Automating embedded analysis capabilities and managing software complexity in multiphysics simulation part II: application to partial differential equations

A template-based generic programming approach was presented in a previous paper that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs). We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application

Poorly differentiated carcinoma arising from adenolymphoma of the parotid gland

BACKGROUND: There is only one previous case report of a poorly differentiated carcinoma arising from an adenolymphoma of the parotid gland (Warthin's tumour). The absence of clinical symptoms, and the aspecificity of the radiological pattern make the diagnosis very difficult. CASE PRESENTATION: We here report the case of a 73-year-old man with Warthin's tumour who was brought to our attention because of a swelling in the parotid region. CONCLUSIONS: In this case with an atypical clinical presentation, the intra-operative examination of a frozen section of the parotid mass allowed us to diagnose the malignant tumour correctly and consequently undertake its radical excision

An extensive bloom of the N₂-fixing cyanobacterium Trichodesmium erythraeum in the central Arabian Sea

We encountered an extensive surface bloom of the N, fixing cyanobactenum Trichodesrniurn erythraeum in the central basin of the Arabian Sea during the spring inter-monsooon of 1995. The bloom, which occurred dunng a period of calm winds and relatively high atmospheric iron content, was metabollcally active. Carbon fixation by the bloom represented about one-quarter of water column primary productivity while input by N₂ flxation could account for a major fraction of the estimated 'new' N demand of primary production. Isotopic measurements of the N in surface suspended material confirmed a direct contribution of N₂ fixation to the organic nltrogen pools of the upper water column. Retrospective analysis of NOAA-12 AVHRR imagery indicated that blooms covered up to 2 X 10⁶ km², or 20% of the Arabian Sea surface, during the period from 22 to 27 May 1995. In addition to their biogeochemical impact, surface blooms of this extent may have secondary effects on sea surface albedo and light penetration as well as heat and gas exchange across the air-sea interface. A preliminary extrapolation based on our observed, non-bloom rates of N₂ fixation from our limited sampling in the spring intermonsoon including a conservative estimate of the input by blooms, suggest N₂ fixation may account for an input of about 1 Tg N yr⁻¹. This is substantial, but relatively minor compared to current estimates of the removal of N through denitrification in the basin. However, N₂ fixation may also occur in the central basin through the mild winter monsoon, be considerably greater during the fall intermonsoon than we observed during the spring intermonsoon, and may also occur at higher levels in the chronically oligotrophic southern basin. Ongoing satellite observations will help to determine more accurately the distribution and density of Trichodesmium in this and other tropical oceanic basins, as well as resolving the actual frequency and duration of bloom occurrence

The influence of thermal cycles on the microstructure of grade 92 steel

The microstructure in the heat-affected zone (HAZ) of welds made from the 9 wt pct chromium martensitic Grade 92 steel is complex and has not yet been completely understood. There is a lack of systematic microstructural investigations to define the different regions of the microstructure across the HAZ of Grade 92 steel welds as a function of the welding process. In this study, the microstructure in the HAZ of an as-fabricated single-pass bead-on-plate weld on a parent metal of Grade 92 steel was systematically investigated by using an extensive range of electron and ion-microscopy-based techniques. A dilatometer was used to apply controlled thermal cycles to simulate the microstructures in the different regions of the HAZ. A wide range of microstructural properties in the simulated materials were then characterized and compared with the experimental observations from the weld HAZ. It was found that the microstructure in the HAZ of a single-pass Grade 92 steel weld can be categorized as a function of a decreasing peak temperature reached as (1) the completely transformed (CT) region, in which the original matrix is completely reaustenitized with complete dissolution of the pre-existing secondary precipitate particles; (2) the partially transformed (PT) region, where the original matrix is partially reaustenitized along with a partial dissolution of the secondary precipitate particles from the original matrix; and (3) the overtempered (OT) region, where the pre-xisting precipitate particles coarsen. The PT region is considered to be the susceptible area for damage in the commonly reported HAZ failures in weldments constructed from these types of steels

Langzeitige Änderungen des Salzgehaltes in der Unterweser

Anhand hundertjähriger Meßreihen wurden langfristige Salzgehaltsänderungen in der Unterweser und ihre möglichen Ursachen untersucht. Dabei wurde angestrebt, die natürlichen und die anthropogenen Einflüsse auf den Salzgehalt zu trennen. Trotz des unvollständigen Datensatzes konnten der Einfluß des Einzugsgebietes und Salzgehaltsschwankungen des angrenzenden Meeresgebietes nahezu eliminiert werden. Wegen der langzeitigen Änderungen der Gezeiten in der Nordsee waren genaue Aussagen über die Auswirkung der in den letzten hundert Jahren in der Unterweser durchgeführten Baumaßnahmen auf den Salzgehalt nicht möglich. Unsere Ergebnisse geben Hinweise für moderne Meßnetze zur Bestimmung der Wasserqualität

Ancient horizontal gene transfer and the last common ancestors

Background The genomic history of prokaryotic organismal lineages is marked by extensive horizontal gene transfer (HGT) between groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated in lineages that have since gone extinct. Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life. Results Organisms existing as part of a diverse ecosystem at the time of LUCA likely shared genetic material between lineages. If these other lineages persisted for some time, HGT with the descendants of LUCA could have continued into the bacterial and archaeal lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein families support the hypothesis that the molecular common ancestors of the most ancient gene families did not all coincide in space and time. This is most apparent in the evolutionary histories of seryl-tRNA synthetase and threonyl-tRNA synthetase protein families, each containing highly divergent “rare” forms, as well as the sparse phylogenetic distributions of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of glycyl-tRNA synthetase. These topologies and phyletic distributions are consistent with horizontal transfers from ancient, likely extinct branches of the tree of life. Conclusions Of all the organisms that may have existed at the time of LUCA, by definition only one lineage is survived by known progeny; however, this lineage retains a genomic record of heterogeneous genetic origins. The evolutionary histories of aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting this signal, as they perform primordial biological functions, have undergone several ancient HGT events, and contain many sites with low substitution rates allowing deep phylogenetic reconstruction. We conclude that some aaRS families contain groups that diverge before LUCA. We propose that these ancient gene variants be described by the term “hypnologs”, reflecting their ancient, reticulate origin from a time in life history that has been all but erased”.National Science Foundation (U.S.) (Grant DEB 0830024)Exobiology Program (U.S.) (Grant NNX10AR85G)United States. National Aeronautics and Space Administration (Postdoctoral Program

New Directions in the Development of Population Estimates in the United States?

The advent of a continuously updated Master Area File (MAF) following the 2000 census represents an information resource that can be tapped for purposes of developing timely, cost-effective, and precise population estimates for even the smallest of geographical units (e.g., census blocks). We argue that the MAF can be enhanced (EMAF) for these purposes. In support of our argument we describe a set of activities needed to develop EMAF, each of which is well within the current capabilities of the U.S. Census Bureau and discuss various costs and benefits of each. We also describe how EMAF would provide population estimates containing a wide range of demographic (e.g., age, race, and sex) and socio-economic characteristics (e.g., educational attainment, income, and employment). As such, it could largely negate and eliminate the need for many of the traditional demographic methods of population estimation and possibly reduce the number of sample surveys. We identify important challenges that must be surmounted in order to realize EMAF and make suggestions for doing so. We conclude by noting that the idea of the EMAF could be of interest to other countries with MAF files and strong administrative records systems that, like the United States, are facing the challenge of producing good population information in the face of increasing census costs

Psychosocial factors and early childhood caries among low-income African–American children in Detroit

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75540/1/j.1600-0528.2006.00352.x.pd

Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations

Hammerhead ribozymes are small self-cleaving RNAs that promote strand scission by internal phosphoester transfer. Comparative sequence analysis was used to identify numerous additional representatives of this ribozyme class than were previously known, including the first representatives in fungi and archaea. Moreover, we have uncovered the first natural examples of “type II” hammerheads, and our findings reveal that this permuted form occurs in bacteria as frequently as type I and III architectures. We also identified a commonly occurring pseudoknot that forms a tertiary interaction critical for high-speed ribozyme activity. Genomic contexts of many hammerhead ribozymes indicate that they perform biological functions different from their known role in generating unit-length RNA transcripts of multimeric viroid and satellite virus genomes. In rare instances, nucleotide variation occurs at positions within the catalytic core that are otherwise strictly conserved, suggesting that core mutations are occasionally tolerated or preferred