Introduction to Domain-Driven Data Mining Special Section

In the last decade, data mining has emerged as one of the most dynamic and lively areas in information technology. Although many algorithms and techniques for data mining have been proposed, they either focus on domain independent techniques or on very specific domain problems. A general requirement in bridging the gap between academia and business is to cater to general domain-related issues surrounding real-life applications, such as constraints, organizational factors, domain expert knowledge, domain adaption, and operational knowledge. Unfortunately, these either have not been addressed, or have not been sufficiently addressed, in current data mining research and development.Domain-Driven Data Mining (D3M) aims to develop general principles, methodologies, and techniques for modeling and merging comprehensive domain-related factors and synthesized ubiquitous intelligence surrounding problem domains with the data mining process, and discovering knowledge to support business decision-making. This paper aims to report original, cutting-edge, and state-of-the-art progress in D3M. It covers theoretical and applied contributions aiming to: 1) propose next-generation data mining frameworks and processes for actionable knowledge discovery, 2) investigate effective (automated, human and machine-centered and/or human-machined-co-operated) principles and approaches for acquiring, representing, modelling, and engaging ubiquitous intelligence in real-world data mining, and 3) develop workable and operational systems balancing technical significance and applications concerns, and converting and delivering actionable knowledge into operational applications rules to seamlessly engage application processes and systems.

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

Background. The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them. Results. Phylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 103 to ca. 104 nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 105 nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches. Conclusions. Our study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.

Pulsating or not? A search for hidden pulsations below the red edge of the ZZ Ceti instability strip

The location of the red edge of the ZZ Ceti instability strip is defined observationally as being the lowest temperature for which a white dwarf with a H-rich atmosphere (DA) is known to exhibit periodic brightness variations. Whether this cut-off in flux variations is actually due to a cessation of pulsation or merely due to the attenuation of any variations by the convection zone, rendering them invisible, is not clear. The latter is a theoretical possibility because with decreasing effective temperature, the emergent flux variations become an ever smaller fraction of the amplitude of the flux variations in the interior. In contrast to the flux variations, the visibility of the velocity variations associated with the pulsations is not thought to be similarly affected. Thus, models imply that were it still pulsating, a white dwarf just below the observed red edge should show velocity variations. In order to test this possibility, we used time-resolved spectra of three DA white dwarfs that do not show photometric variability, but which have derived temperatures only slightly lower than the coolest ZZ Ceti variables. We find that none of our three targets show significant periodic velocity variations, and set 95% confidence limits on amplitudes of 3.0, 5.2, and 8.8 km s(-1). Thus, for two out of our three objects, we can rule out velocity variations as large as 5.4 km s(-1) observed for the strongest mode in the cool white dwarf pulsator ZZ Psc. In order to verify our procedures, we also examined similar data of a known ZZ Ceti, HL Tau 76. Applying external information from the light curve, we detect significant velocity variations for this object with amplitudes of up to 4 km s(-1). Our results suggest that substantial numbers of pulsators having large velocity amplitudes do not exist below the observed photometric red edge and that the latter probably reflects a real termination of pulsations.

Physiological effects of platyhelminth RFamide peptides on muscle-strip preparations of Fasciola hepatica (Trematoda: Digenea)

The effects of each of the known platyhelminth neuropeptides were determined on muscle-strip preparations from the liver fluke, Fasciola hepatica. The activity of synthetic replicates of the C-terminal nonapeptide of neuropeptide F (NPF9, Moniezia expansa), and the FMRFamide-related peptides (FaRPs), GNFFRFamide, RYIRFamide, GYIRFamide and YIRFamide, were examined. Muscle-strip activity was recorded from 1 mm segments of muscle prepared from 28 to 32-day-old worms, using a photo-optic transducer system. None of the peptides (less than or equal to 10 mu M) altered baseline tension significantly; however, each of the peptides increased the amplitude and frequency of muscle contraction. The threshold for activity of each of the peptides examined was, respectively, 1 nM (RYIRFamide), 0.3 mu M (GYIRFamide and YIRFamide), and 10 mu M (GNFFRFamide and NPF9). All of the effects were reversible and repeatable, following wash-out. Muscle-strip integrity was tested following experimentation, using arecoline (10 mu M) and high-K+ bathing medium (90 mM K+).

'Mining money': science, legal technologies & working the borderlands of global finance

This paper explores the roles of science and market devices in the commodification of ‘nature’ and the configuration of flows of speculative capital. It focuses on mineral prospecting and the market for shares in ‘junior’ mining companies. In recent years these companies have expanded the reach of their exploration activities overseas, taking advantage of innovations in exploration methodologies and the liberalisation of fiscal and property regimes in ‘emerging’ mineral rich developing countries. Recent literature has explored how the reconfiguration of notions of ‘risk’ has structured the uneven distribution of rents. It is increasingly evident that neoliberal framing of environmental, political, social and economic risks has set in motion overflows that multinational mining capital had not bargained for (e.g. nationalisation, violence and political resistance). However, the role of ‘geological risk’ in animating flows of mining finance is often assumed as a ‘technical’ given. Yet geological knowledge claims, translated locally, designed to travel globally, assemble heterogeneous elements within distanciated regimes of metrology, valuation and commodity production. This paper explores how knowledge of nature is enrolled within systems of property relations, focusing on the genealogy of the knowledge practices that animate contemporary circuits of speculative mining finance. It argues that the financing of mineral prospecting mobilises pragmatic and situated forms of knowledge rather than actuarially driven calculations that promise predictability. A Canadian public enquiry struck in the wake of scandal associated with Bre-X’s prospecting activities in Indonesia is used to glean insights into the ways in which the construction of a system of public warrant to underpin financial speculation is predicated upon particular subjectivities and the outworking of everyday practices and struggles over ‘value’. Reflection on practical investments in processes of standardisation, rituals of verification and systems of accreditation reveal much about how the materiality of things shape the ways in which regional and global financial circuits are integrated, selectively transforming existing social relations and forms of knowledge production.

Two non-synonymous markers in PTPN21, identified by genome-wide association study data-mining and replication, are associated with schizophrenia

We conducted data-mining analyses of genome wide association (GWA) studies of the CATIE and MGS-GAIN datasets, and found 13 markers in the two physically linked genes, PTPN21 and EML5, showing nominally significant association with schizophrenia. Linkage disequilibrium (LD) analysis indicated that all 7 markers from PTPN21 shared high LD (r(2)>0.8), including rs2274736 and rs2401751, the two non-synonymous markers with the most significant association signals (rs2401751, P=1.10 × 10(-3) and rs2274736, P=1.21 × 10(-3)). In a meta-analysis of all 13 replication datasets with a total of 13,940 subjects, we found that the two non-synonymous markers are significantly associated with schizophrenia (rs2274736, OR=0.92, 95% CI: 0.86-0.97, P=5.45 × 10(-3) and rs2401751, OR=0.92, 95% CI: 0.86-0.97, P=5.29 × 10(-3)). One SNP (rs7147796) in EML5 is also significantly associated with the disease (OR=1.08, 95% CI: 1.02-1.14, P=6.43 × 10(-3)). These 3 markers remain significant after Bonferroni correction. Furthermore, haplotype conditioned analyses indicated that the association signals observed between rs2274736/rs2401751 and rs7147796 are statistically independent. Given the results that 2 non-synonymous markers in PTPN21 are associated with schizophrenia, further investigation of this locus is warranted.