Protozoa of Iowa

Ten years ago, the authors, while working at the University of Iowa Lakeside Laboratory at Lake Okoboji, compiled a list of Protozoa studied that summer. It was felt such a list could be enlarged upon and become a useful reference for workers in the field of Protozoology. As Protozoa have been identified we have added species from the vicinities of Lakeside Laboratory, Des Moines and Iowa City. Most of these were free living, but we have also included some parasitic forms. In addition we have made some attempt to include those mentioned in readily accessible literature, but no attempt has been made to make an exhaustive survey. We intend to supplement this list with additional forms as they are revealed by an intensive search of published material. We believe that this list is sufficiently complete to be of considerable value in its present form

Method for fabricating a low stress x-ray mask using annealable amorphous refractory compounds

X‐ray masks have been fabricated by depositing a compressively stressed refractory material on a wafer, annealing to a zero stress state, and then forming the membrane. Amorphous TaSiN and TaSi alloys deposited with a magnetron sputter tool have been extensively characterized in terms of resistivity, composition, defectivity, surface roughness, and crystalline state. Optimization in terms of these parameters has resulted in base line selection of absorber films of the following compositions: Ta_(61)Si_(17)N_(21) and Ta_(75)Si_(23). The process is shown to be extendable to an entire class of amorphous annealable refractory materials. Careful studies of deposition and annealing conditions have resulted in a 4× reduction of image placement to the 30 nm maximum vector level. Finally, the importance of stress gradients is experimentally verified

Adenoviral-mediated gene transfer of ICP47 inhibits major histocompatibility complex class I expression on vascular cells in vitro

AbstractPurpose: Many viruses have evolved mechanisms to evade detection by the host immune system. The herpes simplex gene ICP47 encodes a protein that binds to the host antigen-processing transporter, inhibiting the formation of major histocompatibility complex class I (MHC-I) antigens in infected cells. MHC-I antigen expression is also important in acute allograft rejection. This study was designed to quantitate the effect of adenoviral-mediated gene transfer of ICP47 on MHC-I cell surface expression of human vascular cells. We hypothesized that the transduction of vascular cells with a replication-incompetent adenoviral vector that was expressing ICP47 (AdICP47) would inhibit constitutive and inducible MHC-I expression and thereby reduce the rate of cytolysis of ICP47-transduced vascular cells by sensitized cytotoxic T lymphocytes (CTL). Methods: A replication-incompetent adenoviral vector, AdICP47, was created to express ICP47 driven by the cytomegalovirus immediate early promoter. Cultured human vascular endothelial and smooth muscle cells and human dermal fibroblasts were transduced with either AdICP47 or the control empty vector AddlE1. Cell surface constitutive and γ-interferon–induced MHC-I expression were quantitated by flow cytometry. A standard 4-hour chromium release cytotoxicity assay was used to determine the percent cytolysis of transduced and nontransduced endothelial cells by sensitized CTL. Finally, to quantitate the specificity of the effect of ICP47 on MHC-I expression, adhesion molecule expression was quantitated in both transduced and nontransduced cells. Results: Constitutive MHC-I expression in AdICP47-transduced endothelial cells was inhibited by a mean of 84% ± 5% (SEM) in five experiments. After 48 hours of exposure to γ-interferon, AdICP47-transduced cells exhibited a mean of 66% ± 8% lower MHC-I expression than nontransduced cells. Similar inhibition in MHC-I expression was achieved in AdICP47-transduced vascular smooth muscle cells and dermal fibroblasts. Percent cytolysis of AdICP47-transduced endothelial cells by CTL was reduced by 72%. Finally, the specificity of the effect of transduction of ICP47 on vascular cell MHC-I expression was confirmed by a lack of significant change in either constitutive or tumor necrosis factor–induced vascular cell adhesion molecule/intercellular adhesion molecule expression. Conclusion: Transduction of vascular cells with AdICP47 strongly inhibits both constitutive and inducible MHC-I expression in human vascular cells. AdICP47-transduced cells exhibited a substantial reduction in cytolysis by CTL. Thus AdICP47 transduction holds promise as a technique to characterize the role of MHC-I expression in acute vascular allograft rejection in vivo and as a potential therapeutic intervention. (J Vasc Surg 2000;31:558-66.

Analytic Quantization of the QCD String

We perform an analytic semi-classical quantization of the straight QCD string with one end fixed and a massless quark on the other, in the limits of orbital and radial dominant motion. We compare our results to the exact numerical semi-classical quantization. We observe that the numerical semi-classical quantization agrees well with our exact numerical canonical quantization.Comment: RevTeX, 10 pages, 9 figure

Studies of Diffuse Interstellar Bands. V. Pairwise Correlations of Eight Strong DIBs and Neutral Hydrogen, Molecular Hydrogen, and Color Excess

We establish correlations between equivalent widths of eight diffuse interstellar bands (DIBs), and examine their correlations with atomic hydrogen, molecular hydrogen, and EB-V . The DIBs are centered at \lambda\lambda 5780.5, 6204.5, 6283.8, 6196.0, 6613.6, 5705.1, 5797.1, and 5487.7, in decreasing order of Pearson\^as correlation coefficient with N(H) (here defined as the column density of neutral hydrogen), ranging from 0.96 to 0.82. We find the equivalent width of \lambda 5780.5 is better correlated with column densities of H than with E(B-V) or H2, confirming earlier results based on smaller datasets. We show the same is true for six of the seven other DIBs presented here. Despite this similarity, the eight strong DIBs chosen are not well enough correlated with each other to suggest they come from the same carrier. We further conclude that these eight DIBs are more likely to be associated with H than with H2, and hence are not preferentially located in the densest, most UV shielded parts of interstellar clouds. We suggest they arise from different molecules found in diffuse H regions with very little H (molecular fraction f<0.01). Of the 133 stars with available data in our study, there are three with significantly weaker \lambda 5780.5 than our mean H-5780.5 relationship, all of which are in regions of high radiation fields, as previously noted by Herbig. The correlations will be useful in deriving interstellar parameters when direct methods are not available. For instance, with care, the value of N(H) can be derived from W{\lambda}(5780.5).Comment: Accepted for publication in The Astrophysical Journal; 37 pages, 11 figures, 6 table

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

Ligand and Receptor Dynamics Contribute to the Mechanism of Graded PPARγ Agonism

SummaryLigand binding to proteins is not a static process, but rather involves a number of complex dynamic transitions. A flexible ligand can change conformation upon binding its target. The conformation and dynamics of a protein can change to facilitate ligand binding. The conformation of the ligand, however, is generally presumed to have one primary binding mode, shifting the protein conformational ensemble from one state to another. We report solution nuclear magnetic resonance (NMR) studies that reveal peroxisome proliferator-activated receptor γ (PPARγ) modulators can sample multiple binding modes manifesting in multiple receptor conformations in slow conformational exchange. Our NMR, hydrogen/deuterium exchange and docking studies reveal that ligand-induced receptor stabilization and binding mode occupancy correlate with the graded agonist response of the ligand. Our results suggest that ligand and receptor dynamics affect the graded transcriptional output of PPARγ modulators

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Smoking and bladder symptoms in women Obstet Gynecol 2011;118:643–