Dip coating process: Silicon sheet growth development for the large-area silicon sheet task of the low-cost silicon solar array project

To date, an experimental dip-coating facility was constructed. Using this facility, relatively thin (1 mm) mullite and alumina substrates were successfully dip-coated with 2.5 - 3.0 ohm-cm, p-type silicon with areas of approximately 20 sq cm. The thickness and grain size of these coatings are influenced by the temperature of the melt and the rate at which the substrate is pulled from the melt. One mullite substrate had dendrite-like crystallites of the order of 1 mm wide and 1 to 2 cm long. Their axes were aligned along the direction of pulling. A large variety of substrate materials were purchased or developed enabling the program to commence a substrate definition evaluation. Due to the insulating nature of the substrate, the bottom layer of the p-n junction may have to be made via the top surface. The feasibility of accomplishing this was demonstrated using single crystal wafers

An Estradiol-Inducible Promoter Enables Fast, Graduated Control of Gene Expression in Fission Yeast [preprint]

The fission yeast Schizosaccharomyces pombe lacks a diverse toolkit of inducible promoters for experimental manipulation. Available inducible promoters suffer from slow induction kinetics, limited control of expression levels and/or a requirement for defined growth medium. In particular, no S. pombe inducible promoter systems exhibit a linear dose response, which would allow expression to be tuned to specific levels. We have adapted a fast, orthogonal promoter system with a large dynamic range and a linear dose response, based on β-estradiol-regulated function of the human estrogen receptor, for use in S. pombe. We show that this promoter system, termed Z3EV, turns on quickly, can reach a maximal induction of 20 fold, and exhibits a linear dose response over its entire induction range, with few off target effects. We demonstrate the utility of this system by regulating the mitotic inhibitor Wee1 to create a strain in which cell size is regulated by β-estradiol concentration. This promoter system will be of great utility for experimentally regulating gene expression in fission yeast

Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions

Background: Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, we study a collection of 75 CLIP-Seq experiments mapping the RNA binding sites for a diverse set of 51 human proteins to explore the role of TEs in post-transcriptional regulation of human mRNAs and lncRNAs via RNA-protein interactions. Results: We detect widespread interactions between RNA binding proteins (RBPs) and many families of TE-derived sequence in the CLIP-Seq data. Further, alignment coverage peaks on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific RBP binding motifs. Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggests that TEs have generally appropriated existing sequence preferences of the RBPs. Depletion assays for numerous RBPs show that TE-derived binding sites affect transcript abundance and splicing similarly to nonrepetitive sites. However, in a few cases the effect of RBP binding depends on the specific TE family bound; for example, the ubiquitously expressed RBP HuR confers transcript stability unless bound to an Alu element. Conclusions: Our meta-analysis suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0537-5) contains supplementary material, which is available to authorized users

Partitioning Complex Networks via Size-constrained Clustering

The most commonly used method to tackle the graph partitioning problem in practice is the multilevel approach. During a coarsening phase, a multilevel graph partitioning algorithm reduces the graph size by iteratively contracting nodes and edges until the graph is small enough to be partitioned by some other algorithm. A partition of the input graph is then constructed by successively transferring the solution to the next finer graph and applying a local search algorithm to improve the current solution. In this paper, we describe a novel approach to partition graphs effectively especially if the networks have a highly irregular structure. More precisely, our algorithm provides graph coarsening by iteratively contracting size-constrained clusterings that are computed using a label propagation algorithm. The same algorithm that provides the size-constrained clusterings can also be used during uncoarsening as a fast and simple local search algorithm. Depending on the algorithm's configuration, we are able to compute partitions of very high quality outperforming all competitors, or partitions that are comparable to the best competitor in terms of quality, hMetis, while being nearly an order of magnitude faster on average. The fastest configuration partitions the largest graph available to us with 3.3 billion edges using a single machine in about ten minutes while cutting less than half of the edges than the fastest competitor, kMetis

Optical Transparency Using Interference Between Two Modes of a Cavity

In electromagnetically-induced transparency (EIT), the absorption of a probe beam is greatly reduced due to destructive interference between two dressed atomic states produced by a strong laser beam. Here we show that a similar reduction in the single-photon absorption rate can be achieved by tuning a probe beam to be halfway between the resonant frequencies of two modes of a cavity. This technique is expected to be useful in enhancing two-photon absorption while reducing losses due to single-photon scattering.Comment: 4 pages, 5 figure

Quantum tunneling in a three dimensional network of exchange coupled single-molecule magnets

A Mn4 single-molecule magnet (SMM) is used to show that quantum tunneling of magnetization (QTM) is not suppressed by moderate three dimensional exchange coupling between molecules. Instead, it leads to an exchange bias of the quantum resonances which allows precise measurements of the effective exchange coupling that is mainly due to weak intermolecular hydrogen bounds. The magnetization versus applied field was recorded on single crystals of [Mn4]2 using an array of micro-SQUIDs. The step fine structure was studied via minor hysteresis loops.Comment: 4 pages, 4 figure

Crop Species Diversity Changes in the United States: 1978-2012

Citation: Aguilar, J., Gramig, G. G., Hendrickson, J. R., Archer, D. W., Forcella, F., & Liebig, M. A. (2015). Crop Species Diversity Changes in the United States: 1978-2012. Plos One, 10(8), 14. doi:10.1371/journal.pone.0136580Anecdotal accounts regarding reduced US cropping system diversity have raised concerns about negative impacts of increasingly homogeneous cropping systems. However, formal analyses to document such changes are lacking. Using US Agriculture Census data, which are collected every five years, we quantified crop species diversity from 1978 to 2012, for the contiguous US on a county level basis. We used Shannon diversity indices expressed as effective number of crop species (ENCS) to quantify crop diversity. We then evaluated changes in county-level crop diversity both nationally and for each of the eight Farm Resource Regions developed by the National Agriculture Statistics Service. During the 34 years we considered in our analyses, both national and regional ENCS changed. Nationally, crop diversity was lower in 2012 than in 1978. However, our analyses also revealed interesting trends between and within different Resource Regions. Overall, the Heartland Resource Region had the lowest crop diversity whereas the Fruitful Rim and Northern Crescent had the highest. In contrast to the other Resource Regions, the Mississippi Portal had significantly higher crop diversity in 2012 than in 1978. Also, within regions there were differences between counties in crop diversity. Spatial autocorrelation revealed clustering of low and high ENCS and this trend became stronger over time. These results show that, nationally counties have been clustering into areas of either low diversity or high diversity. Moreover, a significant trend of more counties shifting to lower rather than to higher crop diversity was detected. The clustering and shifting demonstrates a trend toward crop diversity loss and attendant homogenization of agricultural production systems, which could have far-reaching consequences for provision of ecosystem system services associated with agricultural systems as well as food system sustainability