Linear, Deterministic, and Order-Invariant Initialization Methods for the K-Means Clustering Algorithm

Over the past five decades, k-means has become the clustering algorithm of choice in many application domains primarily due to its simplicity, time/space efficiency, and invariance to the ordering of the data points. Unfortunately, the algorithm's sensitivity to the initial selection of the cluster centers remains to be its most serious drawback. Numerous initialization methods have been proposed to address this drawback. Many of these methods, however, have time complexity superlinear in the number of data points, which makes them impractical for large data sets. On the other hand, linear methods are often random and/or sensitive to the ordering of the data points. These methods are generally unreliable in that the quality of their results is unpredictable. Therefore, it is common practice to perform multiple runs of such methods and take the output of the run that produces the best results. Such a practice, however, greatly increases the computational requirements of the otherwise highly efficient k-means algorithm. In this chapter, we investigate the empirical performance of six linear, deterministic (non-random), and order-invariant k-means initialization methods on a large and diverse collection of data sets from the UCI Machine Learning Repository. The results demonstrate that two relatively unknown hierarchical initialization methods due to Su and Dy outperform the remaining four methods with respect to two objective effectiveness criteria. In addition, a recent method due to Erisoglu et al. performs surprisingly poorly.Comment: 21 pages, 2 figures, 5 tables, Partitional Clustering Algorithms (Springer, 2014). arXiv admin note: substantial text overlap with arXiv:1304.7465, arXiv:1209.196

Brain and ventricular volume in patients with syndromic and complex craniosynostosis

textabstractPurpose: Brain abnormalities in patients with syndromic craniosynostosis can either be a direct result of the genetic defect or develop secondary to compression due to craniosynostosis, raised ICP or hydrocephalus. Today it is unknown whether children with syndromic craniosynostosis have normal brain volumes. The purpose of this study was to evaluate brain and ventricular volume measurements in patients with syndromic and complex craniosynostosis. This knowledge will improve our understanding of brain development and the origin of raised intracranial pressure in syndromic craniosynostosis. Methods: Brain and ventricular volumes were calculated from MRI scans of patients with craniosynostosis, 0.3 to 18.3 years of age. Brain volume was compared to age matched controls from the literature. All patient charts were reviewed to look for possible predictors of brain and ventricular volume. Results: Total brain volume in syndromic craniosynostosis equals that of normal controls, in the age range of 1 to 12 years. Brain growth occurred particularly in the first 5 years of age, after which it stabilized. Within the studied population, ventricular volume was significantly larger in Apert syndrome compared to all other syndromes and in patients with a Chiari I malformation. Conclusions: Patients with syndromic craniosynostosis have a normal total brain volume compared to normal controls. Increased ventricular volume is associated with Apert syndrome and Chiari I malformations, which is most commonly found in Crouzon syndrome. We advice screening of all patients with Apert and Crouzon syndrome for the development of enlarged ventricle volume and the presence of a Chiari I malformation

The Hubble Constant

I review the current state of determinations of the Hubble constant, which gives the length scale of the Universe by relating the expansion velocity of objects to their distance. There are two broad categories of measurements. The first uses individual astrophysical objects which have some property that allows their intrinsic luminosity or size to be determined, or allows the determination of their distance by geometric means. The second category comprises the use of all-sky cosmic microwave background, or correlations between large samples of galaxies, to determine information about the geometry of the Universe and hence the Hubble constant, typically in a combination with other cosmological parameters. Many, but not all, object-based measurements give $H_0$ values of around 72-74km/s/Mpc , with typical errors of 2-3km/s/Mpc. This is in mild discrepancy with CMB-based measurements, in particular those from the Planck satellite, which give values of 67-68km/s/Mpc and typical errors of 1-2km/s/Mpc. The size of the remaining systematics indicate that accuracy rather than precision is the remaining problem in a good determination of the Hubble constant. Whether a discrepancy exists, and whether new physics is needed to resolve it, depends on details of the systematics of the object-based methods, and also on the assumptions about other cosmological parameters and which datasets are combined in the case of the all-sky methods.Comment: Extensively revised and updated since the 2007 version: accepted by Living Reviews in Relativity as a major (2014) update of LRR 10, 4, 200

A review of elliptical and disc galaxy structure, and modern scaling laws

A century ago, in 1911 and 1913, Plummer and then Reynolds introduced their models to describe the radial distribution of stars in `nebulae'. This article reviews the progress since then, providing both an historical perspective and a contemporary review of the stellar structure of bulges, discs and elliptical galaxies. The quantification of galaxy nuclei, such as central mass deficits and excess nuclear light, plus the structure of dark matter halos and cD galaxy envelopes, are discussed. Issues pertaining to spiral galaxies including dust, bulge-to-disc ratios, bulgeless galaxies, bars and the identification of pseudobulges are also reviewed. An array of modern scaling relations involving sizes, luminosities, surface brightnesses and stellar concentrations are presented, many of which are shown to be curved. These 'redshift zero' relations not only quantify the behavior and nature of galaxies in the Universe today, but are the modern benchmark for evolutionary studies of galaxies, whether based on observations, N-body-simulations or semi-analytical modelling. For example, it is shown that some of the recently discovered compact elliptical galaxies at 1.5 < z < 2.5 may be the bulges of modern disc galaxies.Comment: Condensed version (due to Contract) of an invited review article to appear in "Planets, Stars and Stellar Systems"(www.springer.com/astronomy/book/978-90-481-8818-5). 500+ references incl. many somewhat forgotten, pioneer papers. Original submission to Springer: 07-June-201

Adenomatous polyposis coli (APC) gene promoter hypermethylation in primary breast cancers

Similar to findings in colorectal cancers, it has been suggested that disruption of the adenomatous polyposis coli (APC)/β-catenin pathway may be involved in breast carcinogenesis. However, somatic mutations of APC and β- catenin are infrequently reported in breast cancers, in contrast to findings in colorectal cancers. To further explore the role of the APC/β-catenin pathway in breast carcinogenesis, we investigated the status of APC gene promoter methylation in primary breast cancers and in their non-cancerous breast tissue counterparts, as well as mutations of the APC and β- catenin genes. Hypermethylation of the APC promoter CpG island was detected in 18 of 50 (36%) primary breast cancers and in none of 21 non-cancerous breast tissue samples, although no mutations of the APC and β- catenin were found. No significant associations between APC promoter hypermethylation and patient age, lymph node metastasis, oestrogen and progesterone receptor status, size, stage or histological type of tumour were observed. These results indicate that APC promoter CpG island hypermethylation is a cancer-specific change and may be a more common mechanism of inactivation of this tumour suppressor gene in primary breast cancers than previously suspected. © 2001 Cancer Research Campaign http://www.bjcancer.co

Citizen science: a new approach to advance ecology, education, and conservation

Citizen science has a long history in the ecological sciences and has made substantial contributions to science, education, and society. Developments in information technology during the last few decades have created new opportunities for citizen science to engage ever larger audiences of volunteers to help address some of ecology’s most pressing issues, such as global environmental change. Using online tools, volunteers can find projects that match their interests and learn the skills and protocols required to develop questions, collect data, submit data, and help process and analyze data online. Citizen science has become increasingly important for its ability to engage large numbers of volunteers to generate observations at scales or resolutions unattainable by individual researchers. As a coupled natural and human approach, citizen science can also help researchers access local knowledge and implement conservation projects that might be impossible otherwise. In Japan, however, the value of citizen science to science and society is still underappreciated. Here we present case studies of citizen science in Japan, the United States, and the United Kingdom, and describe how citizen science is used to tackle key questions in ecology and conservation, including spatial and macro-ecology, management of threatened and invasive species, and monitoring of biodiversity. We also discuss the importance of data quality, volunteer recruitment, program evaluation, and the integration of science and human systems in citizen science projects. Finally, we outline some of the primary challenges facing citizen science and its future.Dr. Janis L. Dickinson was the keynote speaker at the international symposium at the 61th annual meeting of the Ecological Society of Japan. We appreciate the Ministry of Education, Culture, Sports, Science and Technology in Japan for providing grant to Hiromi Kobori (25282044). Tatsuya Amano is financially supported by the European Commission’s Marie Curie International Incoming Fellowship Programme (PIIF-GA-2011- 303221). The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the funding agencies or the Department of the Interior or the US Government.This is the final version of the article. It was first available from Springer via http://dx.doi.org/10.1007/s11284-015-1314-

From Global to Local and Vice Versa: On the Importance of the 'Globalization' Agenda in Continental Groundwater Research and Policy-Making.

Groundwater is one of the most important environmental resources and its use continuously rises globally for industrial, agricultural, and drinking water supply purposes. Because of its importance, more knowledge about the volume of usable groundwater is necessary to satisfy the global demand. Due to the challenges in quantifying the volume of available global groundwater, studies which aim to assess its magnitude are limited in number. They are further restricted in scope and depth of analysis as, in most cases, they do not explain how the estimates of global groundwater resources have been obtained, what methods have been used to generate the figures and what levels of uncertainty exist. This article reviews the estimates of global groundwater resources. It finds that the level of uncertainty attached to existing numbers often exceeds 100 % and strives to establish the reasons for discrepancy. The outcome of this study outlines the need for a new agenda in water research with a more pronounced focus on groundwater. This new research agenda should aim at enhancing the quality and quantity of data provision on local and regional groundwater stocks and flows. This knowledge enhancement can serve as a basis to improve policy-making on groundwater resources globally. Research-informed policies will facilitate more effective groundwater management practices to ensure a more rapid progress of the global water sector towards the goal of sustainability

ATP release via anion channels

ATP serves not only as an energy source for all cell types but as an ‘extracellular messenger-for autocrine and paracrine signalling. It is released from the cell via several different purinergic signal efflux pathways. ATP and its Mg2+ and/or H+ salts exist in anionic forms at physiological pH and may exit cells via some anion channel if the pore physically permits this. In this review we survey experimental data providing evidence for and against the release of ATP through anion channels. CFTR has long been considered a probable pathway for ATP release in airway epithelium and other types of cells expressing this protein, although non-CFTR ATP currents have also been observed. Volume-sensitive outwardly rectifying (VSOR) chloride channels are found in virtually all cell types and can physically accommodate or even permeate ATP4- in certain experimental conditions. However, pharmacological studies are controversial and argue against the actual involvement of the VSOR channel in significant release of ATP. A large-conductance anion channel whose open probability exhibits a bell-shaped voltage dependence is also ubiquitously expressed and represents a putative pathway for ATP release. This channel, called a maxi-anion channel, has a wide nanoscopic pore suitable for nucleotide transport and possesses an ATP-binding site in the middle of the pore lumen to facilitate the passage of the nucleotide. The maxi-anion channel conducts ATP and displays a pharmacological profile similar to that of ATP release in response to osmotic, ischemic, hypoxic and salt stresses. The relation of some other channels and transporters to the regulated release of ATP is also discussed