ALBERT

Description: Publication and archival of scientific results is still commonly considered the responsability of classical publishing companies. Classical forms of publishing, however, which center around printed narrative articles, no longer seem well-suited in the digital age. In particular, there exist currently no efficient, reliable, and agreed-upon methods for publishing scientific datasets, which have become increasingly important for science. In this article, we propose to design scientific data publishing as a web-based bottom-up process, without top-down control of central authorities such as publishing companies. Based on a novel combination of existing concepts and technologies, we present a server network to decentrally store and archive data in the form of nanopublications, an RDF-based format to represent scientific data. We show how this approach allows researchers to publish, retrieve, verify, and recombine datasets of nanopublications in a reliable and trustworthy manner, and we argue that this architecture could be used as a low-level data publication layer to serve the Semantic Web in general. Our evaluation of the current network shows that this system is efficient and reliable.

Description: Probabilistic programming allows for automatic Bayesian inference on user-defined probabilistic models. Recent advances in Markov chain Monte Carlo (MCMC) sampling allow inference on increasingly complex models. This class of MCMC, known as Hamiltonian Monte Carlo, requires gradient information which is often not readily available. PyMC3 is a new open source probabilistic programming framework written in Python that uses Theano to compute gradients via automatic differentiation as well as compile probabilistic programs on-the-fly to C for increased speed. Contrary to other probabilistic programming languages, PyMC3 allows model specification directly in Python code. The lack of a domain specific language allows for great flexibility and direct interaction with the model. This paper is a tutorial-style introduction to this software package.

Description: The ubiquity of uncertainty across application domains generates a need for principled support for uncertainty management in semantically aware systems. A probabilistic ontology provides constructs for representing uncertainty in domain ontologies. While the literature has been growing on formalisms for representing uncertainty in ontologies, there remains little guidance in the knowledge engineering literature for how to design probabilistic ontologies. To address the gap, this paper presents the Uncertainty Modeling Process for Semantic Technology (UMP-ST), a new methodology for modeling probabilistic ontologies. To explain how the methodology works and to verify that it can be applied to different scenarios, this paper describes step-by-step the construction of a proof-of-concept probabilistic ontology. The resulting domain model can be used to support identification of fraud in public procurements in Brazil. While the case study illustrates the development of a probabilistic ontology in the PR-OWL probabilistic ontology language, the methodology is applicable to any ontology formalism that properly integrates uncertainty with domain semantics.

Description: Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.

Description: BackgroundLarge scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand,de novomethods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results.MethodsThese limitations motivated the development of a newde novometagenomic comparative method, called Simka. This method computes a large collection of standard ecological distances by replacing species counts byk-mer counts. Simka scales-up today’s metagenomic projects thanks to a new parallelk-mer counting strategy on multiple datasets.ResultsExperiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecological distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at thek-mer level is highly correlated with extremely precisede novocomparison techniques which rely on all-versus-all sequences alignment strategy or which are based on taxonomic profiling.

Description: Ascribing function to sequence in the absence of biological data is an ongoing challenge in bioinformatics. Differentiating the toxins of venomous animals from homologues having other physiological functions is particularly problematic as there are no universally accepted methods by which to attribute toxin function using sequence data alone. Bioinformatics tools that do exist are difficult to implement for researchers with little bioinformatics training. Here we announce a machine learning tool called ‘ToxClassifier’ that enables simple and consistent discrimination of toxins from non-toxin sequences with 〉99% accuracy and compare it to commonly used toxin annotation methods. ‘ToxClassifer’ also reports the best-hit annotation allowing placement of a toxin into the most appropriate toxin protein family, or relates it to a non-toxic protein having the closest homology, giving enhanced curation of existing biological databases and new venomics projects. ‘ToxClassifier’ is available for free, either to download (https://github.com/rgacesa/ToxClassifier) or to use on a web-based server (http://bioserv7.bioinfo.pbf.hr/ToxClassifier/).

Description: The information expressed in humanities datasets is inextricably tied to a wider discursive environment that is irreducible to complete formal representation. Humanities scholars must wrestle with this fact when they attempt to publish or consume structured data. The practice of “nanopublication,” which originated in the e-science domain, offers a way to maintain the connection between formal representations of humanities data and its discursive basis. In this paper we describe nanopublication, its potential applicability to the humanities, and our experience curating humanities nanopublications in the PeriodO period gazetteer.

Description: Recent advances in Natural Language Processing and Machine Learning provide us with the tools to build predictive models that can be used to unveil patterns driving judicial decisions. This can be useful, for both lawyers and judges, as an assisting tool to rapidly identify cases and extract patterns which lead to certain decisions. This paper presents the first systematic study on predicting the outcome of cases tried by the European Court of Human Rights based solely on textual content. We formulate a binary classification task where the input of our classifiers is the textual content extracted from a case and the target output is the actual judgment as to whether there has been a violation of an article of the convention of human rights. Textual information is represented using contiguous word sequences, i.e., N-grams, and topics. Our models can predict the court’s decisions with a strong accuracy (79% on average). Our empirical analysis indicates that the formal facts of a case are the most important predictive factor. This is consistent with the theory of legal realism suggesting that judicial decision-making is significantly affected by the stimulus of the facts. We also observe that the topical content of a case is another important feature in this classification task and explore this relationship further by conducting a qualitative analysis.

Description: We consider the problem of detecting and quantifying the periodic component of a function given noise-corrupted observations of a limited number of input/output tuples. Our approach is based on Gaussian process regression, which provides a flexible non-parametric framework for modelling periodic data. We introduce a novel decomposition of the covariance function as the sum of periodic and aperiodic kernels. This decomposition allows for the creation of sub-models which capture the periodic nature of the signal and its complement. To quantify the periodicity of the signal, we derive a periodicity ratio which reflects the uncertainty in the fitted sub-models. Although the method can be applied to many kernels, we give a special emphasis to the Matérn family, from the expression of the reproducing kernel Hilbert space inner product to the implementation of the associated periodic kernels in a Gaussian process toolkit. The proposed method is illustrated by considering the detection of periodically expressed genes in thearabidopsisgenome.

Description: Drug repositioning methods attempt to identify novel therapeutic indications for marketed drugs. Strategies include the use of side-effects to assign new disease indications, based on the premise that both therapeutic effects and side-effects are measurable physiological changes resulting from drug intervention. Drugs with similar side-effects might share a common mechanism of action linking side-effects with disease treatment, or may serve as a treatment by “rescuing” a disease phenotype on the basis of their side-effects; therefore it may be possible to infer new indications based on the similarity of side-effect profiles. While existing methods leverage side-effect data from clinical studies and drug labels, evidence suggests this information is often incomplete due to under-reporting. Here, we describe a novel computational method that uses side-effect data mined from social media to generate a sparse undirected graphical model using inverse covariance estimation with ℓ1-norm regularization. Results show that known indications are well recovered while current trial indications can also be identified, suggesting that sparse graphical models generated using side-effect data mined from social media may be useful for computational drug repositioning.

Description: Edge preserving filters aim to simplify the representation of images (e.g., by reducing noise or eliminating irrelevant detail) while preserving their most significant edges. These filters are typically nonlinear and locally smooth the image structure while minimizing both blurring and over-sharpening of visually important edges. Here we present the Alternating Guided Filter (AGF) that achieves edge preserving smoothing by combining two recently introduced filters: the Rolling Guided Filter (RGF) and the Smooth and iteratively Restore Filter (SiR). We show that the integration of RGF and SiR in an alternating iterative framework results in a new smoothing operator that preserves significant image edges while effectively eliminating small scale details. The AGF combines the large scale edge and local intensity preserving properties of the RGF with the edge restoring properties of the SiR while eliminating the drawbacks of both previous methods (i.e., edge curvature smoothing by RGF and local intensity reduction and restoration of small scale details near large scale edges by SiR). The AGF is simple to implement and efficient, and produces high-quality results. We demonstrate the effectiveness of AGF on a variety of images, and provide a public code to facilitate future studies.

Description: 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.

Description: Scaling up psychotherapy services such as for addiction counseling is a critical societal need. One challenge is ensuring quality of therapy, due to the heavy cost of manual observational assessment. This work proposes a speech technology-based system to automate the assessment of therapist empathy—a key therapy quality index—from audio recordings of the psychotherapy interactions. We designed a speech processing system that includes voice activity detection and diarization modules, and an automatic speech recognizer plus a speaker role matching module to extract the therapist’s language cues. We employed Maximum Entropy models, Maximum Likelihood language models, and a Lattice Rescoring method to characterize highvs.low empathic language. We estimated therapy-session level empathy codes using utterance level evidence obtained from these models. Our experiments showed that the fully automated system achieved a correlation of 0.643 between expert annotated empathy codes and machine-derived estimations, and an accuracy of 81% in classifying highvs.low empathy, in comparison to a 0.721 correlation and 86% accuracy in the oracle setting using manual transcripts. The results show that the system provides useful information that can contribute to automatic quality insurance and therapist training.

Description: Software process improvement (SPI) has been around for decades: frameworks are proposed, success factors are studied, and experiences have been reported. However, the sheer mass of concepts, approaches, and standards published over the years overwhelms practitioners as well as researchers. What is out there? Are there new trends and emerging approaches? What are open issues? Still, we struggle to answer these questions about the current state of SPI and related research. In this article, we present results from an updated systematic mapping study to shed light on the field of SPI, to develop a big picture of the state of the art, and to draw conclusions for future research directions. An analysis of 769 publications draws a big picture of SPI-related research of the past quarter-century. Our study shows a high number of solution proposals, experience reports, and secondary studies, but only few theories and models on SPI in general. In particular, standard SPI models like CMMI and ISO/IEC 15,504 are analyzed, enhanced, and evaluated for applicability in practice, but these standards are also critically discussed, e.g., from the perspective of SPI in small-to-medium-sized companies, which leads to new specialized frameworks. New and specialized frameworks account for the majority of the contributions found (approx. 38%). Furthermore, we find a growing interest in success factors (approx. 16%) to aid companies in conducting SPI and in adapting agile principles and practices for SPI (approx. 10%). Beyond these specific topics, the study results also show an increasing interest into secondary studies with the purpose of aggregating and structuring SPI-related knowledge. Finally, the present study helps directing future research by identifying under-researched topics awaiting further investigation.

Description: Background. Today, redundancy in source code, so-called “clones” caused by copy&paste can be found reliably using clone detection tools. Redundancy can arise also independently, however, not caused by copy&paste. At present, it is not clear how onlyfunctionally similar clones(FSC) differ from clones created by copy&paste. Our aim is to understand and categorise the syntactical differences in FSCs that distinguish them from copy&paste clones in a way that helps clone detection research.Methods. We conducted an experiment using known functionally similar programs in Java and C from coding contests. We analysed syntactic similarity with traditional detection tools and explored whether concolic clone detection can go beyond syntax. We ran all tools on 2,800 programs and manually categorised the differences in a random sample of 70 program pairs.Results. We found no FSCs where complete files were syntactically similar. We could detect a syntactic similarity in a part of the files in

Description: Ebooks of the future may respond to the emotional experience of the reader. (Neuro-) physiological measures could capture a reader’s emotional state and use this to enhance the reading experience by adding matching sounds or to change the storyline therewith creating a hybrid art form in between literature and gaming. We describe the theoretical foundation of the emotional and creative brain and review the neurophysiological indices that can be used to drive future ebook interactivity in a real life situation. As a case study, we report the neurophysiological measurements of a bestselling author during nine days of writing which can potentially be used later to compare them to those of the readers. In designated calibration blocks, the artist wrote emotional paragraphs for emotional (IAPS) pictures. Analyses showed that we can reliably distinguish writing blocks from resting but we found no reliable differences related to the emotional content of the writing. The study shows that measurements of EEG, heart rate (variability), skin conductance, facial expression and subjective ratings can be done over several hours a day and for several days in a row. In follow-up phases, we will measure 300 readers with a similar setup.

Description: Our aim was to determine the possibility of detecting cognitive emotion information (neutral, disgust, shameful, “sensory pleasure”) by using a remote eye tracker within an approximate range of 1 meter. Our implementation was based on a self-learning ANN used for profile building, emotion status identification and recognition. Participants of the experiment were provoked with audiovisual stimuli (videos with sounds) to measure the emotional feedback. The proposed system was able to classify each felt emotion with an average of 90% accuracy (2 second measuring interval).

Description: In this work, DAE Tools modelling, simulation and optimisation software, its programming paradigms and main features are presented. The current approaches to mathematical modelling such as the use of modelling languages and general-purpose programming languages are analysed. The common set of capabilities required by the typical simulation software are discussed, and the shortcomings of the current approaches recognised. A new hybrid approach is introduced, and the modelling languages and the hybrid approach are compared in terms of the grammar, compiler, parser and interpreter requirements, maintainability and portability. The most important characteristics of the new approach are discussed, such as: (1) support for the runtime model generation; (2) support for the runtime simulation set-up; (3) support for complex runtime operating procedures; (4) interoperability with the third party software packages (i.e. NumPy/SciPy); (5) suitability for embedding and use as a web application or software as a service; and (6) code-generation, model exchange and co-simulation capabilities. The benefits of an equation-based approach to modelling, implemented in a fourth generation object-oriented general purpose programming language such as Python are discussed. The architecture and the software implementation details as well as the type of problems that can be solved using DAE Tools software are described. Finally, some applications of the software at different levels of abstraction are presented, and its embedding capabilities and suitability for use as a software as a service is demonstrated.

Description: Container-based application deployments have received significant attention in recent years. Operating system virtualization based on containers as a mechanism to deploy and manage complex, large-scale software systems has become a popular mechanism for application deployment and operation. Packaging application components into self-contained artifacts has brought substantial flexibility to developers and operation teams alike. However, this flexibility comes at a price. Pracitioners need to respect numerous constraints ranging from security and compliance requirements, to specific regulatory conditions. Fulfilling these requirements is especially challenging in specialized domains with large numbers of stakeholders. Moreover, the rapidly growing number of container images to be managed due to the introduction of new or updated applications and respective components, leads to significant challenges for container management and adaptation. In this paper, we introduce Smart Brix, a framework for continuous evolution of container application deployments that tackles these challenges. Smart Brix integrates and unifies concepts of continuous integration, runtime monitoring, and operational analytics. Furthermore, it allows practitioners to define generic analytics and compensation pipelines composed of self-assembling processing components to autonomously validate and verify containers to be deployed. We illustrate the feasibility of our approach by evaluating our framework using a case study from the smart city domain. We show that Smart Brix is horizontally scalable and runtime of the implemented analysis and compensation pipelines scales linearly with the number of container application packages.

Description: We propose a multi-scale image fusion scheme based on guided filtering. Guided filtering can effectively reduce noise while preserving detail boundaries. When applied in an iterative mode, guided filtering selectively eliminates small scale details while restoring larger scale edges. The proposed multi-scale image fusion scheme achieves spatial consistency by using guided filtering both at the decomposition and at the recombination stage of the multi-scale fusion process. First, size-selective iterative guided filtering is applied to decompose the source images into approximation and residual layers at multiple spatial scales. Then, frequency-tuned filtering is used to compute saliency maps at successive spatial scales. Next, at each spatial scale binary weighting maps are obtained as the pixelwise maximum of corresponding source saliency maps. Guided filtering of the binary weighting maps with their corresponding source images as guidance images serves to reduce noise and to restore spatial consistency. The final fused image is obtained as the weighted recombination of the individual residual layers and the mean of the approximation layers at the coarsest spatial scale. Application to multiband visual (intensified) and thermal infrared imagery demonstrates that the proposed method obtains state-of-the-art performance for the fusion of multispectral nightvision images. The method has a simple implementation and is computationally efficient.

Description: Synthesizing human movement is useful for most applications where the use of avatars is required. These movements should be as realistic as possible and thus must take into account anthropometric characteristics (weight, height, etc.), gender, and the performance of the activity being developed. The aim of this study is to develop a new methodology based on the combination of principal component analysis and partial least squares regression model that can generate realistic motion from a set of data (gender, anthropometry and performance). A total of 18 volunteer runners have participated in the study. The joint angles of the main body joints were recorded in an experimental study using 3D motion tracking technology. A five-step methodology has been employed to develop a model capable of generating a realistic running motion. The described model has been validated for running motion, showing a highly realistic motion which fits properly with the real movements measured. The described methodology could be applied to synthesize any type of motion: walking, going up and down stairs, etc. In future work, we want to integrate the motion in realistic body shapes, generated with a similar methodology and from the same simple original data.

Description: Three-dimensional (3D) data of many kinds is produced at an increasing rate throughout all scientific disciplines. The Portable Document Format (PDF) is the de-facto standard for the exchange of electronic documents and allows for embedding three-dimensional models. Therefore, it is a well-suited medium for the visualization and the publication of this kind of data. The generation of the appropriate files has been cumbersome so far. This article presents the first release of a software toolbox which integrates the complete workflow for generating 3D model files and ready-to-publish 3D PDF documents for scholarly publications in a consolidated working environment. It can be used out-of-the-box as a simple working tool or as a basis for specifically tailored solutions. A comprehensive documentation, an example project and a project wizard facilitate the customization. It is available royalty-free and for Windows, MacOS and Linux.

Description: The reality gap is the discrepancy between simulation and reality—the same behavioural algorithm results in different robot swarm behaviours in simulation and in reality (with real robots). In this paper, we study the effect of the reality gap on the psychophysiological reactions of humans interacting with a robot swarm. We compare the psychophysiological reactions of 28 participants interacting with a simulated robot swarm and with a real (non-simulated) robot swarm. Our results show that a real robot swarm provokes stronger reactions in our participants than a simulated robot swarm. We also investigate how to mitigate the effect of the reality gap (i.e., how to diminish the difference in the psychophysiological reactions between reality and simulation) by comparing psychophysiological reactions in simulation displayed on a computer screen and psychophysiological reactions in simulation displayed in virtual reality. Our results show that our participants tend to have stronger psychophysiological reactions in simulation displayed in virtual reality (suggesting a potential way of diminishing the effect of the reality gap).

Description: Two cross-sectional studies investigated the effects of competition and cooperation with virtual players on exercise performance in an immersive Virtual reality (VR) cycle exergame. Study 1 examined the effects of: (1) self-competition whereby participants played the exergame while competing against a replay of their previous exergame session (Ghost condition), and (2) playing the exergame with a virtual trainer present (Trainer condition) on distance travelled and calories expended while cycling. Study 2 examined the effects of (1) competition with a virtual trainer system (Competitive condition) and (2) cooperation with a virtual trainer system (Cooperative condition). Post exergame enjoyment and motivation were also assessed.The results of Study 1 showed that the trainer system elicited a lesser distance travelled than when playing with a ghost or on one’s own. These results also showed that competing against a ghost was more enjoyable than playing on one’s own or with the virtual trainer. There was no significant difference between the participants’ rated enjoyment and motivation and their distance travelled or calories burned. The findings of Study 2 showed that the competitive trainer elicited a greater distance travelled and caloric expenditure, and was rated as more motivating. As in Study 1, enjoyment and motivation were not correlated with distance travelled and calories burned.ConclusionTaken together, these results demonstrate that a competitive experience in exergaming is an effective tool to elicit higher levels of exercise from the user, and can be achieved through virtual substitutes for another human player.

Description: We describe a method for assessing data set complexity based on the estimation of the underlining probability distribution and Hellinger distance. In contrast to some popular complexity measures, it is not focused on the shape of a decision boundary in a classification task but on the amount of available data with respect to the attribute structure. Complexity is expressed in terms of graphical plot, which we call complexity curve. It demonstrates the relative increase of available information with the growth of sample size. We perform theoretical and experimental examination of properties of the introduced complexity measure and show its relation to the variance component of classification error. We then compare it with popular data complexity measures on 81 diverse data sets and show that it can contribute to explaining performance of specific classifiers on these sets. We also apply our methodology to a panel of simple benchmark data sets, demonstrating how it can be used in practice to gain insights into data characteristics. Moreover, we show that the complexity curve is an effective tool for reducing the size of the training set (data pruning), allowing to significantly speed up the learning process without compromising classification accuracy. The associated code is available to download at:https://github.com/zubekj/complexity_curve(open source Python implementation).

Description: Summary.Differential Evolution Entirely Parallel (DEEP) package is a software for finding unknown real and integer parameters in dynamical models of biological processes by minimizing one or even several objective functions that measure the deviation of model solution from data. Numerical solutions provided by the most efficient global optimization methods are often problem-specific and cannot be easily adapted to other tasks. In contrast, DEEP allows a user to describe both mathematical model and objective function in any programming language, such asR,OctaveorPythonand others. Being implemented in C, DEEP demonstrates as good performance as the top three methods from CEC-2014 (Competition on evolutionary computation) benchmark and was successfully applied to several biological problems.Availability.DEEP method is an open source and free software distributed under the terms of GPL licence version 3. The sources are available athttp://deepmethod.sourceforge.net/and binary packages for Fedora GNU/Linux are provided for RPM package manager athttps://build.opensuse.org/project/repositories/home:mackoel:compbio.

Description: We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master’s course at the Universidad Autónoma de Madrid (Spain), the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Order. It also allows a simple representation of misfolded conformations and their free energy. These concepts will motivate evolutionary questions, which we will address by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material (see ‘Data Availability’) to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

Description: Academic publication metadata can be used to analyze the collaboration, productivity and hot topic trends of a research community. In this paper, we study a specific group of authors, namely the top active authors. They are defined as the top 1% authors with uninterrupted and continuous presence in scientific publications over a time window. We take the top active authors in the Computer Science (CS) community over different time windows in the past 50 years, and use them to analyze collaboration, productivity and topic trends. We show that (a) the top active authors are representative of the overall population; (b) the community is increasingly moving in the direction of Team Research, with increased level and degree of collaboration; and (c) the research topics are increasingly inter-related. By focusing on the top active authors, it helps visualize these trends better. Besides, the observations from top active authors also shed light on design of better evaluation framework and resource management for policy makers in academia.

Description: We describe and experimentally validate a question-asking framework for machine-learned linguistic knowledge about human emotions. Using the Socratic method as a theoretical inspiration, we develop an experimental method and computational model for computers to learn subjective information about emotions by playing emotion twenty questions (EMO20Q), a game of twenty questions limited to words denoting emotions. Using human–human EMO20Q data we bootstrap a sequential Bayesian model that drives a generalized pushdown automaton-based dialog agent that further learns from 300 human–computer dialogs collected on Amazon Mechanical Turk. The human–human EMO20Q dialogs show the capability of humans to use a large, rich, subjective vocabulary of emotion words. Training on successive batches of human–computer EMO20Q dialogs shows that the automated agent is able to learn from subsequent human–computer interactions. Our results show that the training procedure enables the agent to learn a large set of emotion words. The fully trained agent successfully completes EMO20Q at 67% of human performance and 30% better than the bootstrapped agent. Even when the agent fails to guess the human opponent’s emotion word in the EMO20Q game, the agent’s behavior of searching for knowledge makes it appear human-like, which enables the agent to maintain user engagement and learn new, out-of-vocabulary words. These results lead us to conclude that the question-asking methodology and its implementation as a sequential Bayes pushdown automaton are a successful model for the cognitive abilities involved in learning, retrieving, and using emotion words by an automated agent in a dialog setting.

Description: Common tasks in document analysis, such as binarization, line extraction etc., are still considered difficult for highly degraded text documents. Having reliable fundamental information regarding the characters of the document, such as the distribution of character dimensions and stroke width, can significantly improve the performance of these tasks. We introduce a novel perspective of the image data which maps the evolution of connected components along the change in gray scale threshold. The maps reveal significant information about the sets of elements in the document, such as characters, noise, stains, and words. The information is further employed to improve state of the art binarization algorithm, and achieve automatically character size estimation, line extraction, stroke width estimation, and feature distribution analysis, all of which are hard tasks for highly degraded documents.

Description: Recently, assurance cases have received much attention in the field of software-based computer systems and IT services. However, software changes very often, and there are no strong regulations for software. These facts are two main challenges to be addressed in the development of software assurance cases. We propose a method of developing assurance cases by means of continuous revision at every stage of the system life cycle, including in operation and service recovery in failure cases. Instead of a regulator, dependability arguments are validated by multiple stakeholders competing with each other. This paper reported our experience with the proposed method in the case of Aspen education service. The case study demonstrates that continuous revisions enable stakeholders to share dependability problems across software life cycle stages, which will lead to the long-term improvement of service dependability.

Description: One of the main motivations behind social network analysis is the quest for understanding opinion formation and diffusion. Previous models have limitations, as they typically assume opinion interaction mechanisms based on thresholds which are either fixed or evolve according to a random process that is external to the social agent. Indeed, our empirical analysis on large real-world datasets such as Twitter, Meme Tracker, and Yelp, uncovers previously unaccounted for dynamic phenomena at population-level, namely the existence of distinctopinion formation phasesandsocial balancing. We also reveal that a phase transition from an erratic behavior to social balancing can be triggered by network topology and by the ratio of opinion sources. Consequently, in order to build a model that properly accounts for these phenomena, we propose a new (individual-level) opinion interaction model based on tolerance. As opposed to the existing opinion interaction models, the new tolerance model assumes that individual’s inner willingness to accept new opinions evolves over time according to basic human traits. Finally, by employing discrete event simulation on diverse social network topologies, we validate our opinion interaction model and show that, although the network size and opinion source ratio are important, the phase transition to social balancing is mainly fostered by the democratic structure of the small-world topology.

Description: A successful software project is the result of a complex process involving, above all, people. Developers are the key factors for the success of a software development process, not merely as executors of tasks, but as protagonists and core of the whole development process. This paper investigates social aspects among developers working on software projects developed with the support of Agile tools. We studied 22 open-source software projects developed using the Agile board of the JIRA repository. All comments committed by developers involved in the projects were analyzed and we explored whether the politeness of comments affected the number of developers involved and the time required to fix any given issue. Our results showed that the level of politeness in the communication process among developers does have an effect on the time required to fix issues and, in the majority of the analysed projects, it had a positive correlation with attractiveness of the project to both active and potential developers. The more polite developers were, the less time it took to fix an issue.

Description: Background.The monophyly of taxa is an important attribute of a phylogenetic tree. A lack of it may hint at shortcomings of either the tree or the current taxonomy, or can indicate cases of incomplete lineage sorting or horizontal gene transfer. Whichever is the reason, a lack of monophyly can misguide subsequent analyses. While monophyly is conceptually simple, it is manually tedious and time consuming to assess on modern phylogenies of hundreds to thousands of species.Results.The R packageMonoPhyallows assessment and exploration of monophyly of taxa in a phylogeny. It can assess the monophyly of genera using the phylogeny only, and with an additional input file any other desired higher order taxa or unranked groups can be checked as well.Conclusion.Summary tables, easily subsettable results and several visualization options allow quick and convenient exploration of monophyly issues, thus makingMonoPhya valuable tool for any researcher working with phylogenies.

Description: BackgroundNames used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae,Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed.MethodsWe analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential ofrbcLandmatKto resolve taxonomic entities within the bamboo subfamily and tribes.ResultsBased on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the generaPhyllostachysandPseudosasafrom the temperate “woody” bamboo tribe (Arundinarieae). Currently availablerbcLandmatKsequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant toDianthus chinensis(Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women.

Description: Timing Speculation (TS) is a widely known method for realizing better-than-worst-case systems. Aggressive clocking, realizable by TS, enable systems to operate beyond specified safe frequency limits to effectively exploit the data dependent circuit delay. However, the range of aggressive clocking for performance enhancement under TS is restricted by short paths. In this paper, we show that increasing the lengths of short paths of the circuit increases the effectiveness of TS, leading to performance improvement. Also, we propose an algorithm to efficiently add delay buffers to selected short paths while keeping down the area penalty. We present our algorithm results for ISCAS-85 suite and show that it is possible to increase the circuit contamination delay by up to 30% without affecting the propagation delay. We also explore the possibility of increasing short path delays further by relaxing the constraint on propagation delay and analyze the performance impact.

Description: In this paper, we describe a novel solution to the problem of virtual machine (VM) consolidation, otherwise known as VM-Packing, as applicable to Infrastructure-as-a-Service cloud data centers. Our solution relies on the observation that virtual machines are not infinitely variable in resource consumption. Generally, cloud compute providers offer them in fixed resource allocations. Effectively this makes all VMs of that allocation type (or instance type) generally interchangeable for the purposes of consolidation from a cloud compute provider viewpoint. The main contribution of this work is to demonstrate the advantages to our approach of deconstructing the VM consolidation problem into a two-step process of multidimensional bin packing. The first step is to determine the optimal, but abstract, solution composed of finite groups of equivalent VMs that should reside on each host. The second step selects concrete VMs from the managed compute pool to satisfy the optimal abstract solution while enforcing anti-colocation and preferential colocation of the virtual machines through VM contracts. We demonstrate our high-performance, deterministic packing solution generation, with over 7,500 VMs packed in under 2 min. We demonstrating comparable runtimes to other VM management solutions published in the literature allowing for favorable extrapolations of the prior work in the field in order to deal with larger VM management problem sizes our solution scales to.

Description: GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of a transcription factor on its target gene, so we created GRNsight. GRNsight automatically lays out either an unweighted or weighted network graph based on an Excel spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows, a Simple Interaction Format (SIF) text file, or a GraphML XML file. When a user uploads an input file specifying an unweighted network, GRNsight automatically lays out the graph using black lines and pointed arrowheads. For a weighted network, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. GRNsight is written in JavaScript, with diagrams facilitated by D3.js, a data visualization library. Node.js and the Express framework handle server-side functions. GRNsight’s diagrams are based on D3.js’s force graph layout algorithm, which was then extensively customized to support the specific needs of GRNs. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop. When a user mouses over an edge, the numerical value of the weight parameter is displayed. Visualizations can be modified by sliders that adjust the force graph layout parameters and through manual node dragging. GRNsight is best-suited for visualizing networks of fewer than 35 nodes and 70 edges, although it accepts networks of up to 75 nodes or 150 edges. GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains. GRNsight serves as an example of following and teaching best practices for scientific computing and complying with FAIR principles, using an open and test-driven development model with rigorous documentation of requirements and issues on GitHub. An exhaustive unit testing framework using Mocha and the Chai assertion library consists of around 160 automated unit tests that examine nearly 530 test files to ensure that the program is running as expected. The GRNsight application (http://dondi.github.io/GRNsight/) and code (https://github.com/dondi/GRNsight) are available under the open source BSD license.

Description: Identifying a temporal pattern of events is a fundamental task of online (real-time) verification. We present efficient schemes for online monitoring of events for identifying desired/undesired patterns of events. The schemes use preprocessing to ensure that the number of comparisons during run-time is minimized. In particular, the first comparison following the time point when an execution sub-sequence cannot be further extended to satisfy the temporal requirements halts the process that monitors the sub-sequence.

Description: OncoLnc is a tool for interactively exploring survival correlations, and for downloading clinical data coupled to expression data for mRNAs, miRNAs, or long noncoding RNAs (lncRNAs). OncoLnc contains survival data for 8,647 patients from 21 cancer studies performed by The Cancer Genome Atlas (TCGA), along with RNA-SEQ expression for mRNAs and miRNAs from TCGA, and lncRNA expression from MiTranscriptome beta. Storing this data gives users the ability to separate patients by gene expression, and then create publication-quality Kaplan-Meier plots or download the data for further analyses. OncoLnc also stores precomputed survival analyses, allowing users to quickly explore survival correlations for up to 21 cancers in a single click. This resource allows researchers studying a specific gene to quickly investigate if it may have a role in cancer, and the supporting data allows researchers studying a specific cancer to identify the mRNAs, miRNAs, and lncRNAs most correlated with survival, and researchers looking for a novel lncRNA involved with cancer lists of potential candidates. OncoLnc is available athttp://www.oncolnc.org.

Description: We presentencube—a qualitative, quantitative and comparative visualisation and analysis system, with application to high-resolution, immersive three-dimensional environments and desktop displays.encubeextends previous comparative visualisation systems by considering: (1) the integration of comparative visualisation and analysis into a unified system; (2) the documentation of the discovery process; and (3) an approach that enables scientists to continue the research process once back at their desktop. Our solution enables tablets, smartphones or laptops to be used as interaction units for manipulating, organising, and querying data. We highlight the modularity ofencube, allowing additional functionalities to be included as required. Additionally, our approach supports a high level of collaboration within the physical environment. We show how our implementation ofencubeoperates in a large-scale, hybrid visualisation and supercomputing environment using the CAVE2 at Monash University, and on a local desktop, making it a versatile solution. We discuss how our approach can help accelerate the discovery rate in a variety of research scenarios.

Description: It is a well-known fact that some criminals follow perpetual methods of operations known as modi operandi. Modus operandi is a commonly used term to describe the habits in committing crimes. These modi operandi are used in relating criminals to crimes for which the suspects have not yet been recognized. This paper presents the design, implementation and evaluation of a new method to find connections between crimes and criminals using modi operandi. The method involves generating a feature matrix for a particular criminal based on the flow of events of his/her previous convictions. Then, based on the feature matrix, two representative modi operandi are generated: complete modus operandi and dynamic modus operandi. These two representative modi operandi are compared with the flow of events of the crime at hand, in order to generate two other outputs: completeness probability (CP) and deviation probability (DP). CP and DP are used as inputs to a fuzzy inference system to generate a score which is used in providing a measurement for the similarity between the suspect and the crime at hand. The method was evaluated using actual crime data and ten other open data sets. In addition, comparison with nine other classification algorithms showed that the proposed method performs competitively with other related methods proving that the performance of the new method is at an acceptable level.

Description: Clawpack is a software package designed to solve nonlinear hyperbolic partial differential equations using high-resolution finite volume methods based on Riemann solvers and limiters. The package includes a number of variants aimed at different applications and user communities. Clawpack has been actively developed as an open source project for over 20 years. The latest major release, Clawpack 5, introduces a number of new features and changes to the code base and a new development model based on GitHub and Git submodules. This article provides a summary of the most significant changes, the rationale behind some of these changes, and a description of our current development model.

Description: End-user programming (EUP) is a common approach for helping ordinary people create small programs for their professional or daily tasks. Since end-users may not have programming skills or strong motivation for learning them, tools should provide what end-users want with minimal costs of learning –i.e., they must decrease the barriers to entry. However, it is often hard to address these needs, especially for fast-evolving domains such as the Web. To better understand these existing and ongoing challenges, we conducted two formative studies with Web users –a semi-structured interview study, and a Wizard-of-Oz study. The interview study identifies challenges that participants have with their daily experiences on the Web. The Wizard-of-Oz study investigates how participants would naturally explain three computational tasks to an interviewer acting as a hypothetical computer agent. These studies demonstrate a disconnect between what end-users want and what existing EUP systems support, and thus open the door for a path towards better support for end user needs. In particular, our findings include: (1) analysis of challenges that end-users experience on the Web with solutions; (2) seven core functionalities of EUP for addressing these challenges; (3) characteristics of non-programmers describing three common computation tasks; (4) design implications for future EUP systems.

Description: The study of social phenomena is becoming increasingly reliant on big data from online social networks. Broad access to social media data, however, requires software development skills that not all researchers possess. Here we present theIUNI Observatory on Social Media, an open analytics platform designed to facilitate computational social science. The system leverages a historical, ongoing collection of over 70 billion public messages from Twitter. We illustrate a number of interactive open-source tools to retrieve, visualize, and analyze derived data from this collection. The Observatory, now available atosome.iuni.iu.edu, is the result of a large, six-year collaborative effort coordinated by the Indiana University Network Science Institute.

Description: This report shares the experience during selection, implementation and maintenance phases of an electronic laboratory notebook (ELN) in a public–private partnership project and comments on user’s feedback. In particular, we address which time constraints for roll-out of an ELN exist in granted projects and which benefits and/or restrictions come with out-of-the-box solutions. We discuss several options for the implementation of support functions and potential advantages of open access solutions. Connected to that, we identified willingness and a vivid culture of data sharing as the major item leading to success or failure of collaborative research activities. The feedback from users turned out to be the only angle for driving technical improvements, but also exhibited high efficiency. Based on these experiences, we describe best practices for future projects on implementation and support of an ELN supporting a diverse, multidisciplinary user group based in academia, NGOs, and/or for-profit corporations located in multiple time zones.

Description: An object-oriented computational framework for the transformation of colour data and colour metric tensors is presented. The main idea of the design is to represent the transforms between spaces as compositions of objects from a class hierarchy providing the methods for both the transforms themselves and the corresponding Jacobian matrices. In this way, new colour spaces can be implemented on the fly by transforming from any existing colour space, and colour data in various formats as well as colour metric tensors and colour difference data can easily be transformed between the colour spaces. This reduces what normally requires several days of coding to a few lines of code without introducing a significant computational overhead. The framework is implemented in the Python programming language.

Description: PhilDB is an open-source time series database that supports storage of time series datasets that are dynamic; that is, it records updates to existing values in a log as they occur. PhilDB eases loading of data for the user by utilising an intelligent data write method. It preserves existing values during updates and abstracts the update complexity required to achieve logging of data value changes. It implements fast reads to make it practical to select data for analysis. Recent open-source systems have been developed to indefinitely store long-period high-resolution time series data without change logging. Unfortunately, such systems generally require a large initial installation investment before use because they are designed to operate over a cluster of servers to achieve high-performance writing of static data in real time. In essence, they have a ‘big data’ approach to storage and access. Other open-source projects for handling time series data that avoid the ‘big data’ approach are also relatively new and are complex or incomplete. None of these systems gracefully handle revision of existing data while tracking values that change. Unlike ‘big data’ solutions, PhilDB has been designed for single machine deployment on commodity hardware, reducing the barrier to deployment. PhilDB takes a unique approach to meta-data tracking; optional attribute attachment. This facilitates scaling the complexities of storing a wide variety of data. That is, it allows time series data to be loaded as time series instances with minimal initial meta-data, yet additional attributes can be created and attached to differentiate the time series instances when a wider variety of data is needed. PhilDB was written in Python, leveraging existing libraries. While some existing systems come close to meeting the needs PhilDB addresses, none cover all the needs at once. PhilDB was written to fill this gap in existing solutions. This paper explores existing time series database solutions, discusses the motivation for PhilDB, describes the architecture and philosophy of the PhilDB software, and performs an evaluation between InfluxDB, PhilDB, and SciDB.

Description: The lotus (Nelumbonaceae:NelumboAdans.) is a highly desired ornamental plant, comprising only two extant species, the sacred lotus (N. nuciferaGaerten.) with red flowers and the American lotus (N. luteaWilld.) with yellow flowers. Flower color is the most obvious difference of two species. To better understand the mechanism of flower color differentiation, the content of anthocyanins and the expression levels of four key structural genes (e.g.,DFR,ANS,UFGTandGST) were analyzed in two species. Our results revealed that anthocyanins were detected in red flowers, not yellow flowers. Expression analysis showed that no transcripts ofGSTgene and low expression level of threeUFGTgenes were detected in yellow flowers. In addition, three regulatory genes (NnMYB5,NnbHLH1andNnTTG1) were isolated from red flowers and showed a high similarity to corresponding regulatory genes of other species. Sequence analysis ofMYB5,bHLH1andTTG1in two species revealed striking differences in coding region and promoter region ofMYB5gene. Population analysis identified threeMYB5variants inNelumbo: a functional allele existed in red flowers and two inactive forms existed in yellow flowers. This result revealed that there was an association between allelic variation inMYB5gene and flower color difference. Yeast two-hybrid experiments showed that NnMYB5 interacts with NnbHLH1, NlbHLH1 and NnTTG1, and NnTTG1 also interacts with NnbHLH1 and NlbHLH1. The over-expression ofNnMYB5led to anthocyanin accumulation in immature seeds and flower stalks and up-regulation of expression ofTT19inArabidopsis. Therefore, NnMYB5 is a transcription activator of anthocyanin synthesis. This study helps to elucidate the function ofNnMYB5and will contribute to clarify the mechanism of flower coloration and genetic engineering of flower color in lotus.

Description: Sex expression and floral morphology studies are central to understand breeding behavior and to define the productive potential of plant genotypes. In particular, the new bioenergy cropJatropha curcasL. has been classified as a monoecious species. Nonetheless, there is no information about its reproductive diversity in the Mesoamerican region, which is considered its center of origin and diversification. Thus, we determined sex expression and floral morphology inJ. curcaspopulations from southern Mexico and Guatemala. Our results showed that most ofJ. curcasspecimens had typical inflorescences with separate sexes (monoecious); meanwhile, the rest were atypical (gynoecious, androecious, andromonoecious, androgynomonoecious). The most important variables to group these populations, based on a discriminant analysis, were: male flower diameter, female petal length and male nectary length. From southern Mexico “Guerrero” was the most diverse population, and “Centro” had the highest variability among the populations from Chiapas. A cluster analysis showed that the accessions from southern Mexico were grouped without showing any correlation with the geographical origin, while those accessions with atypical sexuality were grouped together. To answer the question of how informative are floral morphological traits compared to molecular markers, we perform a Mantel correlation test between the distance matrix generated in this study and the genetic distance matrix (AFLP) previously reported for the same accessions. We found significant correlation between data at the level of accessions. Our results contribute to design genetic improvement programs by using sexually and morphologically contrasting plants from the center of origin.

Description: Due to the rapid development of information technology, the Internet has gradually become a part of everyday life. People would like to communicate with friends to share their opinions on social networks. The diverse behavior on socials networks is an ideal reflection of users’ personality traits. Existing behavior analysis methods for personality prediction mostly extract behavior attributes with heuristic analysis. Although they work fairly well, they are hard to extend and maintain. In this paper, we utilize a deep learning algorithm to build a feature learning model for personality prediction, which could perform an unsupervised extraction of the Linguistic Representation Feature Vector (LRFV) activity without supervision from text actively published on the Sina microblog. Compared with other feature extractsion methods, LRFV, as an abstract representation of microblog content, could describe a user’s semantic information more objectively and comprehensively. In the experiments, the personality prediction model is built using a linear regression algorithm, and different attributes obtained through different feature extraction methods are taken as input of the prediction model, respectively. The results show that LRFV performs better in microblog behavior descriptions, and improves the performance of the personality prediction model.

Description: Background.While significant attention has been paid to the potential risk of pathogenic microbes aboard crewed spacecraft, the non-pathogenic microbes in these habitats have received less consideration. Preliminary work has demonstrated that the interior of the International Space Station (ISS) has a microbial community resembling those of built environments on Earth. Here we report the results of sending 48 bacterial strains, collected from built environments on Earth, for a growth experiment on the ISS. This project was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS).Results.Of the 48 strains sent to the ISS, 45 of them showed similar growth in space and on Earth using a relative growth measurement adapted for microgravity. The vast majority of species tested in this experiment have also been found in culture-independent surveys of the ISS. Only one bacterial strain showed significantly different growth in space.Bacillus safensisJPL-MERTA-8-2 grew 60% better in space than on Earth.Conclusions.The majority of bacteria tested were not affected by conditions aboard the ISS in this experiment (e.g., microgravity, cosmic radiation). Further work onBacillus safensiscould lead to interesting insights on why this strain grew so much better in space.

Description: Statistical analyses of biomechanical finite element (FE) simulations are frequently conducted on scalar metrics extracted from anatomically homologous regions, like maximum von Mises stresses from demarcated bone areas. The advantages of this approach are numerical tabulability and statistical simplicity, but disadvantages include region demarcation subjectivity, spatial resolution reduction, and results interpretation complexity when attempting to mentally map tabulated results to original anatomy. This study proposes a method which abandons the two aforementioned advantages to overcome these three limitations. The method is inspired by parametric random field theory (RFT), but instead uses a non-parametric analogue to RFT which permits flexible model-wide statistical analyses through non-parametrically constructed probability densities regarding volumetric upcrossing geometry. We illustrate method fundamentals using basic 1D and 2D models, then use a public model of hip cartilage compression to highlight how the concepts can extend to practical biomechanical modeling. The ultimate whole-volume results are easy to interpret, and for constant model geometry the method is simple to implement. Moreover, our analyses demonstrate that the method can yield biomechanical insights which are difficult to infer from single simulations or tabulated multi-simulation results. Generalizability to non-constant geometry including subject-specific anatomy is discussed.

Description: In this paper, we introduce a framework for implementing deep copy on top of MPI. The process is initiated by passing just the root object of the dynamic data structure. Our framework takes care of all pointer traversal, communication, copying and reconstruction on receiving nodes. The benefit of our approach is that MPI users can deep copy complex dynamic data structures without the need to write bespoke communication or serialize/deserialize methods for each object. These methods can present a challenging implementation problem that can quickly become unwieldy to maintain when working with complex structured data. This paper demonstrates our generic implementation, which encapsulates both approaches. We analyze the approach with a variety of structures (trees, graphs (including complete graphs) and rings) and demonstrate that it performs comparably to hand written implementations, using a vastly simplified programming interface. We make the source code available completely as a convenient header file.

Description: Software development is becoming more and more collaborative, emphasizing the role of end-users in the development process to make sure the final product will satisfy customer needs. This is especially relevant when developing Domain-Specific Modeling Languages (DSMLs), which are modeling languages specifically designed to carry out the tasks of a particular domain. While end-users are actually the experts of the domain for which a DSML is developed, their participation in the DSML specification process is still rather limited nowadays. In this paper, we propose a more community-aware language development process by enabling the active participation of all community members (both developers and end-users) from the very beginning. Our proposal, called Collaboro, is based on a DSML itself enabling the representation of change proposals during the language design and the discussion (and trace back) of possible solutions, comments and decisions arisen during the collaboration. Collaboro also incorporates a metric-based recommender system to help community members to define high-quality notations for the DSMLs. We also show how Collaboro can be used at the model-level to facilitate the collaborative specification of software models. Tool support is available both as an Eclipse plug-in a web-based solution.

Description: BackgroundAn increasing array of scientific fields face a “data deluge.” However, in many fields data are scarce, with implications for their epistemic status and ability to command funding. Consequently, they often attempt to develop infrastructure for data production, management, curation, and circulation. A component of a knowledge infrastructure may serve one or more scientific domains. Further, a single domain may rely upon multiple infrastructures simultaneously. Studying how domains negotiate building and accessing scarce infrastructural resources that they share with other domains will shed light on how knowledge infrastructures shape science.MethodsWe conducted an eighteen-month, qualitative study of scientists studying the deep subseafloor biosphere, focusing on the Center for Dark Energy Biosphere Investigations (C-DEBI) and the Integrated Ocean Drilling Program (IODP) and its successor, the International Ocean Discovery Program (IODP2). Our methods comprised ethnographic observation, including eight months embedded in a laboratory, interviews (n = 49), and document analysis.ResultsDeep subseafloor biosphere research is an emergent domain. We identified two reasons for the domain’s concern with data scarcity: limited ability to pursue their research objectives, and the epistemic status of their research. Domain researchers adopted complementary strategies to acquire more data. One was to establish C-DEBI as an infrastructure solely for their domain. The second was to use C-DEBI as a means to gain greater access to, and reconfigure, IODP/IODP2 to their advantage. IODP/IODP2 functions as infrastructure for multiple scientific domains, which creates competition for resources. C-DEBI is building its own data management infrastructure, both to acquire more data from IODP and to make better use of data, once acquired.DiscussionTwo themes emerge. One is data scarcity, which can be understood only in relation to a domain’s objectives. To justify support for public funding, domains must demonstrate their utility to questions of societal concern or existential questions about humanity. The deep subseafloor biosphere domain aspires to address these questions in a more statistically intensive manner than is afforded by the data to which it currently has access. The second theme is the politics of knowledge infrastructures. A single scientific domain may build infrastructure for itself and negotiate access to multi-domain infrastructure simultaneously. C-DEBI infrastructure was designed both as a response to scarce IODP/IODP2 resources, and to configure the data allocation processes of IODP/IODP2 in their favor.

Description: Opportunistic data forwarding significantly increases the throughput in multi-hop wireless mesh networks by utilizing the broadcast nature of wireless transmissions and the fluctuation of link qualities. Network coding strengthens the robustness of data transmissions over unreliable wireless links. However, opportunistic data forwarding and network coding are rarely incorporated with TCP because the frequent occurrences of out-of-order packets in opportunistic data forwarding and long decoding delay in network coding overthrow TCP’s congestion control. In this paper, we propose a solution dubbed TCPFender, which supports opportunistic data forwarding and network coding in TCP. Our solution adds an adaptation layer to mask the packet loss caused by wireless link errors and provides early positive feedbacks to trigger a larger congestion window for TCP. This adaptation layer functions over the network layer and reduces the delay of ACKs for each coded packet. The simulation results show that TCPFender significantly outperforms TCP/IP in terms of the network throughput in different topologies of wireless networks.

Description: While traditional methods for calling variants across whole genome sequence data rely on alignment to an appropriate reference sequence, alternative techniques are needed when a suitable reference does not exist. We present a novel alignment and assembly free variant calling method based on information theoretic principles designed to detect variants have strong statistical evidence for their ability to segregate samples in a given dataset. Our method uses the context surrounding a particular nucleotide to define variants. Given a set of reads, we model the probability of observing a given nucleotide conditioned on the surrounding prefix and suffixes of lengthkas a multinomial distribution. We then estimate which of these contexts are stable intra-sample and varying inter-sample using a statistic based on the Kullback–Leibler divergence.The utility of the variant calling method was evaluated through analysis of a pair of bacterial datasets and a mouse dataset. We found that our variants are highly informative for supervised learning tasks with performance similar to standard reference based calls and another reference free method (DiscoSNP++). Comparisons against reference based calls showed our method was able to capture very similar population structure on the bacterial dataset. The algorithm’s focus on discriminatory variants makes it suitable for many common analysis tasks for organisms that are too diverse to be mapped back to a single reference sequence.

Description: The acoustic space in a given environment is filled with footprints arising from three processes: biophony, geophony and anthrophony. Bioacoustic research using passive acoustic sensors can result in thousands of recordings. An important component of processing these recordings is to automate signal detection. In this paper, we describe a new spectrogram-based approach for extracting individual audio events. Spectrogram-based audio event detection (AED) relies on separating the spectrogram into background (i.e., noise) and foreground (i.e., signal) classes using a threshold such as a global threshold, a per-band threshold, or one given by a classifier. These methods are either too sensitive to noise, designed for an individual species, or require prior training data. Our goal is to develop an algorithm that is not sensitive to noise, does not need any prior training data and works with any type of audio event. To do this, we propose: (1) a spectrogram filtering method, the Flattened Local Trimmed Range (FLTR) method, which models the spectrogram as a mixture of stationary and non-stationary energy processes and mitigates the effect of the stationary processes, and (2) an unsupervised algorithm that uses the filter to detect audio events. We measured the performance of the algorithm using a set of six thoroughly validated audio recordings and obtained a sensitivity of 94% and a positive predictive value of 89%. These sensitivity and positive predictive values are very high, given that the validated recordings are diverse and obtained from field conditions. The algorithm was then used to extract audio events in three datasets. Features of these audio events were plotted and showed the unique aspects of the three acoustic communities.

Description: Hypertension or high blood pressure is a condition on the rise. Not only does it affect the elderly but is also increasingly spreading to younger sectors of the population. Treating it involves exhaustive monitoring of patients. A tool adapted to the particular requirements of hypertension can greatly facilitate monitoring and diagnosis. This paper presents HBPF, an efficient cloud-based Home Blood Pressure Framework. This allows hypertensive patients to communicate with their health-care centers, thus facilitating monitoring for both patients and clinicians. HBPF provides a complete, efficient, and cross-platform framework to follow up hypertensive patients with an SLA guarantee. Response time below one second for 80,000 requests and 28% increase in peak throughput going from one to three virtual machines were obtained. In addition, a mobile app (BP) for Android and iOS with a user-friendly interface is also provided to facilitate following up hypertensive patients. Among them, between 54% and 87% favorably evaluated the tool. BP can be downloaded for free from the website Hesoft Group repository (http://www.hesoftgroup.eu).

Description: Online news reading has become a widely popular way to read news articles from news sources around the globe. With the enormous amount of news articles available, users are easily overwhelmed by information of little interest to them. News recommender systems help users manage this flood by recommending articles based on user interests rather than presenting articles in order of their occurrence. We present our research on developing personalized news recommendation system with the help of a popular micro-blogging service, “Twitter.” News articles are ranked based on the popularity of the article identified from Twitter’s public timeline. In addition, users construct profiles based on their interests and news articles are also ranked based on their match to the user profile. By integrating these two approaches, we present a hybrid news recommendation model that recommends interesting news articles to the user based on their popularity as well as their relevance to the user profile.

Description: Annotation of bioassay protocols using semantic web vocabulary is a way to make experiment descriptions machine-readable. Protocols are communicated using concise scientific English, which precludes most kinds of analysis by software algorithms. Given the availability of a sufficiently expressive ontology, some or all of the pertinent information can be captured by asserting a series of facts, expressed as semantic web triples (subject, predicate, object). With appropriate annotation, assays can be searched, clustered, tagged and evaluated in a multitude of ways, analogous to other segments of drug discovery informatics. The BioAssay Ontology (BAO) has been previously designed for this express purpose, and provides a layered hierarchy of meaningful terms which can be linked to. Currently the biggest challenge is the issue of content creation: scientists cannot be expected to use the BAO effectively without having access to software tools that make it straightforward to use the vocabulary in a canonical way. We have sought to remove this barrier by: (1) defining a BioAssay Template (BAT) data model; (2) creating a software tool for experts to create or modify templates to suit their needs; and (3) designing a common assay template (CAT) to leverage the most value from the BAO terms. The CAT was carefully assembled by biologists in order to find a balance between the maximum amount of information captured vs. low degrees of freedom in order to keep the user experience as simple as possible. The data format that we use for describing templates and corresponding annotations is the native format of the semantic web (RDF triples), and we demonstrate some of the ways that generated content can be meaningfully queried using the SPARQL language. We have made all of these materials available as open source (http://github.com/cdd/bioassay-template), in order to encourage community input and use within diverse projects, including but not limited to our own commercial electronic lab notebook products.

Description: We study the interplay between a dynamical process and the structure of the network on which it unfolds using the parameterized Laplacian framework. This framework allows for defining and characterizing an ensemble of dynamical processes on a network beyond what the traditional Laplacian is capable of modeling. This, in turn, allows for studying the impact of the interaction between dynamics and network topology on the quality-measure of network clusters and centrality, in order to effectively identify important vertices and communities in the network. Specifically, for each dynamical process in this framework, we define a centrality measure that captures a vertex’s participation in the dynamical process on a given network and also define a function that measures the quality of every subset of vertices as a potential cluster (or community) with respect to this process. We show that the subset-quality function generalizes the traditional conductance measure for graph partitioning. We partially justify our choice of the quality function by showing that the classic Cheeger’s inequality, which relates the conductance of the best cluster in a network with a spectral quantity of its Laplacian matrix, can be extended to the parameterized Laplacian. The parameterized Laplacian framework brings under the same umbrella a surprising variety of dynamical processes and allows us to systematically compare the different perspectives they create on network structure.

Description: Matrix Depot is a Julia software package that provides easy access to a large and diverse collection of test matrices. Its novelty is threefold. First, it is extensible by the user, and so can be adapted to include the user’s own test problems. In doing so, it facilitates experimentation and makes it easier to carry out reproducible research. Second, it amalgamates in a single framework two different types of existing matrix collections, comprising parametrized test matrices (including Hansen’s set of regularization test problems and Higham’s Test Matrix Toolbox) and real-life sparse matrix data (giving access to the University of Florida sparse matrix collection). Third, it fully exploits the Julia language. It uses multiple dispatch to help provide a simple interface and, in particular, to allow matrices to be generated in any of the numeric data types supported by the language.

Description: Research has suggested that adding contextual information such as reference markers to data sonification can improve interaction with auditory graphs. This paper presents results of an experiment that contributes to quantifying and analysing the extent of such benefits for an integral part of interacting with graphed data: point estimation tasks. We examine three pitch-based sonification mappings; pitch-only, one-reference, and multiple-references that we designed to provide information about distance from an origin. We assess the effects of these sonifications on users’ performances when completing point estimation tasks in a between-subject experimental design against visual and speech control conditions. Results showed that the addition of reference tones increases users accuracy with a trade-off for task completion times, and that the multiple-references mapping is particularly effective when dealing with points that are positioned at the midrange of a given axis.

Description: Recent additions to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall the translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such, they substantially influence the stability of mRNA and the amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance; this makes each of these sequences a potentially interesting case study for the effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present PATACSDB, a resource that contain a comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on the Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A’s allowing for one mismatched base. The PATACSDB database is accessible at:http://sysbio.ibb.waw.pl/patacsdb. The source code is available athttp://github.com/habich/PATACSDB, and it includes the scripts with which the database can be recreated.

Description: Sandboxes are increasingly important building materials for secure software systems. In recognition of their potential to improve the security posture of many systems at various points in the development lifecycle, researchers have spent the last several decades developing, improving, and evaluating sandboxing techniques. What has been done in this space? Where are the barriers to advancement? What are the gaps in these efforts? We systematically analyze a decade of sandbox research from five top-tier security and systems conferences using qualitative content analysis, statistical clustering, and graph-based metrics to answer these questions and more. We find that the term “sandbox” currently has no widely accepted or acceptable definition. We use our broad scope to propose the first concise and comprehensive definition for “sandbox” that consistently encompasses research sandboxes. We learn that the sandboxing landscape covers a range of deployment options and policy enforcement techniques collectively capable of defending diverse sets of components while mitigating a wide range of vulnerabilities. Researchers consistently make security, performance, and applicability claims about their sandboxes and tend to narrowly define the claims to ensure they can be evaluated. Those claims are validated using multi-faceted strategies spanning proof, analytical analysis, benchmark suites, case studies, and argumentation. However, we find two cases for improvement: (1) the arguments researchers present are oftenad hocand (2) sandbox usability is mostly uncharted territory. We propose ways to structure arguments to ensure they fully support their corresponding claims and suggest lightweight means of evaluating sandbox usability.

Description: Background.The decline of submerged plant populations due to high heavy metal (e.g., Cu) levels in sediments and ammonia nitrogen (ammonia-N) accumulation in the freshwater column has become a significant global problem. Previous studies have evaluated the effect of ammonia-N on submerged macrophytes, but few have focused on the influence of sediment Cu on submerged macrophytes and their combined effects.Methods.In this paper, we selected three levels of ammonia-N (0, 3, and 6 mg L−1) and sediment Cu (25.75 ± 6.02 as the control, 125.75 ± 6.02, and 225.75 ± 6.02 mg kg−1), to investigate the influence of sediment Cu and ammonia-N on submergedVallisneria natans. We measured the relative growth rate (RGR), above- and below- ground biomass, chlorophyll, non-protein thiol (NP-SH), and free proline.Results and Discussion.The below-ground biomass ofV. natansdecreased with increasing Cu sediment levels, suggesting that excessive sediment Cu can result in significant damage to the root ofV. natans. Similarly, the above-ground biomass significantly decreased with increasing ammonia-N concentrations, indicating that excessive water ammonia-N can cause significant toxicity to the leaf ofV. natans. In addition, high ammonia-N levels place a greater stress on submerged plants than sediment Cu, which is indicated by the decline of RGR and chlorophyll, and the increase of (NP-SH) and free proline. Furthermore, high sediment Cu causes ammonia-N to impose greater injury on submerged plants, and higher sediment Cu levels ($mathrm{Cu}geq 125.75$ mg kg−1) led to the tolerant values of ammonia-N forV. natansdecreasing from 6 to 3 mg L−1. This study suggests that high sediment Cu restricts the growth of plants and intensifies ammonia-N damage toV. natans.

Description: BackgroundThe benefit of maintenance therapy has been confirmed in patients with non-progressing non-small cell lung cancer (NSCLC) after first-line therapy by many trials and meta-analyses. However, since few head-to-head trials between different regimens have been reported, clinicians still have little guidance on how to select the most efficacious single-agent regimen. Hence, we present a network meta-analysis to assess the comparative treatment efficacy of several single-agent maintenance therapy regimens for stage III/IV NSCLC.MethodsA comprehensive literature search of public databases and conference proceedings was performed. Randomized clinical trials (RCTs) meeting the eligible criteria were integrated into a Bayesian network meta-analysis. The primary outcome was overall survival (OS) and the secondary outcome was progression free survival (PFS).ResultsA total of 26 trials covering 7,839 patients were identified, of which 24 trials were included in the OS analysis, while 23 trials were included in the PFS analysis. Switch-racotumomab-alum vaccine and switch-pemetrexed were identified as the most efficacious regimens based on OS (HR, 0.64; 95% CrI, 0.45–0.92) and PFS (HR, 0.54; 95% CrI, 0.26–1.04) separately. According to the rank order based on OS, switch-racotumomab-alum vaccine had the highest probability as the most effective regimen (52%), while switch-pemetrexed ranked first (34%) based on PFS.ConclusionsSeveral single-agent maintenance therapy regimens can prolong OS and PFS for stage III/IV NSCLC. Switch-racotumomab-alum vaccine maintenance therapy may be the most optimal regimen, but should be confirmed by additional evidence.

Description: Small non-coding RNAs include powerful regulators of gene expression, transposon mobility and virus activity. Among the various categories, mature microRNAs (miRNAs) guide the translational repression and decay of several targeted mRNAs. The biogenesis of miRNAs depends on few gene products, essentially conserved from basal to higher metazoans, whose protein domains allow specific interactions with dsRNA. Here, we report the identification of key genes responsible of the miRNA biogenesis in 32 bivalves, with particular attention to the aquaculture speciesMytilus galloprovincialisandCrassostrea gigas. In detail, we have identified and phylogenetically compared eight evolutionary conserved proteins: DROSHA, DGCR8, EXP5, RAN, DICER TARBP2, AGO and PIWI. In mussels, we recognized several other proteins participating in the miRNA biogenesis or in the subsequent RNA silencing. According to digital expression analysis, these genes display low and not inducible expression levels in adult mussels and oysters whereas they are considerably expressed during development. As miRNAs play an important role also in the antiviral responses, knowledge on their production and regulative effects can shed light on essential molecular processes and provide new hints for disease prevention in bivalves.

Description: Deforestation and changes in land use have reduced the tropical dry forest to isolated forest patches in northwestern Costa Rica. We examined the effect of patch area and length of the dry season on nestedness of the entire avian community, forest fragment assemblages, and species occupancy across fragments for the entire native avifauna, and for a subset of forest dependent species. Species richness was independent of both fragment area and distance between fragments. Similarity in bird community composition between patches was related to habitat structure; fragments with similar forest structure have more similar avian assemblages. Size of forest patches influenced nestedness of the bird community and species occupancy, but not nestedness of assemblages across patches in northwestern Costa Rican avifauna. Forest dependent species (species that require large tracts of mature forest) and assemblages of these species were nested within patches ordered by a gradient of seasonality, and only occupancy of species was nested by area of patches. Thus, forest patches with a shorter dry season include more forest dependent species.

Description: Background.Calomera littoralisis a Palearctic species, widely distributed in Europe; inhabiting predominantly its Atlantic, Mediterranean and Black Sea coastlines.Methods.Its phylogeography on the Balkan Peninsula and on the north-western Black Sea coast was inferred using a 697 bp long portion of the mitochondrial COI gene, amplified from 169 individuals collected on 43 localities.Results.The results revealed two genetically divergent groups/lineages, the southern one inhabiting both the Balkan Peninsula and the Pontic Region and the northern one found exclusively in the Pontic Region. Species delimitation based on DNA barcoding gap suggested an interspecific level of divergence between these groups. Multivariate analysis of eight male and female morphometric traits detected no difference between the groups, implying they may represent cryptic species. The Bayesian time-calibrated reconstruction of phylogeny suggested that the lineages diverged ca. 2.3 Ma, in early Pleistocene.Discussion.The presence of the two genetically divergent groups results most likely from contemporary isolation of the Pontic basin from the Mediterranean that broke the continuous strip of coastal habitats inhabited byC. littoralis. Demographic analyses indicated that both lineages have been in demographic and spatial expansion since ca. 0.15 Ma. It coincides with the terminal stage of MIS-6, i.e., Wartanian/Saalian glaciation, and beginning of MIS-5e, i.e., Eemian interglacial, during which, due to eustatic sea level rise, a wide connection between Mediterranean and the Pontic basin was re-established. This, along with re-appearance of coastal habitats could initiate north-east expansion of the southern lineage and its secondary contact with the northern one. The isolation of the Pontic basin from the Mediterranean during the Weichselian glaciation most likely did not have any effect on their phylogeography.

Description: Background and Objectives.The medial circumflex femoral artery (MCFA) is a common branch of the deep femoral artery (DFA) responsible for supplying the femoral head and the greater trochanteric fossa. The prevalence rates of MCFA origin, its branching patterns and its distance to the mid-inguinal point (MIP) vary significantly throughout the literature. The aim of this study was to determine the true prevalence of these characteristics and to study their associated anatomical and clinical relevance.Methods.A search of the major electronic databases Pubmed, EMBASE, Scopus, ScienceDirect, Web of Science, SciELO, BIOSIS, and CNKI was performed to identify all articles reporting data on the origin of the MCFA, its branching patterns and its distance to the MIP. No data or language restriction was set. Additionally, an extensive search of the references of all relevant articles was performed. All data on origin, branching and distance to MIP was extracted and pooled into a meta-analysis using MetaXL v2.0.Results.A total of 38 (36 cadaveric and 2 imaging) studies (n= 4,351 lower limbs) were included into the meta-analysis. The pooled prevalence of the MCFA originating from the DFA was 64.6% (95% CI [58.0–71.5]), while the pooled prevalence of the MCFA originating from the CFA was 32.2% (95% CI [25.9–39.1]). The CFA-derived MCFA was found to originate as a single branch in 81.1% (95% CI [70.1–91.7]) of cases with a mean pooled distance of 50.14 mm (95% CI [42.50–57.78]) from the MIP.Conclusion.The MCFA’s variability must be taken into account by surgeons, especially during orthopedic interventions in the region of the hip to prevent iatrogenic injury to the circulation of the femoral head. Based on our analysis, we present a new proposed classification system for origin of the MCFA.

Description: The most common coral monitoring methods estimate coral abundance as percent cover, either viain situobservations or derived from images. In recent years, growing interest and effort has focused on colony-based (demographic) data to assess the status of coral populations and communities. In this study, we relied on two separate data sets (photo-derived percent cover estimates, 2002–12, and opportunisticin situdemographic sampling, 2004 and 2012) to more fully infer decadal changes in coral communities at a small, uninhabited Caribbean island. Photo-derived percent cover documented drastic declines in coral abundance including disproportionate declines inOrbicellaspp. While overallin situestimates of total coral density were not different between years, densities of several rarer taxa were.Meandrina meandritesandStephanocoenia interseptaincreased whileLeptoseris cucullatadecreased significantly, changes that were not discernable from the photo-derived cover estimates. Demographic data also showed significant shifts to larger colony sizes (both increased mean colony sizes and increased negative skewness of size frequency distributions, but similar maximum colony sizes) for most taxa likely indicating reduced recruitment.Orbicellaspp. differed from this general pattern, significantly shifting to smaller colony sizes due to partial mortality. Both approaches detected significant decadal changes in coral community structure at Navassa, though the demographic sampling provided better resolution of more subtle, taxon-specific changes.

Description: Background:Surgical treatments for adult spinal deformities often include pelvic fixation, and the feasibility of sacral-2 alar iliac (S2AI) screw fixation has been shown previously. However, sometimes S2AI screw fixation cannot be applied due to the presence of an osteolytic lesion or trauma or because the biomechanical properties of only an S2AI screw is insufficient. Therefore, we questioned the feasibility of using sacral AI screws in other segments and determined whether S3AI and S4AI screws have the potential to be used for sacral fractures. The aim of this study was to investigate the feasibility and radiological features of sacral AI fixation in S1–S4 in an adult population using 3D imaging techniques.Methods:Computed tomography (CT) scans were taken of 45 patients and were imported into Mimics (Version 10.01, Materialise, Belgium) software to reconstruct the 3D digital images. Next, a cylinder (radius of 3.5 mm) was drawn to imitate the screw trajectory of a S1–4 AI screw, and every imitated screw in each segment was adjusted to a maximum upward and downward angle to acquire the feasible region. The parameters of the S1–4AI screw trajectories were measured.Results:Sacral AI screws could be successfully imitated using 3D digital imaging. The S4AI screw trajectory could be obtained in 19 of 45 patient images (42.2%), while the feasibility rates of S1AI, S2AI, and S3AI screw fixation were 100%, 100%, and 91.1% (41/45), respectively. The feasible regions of S1AI, S2AI, and S3AI screw trajectories were wide enough, while the adjustable angle of S4AI screws was very small.Conclusion:It is feasible to place S1–2AI screws in the entire adult population and S3–4AI screws in some of the adult population. Furthermore, our study suggested that 3D digital images are suitable to study the feasibility of new screw fixation.

Description: Hepatocyte growth factor (HGF) is a paracrine hormone that plays an important role in epithelial-mesenchymal transition. HGF secreted by mesenchymal cells affects many properties of epithelial cells, such as proliferation, motility, and morphology. HGF has been reported to promote follicular growth. The purpose of the present study is to investigate the therapeutic role of HGF in hair loss treatment. A recombinant vector containing the human HGF (hHGF) gene (pTARGET-hHGF) was constructed, and the expression of hHGF in vitro was quantitatively and qualitatively evaluated. The effect of hHGF on hair growth was tested in mice, and results demonstrated that pTARGET-hHGF was successfully delivered into fibroblasts in vitro leading to a high expression of hHGF. Local injections of the pTARGET-hHGF recombinant vector into mice resulted in multiple beneficial effects compared to placebo, including faster hair regeneration, improved follicle development, and significantly increased HGF receptor (HGF-R). In conclusion, we have established a nonviral vector of hHGF which could be utilized to manipulate the sheath fibroblasts surrounding hair follicles (HF), thereby stimulating hair regeneration.

Description: The conserved nature of sleep in Drosophila has allowed the fruit fly to emerge in the last decade as a powerful model organism in which to study sleep. Recent sleep studies in Drosophila have focused on the discovery and characterization of hyposomnolent mutants. One common feature of these animals is a change in sleep architecture: sleep bout count tends to be greater, and sleep bout length lower, in hyposomnolent mutants. I propose a mathematical model, produced by least-squares nonlinear regression to fit the formY=aX∧b, which can explain sleep behavior in the healthy animal as well as previously-reported changes in total sleep and sleep architecture in hyposomnolent mutants. This model, fit to sleep data, yields coefficient of determinationRsquared, which describes goodness of fit.Rsquared is lower, as compared to control, in hyposomnolent mutantsinsomniacandfumin. My findings raise the possibility that lowRsquared is a feature of all hyposomnolent mutants, not justinsomniacandfumin. If this were the case,Rsquared could emerge as a novel means by which sleep researchers might assess sleep dysfunction.

Description: Studies linking postcranial morphology with locomotion in mammals are common. However, such studies are mostly restricted to caviomorphs in rodents. We present here data from various families, belonging to the three main groups of rodents (Sciuroidea, Myodonta, and Ctenohystrica). The aim of this study is to define morphological indicators for the astragalus and calcaneus, which allow for inferences to be made about the locomotor behaviours in rodents. Several specimens were dissected and described to bridge the myology of the leg with the morphology of the bones of interest. Osteological characters were described, compared, mechanically interpreted, and correlated with a “functional sequence” comprising six categories linked to the lifestyle and locomotion (jumping, cursorial, generalist, fossorial, climber and semi-aquatic). Some character states are typical of some of these categories, especially arboreal climbers, fossorial and “cursorial-jumping” taxa. Such reliable characters might be used to infer locomotor behaviours in extinct species. Linear discriminant analyses (LDAs) were used on a wider sample of species and show that astragalar and calcaneal characters can be used to discriminate the categories among extant species whereasa posterioriinferences on extinct species should be examined with caution.

Description: We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404--411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs) were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in the realms of oceanography and marine ecology.

Description: Objective.We hypothesized that a significant percentage of patients who are referred to the Emergency Department (ED) after calling their primary care physician’s (PCP) office receive such instructions without the input of a physician.Methods.We enrolled a convenience sample of stable adults at an inner-city ED. Patients provided written answers to structured questions regarding PCP contact prior to the ED visit. Continuous data are presented as means ± standard deviation; categorical data as frequency of occurrence. 95% confidence intervals were calculated.Results.The study group of 660 patients had a mean age of 41.7 ± 14.7 years and 72.6% had income below $20,000/year. 472 patients (71.51%; 67.9%–74.8%) indicated that they had a PCP. A total of 155 patients (23.0%; 19.9%–26.4%) called to contact their PCP prior to ED visit. For patients who called their PCP office and were directed by phone to the ED, the referral pattern was observed as follows: 31/98 (31.63%; 23.2%–41.4%) by a non-health care provider without physician input, 11/98 (11.2%; 6.2%–19.1%) by a non-healthcare provider after consultation with a physician, 12/98 (12.3%; 7.7%–20.3%) by a nurse without physician input, and 14/98 (14.3%; 8.6%–22.7%) by a nurse after consultation with physician. An additional 11/98, 11.2%; 6.2–19.1%) only listened to a recorded message and felt the message was directing them to the ED.Conclusion.A relatively small percentage of patients were referred to the ED without the consultation of a physician in our overall population. However, over half of those that contacted their PCP’s office felt directed to the ED by non-health care staff.

Description: Anemones of genusExaiptasiaare used as model organisms for the study of cnidarian-dinoflagellate (genusSymbiodinium) endosymbiosis. However, while most reef-building corals harborSymbiodiniumof clade C,Exaiptasiaspp. anemones mainly harbor clade BSymbiodinium(ITS2 type B1) populations. In this study, we reveal for the first time that bleachedExaiptasia pallidaanemones can establish a symbiotic relationship with a clade CSymbiodinium(ITS2 type C1). We further found that anemones can transmit the exogenously supplied clade CSymbiodiniumcells to their offspring by asexual reproduction (pedal laceration). In order to corroborate the establishment of stable symbiosis, we used microscopic techniques and genetic analyses to examine several generations of anemones, and the results of these endeavors confirmed the sustainability of the system. These findings provide a framework for understanding the differences in infection dynamics between homologous and heterologous dinoflagellate types using a model anemone infection system.

Description: We describe a new species ofPsychrophrynellafrom the humid montane forest of the Department Cusco in Peru. Specimens were collected at 2,670–3,165 m elevation in the Área de Conservación Privada Ukumari Llakta, Japumayo valley, near Comunidad Campesina de Japu, in the province of Paucartambo. The new species is readily distinguished from all other species ofPsychrophrynellabutP. bagrecitoandP. usurpatorby possessing a tubercle on the inner edge of the tarsus, and from these two species by its yellow ventral coloration on abdomen and limbs. Furthermore, the new species is likeP. bagrecitoandP. usurpatorin having an advertisement call composed of multiple notes, whereas other species ofPsychrophrynellawhose calls are known have a pulsed call (P. teqta) or a short, tonal call composed of a single note. The new species has a snout-vent length of 16.1–24.1 mm in males and 23.3–27.7 mm in females. Like other recently described species in the genus, this newPsychrophrynellainhabits high-elevation forests in the tropical Andes and likely has a restricted geographic distribution.

Description: The genusElatinecontainsca25 species, all of which are small, herbaceous annuals distributed in ephemeral waters on both hemispheres. However, due to a high degree of morphological variability (as a consequence of their amphibious life-style), the taxonomy of this genus remains controversial. Thus, to fill this gap in knowledge, we present a detailed molecular phylogenetic study of this genus based on nuclear (rITS) and plastid (accD-psaI,psbJ-petA,ycf6-psbM-trnD) sequences using 27 samples from 13 species. On the basis of this phylogenetic analysis, we provide a solid phylogenetic background for the modern taxonomy of the European members of the genus. Traditionally accepted sections of this tree (i.e., CryptaandElatinella) were found to be monophyletic; onlyE. borchoni—found to be a basal member of the genus—has to be excluded from the latter lineage to achieve monophyly. A number of taxonomic conclusions can also be drawn:E. hexandra, a high-ploid species, is most likely a stabilised hybrid between the main sections;E. campylospermamerits full species status based on both molecular and morphological evidence;E. gussoneiis a more widespread and genetically diverse species with two main lineages; and the presence of the AsianE. ambiguain the European flora is questionable. The main lineages recovered in this analysis are also supported by a number of synapomorphic morphological characters as well as uniform chromosome counts. Based on all the evidence presented here, two new subsections withinElatinellaare described: subsectionHydropiperaconsisting of the temperate species of the section, and subsectionMacropodaeincluding the Mediterranean species of the section.

Description: Nitrite-dependent anaerobic methane oxidation (n-damo) is a recently discovered biological process which has been arousing global attention because of its potential in minimizing greenhouse gases emissions. In this study, molecular biological techniques and potential n-damo activity batch experiments were conducted to investigate the presence and diversity of M. oxyfera bacteria in paddy field, corn field, and wastewater treatment plant (WWTP) sites in northern China, as well as lab-scale n-damo enrichment culture. N-damo enrichment culture showed the highest abundance of M. oxyfera bacteria, and positive correlation was observed between potential n-damo rate and abundance of M. oxyfera bacteria. Both paddy field and corn field sites were believed to be better inoculum than WWTP for the enrichment of M. oxyfera bacteria due to their higher abundance and the diversity of M. oxyfera bacteria. Comparative analysis revealed that long biomass retention time, low NH${}_{4}^{+}$ and high NO${}_{2}^{-}$ content were suitable for the growth of M. oxyfera bacteria.

Description: BackgroundThe aim of this study was to determine the expression stabilities of 12 common internal reference genes for the relative quantitation analysis of target gene expression performed by reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) in human laryngeal cancer.MethodsHep-2 cells and 14 laryngeal cancer tissue samples were investigated. The expression characteristics of 12 internal reference gene candidates (18S rRNA, GAPDH, ACTB, HPRT1, RPL29, HMBS, PPIA, ALAS1, TBP, PUM1, GUSB, and B2M) were assessed by RT-qPCR. The data were analyzed by three commonly used software programs: geNorm, NormFinder, and BestKeeper.ResultsThe use of the combination of four internal reference genes was more appropriate than the use of a single internal reference gene. The optimal combination was PPIA + GUSB + RPL29 + HPRT1 for both the cell line and tissues; while the most appropriate combination was GUSB + RPL29 + HPRT1 + HMBS for the tissues.ConclusionsOur recommended internal reference genes may improve the accuracy of relative quantitation analysis of target gene expression performed by the RT-qPCR method in further gene expression research on laryngeal tumors.

Description: The tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in the mean time of 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

Description: BackgroundShugoshins (SGOs) are proteins that protect cohesins located at the centromeres of sister chromatids from their early cleavage during mitosis and meiosis in plants, fungi, and animals. Their function is to prevent premature sister-chromatid disjunction and segregation. The study focused on the structural differences among SGOs acting during mitosis and meiosis that cause differences in chromosome behavior in these two types of cell division in different organisms.MethodsA bioinformatical analysis of protein domains, conserved amino acid motifs, and physicochemical properties of 32 proteins from 25 species of plants, fungi, and animals was performed.ResultsWe identified a C-terminal amino acid motif that is highly evolutionarily conserved among the SGOs protecting centromere cohesion of sister chromatids in meiotic anaphase I, but not among mitotic SGOs. This meiotic motif is arginine-rich in vertebrates. SGOs differ in different eukaryotic kingdoms by the sets and locations of amino acid motifs and the number of α-helical regions in the protein molecule.DiscussionThese structural differences between meiotic and mitotic SGOs probably could be responsible for the prolonged SGOs resistance to degradation during meiotic metaphase I and anaphase I. We suggest that the “arginine comb” in C-end meiotic motifs is capable of interaction by hydrogen bonds with guanine bases in the minor groove of DNA helix, thus protecting SGOs from hydrolysis. Our findings support independent evolution of meiosis in different lineages of multicellular organisms.

Description: Drosophila embryogenesis has proven to be an extremely powerful system for developmental gene discovery and characterization. We isolated five new EMS-induced alleles that do not complement thel(3R)5G83lethal line isolated in the Nüsslein-Volhard and Wieschaus screens. We have named this locuschem. Lethality of the new alleles as homozygous zygotic mutants is not completely penetrant, and they have an extended phenocritical period. Like the original allele, a fraction of mutant embryos die with cuticular defects, notably head involution and dorsal closure defects. Embryonic defects are much more extreme in germline clones, where the majority of mutant embryos die during embryogenesis and do not form cuticle, implying a strongchemmaternal contribution.chemmutations genetically interact with mutations in cytoskeletal genes (arm) and with mutations in the epithelial polarity genescoracle, crumbs,andyurt.chemmutants dorsal open defects are similar to those present inyurtmutants, and, likewise, they have epithelial polarity defects.chem1andchem3mutations suppressyurt3, andchem3mutants suppresscrumbs1mutations. In contrast,chem1andcoracle2mutations enhance each other. Compared to controls, inchemmutants in embryonic lateral epithelia Crumbs expression is mislocalized and reduced, Coracle is increased and mislocalized basally at embryonic stages 13–14, then reduced at stage 16. Arm expression has a similar pattern but levels are reduced.

Description: BackgroundTerritory owners usually defeat intruders. One explanation for this observation is the uncorrelated asymmetry hypothesis which argues that contests might be settled by an arbitrary convention such as “owners win.” We studied the effect of territorial residency on contest asymmetries in the white-eared hummingbird (Hylocharis leucotis) in a fir forest from central Mexico.MethodsTwenty white-eared male adult hummingbird territories were monitored during a winter season, recording the territorial behavior of the resident against intruding hummingbirds. The size and quality of the territory were related to the probability that the resident would allow the use of flowers by the intruder. Various generalized models (logistical models) were generated to describe the probabilities of victory for each individual resident depending on the different combinations of three predictor variables (territory size, territory quality, and intruder identity).ResultsIn general, small and low quality territory owners tend to prevent conspecific intruders from foraging at a higher rate, while they frequently fail to exclude heterospecific intruders such as the magnificent hummingbird (Eugenes fulgens) or the green violetear hummingbird (Colibri thalassinus) on any territory size. Our results showed that the identity of the intruder and the size and quality of the territory determined the result of the contests, but not the intensity of defense.DiscussionInitially, the rule that “the resident always wins” was supported, since no resident was expelled from its territory during the study. Nevertheless, the resident-intruder asymmetries during the course of a day depended on different factors, such as the size and quality of the territory and, mainly, the identity of the intruders. Our results showed that flexibility observed in contest tactics suggests that these tactics are not fixed but are socially plastic instead and they can be adjusted to specific circumstances.

Description: After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably owing to the large diversity of cell walls that exist in the three domains of life. Many prokaryotic cell walls, however, are synthesized using glycosylation pathways with similar polyisoprenol lipid carriers and topology (i.e., orientation across the cell membranes). Here, we provide the first systematic phylogenomic report on the polyisoprenol biosynthesis pathways in the three domains of life. This study shows that, whereas the last steps of the polyisoprenol biosynthesis are unique to the respective domain of life of which they are characteristic, the enzymes required for basic unsaturated polyisoprenol synthesis can be traced back to the respective last common ancestor of each of the three domains of life. As a result, regardless of the topology of the tree of life that may be considered, the most parsimonious hypothesis is that these enzymes were inherited in modern lineages from the cenancestor. This observation supports the presence of an enzymatic mechanism to synthesize unsaturated polyisoprenols in the cenancestor and, since these molecules are notorious lipid carriers in glycosylation pathways involved in the synthesis of a wide diversity of prokaryotic cell walls, it provides the first indirect evidence of the existence of a hypothetical unknown cell wall synthesis mechanism in the cenancestor.

Description: Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome forHelwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels. TheHelwingiagenome consists of 158,362 bp containing a pair of inverted repeat (IR) regions of 25,996 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

Description: Molecular mechanisms underlying RNA splicing regulation in response to viral infection are poorly understood. Classical swine fever (CSF), one of the most economically important and highly contagious swine diseases worldwide, is caused by classical swine fever virus (CSFV). Here, we used high-throughput sequencing to obtain the digital gene expression (DGE) profile in swine umbilical vein endothelial cells (SUVEC) to identify different response genes for CSFV by using both Shimen and C strains. The numbers of clean tags obtained from the libraries of the control and both CSFV-infected libraries were 3,473,370, 3,498,355, and 3,327,493 respectively. In the comparison among the control, CSFV-C, and CSFV-Shimen groups, 644, 158, and 677 differentially expressed genes (DEGs) were confirmed in the three groups. Pathway enrichment analysis showed that many of these DEGs were enriched in spliceosome, ribosome, proteasome, ubiquitin-mediated proteolysis, cell cycle, focal adhesion, Wnt signalling pathway, etc., where the processes differ between CSFV strains of differing virulence. To further elucidate important mechanisms related to the differential infection by the CSFV Shimen and C strains, we identified four possible profiles to assess the significantly expressed genes only by CSFV Shimen or CSFV C strain. GO analysis showed that infection with CSFV Shimen and C strains disturbed ‘RNA splicing’ of SUVEC, resulting in differential ‘gene expression’ in SUVEC. Mammalian target of rapamycin (mTOR) was identified as a significant response regulator contributed to impact on SUVEC function for CSFV Shimen. This computational study suggests that CSFV of differing virulence could induce alterations in RNA splicing regulation in the host cell to change cell metabolism, resulting in acute haemorrhage and pathological damage or infectious tolerance.

Description: Insect herbivores can shift the composition of a plant community, but the mechanism underlying such shifts remains largely unexplored. A possibility is that insects alter the competitive symmetry between plant species. The effect of herbivory on competition likely depends on whether the plants are subjected to aboveground or belowground herbivory or both, and also depends on soil nitrogen levels. It is unclear how these biotic and abiotic factors interactively affect competition. In a greenhouse experiment, we measured competition between two coexisting grass species that respond differently to nitrogen deposition:Dactylis glomerataL., which is competitively favoured by nitrogen addition, andFestuca rubraL., which is competitively favoured on nitrogen-poor soils. We predicted: (1) that aboveground herbivory would reduce competitive asymmetry at high soil nitrogen by reducing the competitive advantage ofD. glomerata; and (2), that belowground herbivory would relax competition at low soil nitrogen, by reducing the competitive advantage ofF. rubra. Aboveground herbivory caused a 46% decrease in the competitive ability ofF. rubra, and a 23% increase in that ofD. glomerata, thus increasing competitive asymmetry, independently of soil nitrogen level. Belowground herbivory did not affect competitive symmetry, but the combined influence of above- and belowground herbivory was weaker than predicted from their individual effects. Belowground herbivory thus mitigated the increased competitive asymmetry caused by aboveground herbivory.D. glomerataremained competitively dominant after the cessation of aboveground herbivory, showing that the influence of herbivory continued beyond the feeding period. We showed that insect herbivory can strongly influence plant competitive interactions. In our experimental plant community, aboveground insect herbivory increased the risk of competitive exclusion ofF. rubra. Belowground herbivory appeared to mitigate the influence of aboveground herbivory, and this mechanism may play a role for plant species coexistence.

Description: The integration of invasive species into native food webs represent multifarious dynamics of ecological and evolutionary processes. We document incorporation ofPrunus serotina(black cherry) into native insect food webs. We find thatP. serotinaharbours a herbivore community less dense but more diverse than its native relative,P. padus(bird cherry), with similar proportions of specialists and generalists. While herbivory onP. padusremained stable over the past century, that onP. serotinagradually doubled. We show thatP. serotinamay have evolved changes in investment in cyanogenic glycosides compared with its native range. In the leaf beetleGonioctena quinquepunctata, recently shifted from nativeSorbus aucupariatoP. serotina, we find divergent host preferences onSorbus- versusPrunus-derived populations, and weak host-specific differentiation among 380 individuals genotyped for 119 SNP loci. We conclude that evolutionary processes may generate a specialized herbivore community on an invasive plant, allowing prognoses of reduced invasiveness over time. On the basis of the results presented here, we would like to caution that manual control might have the adverse effect of a slowing down of processes of adaptation, and a delay in the decline of the invasive character ofP. serotina.

Description: Pleurocystitid rhombiferans are among the most unusual echinoderms whose mode of life has been long debated. These echinoderms are usually interpreted as vagile epibenthic echinoderms, moving over the sea bottom by means of a flexible stem. Although their life habits and posture are reasonably well understood, the mechanisms that control the movement of stem are highly controversial. Specifically, it is unknown whether the stem flexibility was under the control of muscles or ligamentary mutable collagenous tissues (MCTs). Here, we reconstruct palaeoanatomy of the two Ordovician pleurocystitid rhombiferans (PleurocystitesandAmecystis) based on stereom microstructure. We show that the articular facets of columnals in pleurocystitid rhombiferans are composed of fine labyrinthic stereom. Comparison with modern echinoderms suggests that this type of stereom was associated with muscles implying that their stem was a muscular locomotory organ supporting an active mode of life.

Description: Vertebrate mothers transfer diverse compounds to developing embryos that can affect their development and final phenotype (i.e., maternal effects). However, the way such effects modulate offspring phenotype, in particular their immunity, remains unclear. To test the impact of maternal effects on offspring development, we treated wild breeding house sparrows (Passer domesticus) in Sevilla, SE Spain with Newcastle disease virus (NDV) vaccine. Female parents were vaccinated when caring for first broods, eliciting a specific immune response to NDV. The immune response to the same vaccine, and to the PHA inflammatory test were measured in 11-day-old chicks from their following brood. Vaccinated chicks from vaccinated mothers developed a stronger specific response that was related to maternal NDV antibody concentration while rearing their chicks. The chicks’ carotenoid concentration and total antioxidant capacity in blood were negatively related to NDV antibody concentration, whereas no relation with PHA response was found. Specific NDV antibodies could not be detected in 11-day-old control chicks from vaccinated mothers, implying that maternally transmitted antibodies are not directly involved but may promote offspring specific immunity through a priming effect, while other immunity components remain unaffected. Maternally transmitted antibodies in the house sparrow are short-lived, depend on maternal circulation levels and enhance pre-fledging chick specific immunity when exposed to the same pathogens as the mothers.

Description: Applying analgesics to feed is a potentially easy method of providing pain-relief to sheep and lambs that undergo painful husbandry procedures. To be effective, the medicated feed needs to be readily accepted by sheep and its consumption needs to result in therapeutic concentrations of the drug. In the present experiment, pelleted feed was supplemented with flunixin (4.0 mg/kg live weight) and offered to eight sheep. To test the palatability of flunixin, the individually penned sheep were offered normal feed and feed supplemented with flunixin in separate troughs for two consecutive days. A trend for a day by feed-type (control versus flunixin supplemented) interaction suggested that sheep may have had an initial mild aversion to pellets supplemented with flunixin on the first day of exposure, however, by on the second day there was no difference in consumption of normal feed and feed supplemented with flunixin. To test pharmacokinetics, sheep were offered 800 g of flunixin supplemented feed for a 12 h period. Blood samples were taken over 48 h and plasma drug concentrations were determined using ultra-high-pressure liquid chromatography, negative electrospray ionisation and tandem mass spectrometry. The mean ± S.D. time required to reach maximum concentration was 6.00 ± 4.14 h and ranged from 1 to 12 h. Average maximum plasma concentration was 1.78 ± 0.48 µg/mL and ranged from 1.61 to 2.80 µg/mL. The average half-life of flunixin was 7.95 ± 0.77 h and there was a mean residence time of 13.62 ± 1.17 h. Free access to flunixin supplemented feed enabled all sheep to obtain inferred therapeutic concentrations of flunixin in plasma within 6 h of starting to consume the feed. Provision of an analgesic in feed may be an alternative practical method for providing pain relief to sheep.

Description: Normalization to reference genes is the most common method to avoid bias in real-time quantitative PCR (qPCR), which has been widely used for quantification of gene expression. Despite several studies on gene expression,Lilium, and particularlyL. regale, has not been fully investigated regarding the evaluation of reference genes suitable for normalization. In this study, nine putative reference genes, namely18S rRNA,ACT,BHLH,CLA,CYP,EF1,GAPDH,SANDandTIP41, were analyzed for accurate quantitative PCR normalization at different developmental stages and under different stress conditions, including biotic (Botrytis elliptica), drought, salinity, cold and heat stress. All these genes showed a wide variation in their Cq (quantification Cycle) values, and their stabilities were calculated by geNorm, NormFinder and BestKeeper. In a combination of the results from the three algorithms,BHLHwas superior to the other candidates when all the experimental treatments were analyzed together;CLAandEF1were also recommended by two of the three algorithms. As for specific conditions,EF1under various developmental stages,SANDunder biotic stress,CYP/GAPDHunder drought stress, andTIP41under salinity stress were generally considered suitable. All the algorithms agreed on the stability ofSANDandGAPDHunder cold stress, while onlyCYPwas selected under heat stress by all of them. Additionally, the selection of optimal reference genes under biotic stress was further verified by analyzing the expression level ofLrLOXin leaves inoculated withB. elliptica. Our study would be beneficial for future studies on gene expression and molecular breeding ofLilium.