Freeform Deposition Method for Coolant Channel Closeout

A method is provided for fabricating a coolant channel closeout jacket on a structure having coolant channels formed in an outer surface thereof. A line of tangency relative to the outer surface is defined for each point on the outer surface. Linear rows of a metal feedstock are directed towards and deposited on the outer surface of the structure as a beam of weld energy is directed to the metal feedstock so-deposited. A first angle between the metal feedstock so-directed and the line of tangency is maintained in a range of 20-90.degree.. The beam is directed towards a portion of the linear rows such that less than 30% of the cross-sectional area of the beam impinges on a currently-deposited one of the linear rows. A second angle between the beam and the line of tangency is maintained in a range of 5-65 degrees

Predicting functional upstream open reading frames in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Some upstream open reading frames (uORFs) regulate gene expression (i.e., they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of experimentally verified functional uORFs are needed. Unfortunately, wet-experiments to verify that uORFs are functional are expensive.</p> <p>Results</p> <p>In this paper, a new computational approach to predicting functional uORFs in the yeast <it>Saccharomyces cerevisiae </it>is presented. Our approach is based on inductive logic programming and makes use of a novel combination of knowledge about biological conservation, Gene Ontology annotations and genes' responses to different conditions. Our method results in a set of simple and informative hypotheses with an estimated sensitivity of 76%. The hypotheses predict 301 further genes to have 398 novel functional uORFs. Three (<it>RPC11</it>, <it>TPK1</it>, and <it>FOL1</it>) of these 301 genes have been hypothesised, following wet-experiments, by a related study to have functional uORFs. A comparison with another related study suggests that eleven of the predicted functional uORFs from genes <it>LDB17</it>, <it>HEM3</it>, <it>CIN8</it>, <it>BCK2</it>, <it>PMC1</it>, <it>FAS1</it>, <it>APP1</it>, <it>ACC1</it>, <it>CKA2</it>, <it>SUR1</it>, and <it>ATH1 </it>are strong candidates for wet-lab experimental studies.</p> <p>Conclusions</p> <p>Learning based prediction of functional uORFs can be done with a high sensitivity. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help to elucidate the regulatory roles of uORFs.</p

Valuing Transgenic Cotton Technologies Using a Risk/Return Framework

Stochastic Efficiency with Respect to a Function (SERF) is used to rank transgenic cotton technology groups and place an upper and lower bound on their value. Yield and production data from replicated plot experiments are used to build cumulative distribution functions of returns for nontransgenic, Roundup Ready, Bollgard, and stacked gene cotton cultivars. Analysis of Arkansas data indicated that the stacked gene and Roundup Ready technologies would be preferred by a large number of risk neutral and risk averse producers as long as the costs of the technology and seed are below the lower bounds calculated in this manuscript.cotton, financial risk, market value, SERF, transgenic, Agribusiness, Crop Production/Industries, Risk and Uncertainty, Q12, Q16,

Refining multiple sequence alignments with conserved core regions

Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core (block) model of a protein family. Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile and at the same time preserves the family's overall block model. Large-scale benchmarking studies showed a noticeable improvement of alignment after refinement. This can be inferred from the increased alignment score and enhanced sensitivity for database searching using the sequence profiles derived from refined alignments compared with the original alignments. A standalone version of the program is available by ftp distribution () and will be incorporated into the next release of the Cn3D structure/alignment viewer

Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light

Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400–700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700–800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL–PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL

Effect of Particle Size on Droplet Infiltration into Hydrophobic Porous Media As a Model of Water Repellent Soil

The wettability of soil is of great importance for plants and soil biota, and in determining the risk for preferential flow, surface runoff, flooding,and soil erosion. The molarity of ethanol droplet (MED) test is widely used for quantifying the severity of water repellency in soils that show reduced wettability and is assumed to be independent of soil particle size. The minimum ethanol concentration at which droplet penetration occurs within a short time (≤10 s) provides an estimate of the initial advancing contact angle at which spontaneous wetting is expected. In this study, we test the assumption of particle size independence using a simple model of soil, represented by layers of small (0.2–2 mm) diameter beads that predict the effect of changing bead radius in the top layer on capillary driven imbibition. Experimental results using a three-layer bead system show broad agreement with the model and demonstrate a dependence of the MED test on particle size. The results show that the critical initial advancing contact angle for penetration can be considerably less than 90° and varies with particle size, demonstrating that a key assumption currently used in the MED testing of soil is not necessarily valid

Betti numbers for numerical semigroup rings

We survey results related to the magnitude of the Betti numbers of numerical semigroup rings and of their tangent cones.Comment: 22 pages; v2: updated references. To appear in Multigraded Algebra and Applications (V. Ene, E. Miller Eds.

Novel insights into the molecular mechanisms underlying risk of colorectal cancer from smoking and red/processed meat carcinogens by modeling exposure in normal colon organoids

Tobacco smoke and red/processed meats are well-known risk factors for colorectal cancer (CRC). Most research has focused on studies of normal colon biopsies in epidemiologic studies or treatment of CRC cell lines in vitro. These studies are often constrained by challenges with accuracy of self-report data or, in the case of CRC cell lines, small sample sizes and lack of relationship to normal tissue at risk. In an attempt to address some of these limitations, we performed a 24-hour treatment of a representative carcinogens cocktail in 37 independent organoid lines derived from normal colon biopsies. Machine learning algorithms were applied to bulk RNA-sequencing and revealed cellular composition changes in colon organoids. We identified 738 differentially expressed genes in response to carcinogens exposure. Network analysis identified significantly different modules of co-expression, that included genes related to MSI-H tumor biology, and genes previously implicated in CRC through genome-wide association studies. Our study helps to better define the molecular effects of representative carcinogens from smoking and red/processed meat in normal colon epithelial cells and in the etiology of the MSI-H subtype of CRC, and suggests an overlap between molecular mechanisms involved in inherited and environmental CRC risk. Keywords: colon organoids; microsatellite instability; single-cell deconvolution; smoking; weighted gene co-expression network analysis

Community Attitudes and Practices of Urban Residents Regarding Predation by Pet Cats on Wildlife: An International Comparison

International differences in practices and attitudes regarding pet cats\u27 interactions with wildlife were assessed by surveying citizens from at least two cities in Australia, New Zealand, the UK, the USA, China and Japan. Predictions tested were: (i) cat owners would agree less than non-cat owners that cats might threaten wildlife, (ii) cat owners value wildlife less than non-cat owners, (iii) cat owners are less accepting of cat legislation/restrictions than non-owners, and (iv) respondents from regions with high endemic biodiversity (Australia, New Zealand, China and the USA state of Hawaii) would be most concerned about pet cats threatening wildlife. Everywhere non-owners were more likely than owners to agree that pet cats killing wildlife were a problem in cities, towns and rural areas. Agreement amongst nonowners was highest in Australia (95%) and New Zealand (78%) and lowest in the UK (38%). Irrespective of ownership, over 85% of respondents from all countries except China (65%) valued wildlife in cities, towns and rural areas. Non-owners advocated cat legislation more strongly than owners except in Japan. Australian non-owners were the most supportive (88%), followed by Chinese non-owners (80%) and Japanese owners (79.5%). The UK was least supportive (non-owners 43%, owners 25%). Many Australian (62%), New Zealand (51%) and Chinese owners (42%) agreed that pet cats killing wildlife in cities, towns and rural areas was a problem, while Hawaiian owners were similar to the mainland USA (20%). Thus high endemic biodiversity might contribute to attitudes in some, but not all, countries. Husbandry practices varied internationally, with predation highest where fewer cats were confined. Although the risk of wildlife population declines caused by pet cats justifies precautionary action, campaigns based on wildlife protection are unlikely to succeed outside Australia or New Zealand. Restrictions on roaming protect wildlife and benefit cat welfare, so welfare is a better rationale