A computer-aided diagnostic system to characterize CT focal liver lesions: design and optimization of a neural network classifier

In this paper, a computer-aided diagnostic (CAD) system for the classification of hepatic lesions from computed tomography (CT) images is presented. Regions of interest (ROIs) taken from nonenhanced CT images of normal liver, hepatic cysts, hemangiomas, and hepatocellular carcinomas have been used as input to the system. The proposed system consists of two modules: the feature extraction and the classification modules. The feature extraction module calculates the average gray level and 48 texture characteristics, which are derived from the spatial gray-level co-occurrence matrices, obtained from the ROIs. The classifier module consists of three sequentially placed feed-forward neural networks (NNs). The first NN classifies into normal or pathological liver regions. The pathological liver regions are characterized by the second NN as cyst or "other disease." The third NN classifies "other disease" into hemangioma or hepatocellular carcinoma. Three feature selection techniques have been applied to each individual NN: the sequential forward selection, the sequential floating forward selection, and a genetic algorithm for feature selection. The comparative study of the above dimensionality reduction methods shows that genetic algorithms result in lower dimension feature vectors and improved classification performance.

Climate Engineering: gesellschaftliches Konfliktpotenzial und öffentliche Partizipationsmöglichkeiten

Aufbauend auf den Ergebnissen einer Literatur- und Medienanalyse wurde erstmals zum Thema Climate Engineering ein sogenanntes Gruppen-Delphi durchgeführt, um aktuelle und argumentativ fundierte Einschätzungen von Experten zu den möglichen sozialen und kulturellen Folgen von Climate Engineering, insbesondere auch in Deutschland, zu erhalten. Die Ergebnisse dieser diskursiven Form der Expertenbefragung zeigen deutlich, dass die Verfahren des Climate Engineering differenziert betrachtet und bewertet werden müssen. Auf Akzeptanzprobleme stoßen vor allem Maßnahmen, bei denen hohe Unsicherheit über die potenziellen Nebenwirkungen besteht. In der Literatur und unter den Experten besteht Einigkeit darüber, dass es bereits jetzt, in der Frühphase der Entwicklung von Climate Engineering-Strategien, notwendig sei, die Bürger über diese Technologien und Strategien aufzuklären.

Iowa State Daily (April 5, 2012)

ContentsEnjoy a caveman's dietFair focuses on science, technology, math fieldsStudents present research at CapitolRacism finds its sociological roots Track and field looks to future of conference

How Noninvasive Haemoglobin Measurement with Pulse CO-Oximetry Can Change Your Practice: An Expert Review

Trauma related haemorrhagic anaemia is rarely diagnosed by physical examination alone but typically includes measurement of blood haemoglobin, one of the most frequently ordered laboratory tests. Recently, noninvasive technologies have been developed that allow haemoglobin to be measured immediately without the need for intravenous access or having to take venous, arterial, or capillary blood. Moreover, with these technologies haemoglobin can be continuously measured in patients with active bleeding, to guide the start and stop of blood transfusions and to detect occult bleeding. Recent studies on the accuracy of the devices showed promising results in terms of accuracy of hemoglobin measurement compared to laboratory determination. The present review gives an overview on the technology itself and reviews the current literature on the subject.

Quantum and classical criticality in a dimerized quantum antiferromagnet

A quantum critical point (QCP) is a singularity in the phase diagram arising because of quantum mechanical fluctuations. The exotic properties of some of the most enigmatic physical systems, including unconventional metals and superconductors, quantum magnets and ultracold atomic condensates, have been related to the importance of critical quantum and thermal fluctuations near such a point. However, direct and continuous control of these fluctuations has been difficult to realize, and complete thermodynamic and spectroscopic information is required to disentangle the effects of quantum and classical physics around a QCP. Here we achieve this control in a high-pressure, high-resolution neutron scattering experiment on the quantum dimer material TlCuCl3. By measuring the magnetic excitation spectrum across the entire quantum critical phase diagram, we illustrate the similarities between quantum and thermal melting of magnetic order. We prove the critical nature of the unconventional longitudinal (Higgs) mode of the ordered phase by damping it thermally. We demonstrate the development of two types of criticality, quantum and classical, and use their static and dynamic scaling properties to conclude that quantum and thermal fluctuations can behave largely independently near a QCP.

Cosmogenic 180W variations in meteorites and re-assessment of a possible 184Os–180W decay system

We measured tungsten (W) isotopes in 23 iron meteorites and the metal phase of the CB chondrite Gujba in order to ascertain if there is evidence for a large-scale nucleosynthetic heterogeneity in the p-process isotope 180W in the solar nebula as recently suggested by Schulz et al. (2013). We observed large excesses in 180W (up to ≈ 6 ε) in some irons. However, significant within-group variations in magmatic IIAB and IVB irons are not consistent with a nucleosynthetic origin, and the collateral effects on 180W from an s-deficit in IVB irons cannot explain the total variation. We present a new model for the combined effects of spallation and neutron capture reactions on 180W in iron meteorites and show that at least some of the observed within-group variability is explained by cosmic ray effects. Neutron capture causes burnout of 180W, whereas spallation reactions lead to positive shifts in 180W. These effects depend on the target composition and cosmic-ray exposure duration; spallation effects increase with Re/W and Os/W ratios in the target and with exposure age. The correlation of 180W/184W with Os/W ratios in iron meteorites results in part from spallogenic production of 180W rather than from 184Os decay, contrary to a recent study by Peters et al. (2014). Residual ε180W excesses after correction for an s-deficit and for cosmic ray effects may be due to ingrowth of 180W from 184Os decay, but the magnitude of this ingrowth is at least a factor of ≈2 smaller than previously suggested. These much smaller effects strongly limit the applicability of the putative 184Os-180W system to investigate geological problems.

Economic analysis of soil conservation: Case studies from the highlands of Amhara Region, Ethiopia

Soil degradation is widespread in the Ethiopian Highlands. Its negative impacts on soil productivity contribute to the extreme poverty of the rural population. Soil conservation is propagated as a means of reducing soil erosion, however, it is a costly investment for small-scale farming households. The present study is an attempt to show whether or not selected mechanical Soil and Water Conservation (SWC) technologies are profitable from a farmer’s point of view. A financial Cost-Benefit Analysis (CBA) is carried out to assess whether or not the considered SWC technologies are profitable from a farmer’s point of view. The CBA is supplemented by an evaluation of aspects from the economic and institutional environment. Whether or not soil conservation is profitable from a farmer’s point of view depends on a broad range of factors from the ecological, economic, political, institutional and socio-cultural sphere and also depends on the technology and the prevailing farming system. Because these factors are closely interlinked, it is often not sufficient to change or influence one to make SWC profitable. Several recommendations are formulated with regard to improving the profitability of SWC investments from a farmer’s point of view. Because the reasons for unsustainable resource use are manifold and highly interlinked, only a multi-stakeholder, multi-level and multi-objective approach is likely to offer solutions that address the underlying problems adequately.

Optical Light Curve Observations to Determine Attitude States of Space Debris

The currently proposed space debris remediation measures include the active removal of large objects and “just in time” collision avoidance by deviating the objects using, e.g., ground-based lasers. Both techniques require precise knowledge of the attitude state and state changes of the target objects. In the former case, to devise methods to grapple the target by a tug spacecraft, in the latter, to precisely propagate the orbits of potential collision partners as disturbing forces like air drag and solar radiation pressure depend on the attitude of the objects. Non-resolving optical observations of the magnitude variations, so-called light curves, are a promising technique to determine rotation or tumbling rates and the orientations of the actual rotation axis of objects, as well as their temporal changes. The 1-meter telescope ZIMLAT of the Astronomical Institute of the University of Bern has been used to collect light curves of MEO and GEO objects for a considerable period of time. Recently, light curves of Low Earth Orbit (LEO) targets were acquired as well. We present different observation methods, including active tracking using a CCD subframe readout technique, and the use of a high-speed scientific CMOS camera. Technical challenges when tracking objects with poor orbit redictions, as well as different data reduction methods are addressed. Results from a survey of abandoned rocket upper stages in LEO, examples of abandoned payloads and observations of high area-to-mass ratio debris will be resented. Eventually, first results of the analysis of these light curves are provided.

Particle Accelerators and Detectors for medical Diagnostics and Therapy

This Habilitationsschrift (Habilitation thesis) is focused on my research activities on medical applications of particle physics and was written in 2013 to obtain the Venia Docendi (Habilitation) in experimental physics at the University of Bern. It is based on selected publications, which represented at that time my major scientific contributions as an experimental physicist to the field of particle accelerators and detectors applied to medical diagnostics and therapy. The thesis is structured in two parts. In Part I, Chapter 1 presents an introduction to accelerators and detectors applied to medicine, with particular focus on cancer hadrontherapy and on the production of radioactive isotopes. In Chapter 2, my publications on medical particle accelerators are introduced and put into their perspective. In particular, high frequency linear accelerators for hadrontherapy are discussed together with the new Bern cyclotron laboratory. Chapter 3 is dedicated to particle detectors with particular emphasis on three instruments I contributed to propose and develop: segmented ionization chambers for hadrontherapy, a proton radiography apparatus with nuclear emulsion films, and a beam monitor detector for ion beams based on doped silica fibres. Selected research and review papers are contained in Part II. For copyright reasons, they are only listed and not reprinted in this on-line version. They are available on the websites of the journals.

RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION

My dissertation focuses on two aspects of RNA sequencing technology. The first is the methodology for modeling the overdispersion inherent in RNA-seq data for differential expression analysis. This aspect is addressed in three sections. The second aspect is the application of RNA-seq data to identify the CpG island methylator phenotype (CIMP) by integrating datasets of mRNA expression level and DNA methylation status. Section 1: The cost of DNA sequencing has reduced dramatically in the past decade. Consequently, genomic research increasingly depends on sequencing technology. However it remains elusive how the sequencing capacity influences the accuracy of mRNA expression measurement. We observe that accuracy improves along with the increasing sequencing depth. To model the overdispersion, we use the beta-binomial distribution with a new parameter indicating the dependency between overdispersion and sequencing depth. Our modified beta-binomial model performs better than the binomial or the pure beta-binomial model with a lower false discovery rate. Section 2: Although a number of methods have been proposed in order to accurately analyze differential RNA expression on the gene level, modeling on the base pair level is required. Here, we find that the overdispersion rate decreases as the sequencing depth increases on the base pair level. Also, we propose four models and compare them with each other. As expected, our beta binomial model with a dynamic overdispersion rate is shown to be superior. Section 3: We investigate biases in RNA-seq by exploring the measurement of the external control, spike-in RNA. This study is based on two datasets with spike-in controls obtained from a recent study. We observe an undiscovered bias in the measurement of the spike-in transcripts that arises from the influence of the sample transcripts in RNA-seq. Also, we find that this influence is related to the local sequence of the random hexamer that is used in priming. We suggest a model of the inequality between samples and to correct this type of bias. Section 4: The expression of a gene can be turned off when its promoter is highly methylated. Several studies have reported that a clear threshold effect exists in gene silencing that is mediated by DNA methylation. It is reasonable to assume the thresholds are specific for each gene. It is also intriguing to investigate genes that are largely controlled by DNA methylation. These genes are called “L-shaped” genes. We develop a method to determine the DNA methylation threshold and identify a new CIMP of BRCA. In conclusion, we provide a detailed understanding of the relationship between the overdispersion rate and sequencing depth. And we reveal a new bias in RNA-seq and provide a detailed understanding of the relationship between this new bias and the local sequence. Also we develop a powerful method to dichotomize methylation status and consequently we identify a new CIMP of breast cancer with a distinct classification of molecular characteristics and clinical features.

Hacia un enfoque analítico y de políticas para las interacciones entre ciencia, universidad y sociedad en la región latinoamericana

El objetivo de este trabajo es argumentar sobre la importancia del enfoque de redes de conocimiento, generado en el campo de los estudios sociales de la ciencia y la tecnología (CTS), para el análisis de las relaciones entre ciencia, universidad y sociedad. La construcción de procesos interactivos, cooperativos entre actores y el aprendizaje constituyen dimensiones clave para producir y utilizar conocimiento en la mejora del bienestar social de nuestras poblaciones. El trabajo expone brevemente las concepciones que han dominado en las políticas de ciencia y tecnología en la región latinoamericana; se argumenta sobre la importancia de los enfoques de redes de conocimiento y de la perspectiva regional y local al interior de los países, tanto para analizar la generación, intercambio y uso de conocimiento como para el diseño e implementación de políticas públicas de ciencia, tecnología e innovación; se documenta si en las nuevas concepciones de políticas de ciencia, tecnología e innovación en América Latina que destacan la importancia de la inclusión social se está adoptando el enfoque de redes de conocimiento y la perspectiva regional; y, se ofrecen, a manera de conclusiones, algunas argumentaciones sobre el futuro de las relaciones entre universidad y sociedad en lo que al desarrollo científico y tecnológico se refiere.

Hacia un enfoque analítico y de políticas para las interacciones entre ciencia, universidad y sociedad en la región latinoamericana

El objetivo de este trabajo es argumentar sobre la importancia del enfoque de redes de conocimiento, generado en el campo de los estudios sociales de la ciencia y la tecnología (CTS), para el análisis de las relaciones entre ciencia, universidad y sociedad. La construcción de procesos interactivos, cooperativos entre actores y el aprendizaje constituyen dimensiones clave para producir y utilizar conocimiento en la mejora del bienestar social de nuestras poblaciones. El trabajo expone brevemente las concepciones que han dominado en las políticas de ciencia y tecnología en la región latinoamericana; se argumenta sobre la importancia de los enfoques de redes de conocimiento y de la perspectiva regional y local al interior de los países, tanto para analizar la generación, intercambio y uso de conocimiento como para el diseño e implementación de políticas públicas de ciencia, tecnología e innovación; se documenta si en las nuevas concepciones de políticas de ciencia, tecnología e innovación en América Latina que destacan la importancia de la inclusión social se está adoptando el enfoque de redes de conocimiento y la perspectiva regional; y, se ofrecen, a manera de conclusiones, algunas argumentaciones sobre el futuro de las relaciones entre universidad y sociedad en lo que al desarrollo científico y tecnológico se refiere.

Hacia un enfoque analítico y de políticas para las interacciones entre ciencia, universidad y sociedad en la región latinoamericana

El objetivo de este trabajo es argumentar sobre la importancia del enfoque de redes de conocimiento, generado en el campo de los estudios sociales de la ciencia y la tecnología (CTS), para el análisis de las relaciones entre ciencia, universidad y sociedad. La construcción de procesos interactivos, cooperativos entre actores y el aprendizaje constituyen dimensiones clave para producir y utilizar conocimiento en la mejora del bienestar social de nuestras poblaciones. El trabajo expone brevemente las concepciones que han dominado en las políticas de ciencia y tecnología en la región latinoamericana; se argumenta sobre la importancia de los enfoques de redes de conocimiento y de la perspectiva regional y local al interior de los países, tanto para analizar la generación, intercambio y uso de conocimiento como para el diseño e implementación de políticas públicas de ciencia, tecnología e innovación; se documenta si en las nuevas concepciones de políticas de ciencia, tecnología e innovación en América Latina que destacan la importancia de la inclusión social se está adoptando el enfoque de redes de conocimiento y la perspectiva regional; y, se ofrecen, a manera de conclusiones, algunas argumentaciones sobre el futuro de las relaciones entre universidad y sociedad en lo que al desarrollo científico y tecnológico se refiere.

Simulated agricultural subsistence, timing of transition, and percentage of immigrant farmers

Farming and herding were introduced to Europe from the Near East and Anatolia; there are, however, considerable arguments about the mechanisms of this transition. Were it the people who moved and either outplaced, or admixed with, the indigenous hunter-gatherer groups? Or was it material and information that moved---the Neolithic Package---consisting of domesticated plants and animals and the knowledge of their use? The latter process is commonly referred to as cultural diffusion and the former as demic diffusion. Despite continuous and partly combined efforts by archaeologists, anthropologists, linguists, palaeontologists and geneticists, a final resolution of the debate has not yet been reached. In the present contribution we interpret results from the Global Land Use and technological Evolution Simulator (GLUES). GLUES is a mathematical model for regional sociocultural development, embedded in the geoenvironmental context, during the Holocene. We demonstrate that the model is able to realistically hindcast the expansion speed and the inhomogeneous space-time evolution of the transition to agropastoralism in western Eurasia. In contrast to models that do not resolve endogenous sociocultural dynamics, our model describes and explains how and why the Neolithic advanced in stages. We uncouple the mechanisms of migration and information exchange and also of migration and the spread of agropastoralism. We find that: (1) An indigenous form of agropastoralism could well have arisen in certain Mediterranean landscapes, but not in Northern and Central Europe, where it depended on imported technology and material. (2) Both demic diffusion by migration and cultural diffusion by trade may explain the western European transition equally well. (3) Migrating farmers apparently contribute less than local adopters to the establishment of agropastoralism. Our study thus underlines the importance of adoption of introduced technologies and economies by resident foragers.