Modeling the Uptake and Transpiration of TCE Using Phreatophytic Trees

Phytoremediation is a recent addition to the numerous methods used today to remediate ground water contaminants. It is proving more effective and efficient compared to existing remediation techniques. The use of phreatophytes, or water seeking trees, has great potential for phytoremediation. These trees are fast growing, long lived, grow their roots down to the ground water table, transpire large amounts of water, and are proven to actively remove contaminants from the soil horizon. The purpose of this research is to develop quantitative concepts for understanding the dynamics of TCE uptake and transpiration by phreatophytic trees over a short rotation woody crop time frame. This will he done by constructing a system dynamics model of this process and running it over a wide range of conditions. This research will offer managers a tool to simulate long-term uptake and transpiration of TCE at potential sites. The results of this study indicate that TCE is actively removed from the soil horizon by phreatophytic trees and a significant proportion of this TCE is then transpired. Changes in soil horizon parameters, xylem flow rates, and variables in the uptake equation greatly influence TCE uptake rates as well as transpiration. Also, parameters used in equations representing flows in and out of the leaf greatly influence transpiration. Better understanding of these processes is essential for managers to accurately predict the amount of TCE removed and transpired during potential phytoremediation projects

Effect of alloying on the microstructure, phase stability, hardness and partitioning behavior of a new dual-superlattice nickel-based superalloy

A novel y-y'-y" dual-superlattice superalloy, with promising mechanical properties up to elevated temperatures was recently reported. The present work employs state of the art chemical and spatial characterization techniques to study the effect systematic additions of Mo, W and Fe and variations in Nb and Al contents have on the phase fraction, thermal stability, elemental partitioning and mechanical properties. Alloys were produced through arc melting followed by heat treatment. Multi-scale characterization techniques and hardness testing were employed to characterize their microstructure, thermal stability and mechanical properties. Alterations in such properties or in elemental partitioning behaviour were then explained through thermodynamic modelling. A modest addition of 1.8 at.% Mo had a strong effect on the microstructure and thermal stability: it minimized microstructural coarsening during heat treatments while not significantly decreasing the y' solvus temperature. A reduction of Nb by 0.6 at.%, strongly reduced the y" volume fraction, without affecting the y' volume fraction. The reduced precipitate fraction led to a significant reduction in alloy hardness. Fe, added to achieve better processability and reduced material cost, decreased the y' solvus temperature and caused rapid microstructural coarsening during heat treatments, without affecting alloy hardness. A reduction of Al by 0.4 at.%, reduced the y' volume fraction and the y' solvus temperature, also without affecting alloy hardness. The addition of 0.9 at.% W decreased the y' solvus temperature but increased both precipitate volume fractions. These data will be invaluable to optimize current alloy design and to inform future alloy design efforts

Control of Vertebrate Skeletal Mineralization by Polyphosphates

BACKGROUND:Skeletons are formed in a wide variety of shapes, sizes, and compositions of organic and mineral components. Many invertebrate skeletons are constructed from carbonate or silicate minerals, whereas vertebrate skeletons are instead composed of a calcium phosphate mineral known as apatite. No one yet knows why the dynamic vertebrate skeleton, which is continually rebuilt, repaired, and resorbed during growth and normal remodeling, is composed of apatite. Nor is the control of bone and calcifying cartilage mineralization well understood, though it is thought to be associated with phosphate-cleaving proteins. Researchers have assumed that skeletal mineralization is also associated with non-crystalline, calcium- and phosphate-containing electron-dense granules that have been detected in vertebrate skeletal tissue prepared under non-aqueous conditions. Again, however, the role of these granules remains poorly understood. Here, we review bone and growth plate mineralization before showing that polymers of phosphate ions (polyphosphates: (PO(3)(-))(n)) are co-located with mineralizing cartilage and resorbing bone. We propose that the electron-dense granules contain polyphosphates, and explain how these polyphosphates may play an important role in apatite biomineralization. PRINCIPAL FINDINGS/METHODOLOGY:The enzymatic formation (condensation) and destruction (hydrolytic degradation) of polyphosphates offers a simple mechanism for enzymatic control of phosphate accumulation and the relative saturation of apatite. Under circumstances in which apatite mineral formation is undesirable, such as within cartilage tissue or during bone resorption, the production of polyphosphates reduces the free orthophosphate (PO(4)(3-)) concentration while permitting the accumulation of a high total PO(4)(3-) concentration. Sequestering calcium into amorphous calcium polyphosphate complexes can reduce the concentration of free calcium. The resulting reduction of both free PO(4)(3-) and free calcium lowers the relative apatite saturation, preventing formation of apatite crystals. Identified in situ within resorbing bone and mineralizing cartilage by the fluorescent reporter DAPI (4',6-diamidino-2-phenylindole), polyphosphate formation prevents apatite crystal precipitation while accumulating high local concentrations of total calcium and phosphate. When mineralization is required, tissue non-specific alkaline phosphatase, an enzyme associated with skeletal and cartilage mineralization, cleaves orthophosphates from polyphosphates. The hydrolytic degradation of polyphosphates in the calcium-polyphosphate complex increases orthophosphate and calcium concentrations and thereby favors apatite mineral formation. The correlation of alkaline phosphatase with this process may be explained by the destruction of polyphosphates in calcifying cartilage and areas of bone formation. CONCLUSIONS/SIGNIFICANCE:We hypothesize that polyphosphate formation and hydrolytic degradation constitute a simple mechanism for phosphate accumulation and enzymatic control of biological apatite saturation. This enzymatic control of calcified tissue mineralization may have permitted the development of a phosphate-based, mineralized endoskeleton that can be continually remodeled

Interactions of Candida albicans with host epithelial surfaces

Candida albicans is an opportunistic, fungal pathogen of humans that frequently causes superficial infections of oral and vaginal mucosal surfaces of debilitated and susceptible individuals. The organism is however, commonly encountered as a commensal in healthy individuals where it is a component of the normal microflora. The key determinant in the type of relationship that Candida has with its host is how it interacts with the epithelial surface it colonises. A delicate balance clearly exists between the potentially damaging effects of Candida virulence factors and the nature of the immune response elicited by the host. Frequently, it is changes in host factors that lead to Candida seemingly changing from a commensal to pathogenic existence. However, given the often reported heterogeneity in morphological and biochemical factors that exist between Candida species and indeed strains of C. albicans, it may also be the fact that colonising strains differ in the way they exploit resources to allow persistence at mucosal surfaces and as a consequence this too may affect the way Candida interacts with epithelial cells. The aim of this review is to provide an overview of some of the possible interactions that may occur between C. albicans and host epithelial surfaces that may in turn dictate whether Candida removal, its commensal persistence or infection follows

Influenza A Virus Coding Regions Exhibit Host-Specific Global Ordered RNA Structure

Influenza A is a significant public health threat, partially because of its capacity to readily exchange gene segments between different host species to form novel pandemic strains. An understanding of the fundamental factors providing species barriers between different influenza hosts would facilitate identification of strains capable of leading to pandemic outbreaks and could also inform vaccine development. Here, we describe the difference in predicted RNA secondary structure stability that exists between avian, swine and human coding regions. The results predict that global ordered RNA structure exists in influenza A segments 1, 5, 7 and 8, and that ranges of free energies for secondary structure formation differ between host strains. The predicted free energy distributions for strains from avian, swine, and human species suggest criteria for segment reassortment and strains that might be ideal candidates for viral attenuation and vaccine development

Dark Stars: A New Study of the FIrst Stars in the Universe

We have proposed that the first phase of stellar evolution in the history of the Universe may be Dark Stars (DS), powered by dark matter heating rather than by nuclear fusion. Weakly Interacting Massive Particles, which may be their own antipartners, collect inside the first stars and annihilate to produce a heat source that can power the stars. A new stellar phase results, a Dark Star, powered by dark matter annihilation as long as there is dark matter fuel, with lifetimes from millions to billions of years. We find that the first stars are very bright ($\sim 10^6 L_\odot$) and cool ($T_{surf} < 10,000$K) during the DS phase, and grow to be very massive (500-1000 times as massive as the Sun). These results differ markedly from the standard picture in the absence of DM heating, in which the maximum mass is about 140$M_\odot$ and the temperatures are much hotter ($T_{surf} > 50,000$K); hence DS should be observationally distinct from standard Pop III stars. Once the dark matter fuel is exhausted, the DS becomes a heavy main sequence star; these stars eventually collapse to form massive black holes that may provide seeds for supermassive black holes observed at early times as well as explanations for recent ARCADE data and for intermediate black holes.Comment: article to be published in special issue on Dark Matter and Particle Physics in New Journal of Physic

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment