A Taxonomy of Big Data for Optimal Predictive Machine Learning and Data Mining

Big data comes in various ways, types, shapes, forms and sizes. Indeed, almost all areas of science, technology, medicine, public health, economics, business, linguistics and social science are bombarded by ever increasing flows of data begging to be analyzed efficiently and effectively. In this paper, we propose a rough idea of a possible taxonomy of big data, along with some of the most commonly used tools for handling each particular category of bigness. The dimensionality p of the input space and the sample size n are usually the main ingredients in the characterization of data bigness. The specific statistical machine learning technique used to handle a particular big data set will depend on which category it falls in within the bigness taxonomy. Large p small n data sets for instance require a different set of tools from the large n small p variety. Among other tools, we discuss Preprocessing, Standardization, Imputation, Projection, Regularization, Penalization, Compression, Reduction, Selection, Kernelization, Hybridization, Parallelization, Aggregation, Randomization, Replication, Sequentialization. Indeed, it is important to emphasize right away that the so-called no free lunch theorem applies here, in the sense that there is no universally superior method that outperforms all other methods on all categories of bigness. It is also important to stress the fact that simplicity in the sense of Ockham’s razor non-plurality principle of parsimony tends to reign supreme when it comes to massive data. We conclude with a comparison of the predictive performance of some of the most commonly used methods on a few data sets.

Supporting learners’ agentic engagement with feedback:a systematic review and a taxonomy of recipience processes

Much has been written in the educational psychology literature about effective feedback and how to deliver it. However, it is equally important to understand how learners actively receive, engage with, and implement feedback. This article reports a systematic review of the research evidence pertaining to this issue. Through an analysis of 195 outputs published between 1985 and early 2014, we identified various factors that have been proposed to influence the likelihood of feedback being used. Furthermore, we identified diverse interventions with the common aim of supporting and promoting learners' agentic engagement with feedback processes. We outline the various components used in these interventions, and the reports of their successes and limitations. Moreover we propose a novel taxonomy of four recipience processes targeted by these interventions. This review and taxonomy provide a theoretical basis for conceptualizing learners' responsibility within feedback dialogues and for guiding the strategic design and evaluation of interventions. Receiving feedback on one's skills and understanding is an invaluable part of the learning process, benefiting learners far more than does simply receiving praise or punishment (Black & Wiliam, 1998 Black, P., & Wiliam, D. (1998). Assessment and classroom learning. Assessment in Education: Principles, Policy & Practice, 5, 7–74. doi:10.1080/0969595980050102[Taylor & Francis Online]; Hattie & Timperley, 2007 Hattie, J., & Timperley, H. (2007). The power of feedback. Review of Educational Research, 77, 81–112. doi:10.3102/003465430298487[CrossRef], [Web of Science ®]). Inevitably, the benefits of receiving feedback are not uniform across all circumstances, and so it is imperative to understand how these gains can be maximized. There is increasing consensus that a critical determinant of feedback effectiveness is the quality of learners' engagement with, and use of, the feedback they receive. However, studies investigating this engagement are underrepresented in academic research (Bounds et al., 2013 Bounds, R., Bush, C., Aghera, A., Rodriguez, N., Stansfield, R. B., & Santeen, S. A. (2013). Emergency medicine residents' self-assessments play a critical role when receiving feedback. Academic Emergency Medicine, 20, 1055–1061. doi:10.1111/acem.12231[CrossRef], [PubMed], [Web of Science ®]), which leaves a “blind spot” in our understanding (Burke, 2009 Burke, D. (2009). Strategies for using feedback students bring to higher education. Assessment & Evaluation in Higher Education, 34, 41–50. doi:10.1080/02602930801895711[Taylor & Francis Online], [Web of Science ®]). With this blind spot in mind, the present work sets out to systematically map the research literature concerning learners' proactive recipience of feedback. We use the term “proactive recipience” here to connote a state or activity of engaging actively with feedback processes, thus emphasizing the fundamental contribution and responsibility of the learner (Winstone, Nash, Rowntree, & Parker, in press Winstone, N. E., Nash, R. A., Rowntree, J., & Parker, M. (in press). ‘It'd be useful, but I wouldn't use it’: Barriers to university students' feedback seeking and recipience. Studies in Higher Education. doi: 10.1080/03075079.2015.1130032[Taylor & Francis Online]). In other words, just as Reeve and Tseng (2011 Reeve, J., & Tseng, M. (2011). Agency as a fourth aspect of student engagement during learning activities. Contemporary Educational Psychology, 36, 257–267. doi:10.1016/j.cedpsych.2011.05.002[CrossRef], [Web of Science ®]) defined “agentic engagement” as a “student's constructive contribution into the flow of the instruction they receive” (p. 258), likewise proactive recipience is a form of agentic engagement that involves the learner sharing responsibility for making feedback processes effective.

Taxonomy and distribution of taxa in the genus Gomphonema from the Florida Everglades, U.S.A.

Located at a subtropical latitude, the expansive Florida Everglades contains a mixture of tropical and temperate diatom taxa, as well as a unique flora adapted to the calcareous, often excessively hot, seasonally flooded wetland conditions. This flora has been poorly documented taxonomically, although diatoms are recognized as important indicators of environmental change in this threatened ecosystem. Gomphonema is a dominant genus in the freshwater marsh, and is represented by highly variable species complexes, including Gomphonema gracile Ehrenberg, Gomphonema intricatum var. vibrio Ehrenberg sensu Fricke, Gomphonema vibrioides Reichardt & Lange-Bertalot and Gomphonema parvulum (Kützing) Grunow. These taxa have been shown to exhibit wide morphological variation in other regions, resulting in considerable nomenclatural confusion. We collected Gomphonema from 237 sites distributed throughout the freshwater Everglades and used qualitative and quantitative morphological data to identify 20 distinguishable populations. Taxonomie assignments were based on descriptions and/or observations of type material of relevant taxa when possible, but deviations from original morphological range descriptions were common. We then compared morphological variation in Everglades Gomphonema taxa to that reported for the same taxa in other regions and suggest revisions of taxonomie concepts when necessary.

Reporting behaviour change interventions : do the behaviour change technique taxonomy v1, and training in its use, improve the quality of intervention descriptions?

Acknowledgements This research was funded by the MRC via its Methodology Panel: ‘Strengthening evaluation and implementation by specifying components of behaviour change interventions’ Ref: G0901474/1. We thank the participants who took part in the studies that form this research. We also thank Derek Johnston (Emeritus Professor, University of Aberdeen) for his guidance on statistical analyses.

Phylogenetic relationships among hadal amphipods of the Superfamily Lysianassoidea : Implications for taxonomy and biogeography

Date of Acceptance: 30/8/15 Acknowledgements We thank the chief scientists, crew and company of the Japanese RV Hakuho-Maru (KH0703 and KH0803), the RV Tansei-Maru (KT-09-03), the RV Kairei (KR0716), the German FS Sonne (SO197 and SO 209) and the New Zealand RV Kaharoa (KAH0190, KAH1109, KAH1202, KAH1301 and KAH1310). This work was supported by the HADEEP projects, funded by the Nippon Foundation, Japan (2009765188), the Natural Environmental Research Council, UK (NE/E007171/1) and the Total Foundation, France. We acknowledge additional support from the Marine Alliance for Science and Technology for Scotland (MASTS) funded by the Scottish Funding Council (Ref: HR09011) and contributing institutions. We also acknowledge support from the Leverhulme Research Fellowship granted to SBP. Additional sea time was supported by NIWA’s ‘Impact of Resource Use on Vulnerable Deep-Sea Communities’ project (CO1_0906). From NIWA we thank Malcolm Clark, Ashley Rowden, Kareen Schnabel, Sadie Mills for logistical support at the NIWA Invertebrate Collection. We also thank Fredrik Søreide from Promare, USA, for supply of the Puerto-Rico samples, Marius Wenzel for helpful comments on manuscript drafts, and Dr. Tammy Horton (NOCS, UK) for identifying some of the earlier amphipod samples

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.

Molecular Taxonomy of Deep Sea Fishes Off the southern coast of India

CMFRI,

Taxonomy of Institutional Issues that Act as Barriers to the Implementation of Pavement Management Systems, 1994

The benefits of pavement management system when fully implemented are well known and the history of successful implementation is rich. Implementation occurs, for purposes of this paper, when the pavement management system is the critical component for making pavement decisions. This paper addresses the issues that act as barriers to full implementation of pavement management systems. Institutional barriers, not technical and financial barriers, are more commonly responsible for a pavement management systems falling short of full implementation. The paper groups these institutional issues into a general taxonomy. In general, more effort needs to be put forth by highway agencies to overcome institutional issues. Most agencies approach pavement management as a technical process, but more commonly, institutional issues become more problematic and thus require more attention paid to institutional issues. The paper concludes by summarizing the implementation process being taken by the Iowa Department of Transportation. The process was designed to overcome institutional barriers and facilitate the complete and full implementation of their pavement management system.

DNA Barcoding as a tool for Zoological Taxonomy: Identification of bony fish in the Mediterranean Sea

The description of all the species present in nature is a vast task to be fulfilled by using the classical approach of morphological description of the organisms. In recent years, the traditional taxonomy, based primarily on identification keys of species, has shown a number of limitations in the use of the distinctive features in many animal taxa and inconsistencies with the genetic data. Furthermore, the increasing need to get a true estimate of biodiversity has led Zoological Taxonomy to seek new approaches and methodologies to support the traditional methods. The classification procedure has added modern criteriasuch as the evolutionary relationships and the genetic, biochemical and morphological characteristics of the organisms.Until now the Linnean binomial was the only abbreviated code associated with the description of the morphology of a species. The new technologies aim to achieve a short nucleotide sequence of the DNA to be used as an unique and solely label for a particular species, a specific genetic barcode. For both morphological and genetic approaches, skills and experience are required. Taxonomy is one of zoological disciplines that has been benefited from the achievements reached by modern molecular biotechnology. Using a molecular approach it is possible to identify cryptic species, to establish a family relationship between species and their membership of taxonomic categories or to reconstruct the evolutionary history of a taxon.

Taxonomy of the order Mononegavirales: update 2016

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

A rehabilitation intervention to promote physical recovery following intensive care: a detailed description of construct development, rationale and content together with proposed taxonomy to capture processes in a randomised controlled trial.

Background: increasing numbers of patients are surviving critical illness, but survival may be associated with a constellation of physical and psychological sequelae that can cause on going disability and reduced health-related quality of life. Limited evidence currently exists to guide the optimum structure, timing, and content of rehabilitation programmes. There is a need to both develop and evaluate interventions to support and expedite recovery during the post-ICU discharge period. This paper describes the construct development for a complex rehabilitation intervention intended to promote physical recovery following critical illness. The intervention is currently being evaluated in a randomised trial (ISRCTN09412438; funder Chief Scientists Office, Scotland). Methods: the intervention was developed using the Medical Research Council (MRC) framework for developing complex healthcare interventions. We ensured representation from a wide variety of stakeholders including content experts from multiple specialties, methodologists, and patient representation. The intervention construct was initially based on literature review, local observational and audit work, qualitative studies with ICU survivors, and brainstorming activities. Iterative refinement was aided by the publication of a National Institute for Health and Care Excellence guideline (No. 83), publicly available patient stories (Healthtalkonline), a stakeholder event in collaboration with the James Lind Alliance, and local piloting. Modelling and further work involved a feasibility trial and development of a novel generic rehabilitation assistant (GRA) role. Several rounds of external peer review during successive funding applications also contributed to development. Results: the final construct for the complex intervention involved a dedicated GRA trained to pre-defined competencies across multiple rehabilitation domains (physiotherapy, dietetics, occupational therapy, and speech/language therapy), with specific training in post-critical illness issues. The intervention was from ICU discharge to 3 months post-discharge, including inpatient and post-hospital discharge elements. Clear strategies to provide information to patients/families were included. A detailed taxonomy was developed to define and describe the processes undertaken, and capture them during the trial. The detailed process measure description, together with a range of patient, health service, and economic outcomes were successfully mapped on to the modified CONSORT recommendations for reporting non-pharmacologic trial interventions. Conclusions: the MRC complex intervention framework was an effective guide to developing a novel post-ICU rehabilitation intervention. Combining a clearly defined new healthcare role with a detailed taxonomy of process and activity enabled the intervention to be clearly described for the purpose of trial delivery and reporting. These data will be useful when interpreting the results of the randomised trial, will increase internal and external trial validity, and help others implement the intervention if the intervention proves clinically and cost effective.

Towards an integrated taxonomy of the Merodon equestris species complex (Diptera: Syrphidae) including description of a new species, with additional data on Iberian Merodon

Study of specimens of Merodon Meigen collected in southwestern Europe resulted in new data and taxonomic changes for this genus. The cryptic species Merodon confusus sp. nov. (Merodon equestris species group) is described based on specimens collected in Cabañeros National Park, central Spain. Morphological and molecular diagnostic characters are provided to separate members of the species group. Merodon aeneus fulvus Gil Collado is proposed as a junior synonym of Merodon pumilus Macquart. The first Iberian record of Merodon rufus Meigen is reported and updates of the revision of Iberian Merodon are provided.