Econometric Estimation of Groundwater Depth Change for the High Plains Aquifer

This article presents a new method for estimating changes in depth to groundwater at a yearly, county level and incorporates these estimates as the dependent variable of econometric models for the High Plains aquifer. The High Plains (Ogallala) aquifer underlies eight states in the central United States and is the primary source of irrigation water for this large food producing region. The stock of groundwater is a finite, non-renewable resource with minimal recharge in most areas. Many fields of study, including hydrology and agricultural economics, are interested in depth to groundwater changes because they serve as a proxy for estimating groundwater stock changes. Economic data exist at the yearly, county level, but there are currently no yearly estimates for depth to groundwater changes making it difficult to reliably utilize economic optimization and production models that depend on groundwater data. Including the new estimates generated in this study as the dependent variable with climate, recharge, and irrigation as independent variables in panel econometric models (Pooled OLS, Random Effects, and Fixed Effects) with counties as the individuals produced statistically significant results. Further, models were found which consistently performed best when comparing coefficients and predicted values with outside estimates from hydrology studies. Advisor: Lilyan E. Fulginit

Exploring the Cost Function in Color Perception and Memory:An Information-Theoretic Model of Categorical Effects in Color Matching

Recent evidence indicates that color categories can exert astrong influence over color matching in both perception andmemory. We explore this phenomenon by analyzing the costfunction for perceptual error. Our analysis is developed withinthe mathematical framework of rate–distortion theory. Ac-cording to our approach, the goal of perception is to minimizethe expected cost of error while subject to a strong constrainton the capacity of perceptual processing. We propose that thecost function in color perception is defined by the sum of twocomponents: a metric cost associated with the magnitude of er-ror in color space, and a cost associated with perceptual errorsthat cross color category boundaries. A computational modelembodying this assumption is shown to produce an excellent fitto empirical data. The results generally suggest that what ap-pear as ‘errors’ in working memory performance may reflectreasonable and systematic behaviors in the context of costs

Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production

In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed. It was not clear if these differences were due to changes in genomic sequence, the protein sequence or the frequency of frameshifting. Here, viruses with synonymous codon changes are shown to produce different ratios of genomic and subgenomic RNA. These findings demonstrate that the protein sequence is not the primary cause of altered genomic and subgenomic RNA production. The synonymous codon changes affect both the structure of the frameshift signal and frameshifting efficiency. Small differences in frameshifting efficiency result in dramatic differences in genomic RNA production and TCID50 suggesting that the frameshifting frequency must stay above a certain threshold for optimal virus production. The data suggest that either the RNA sequence or the ratio of viral proteins resulting from different levels of frameshifting affects viral replication

Cartan subalgebras in C*-algebras of Hausdorff etale groupoids

The reduced $C^*$-algebra of the interior of the isotropy in any Hausdorff \'etale groupoid $G$ embeds as a $C^*$-subalgebra $M$ of the reduced $C^*$-algebra of $G$. We prove that the set of pure states of $M$ with unique extension is dense, and deduce that any representation of the reduced $C^*$-algebra of $G$ that is injective on $M$ is faithful. We prove that there is a conditional expectation from the reduced $C^*$-algebra of $G$ onto $M$ if and only if the interior of the isotropy in $G$ is closed. Using this, we prove that when the interior of the isotropy is abelian and closed, $M$ is a Cartan subalgebra. We prove that for a large class of groupoids $G$ with abelian isotropy---including all Deaconu--Renault groupoids associated to discrete abelian groups---$M$ is a maximal abelian subalgebra. In the specific case of $k$-graph groupoids, we deduce that $M$ is always maximal abelian, but show by example that it is not always Cartan.Comment: 14 pages. v2: Theorem 3.1 in v1 incorrect (thanks to A. Kumjain for pointing out the error); v2 shows there is a conditional expectation onto $M$ iff the interior of the isotropy is closed. v3: Material (including some theorem statements) rearranged and shortened. Lemma~3.5 of v2 removed. This version published in Integral Equations and Operator Theor

MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma

Glioblastomas (GBMs) diffusely infiltrate the brain, making complete removal by surgical resection impossible. The mixture of neoplastic and nonneoplastic cells that remain after surgery form the biological context for adjuvant therapeutic intervention and recurrence. We performed RNA-sequencing (RNA-seq) and histological analysis on radiographically guided biopsies taken from different regions of GBM and showed that the tissue contained within the contrast-enhancing (CE) core of tumors have different cellular and molecular compositions compared with tissue from the nonenhancing (NE) margins of tumors. Comparisons with the The Cancer Genome Atlas dataset showed that the samples from CE regions resembled the proneural, classical, or mesenchymal subtypes of GBM, whereas the samples from the NE regions predominantly resembled the neural subtype. Computational deconvolution of the RNA-seq data revealed that contributions from nonneoplastic brain cells significantly influence the expression pattern in the NE samples. Gene ontology analysis showed that the cell type-specific expression patterns were functionally distinct and highly enriched in genes associated with the corresponding cell phenotypes. Comparing the RNA-seq data from the GBM samples to that of nonneoplastic brain revealed that the differentially expressed genes are distributed across multiple cell types. Notably, the patterns of cell type-specific alterations varied between the different GBM subtypes: the NE regions of proneural tumors were enriched in oligodendrocyte progenitor genes, whereas the NE regions of mesenchymal GBM were enriched in astrocytic and microglial genes. These subtypespecific patterns provide new insights into molecular and cellular composition of the infiltrative margins of GBM

High performance aluminum–cerium alloys for high-temperature applications

Light-weight high-temperature alloys are important to the transportation industry where weight, cost, and operating temperature are major factors in the design of energy efficient vehicles. Aluminum alloys fill this gap economically but lack high-temperature mechanical performance. Alloying aluminum with cerium creates a highly castable alloy, compatible with traditional aluminum alloy additions, that exhibits dramatically improved high-temperature performance. These compositions display a room temperature ultimate tensile strength of 400 MPa and yield strength of 320 MPa, with 80% mechanical property retention at 240 °C. A mechanism is identified that addresses the mechanical property stability of the Al-alloys to at least 300 °C and their microstructural stability to above 500 °C which may enable applications without the need for heat treatment. Finally, neutron diffraction under load provides insight into the unusual mechanisms driving the mechanical strength

RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis

Increased autophagy in EphrinB2-deficient osteocytes is associated with elevated secondary mineralization and brittle bone

Mineralized bone forms when collagen-containing osteoid accrues mineral crystals. This is initiated rapidly (primary mineralization), and continues slowly (secondary mineralization) until bone is remodeled. The interconnected osteocyte network within the bone matrix differentiates from bone-forming osteoblasts; although osteoblast differentiation requires EphrinB2, osteocytes retain its expression. Here we report brittle bones in mice with osteocyte-targeted EphrinB2 deletion. This is not caused by low bone mass, but by defective bone material. While osteoid mineralization is initiated at normal rate, mineral accrual is accelerated, indicating that EphrinB2 in osteocytes limits mineral accumulation. No known regulators of mineralization are modified in the brittle cortical bone but a cluster of autophagy-associated genes are dysregulated. EphrinB2-deficient osteocytes displayed more autophagosomes in vivo and in vitro, and EphrinB2-Fc treatment suppresses autophagy in a RhoA-ROCK dependent manner. We conclude that secondary mineralization involves EphrinB2-RhoA-limited autophagy in osteocytes, and disruption leads to a bone fragility independent of bone mass.Mineralized bone forms when collagen-containing osteoid accrues mineral crystals. This is initiated rapidly (primary mineralization), and continues slowly (secondary mineralization) until bone is remodeled. The interconnected osteocyte network within the bone matrix differentiates from bone-forming osteoblasts; although osteoblast differentiation requires EphrinB2, osteocytes retain its expression. Here we report brittle bones in mice with osteocyte-targeted EphrinB2 deletion. This is not caused by low bone mass, but by defective bone material. While osteoid mineralization is initiated at normal rate, mineral accrual is accelerated, indicating that EphrinB2 in osteocytes limits mineral accumulation. No known regulators of mineralization are modified in the brittle cortical bone but a cluster of autophagy-associated genes are dysregulated. EphrinB2-deficient osteocytes displayed more autophagosomes in vivo and in vitro, and EphrinB2-Fc treatment suppresses autophagy in a RhoA-ROCK dependent manner. We conclude that secondary mineralization involves EphrinB2-RhoA-limited autophagy in osteocytes, and disruption leads to a bone fragility independent of bone mass

Meloneis Gen. Nov., a New Epipsammic Genus of Rhaphoneidaceae (Bacillariophyceae)

The diatom family Rhaphoneidaceae is characterized by high generic diversity and low species diversity with most genera known to have long stratigraphic ranges. The genera within this family are neritic marine, and mostly epipsammic. A new modern and epipsammic genus, Meloneis gen. nov., is described herein and is compared to all genera within Rhaphoneidaceae and especially to Rhaphoneis Ehrenberg s.l. Within Meloneis three new species and one variety are distinguished and described herein: M. mimallis sp. nov., M. mimallis var. zephyria var. nov., M. akytos sp. nov., and M. gorgis sp. nov