Are Forward Designed or Reverse-Engineered UML Diagrams More Helpful for Code Maintenance?: A Controlled Experiment

Context: UML has been the de facto standard notation for modeling object-oriented software systems since its appearance in 1997. UML diagrams are important for maintainers of a system, especially when the software was developed by a different team. These diagrams of the system are not always available, however, and are commonly recovered using Reverse Engineering (RE) techniques. When obtained through RE, UML diagrams have a high level of detail as compared to those developed in the forward design activity. Method: In this paper we report on a comparison of the attitude and performance of maintainers when using these two kinds of diagrams during the maintenance of source code. Our findings were obtained by carrying out a controlled experiment with 40 students of a Master’s degree in Computer Science. Results: The results show a preference for forward design diagrams but do not display significant differences in task performance. The post-experiment survey results have led us to conclude that the subjects did not consider RE diagrams helpful; they found them difficult to understand, particularly the sequence diagrams. In the case of forward design diagrams, subjects considered sequence diagrams as useful, but they did not really employ them. Conclusions: Based on our findings, as regards performance of maintainers, there are no objective results which favor the use of one of these types of diagram in particular, i.e., UML diagrams which come from forwards design, on the one hand, and diagrams obtained from RE, on the other. Subjective opinions do, however, lead us to recommend the use of diagrams created during design. Nevertheless, we realize that the results should be considered as preliminary ones; further replications of this experiment are planned, using students and professionals, the aim being to obtain more conclusive results.Ministerio de Economía y Competitividad TIN2012-37493-C03-0

Seasonal impact of grazing, viral mortality, resource availability and light on the group-specific growth rates of coastal Mediterranean bacterioplankton

Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups display the highest growth rates, contributing to the recycling of organic matter to a much greater extent than what their abundances alone would predict.En prensa2,92

Biofunctionalization of cork with Moringa oleifera seeds and use of PMA staining and qPCR to detect viability of Escherichia coli

Cork matrices biofunctionalized with Moringa oleifera seed extracts (MoSe) have potential for use as a biofilter with antibacterial properties to reduce waterborne pathogens. The aim of this study was to evaluate the effect of cork biofunctionalized with active antimicrobial compounds of MoSe (f-cork) on the inhibition of Escherichia coli (InhEc). The LacZ gene from a strain of E. coli was used as the target sequence using viability quantification Polymerase Chain Reaction (qPCR) and differentiation of viable and dead bacteria through selective cell viability PMA staining. To perform this, a 27−4 fractional factorial design and a biofiltration system were used to evaluate the effect of the active protein in MoSe immobilized in granulated cork on InhEc. We found that the potential for antimicrobial activity increased with f-cork for an effective maximal bacterial reduction (99.99%; p < 0.05). The effect of f-cork functionalized with MoSe on E. coli viability was of 0.024% and 0.005% for the cells exposed to PMA, respectively, being the relevant conditions in treatment 2: (0 L/min) without aeration, (5%) MoSe and (5 mm) cork particle. In conclusion, the f-cork functionalized with MoSe presented biosorbent and antibacterial properties that effectively reduced the E. coli growth

Phenotypic Differences in a PRPH2 Mutation in Members of the Same Family Assessed with OCT and OCTA

Choroidal dystrophies comprise a group of chorioretinal degenerations. However, the different findings observed among these patients make it difficult to establish a correct clinical diagnosis. The objective of this study was to characterize new clinical findings by optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA) in these patients. Four family members with a PRPH2 gene mutation (p.Arg195Leu) were included. OCT was performed at the macula, and the thickness of the outer and inner retina, total retina, and choroid was measured. The features of the vascular network were analyzed by OCTA. Patients showed a decreased outer nuclear layer in the avascular area compared with the controls. Two patients presented greater foveal and parafoveal degeneration of the outer retina, whereas the most degenerated area in the rest was the perifovea. Disruption of the third outer band at the foveola is one of the first-altered outer bands. Slow blood flow areas or capillary dropout were main signs in the deep capillary plexus. Microaneurysms were frequently observed in less degenerated retinas. Vascular loops and intraretinal microvascular abnormalities (IRMAs) were present in the superficial plexus. Extensive degeneration of the choriocapillaris was detected. Phenotypic differences were found between patients: two showed central areolar choroidal dystrophy and the rest had extensive chorioretinal atrophy. These signs observed in OCT and OCTA can help to more appropriately define the clinical disease in patients with choroidal dystrophies.This research was funded by grants from the Spanish Ministry of Science and Innovation (FEDER- PID2019-106230RB-I00, RD16/0008/0001), Spanish Ministry of Universities (FPU16/04114 and FPU18/02964), Instituto de Salud Carlos III (RETICS-FEDER RD16/0008/0016), Asociación Retina Asturias/Cantabria, FARPE-FUNDALUCE, and Generalitat Valenciana (IDIFEDER/2017/064)

Impact of Maturation and Vitrification Time of Human GV Oocytes on the Metaphase Plate Configuration

The combination of in vitro maturation (IVM) techniques and oocyte vitrification (OV) could increase the number of useful oocytes in different types of patients. IVM and subsequent OV is the most widely used clinical strategy. Would the results improve if we reverse the order of the techniques? Here, we evaluated survival, in vitro maturation, time to extrude the first polar body (PB), and the metaphase plate configuration of human prophase I (GV) oocytes before or after their vitrification. Specific, 195 GV oocytes from 104 patients subjected to controlled ovarian stimulation cycles were included. We stablished three experimental groups: GV oocytes vitrified and IVM (Group GV-Vit), GV oocytes IVM and vitrified at MII stage (Group MII-Vit), and GV oocytes IVM (Group not-Vit). All of them were in vitro matured for a maximum of 48 h and fixed to study the metaphase plate by confocal microscopy. According to our results, the vitrification of immature oocytes and their subsequent maturation presented similar survival, maturation, and metaphase plate conformation rates, but a significantly higher percentage of normal spindle than the standard strategy. Additionally, the extension of IVM time to 48 h did not seem to negatively affect the oocyte metaphase plate configuration.This research was funded by Department of Biotechnology of the University of Alicante (VIGROB-186)

Mesonia oceanica sp. Nov., isolated from oceans during the tara oceans expedition, with a preference for mesopelagic waters

Strain ISS653T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bac-terium, strictly aerobic and chemoorganotrophic, slightly halophilic (1-15% NaCl) and mesophilic (4-37 °C), oxidase-and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15:0, iso-C15:0 2-OH, and iso-C17:0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2%), Salegentibacter mishustinae (93.1%) and Mesonia mobilis (92.9%) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81% AAI; 78.9% ANI), M. phycicola (76% AAI; 76.3% ANI), Mesonia maritima (72% AAI, 74.9% ANI), Mesonia hippocampi (64% AAI, 70.8% ANI) and Mesonia algae (68% AAI; 72.2% ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653T in a clade with species of the genus Mesonia. We conclude that strain ISS653T represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653T (=CECT 9532T=LMG 31236T) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans

Análisis de la microbiota de branquias de Sparus aurata tras la inclusión de la microalga Nannochloropsis gaditana en la dieta

The inclusion of microalgae in the diet of farmed fish such as sea bream (Sparus aurata) is proposed as a sustainable alternative to the traditional diet with fishmeal, since numerous benefits have been reported to the fish. The gills act as the first defence barrier against pathogenic organisms and have an autochthonous microbiota that contributes to this function, in the fact that it is important to know if diets supplemented with microalgae can cause any alteration. In this work, three diets (control, raw Nannochloropsis gaditana seaweed and hydrolyzed seaweed) were fed to juvenile sea bream for 90 days, later they were sacrificed and their organs frozen. 16S rRNA was sequenced on an Illumina® platform and bioinformatic analysis with MOTHUR was performed. A significant increase in the richness index (Chao1) was shown in the microbiota of the gills of the fish fed N. gaditana. The most significant changes occurred in the fish fed the raw algae, with a notable increase in the genus Shewanella in this group.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Empirical leucine-to-carbon conversion factors for estimating heterothrophic bacterial production in surface waters of the world oceans

Comunicación oralBacterial biomass production is a key parameter for evaluating the role of bacterioplankton in ocean carbon cycling. However, bacterial production cannot be directly measured and is typically estimated from the incorporation rates of radiolabelled leucine. The conversion of leucine uptake rates into bacterial carbon production rates requires the use of conversion factors (CFs) which must be empirically determined. Despite the empirical leucine-to-carbon CFs vary widely across environments very little is known about its potential controlling factors. We conducted a set of 10 surface seawater cultures experiments where the growth of the natural bacterial assemblage was promoted by filtration (removal of grazers) or by both filtration and dilution. Sampling stations were located between 30 ºN and 30 ºS, including the Atlantic, Pacific and Indian oceans. CFs varied from 0.13 to 1.47 Kg C mol Leu-1, being higher in the filtrated than in the filtrated and diluted treatment. The abundance of picocyanobacteria explained 60% of the observed variability. Our results further suggest that the composition of bacterioplankton, as assessed by ARISA fingerprinting, may partially explain the observed variation in CFs

¿Catástrofes ecológicas en la estepa? Arqueología del Paisaje en el complejo minerometalúrgico de Kargaly (Región de Orenburg, Rusia)

Kargaly is one of the most important centers of mining and metallurgy in the great Eurasian steppe. Dr. E.N. Chernykh and his team (Institute of Archaeology, Russian Academy of Sciences, Moscow) and various researchers at the CSIC and other Spanish institutions have developed a joint project to undertake a comprehensive study of the site's two main phases of occupation, the Bronze Age (2nd millenium BC) and the first Russian industrialization (1745-1900 AD). The Russian members of the joint team are in charge of the archaeological investigations, while the Spanish members are studying metallurgical and mining technology and production, on the one hand, and the environmental context and impact of these activities, on the other. This article presents the research design and first results of the Palaeoenvironmental research at Kargaly. This work has two aspects. The first consisted of obtaining one of the most complete palaeoenvironmental data sets from the steppes through both the systematic sampling of archaeological sites to recover charcoal, seeds, fruits and pollen and the taking of palynological cores from natural deposits, on the other Both sampling programs were supported by radiocarbon dates. The second aspect, to which the greater part of this article is devoted, was dedicated to contextualizing the palaeobotanical evidence by studying the present-day landscape, with particular attention to understanding the processes which shape the variability of the pollen rain. Our purpose was to obtain explicit and measurable calibrative criteria which would enable us to answer the palaeoenvironmental questions raised by our archaeological and archaeometallurgical research. These questions include, most importantly, the following: what was the extent of forest (the energy base for the mining/metallurgical complex) during the Bronze Age? and how do we evaluate subsistence practices? (an issue related to the origins of agriculture on the steppe). Answering both questions require us to go beyond conventional palaeoenvironmental practice, since they require very specific information about the past spatial distribution of vegetation on both local and regional scales. We propose a methodological perspective that places the practice of palynology in archaeology within the goals, theoretical premisses, and methods of Landscape Archaeology. Using this framework we evaluate and identify the limitation of conventional palaeoenvironmental practice (particularly the use of pollen analysis in archaeology) and we develop an intensive application of model-based approach to palynology, one that combines study of the pollen rain with mathematical modelling of the landscape. To put it into practice we used modern methods of terrestrial observation, such as satellite imagery, grounded in the use of Geo graphical Information Systems (GIS) and global positioning (GPS) technology.Kargaly es uno de los centros de minería y metalurgia del cobre más significativos de la Gran Estepa Euroasiática. El Dr. E.N. Chernyj y su equipo (Instituto de Arqueología, Academia Rusa de Ciencias, Moscú) y varios investigadores del CSIC y de otras instituciones españolas desarrollan allí un proyecto conjunto para el estudio integral de sus dos fases de explotación: la Edad del Bronce (II milenio AC) y la primera industrialización rusa (1745-1900 AD). Los miembros rusos del equipo están a cargo de la investigación arqueológica de este proyecto coordinado y los miembros españoles del estudio de los aspectos tecnológicos y productivos de la minería y la metalurgia, por un lado, y del contexto ambiental de ambas actividades, así como de su impacto sobre el territorio por otro. El propósito de este artículo es presentar los planteamientos y primeros resultados del programa de estudios paleoambientales, que consta de dos fases. La primera dio lugar a uno de los registros paleoambientales más completos de esta región mediante muestreo sistemático antracológico, paleocarpológico y palinológico en varios yacimientos arqueológicos, y sondeos palinológicos en depósitos naturales. En ambos casos se contó con el apoyo de dataciones radiocarbónicas. La segunda fase, a la que se dedica la mayor parte del artículo, se orientó a la contextualización de ese registro mediante una investigación sobre el paisaje actual, con especial énfasis en la comprensión de los procesos de formación de la lluvia polínica. Su finalidad es obtener criterios explícitos y controlables de calibración para la interpretación de las cuestiones paleoambientales demandadas por la investigación arqueológica y arqueometalúrgica. Destaca entre ellas la evaluación de los recursos forestales durante la Edad del Bronce, base energética del complejo minero metalúrgico, y el problema del reconocimiento de las prácticas subsistenciales, en relación con la discusión sobre el comienzo de la economía productora en la Gran Estepa Euroasiática. Ambas rebasan el marco de la práctica paleoambiental convencional, al requerir información muy específica sobre la distribución espacial en el pasado de la vegetación a escala local y regional. Se propone un enfoque metodológico que enmarca la práctica de la palinología arqueológica en los objetivos, planteamientos teóricos y métodos de la Arqueología del Paisaje. Desde este marco se evalúan y diagnostican las limitaciones de la práctica convencional de la Arqueología paleoambiental (particularmente la palinología arqueológica) y se ofrece una aplicación intensiva del "enfoque modelizador" en paleopalinología basada en la combinación de métodos de modelización matemática del paisaje y de la lluvia polínica. Para su puesta en práctica se aplican métodos avanzados de observación de la Tierra, como la Teledetección espacial, apoyados en el uso intensivo de la tecnología de los Sistemas de Información Geográfica (GIS) y las técnicas de posicionamiento global (GPS)