On the Schoenberg Transformations in Data Analysis: Theory and Illustrations

The class of Schoenberg transformations, embedding Euclidean distances into higher dimensional Euclidean spaces, is presented, and derived from theorems on positive definite and conditionally negative definite matrices. Original results on the arc lengths, angles and curvature of the transformations are proposed, and visualized on artificial data sets by classical multidimensional scaling. A simple distance-based discriminant algorithm illustrates the theory, intimately connected to the Gaussian kernels of Machine Learning

Simultaneous determination of natural and synthetic steroid estrogens and their conjugates in aqueous matrices by liquid chromatography / mass spectrometry

An analytical method for the simultaneous determination of nine free and conjugated steroid estrogens was developed with application to environmental aqueous matrices. Solid phase extraction (SPE) was employed for isolation and concentration, with detection by liquid chromatography/mass spectrometry (LC/MS) using electrospray ionisation (ESI) in the negative mode. Method recoveries for various aqueous matrices (wastewater, lake and drinking water) were determined, recoveries proving to be sample dependent. When spiked at 50 ng/l concentrations in sewage influent, recoveries ranged from 62-89 % with relative standard deviations (RSD) < 8.1 %. In comparison, drinking water spiked at the same concentrations had recoveries between 82-100 % with an RSD < 5%. Ion suppression is a known phenomenon when using ESI; hence its impact on method recovery was elucidated for raw sewage. Both ion suppression from matrix interferences and the extraction procedure has bearing on the overall method recovery. Analysis of municipal raw sewage identified several of the analytes of interest at ng/l concentrations, estriol (E3) being the most abundant. Only one conjugate, estrone 3-sulphate (E1-3S) was observe

Anaerobic removal of 1-methoxy-2-propanol under ambient temperature in an EGSB reactor

Two laboratory-scale expanded granular sludge bed (EGSB) reactors were operated at 18 and 25 C, respectively, for the treatment of synthetic wastewater composed of ethanol and 1-methoxy-2-propanol (M2P) in a mass ratio of 4:1. Reactors were operated first with continuous wastewater supply and after with discontinuous substrate supply (5 days a week, 16 h a day) to simulate shift working conditions. Under continuous wastewater supply chemical oxygen demand (COD), removal efficiency higher than 95 % was achieved at the end of the trial applying organic loading rates (OLR) of 29 and 43 kg COD m-3 day-1 at 18 and 25 C; thus, corresponding to M2P OLR of 6.4 and 9.3 kg COD m-3 day-1, respectively. During intermittent supply of substrate, good performance was recorded at both temperatures with an OLR of 30 kg COD m-3 day-1 (M2P OLR of 6.6 kg COD m-3 day-1). After 56 h without substrate supply, a decline in methane yield of 15¿30 % was observed due to the deactivation of the biomass. Specific methanogenic activity (SMA) assays were carried out at the end of the experiments. SMA values using 1-methoxy-2-propanol as substrate were 24.3 and 7.8 ml CH4 gVSS-1 day-1 at 25 C and at 18 C, respectively. This is the first attempt to investigate the removal of 1-methoxy-2-propanol by EGSB reactors

Symmetry structure in discrete models of biochemical systems : natural subsystems and the weak control hierarchy in a new model of computation driven by interactions

© 2015 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.Interaction Computing (IC) is inspired by the observation that cell metabolic/regulatory systems construct order dynamically, through constrained interactions between their components and based on a wide range of possible inputs and environmental conditions. The goals of this work are (1) to identify and understand mathematically the natural subsystems and hierarchical relations in natural systems enabling this, and (2) to use the resulting insights to define a new model of computation based on interactions that is useful for both biology and computation. The dynamical characteristics of the cellular pathways studied in Systems Biology relate, mathematically, to the computational characteristics of automata derived from them, and their internal symmetry structures to computational power. Finite discrete automata models of biological systems such as the lac operon, Krebs cycle, and p53-mdm2 genetic regulation constructed from Systems Biology models have canonically associated algebraic structures { transformation semigroups. These contain permutation groups (local substructures exhibiting symmetry) that correspond to "pools of reversibility". These natural subsystems are related to one another in a hierarchical manner by the notion of "weak control ". We present natural subsystems arising from several biological examples and their weak control hierarchies in detail. Finite simple non-abelian groups (SNAGs) are found in biological examples and can be harnessed to realize nitary universal computation. This allows ensembles of cells to achieve any desired finitary computational transformation, depending on external inputs, via suitably constrained interactions. Based on this, interaction machines that grow and change their structure recursively are introduced and applied, providing a natural model of computation driven by interactions.Peer reviewe

Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific

Natural Environment Research Council (NERC) (NE/E01559X/1)

Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseqTM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs

Teachers' ideas versus experts' descriptions of 'the good teacher' in postgraduate medical education: implications for implementation. A qualitative study

Contains fulltext : 96394.pdf (publisher's version ) (Open Access)BACKGROUND: When innovations are introduced in medical education, teachers often have to adapt to a new concept of what being a good teacher includes. These new concepts do not necessarily match medical teachers' own, often strong beliefs about what it means to be a good teacher.Recently, a new competency-based description of the good teacher was developed and introduced in all the Departments of Postgraduate Medical Education for Family Physicians in the Netherlands. We compared the views reflected in the new description with the views of teachers who were required to adopt the new framework. METHODS: Qualitative study. We interviewed teachers in two Departments of Postgraduate Medical Education for Family Physicians in the Netherlands. The transcripts of the interviews were analysed independently by two researchers, who coded and categorised relevant fragments until consensus was reached on six themes. We investigated to what extent these themes matched the new description. RESULTS: Comparing the teachers' views with the concepts described in the new competency-based framework is like looking into two mirrors that reflect clearly dissimilar images. At least two of the themes we found are important in relation to the implementation of new educational methods: the teachers' identification and organisational culture. The latter plays an important role in the development of teachers' ideas about good teaching. CONCLUSIONS: The main finding of this study is the key role played by the teachers' feelings regarding their professional identity and by the local teaching culture in shaping teachers' views and expectations regarding their work. This suggests that in implementing a new teaching framework and in faculty development programmes, careful attention should be paid to teachers' existing identification model and the culture that fostered it

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns