent clones must be monitored as they can cause complex infections in susceptible hosts

Applying the clustering technique for characterising maintenance outsourcing

Objetivo Utilizar técnicas de clustering para caracterizar a los proveedores de servicios de mantenimiento de una institución de salud. Métodos El estudio analiza el inventario del equipamiento perteneciente a 7 áreas pilotos (264 equipos médicos). Se aplican técnicas de clustering usando 26 variables. Entre las más significativas: el tiempo de respuesta (RT), la duración de las intervenciones (DR), la disponibilidad y el tiempo de cambio de estado (TAT). Resultados La obsolescencia del equipo biomédico en promedio es de 0,78. Se identifican 4 grupos de proveedores de servicios. Grupos (1 y 3): Mejor desempeño, menores valores de TAT, RT y DR; cuyos proveedores son: O, L, C, B, I, S, H, F, G; representan el 56 % del total; con valores de TAT entre: 1,4 días <TAT < 2,56 días como promedio. Grupo (0): Desempeño medio, cuyos proveedores son: V, M, K, Z, T, Y; representan el 38 %; con valores de TAT iguales a 9,79 días como promedio. Grupo (2): con bajos desempeños, por poseer valores altos de TAT (101 días como promedio); con único proveedor: J, representa el 6 % del total de la muestra analizada. Conclusiones La metodología empleada permitió caracterizar el inventario de equipos médicos y a los proveedores de servicios de mantenimiento. La técnica de conglomerados demostró ser efectiva para identificar los proveedores más competitivos. Palabras Clave: Disponibilidad de servicios de salud, servicios contratados, análisis por conglomerados, servicio de mantenimiento e ingeniería en hospital, ingeniería biomédicaUsing clustering techniques for characterising companies providing health institutions with maintenance services.METHODS: The study analysed seven pilot areas' equipment inventory (264 medical devices). Clustering techniques were applied using 26 variables. Response time (RT), operation duration (OD), availability and turnaround time (TAT) were amongst the most significant ones.RESULTS: Average biomedical equipment obsolescence value was 0.78. Four service provider clusters were identified: clusters 1 and 3 had better performance, lower TAT, RT and DR values (56 % of the providers coded O, L, C, B, I, S, H, F and G, had 1 to 4 day TAT values: <TAT < 2.56 days on average). Cluster 0 had medium performance (38 % of providers coded V, M, K, Z, T and Y, having an average 9.79 TAT value). Cluster 2 (6 % - provider J) had low performance, having very a high TAT level (101 days on average).CONCLUSIONS: The methodology allowed medical equipment inventory and maintenance service suppliers to be characterised. The cluster technique was effective in identifying the most competitive suppliers

α-FAPbI3 powder presynthesized by microwave irradiation for photovoltaic applications

The development of up-scalable and high-throughput methodologies to fabricate high-efficiency lead halide perovskite solar cells (PSCs) based on α-phase formamidinium lead iodide (FAPbI3) is one of the main challenges of making solar energy economical. In this context, PSCs based on α-phase formamidinium lead iodide (FAPbI3) are receiving special attention as this perovskite has the highest theoretical photoconversion efficiency (PCE). This manuscript reports an easy, fast and environmentally-friendly way to prepare α-FAPbI3 black powders by a microwave-assisted synthesis and their application in solar cells. The α-FAPbI3 powders consist of micrometric particles that can be stored for weeks in a closed vial at ambient conditions. This technique presents an enormous potential for upscaling FAPbI3 powders synthesis prerequisite necessary for large scale commercialization. The performance of the presynthesized FAPbI3-based solar cell was comparable with that of PSCs fabricated with the conventional procedure from precursors solutions, leading to a maximum PCE value of 18.15%, with an VOC=1.07 V, a Jsc=24.28 mA/cm2 and an FF=70%. The presynthesized FAPbI3-based solar cell was further modified through the addition of methylammonium chloride (MACl) in order to study the generality of the approach. The optical band gap for the presynthesized perovskite shifted from ∼1.43 eV to ∼1.55 eV with the MACl addition (30 mol%), indicating the formation of a mixed methylammonium and formamidinium based perovskite material (MAFAPbI3). In addition, the incorporation of MACl led to an increase in the grain size and the disappearance of the residual δ-phase perovskite, thus improving the efficiency of the final device.Funding for open access charge: CRUE-Universitat Jaume

Development and validation of a method for the analysis of Ochratoxin A in roasted coffee by liquid chromatography/electrospray-mass spectrometry in Tandem (LC/ESI-MS/MS)

A method using LC/ESI-MS/MS for the quantitative analysis of Ochratoxin A in roasted coffee was described. Linearity was demonstrated (r = 0.9175). The limits of detection and quantification were 1.0 and 3.0 ng g-1, respectively. Trueness, repeatability and intermediate precision values were 89.0-108.8%; 2.4-13.7%; 12.5-17.8%, respectively. To the best of our knowledge, this is the first report in which Ochratoxin A in roasted coffee is analysed by LC/ESI-MS/MS, contributing to the field of mycotoxin analysis, and it will be used for future production of Certified Reference Material

Atlantic mammal traits: a dataset of morphological traits of mammals in the atlantic forest of south America

Measures of traits are the basis of functional biological diversity. Numerous works consider mean species-level measures of traits while ignoring individual variance within species. However, there is a large amount of variation within species and it is increasingly apparent that it is important to consider trait variation not only between species, but also within species. Mammals are an interesting group for investigating trait-based approaches because they play diverse and important ecological functions (e.g., pollination, seed dispersal, predation, grazing) that are correlated with functional traits. Here we compile a data set comprising morphological and life history information of 279 mammal species from 39,850 individuals of 388 populations ranging from −5.83 to −29.75 decimal degrees of latitude and −34.82 to −56.73 decimal degrees of longitude in the Atlantic forest of South America. We present trait information from 16,840 individuals of 181 species of non-volant mammals (Rodentia, Didelphimorphia, Carnivora, Primates, Cingulata, Artiodactyla, Pilosa, Lagomorpha, Perissodactyla) and from 23,010 individuals of 98 species of volant mammals (Chiroptera). The traits reported include body mass, age, sex, reproductive stage, as well as the geographic coordinates of sampling for all taxa. Moreover, we gathered information on forearm length for bats and body length and tail length for rodents and marsupials. No copyright restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.Fil: Gonçalves, Fernando. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Bovendorp, Ricardo S.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Beca, Gabrielle. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Bello, Carolina. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Costa Pereira, Raul. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Muylaert, Renata L.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Rodarte, Raisa R.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Villar, Nacho. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Souza, Rafael. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Graipel, Maurício E.. Universidade Federal de Santa Catarina; BrasilFil: Cherem, Jorge J.. Caipora Cooperativa, Florianopolis; BrasilFil: Faria, Deborah. Universidade Estadual de Santa Cruz; BrasilFil: Baumgarten, Julio. Universidade Estadual de Santa Cruz; BrasilFil: Alvarez, Martín R.. Universidade Estadual de Santa Cruz; BrasilFil: Vieira, Emerson M.. Universidade do Brasília; BrasilFil: Cáceres, Nilton. Universidade Federal de Santa María. Santa María; BrasilFil: Pardini, Renata. Universidade de Sao Paulo; BrasilFil: Leite, Yuri L. R.. Universidade Federal do Espírito Santo; BrasilFil: Costa, Leonora Pires. Universidade Federal do Espírito Santo; BrasilFil: Mello, Marco Aurelio Ribeiro. Universidade Federal de Minas Gerais; BrasilFil: Fischer, Erich. Universidade Federal do Mato Grosso do Sul; BrasilFil: Passos, Fernando C.. Universidade Federal do Paraná; BrasilFil: Varzinczak, Luiz H.. Universidade Federal do Paraná; BrasilFil: Prevedello, Jayme A.. Universidade do Estado de Rio do Janeiro; BrasilFil: Cruz-Neto, Ariovaldo P.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Carvalho, Fernando. Universidade do Extremo Sul Catarinense; BrasilFil: Reis Percequillo, Alexandre. Universidade de Sao Paulo; BrasilFil: Paviolo, Agustin Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; ArgentinaFil: Duarte, José M. B.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil. Fundación Oswaldo Cruz; BrasilFil: Bernard, Enrico. Universidade Federal de Pernambuco; BrasilFil: Agostini, Ilaria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; ArgentinaFil: Lamattina, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Ministerio de Salud de la Nación; ArgentinaFil: Vanderhoeven, Ezequiel Andres. Ministerio de Salud de la Nación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentin

The contribution of meteorological parameters and the COVID-19 partial lockdown on air quality in Rio de Janeiro, Brazil

This study evaluated the pollutant levels (NO2, SO2, CO, and O3), air quality index (AQI) and the influence of meteorological variables and coronavirus disease (COVID-19) pandemic on the air quality in Rio de Janeiro. The data set used comprises periods before (March-April, 2019) and during pandemic (March-April, 2020). According to the AQI results, on most days, the air quality was ranked as “good”. Brazilian air quality standards for SO2, O3, and NO2 were not exceeded in any of the monitoring stations during partial lockdown, while CO exceeded in all periods in one site due to industrial emission. Comparing both periods, descriptive statistics for the meteorological parameters presented no differences, which suggests similar conditions. However, when evaluated week by week in 2020, weather conditions presented some differences that probably affected pollutant concentrations. The correlations between O3 and NO2 and some meteorological parameters indicate that variations in both favored ozone formation, since it is a photochemical process favored by temperature and solar radiation and that, in Rio de Janeiro, low NO2 concentrations lead to increased O3. The improvements on air quality during the partial lockdown may be attributed mainly to a reduction on emission sources rather than weather conditions.Campus Lima Centr