Indication strength of coenological similarity patterns based on genus-level taxon lists and prevalence distribution

Several methods and indicators can be used to evaluate the coenological state of a given habitat, the ones which can be created simply, quickly, standardizably and reliably and which can be used to exactly quantify the state of a given habitat in point of numbers can be of outstanding practical importance in ecology. One possible method is the examination of the genera which can be found in a given habitat in great abundance and have little number of species and various ecological characteristics. For this purpose one of the most appropriate groups is that of ground-dwelling oribatid mites (Acari: Oribatida). In our research, joining the bioindication methodological project of the “Adaptation to Climate Change” Research Group of the Hungarian Academy of Sciences, the indication strength of genus-level taxon lists and the effects of the main pattern-generating factors creating similarity patterns were analysed with the help of data series on oribatid mites collected by us and originating from literature. Our aim was to develop a method with the help of which the difference expressed with distance functions between two oribatid mite genus lists originating from any sources can correspond to spatial and temporal scales. Our results prove that these genus lists are able to express the spatial distance of the habitats. With the help of this base of comparison changes in disturbed or transformed habitats can be expressed by means of oribatid mite communities, with spatial and temporal distances.

Discovery of "Warm Dust" galaxies in clusters at z ~ 0.3: evidence for stripping of cool dust in the dense environment?

Using far-infrared imaging from the "Herschel Lensing Survey," we derive dust properties of spectroscopically confirmed cluster member galaxies within two massive systems at z ~ 0.3: the merging Bullet Cluster and the more relaxed MS2137.3-2353. Most star-forming cluster sources (~90%) have characteristic dust temperatures similar to local field galaxies of comparable infrared (IR) luminosity (T_dust ~ 30 K). Several sub-luminous infrared galaxy (LIRG; L_IR < 10^11 L_☉) Bullet Cluster members are much warmer (T_dust > 37 K) with far-infrared spectral energy distribution (SED) shapes resembling LIRG-type local templates. X-ray and mid-infrared data suggest that obscured active galactic nuclei do not contribute significantly to the infrared flux of these "warm dust" galaxies. Sources of comparable IR luminosity and dust temperature are not observed in the relaxed cluster MS2137, although the significance is too low to speculate on an origin involving recent cluster merging. "Warm dust" galaxies are, however, statistically rarer in field samples (>3σ), indicating that the responsible mechanism may relate to the dense environment. The spatial distribution of these sources is similar to the whole far-infrared bright population, i.e., preferentially located in the cluster periphery, although the galaxy hosts tend toward lower stellar masses (M_* < 10^10 M_☉). We propose dust stripping and heating processes which could be responsible for the unusually warm characteristic dust temperatures. A normal star-forming galaxy would need 30%-50% of its dust removed (preferentially stripped from the outer reaches, where dust is typically cooler) to recover an SED similar to a "warm dust" galaxy. These progenitors would not require a higher IR luminosity or dust mass than the currently observed normal star-forming population.

Biological fluorination from the sea : discovery of a SAM-dependent nucleophilic fluorinating enzyme from the marine-derived bacterium Streptomyces xinghaiensis NRRL B24674

We thank Prof. David O’Hagan and Dr Qingzhi Zhang (University of St Andrews, UK) for their helpful discussion and for providing the synthetic 50 -FDA sample. This work is supported by National Natural Science Foundation of China (No. 81503086), a starting funding (No. 20140520) from Tianjin University of Science & Technology, a research funding of “1000 Talents Plan” of Tianjin (to LM) and Foundation of Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education and Tianjin Key Lab of Industrial Microbiology (No. 2015IM106)

Reference list of 265 sources used for the discovery of relationships between data clusters and metadata properties

Visual cluster analysis provides valuable tools that help analysts to understand large data sets in terms of representative clusters and relationships thereof. Often, the found clusters are to be understood in context of belonging categorical, numerical or textual metadata which are given for the data elements. While often not part of the clustering process, such metadata play an important role and need to be considered during the interactive cluster exploration process. Traditionally, linked-views allow to relate (or loosely speaking: correlate) clusters with metadata or other properties of the underlying cluster data. Manually inspecting the distribution of metadata for each cluster in a linked-view approach is tedious, specially for large data sets, where a large search problem arises. Fully interactive search for potentially useful or interesting cluster to metadata relationships may constitute a cumbersome and long process. To remedy this problem, we propose a novel approach for guiding users in discovering interesting relationships between clusters and associated metadata. Its goal is to guide the analyst through the potentially huge search space. We focus in our work on metadata of categorical type, which can be summarized for a cluster in form of a histogram. We start from a given visual cluster representation, and compute certain measures of interestingness defined on the distribution of metadata categories for the clusters. These measures are used to automatically score and rank the clusters for potential interestingness regarding the distribution of categorical metadata. Identified interesting relationships are highlighted in the visual cluster representation for easy inspection by the user. We present a system implementing an encompassing, yet extensible, set of interestingness scores for categorical metadata, which can also be extended to numerical metadata. Appropriate visual representations are provided for showing the visual correlations, as well as the calculated ranking scores. Focusing on clusters of time series data, we test our approach on a large real-world data set of time-oriented scientific research data, demonstrating how specific interesting views are automatically identified, supporting the analyst discovering interesting and visually understandable relationships.

Discovery of relict subglacial lakes and their geometry and mechanism of drainage

Recent proxy measurements reveal that subglacial lakes beneath modern ice sheets periodically store and release large volumes of water, providing an important but poorly understood influence on contemporary ice dynamics and mass balance. This is because direct observations of how lake drainage initiates and proceeds are lacking. Here we present physical evidence of the mechanism and geometry of lake drainage from the discovery of relict subglacial lakes formed during the last glaciation in Canada. These palaeo-subglacial lakes comprised shallow (<10 m) lenses of water perched behind ridges orientated transverse to ice flow. We show that lakes periodically drained through channels incised into bed substrate (canals). Canals sometimes trend into eskers that represent the depositional imprint of the last high-magnitude lake outburst. The subglacial lakes and channels are preserved on top of glacial lineations, indicating long-term re-organization of the subglacial drainage system and coupling to ice flow.

Discovery of WASP-113b and WASP-114b, two inflated hot-Jupiters with contrasting densities

We present the discovery and characterisation of the exoplanets WASP-113b and WASP-114b by the WASP survey, SOPHIE and CORALIE. The planetary nature of the systems was established by performing follow-up photometric and spectroscopic observations. The follow-up data were combined with the WASP-photometry and analysed with an MCMC code to obtain system parameters. The host stars WASP-113 and WASP-114 are very similar. They are both early G-type stars with an effective temperature of ~5900K, [Fe/H] ~0.12 and T_{eff} ~4.1 dex. However, WASP-113 is older than WASP-114. Although the planetary companions have similar radii, WASP-114b is almost 4 times heavier than WASP-113b. WASP-113b has a mass of 0.48 M_{Jup} and an orbital period of ~4.5 days; WASP-114b has a mass of 1.77 M_{Jup} and an orbital period of ~1.5 days. Both planets have inflated radii, in particular WASP-113 with a radius anomaly of Re=0.35. The high scale height of WASP-113b (~950 km ) makes it a good target for follow-up atmospheric observations.

Discovery of Novel Bacterial Cell-Penetrating Phylloseptins in Defensive Skin Secretions of the South American Hylid Frogs, Phyllomedusa duellmani and Phyllomedusa coelestis

Phylloseptin (PS) peptides, derived from South American hylid frogs (subfamily Phyllomedusinae), have been found to have broad-spectrum antimicrobial activities and relatively low haemolytic activities. Although PS peptides have been identified from several well-known and widely-distributed species of the Phyllomedusinae, there remains merit in their study in additional, more obscure and specialised members of this taxon. Here, we report the discovery of two novel PS peptides, named PS-Du and PS-Co, which were respectively identified for the first time and isolated from the skin secretions of Phyllomedusa duellmani and Phyllomedusa coelestis. Their encoding cDNAs were cloned, from which it was possible to deduce the entire primary structures of their biosynthetic precursors. Reversed-phase high-performance liquid chromatography (RP-HPLC) and tandem mass spectrometry (MS/MS) analyses were employed to isolate and structurally-characterise respective encoded PS peptides from skin secretions. The peptides had molecular masses of 2049.7 Da (PS-Du) and 1972.8 Da (PS-Co). They shared typical N-terminal sequences and C-terminal amidation with other known phylloseptins. The two peptides exhibited growth inhibitory activity against E. coli (NCTC 10418), as a standard Gram-negative bacterium, S. aureus (NCTC 10788), as a standard Gram-positive bacterium and C. albicans (NCPF 1467), as a standard pathogenic yeast, all as planktonic cultures. Moreover, both peptides demonstrated the capability of eliminating S. aureus biofilm.

Discovery of a New Retrograde Trans-Neptunian Object: Hint of a Common Orbital Plane for Low Semimajor Axis, High-inclination TNOs and Centaurs

Although the majority of Centaurs are thought to have originated in the scattered disk, with the high-inclination members coming from the Oort cloud, the origin of the high-inclination component of trans-Neptunian objects (TNOs) remains uncertain. We report the discovery of a retrograde TNO, which we nickname “Niku,” detected by the Pan-STARRS 1 Outer Solar System Survey. Our numerical integrations show that the orbital dynamics of Niku are very similar to that of 2008 KV42 (Drac), with a half-life of ˜500 Myr. Comparing similar high-inclination TNOs and Centaurs (q > 10 au, a <100 au, and i > 60°), we find that these objects exhibit a surprising clustering of ascending node, and occupy a common orbital plane. This orbital configuration has high statistical significance: 3.8-σ. An unknown mechanism is required to explain the observed clustering. This discovery may provide a pathway to investigating a possible reservoir of high-inclination objects.

Automated Discovery of Social Networks in Online Learning Communities

As a way to gain greater insights into the operation of online communities, this dissertation applies automated text mining techniques to text-based communication to identify, describe and evaluate underlying social networks among online community members. The main thrust of the study is to automate the discovery of social ties that form between community members, using only the digital footprints left behind in their online forum postings. Currently, one of the most common but time consuming methods for discovering social ties between people is to ask questions about their perceived social ties. However, such a survey is difficult to collect due to the high investment in time associated with data collection and the sensitive nature of the types of questions that may be asked. To overcome these limitations, the dissertation presents a new, content-based method for automated discovery of social networks from threaded discussions, referred to as ‘name network’. As a case study, the proposed automated method is evaluated in the context of online learning communities. The results suggest that the proposed ‘name network’ method for collecting social network data is a viable alternative to costly and time-consuming collection of users’ data using surveys. The study also demonstrates how social networks produced by the ‘name network’ method can be used to study online classes and to look for evidence of collaborative learning in online learning communities. For example, educators can use name networks as a real time diagnostic tool to identify students who might need additional help or students who may provide such help to others. Future research will evaluate the usefulness of the ‘name network’ method in other types of online communities.

Eco-Taxonomic Insights into Actinomycete Symbionts of Termites for Discovery of Novel Bioactive Compounds

Termites play a major role in foraging and degradation of plant biomass as well as cultivating bioactive microorganisms for their defense. Current advances in "omics'' sciences are revealing insights into function-related presence of these symbionts, and their related biosynthetic activities and genes identified in gut symbiotic bacteria might offer a significant potential for biotechnology and biodiscovery. Actinomycetes have been the major producers of bioactive compounds with an extraordinary range of biological activities. These metabolites have been in use as anticancer agents, immune suppressants, and most notably, as antibiotics. Insect-associated actinomycetes have also been reported to produce a range of antibiotics such as dentigerumycin and mycangimycin. Advances in genomics targeting a single species of the unculturable microbial members are currently aiding an improved understanding of the symbiotic interrelationships among the gut microorganisms as well as revealing the taxonomical identity and functions of the complex multilayered symbiotic actinofloral layers. If combined with target-directed approaches, these molecular advances can provide guidance towards the design of highly selective culturing methods to generate further information related to the physiology and growth requirements of these bioactive actinomycetes associated with the termite guts. This chapter provides an overview on the termite gut symbiotic actinoflora in the light of current advances in the "omics'' science, with examples of their detection and selective isolation from the guts of the Sunshine Coast regional termite Coptotermes lacteus in Queensland, Australia.

Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis

Mycobacterium avium subsp. paratuberculosis is an important animal pathogen widely disseminated in the environment that has also been associated with Crohn's disease in humans. Three M. avium subsp. paratuberculosis genomotypes are recognized, but genomic differences have not been fully described. To further investigate these potential differences, a 60-mer oligonucleotide microarray (designated the MAPAC array), based on the combined genomes of M. avium subsp. paratuberculosis (strain K-10) and Mycobacterium avium subsp. hominissuis (strain 104), was designed and validated. By use of a test panel of defined M. avium subsp. paratuberculosis strains, the MAPAC array was able to identify a set of large sequence polymorphisms (LSPs) diagnostic for each of the three major M. avium subsp. paratuberculosis types. M. avium subsp. paratuberculosis type II strains contained a smaller genomic complement than M. avium subsp. paratuberculosis type I and M. avium subsp. paratuberculosis type III genomotypes, which included a set of genomic regions also found in M. avium subsp. hominissuis 104. Specific PCRs for genes within LSPs that differentiated M. avium subsp. paratuberculosis types were devised and shown to accurately screen a panel (n = 78) of M. avium subsp. paratuberculosis strains. Analysis of insertion/deletion region INDEL12 showed deletion events causing a reduction in the complement of mycobacterial cell entry genes in M. avium subsp. paratuberculosis type II strains and significantly altering the coding of a major immunologic protein (MPT64) associated with persistence and granuloma formation. Analysis of MAPAC data also identified signal variations in several genomic regions, termed variable genomic islands (vGIs), suggestive of transient duplication/deletion events. vGIs contained significantly low GC% and were immediately flanked by insertion sequences, integrases, or short inverted repeat sequences. Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology.

Weak reasoning argumentative theory. A dialogical approach for the discovery of philosophy in high schools

In the literature on philosophical practices, despite the crucial role that argumentation plays in these activities, no specific argumentative theories have ever been proposed to assist the figure of the facilitator in conducting philosophical dialogue and to enhance student’s critical thinking skills. The dissertation starts from a cognitive perspective that challenges the classic Cartesian notion of rationality by focusing on limits and biases of human reasoning. An argumentative model (WRAT – Weak Reasoning Argumentative Theory) is then outlined in order to respond to the needs of philosophical dialogue. After justifying the claim that this learning activity, among other inductive methodologies, is the most suitable for critical thinking education, I inquired into the specific goal of ‘arguing’ within this context by means of the tools provided by Speech Act Theory: the speaker’s intention is to construct new knowledge by questioning her own and other’s beliefs. The model proposed has been theorized on this assumption, starting from which the goals, and, in turn, the related norms, have been pinpointed. In order to include all the epistemic attitudes required to accomplish the complex task of arguing in philosophical dialogue, I needed to integrate two opposed cognitive accounts, Dual Process Theory and Evolutionary Approach, that, although they provide incompatible descriptions of reasoning, can be integrated to provide a normative account of argumentation. The model, apart from offering a theoretical contribution to argumentation studies, is designed to be applied to the Italian educational system, in particular to classes in technical and professional high schools belonging to the newly created network Inventio. This initiative is one of the outcomes of the research project by the same name, which also includes an original Syllabus, research seminars, a monitoring action and publications focused on introducing philosophy, in the form of workshop activities, into technical and professional schools.

(Table 2) Similarity Indexes (Pearson's correlation coefficient) of the silicoflagellate assemblages of IODP Exp302

The silicoflagellate and ebridian assemblages in early middle Eocene Arctic cores obtained by IODP Expedition 302 (ACEX) were studied in order to decipher the paleoceanography of the upper water column. The assemblages in Lithologic Unit 2 (49.7-45.1 Ma), one of the biosiliceous intervals, were usually endemic as compared to the assemblages that occurred outside of the Arctic Ocean. The presence of these endemic assemblages is probably due to a unique environmental setting, controlled by the degree of mixing between the low-salinity Arctic waters and relatively high salinity waters supplied from outside the Arctic Ocean, such as the Atlantic and possibly the Western Siberian Sea. Using the basin-to-basin fractionation model, the early middle Eocene Arctic Ocean corresponds to an estuarine circulation type, which includes the modern-day Black Sea. The abundant down-core occurrence of ebridians strongly suggests the past presence of low-salinity waters, and may indicate that low oxygen concentrations prevailed in the euphotic layer, on the basis of the ecology of the modern ebridian Hermesinum adriaticum.

SELF-SIMILARITY AND LAMPERTI CONVERGENCE FOR FAMILIES OF STOCHASTIC PROCESSES

We define a new type of self-similarity for one-parameter families of stochastic processes, which applies to certain important families of processes that are not self-similar in the conventional sense. This includes Hougaard Levy processes such as the Poisson processes, Brownian motions with drift and the inverse Gaussian processes, and some new fractional Hougaard motions defined as moving averages of Hougaard Levy process. Such families have many properties in common with ordinary self-similar processes, including the form of their covariance functions, and the fact that they appear as limits in a Lamperti-type limit theorem for families of stochastic processes.

Circular proteins in plants - Solution structure of a novel macrocyclic trypsin inhibitor from Momordica cochinchinensis

Much interest has been generated by recent reports on the discovery of circular (i.e. head-to-tail cyclized) proteins in plants. Here we report the three-dimensional structure of one of the newest such circular proteins, MCoTI-II, a novel trypsin inhibitor from Momordica cochinchinensis, a member of the Cucurbitaceae plant family. The structure consists of a small beta -sheet, several turns, and a cystine knot arrangement of the three disulfide bonds. Interestingly, the molecular topology is similar to that of the plant cyclotides (Craik, D. J., Daly, N. L., Bond, T., and Waine, C. (1999) J. Mol. Biol, 294, 1327-1336), which derive from the Rubiaceae and Violaceae plant families, have antimicrobial activities, and exemplify the cyclic cystine knot structural motif as part of their circular backbone. The sequence, biological activity, and plant family of MCoTI-II are all different from known cyclotides. However, given the structural similarity, cyclic backbone, and plant origin of MCoTI-II, we propose that MCoTI-II can be classified as a new member of the cyclotide class of proteins. The expansion of the cyclotides to include trypsin inhibitory activity and a new plant family highlights the importance and functional variability of circular proteins and the fact that they are more common than has previously been believed, Insights into the possible roles of backbone cyclization have been gained by a comparison of the structure of MCoTI-II with the homologous acyclic trypsin inhibitors CMTI-I and EETI-II from the Cucurbitaceae plant family.