bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of autotomy and regeneration on the locomotion and behavior or brittle stars (Echinodermata: Ophiuroidea) of Moorea, French Polynesia
Authors: Shaeffer Chandler M
Published: January 2018

Autotomy and regeneration of body parts is a defense mechanism that a multitude of taxa have evolved in order to escape predation. While both autotomy and regeneration are very commonly observed traits in brittle stars, little has been studied about them in relation to many aspects of their ecology, including its effects on their locomotion and behavior. This study compared the tendency to autotomize across brittle star taxa by way of a field survey and quantified the effects of autotomy on the locomotion and behavioral ecology of genus Ophiocoma. This was done by taking and analyzing videos the movements of eighteen individuals over the course of four weeks, comparing locomotive and behavioral changes over the course of the autotomization and regenerative process. Of the three genera of large epibenthic brittle star found, there was no one genus that seemed more likely to autotomize than another. When examining the effects of autotomy on Ophiocoma, there were very few differences among any of the sampling periods or treatments. Any changes occurred immediately after autotomy, but did not persist for more than that one sampling period, and yielded results comparable to those of pre-autotomy one week into regeneration. This may imply that Ophiocoma—and brittle stars as a whole—are extremely well adapted to autotomy as a defense strategy, more so than many other taxa who also employ autotomy as a defense mechanism.
Cryoelectrolysis - electrolytic processes in a frozen physiological saline medium
Authors: Lugnani Franco , Macchioro Matteo , Rubinsky Boris
Published: January 2018

Background: Cryoelectrolysis is a new minimally invasive tissue ablation surgical technique that combines the processes of electrolysis and solid/liquid phase transformation (freezing).

Method: Performing a typical cryoelectrolytic ablation protocol in a tissue simulant made of physiological saline gel with a pH dye, we observed several new physical and electrochemical phenomena of relevance to tissue ablation.

Results: We found that electrolysis can occur simultaneously with phase transformation, at high subzero freezing temperatures, above the eutectic temperature of the frozen salt solution. Another interesting finding is that electro-osmotic flows affect the process of cryoelectrolysis at the anode and cathode, in different ways.

Discussion: The observations are consistent with a mechanism involving ionic movement through the concentrated saline solution channels between ice crystals, at subfreezing temperatures above the eutectic. The findings in this paper may become the scientific basis for designing future cryoelectrolytic ablation surgery protocols.
Cryoelectrolysis - electrolytic processes in a frozen physiological saline medium
Authors: Lugnani Franco , Macchioro Matteo , Rubinsky Boris
Published: January 2018

Background: Cryoelectrolysis is a new minimally invasive tissue ablation surgical technique that combines the ablation techniques of electrolytic ablation with cryosurgery. The goal of this study is to examine the hypothesis that electrolysis can take place in a frozen aqueous saline solution.

Method: To examine the hypothesis we performed a cryoelectrolytic ablation protocol in which electrolysis and cryosurgery are delivered simultaneously in a tissue simulant made of physiological saline gel with a pH dye. We measured current flow, voltage and extents of freezing and pH dye staining.

Results: Using optical measurements and measurements of currents, we have shown that electrolysis can occur in frozen physiological saline, at high subzero freezing temperatures, above the eutectic temperature of the frozen salt solution. It was observed that electrolysis occurs when the tissue resides at high subzero temperatures during the freezing stage and essentially throughout the entire thawing stage. We also found that during thawing, the frozen lesion temperature raises rapidly to high subfreezing values and remains at those values throughout the thawing stage. Substantial electrolysis occurs during the thawing stage. Another interesting finding is that electro-osmotic flows affect the process of cryoelectrolysis at the anode and cathode, in different ways.

Discussion: The results showing that electrical current flow and electrolysis occur in frozen saline solutions imply a mechanism involving ionic movement in the fluid concentrated saline solution channels between ice crystals, at high subfreezing temperatures. Temperatures higher than the eutectic are required for the brine to be fluid. The particular pattern of temperature and electrical currents during the thawing stage of frozen tissue, can be explained by the large amounts of energy that must be removed at the outer edge of the frozen lesion because of the solid/liquid phase transformation on that interface.

Conclusion: Electrolysis can occur in a frozen domain at high subfreezing temperature, probably above the eutectic. It appears that the most effective period for delivering electrolytic currents in cryoelectrolysis is during the high subzero temperatures stage while freezing and immediately after cooling has stopped, throughout the thawing stage.
A scaled-down workflow for Illumina shotgun sequencing library preparation: lower input and improved performance at small fraction of the cost
Authors: Tan Jo Ann , Mikheyev Alexander S
Published: January 2018

The high cost of library preparation remains a major obstacle to sequencing large numbers of individual genomes. Illumina’s proprietary tagmentation technology allows for rapid and easy preparation of sequencing libraries, but remains prohibitively expensive for many users. Here we propose a modified version of the protocol, which uses Illumina reagents at 1/20th the scale. We show that the scaled-down protocol performs comparably to that of the manufacturer on a non-model insect genome. Surprisingly, the scaled-down protocol also produced 14% fewer PCR duplicates that the full-scale protocol. Since PCR duplicates effectively wasted redundant data, our protocol presented here can help save not just library preparation costs, but sequencing costs as well.
Protein structure refinement using a quantum mechanics-based chemical shielding predictor
Authors: Bratholm Lars A. , Jensen Jan H.
Published: January 2018

The accurate prediction of protein chemical shifts using quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of protein backbone and CB chemical shifts (ProCS15, PeerJ 2016, 3:e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: Simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1 - 0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If a residue-specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiment that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differs in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.
SNF: Synthesizing high performance NFV service chains
Authors: Katsikas Georgios P , Enguehard Marcel , Kuźniar Maciej , Maguire Jr. Gerald Q , Kostić Dejan
Published: January 2018

In this paper we introduce SNF, a framework that synthesizes (S) network function (NF) service chains by eliminating redundant I/O and repeated elements, while consolidating stateful cross layer packet operations across the chain. SNF uses graph composition and set theory to determine traffic classes handled by a service chain composed of multiple elements. It then synthesizes each traffic class using a minimal set of new elements that apply single-read-single-write and early-discard operations.

Our SNF prototype takes a baseline state-of-the-art network functions virtualization (NFV) framework to the level of performance required for practical NFV service deployments. Software-based SNF realizes long (up to 10 NFs) and stateful service chains that achieve line-rate 40 Gbps throughput (up to 8.5x greater than the baseline NFV framework). Hardware-assisted SNF, using a commodity OpenFlow switch, shows that our approach scales at 40 Gbps for Internet Service Provider-level NFV deployments.
3D-Analysis of a non-planispiral ammonoid from the Hunsrück Slate: natural or pathological variation?
Authors: Stilkerich Julia , Smrecak Trisha A , De Baets Kenneth
Published: January 2018

We herein examine the only known non-planispirally coiled early Devonian ammonoid, the holotype specimen of Ivoites opitzi, to investigate if the host was encrusted in vivo and if these sclerobionts were responsible for the trochospiral coiling observed on this unique specimen. To test if the presence of runner-like sclerobionts infested the historically collected specimen of Ivoites opitzi during its life, we used microCT to produce a three-dimensional model of the surface of the specimen. Our results indicate that sclerobionts grew across the outer rim (venter) on both sides of the ammonoid conch at exactly the location where the deviation from the planispiral was recognized, and where subsequent ammonoid growth would likely preclude encrustation. This indicates in vivo encrustation of the I. opitzi specimen, and represents the earliest documentation of the phenomenon. Further, this suggests that non-planispiral coiling in I. opitzi was pathologically induced and does not represent natural morphological variation in the species. Despite the observed anomalies in coiling, the specimen reached adulthood and retains important identifying morphological features, suggesting the ammonoid was minimally impacted by encrustation in life. As such, appointing a new type specimen – as suggested by some authors – for the species is not necessary. In addition, we identify the sclerobionts responsible for modifying the coiling of this specimen as hederelloids, a peculiar group of sclerobionts likely related to phoronids. Hederelloids in the Devonian are commonly found encrusting on fossils collected in moderately deep environments within the photic zone and are rarely documented in dysphotic and aphotic samples. This indicates that when the ammonoid was encrusted it lived within the euphotic zone and supports the latest interpretations of the Hunsrück Slate depositional environment.
A systematic literature review of how mutation testing supports test activities
Authors: Zhu Qianqian , Panichella Annibale , Zaidman Andy
Published: January 2018

Mutation testing has been very actively investigated by researchers since the 1970s and remarkable advances have been achieved in its concepts, theory, technology and empirical evidence. While the latest realisations have been summarised by existing literature review, we lack insight into how mutation testing is actually applied. Our goal is to identify and classify the main applications of mutation testing and analyse the level of replicability of empirical studies related to mutation testing. To this aim, this paper provides a systematic literature review on the application perspective of mutation testing based on a collection of 159 papers published between 1981 and 2015. In particular, we analysed in which testing activities mutation testing is used, which mutation tools and which mutation operators are employed. Additionally, we also investigated how the core inherent problems of mutation testing, i.e. the equivalent mutant problem and the high computational cost, are addressed during the actual usage. The results show that most studies use mutation testing as an assessment tool targeting unit tests, and many of the supporting techniques for making mutation testing applicable in practice are still underdeveloped. Based on our observations, we made nine recommendations for the future work, including an important suggestion on how to report mutation testing in testing experiments in an appropriate manner.
A laid-­back trip through the Hennigian forests (Notes from naturalists)
Authors: Mavrodiev Evgeny V , Dell Christopher A.
Published: January 2018

Binary matrix with an a priori defined plesiomorphic character-­state may be simply re-­written as a set of branching diagrams (as a “Hennigian forest”). The last might be analyzed by the average consensus method. This procedure eventually avoids the taxon-­character matrix from the analysis of the data. Within this framework, the criteria of the best topologies based on the character-­state changes are unnecessary. The solely ‘reversal’‐based groups always appear within the average consensus topologies despite the lack of direct evidence from the primary data.
A laid-­back trip through the Hennigian forests (Notes from naturalists)
Authors: Mavrodiev Evgeny V , Dell Christopher A.
Published: January 2018

Binary matrix with an a priori defined plesiomorphic character-­state may be re-­written as a set of branching diagrams (as a “Hennigian forest”). The last might be analyzed by the average consensus method. This procedure eventually avoids the taxon-­character matrix from the analysis of the data. Within this framework, the criteria of the best topologies based on the character-­state changes are unnecessary. The solely ‘reversal’‐based groups are always appear within the average consensus topologies despite the lack of direct evidence from the primary data.
A laid-­back trip through the Hennigian forests (Notes from Naturalists)
Authors: Mavrodiev Evgeny V , Dell Christopher A.
Published: January 2018

Binary matrix with a priori defined plesiomorphic character‐state may be re-­written as a simple set of branching diagrams (as a “Hennigian forest”). The last might be analyzed by the average consensus method. This procedure eventually avoids the taxon-­‐character matrix from the analysis of the data. Within this framework, the criteria of the best topologies based on the character-­‐state changes are unnecessary. The solely ‘reversal’-­based groups are always appear within the average consensus topologies despite the lack of evidence from the primary data.
The outcomes of most aggressive interactions among closely related bird species are asymmetric
Authors: Martin Paul R , Freshwater Cameron , Ghalambor Cameron K
Published: January 2018

Aggressive interactions among closely related species are common. These can play an important role as a selective pressure shaping species, traits and assemblages. The nature of this selective pressure depends on whether the outcomes of aggressive contests are asymmetric between species (i.e., one species is consistently dominant), yet few studies have estimated the prevalence of asymmetric versus symmetric outcomes to aggressive contests. Here we use previously published data involving 26,656 interactions between 270 species pairs of birds from 26 taxonomic families to address the question: How often are aggressive interactions among closely related bird species asymmetric? We define asymmetry using (i) the proportion of contests won by one species, and (ii) statistical tests for asymmetric outcomes of aggressive contests. We calculate these asymmetries using data summed across different sites for each species pair, and compare results to asymmetries calculated using data separated by location. We find that 80% of species pairs had aggressive outcomes where one species won 80% or more of aggressive contests. We also find that the majority of aggressive interactions among closely related species show statistically significant asymmetries, and above a sample size of 52 interactions, all outcomes are asymmetric following binomial tests. Results using data partitioned by location showed similar patterns. Species pairs with dominance data from multiple sites showed the same dominance relationship across locations in 93% of the species pairs. Overall, our results suggest that the outcome of aggressive interactions among closely related species are usually consistent and asymmetric, and should thus favor ecological and evolutionary strategies specific to the position of a species within a dominance hierarchy.
Tet(C) gene transfer between Chlamydia suis strains occurs by homologous recombination after co-infection: Implications for spread of tetracycline-resistance among Chlamydiaceae
Authors: Marti Hanna , Kim Hoyon , Joseph Sandeep , Dojiri Stacey S , Read Timothy , Dean Deborah
Published: January 2018

Chlamydia suis is a swine pathogen that also causes zoonotic infections. Many strains contain a tet(C) cassette conferring tetracycline resistance originally acquired by horizontal gene transfer from a Gram-negative donor. As we and others have described the capacity for Chlamydiaceae to exchange DNA by homologous recombination, tet(C)-containing C. suis strains represent a potential source for antibiotic-resistance spread within and between Chlamydia species. Here, we examine the genetics of tet(C)-transfer among C. suis strains. Tetracycline-sensitive C. suis strain S45 was simultaneously or sequentially co-infected with tetracycline-resistant C. suis strains in McCoy cells. Potential recombinants were clonally purified by plaque assay. C. suis strain Rogers132, which lacks IS200/IS605 transposases, was the most efficient donor, producing three confirmed recombinants of 56 (5.4%) clones with a minimal inhibitory concentration (MIC) of ~8µg/mL. Resistance was stable when recombinants were grown initially in tetracycline at twice the MIC of S45 (0.032 µg/mL). Genomic analysis revealed that tet(C) had integrated into the S45 genome by homologous recombination at two sites in different recombinants: a 55kb exchange between nrqF and pckG, and a 175kb exchange between kdsA and cysQ. Neither site was associated with repeats or motifs associated with recombination hotspots. Our findings show that cassette transfer into S45 has low frequency, does not require IS200/IS605 transposases, is stable if initially grown in tetracycline, and results in multiple genomic configurations. We provide a model for stable cassette transfer to better understand the capability for cassette acquisition by Chlamydia species that infect humans, a matter of public health importance.
Development and characterization of 29 polymorphic microsatellite loci of Megalobrama pellegrini by next-generation sequencing technology and cross-species amplification in related species
Authors: Song Wen , Zhu Dongmei , Lv Yefeng , Wang Weimin
Published: January 2018

Megalobrama pellegrini is one of the economically important freshwater fish in China. Here, we developed 29 polymorphic microsatellite loci of M. pellegrini. The number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (HO), expected heterozygosity (HE) and polymorphic information content (PIC) ranged from 3 to 11 (mean±SD 5.4828±1.9571), 2.8708 to 9.6257 (mean±SD 5.0865±1.6681), 0.4333 to 0.9333 (mean±SD 0.7874±0.1213), 0.6627 to 0.9113 (mean±SD 0.7946±0.0751) and 0.5785 to 0.8868 (mean±SD 0.7439±0.0950), respectively. Cross-species amplification was successful at most loci for related species such as M. amblycephala, M. hoffmanni, M. skolkovii and Parabramis pekinensis. The transferability rate of the 29 polymorphic microsatellite markers in M. amblycephala, M. hoffmanni, M. skolkovii and P. pekinensis were 96.55%, 86.21%, 86.21% and 75.86%, respectively. These polymorphic microsatellites are not only useful in genetic study and conservation of M. pellegrini, but also an effective tool for identifying the related species. We could use 5 microsatellite markers (HHF-63, HHF-104, HHF-113, HHF-148, HHF-163) to distinguish the 5 species.
Are coupled file changes suggestions useful?
Authors: Ramadani Jasmin , Wagner Stefan
Published: January 2018

Background. Software maintenance is an important activity in the process of software engineering where over time maintenance team members leave and new members join. The identification of files being changes together frequently has been proposed several times. Yet, existing studies about these file changes ignore the feedback from developers as well as the impact on the performance of maintenance and rely on the analysis findings and expert evaluation.

Methods. We conducted an experiment with the goal to investigate the usefulness of coupled file changes during maintenance tasks when developers are inexperienced in programming or when they are new on the project. Using data mining on software repositories we can identify files that changed most frequently together in the past. We extract coupled file changes from the Git repository of a Java software system and join them with corresponding attributes from the versioning and issue tracking system and the project documentation. We present a controlled experiment involving 36 student participants where we investigate if coupled file change suggestions influence the correctness of the task solutions and the time to complete them.

Results. The results show that coupled file change suggestions significantly increase the correctness of the solutions. However, there is only a small effect on the time to complete the tasks. We also derived a set of the most useful attributes based on the developers feedback.

Discussion. Coupled file changes and a limited number of the proposed attributes are useful for inexperienced developers working on maintenance tasks whereby although the developers using these suggestions solved more tasks, they still need time to organize and understand and implement this information.
External bacterial diversity on bats in the southwestern United States: Changes in bacterial community structure above and below ground
Authors: Winter Ara S , Kimble Jason C , Young Jesse M , Buecher Debbie C. , Valdez Ernest W. , Hathaway Jennifer J.M. , Porras-Alfaro Andrea , Read Kaitlyn J. H. , Northup Diana E.
Published: January 2018

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide potential defenses against invading pathogens. However, we have little to no understanding of the external bacterial microbiome on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiomes due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiome communities, and the lack of white-nose syndrome (a newly emergent fungal disease of bats) presence in the Southwest. We studied the extent to which changes in distributions of bacteria on external bat surfaces are a function of geographic location and ecoregion, and whether the sampled bats were caught in caves or surface-netted. To test these variables we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 186 bats from 14 species sampled across southeastern New Mexico to northwestern Arizona. Community similarity patterns and random forest models, and generalized linear mixed-effects models show that factors such as location (e.g. cave-caught vs. surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of external bat bacteria in a WNS-free environment and provide a baseline of bat external microbiomes that can be explored for potential natural defenses against pathogens.
Highlights of the 1st Argentine Symposium of Young Bioinformatics Researchers (1SAJIB) organized by the ISCB RSG-Argentina
Authors: Parra R. Gonzalo , Defelipe Lucas A , Guzovsky A. Brenda , Monzon Alexander M , Cravero Fiorella , Mancini Estefanía , Moreyra Nicolás , Padilla Franzotti Carla L , Revuelta Maria V , Freiberger Maria I , Gonzalez Nahuel N , Gonzalez German A , Orts Facundo , Stocchi Nicolas , Hasenahuer Marcia A , Teppa Elin , Zea Diego J , Palopoli Nicolas
Published: January 2018

The 1st Argentine Symposium of Young Bioinformatics Researchers took place on 9-10 May 2016 at Universidad de Buenos Aires, Buenos Aires, Argentina. This event evolved from a previous meeting series known as Argentine Student Council Symposium that have been successfully organized since 2012 by the Regional Student Group of Argentina (RSG-Argentina). The change in name reflects the new vision of the organizing committee to gather together all students at Bachelor, Master and PhD levels, postdocs and researchers that are still not Principal Investigator. Here we summarize the main activities and outcomes from this year’s meeting and offer some insights into our future plans.
Cropping system diversification for food production in Mindanao rubber plantations: A rice cultivar mixture and rice intercropped with mungbean
Authors: Hondrade Rosa Fe , Hondrade Edwin , Zheng Lianqing , Elazegui Francisco , Duque JLE , Mundt Christopher C , Vera Cruz Casiana M , Garrett Karen A
Published: January 2018

Including food production in non-food systems, such as rubber plantations and biofuel or bioenergy crops, may contribute to household food security. We evaluated the potential for use of rice, mungbean, rice cultivar mixtures, and rice intercropped with mungbean in experiments planted in young rubber plantations in the Arakan Valley of Mindanao. Rice mixtures consisted of two- or three-row strips of cultivar Dinorado, a cultivar with higher value but lower yield, and high-yielding cultivar UPL Ri-5. Rice and mungbean intercropping treatments consisted of different combinations of two- or three-row strips of rice and mungbean. We used generalized linear mixed models to evaluate the yield of each crop alone and in the mixture or intercropping treatments, as well as a land equivalent ratio for yield, and weed biomass, the severity of panicle blast, brown spot, and brown leaf spot, and rice bug abundance. We also analyzed the yield ranking of each cropping system across site-year combinations to determine mean relative performance and yield stability. When weighted by their relative economic value, UPL Ri-5 had the highest mean performance, but with decreasing performance in low-yielding environments. A rice and mungbean intercropping system had the second highest performance, tied with high-value Dinorado but without decreasing performance in low-yielding environments. Rice and mungbean intercropped with rubber have been adapted by farmers in the Arakan Valley.
Simulating business processes of manufacturing SMEs on the cloud
Authors: Terstyanszky Gabor , Kiss Tamas , Ozkok Ahmet , Isler Veysi
Published: January 2018

Simulating the efficiency of business processes could reveal crucial bottlenecks for manufacturing companies and could lead to significant optimizations resulting in decreased time to market, more efficient resource utilization, and larger profit. While such business optimization software is widely utilized by larger companies, SMEs typically do not have the required expertise and resources to efficiently exploit these advantages. The aim of this work is to explore how simulation software vendors and consultancies can extend their portfolio to SMEs by providing business process optimization based on a cloud computing platform. By executing simulation runs on the cloud, software vendors and associated business consultancies can get access to large computing power and data storage capacity on demand, run large simulation scenarios on behalf of their clients, analyze simulation results, and advise their clients regarding process optimization. The solution is mutually beneficial for both vendor/consultant and the end-user SME. End-user companies will only pay for the service without requiring large upfront costs for software licenses and expensive hardware. Software vendors can extend their business towards the SME market with potentially huge benefits.
The effect of changing topography on the coordinated marching of locust nymphs
Authors: Amichay Guy , Ariel Gil , Ayali Amir
Published: January 2018

Collective motion has traditionally been studied in the lab in homogeneous, obstacle-free environments, with little work having been conducted with changing landscapes or topography. Here, the impact of spatial heterogeneity on the collective motion exhibited by marching desert locust nymphs was studied under controlled lab conditions. Our experimental circular arenas, incorporating a funnel-like narrowing followed by re-widening, did not constitute a major barrier to the locusts; but, rather, mimicked a changing topography in the natural environment. We examined its effects on macroscopic features of the locust collective behavior, as well as the any changes in their marching kinematics. A major finding was that of the limited extent to which the changing topography affected system-level features of the marching locust group, such as the order parameter and the fraction of walking individuals, despite increased crowding at the funnel. Overall, marching kinematics was also very little affected, suggesting that locust marching bands adjust to the environment, with little effect on the overall dynamics of the group. These findings are in contrast to recent theoretical results predicting that environmental heterogeneities qualitatively alter the dynamics of collectively moving particles; and highlight the crucial role of rapid individual plasticity and adaptability in the dynamics of flocks and swarms. Our study has revealed other important features of the marching behavior of the desert locust in addition to its robustness: the locusts demonstrated both, clear thigmotaxis and a tendency to spread-out and fill the available space.
SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies
Authors: Bergmann Frank T , Nickerson David , Waltemath Dagmar , Scharm Martin
Published: January 2018

The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications and co-simulation of SBML and CellML models. This online application allows for creating, editing, simulating and validating SED-ML documents. It lowers the bar on working with SED-ML documents and helps users create valid simulation descriptions for models in CellML and SBML formats.

Availability and Implementation: sysbioapps.dyndns.org/SED-ML_Web_Tools.
The relationship between sap flow density and environmental factors in the Yangtze River Delta region
Authors: Liu Xin , Zhang Bo , DeAngelis Donald L , Zhang Jinchi , Zhuang Jiayao , Han Cheng , Zhai Lu , Zhao Wenrui , Wang Ling
Published: January 2018

Transpiration is an important component of the water balance in forest ecosystems. Quercus acutissima and Cunninghamia lanceolata are two important, fast-growing and commercial tree species that have been extensively used for vegetation restoration, water conservation and building artificial forests in the Yangtze River Delta Region of China. The primary objective of this study was to characterize sap ﬂow densities of the two species by comparing diurnal, nocturnal and seasonal sap ﬂow patterns and their relationships with environmental factors. Sap ﬂow densities (Sd) were measured between September 2012 and August 2013 using the commercially-available thermal dissipation probes. Hourly meteorological data were measured in an open ﬁeld, located 200 m away from the study site. Standard meteorological data were logged hourly at this site, including photosynthetically active radiation (Par), air temperature (Ta), relative air humidity (Rh), vapor pressure deficit (Vpd) and precipitation (P). Soil water content (Swc) data were logged hourly in different layers at Q.acutissima and C.lanceolata forests. Results indicated that the mean Sd in summer was higher than that in spring and autumn, and was lowest in winter. The Sd of Q. acutissima showed distinct diurnal patterns during the growth period (between May and October), and C. lanceolata followed similar sap ﬂow patterns in all months except February. Nocturnal sap flow densities (Sdn) were noticeable and both species followed similar patterns during the growth period, in which Q. acutissima followed a power function from April to November and C. lanceolata followed similar patterns in all months except February. Pearson correlation analysis suggested that the sap flow density responded to environmental factors differently among each of the growing stages. The diurnal sap flow density (Sdd) was more sensitive to environmental factors than Sdn. The Sd during the growth period was more sensitive to environmental factors than in the dormant period. Par, Vpd and Ta were significantly correlated with Sdd in the whole year. In the nighttime, the sap flow density was also effected by the Vpd, Ta and Rh. The results of this study can be used to estimate the transpiration of Q. acutissima and C. lanceolata.
Why to choose Random Forest to predict rare species distribution with few samples in large undersampled areas? Three Asian crane species models provide supporting evidence
Authors: Mi Chunrong , Huettmann Falk , Guo Yumin , Han Xuesong , Wen Lijia
Published: January 2018

Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution, and more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane (Grus monacha, n=33), White-naped Crane (Grus vipio, n=40), and Black-necked Crane (Grus nigricollis, n=75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models) Besides, we developed an ensemble forecast by averaging predicted probability of above four models results. Commonly-used model performance metrics (Area under ROC (AUC) and true skill statistic (TSS)) were employed to evaluate model accuracy. Latest satellite tracking data and compiled literature data were used as two independent testing datasets to confront model predictions. We found Random Forest demonstrated the best performance for the most assessment method, provided a better model fit to the testing data, and achieved better species range maps for each crane species in undersampled areas. Random Forest has been generally available for more than 20 years, and by now, has been known to perform extremely well in ecological predictions. However, while increasingly on the rise its potential is still widely underused in conservation, (spatial) ecological applications and for inference. Our results show that it informs ecological and biogeographical theories as well as being suitable for conservation applications, specifically when the study area is undersampled. This method helps to save model-selection time and effort, and it allows robust and rapid assessments and decisions for efficient conservation.
A microservice-based portal for X-ray transient and variable sources
Authors: D'Agostino Daniele , Roverelli Luca , Zereik Gabriele , De Luca Andrea , Salvaterra Ruben , Belfiore Andrea , Lisini Gianni , Novara Giovanni , Tiengo Andrea
Published: January 2018

Modern soft X-ray observatories can yield unique insights into time domain astrophysics, and a huge amount of information is stored - and largely unexploited - in data archives. Like a treasure-hunt, the EXTraS project is harvesting the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon Imaging Camera (EPIC) instrument onboard the ESA XMM-Newton, in 16 years of observations. Part of this analysis is performed through a dedicated science gateway, the EXTraS portal, whose initial release is the subject of this paper. In particular the focus is on its light software architecture, based on the use of microservices, providing a better resilience and more decoupled development lifecycle with respect to the approaches followed by the most used science gateway toolkits. The full paper is available at http://ceur-ws.org/Vol- 1871/paper8.pdf
A tutorial on how to use Gradepro GDT Tool for writing reviews
Authors: Basu Arindam
Published: January 2018

This is a tutorial on how to use the GRADEPro GDT guidelines development tool for appraisal of articles. The tutorial assumes that the student has little experience of working with Gradepro and walks through in several steps how to use this tool. Grading of evidence is an essential action to be taken by practitioners of evidence based medicine and public health yet the tools are not very intuitive. Grading of evidence puts the focus of evidence appraisal on outcomes. Select outcomes first at most seven outcomes and use this tool to appraise articles and bodies of evidence. In this article, we shall use two articles -- one a primary study, and another, a Cochrane Review to critically appraise a body of evidence focused on health outcomes. We will then demonstrate that it is possible not only to appraise one outcome and an individual study but also bodies of studies such as that based on a Cochrane Meta analysis. Taking an example of grommet insertion for children with otitis media with effusion, we show the advantage of using a tool for setting up meta analysis and conducting web based analysis of literature data.
Haplotype distribution and connectivity of the white sea urchin Tripneustes ventricosus across the Brazilian biogeographic province
Authors: Godinho Wander O , Maggioni Rodrigo , Lacerda Ana L , Lotufo Tito M C
Published: January 2018

Sea urchins play important roles in marine ecosystems as key herbivores and some species have wide geographic range. The Atlantic white sea urchin Tripneustes ventricosus is abundant in many rock reefs of the eastern and western Atlantic, and may be found in high densities in Atolls and Archipelagos. Despite the importance of sea urchins in insular ecosystems, there is no study evaluating the genetic structure and the origin of the white sea urchin in isolated ecosystems. Such information is crucial to understand the connectivity and genetic diversity of these populations from the tropical Atlantic provinces. To evaluate the origin of the white sea urchin in Fernando de Noronha Archipelago and the genetic features of this population, we conducted studies on the population structure of the white sea urchin using mitochondrial DNA (COI), in two regions within the Brazilian biogeographic province and compared with other regions in the Atlantic. The white sea urchin from Fernando de Noronha was found to be genetically distinct, with FST ranging from 0.3 to 0.9 from other populations in Atlantic. The sharing of haplotypes between the Brazilian coast and the archipelago suggests that insular species derived from the Brazilian coast, rather than the East Atlantic. Moreover, all other Atlantic populations were genetically isolated, with low genetic diversity being a common characteristic among them (ranging from 0.0011 to 0.0022). The low connectivity found within populations might be related to the presence of soft barriers among the Brazilian biogeographic province. The low nucleotide diversity may also suggest that T. ventricosus may have undergone bottleneck processes at some stage of their evolution. This study has important implications on the geographic distribution, population structure and gene flow of the white sea urchin among the Atlantic regions. Further studies should evaluate the biological and ecological aspects of the species in both insular and continental marine ecosystems.
The nematode homologue of Mediator complex subunit 28, F28F8.5, is a critical regulator of C. elegans development
Authors: Kostrouchová Markéta , Kostrouch David , Chughtai Ahmed A , Kaššák Filip , Novotný Jan P. , Kostrouchová Veronika , Benda Aleš , Krause Michael W. , Saudek Vladimír , Kostrouchová Marta , Kostrouch Zdenek
Published: January 2018

The evolutionarily conserved Mediator complex is a critical player in regulating transcription. Comprised of approximately two dozen proteins, Mediator integrates diverse regulatory signals through direct protein-protein interactions that, in turn, modulate the influence of Mediator on RNA Polymerase II activity. One Mediator subunit, MED28, is known to interact with cytoplasmic structural proteins, providing a potential direct link between cytoplasmic dynamics and the control of gene transcription. Although identified in many animals and plants, MED28 is not present in yeast; no bona fide MED28 has been described previously in C. elegans. Here, we identify bioinformatically F28F8.5, an uncharacterized predicted protein, as the nematode homologue of MED28. As in other metazoa, F28F8.5 has dual nuclear and cytoplasmic localization and plays critical roles in the regulation of development. F28F8.5 is a vital gene and its null mutants have severely malformed gonads and do not reproduce. Our results indicate that F28F8.5 is a homologue of MED28 and suggest that the potential to link cytoplasmic and nuclear events is conserved between MED28 vertebrate and nematode homologues.
Identifying zooplankton community changes between shallow and upper-mesophotic reefs on the Mesoamerican Barrier Reef, Caribbean
Authors: Andradi-Brown Dominic A , Head Catherine , Exton Dan A , Hunt Christina L , Hendrix Alicia , Gress Erika , Rogers Alex D
Published: January 2018

Mesophotic coral ecosystems (MCEs, reefs 30 -150m) are understudied, yet the limited research conducted has been biased towards large sessile taxa, such as scleractinian corals and sponges, or mobile taxa such as fish. Here we investigate zooplankton communities on shallow reefs and MCEs around Utila, on the southern Mesoamerican Barrier Reef using planktonic light traps. Zooplankton samples were sorted into broad taxonomic groups. Our results indicate similar taxonomic zooplankton richness and overall biomass between shallow reefs and MCEs, but that abundance of larger bodied (>2 mm) zooplanktonic groups, including decapod crab zoea, mysid shrimps and peracarid crustaceans was higher on MCEs than shallow reefs. Our findings highlight the important of considering zooplankton when identifying broader reef community shifts across the shallow reef to MCE depth gradient.
MiCADO – Towards a microservice-based cloud application-level dynamic orchestrator
Authors: Visti Hannu , Kiss Tamas , Terstyanszky Gabor , Gesmier Gregoire , Winter Stephen
Published: January 2018

In order to satisfy end-user requirements, many scientific and commercial applications require access to dynamically adjustable infrastructure resources. Cloud computing has the potential to provide these dynamic capabilities. However, utilising these capabilities from application code is not trivial and requires application developers to understand low-level technical details of clouds. This paper investigates how a generic framework can be developed that supports the dynamic orchestration of cloud applications both at deployment and at run-time. The advantages and challenges of designing such framework based on microservices is analysed, and a generic framework, called MiCADO – (Microservices-based Cloud Application-level Dynamic Orchestrator) is proposed. A first prototype implementation of MiCADO to support data intensive commercial web applications is also presented.
Elucidating the diet and foraging ecology of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing
Authors: Aziz Sheema Abdul , Clements Gopalasamy Reuben , Peng Lee Yin , Campos-Arceiz Ahimsa , McConkey Kim R , Forget Pierre-Michel A.A. , Gan Han Ming
Published: January 2018

There is an urgent need to identify and understand the ecosystem services provided by threatened animal species such as flying foxes. The first step towards this is to obtain comprehensive data on their diet. However, the volant and nocturnal nature of flying foxes presents a challenging situation, and conventional microhistological approaches to studying their diet can be laborious and time-consuming, and provide incomplete information. We used Illumina Next-Generation Sequencing (NGS) as a novel, non-invasive method for analysing the diet of the island flying fox (Pteropus hypomelanus) on Tioman Island, Peninsular Malaysia. Through NGS analysis of flying fox droppings over eight months, we identified at least 29 Operationally Taxonomic Units comprising the diet of this giant pteropodid, spanning 19 genera and 18 different plant families, including one new family not previously recorded for pteropodid diet. NGS was just as successful as conventional microhistological analysis in detecting plant taxa from droppings, but also uncovered six additional plant taxa. The island flying fox’s diet appeared to be dominated by figs (Ficus sp.), which was the most abundant plant taxon detected in the droppings every single month. Our study has shown that NGS can add value to the conventional microhistological approach in identifying food plant species from flying fox droppings. However, accurate and detailed identification requires a comprehensive database of the relevant plant DNA, which may require collection of botanical specimens from the study site. Although this method cannot be used to quantify true abundance or proportion of plant species, nor plant parts consumed, it ultimately provides a very important first step towards identifying plant taxa in pteropodid diet.