First-principles study of illite-smectite and implications for clay mineral systems

Illite-smectite interstratified clay minerals are ubiquitous in sedimentary basins and they have been linked to the maturation, migration and trapping of hydrocarbons, rock cementation, evolution of porewater chemistry during diagenesis and the development of pore pressure. But, despite the importance of these clays, their structures are controversial. Two competing models exist, each with profoundly different consequences for the understanding of diagenetic processes: model A views such interstratified clays as a stacking of layers identical to endmember illite and smectite layers, implying discrete and independently formed units (fundamental particles), whereas model B views the clays as composed of crystallites with a unique structure that maintains coherency over much greater distances, in line with local charge balance about interlayers. Here we use first-principles density-functional theory to explore the energetics and structures of these two models for an illite-smectite interstratified clay mineral with a ratio of 1:1 and a Reichweite parameter of 1. We find that the total energy of model B is 2.3 kJ atom(-1) mol(-1) lower than that of model A, and that this energy difference can be traced to structural distortions in model A due to local charge imbalance. The greater stability of model B requires re-evaluation of the evolution of the smectite-to-illite sequence of clay minerals, including the nature of coexisting species, stability relations, growth mechanisms and the model of fundamental particles.     

Response of winterfat ( Ceratoides lanata ) communities to release from grazing pressure

Sixteen study sites were established in grazed and ungrazed stands of winterfat in Kane County, Utah. The area is located within the winter range of cattle and along U.S. Highway 89 between Kanab, Utah, and Page, Arizona. Road construction in 1957 dissected several winterfat communities, and following fencing part of the communities were released from grazing. Differences in species composition, vegetation, and soil characteristics between grazed and ungrazed sites were assessed. Major differences in site characteristics appeared due to the influence of winter grazing by cattle. Winterfat and Indian ricegrass showed increased cover on the nongrazed sites following release from grazing pressure. Winterfat also showed significant negative interspecific association patterns with all major species.     

Comparative habitat and community relationships of Atriplex confertifolia and Sarcobatus vermiculatus in central Utah

Thirty-four study sites were established in shadscale ( Atriplex confertifolia [Torr. & Frem.] Wats.) and greasewood ( Sarcobatus vermiculatus [Hoov. Torr. in Emory) communities bordering Utah Lake in central Utah. Differences in species composition, vegetation, and soil characteristics were assessed. Significant differences in soil factors between the two communities were found for sand, calcium, manganese, zinc, and copper. Soluble salts and sodium concentrations were generally higher in the greasewood type, but differences were not significant. Major differences were found in understory species, with burr buttercup ( Ranunculus testiculatus Grantz) showing significantly greater cover in the shadscale community and cheatgrass ( Bromus tectorum L.) showing significantly greater cover in the greasewood community.     

From Bureaucracy to Learning Organization: Critical Minimum Specification Design as Space for Sensemaking

What does it take of a municipal organization to be a significant participant in the dynamic, learning oriented interaction within a triple helix constellation of partners aimed at regional development? The short answer is that it needs to develop the receptivity (Morgan, 1996) and the flexibility to act in novel ways, which are the traits of a learning organization. However, how these abilities are enhanced in organizations that are basically organized as bureaucracies aimed at maintaining a stable and standardized function of its operations, is an under-researched phenomenon within the triple helix discussions. In this paper, I investigate this question through an analysis of a change and development process within a municipal organization that aimed to enhance the capacity of the organization to interact receptively and dynamically with their environment, by changing their organizational structure from a bureaucratic to a post-bureaucratic type. The main finding is that rather than the new formal structure as such; it is the process of sensemaking following the introduction of this new formal structure that creates the capacity for learning and development. However, this outcome is dependent on the sensemaking process being turned over from a defensive mode into a learning oriented mode. The paper explores how this turn may be facilitated.     

Surface-enhanced Raman scattering on dual-layer metallic grating structures

Dual-layer Metallic grating (DMG) structures as surface-enhanced Raman scattering (SERS) substrates are studied using ben-zenethiol as the probe analyte. The DMG structure consists of a SiO₂ grating and 100-nm-thick gold coating layers. An enhancement factor of 10⁵ is achieved by optimizing the SiO₂ grating height within the range from 165 to 550 nm. The enhancement factor dependence on the SiO₂ grating height is due to the surface plasmon excitation, which is dependent on the polarization of the incident light, and confirmed by finite difference time domain simulations. This study demonstrates the advantages of high uniformity, reproducibility and sensitivity in the DMG structures for SERS applications.     

A classifying procedure for signalling turning points

A Hidden Markov Model (HMM) is used to classify an out‐of‐sample observation vector into either of two regimes. This leads to a procedure for making probability forecasts for changes of regimes in a time series, i.e. for turning points. Instead of estimating past turning points using maximum likelihood, the model is estimated with respect to known past regimes. This makes it possible to perform feature extraction and estimation for different forecasting horizons. The inference aspect is emphasized by including a penalty for a wrong decision in the cost function. The method, here called a ‘Markov Bayesian Classifier (MBC)’, is tested by forecasting turning points in the Swedish and US economies, using leading data. Clear and early turning point signals are obtained, contrasting favourably with earlier HMM studies. Some theoretical arguments for this are given. Copyright © 2004 John Wiley & Sons, Ltd.     

High-resolution mapping of meiotic crossovers and non-crossovers in yeast

Meiotic recombination has a central role in the evolution of sexually reproducing organisms. The two recombination outcomes, crossover and non-crossover, increase genetic diversity, but have the potential to homogenize alleles by gene conversion. Whereas crossover rates vary considerably across the genome, non-crossovers and gene conversions have only been identified in a handful of loci. To examine recombination genome wide and at high spatial resolution, we generated maps of crossovers, crossover-associated gene conversion and non-crossover gene conversion using dense genetic marker data collected from all four products of fifty-six yeast (Saccharomyces cerevisiae) meioses. Our maps reveal differences in the distributions of crossovers and non-crossovers, showing more regions where either crossovers or non-crossovers are favoured than expected by chance. Furthermore, we detect evidence for interference between crossovers and non-crossovers, a phenomenon previously only known to occur between crossovers. Up to 1% of the genome of each meiotic product is subject to gene conversion in a single meiosis, with detectable bias towards GC nucleotides. To our knowledge the maps represent the first high-resolution, genome-wide characterization of the multiple outcomes of recombination in any organism. In addition, because non-crossover hotspots create holes of reduced linkage within haplotype blocks, our results stress the need to incorporate non-crossovers into genetic linkage analysis.     

TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis

Although there has been much success in identifying genetic variants associated with common diseases using genome-wide association studies (GWAS), it has been difficult to demonstrate which variants are causal and what role they have in disease. Moreover, the modest contribution that these variants make to disease risk has raised questions regarding their medical relevance. Here we have investigated a single nucleotide polymorphism (SNP) in the TNFRSF1A gene, that encodes tumour necrosis factor receptor 1 (TNFR1), which was discovered through GWAS to be associated with multiple sclerosis (MS), but not with other autoimmune conditions such as rheumatoid arthritis, psoriasis and Crohn’s disease. By analysing MS GWAS data in conjunction with the 1000 Genomes Project data we provide genetic evidence that strongly implicates this SNP, rs1800693, as the causal variant in the TNFRSF1A region. We further substantiate this through functional studies showing that the MS risk allele directs expression of a novel, soluble form of TNFR1 that can block TNF. Importantly, TNF-blocking drugs can promote onset or exacerbation of MS, but they have proven highly efficacious in the treatment of autoimmune diseases for which there is no association with rs1800693. This indicates that the clinical experience with these drugs parallels the disease association of rs1800693, and that the MS-associated TNFR1 variant mimics the effect of TNF-blocking drugs. Hence, our study demonstrates that clinical practice can be informed by comparing GWAS across common autoimmune diseases and by investigating the functional consequences of the disease-associated genetic variation.