A taxonomy of heterogeneity and dynamics in particle swarm optimisation

We propose a taxonomy for heterogeneity and dynamics of swarms in PSO, which separates the consideration of homogeneity and heterogeneity from the presence of adaptive and non-adaptive dynamics, both at the particle and swarm level. It thus supports research into the separate and combined contributions of each of these characteristics. An analysis of the literature shows that most recent work has focussed on only parts of the taxonomy. Our results agree with prior work that both heterogeneity and dynamics are useful. However while heterogeneity does typically improve PSO, this is often dominated by the improvement due to dynamics. Adaptive strategies used to generate heterogeneity may end up sacrificing the dynamics which provide the greatest performance increase. We evaluate exemplar strategies for each area of the taxonomy and conclude with recommendations.

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.

Changes in Community Structure of Sediment Bacteria Along the Florida Coastal Everglades Marsh–Mangrove–Seagrass Salinity Gradient

Community structure of sediment bacteria in the Everglades freshwater marsh, fringing mangrove forest, and Florida Bay seagrass meadows were described based on polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) patterns of 16S rRNA gene fragments and by sequencing analysis of DGGE bands. The DGGE patterns were correlated with the environmental variables by means of canonical correspondence analysis. There was no significant trend in the Shannon–Weiner index among the sediment samples along the salinity gradient. However, cluster analysis based on DGGE patterns revealed that the bacterial community structure differed according to sites. Not only were these salinity/vegetation regions distinct but the sediment bacteria communities were consistently different along the gradient from freshwater marsh, mangrove forest, eastern-central Florida Bay, and western Florida Bay. Actinobacteria- and Bacteroidetes/Chlorobi-like DNA sequences were amplified throughout all sampling sites. More Chloroflexi and members of candidate division WS3 were found in freshwater marsh and mangrove forest sites than in seagrass sites. The appearance of candidate division OP8-like DNA sequences in mangrove sites distinguished these communities from those of freshwater marsh. The seagrass sites were characterized by reduced presence of bands belonging to Chloroflexi with increased presence of those bands related to Cyanobacteria, γ-Proteobacteria, Spirochetes, and Planctomycetes. This included the sulfate-reducing bacteria, which are prevalent in marine environments. Clearly, bacterial communities in the sediment were different along the gradient, which can be explained mainly by the differences in salinity and total phosphorus.

Patterns of Soil Bacteria and Canopy Community Structure Related to Tropical Peatland Development

Natural environmental gradients provide important information about the ecological constraints on plant and microbial community structure. In a tropical peatland of Panama, we investigated community structure (forest canopy and soil bacteria) and microbial community function (soil enzyme activities and respiration) along an ecosystem development gradient that coincided with a natural P gradient. Highly structured plant and bacterial communities that correlated with gradients in phosphorus status and soil organic matter content characterized the peatland. A secondary gradient in soil porewater NH4 described significant variance in soil microbial respiration and β-1-4-glucosidase activity. Covariation of canopy and soil bacteria taxa contributed to a better understanding of ecological classifications for biotic communities with applicability for tropical peatland ecosystems of Central America. Moreover, plants and soils, linked primarily through increasing P deficiency, influenced strong patterning of plant and bacterial community structure related to the development of this tropical peatland ecosystem.

Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea

We investigated the occurrence and activity of anaerobic ammonia oxidation (anammox) bacteria in sandy and muddy sand sediments of the southern North Sea. The presence of anammox bacteria was established through the detection of specific phosphocholine-monoether ladderane lipids, 16S rRNA gene, and hydrazine synthase (hzsA) genes. Anammox activity was measured in intact sediment cores (in situ rate) and in sediment slurries (potential rate) as the rate of N2 evolution from 15N-labeled substrates and compared to the transcriptional activity of genes of anammox bacteria. The contribution of anammox to N2 production ranged between 0% and 29%. The potential rate of anammox agreed well with the abundance of anammox bacteria 16S rRNA and hzsA gene copies and the transcriptional activity of the anammox bacteria 16S rRNA gene. We found a higher abundance and activity of anammox bacteria in sediments with higher organic carbon content and also higher activity in summer than in winter. The abundance of anammox bacteria and their potential anammox rates were similar to those reported for other marine coastal sediments, suggesting that potentially they are important contributors to the nitrogen cycle in sandy sediments of shallow continental shelf areas.

SILVER NANOPARTICLES AND THE PLANT-ASSOCIATING ABILITIES OF RHIZOBIACEAE BACTERIA

The use of nanoparticle technology in consumer products has been increasing due to their broad-spectrum antimicrobial properties. Specifically, silver nanoparticles (AgNPs) can demonstrate distinct physiochemical properties compared to bulk silver, including a large surface area to volume ratio that allows for higher reactivity with bacterial cell surfaces. AgNPs are being released into the environment, including soil ecosystems through various pathways such as points of production or during disposal of silver-containing products. This raises the concern about the potential impact on beneficial soil bacteria and their surrounding ecosystems. Members of the Rhizobiaceae family play important roles in nutrient cycling and contribute to overall soil fertility and the experiments in this thesis address the potential for AgNP-mediated toxicity on these plant-associating bacteria. Respiration analysis of Bradyrhizobium japonicum, Azospirillum brasilense, and Agrobacterium tumefaciens has revealed that AgNPs can negatively impact the growth and survival of these bacterial species, with B. japonicum being the most susceptible. Additionally, swimming motility assays using B. japonicum showed a significant decrease in colony diameter when treated with AgNPs (50 ppm). A significant decrease in root colonization of Triticum aestivum roots by A. brasilense was observed as AgNP treatment concentrations increased. Although some of the experiments could not be completed, taken together, these experiments and the research reported herein highlights the potential toxicological effects of AgNPs on bacterial species vital to the growth and health of agriculturally important crops.

The role of anaerobic bacteria in the cystic fibrosis airway

PURPOSE OF REVIEW: Anaerobic bacteria are not only normal commensals, but are also considered opportunistic pathogens and have been identified as persistent members of the lower airway community in people with cystic fibrosis of all ages and stages of disease. Currently, the role of anaerobic bacteria in cystic fibrosis lower airway disease is not well understood. Therefore, this review describes the recent studies relating to the potential pathophysiological role(s) of anaerobes within the cystic fibrosis lungs.

RECENT FINDINGS: The most frequently identified anaerobic bacteria in the lower airways are common to both cystic fibrosis and healthy lungs. Studies have shown that in cystic fibrosis, the relative abundance of anaerobes fluctuates in the lower airways with reduced lung function and increased inflammation associated with a decreased anaerobic load. However, anaerobes found within the lower airways also produce virulence factors, may cause a host inflammatory response and interact synergistically with recognized pathogens.

SUMMARY: Anaerobic bacteria are potentially members of the airway microbiota in health but could also contribute to the pathogenesis of lower airway disease in cystic fibrosis via both direct and indirect mechanisms. A personalized treatment strategy that maintains a normal microbial community may be possible in the future.

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.

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).

Viability of probiotic bacteria and some chemical and sensory characteristics in cornelian cherry juice during cold storage

Background: Increased popularity of vegetarianism, lactose intolerance, and the high cholesterol content in dairy products, are all factors that have recently increased the demand for nondairy probiotic products. The objective of this study is to evaluate the effect of refrigeration on the viability of probiotics and asses someof the chemical and sensory characteristics in cornelian cherry juice. Results: The Iranian native probiotic strain (L. casei T4) showed greater viability compared to industrial types (viable count of 8.67 log cfu/mL versus <6.0 log cfu/mL at d 28). However, this most tolerant Iranian strain, could not withstand the conditions of ‘Natural juice’ at pH 2.6 for more than 7 d. Following a pH adjusted treatment (to pH ~3.5), the viability of the strain was improved to 28 d with some evidence of increased growth of the probiotic. However, the level of antioxidant activity, anthocyanin and phenolic compounds, revealed a slight decrease during cold storage. The changes in the chemical profile of the sample containing L. casei T4 indicated fermentation activity during cold storage. Sensory evaluation results showed significant differences between samples containing L. casei TD4 and other samples in taste, odor and overall acceptance in a complimentary way. Conclusions: The results showed that low pH and presence of inhibitor phenolic compounds of cornelian cherry juice have negative effect on viability of probiotics, especially industrial strains during refrigerated storage.

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.

Taxonomy of rare congenital metabolic bone disorders

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