Contributors: Li Li, Xiqun (Micheal) Chen, Lei Zhang
... How to calibrate the parameters of car-following models based on observed traffic data is a vital problem in traffic simulation. Usually, the core of calibration is cast into an optimization problem, in which the decision variables are car-following model parameters and the objective function usually characterizes the difference between empirical vehicle movements and their simulated correspondences. Since the objective function is usually nonlinear and non-convex, various greedy or stochastic algorithms had been proposed during the last two decades. However, the performance of these algorithms remains to be further examined. In this paper, we revisit this important problem with a special focus on the geometric feature of the objective function. First, we prove that, from a global perspective, most existing objective functions are Lipschitz continuous. Second, we show that, from a local perspective, many of these objective functions are relatively flat around the global optimal solution. Based on these two features, we propose a new global optimization algorithm that integrates global direct search and local gradient search to find the optimal solution in an efficient manner. We compare this new algorithm with several existing algorithms, including Nelder–Mead (NM) algorithm, sequential quadratic programming (SQP) algorithm, genetic algorithm (GA), and simultaneous perturbation stochastic approximation (SPSA) algorithm, on NGSIM trajectory datasets. Results demonstrate that the proposed algorithm has a fast convergence speed and a high probability of finding the global optimal solution. Moreover, it has only two major configuration parameters that can be easily determined in practice.
Short Communication - Dietary preferences of Hawaiian tree snails to inform culture for conservation
Contributors: Richard O'Rorke, Brenden S. Holland, Gerry M. Cobian, Kapono Gaughen, Anthony S. Amend
... One strategy to safeguard endangered species against extinction is raising subpopulations in ex situ facilities. Feeding animals ex situ is difficult when their diet is cryptic. We present a combined molecular and behavioral approach to assess the diet of Achatinella, a critically endangered genus of tree snail, to determine how diet of captive snails differs from wild snails. Cultured snails are currently fed biofilms growing on leaf surfaces, as well as a Cladosporium fungus isolated from this same habitat. Amplicon sequencing of DNA extracted from feces of wild and cultured snails confirms that this Cladosporium is abundant in the wild (~1.5% of sequences), but it dominates the ex situ snails' diet (~38%) and the diet of captive snails is still significantly less diverse than wild snails. To test the hypothesis that snails have diet preferences, we conducted feeding trials. These used a surrogate snail species, Auriculella diaphana, which is a confamilial Oahu endemic, though non-federally listed. Contrary to our expectations we found that snails do have feeding preferences. Furthermore, our feeding preference trials show that over all other feeding options snails most preferred the “no-microbe” control, which consisted only of potato dextrose agar (PDA). PDA is rich in simple carbohydrates, in contrast to the oligotrophic environment of wild tree-snails. These results suggest further research should focus on calorie budgets of snails, devising new approaches to supplementing their ex situ diet and determining whether a wild diet is an optimum diet.
Contributors: Olivier Le Tonquèze, Bernhard Gschloessl, Vincent Legagneux, Luc Paillard, Yann Audic
... The specific interactions between RNA-binding proteins and their target RNAs are an essential level to control gene expression. By combining ultra-violet cross-linking and immunoprecipitation (CLIP) and massive SoliD sequencing we identified the RNAs bound by the RNA-binding protein CELF1, in human HeLa cells. The CELF1 binding sites deduced from the sequence data allow characterizing specific features of CELF1-RNA association. We present therefore the first map of CELF1 binding sites in human cells.
Does nutrient enrichment compensate fungicide effects on litter decomposition and decomposer communities in streams?
Contributors: Diego Fernández, Mallikarjun Tummala, Verena C. Schreiner, Sofia Duarte, Cláudia Pascoal, Carola Winkelmann, Daniela Mewes, Katherine Muñoz, Ralf B. Schäfer
... Nutrient and pesticide pollution are widespread agricultural stressors. Fungicides may affect freshwater fungi, which play an important role in litter decomposition (LD), whereas moderate nutrient enrichment can stimulate LD. We examined potential interaction effects of nutrients and fungicides on decomposer communities and LD in a 14-day two-factorial (fungicide and nutrient treatments) mesocosm experiment. Fungicide exposure was limited to 4days to simulate episodic contamination. Only the microbial community responded significantly to the experimental factors, though non-significant increases >20% were found for invertebrate decomposer weight gain and LD under high-nutrient conditions. Fungal community structure responded more strongly to fungicides than sporulation. Sporulation responded strongest to nutrients. Bacterial community structure was affected by both factors, although only nutrients influenced bacterial density. Our results suggest effects from fungicides at field-relevant levels on the microbial community. Whether these changes propagate to invertebrate communities and LD remains unclear and should be analysed under longer and recurrent fungicide exposure.
Contributors: Panos Bravakos, Georgios Kotoulas, Katerina Skaraki, Adriani Pantazidou, Athena Economou-Amilli
... Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S–23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes.
Refining measurements of lateral channel movement from image time series by quantifying spatial variations in registration error
Contributors: Devin M. Lea, Carl J. Legleiter
... Remotely sensed data provides information on river morphology useful for examining channel change at yearly-to-decadal time scales. Although previous studies have emphasized the need to distinguish true geomorphic change from errors associated with image registration, standard metrics for assessing and summarizing these errors, such as the root-mean-square error (RMSE) and 90th percentile of the distribution of ground control point (GCP) error, fail to incorporate the spatial structure of this uncertainty. In this study, we introduce a framework for evaluating whether observations of lateral channel migration along a meandering channel are statistically significant, given the spatial distribution of registration error. An iterative leave-one-out cross-validation approach was used to produce local error metrics for an image time series from Savery Creek, Wyoming, USA, and to evaluate various transformation equations, interpolation methods, and GCP placement strategies. Interpolated error surfaces then were used to create error ellipses representing spatially variable buffers of detectable change. Our results show that, for all five sequential image pairs we examined, spatially distributed estimates of registration error enabled detection of a greater number of statistically significant lateral migration vectors than the spatially uniform RMSE or 90th percentile of GCP error. Conversely, spatially distributed error metrics prevented changes from being mistaken as real in areas of greater registration error. Our results also support the findings of previous studies: second-order polynomial functions on average yield the lowest RMSE, and errors are reduced by placing GCPs on the floodplain rather than on hillslopes. This study highlights the importance of characterizing the spatial distribution of image registration errors in the analysis of channel change.
Contributors: Boqiang Lin, Xuan Xie
... In a joint U.S.–China statement on climate change, the Chinese government declared to peak CO2 emissions around 2030. This demonstrates the government's determination to deal with carbon emission and climate change. Although the food industry is not a carbon emission-intensive industry, its large scale makes the emission reduction in the industry very important. Based on the input–output structural decomposition method, this paper calculates the CO2 emissions of China's food industry from 1991 to 2012, and decomposes the change in CO2 emissions of the industry during 1992–1997, 1997–2002, 2002–2007 and 2007–2010 into four main effects: emission factor, energy structure, energy intensity, and total output (including four sub-effects: intermediate use, domestic final demand, import substitution and export extension). The results show that changes in CO2 emissions in the food industry mainly depends on total output effect and energy intensity effect. Energy intensity effect is the most important factor reducing CO2 emissions, as it reduced cumulative 213 million tons (Mt) CO2 emissions of the industry. Among total output effect, the effects of intermediate use and domestic final demand are the two biggest contributors to carbon emissions. Finally, we provide some policy advices for constraining and reducing CO2 emissions of China's food industry. The advices include increasing R&D investment and the substitution of energy with other input factors to decrease energy intensity, increasing the added value of the food industry, optimizing the energy structure with more clean and low-carbon energy, and maintaining the prices of raw materials of the food industry (i.e. agricultural products) with taxes or subsidies.
Ancient Neotropical origin and recent recolonisation: Phylogeny, biogeography and diversification of the Riodinidae (Lepidoptera: Papilionoidea)
Contributors: Marianne Espeland, Jason P.W. Hall, Philip J. DeVries, David C. Lees, Mark Cornwall, Yu-Feng Hsu, Li-Wei Wu, Dana L. Campbell, Gerard Talavera, Roger Vila
... We present the first dated higher-level phylogenetic and biogeographic analysis of the butterfly family Riodinidae. This family is distributed worldwide, but more than 90% of the c. 1500 species are found in the Neotropics, while the c. 120 Old World species are concentrated in the Southeast Asian tropics, with minor Afrotropical and Australasian tropical radiations, and few temperate species. Morphologically based higher classification is partly unresolved, with genera incompletely assigned to tribes. Using 3666bp from one mitochondrial and four nuclear markers for each of 23 outgroups and 178 riodinid taxa representing all subfamilies, tribes and subtribes, and 98 out of 145 described genera of riodinids, we estimate that Riodinidae split from Lycaenidae about 96Mya in the mid-Cretaceous and started to diversify about 81Mya. The Riodinidae are monophyletic and originated in the Neotropics, most likely in lowland proto-Amazonia. Neither the subfamily Euselasiinae nor the Nemeobiinae are monophyletic as currently constituted. The enigmatic, monotypic Neotropical genera Styx and Corrachia (most recently treated in Euselasiinae: Corrachiini) are highly supported as derived taxa in the Old World Nemeobiinae, with dispersal most likely occurring across the Beringia land bridge during the Oligocene. Styx and Corrachia, together with all other nemeobiines, are the only exclusively Primulaceae-feeding riodinids. The steadily increasing proliferation of the Neotropical Riodininae subfamily contrasts with the decrease in diversification in the Old World, and may provide insights into factors influencing the diversification rate of this relatively ancient clade of Neotropical insects.
Original Article - Tumor heterogeneity uncovered by dynamic expression of long noncoding RNA at single-cell resolution
Contributors: Wangxiong Hu, Tingzhang Wang, Yanmei Yang, Shu Zheng
... The expression of long noncoding RNA (lncRNA) is thought to be more cell-type specific than the expression of protein-coding genes. However, the expression profile of individual cells regarding lncRNA remains to be elucidated. Here, we comprehensively investigated the pattern of lncRNA expression across five glioblastoma tumors (414 cells) and two cell lines (GBM6 and GBM8, 127 cells). We found that there were more than 1,000 lncRNAs that varied between any two cells and that there was frequent gain and loss of lncRNA expression during tumor cell proliferation, suggesting a great heterogeneity in lncRNA expression across different single cells in glioblastoma.
Data in Brief - Generating and evaluating a ranked candidate gene list for potential vertebrate heart field regulators
Contributors: G. Musso, C. Mosimann, D. Panáková, A. Burger, Y. Zhou, L.I. Zon, C.A. MacRae
... The vertebrate heart develops from two distinct lineages of cardiomyocytes that arise from the first and second heart fields (FHF and SHF, respectively). The FHF forms the primitive heart tube, while adding cells from the SHF allows elongation at both poles of the tube. Initially seen as an exclusive characteristic of higher vertebrates, recent work has demonstrated the presence of a distinct FHF and SHF in lower vertebrates, including zebrafish. We found that key transcription factors that regulate septation and chamber formation in higher vertebrates, including Tbx5 and Pitx2, influence relative FHF and SHF contributions to the zebrafish heart tube. To identify molecular modulators of heart field migration, we used microarray-based expression profiling following inhibition of tbx5a and pitx2ab in embryonic zebrafish (Mosimann & Panakova, et al, 2015; GSE70750). Here, we describe in more detail the procedure used to process, prioritize, and analyze the expression data for functional enrichment.