Parallel particle swarm optimization based on spark for academic paper co-authorship prediction

The particle swarm optimization (PSO) algorithm has been widely used in various optimization problems. Although PSO has been successful in many fields, solving optimization problems in big data applications often requires processing of massive amounts of data, which cannot be handled by traditional PSO on a single machine. There have been several parallel PSO based on Spark, however they are almost proposed for solving numerical optimization problems, and few for big data optimization problems. In this paper, we propose a new Spark-based parallel PSO algorithm to predict the co-authorship of academic papers, which we formulate as an optimization problem from massive academic data. Experimental results show that the proposed parallel PSO can achieve good prediction accuracy

Testicular fat deposition attenuates reproductive performance via decreased follicle-stimulating hormone level and sperm meiosis and testosterone synthesis in mouse

Objective Testicular fat deposition has been reported to affect animal reproduction. However, the underlying mechanism remains poorly understood. The present study explored whether sperm meiosis and testosterone synthesis contribute to mouse testicular fat deposition-induced reproductive performance. Methods High fat diet (HFD)-induced obesity CD1 mice (DIO) were used as a testicular fat deposition model. The serum hormone test was performed by agent kit. The quality of sperm was assessed using a Sperm Class Analyzer. Testicular tissue morphology was analyzed by histochemical methods. The expression of spermatocyte marker molecules was monitored by an immuno-fluorescence microscope during meiosis. Analysis of the synthesis of testosterone was performed by real-time polymerase chain reaction and reagent kit. Results It was found that there was a significant increase in body weight among DIO mice, however, the food intake showed no difference compared to control mice fed a normal diet (CTR). The number of offspring in DIO mice decreased, but there was no significant difference from the CTR group. The levels of follicle-stimulating hormone were lower in DIO mice and their luteinizing hormone levels were similar. The results showed a remarkable decrease in sperm density and motility among DIO mice. We also found that fat accumulation affected the meiosis process, mainly reflected in the cross-exchange of homologous chromosomes. In addition, overweight increased fat deposition in the testis and reduced the expression of testosterone synthesis-related enzymes, thereby affecting the synthesis and secretion of testosterone by testicular Leydig cells. Conclusion Fat accumulation in the testes causes testicular cell dysfunction, which affects testosterone hormone synthesis and ultimately affects sperm formation. Keywords Cholesterol Metabolism, Overweight, Spermatogenesis, Testosteron

The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics

Water bloom development due to eutrophication constitutes a case of niche specialization among planktonic cyanobacteria, but the genomic repertoire allowing bloom formation in only some species has not been fully characterized. We posited that the habitat relevance of a trait begets its underlying genomic complexity, so that traits within the repertoire would be differentially more complex in species successfully thriving in that habitat than in close species that cannot. To test this for the case of bloom-forming cyanobacteria, we curated 17 potentially relevant query metabolic pathways and five core pathways selected according to existing ecophysiological literature. The available 113 genomes were split into those of blooming (45) or nonblooming (68) strains, and an index of genomic complexity for each strain’s version of each pathway was derived. We show that strain versions of all query pathways were significantly more complex in bloomers, with complexity in fact correlating positively with strain blooming incidence in 14 of those pathways. Five core pathways, relevant everywhere, showed no differential complexity or correlations. Gas vesicle, toxin and fatty acid synthesis, amino acid uptake, and C, N, and S acquisition systems were most strikingly relevant in the blooming repertoire. Further, we validated our findings using metagenomic gene expression analyses of blooming and non- blooming cyanobacteria in natural settings, where pathways in the repertoire were differentially overexpressed according to their relative complexity in bloomers, but not in nonbloomers. We expect that this approach may find applications to other habitats and organismal groups

Probiotic Yeast Inhibits VEGFR Signaling and Angiogenesis in Intestinal Inflammation

Background and Aims Saccharomyces boulardii (Sb) can protect against intestinal injury and tumor formation, but how this probiotic yeast controls protective mucosal host responses is unclear. Angiogenesis is an integral process of inflammatory responses in inflammatory bowel diseases (IBD) and required for mucosal remodeling during restitution. The aim of this study was to determine whether Sb alters VEGFR (vascular endothelial growth factor receptor) signaling, a central regulator of angiogenesis. Methods: HUVEC were used to examine the effects of Sb on signaling and on capillary tube formation (using the ECMatrix™ system). The effects of Sb on VEGF-mediated angiogenesis were examined in vivo using an adenovirus expressing VEGF-A(164) in the ears of adult nude mice (NuNu). The effects of Sb on blood vessel volume branching and density in DSS-induced colitis was quantified using VESsel GENeration (VESGEN) software. Results: 1) Sb treatment attenuated weight-loss (p<0.01) and histological damage (p<0.01) in DSS colitis. VESGEN analysis of angiogenesis showed significantly increased blood vessel density and volume in DSS-treated mice compared to control. Sb treatment significantly reduced the neo-vascularization associated with acute DSS colitis and accelerated mucosal recovery restoration of the lamina propria capillary network to a normal morphology. 2) Sb inhibited VEGF-induced angiogenesis in vivo in the mouse ear model. 3) Sb also significantly inhibited angiogenesis in vitro in the capillary tube assay in a dose-dependent manner (p<0.01). 4) In HUVEC, Sb reduced basal VEGFR-2 phosphorylation, VEGFR-2 phosphorylation in response to VEGF as well as activation of the downstream kinases PLCγ and Erk1/2. Conclusions: Our findings indicate that the probiotic yeast S boulardii can modulate angiogenesis to limit intestinal inflammation and promote mucosal tissue repair by regulating VEGFR signaling

Global-regional nested simulation of particle number concentration by combing microphysical processes with an evolving organic aerosol module

Aerosol microphysical processes are essential for the next generation of global and regional climate and air quality models to determine particle size distribution. The contribution of organic aerosols (OAs) to particle formation, mass, and number concentration is one of the major uncertainties in current models. A new global–regional nested aerosol model was developed to simulate detailed microphysical processes. The model combines an advanced particle microphysics (APM) module and a volatility basis set (VBS) OA module to calculate the kinetic condensation of low-volatility organic compounds and equilibrium partitioning of semi-volatile organic compounds in a 3-D framework using global–regional nested domain. In addition to the condensation of sulfuric acid, the equilibrium partitioning of nitrate and ammonium, and the coagulation process of particles, the microphysical processes of the OAs are realistically represented in our new model. The model uses high-resolution size bins to calculate the size distribution of new particles formed through nucleation and subsequent growth. The multi-scale nesting enables the model to perform high-resolution simulations of the particle formation processes in the urban atmosphere in the background of regional and global environments. By using the nested domains, the model reasonably reproduced the OA components obtained from the analysis of aerosol mass spectrometry measurements through positive matrix factorization and the particle number size distribution in the megacity of Beijing during a period of approximately a month. Anthropogenic organic species accounted for 67 % of the OAs of secondary particles formed by nucleation and subsequent growth, which is considerably larger than that of biogenic OAs. On the global scale, the model well predicted the particle number concentration in various environments. The microphysical module combined with the VBS simulated the universal distribution of organic components among the different aerosol populations. The model results strongly suggest the importance of anthropogenic organic species in aerosol particle formation and growth at polluted urban sites and over the whole globe.Aerosol microphysical processes are essential for the next generation of global and regional climate and air quality models to determine particle size distribution. The contribution of organic aerosols (OAs) to particle formation, mass, and number concentration is one of the major uncertainties in current models. A new global-regional nested aerosol model was developed to simulate detailed microphysical processes. The model combines an advanced particle microphysics (APM) module and a volatility basis set (VBS) OA module to calculate the kinetic condensation of low-volatility organic compounds and equilibrium partitioning of semi-volatile organic compounds in a 3-D framework using global-regional nested domain In addition to the condensation of sulfuric acid, the equilibrium partitioning of nitrate and ammonium, and the coagulation process of particles, the microphysical processes of the OAs are realistically represented in our new model. The model uses high-resolution size bins to calculate the size distribution of new particles formed through nucleation and subsequent growth. The multi-scale nesting enables the model to perform high-resolution simulations of the particle formation processes in the urban atmosphere in the background of regional and global environments. By using the nested domains, the model reasonably reproduced the OA components obtained from the analysis of aerosol mass spectrometry measurements through positive matrix factorization and the particle number size distribution in the megacity of Beijing during a period of approximately a month. Anthropogenic organic species accounted for 67 % of the OAs of secondary particles formed by nucleation and subsequent growth, which is considerably larger than that of biogenic OAs. On the global scale, the model well predicted the particle number concentration in various environments. The microphysical module combined with the VBS simulated the universal distribution of organic components among the different aerosol populations. The model results strongly suggest the importance of anthropogenic organic species in aerosol particle formation and growth at polluted urban sites and over the whole globe.Peer reviewe

Suckling Piglet Intestinal Enterocyte Nutrient Metabolism Changes

Background/Aims: Intestinal morphology and the types of enterocytes are changed in piglets during the suckling period, but it is unclear whether these changes are associated with metabolic changes in epithelium. The present study was conducted to test the hypothesis that glucose, fatty acids, and amino acid metabolism in differentiated piglet enterocytes changed during suckling. Methods: Twenty-four piglets (Duroc × [Landrace × Yorkshire]) from 8 litters (3 piglets/litter) were selected. A single piglet from each litter was randomly selected and euthanized at days 7, 14, and 21. Differentiated enterocytes (DE) were isolated from their mid-jejunum. Isobaric tags for relative and absolute quantification and subsequent liquid chromatography-tandem mass spectrometry were used to identify and measure protein synthesis. Results: The results showed that various activities, including: cellular processes; metabolic processes; biological regulation; pigmentation; and, localization, in DEs changed during suckling. Metabolic process analyses revealed that protein expression related to glycolysis and citrate cycle was decreased from day 7 to day 14. The number of differentiated enterocytes of 21 d piglets increased compared to 7 d piglets. Most of the proteins involved in fatty acid and amino acids metabolism had decreased DE expression between day 7 and day 14. Some, but not all, detected proteins down-regulated in DEs of 21 day piglets compared to 7 day piglets. Conclusion: These results indicate that glucose, fatty acids, and amino acids metabolism changed during suckling. This may provide useful information for designing feed formulas and regulating piglet intestinal growth and development