Nine Quick Tips for Analyzing Network Data

These tips provide a quick and concentrated guide for beginners in the analysis of network data

PIA : more accurate taxonomic assignment of metagenomic data demonstrated on sedaDNA from the North sea

Assigning metagenomic reads to taxa presents significant challenges. Existing approaches address some issues, but are mostly limited to metabarcoding or optimized for microbial data. We present PIA (Phylogenetic Intersection Analysis): a taxonomic binner that works from standard BLAST output while mitigating key effects of incomplete databases. Benchmarking against MEGAN using sedaDNA suggests that, while PIA is less sensitive, it can be more accurate. We use known sequences to estimate the accuracy of PIA at up to 96% when the real organism is not represented in the database. For ancient DNA, where taxa of interest are frequently over-represented domesticates or absent, poorly-known organisms, more accurate assignment is critical, even at the expense of sensitivity. PIA offers an approach to objectively filter out false positive hits without the need to manually remove taxa and so make presuppositions about past environments and their palaeoecologies

Beak colour dynamically signals changes in fasting status and parasite loads in king penguins

This research was funded by the French Polar Institute (IPEV–Research Program 119) and the French National Centre for Scientific Research (CNRS-INEE). Field logistic support was provided by Terres Australes et Antarctiques Françaises. Q.S. was funded by a doctoral fellowship from the Ministère Français de l’Education Supérieur et de la Recherche. We thank all over-wintering assistants: Benoit Gineste, Sylvia Pardonnet, Laureline Durand, Emilie Lefol and Hédi Saadaoui for field work and Emilio Rojas for helpful discussion on the analyses. We apologize to our stick insect (Carausius morosus) for bearing with VAV’s inquisitive curiosity during our debates on color ornaments in king penguins. We sincerely thank the editor and 2 anonymous reviewers for their helpful comments on a previous version of the paper.Peer reviewedPostprin

Statistical tests to compare motif count exceptionalities

BACKGROUND: Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. RESULTS: We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. CONCLUSION: The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use

Affective Learning Outcomes Assessment as a Path to Online Dialogic Student Development

Meaning-centered education (Kovbasyuk & Blessinger, 2013) suggests that students benefit from incorporating learning outcomes from non-cognitive domains. A radical idea in a world focused on standardization, this paradigm nevertheless holds great value for educators and students alike as we can never “find a behaviour or a state which is purely cognitive without affect nor a purely affective state without a cognitive element” (Piaget as cited in Clark & Fiske, 1982, p.130). Infusing an online curriculum with weekly formative assessment activities allowed instructors to monitor students’ states of mind while reducing negative emotional effects on learning by incorporating that feedback. Extended analysis promoted a deeper understanding of the roles that emotions and attitudes play in achieving affective learning outcomes

Intelligence territoriale et éducation au développement durable:une vision systémique de l'éducation au développement durable au service du territoire

International audienceCet article pose les bases d'une recherche sur la territorialisation de l'éducation au développement durable. Il s'agit d'étudier les conditions de mise en oeuvre d'une éducation au développement durable territorialisée qui intègre toutes les dimensions du développement durable (économique, environnementale, sociale, culturelle). Cette EDD devant être capable d'associer toutes les catégories d'acteurs territoriaux dans une perspective de co-production de compétences au service de projets de développement locaux, condition de l'émergence de territoires apprenants. L'approche dans une perspective systémique, s'adosse aux travaux de l'intelligence territoriale, ellemobilise les méthodologies du diagnostic territorial et de l'ingénierie de formation

Modelling of multiple impacts for the prediction of distortions and residual stresses induced by ultrasonic shot peening (USP)

During a manufacturing process, the ultrasonic shot peening (USP) technique can be used as the final surface treatment. The aim of this operation is to introduce surface compressive residual stresses in order to prevent crack propagation advancement. Although the numerical simulation method is able to predict the level of residual stresses in a peened part, the 3D modelling of the real USP process, in which many successive and shifted impacts take place, is very delicate to perform and costly in terms of computing time and memory space required. In this paper, a two step method based at first on the calculation of the averaged plastic strain tensor in a half-space by using a semi-analytical method and in a second time on the transfer of this plastic strain field to a finite element model is proposed in order to simulate the effects of the USP process in thin structures. The accuracy and advantages of the semi-analytical method are validated by a benchmark with several finite element codes. Experiments, similar to the Almen test, are performed on thin plates of Inconel 600. Numerical results in terms of distortions and residual stresses are compared with the experimental data

“Is This Enough?” Digitizing Liz Lerman Dance Exchange Archives Media

Special Collections in Performing Arts (SCPA) at University of Maryland Libraries collects performing arts materials that preserve performance practice, instruction, and scholarship, including the full scope of audiovisual (AV) formats. The Liz Lerman Dance Exchange Archives at SCPA contains, among common print archival materials, a significant number of AV materials. This collection is examplar of the numerous challenges facing AV digitization and preservation projects in university libraries and archives, including determining metadata standards and best practices, describing at the appropriate level, handling technical and personnel issues, and working with vendors. In this article we outline the decisions made for this project, our ultimate workflow, lessons learned, and future plans

Organisation, agrégation et visualisation d'informations médiatiques

International audienceThis article presents some data processing technics for GEOMEDIA, a platform for visualization and analysis of media information. In order to handle the complexity and the large amount of media data, we proceed in three stages. (1) Organization of the information flow in order to extract its global structure: Three dimensions (Agents x Dates x Themes) are settled for data classifying. We use the concept of " agent " , originated from Artificial Intelligence, in order to generalize the concept of " space ". (2) Aggregation of information in order to obtain a macroscopic point of view: Aggregation processes automatically decrease the structural complexity of data. Thus, they generate high-level abstractions. (3) Visualization of aggregated data: spatial projections on geometric, territorial or reticular spaces, temporal projections on timelines, thematic projections on tag clouds, etc.Cet article présente une méthode de traitement de données pour GEOMEDIA, une plateforme de visualisation et d'analyse d'informations médiatiques. Devant la complexité et la quantité des données médiatiques, nous avons trois objectifs. (1) Organisation du déluge d'informations pour en extraire la structure générale : trois dimensions (Agents × Dates × Thèmes) sont retenues pour classer les articles. Nous utilisons la notion d'« agent », issue de l'Intelligence Artificielle, pour généraliser la notion d'« espace ». (2) Agrégation de l'information pour obtenir un point de vue macroscopique sur la structure de données : des procédures automatiques d'agrégation réduisent la complexité structurelle et engendrent ainsi des abstractions de haut-niveaux. (3) Visualisation des données agrégées : projections spatiales sur des cartes géométriques, territoriales ou réticulaires, projections temporelles sur des frises chronologiques, projections thématiques sur des nuages sémantiques, etc