Test Derivation from Timed Automata

A real-time system is a discrete system whose state changes occur in real-numbered time [AH97]. For testing real-time systems, specification languages must be extended with constructs for expressing real-time constraints, the implementation relation must be generalized to consider the temporal dimension, and the data structures and algorithms used to generate tests must be revised to operate on a potentially infinite set of states

Robustness of fossil fish teeth for seawater neodymium isotope reconstructions under variable redox conditions in an ancient shallow marine setting

Fossil fish teeth from pelagic open ocean settings are considered a robust archive for preserving the neodymium (Nd) isotopic composition of ancient seawater. However, using fossil fish teeth as an archive to reconstruct seawater Nd isotopic compositions in different sedimentary redox environments and in terrigenous‐dominated, shallow marine settings is less proven. To address these uncertainties, fish tooth and sediment samples from a middle Eocene section deposited proximal to the East Antarctic margin at Integrated Ocean Drilling Program Site U1356 were analyzed for major and trace element geochemistry, and Nd isotopes. Major and trace element analyses of the sediments reveal changing redox conditions throughout deposition in a shallow marine environment. However, variations in the Nd isotopic composition and rare earth element (REE) patterns of the associated fish teeth do not correspond to redox changes in the sediments. REE patterns in fish teeth at Site U1356 carry a typical mid‐REE‐enriched signature. However, a consistently positive Ce anomaly marks a deviation from a pure authigenic origin of REEs to the fish tooth. Neodymium isotopic compositions of cleaned and uncleaned fish teeth fall between modern seawater and local sediments and hence could be authigenic in nature, but could also be influenced by sedimentary fluxes. We conclude that the fossil fish tooth Nd isotope proxy is not sensitive to moderate changes in pore water oxygenation. However, combined studies on sediments, pore waters, fish teeth, and seawater are needed to fully understand processes driving the reconstructed signature from shallow marine sections in proximity to continental sources

Atomistic simulation of the measurement of mechanical properties of gold nanorods by AFM

Mechanical properties of nanoscale objects can be measured with an atomic force microscope (AFM) tip. However, the continuum models typically used to relate the force measured at a certain indentation depth to quantities such as the elastic modulus, may not be valid at such small scales, where the details of atomistic processes need to be taken into account. On the other hand, molecular dynamics (MD) simulations of nanoindentation, which can offer understanding at an atomistic level, are often performed on systems much smaller than the ones studied experimentally. Here, we present large scale MD simulations of the nanoindentation of single crystal and penta-twinned gold nanorod samples on a silicon substrate, with a spherical diamond AFM tip apex. Both the sample and tip sizes and geometries match commercially available products, potentially linking simulation and experiment. Different deformation mechanisms, involving the creation, migration and annihilation of dislocations are observed depending on the nanorod crystallographic structure and orientation. Using the Oliver-Pharr method, the Young's moduli of the (100) terminated and (110) terminated single crystal nanorods, and the penta-twinned nanorod, have been determined to be 103 +/- 2, 140 +/- 4 and 108 +/- 2 GPa, respectively, which is in good agreement with bending experiments performed on nanowires.Peer reviewe

IR Astrometry and Photometry of the Abell 1882 Supergroup

Previously observed characteristics of the Abell 1 882 supergroup show signs of early stages of cluster formation. Supergroups and clusters have already been studied, but the unique stage of Abell 1 882 will aid in understanding the process of galaxy cluster formation. The data set contains observations from the Infrared Side Port Imager at the 4.0-m Blanco telescope at the Cerro Tololo Inter-American Observatory (CTIO) during May 2010. The data reduction process, unique challenges of working with infrared data, and preliminary results will be discussed. Rohl worked with Gomez from January through March 201 1 as a research assistant with the Research Experience for Undergraduates (REV) program of the National Science Foundation. The program was hosted at CTIO in cooperation with Gemini Observatory in La Serena, Chile

Mediterranean Outflow and surface water variability off southern Portugal during the early Pleistocene: A snapshot at Marine Isotope Stages 29 to 34 (1020-1135 ka)

Centennial-to-millennial scale records from IODP Site U1387, drilled during IODP Expedition 339 into the Faro Drift at 558 m water depth, now allow evaluating the climatic history of the upper core of the Mediterranean Outflow (MOW) and of the surface waters in the northern Gulf of Cadiz during the early Pleistocene. This study focuses on the period from Marine Isotope Stages (MIS) 29 to 34, i.e. the interval surrounding extreme interglacial MIS 31. Conditions in the upper MOW reflect obliquity, precession and millennial-scale variations. The benthic delta O-18 signal follows obliquity with the exception of an additional, smaller delta O-18 peak that marks the MIS 32/31 transition. Insolation maxima (precession minima) led to poor ventilation and a sluggish upper MOW core, whereas insolation minima were associated with enhanced ventilation and often also increased bottom current velocity. Millennial-scale periods of colder sea-surface temperatures (SST) were associated with short-term maxima in flow velocity and better ventilation, reminiscent of conditions known from MIS 3.A prominent contourite layer, coinciding with insolation cycle 100, was formed during MIS 31 and represents one of the few contourites developing within an interglacial period. MIS 31 surface water conditions were characterized by an extended period (1065-1091 ka) of warm SST, but SST were not much warmer than during MIS 33. Interglacial to glacial transitions experienced 2 to 3 stadial/interstadial cycles, just like their mid-to-late Pleistocene counterparts. Glacial MIS 30 and 32 recorded periods of extremely cold (<12 degrees C) SST that in their climatic impact were comparable with the Heinrich events of the mid and late Pleistocene. Glacial MIS 34, on the other hand, was a relative warm glacial period off southern Portugal. Overall, surface water and MOW conditions at Site U1387 show a strong congruence with Mediterranean climate, whereas millennial-scale variations are closely linked to North Atlantic circulation changes. (C) 2015 Elsevier B.V. All rights reserved.Fundação para a Ciência e a Tecnologia (FCT; Portugal) through MOWCADYN project [PTDC/MAR-PRO/3761/2012]; FCT [SFRH/BPD/66025/2009]; Deutsche Forschungsgemeinschaft (DFG) [BA 3809/4, RO 1113/6]; MARUM Research Center; Spanish Ministry of Science and Innovation [CTM 2011-24079]; European Union [228344-EUROFLEETS]info:eu-repo/semantics/publishedVersio

Chorography: history, theory and potential for archaeological research

Chorography is a little-known field of theory and practice concerned with the significance of place, regional description/characterization, local history, and representation. A well-established discipline and methodology with demonstrable roots in antiquity and an important role in the development of antiquarian research, regional studies and the establishment of modern archaeology, chorography is useful for understanding the history of scholarship and may continue to provide sound theoretical principles and practical methods for new explorations of archaeological monuments and landscapes. This paper discusses the historical uses of chorography, beginning with practitioners from classical antiquity but emphasizing the uniquely British chorographic tradition of the sixteenth through eighteenth centuries. Attention is also given to more recent efforts at exploring this tradition by literary scholars, historiographers and archaeological theorists. Careful analysis of works of—and about—chorography allows for the explication of key theoretical principles and practical methods, which are presented and elaborated upon. It is argued that chorography offers a coherent, viable and valuable approach to evaluating the long-term significance of landscapes, monuments and regions, crossing conventional disciplinary divides and connecting past and present. The paper concludes with some thoughts on the benefits of chorography for contemporary research and its potential role in modern archaeology

Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles

The stability, activity, and solubility of a protein sequence are determined by a delicate balance of molecular interactions in a variety of conformational states. Even so, most computational protein design methods model sequences in the context of a single native conformation. Simulations that model the native state as an ensemble have been mostly neglected due to the lack of sufficiently powerful optimization algorithms for multistate design. Here, we have applied our multistate design algorithm to study the potential utility of various forms of input structural data for design. To facilitate a more thorough analysis, we developed new methods for the design and high-throughput stability determination of combinatorial mutation libraries based on protein design calculations. The application of these methods to the core design of a small model system produced many variants with improved thermodynamic stability and showed that multistate design methods can be readily applied to large structural ensembles. We found that exhaustive screening of our designed libraries helped to clarify several sources of simulation error that would have otherwise been difficult to ascertain. Interestingly, the lack of correlation between our simulated and experimentally measured stability values shows clearly that a design procedure need not reproduce experimental data exactly to achieve success. This surprising result suggests potentially fruitful directions for the improvement of computational protein design technology

Are structural biases at protein termini a signature of vectorial folding?

Experimental investigations of the biosynthesis of a number of proteins have pointed out that part of the native structure can be acquired already during translation. We carried out a comprehensive statistical analysis of some average structural properties of proteins that have been put forward as possible signatures of this progressive buildup process. Contrary to a widespread belief, it is found that there is no major propensity of the amino acids to form contacts with residues that are closer to the N terminus. Moreover, it is found that the C terminus is significantly more compact and locally-organized than the N one. Also this bias, though, is unlikely to be related to vectorial effects, since it correlates with subtle differences in the primary sequence. These findings indicate that even if proteins aquire their structure vectorially no signature of this seems to be detectable in their average structural properties.Comment: 7 pages, 3 figures, 1 tabl

Mapping the genetic architecture of gene expression in human liver

Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order disease traits. Therefore, identifying the molecular phenotypes that vary in response to changes in DNA and that also associate with changes in disease traits has the potential to provide the functional information required to not only identify and validate the susceptibility genes that are directly affected by changes in DNA, but also to understand the molecular networks in which such genes operate and how changes in these networks lead to changes in disease traits. Toward that end, we profiled more than 39,000 transcripts and we genotyped 782,476 unique single nucleotide polymorphisms (SNPs) in more than 400 human liver samples to characterize the genetic architecture of gene expression in the human liver, a metabolically active tissue that is important in a number of common human diseases, including obesity, diabetes, and atherosclerosis. This genome-wide association study of gene expression resulted in the detection of more than 6,000 associations between SNP genotypes and liver gene expression traits, where many of the corresponding genes identified have already been implicated in a number of human diseases. The utility of these data for elucidating the causes of common human diseases is demonstrated by integrating them with genotypic and expression data from other human and mouse populations. This provides much-needed functional support for the candidate susceptibility genes being identified at a growing number of genetic loci that have been identified as key drivers of disease from genome-wide association studies of disease. By using an integrative genomics approach, we highlight how the gene RPS26 and not ERBB3 is supported by our data as the most likely susceptibility gene for a novel type 1 diabetes locus recently identified in a large-scale, genome-wide association study. We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process. © 2008 Schadt et al

The Efficacy of Magnetis Polus Australis 7CH and 30CH in the treatment of Onychocryptosis of the Hallux

Onychocryptosis (ingrown nails) is the most common of pedal foot maladies seen by podiatrists (Armstrong et al., 2000) and makes up 3-5% of all foot problems. This condition is characterized by the nail plate growing into and cutting the lateral nail fold. Symptoms include erythema (redness) of the lateral nail fold, oedema (swelling) of the lateral nail fold and tenderness to pressure (Zuber, 2002). Within the Materia Medica, the homoeopathic remedy Magnetis Polus Australis is indicated for the treatment of the symptom of “ingrowing toenail” (Vermeulen, 1997). Although used for nearly 200 years, no research has been conducted to verify this claim. The study aimed at determining whether Magnetis Polus Australis in the 7th and 30th centesimal potencies is effective in treating the symptoms of onychocryptosis of the hallux such as pain, tenderness to pressure, oedema and erythema. The study, a double-blind placebo study, involved thirty participants. The placebo group included ten participants and the experimental group included twenty participants, ten of which received the 7CH and the other ten received the 30CH. Each group took the homoeopathic or placebo medication orally twice daily for a period of three weeks. The participants were followed-up with an assessment questionnaire every two weeks for a one month period. At the end of the research period these questionnaires with the data were collected and statistically analyzed using chi-squared tests. The study indicated that Magnetis Polus Australis has a positive effect in the treatment of onychocryptosis of the hallux and has demonstrated effectiveness in reducing inflammation associated with it. Overall the 30th centesimal potency shows the highest percentage of improvement in the symptoms of onychocryptosis, though the percentages between the two experimental groups were very close. Further research using a larger research sample group is required to confirm these initial findings.Dr. E.M. Solomon Mr. B. Zipfe