DVMS 1.5: A user manual (the data visualization and modeling system)

The data available during the drug discovery process is vast in amount and diverse in nature. To gain useful information from such data, an effective visualisation tool is required. To provide better visualisation facilities to the domain experts (screening scientist, biologist, chemist, etc.),we developed a software which is based on recently developed principled visualisation algorithms such as Generative Topographic Mapping (GTM) and Hierarchical Generative Topographic Mapping (HGTM). The software also supports conventional visualisation techniques such as Principal Component Analysis, NeuroScale, PhiVis, and Locally Linear Embedding (LLE). The software also provides global and local regression facilities . It supports regression algorithms such as Multilayer Perceptron (MLP), Radial Basis Functions network (RBF), Generalised Linear Models (GLM), Mixture of Experts (MoE), and newly developed Guided Mixture of Experts (GME). This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install & use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

Introduction

Werner Sombart (1863-1941) was a famous and controversial social scientist in Germany during the early 20th century. Highly influential, his work and reputation have been indelibly tainted by his embrace of National Socialism in the last decade of his life. Although Sombart left an enormous opus spanning disciplinary boundaries, the scholarly assessment of and intellectual reaction to his work inside and outside of Germany is divided, and ambivalent. Best known for his analyses of capitalism - his essay "Why is There No Socialism in the United States?" remains a classic - Sombart consistently responded to the social and political developments that have shaped the 20th century. This collection provides a representative sampling of those portions of Sombart's work that have stood the test of time. The volume opens with a substantial introduction by the editors reviewing Sombart's life and career, the evolution of his major intellectual concerns, his relation to Marx and Weber, and his political affiliation with the Nazis. Their selection of texts emphasizes areas of his economic and cultural thought that remain relevant to intellectual trends in the social sciences, particularly those trends that seek a more broadly based, cross-disciplinary approach to the relationship of culture and economics. Sombart's writings on capitalism are represented by essays on the nature and origin of the market system and the diversity of its actors and motives among the bourgeoisie and the proletariat. Also included is an excerpt from Sombart's controversial volume "The Jews and Modern Capitalism" exploring the widely perceived relation between economic life and Judaism as a religion. In essays on the economics of cultural processes, Sombart's comprehensive and expansive idea of cultural science yields remarkable and prophetic insights into the nature of urbanism, luxury consumption, fashion and the cultural secularization of love. The volume's final section consists of Sombart's reflections on the social influences of technology, the economic life of the future, and on socialism, including the influential essay "Why is There No Socialism in the United States?". Encapsulating the most valuable aspects of his work, this study provides clear demonstration of Sombart's sense for fine cultural distinctions and broad cultural developments and the predictive power of his analyses. It should be of interest to sociologists, economists, political scientists and specialists in cultural studies.

Economic life in the modern age

Werner Sombart (1863-1941) may well have been the most famous and controversial social scientist in Germany during the early twentieth century. Highly influential, his work and reputation have been indelibly tainted by his embrace of National Socialism in the last decade of his life. Although Sombart left an enormous opus spanning disciplinary boundaries, intellectual reaction to his work inside and outside of Germany is divided and ambivalent. Sombart consistently responded to the social and political developments that have shaped the twentieth century. Economic Life in the Modern Age provides a representative sampling of those portions of Sombart's work that have stood the test of time. The volume opens with a substantial introduction reviewing Sombart's life and career, the evolution of his major intellectual concerns, his relation to Marx and Weber, and his political affiliation with the Nazis. The editors' selection of texts emphasizes areas of Sombart's economic and cultural thought that remain relevant, particularly to those intellectual trends that seek a more broadly based, cross-disciplinary approach to culture and economics. Sombart's writings on capitalism are represented by essays on the nature and origin of the market system and the diversity of motives among the bourgeoisie and the proletariat. Also included is an excerpt from Sombart's controversial The Jews and Modern Capitalism, exploring the widely perceived relation between economic life and Judaism as a religion. In essays on the economics of cultural processes, Sombart's comprehensive and expansive idea of cultural science yields prophetic insights into the nature of urbanism, luxury consumption, fashion, and the cultural secularization of love. The volume's final section consists of Sombart's reflections on the social influences of technology, the economic life of the future, and on socialism, including the influential essay "Why is there no Socialism in the United States." Encapsulating the most valuable aspects of his work, Economic Life in the Modern Age provides clear demonstration of Sombart's sense for fine cultural distinctions and broad cultural developments and the predictive power of his analyses. It will be of interest to sociologists, economists, political scientists, and specialists in cultural studies.

Gender and subject in higher education

This thesis is concerned with the issue of gender inequality in higher education. It examines the relationship between gender and subject specialisation, looking in particular at the reasons for the predominance, at undergraduate level, of men in the physical sciences, and of women in the humanities. It investigates ideas of `masculinity' and `femininity' and how these relate to constructions of `science' and `arts'. The thesis argues that students choose which subject to study on the basis of certain qualities these subjects are seen to hold, and that these qualities have close connections with beliefs about `masculinity' and `femininity'. It examines this through an interview study of male and female students on six higher education courses: two university courses of physics, two university courses of English, a polytechnic course in communications and a polytechnic course in physical science. The interview study demonstrates that the science subjects are perceived by science students as more certain, more useful and more important than the humanities, and emphasise the value of their degree in gaining a well-paid and important job. Female science students, however, experience conflict between being `a good scientist' and being `feminine'. English and communications students emphasise the breadth, uncertainty and individuality of their subjects, and find science restrictive and narrow. They make little link between their degree and their future career. Men, however, feel no conflict between their identity as men and their chosen subject. It is argued that there is a close link between the construction of masculinity and the construction of physical science, but that English and communications are more ambivalent: in some senses `masculine', in some `feminine'. Men are advantaged in these subjects because of their greater visibility and assertiveness. The thesis concludes that the division between `science' and `arts' reinforces ideas of masculinity and femininity, and argues that female `failure' in education is in part the result of higher education's inability to transcend that division.

Pragmatic algorithms for implementing geostatistics with large datasets

With the ability to collect and store increasingly large datasets on modern computers comes the need to be able to process the data in a way that can be useful to a Geostatistician or application scientist. Although the storage requirements only scale linearly with the number of observations in the dataset, the computational complexity in terms of memory and speed, scale quadratically and cubically respectively for likelihood-based Geostatistics. Various methods have been proposed and are extensively used in an attempt to overcome these complexity issues. This thesis introduces a number of principled techniques for treating large datasets with an emphasis on three main areas: reduced complexity covariance matrices, sparsity in the covariance matrix and parallel algorithms for distributed computation. These techniques are presented individually, but it is also shown how they can be combined to produce techniques for further improving computational efficiency.

Reflection and reflexivity in reviewing and evaluating CDIO:an empirical approach to evaluation

Facilitated by an Engineer and a Social Scientist, both of whom have expertise in Engineering Education Research and Evaluation (EERE), this interactive workshop is divided into three main sections, each one focusing on a different area of evaluation. It will build on research conducted at Aston University School of Engineering and Applied Science to explore and critique the value of introducing CDIO across the first year undergraduate curriculum. Participants will be invited to consider the pedagogical and engineering related challenges of evaluating the academic and practical value of CDIO as a strategy for learning and teaching in the discipline. An empirical approach to evaluation developed by the researchers to provide empirically grounded evidence of the pedagogical and vocational value of CDIO will form the theoretical and conceptual basis of the workshop. This approach is distinctive in that it encapsulates both engineering and social science methods of evaluation. It is also contemporaneous in nature, with the researchers acting as a ‘fly on the wall’ capturing data as the programme unfolds. Through facilitated discussion and participation, the workshop will provide colleagues with the opportunity to develop a cross-disciplinary, empirically grounded research proposal specifically for the purposes of critically evaluating CDIO. It is anticipated that during the workshop, colleagues will work together in small groups. Suitable pedagogical approaches and tools will be suggested and a purposefully developed Engineering Education Research Guide, written by the workshop facilitators, will be given to all participants to inform and support the Workshop approach.

Form follows function:model-driven engineering for clinical trials

We argue that, for certain constrained domains, elaborate model transformation technologies-implemented from scratch in general-purpose programming languages-are unnecessary for model-driven engineering; instead, lightweight configuration of commercial off-the-shelf productivity tools suffices. In particular, in the CancerGrid project, we have been developing model-driven techniques for the generation of software tools to support clinical trials. A domain metamodel captures the community's best practice in trial design. A scientist authors a trial protocol, modelling their trial by instantiating the metamodel; customized software artifacts to support trial execution are generated automatically from the scientist's model. The metamodel is expressed as an XML Schema, in such a way that it can be instantiated by completing a form to generate a conformant XML document. The same process works at a second level for trial execution: among the artifacts generated from the protocol are models of the data to be collected, and the clinician conducting the trial instantiates such models in reporting observations-again by completing a form to create a conformant XML document, representing the data gathered during that observation. Simple standard form management tools are all that is needed. Our approach is applicable to a wide variety of information-modelling domains: not just clinical trials, but also electronic public sector computing, customer relationship management, document workflow, and so on. © 2012 Springer-Verlag.

Analysis of protein carbonylation - pitfalls and promise in commonly used methods

Abstract Oxidation of proteins has received a lot of attention in the last decades due to the fact that they have been shown to accumulate and to be implicated in the progression and the patho-physiology of several diseases such as Alzheimer, coronary heart diseases, etc. This has also resulted in the fact that research scientist became more eager to be able to measure accurately the level of oxidized protein in biological materials, and to determine the precise site of the oxidative attack on the protein, in order to get insights into the molecular mechanisms involved in the progression of diseases. Several methods for measuring protein carbonylation have been implemented in different laboratories around the world. However, to date no methods prevail as the most accurate, reliable and robust. The present paper aims at giving an overview of the common methods used to determine protein carbonylation in biological material as well as to highlight the limitations and the potential. The ultimate goal is to give quick tips for a rapid decision making when a method has to be selected and taking into consideration the advantage and drawback of the methods.

Curriculum Vitae of Petar R. Popivanov

Petar Radoev Popivanov was born on April 6, 1946 in Sofia. Traces of this branch of Popivanov’s are found in the late 1700’s in Lyaskovets, a small town near Veliko Tarnovo, the old capital of the second Bulgarian kingdom. In the family tree one finds in the last 200 years or so lawyers, men of learning, men of politics, military officers, physicians, priests. In particular, his father Radoy Popivanov (1913-2010) was a well known Bulgarian scientist in Biology and Immunogenetics and a Full Member of the Bulgarian Academy of Sciences (BAS).

Expert report writing in toxicology:forensic, scientific and legal aspects

Every year throughout the world, individuals' health is damaged by their exposure to toxic chemicals at work. In most cases these problems will resolve, but many will sustain permanent damage. Whilst any justified claim for compensation requires medical and legal evidence a crucial and often controversial component of this process is the establishment of a causal link between the individual's condition and exposure to a specific chemical or substance. Causation, in terms of how a substance or substances led the claimant to his or her current plight, can be difficult to establish and the main purpose of this book, is to provide the aspiring expert report writer with a concise, practical guide that uses case histories to illuminate the process of establishing causation in occupational toxicity proceedings. In summary: A practical, accessible guide to the preparation of balanced, scientifically sound expert reports in the context of occupational toxicology. Focuses on the scientist's role in establishing a causal link between exposure to toxins and an individual's ill health. Includes real-life case histories drawn from the Author's 15 years experience in this area to illustrate the principles involved. Expert Report Writing in Toxicology: Forensic, Scientific and Legal Aspects proves invaluable to scientists across a range of disciplines needing guidance as to what is expected of them in terms of the best use of their expertise and how to present their findings in a manner that is authoritative, balanced and informative.

Greetings, Earthlings

This blow to the myth of distinct male and female brains is welcome, says Gina Rippon

Fever : friend or foe?

It has long been suspected that some fevers should be allowed to run their course. Now doctors are finally acting on new evidence. © 2010 Reed Business Information Ltd, England.

Presumptive Identification of the Fungal Communities in Cystic Fibrosis Patients' Sputum Using Amplicon Length Heterogeneity Polymerase Chain Reaction

This thesis would not have been possible without the aid of my family, friends, laboratory members, and professors. First and foremost, I would like to thank Dr. Kalai Mathee for allowing me to enter her lab in August 2007 and enabling to embark on this journey. This experience has transformed me into more mature scientist, teaching me how to ask the right questions and the process needed to solve them. I would also like to acknowledge Dr. Lisa Schneper. She has helped me throughout the whole process, by graciously giving me input at every step of the way. I would like to express gratitude to Dr. Jennifer Richards for all her input in writing the thesis. She has been a great teacher and being in her class has been a pleasure. Moreover, I would like to thank all the committee members for their constructive criticism throughout the process. When I entered the lab in August, there was one person who literally was by my side, Melissa Doud. Without your input and guidance I would not have even been able to do these experiments. I would also like to thank you and Dr. Light for allowing me to meet some cystic fibrosis patients. It has allowed me to put a face on the disease, and help the patients' fight. For a period before I had entered the lab, Ms. Doud had an apprentice, who started the fungal aspect of the project, Caroline Veronese. Her initial work has enabled me to prefect the protocols and complete the ITS 1 region.One very unique aspect about Dr. Mathee's lab is the camaraderie. I would like to thank all the lab members for the good times in and out of the lab. These individuals have been able to make smile and laugh in parties and lab meetings. I would like to individually thank Balachandar Dananjeyan, Deepak Balasubramanian, and V arinderpal Singh Pannu for all the PCR help and Natalie Maricic for the laughs and being a great classmate. Last, but not least, I would like to acknowledge my family and friends for their support and keeping me sane: Cecilia, my mother, Mohammad, my father, Amir, my older brother, Billal, my younger brother, Ouday Akkari and Stephanie De Bedout, my best friends.

Tropical seagrass-associated macroalgae distributions and trends relative to water quality

Tropical coastal marine ecosystems including mangroves, seagrass beds and coral reef communities are undergoing intense degradation in response to natural and human disturbances, therefore, understanding the causes and mechanisms present challenges for scientist and managers. In order to protect our marine resources, determining the effects of nutrient loads on these coastal systems has become a key management goal. Data from monitoring programs were used to detect trends of macroalgae abundances and develop correlations with nutrient availability, as well as forecast potential responses of the communities monitored. Using eight years of data (1996–2003) from complementary but independent monitoring programs in seagrass beds and water quality of the Florida Keys National Marine Sanctuary (FKNMS), we: (1) described the distribution and abundance of macroalgae groups; (2) analyzed the status and spatiotemporal trends of macroalgae groups; and (3) explored the connection between water quality and the macroalgae distribution in the FKNMS. In the seagrass beds of the FKNMS calcareous green algae were the dominant macroalgae group followed by the red group; brown and calcareous red algae were present but in lower abundance. Spatiotemporal patterns of the macroalgae groups were analyzed with a non-linear regression model of the abundance data. For the period of record, all macroalgae groups increased in abundance (Abi) at most sites, with calcareous green algae increasing the most. Calcareous green algae and red algae exhibited seasonal pattern with peak abundances (Φi) mainly in summer for calcareous green and mainly in winter for red. Macroalgae Abi and long-term trend (mi) were correlated in a distinctive way with water quality parameters. Both the Abi and mi of calcareous green algae had positive correlations with NO3−, NO2−, total nitrogen (TN) and total organic carbon (TOC). Red algae Abi had a positive correlation with NO2−, TN, total phosphorus and TOC, and the mi in red algae was positively correlated with N:P. In contrast brown and calcareous red algae Abi had negative correlations with N:P. These results suggest that calcareous green algae and red algae are responding mainly to increases in N availability, a process that is happening in inshore sites. A combination of spatially variable factors such as local current patterns, nutrient sources, and habitat characteristics result in a complex array of the macroalgae community in the seagrass beds of the FKNMS.