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Search Results: 1 - 10 of 2241 matches for " Ralph Pethica "
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Evolutionarily consistent families in SCOP: sequence, structure and function
Ralph B Pethica, Michael Levitt, Julian Gough
BMC Structural Biology , 2012, DOI: 10.1186/1472-6807-12-27
Abstract: Several phylogenetic trees were generated for each superfamily: one derived from a multiple sequence alignment, one based on structural distances, and the final two from presence/absence of GO terms or EC numbers assigned to domains. The topologies of the resulting trees and confidence values were compared to the SCOP family classification.We show that SCOP family groupings are evolutionarily consistent to a very high degree with respect to classical sequence phylogenetics. The trees built from (automatically generated) structural distances correlate well, but are not always consistent with SCOP (hand annotated) groupings. Trees derived from functional data are less consistent with the family level than those from structure or sequence, though the majority still agree. Much of GO and EC annotation applies directly to one family or subset of the family; relatively few terms apply at the superfamily level. Maximum sequence diversity within a family is on average 22% but close to zero for superfamilies.Proteins are made up of domains. Protein domains in this context can be regarded as the building blocks of proteins, and the smallest units of protein evolution. A small protein may consist of a single domain, larger proteins maybe contain multiple domains. A domain can be defined as a protein unit which is seen in nature either on its own or in combination with other different domains.Detecting the evolutionary relationship between two or more domains using sequence information alone is often not possible, as sequences often diverge beyond the point of detection by comparison methods. Lack of sequence information does not necessarily show that there is no relationship between domains. If the three dimensional structure of the domains is known, evolutionary relationships can usually be recognised. The Structural Classification of Proteins (SCOP) [1-3], is a hierarchical classification system of proteins for which atomic resolution three dimensional structures are known;
TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web
Ralph Pethica,Gary Barker,Tim Kovacs,Julian Gough
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008934
Abstract: Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees.
Direct measurement of molecular stiffness and damping in confined water layers
Steve Jeffery,Peter M. Hoffmann,John B. Pethica,Chandra Ramanujan,H. ?zgür ?zer,Ahmet Oral
Physics , 2003, DOI: 10.1103/PhysRevB.70.054114
Abstract: We present {\em direct} and {\em linear} measurements of the normal stiffness and damping of a confined, few molecule thick water layer. The measurements were obtained by use of a small amplitude (0.36 $\textrm{\AA}$), off-resonance Atomic Force Microscopy (AFM) technique. We measured stiffness and damping oscillations revealing up to 7 layers separated by 2.56 $\pm$ 0.20 $\textrm{\AA}$. Relaxation times could also be calculated and were found to indicate a significant slow-down of the dynamics of the system as the confining separation was reduced. We found that the dynamics of the system is determined not only by the interfacial pressure, but more significantly by solvation effects which depend on the exact separation of tip and surface. Thus ` solidification\rq seems to not be merely a result of pressure and confinement, but depends strongly on how commensurate the confining cavity is with the molecule size. We were able to model the results by starting from the simple assumption that the relaxation time depends linearly on the film stiffness.
Scrutinizing the atmospheric greenhouse effect and its climatic impact  [PDF]
Gerhard Kramm, Ralph Dlugi
Natural Science (NS) , 2011, DOI: 10.4236/ns.2011.312124
Abstract: In this paper, we scrutinize two completely different explanations of the so-called atmospheric greenhouse effect: First, the explanation of the American Meteorological Society (AMS) and the World Meteorological Organization (W?MO) quan- tifying this effect by two characteristic temperatures, secondly, the explanation of Ramanathan et al. [1] that is mainly based on an energy-flux budget for the Earth-atmosphere system. Both explanations are related to the global scale. In addition, we debate the meaning of climate, climate change, climate variability and climate variation to outline in which way the atmospheric greenhouse effect might be responsible for climate change and climate variability, respectively. In doing so, we distinguish between two different branches of climatology, namely 1) physical climatology in which the boundary conditions of the Earth-atmosphere system play the dominant role and 2) statistical climatology that is dealing with the statistical description of fortuitous weather events which had been happening in climate periods; each of them usually comprises 30 years. Based on our findings, we argue that 1) the so-called atmospheric greenhouse effect cannot be proved by the statistical description of fortuitous weather events that took place in a climate period, 2) the description by AMS and W?MO has to be discarded because of physical reasons, 3) energy-flux budgets for the Earth-atmosphere system do not provide tangible evidence that the atmospheric greenhouse effect does exist. Because of this lack of tangible evidence it is time to acknowledge that the atmospheric greenhouse effect and especially its climatic impact are based on meritless conjectures.
Determination of Total Galactose from Dried Blood Spots—Extensive Assay Evaluation of a CE-Marked Test-Kit  [PDF]
Ralph Fingerhut, Toni Torresani
Journal of Analytical Sciences, Methods and Instrumentation (JASMI) , 2013, DOI: 10.4236/jasmi.2013.33020

Most newborn screening laboratories use CE-marked or FDA-approved test-kits, like in routine clinical chemistry. National regulations require only minimal evaluation from the customer, if the test-kits are used as specified by the manufacturer. The microtiter-based kit-concept is often based on the perception, that the laboratory always processes whole microtiter plates. However, in the daily routine, this is rather a rare exception, which leads to much higher costs per newborn, compared to the costs per assay in the test-kits. In addition the amount of wasted resources is quite high. Performance of the Neonatal Total Galactose kit from Perkin Elmer was tested. We have determined specificity, limit of detection (LOD), limit of quantitation (LOQ), intra and inter assay variation, recovery, stability of measuring signal and reagents. Results were also compared with the Astoria Pacific Spot Check System. In addition, we had (by chance) the opportunity to test 2 kits, which were already expired for more than 3 years. LOD was 165 - 306 μmol/L and LOQ 475 - 703 μmol/L, depending on the definition of LOD/LOQ. Mean recovery was 112.8%, intra assay CVs were 11.3, 7.3, 4.0, and 3.0, and inter assay CVs 28.7, 15.9, 7.8, and 9.3, at 220, 590, 1200, and 2060 μmol/L respectively. Reconstituted and mixed reagents must be used within some hours, and were unstable even if stored at -20℃. However, if the reconstituted galactose substrate reagent and galactose oxidase reagent were only mixed according to the daily requirements, and the rest stored separately at -20℃, they were stable for at least 12 days. The performance of the expired test-kits did not differ from the others. The performance of the Total Galactose kit is comparable to other tests used for newborn screening. However, we could significantly reduce the costs per newborn and reduce unnecessary production of waste, by thorough validation and modification of the assay procedures.

The Potential of Adaptive Mentorship©: Experts’ Perspectives  [PDF]
Edwin Ralph, Keith Walker
Open Journal of Social Sciences (JSS) , 2014, DOI: 10.4236/jss.2014.28013
Abstract: In recent years, global interest in the processes of mentorship and coaching has expanded across all disciplinary fields. Educational institutions, commercial enterprises, and other organizations have integrated mentorship processes into their educational programs to help prepare/train protégés for entry into a specific professions or occupations and/or to upgrade their related skills/knowledge. Over the past quarter century, in partial response to the popularity of mentoring, the authors have developed a mentoring model called Adaptive Mentorship© (AM). Research conducted by the authors and others has affirmed AM’s value in improving mentoring practice in a variety of disciplines. In the present article, the authors summarize assessments of the model that they solicited during the past five years from 49 multi-disciplinary groups or panels of experts. The experts’ positive statements regarding AM outweighed their cautionary comments by a ratio of 2:1. The strengths that they identified were that AM conceptualized the entire mentorship process in an understandable manner, and that it helped reveal potential interpersonal conflicts as well as practical solutions for them. The caveats identified by the experts were that personnel employing the AM model must apply it sensibly, sensitively, and flexibly—especially in cross-cultural contexts.
Revisiting the Effect of Crude Oil Price Movements on US Stock Market Returns and Volatility  [PDF]
Ralph Sonenshine, Michael Cauvel
Modern Economy (ME) , 2017, DOI: 10.4236/me.2017.85053
Abstract: From mid-2014 to 2016, oil prices plunged rapidly causing significant volatility in the US and global equity markets. This change in crude oil prices occurred after a significant run up in oil prices three to four years earlier. Each change in the growth trajectory of oil prices affects stock market returns. How and why do oil price shocks affect the expected stock market returns among key sectors of the economy? This paper explores this issue by examining how the magnitude of crude oil price changes affects the stock market returns and variances of key producing, banking and consuming segments of the US economy. Our findings provide some explanations for the asymmetric responses to positive and negative oil shocks found in these key sectors of the economy.
Epistatic Relationships in the BRCA1-BRCA2 Pathway
Ralph Scully
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1002183
The Limits to Transforming the Environment and the Limits to Sociological Knowledge
Ralph Schroeder
Sustainability , 2010, DOI: 10.3390/su2082483
Abstract: This paper argues that the social sciences are fragmented in addressing the environmental challenge of increasing resource depletion. To address this problem, the paper puts forward a framework which encompasses several disciplinary approaches, and above all a long-term historical perspective and a realist sociology of science and technology which, in combination, provide a means of understanding the disruptive changes in the transformation of the environment. The paper then focuses on energy and gives an overview of the various social forces that can potentially counteract the future tensions arising from the foreseeable depletion of energy sources. It argues that only some of these countervailing forces—namely state intervention and technological innovation—provide viable potential solutions to these tensions. However, these solutions themselves face severe constraints. The paper concludes by arguing that a realistic assessment of constraints is the most useful, though limited, service that social science can contribute to our understanding of the relation between social and environmental transformation.
Environmental Literacy in Science and Society: From Knowledge to Decisions. By Roland W. Scholz. Cambridge University Press: New York, USA, 2011; Hardback, 631 pp; ISBN 978-0-521-19271-2; Paperback, ISBN 978-0-521-18333-8
Ralph Hansmann
Sustainability , 2012, DOI: 10.3390/su4050863
Abstract: The book Environmental Literacy in Science and Society contributes to the scientific understanding and sustainability-oriented management of Human–Environment Systems (HES) based on processes of transdisciplinarity and mutual learning. It presents a historical analysis, and modern explanations, of crucial concepts and developments regarding environmental literacy in science and society. In addition, it presents an original framework for the analysis of HES in which these are seen as inextricably coupled transactional systems. This framework is applied in the book to sustainability learning and decision making in real-world problem-solving processes with respect to complex, ill-defined problems that pose threads to the balance of certain aspects of HES or to the anthroposphere as a whole. [...]
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