bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of root exudates of woody species on the soil anti-erodibility in the rhizosphere in a karst region, China
Authors: Wang Zhen Hong , Fang Hong , Chen Mouhui
Published: January 2018

Introduction: The rhizospheres, the most active interfaces between plants and soils, play a central role in a long-term maintenance of the biosphere. The anti-erodibility of soils (AES) regulated by the root exudates is crucial to the stability of the rhizospheres. However, scientists still remain unclear regarding the key organic matter in the root exudates to affect the AES and interspecific variation. Methods: We used an incubation of soils to test the effects of the root exudates from 8 woody plant species on a change in soil aggregation, and identified the organic matter in these root exudates with gas chromatograph-mass spectrometer (GC-MS) and biochemical methods. Furthermore, the relationships between the organic matter in the exudates and the AES in the rhizosperes of the 34 additional tree species were analyzed. Results: The water-stable aggregates of the soils incubated with the root exudates increased by 15-50% on average compared with controls, and the interspecific differences were significant. The root exudates included hundreds of specific organic matter, in which hydrocarbon, total sugar, total amino acids and phenolic compounds were crucial to the AES. These types of the matter could explain about 20-75% of the variation in total effects of the root exudates on the AES quantified by aggregate status, degree of aggregation, dispersion ratio and dispersion coefficient. Discussion: Effects of the root exudates on the AES and the interspecific variation are as important as those of root density, litters and vegetation covers. A range of studies have explored the effects of root density, litters, vegetation covers and types on the AES, but little attention has been given to the effects of the root exudates on the AES. Different plants secrete the different relative contents of the organic matter resulting in the variation of the effects of the root exudates on the AES. Our study quantified the causal relationships between the root exudates and the AES from modeling experiments in laboratory to actual effects in the field, and indicated the interspecific variation of the AES and the organic matter in the root exudates. Conclusions: The study recognized more organic compounds in the exudates related to the AES. These results can enhance the understanding of the stability of the soils in a slope and be applied to ecosystem restoration.
Effects of root exudates of woody species on the soil anti-erodibility in the rhizosphere in a karst region, China
Authors: Wang Zhenhong , Fang Hong , Chen Mouhui
Published: January 2018

Introduction: Rhizospheres, the most active interfaces between plants and soils, play a central role in a long-term maintenance of the biosphere. The anti-erodibility of soils (AES) regulated by the root exudates is crucial to the stability of the rhizospheres. However, scientists still remain unclear regarding the key organic matter in the root exudates to affect the AES and interspecific variation. Methods: We used an incubation of soils to test the effects of the root exudates from 8 woody plant species on a change in soil aggregation, and identified the organic matter in these root exudates with gas chromatograph-mass spectrometer (GC-MS) and biochemical methods. Furthermore, the relationships between the organic matter in the exudates and the AES in the rhizosperes of the 34 additional tree species were analyzed. Results: The water-stable aggregates of the soils incubated with the root exudates increased by 15-50% on average compared with controls, and the interspecific differences were significant. The root exudates included hundreds of specific organic matter, in which hydrocarbon, total sugar, total amino acids and phenolic compounds were crucial to the AES. These types of the matter could explain about 20-75% of the variation in total effects of the root exudates on the AES quantified by aggregate status, degree of aggregation, dispersion ratio and dispersion coefficient. Discussion: Effects of the root exudates on the AES and the interspecific variation are as important as those of root density, litters and vegetation covers. A range of studies have explored the effects of root density, litters, vegetation covers and types on the AES, but little attention has been given to the effects of the root exudates on the AES. Different plants secrete the different relative contents of the organic matter resulting in the variation of the effects of the root exudates on the AES. Our study quantified the causal relationships between the root exudates and the AES from modeling experiments in laboratory to actual effects in the field, and indicated the interspecific variation of the AES and the organic matter in the root exudates. Conclusions: The study recognized more organic compounds in the exudates related to the AES. These results can enhance the understanding of the stability of the soils in a slope and be applied to ecosystem restoration.
Reptile diversity and community composition in the Puyango dry forest
Authors: Ana Acosta Vásconez , Diego Cisneros-Heredia ,   Diego Cisneros-Heredia
Published: January 2018

Reptiles are key animals in vertebrate communities in most ecosystems. However, there is little information on their diversity and abundance in dry forests of Ecuador. Between 2013 and 2014 we studied the reptile diversity and natural history of the Puyango Protected Forest, on the border between the province of Loja and El Oro, Ecuador. This area protects relicts of dry deciduous forest in hills and patches of semi-deciduous forest around ravines. We used belt transects in three different streams and irregular band transects in trails, together with pitfall traps, funnel traps, and litter quadrants. The richness of the Puyango Protected Forest represents a small percentage of the Ecuadorian reptile diversity, but covers much of the representative phylogenetic groups of tropical dry forests of the world. Sampling was effective to determine saurian diversity, but more sampling is needed to estimate snake diversity. Evidence of the presence of 21 species, divided into 10 families, was obtained; of which 14 are snakes (including a potential new species of the genus Epictia) and seven are lizards. Natural history is described for each species, including time and space use, and their conservation status is analyzed. The reptile community is characterized by a relative homogeneity over the vegetation remnants and the highest abundances correspond to saurian species.
A probabilistic model to recover genomes in shotgun metagenomics
Authors: Dröge Johannes , Schoenhuth Alexander , McHardy Alice C
Published: January 2018

Shotgun metagenomics of microbial communities reveals information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial, but very challenging step, due to the complexity of the underlying biological system and technical factors. Microbial communities are heterogeneous, with oftentimes hundreds of present genomes deriving from different species or strains, all at varying abundances and with different degrees of similarity to each other and reference data. We present a versatile probabilistic model for genome recovery and analysis, which aggregates three types of information that are commonly used for genome recovery from metagenomes. As potential applications we showcase metagenome contig classification, genome sample enrichment and genome bin comparisons. The open source implementation MGLEX is available via the Python Package Index and on GitHub and can be embedded into metagenome analysis workflows and programs.
Microbiome of the sexual scent organ of Leptonycteris yerbabuenae
Authors: Gaona Osiris , Cerqueda-García Daniel , Martínez-Martínez Daniel , Moya Andrés , Falcón Luisa I.
Published: January 2018

Microorganisms are tightly bounded to the animals on Earth. Bacteria, among other types of microbes, interact with their hosts in several ways regarding metabolic pathways, development, complex behavioral processes such as mate recognition, among others. The adult males of Leptonycteris yerbabuenae, a nectarivorous bat, develop an interscapular odoriferous patch during the mating season. Here we present a description of the microbiota associated to this sebaceous patch 11 adult males, and studied it in terms of their taxonomical information. The variability between samples was not relevant to this study, and the most abundant phyla were Firmicutes and Proteobacteria, with dominanting classes including Gammaproteobacteria, Clostridia and Bacilli. The two most abundant species were Aggregatibacter pneumotropica and Actinomyces europaeus and other Streptococcus minor, Pseudomonas stutzeri, P. viridiflava and Staphylococcus epidermis, which are relevant in both normal and wounded human skin. Furthermore, the species present in this mating organ are involved in metabolic pathways related to fatty acid transformation to volatile molecules, which could be playing a key role in mate recognition.
A benchmark for evaluation of phylogeny reconstruction programs
Authors: Spirin Sergei
Published: January 2018

There are a lot of algorithms and programs for reconstruction of phylogeny of a set of proteins basing on multiple sequence alignment. Many programs allow users to choose a number of parameters, for example, a model for maximum likelihood programs. Different programs and different parameters often produce different results. However at the moment all published benchmarks for evaluation of relative accuracy of programs or different choices of parameters are based on simulated sequences. The aim of the present work is to create a benchmark that allows a comparison of phylogenetic programs on large sets of alignments of natural protein sequences.
Spatiotemporal succession of ammonia-oxidizing archaea abundance and composition in a created riparian wetland
Authors: Su Yu , Zhu Guibing , Wang Baoling , Wang Yu , Zhuang Linjie , Wang Weidong
Published: January 2018

Cascaded performance and compartments of constructed wetlands may harbor the internal eco-environmental gradients and further differentiate the niche and community structure of ammonia-oxidizing archaea (AOA). Here, we used quantitative PCR and 454 pyrosequencing of AOA amoA gene to investigate the abundance, diversity, composition, and driving factors of sedimentary AOA community in a created riparian wetland---Shijiuyang constructed wetland (SJY-CW) in China. Results showed that the heterogeneous wetland with serial-connected combinations of pretreatment pond, plant-bed/ditch system, and post-treatment pond as well as the third through fifth year succession (2011--2013, corresponding to the third through fifth year of actual operation after the initial two-year trial operation) had exerted significant spatiotemporal niche selection effects on AOA abundance and composition. AOA abundance in the pre- and post-treatment ponds was almost invariant in 2011--2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with the succession of SJY-CW. The AOA abundance ended up with one order of magnitude lower and tended to be consistent in the whole wetland. In contrast to abundance, the temporal niche differentiation of AOA diversity was insignificant. Nonetheless, a rough decrease trend was detected for the average community richness index Chao1 and diversity index Shannon H' in 2011--2013. Community structure analysis showed that Nitrososphaera was dominant genus, while Nitrosopumilus cluster and Nitrososphaera sister cluster increased with the succession of SJY-CW. Hierarchical clustering analysis and redundancy analysis both verified the horizontal shifts of AOA communities and these shifts inclined to occur in the most heterogeneous plant-bed/ditch system. Operational duration of the wetland which comprehensively reflected the wetland hydrology, water quality, and associated functions became the key factor driving the AOA abundance and community shift in SJY-CW sediments. In a nutshell, with the third through fifth year succession of wetland, the sedimentary ammonia-oxidizing archaea tended to be characterized by temporally decreased and spatially consistent abundance, while spatially variable and temporally decreased richness and diversity; regarding the AOA community structure, temporally from local species and relatively uniform distribution to mixing with allochthonous species and highly diversified distribution, while spatially occurring significant horizontal shifts of AOA amoA genes. These results showed the considerable if not significant niche selection effect of AOA abundance, diversity, and community structure with the operation of SJY-CW, and this will have some implications on the microbial ecology of archaeal ammonia-oxidization in a man-made wetland ecosystem.
Do current definitions and methods promote the general application of functional traits and functional diversity
Authors: Zhu Linhai , Lefcheck Jonathan S , Fu Bojie
Published: January 2018

The use of functional traits has increased exponentially in ecology, particularly in attempting to explain ecosystem functioning. This popularity has led to many proposed definitions of functional traits, which in turn has informed recommendations about how to gather, summarize, and analyze trait data. In this paper, we revisit the definition of the functional trait from the perspective of physiological, community and ecosystem ecologists, and reason towards a broad, unrestrictive, and applicable definition. We then demonstrate how a popular technique, ordination, which is used to collapse multivariate trait data into orthogonal axes, undermines this definition and the primary benefit of functional traits. We outline the conceptual pitfalls associated with ordination, and make specific suggestions about alternative methods that progress functional traits as generalizable proxies for how organisms affect ecosystem processes. We hope these suggestions will improve our ability to move towards an ecological synthesis using a trait-based approach.
Is the use of unconstrained ordination appropriate for understanding plant ecological strategies and ecosystem functioning?
Authors: Zhu Linhai , Lefcheck Jonathan S , Fu Bojie
Published: January 2018

The use of functional traits has increased exponentially in ecology, particularly in attempting to understand plant strategies and ecosystem functioning. This popularity has led to many proposed definitions of functional traits, which in turn has informed recommendations about how to gather, summarize, and analyze trait data. In this paper, we revisit the definition of the functional trait from the perspective of physiological, community and ecosystem ecology, and reason towards a broad, unrestrictive, and applicable definition. We then outline the conceptual mismatch between this definition and the popular practice of summarizing trait information using unconstrained ordination . We make specific suggestions about alternative methods to gain a mechanistic insight into how traits translate into functions. We hope this paper will improve our ability to move towards an ecological synthesis using a trait-based approach.
Speeding-up mutation testing via data compression and state infection
Authors: Zhu Qianqian , Panichella Annibale , Zaidman Andy
Published: January 2018

Mutation testing is widely considered as a high-end test criterion due to the vast number of mutants it generates. Although many efforts have been made to reduce the computational cost of mutation testing, its scalability issue remains in practice. In this paper, we introduce a novel method to speed up mutation testing based on state infection information. In addition to filtering out uninfected test executions, we further select a subset of mutants and a subset of test cases to run leveraging data-compression techniques. In particular, we adopt Formal Concept Analysis (FCA) to group similar mutants together and then select test cases to cover these mutants. To evaluate our method, we conducted an experimental study on six open source Java projects. We used EvoSuite to automatically generate test cases and to collect mutation data. The initial results show that our method can reduce the execution time by 83.93% with only 0.257% loss in precision.
Evaluation of the IEEE 802.11p multi-channel operation in vehicular networks
Authors: Behravesh Ehsun , Butler Andrew
Published: January 2018

This paper explores recent improvements in 802.11p multi-channel protocol in vehicular ad-hoc networks. We provide definitions for a vehicular network and explore the operation of 802.11 within a vehicular network. We also study on areas of improvements of this protocol and briefly discuss on advantages and disadvantages of each solution.Various solutions that various researchers have done to improve the 802.11p multi-channel protocol as it applies to vehicular networks are explored in this paper.
The solution of large-scale Minimum Cost SAT Problem as a tool for data analysis in bioinformatics
Authors: Felici Giovanni , Ferone Daniele , Festa Paola , Napoletano Antonio , Pastore Tommaso
Published: January 2018

Data mining is one of the main activities in bioinformatics, specifically to extract knowledge from massive data sets related with gene expression measurement, CNV, DNA strings, and others. A long array of methods are used to perform such task, ranging from the more established parametric statistical analysis to non parametric techniques, to classification methods that have been developed in knowledge engineering and artificial intelligence. In this paper, we consider a method for extracting logic formulas from data that relies on a large body of literature in integer and logic optimization, originally presented in [1], that has been largely and successfully applied to different problems in bioinformatics ([2], [3], [4], [5], [6]). Such method is based on the iterative solution of Minimum Cost SAT Problems and is able to extract logic formulas in DNF form that possess interesting features for their interpretation. While leaving the discussion of the main features and motivations of this approach to the related literature, in this talk we focus on the problem of solving efficiently very large scale instances of this well known logic programming problem and propose a new GRASP approach that, being able to exploit the specific structure of the problem, largely outperforms other established solvers for the same problem.

References

[1] G. Felici, K. Truemper. A Minsat Approach for Learning in Logic Domains, INFORMS Journal on Computing 14(1): 20-36 (2002).

[2] P. Bertolazzi, G. Felici, E. Weitschek. Learning to classify species with barcodes, BMC Bioinformatics, 10:1-12 (2009).

[3] M. Arisi, R. D’Onofrio, A. Brandi, S. Felsani, G. Capsoni, G. Drovandi, G. Felici, E. Weitschek, P. Bertolazzi, A. Cattaneo. Gene Expression Biomarkers in the Brain of a Mouse Model for Alzheimer’s Disease: Mining of Microarray Data by Logic Classification and Feature Selection. Journal of Alzheimer's Disease, 24(4) 721-738 (2011).

[4] E. Weitschek, A. Lo Presti, G. Drovandi, G. Felici, M. Ciccozzi, M. Ciotti, P. Bertolazzi. Human polyomaviruses identification by logic mining techniques. BMC Virology Journal, 9:58 (2012).

[5] E. Weitschek, G. Fiscon, G. Felici. Supervised DNA Barcodes species classification: analysis, comparisons and results, BMC BioData Mining, 7:4 (2014).

[6] P. Bertolazzi, G. Felici, P. Festa, G. Fiscon, E. Weitschek. Integer Programming models for Feature Selection: new extensions and a randomized solution algorithm, European Journal of Operational Research, 250-389–399, 250 (2016).
Characterization of fermented Okara powder and its effect on lipid oxidation of emulsion-type pork sausage during cold storage
Authors: Tu Chuanhai , Zhang Shanshan , Zhang Qiuqin , Xiao Yu , Xing Guangliang , Dong Mingsheng
Published: January 2018

In the present study, Okara, a soybean by-product from the production of tofu and soymilk, was processed by solid state fermentation (SSF) with Neurospora crassa Mai 1-1, a filamentous and edible fungus which was firstly isolated in our group. The proximate composition, dietary fiber content, water-soluble polysaccharides and antioxidant activity of Okara was investigated. The crude fat and protein, soluble dietary fiber content and ergosterol content of Okara was significantly increased by SSF with N.crassa . And the antioxidant activity (evaluated by the ABTS radical cation scavenging activity and DPPH radical scavenging activity) of Okara was significantly enhanced by SSF with N. crassa . In addition, emulsion-type sausage was taken as a model system for farther investigation, sausage with fermented Okara power had reduced values of thiobarbituric acid reactive substances (TBARS) ( p < 0.05 ), peroxide value. Therefore, this study demonstrated that fermented Okara showed higher nutrition value and antioxidant activity compared to the non-fermented Okara counterpart, and as an additive has good effect on antioxidant of emulsion-type sausage.
Reinstatement of Pedicularis delavayi (Orobanchaceae): a species separating from P. siphonantha revealed by phylogenetic analyses
Authors: Yu Wen-Bin , Wang Hong , Liu Min-Lu , Grabovskaya-Borodina Alisa E. , Li De-Zhu
Published: January 2018

Background. Morphological identification of Pedicularis depends on floral characters because interspecific variations these characters is very large. However, some important characters may be lost during the process of pressing the specimen. Pedicularis delavayi was described from Lijiang, northwestern Yunnan, and it was widely adopted as a variety of P. siphonantha. Unfortunately, the name “P. siphonantha var. delavayi’ incorrectly referred to P. milliana/P. tenuituba in some identified specimens and publications. Moreover, phylogenetic relationships between P. delavayi and P. siphonantha and its allies (P. millana and P. tenuituba) were not fully resolved. Methods. In total, we sampled 75 individuals representing 56 taxa. Of them, 10 taxa were from P. siphonantha group, and 11 individuals of P. delavayi represented 9 populations. One nuclear gene (nrITS) and four chloroplast genes/regions (matK, rbcL, trnH-psbA, and trnL-F) were sequenced for phylogenetic analyses. The nrITS and plastid datasets were combined to analyze. Bayesian Inference (BI) and Maximum Likelihood (ML) methods were used to reconstruct phylogenetic trees. Species identification, morphological comparison and line drawing were based on field observation, dried herbarium specimens and FFA-fixed samples. Results. Phylogenetic analyses showed that the P. siphonantha group was polyphyletic: monophyletic P. delavayi, sister to P. obliquigaleata, fell into clade A; and the remaining species of P. siphonantha group was in clade B as monophyletic (i.e. P. siphonantha lineage). In the P. siphonantha lineage, P. milliana, P. siphonantha, and P. tenuituba (= P. siphonantha var. stictochila) were well supported as monophyletic, and P. dolichosiphon (≡ P. siphonantha var. dolichosiphon) was sister to P. leptosiphon. Morphologically, P. delavayi differs from species of the P. siphonantha lineage in having a long petiole (~ 50 mm) and pedicel (~ 40 mm), a ridged corolla tube, and a folded lower-lip of the corolla. Discussion. Phylogenetic analyses showed evolution of P. delavayi was independent from the P. siphonantha lineage. The long-tubular corollas in P. delavayi and P. siphonantha lineage might be a convergent character. Both morphological and phylogenetic evidence strongly supported to reinstate P. delavayi as an independent species. In addition, P. neolatituba was proposed to reduce as a new synonymy of P. delavayi.
Basal tolerance to heat and cold exposure of the spotted wing drosophila, Drosophila suzukii
Authors: Enriquez Thomas , Colinet Hercé
Published: January 2018

The spotted wing Drosophila, Drosophila suzukii, is a new pest in Europe and America which causes severe damages to stone fruits crops. Temperature and humidity are among the most important abiotic factors governing insect life. In many situations, temperature can become stressful thus compromising fitness and survival. The ability to cope with thermal stress depends on basal level of thermal tolerance. Basic knowledge on temperature-dependent mortality of D. suzukii is essential to facilitate management of this pest. The objective of the present study was to investigate D. suzukii basal cold and heat tolerance. Adults and pupae were submitted to six low (-5 to 7.5 °C) and seven high temperatures (30 to 37 °C) for various durations, and survival-time-temperature relationships were investigated. In addition, pupal thermal tolerance was analyzed under low vs. high relative humidity. Our results showed that males had higher cold survival than females, and pupae appeared less cold-tolerant than adults. Above 5 °C, adult cold mortality became minor, even after prolonged exposures (i.e. one month). Males were less heat tolerant than females, and pupae showed a better survival to extreme high temperatures than adults. Low relative humidity did not affect D. suzukii cold survival, but reduced survival under heat stress. Overall, this study shows that survival of D. suzukii under heat and cold conditions depends on both stress intensity and duration, and the methodological approach used here, which was based on thermal tolerance landscapes, provides a comprehensive description of D. suzukii thermal tolerance and limits.
Formatting Open Science: agile creation of multiple document types by writing academic manuscripts in pandoc markdown
Authors: Krewinkel Albert , Winkler Robert
Published: January 2018

The timely publication of scientific results is essential for dynamic advances in science. The ubiquitous availability of computers which are connected to a global network made the rapid and low-cost distribution of information through electronic channels possible. New concepts, such as Open Access publishing and preprint servers are currently changing the traditional print media business towards a community-driven peer production. However, the cost of scientific literature generation, which is either charged to readers, authors or sponsors, is still high. The main active participants in the authoring and evaluation of scientific manuscripts are volunteers, and the cost for online publishing infrastructure is close to negligible. A major time and cost factor though is the formatting of manuscripts in the production stage. In this article we demonstrate the feasibility to write scientific manuscripts in plain markdown (MD) text files, which can be easily converted into common publication formats, such as PDF, HTML or EPUB, using pandoc. The simple syntax of markdown assures the long-term readability of raw files and the development of software and workflows. We show the implementation of typical elements of scientific manuscripts -- formulas, tables, code blocks and citations -- and present tools for editing, collaborative writing and version control. We give an example on how to prepare a manuscript with distinct output formats, a DOCX file for submission to a journal and a LATEX/PDF version for deposition as a PeerJ preprint. Reducing the work spent on manuscript formatting translates directly to time and cost savings for writers, publishers, readers and sponsors. Therefore, the adoption of the MD format contributes to the agile production of open science literature.
Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar
Authors: Krewinkel Albert , Winkler Robert
Published: January 2018

The timely publication of scientific results is essential for dynamic advances in science. The ubiquitous availability of computers which are connected to a global network made the rapid and low-cost distribution of information through electronic channels possible. New concepts, such as Open Access publishing and preprint servers are currently changing the traditional print media business towards a community-driven peer production. However, the cost of scientific literature generation, which is either charged to readers, authors or sponsors, is still high. The main active participants in the authoring and evaluation of scientific manuscripts are volunteers, and the cost for online publishing infrastructure is close to negligible. A major time and cost factor is the formatting of manuscripts in the production stage. In this article we demonstrate the feasibility of writing scientific manuscripts in plain markdown (MD) text files, which can be easily converted into common publication formats, such as PDF, HTML or EPUB, using pandoc. The simple syntax of markdown assures the long-term readability of raw files and the development of software and workflows. We show the implementation of typical elements of scientific manuscripts – formulas, tables, code blocks and citations – and present tools for editing, collaborative writing and version control. We give an example on how to prepare a manuscript with distinct output formats, a DOCX file for submission to a journal, and a LATEX/PDF version for deposition as a PeerJ preprint. Further, we implemented new features for supporting ‘semantic web’ applications, such as the ‘journal article tag suite’ - JATS, and the ‘citation typing ontology’ - CiTO standard. Reducing the work spent on manuscript formatting translates directly to time and cost savings for writers, publishers, readers and sponsors. Therefore, the adoption of the MD format contributes to the agile production of open science literature. Pandoc Scholar is freely available from https://github.com/pandoc-scholar.
Metabolic responses of photosynthetic sea slugs to a changing environment
Authors: Van Wert Jacey C
Published: January 2018

Sacoglossan sea slugs have complex interactions with their environment. They are well known for their ability to sequester stolen chloroplasts and utilize them for photoautotrophic CO2 fixation, yet the dependence on this is not clear in most species. Elysia stylifera is an Indo-Pacific tropical sacoglossan that selectively consumes Halimeda macroalgae and retains its chloroplasts for two weeks. This association is prone to change as their habitats are subjected to increased ocean warmth and acidification, altering algal distribution and decreasing photosynthetic efficiency. This study aimed to investigate the metabolic response of E. stylifera to projected environmental changes. Elysia stylifera were subjected to ambient (28°C) or warm (30°C) conditions and five days of food deprivation. On the first and fifth day of starvation, the respiration rates of individuals were measured in the dark to quantify slug response, as well as in the light to characterize their response when given the ability to photosynthesize. Dark treatments showed that slugs deprived of food undergo metabolic suppression in current conditions, but may not undergo suppression in projected warm conditions. The difference between oxygen consumption in dark and light treated slugs demonstrated photosynthesis occurred, but that it was reduced under all stressors. This study reveals that forecasted ocean warming may not be favorable for short-term photosynthetic sea slugs because of its impact on both the sea slugs and their ingested kleptoplasts. It also presents new uncertainties about the benefits of kleptoplasty and how it may transform with climate change.
The effects of sound on the survivorship and embryonic development of a marine gastropod Stylocheilus striatus, (aplysiidae)
Authors: Spankowski Robert J
Published: January 2018

How anthropogenic noise pollution affects marine organisms is drawing increasing international concern. There is evidence for anthropogenic noise having negative and harmful effects on the health, development and behavior of many terrestrial species; however, there are few examples of how specific frequencies of sound affect the survivorship and embryonic development of marine invertebrates. This experiment examines the effects of specific frequencies of sound on the survivorship and embryonic development of a marine gastropod, Stylocheilus striatus on the island of Mo’orea, French Polynesia. It was found that high frequency sound treatments caused a delay in the embryonic development of S. striatus embryos by 3 days while decreasing veliger survivorship by 37%. Additionally, high frequency treatments were shown to cause an observed morphological difference in shell morphology as compared to control and low frequency treatment groups. This study can be used to aid in the management and planning of future conservation polices regarding sound pollution and marine invertebrate gastropods as their presence is crucial for reef health and community structure.
The thermal range of the cushion sea star, Culcita novaeguineae, distribution and its behavioral response to warmer waters
Authors: Yokley Alexandra G
Published: January 2018

Overproduction of greenhouse gases is driving climate change and increasing the average temperature of oceans worldwide. As a result, organisms are exhibiting behavioral changes and species are shifting their natural distribution. This study aimed to assess the effects of temperature on C. novaeguineae distribution and movement in order to predict the effects of rising sea temperature on this echinoderm’s behavior and ecology. The distribution study measured the temperature gradient of the cushion star’s current habitat in order to determine how temperature changes with respect to depth. Additionally, the cushion star’s distribution range in relation to depth and sea temperature was examined to demonstrate how temperature influences cushion star range. The field experiment was conducted to determine the effects of increased temperature on C. novaeguineae behavior. Movement, a common mechanism used by ectotherms to escape heat stress, was measured as the response variable in cushion stars heat shocked in ocean waters 3°C above their expected upper thermal limit and in control organisms kept in ambient ocean waters of 31°C. The results of the distribution survey found that temperature decreased as depth increased. And cushion stars were generally found at 1, 2, and 3 meters and in temperatures between 29°C and 31°C. The field experiment revealed that the heat shocked individuals moved 3.2 times further than the control organisms and twice the number of heat shocked cushion stars moved into deeper waters than control organisms. This study suggests that temperature is the major factor affecting cushion star distribution and increased temperature promotes movement into greater depths. Consequently, as the ocean continues to warm, cushion stars may move into deeper waters to find relief from the heat stress, altering the structure of the shallow, coral reef ecosystem in which cushion stars are currently abundant.
Distribution of carbapenemases and efflux pump in carbopenems-resistance Acinetobacter baumannii
Authors: Qiu Zhu-Qiang , Zhu Li-Jing , Hou Pan-Fei
Published: January 2018

Acinetobacter baumannii has emerged as an important pathogen related to serious infections and nosocomial outbreaks around the world. The aim of this study was to detect the distribution of carbapenemases and efflux pump in carbopenems-resistance Acinetobacter baumannii(CRAB). In this study, 100 isolates of CRAB were collected from clinical specimens. Agar dilution was conducted to determine the minimum inhibitory concentrations (MICs) to 15 kinds of antibiotic. Genes of carbapenemases and efflux pumps were amplified by PCR. The expression difference of pump genes was also analyzed by real-time PCR between CRAB and carbopenems- sensitive Acinetobacter baumannii (CSAB). We found that most antibiotics, including aminoglycosides, fluoroquinolones and cephalosporins showed high MIC values in CRAB. While, all isolates were sensitive to polymyxin B. Among CRAB, 54, 32 and 16 isolates were positive for SHV-12，PER-1 and TEM-1, respectively. 86 isolates were positive for OXA-23. 55, 33 and 5 isolates carried adeB, adeJ and adeE genes. The expression level of adeB in CRAB was ten times higher than that in CSAB. Moreover, isolates with single adeE gene were detected for the first time in Acinetobacter baumannii.
Molecular simulations for investigating the role of food polyphenols
Authors: Scafuri Bernardina , Marabotti Anna , Facchiano Angelo
Published: January 2018

Food components are object of many studies aimed to identify compounds responsible of positive effects in nutrition and food science. Compound categories include antioxidants, whose positive activity is commonly related to their activity in deactivating free radicals. Polyphenols are of particular interest, and studies demonstrate many positive effects. We have recently investigated the role of apple polyphenols, in particular for the effects reported in literature in the past years, and we evidenced possible protein targets for polyphenols found in apple but present also in other fruits and vegetables. Our results open the perspective of identifying metabolic pathways affected by polyphenols. To this aim, we are investigating in more detail the potential protein targets already identified in our study, and defining the possible role of each compound investigated in the modulation of the related target activity. This ongoing study is based on the integration of techniques and resources previously used in our studies, as molecular simulations of protein-ligand docking, mutation effects, pathways analysis, and online bioinformatics resources for collecting information about proteins and their structural and functional properties.
The oldest vertebrate trace fossils from Comb Ridge (Bears Ears Region, southeastern Utah)
Authors: Gay Robert J , Jenkins Xavier A , Lepore Taormina
Published: January 2018

Vertebrate trace fossils are common in Upper Triassic deposits across the American southwest. These ichnofauna are dominated by Grallator, Brachychirotherium, and Pseudotetrasauropus, and lack ichnotaxa traditionally considered to be Early Jurassic in age, such as Eubrontes and Anomoepus. While known from Indian Creek and Lisbon Valley, Utah, vertebrate trace fossils have not been previously reported from Comb Ridge, Utah. This is significant considering that lithostratigraphic work has been ongoing at Comb Ridge since the 1990s in the elsewhere fossiliferous ‘Big Indian Rock Beds’, in the US Highway 163 roadcut that transects Comb Ridge. 2016 fieldwork by the Museums of Western Colorado: Dinosaur Journey recovered two sandstone slabs that had been dislodged from a river channel sand in the Church Rock Member of the Chinle Formation. The slabs preserve the first documented Triassic vertebrate trace fossils from Comb Ridge: a single pes impression of the ichnogenus Grallator, and several manus and at least one pes impression of a small archosaur. We tentatively refer this second track set to the ichnogenus Brachychirotherium. Taken together, these specimens provide evidence for a more diverse vertebrate fauna in the Church Rock Member of the Chinle Formation at Comb Ridge than indicated by the current body fossil record.
Mountain colonisation, miniaturisation and ecological evolution in a radiation of direct developing New Guinea Frogs (Choerophryne, Microhylidae)
Authors: Oliver Paul M , Iannella Amy , Richards Stephen J , Lee Michael S.Y
Published: January 2018

Aims. Mountain ranges in the tropics are characterised by high levels of localised endemism, often-aberrant evolutionary trajectories, and some of the world’s most diverse regional biotas. Here we investigate the evolution of montane endemism, ecology and body size in a clade of direct-developing frogs (Choerophryne, Microhylidae) from New Guinea. Methods. Phylogenetic relationships were estimated from a mitochondrial molecular dataset using Bayesian and maximum likelihood approaches. Ancestral state reconstruction was used to infer the evolution of elevational distribution, ecology (indexed by male calling height), and body size, and phylogenetically corrected regression was employed to examine the relationships between these three traits. Results. We obtained strong support for a monophyletic lineage comprising the majority of taxa sampled. Within this clade we identified one subclade that appears to have diversified primarily in montane habitats of the Central Cordillera (> 1000 m. a.s.l), with subsequent dispersal to isolated North Papuan Mountains. A second subclade (characterised by moderately to very elongated snouts) appears to have diversified primarily in hill forests (< 1000 m a.s.l.), with inferred independent upwards colonisations of isolated montane habitats, especially in isolated North Papuan Mountains. We found no clear relationship between extremely small body size (adult SVL less than 15mm) and elevation, but a stronger relationship with ecology – smaller species tend to be more terrestrial. Conclusions. Orogeny and climatic oscillations have interacted to generate high montane biodiversity in New Guinea via both localised diversification within montane habitats (centric endemism) and periodic dispersal across lowland regions (eccentric endemism). The correlation between extreme miniaturisation and terrestrial habits reflects a general trend in frogs, suggesting that ecological or physiological constraints limit niche usage by miniaturised frogs, even in extremely wet environments such as tropical mountains.
Signature-based detection of behavioural deviations in flight simulators - Experiments on FlightGear and JSBSim
Authors: Boisselle Vincent , Destefanis Giuseppe , De Marco Agostino , Adams Bram
Published: January 2018

Flight simulators are systems composed of numerous off-the-shelf components that allow pilots and maintenance crew to prepare for common and emergency flight procedures for a given aircraft model. A simulator must follow severe safety specifications to guarantee correct behaviour and requires an extensive series of prolonged manual tests to identify bugs or safety issues. In order to reduce the time required to test a new simulator version, this paper presents rule-based models able to automatically identify unexpected behaviour (deviations). The models represent signature trends in the behaviour of a successful simulator version that are compared to the behaviour of a new simulator version. Empirical analysis on nine types of injected faults in the popular FlightGear and JSBSim open source simulators shows that our approach does not miss any deviating behaviour considering faults which change the flight environment, and that we are able to find all the injected deviations in 4 out 7 functional faults and 75% of the deviations in 2 other faults.
Self-management open online trials in health [SMOOTH] an analysis of existing online trials [Protocol]
Authors: Price Amy , Burls Amanda , Vasanthan Lenny , Clarke Mike , Liew Su May , Brice Anne
Published: January 2018

BACKGROUND: The use of public engagement and self-management in online clinical trials is growing with benefits, boundaries and minimal methodological guidance. This analysis explores whether running self-recruited online trials can provide trustworthy and useful answers to research questions. AIM: To systematically explore existing self-recruited online randomized controlled trials of self-management interventions and analyze the trials to assess their strengths and weaknesses, the quality of trials reporting and to report how participants were involved in the research process. METHODS: The Online Randomized Controlled Trials of Health Information Database (ORCHID) will be used as a sampling framework to identify a subset of self-management self-recruited interventions. The trials will be used to explore the qualities of self-recruited online randomized controlled trials and to evaluate how useful they are for obtaining trustworthy answers to questions about health self-management and citizen research involvement. This research employs participatory action research where researchers and participants work as collaborators. SUMMARY: This analysis can provide an overall view of effective methods for online trials and to provide insights into integration for online trials development as early as the protocol planning stage.
Impacts of deforestation on passerine avifauna in the Opunohu Valley of Mo'orea, French Polynesia
Authors: ZoBell Vanessa M. , Furnas Brett J
Published: January 2018

Human expansion has negatively impacted biodiversity. Oceanic islands have some of the most diverse, endemic biodiversity. Endemism leads to vulnerability due to the isolated and discrete nature of oceanic islands. Birds are indicator species that adapt to change very quickly. By analyzing birds, we can investigate how changes in behavior and abundance may occur for different species in the future. Nine passerine bird species were studied with automated acoustic recording devices. Recording devices were places in agricultural, forest, and mixed habitats. Three invasive species preferred agriculture areas and low canopy cover, based on call frequency and detection probability. Native bird detectability was significantly lower than invasive bird detectability. Occupancy was above 0.8 for all species, except for the gray-green fruit dove that was >0.6. Native bird populations are at risk, based on their calling number and detection probability.
A 20-year comparison of shrimp populations in the Opunohu Valley of Moorea, French Polynesia
Authors: Goldstein Ari H
Published: January 2018

Global change is a central issue in many fields of science, particularly related to climate. One impact of climate change is changing weather patterns. This study focuses on the effects of changes in rainfall on freshwater stream ecosystems. Streams on small tropical islands are extremely fragile ecosystems. On the South Pacific volcanic island of Moorea, French Polynesia, lies the Opunohu Valley watershed. The Opunohu valley watershed is inhabited by three species of shrimp: Macrobrachium sp., Atyoida pilipes, and Caridina weberi. These shrimps are key components of their ecosystem because they break down organic material that falls into the stream thereby creating habitat for many other living organisms. Thus, they are a good measure of stream ecosystem health. This study focused on nine different sites throughout Opunohu valley. These sites had been surveyed in 1996 by C. Feldman. Comparisons to survey data collected in 1996 revealed no significant changes over time, demonstrating that shrimp populations have not declined or increased significantly in the last two decades.