gebhart/patrepeval huggingface dataset:
Phylogeography and host association in a pollinating seed parasite <i>Greya politella</i> (Lepidoptera: Prodoxidae) (1997)

Inferring the historical context of ecological diversification is an important step in understanding the way that population-level processes result in a diversity of species and interactions in communities. We performed a phylogeographic analysis of mitochondrial DNA haplotypes from the pollinating seed parasite Greya politella (Lepidoptera: Prodoxidae) in order to determine the degree to which populations were structured according to geographical location and host-plant association. Ninety-eight individuals were sampled from 29 locations ranging from southern California to western Idaho. Restriction-site variation in 87 individuals (27 populations) was screened by digestion with 11 endonucleases, followed by Southern blotting; 38 restriction-site positions were mapped by double digests. Haplotypes were further defined by generating fragments 251 bases in length via PCR, screening them for sequence variation using denaturing gel gradient electrophoresis (DGGE), and sequencing the resulting variants. Parsimony analysis of the resulting 12 restriction-site and 15 sequence haplotypes indicated strong geographical structuring of populations: (i) most populations were monomorphic for haplotype; (ii) haplotypes from California and the Pacific Northwest (Oregon, Washington and Idaho) formed robust monophyletic groups. Population structure was significant both within and between the two regions, as reflected by NST. Patterns of host-plant association and haplotype phylogeny suggest that populations have recently undergone host-plant shifts in many different parts of the species range, although the direction and number of host shifts cannot be determined at the present level of sampling resolution.
Tetracycline-Inducible Gene Expression and Gene Deletion in <i>Candida albicans</i> (2005)

The genetic analysis of Candida albicans, the major fungal pathogen of humans, is hampered by its diploid genome, the absence of a normal sexual cycle, and a nonstandard codon usage. Although effective methods to study gene function have been developed in the past years, systems to control gene expression in C. albicans are limited. We have established a system that allows induction of gene expression in C. albicans by the addition of tetracycline (Tet). By fusing genetically modified versions of the reverse Tet repressor from Escherichia coli and the transcription activation domain of the Gal4 protein from Saccharomyces cerevisiae, a C. albicans-adapted reverse Tet-dependent transactivator (rtTA) was created that was expressed from the constitutive ADH1 or the opaque-specific OP4 promoter. To monitor Tet-inducible gene expression, the caGFP reporter gene was placed under the control of a Tet-dependent promoter, obtained by fusing a minimal promoter from C. albicans to seven copies of the Tet operator sequence. Fluorescence of the cells demonstrated that gene expression could be efficiently induced by the addition of doxycycline in yeast, hyphal, and opaque cells of C. albicans. The Tet-inducible gene expression system was then used to manipulate the behavior of the various growth forms of C. albicans. Tet-induced expression of a dominant-negative CDC42 allele resulted in growth arrest as large, multinucleate cells. Filamentous growth was efficiently inhibited under all tested hyphal-growth-promoting conditions by Tet-inducible expression of the NRG1 repressor. Tet-induced expression of the MTLa1 gene in opaque cells of an MTLalpha strain forced the cells to switch to the white phase, whereas Tet-induced expression of the MTLa2 transcription factor induced shmooing. When the ecaFLP gene, encoding the site-specific recombinase FLP, was placed under the control of the Tet-dependent promoter, Tet-inducible deletion of genes which were flanked by the FLP target sequences was achieved with high efficiency to generate conditional null mutants. In combination with the dominant selection marker caSAT1, the Tet-inducible gene expression system was also applied in C. albicans wild-type strains, including drug-resistant clinical isolates that overexpressed the MDR1, CDR1, and CDR2 multidrug efflux pumps. This system, therefore, allows a growth medium-independent, Tet-inducible expression and deletion of genes in C. albicans and provides a convenient, versatile new tool to study gene function and manipulate cellular behavior in this model pathogenic fungus.
Microlens array production in a microtechnological dry etch and reflow process for display applications (2012)

The fabrication of arrays consisting of densely ordered circular convex microlenses with diameters of 126 µ m made of quartz glass in a photoresist reflow and dry etch structure transition process is demonstrated. The rectangular lens arrays with dimensions of 6 mm × 9 mm were designed for focussing collimated light on the pixel center regions of a translucent interference display, which also was produced in microtechnological process steps. The lenses focus light on pixel centers and thus serve for increasing display brightness and contrast since incoming collimated light is partially blocked by opaque metallic ring contacts at the display pixel edges. The focal lengths of the lenses lie between 0.46 mm and 2.53 mm and were adjusted by varying the ratio of the selective dry etch rate of photoresist and quartz glass. Due to volume shrinking and edge line pinning of the photoresist structures the lenses curvatures emerge hyperbolic, leading to improved focussing performance.
Practice Guidelines for the Treatment of Lyme Disease (2000)

Gary P. Wormser,1 Robert B. Nadelman,1 'Division of Infectious Diseases, Department of Medicine, New York Raymond J. Dattwyler,2 David T. Dennis,6 Medical College, Valhalla, 2Division of Allergy, Immunology Eugene D. Shapiro,7 Allen C. Steere,9 and Lyme Disease, Department of Medicine, 3Department Thoma J. Rush,' D l W. R n, of Neurology, and 4Department of Medicine, Health Sciences Center, Thomas J. Rush,5 Daniel W. Rahn,10 T a sa J. R ,' 'Danid W Prang, State University of New York at Stony Brook, and 5private practice, Patricia K. Coyle,3 David H. Persing,1 Briarcliff Manor, New York; 6Division of Vector-Borne Infectious Durland Fish,8 and Benjamin J. Luft4 Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado; Departments of 7Pediatrics and 8Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut; 9Tufts University School of Medicine, New England Medical Center, Boston, Massachusetts; 'OOffice of Medical Management, Medical College of Georgia, Augusta; and Diagnostics Development, Corixa Corporation, and Infectious Disease Research Institute, Seattle Life Sciences Center, Seattle, Washington
Electron-induced nitridation of GaAs(100) with ammonia (1993)

Nitridation of GaAs(100) was observed at temperatures ranging from 323 to 523 K by simultaneous exposure of the substrate to a molecular ammonia flux and electron irradiation in an ultrahigh vacuum environment. Incident electron energies of 350–3000 eV were employed. A GaN surface film formed. GaN formation was related to the amount of chemisorbed NH3 and the electron beam flux. The nitridation process was nonthermal. Two possible reaction schemes involving dissociative electron attachment and dissociative electron ionization are discussed.
An error simulation based approach to measure error coverage of formal properties (2002)

Many approaches have been proposed for digital system verification, either based on simulation strategies or on formal verification techniques. Both of them show advantages and drawbacks and new mixed approaches have been presented in order to improve the verification process. Specifically, the adoption of formal methods still lacks a coverage metrics to let the verification engineer get a measure of which portion of the circuit is already covered by the written properties that far and which parts still need to be addressed. The present paper describes a new simulation based methodology aimed at measuring the error coverage achieved by temporal assertions proved by model checking. The approach has been applied to the description of a protocol converter block, and some preliminary results are presented in the paper.
Mathematical And Computational Methods For Freeform Optical Shape Description (2013)

Slow-servo single-point diamond turning as well as advances in computer controlled small lap polishing enable the fabrication of freeform optics, specifically, optical surfaces for imaging applications that are not rotationally symmetric. Freeform optical elements will have a profound importance in the future of optical technology. Orthogonal polynomials added onto conic sections have been extensively used to describe optical surface shapes. The optical testing industry has chosen to represent the departure of a wavefront under test from a reference sphere in terms of orthogonal φ-polynomials, specifically Zernike polynomials. Various forms of polynomials for describing freeform optical surfaces may be considered, however, both in optical design and in support of fabrication. More recently, radial basis functions were also investigated for optical shape description. In the application of orthogonal φ-polynomials to optical freeform shape description, there are important limitations, such as the number of terms required as well as edge-ringing and ill-conditioning in representing the surface with the accuracy demanded by most stringent optics applications. The first part of this dissertation focuses upon describing freeform optical surfaces with φ-polynomials and shows their limitations when including higher orders together with possible remedies. We show that a possible remedy is to use edge-clusteredfitting grids. Provided different grid types, we furthermore compared the efficacy of using different types of φ-polynomials, namely Zernike and gradient orthogonal Q-polynomials. In the second part of this thesis, a local, efficient and accurate hybrid method is developed in order to greatly reduce the order of polynomial terms required to achieve higher level of accuracy in freeform shape description that were shown to require thousands of terms including many higher order terms under prior art. This comes at the expense of multiple sub-apertures, and as such iv computational methods may leverage parallel processing. This new method combines the assets of both radial basis functions and orthogonal phi-polynomials for freeform shape description and is uniquely applicable across any aperture shape due to its locality and stitching principles. Finally in this thesis, in order to comprehend the possible advantages of parallel computing for optical surface descriptions, the benefits of making an effective use of impressive computational power offered by multi-core platforms for the computation of φ-polynomials are investigated. The φ-polynomials, specifically Zernike and gradient orthogonal Q-polynomials, are implemented with a set of recurrence based parallel algorithms on Graphics Processing Units (GPUs). The results show that more than an order of magnitude speedup is possible in the computation of φ-polynomials over a sequential implementation if the recurrence based parallel algorithms are adopted.
Effect of PEG4000 on cellulase catalysis in the lignocellulose saccharification processes (2010)

Abstract BACKGROUND: Lignocellulose is a large source of biomass. However, the conversion ratio of lignocellulose into fermentable sugars is quite low, and the saccharification process requires lots of enzyme. In order to improve biocatalysis efficiency of cellulase for lignocellulose, poly ethylene glycol (PEG4000) is added to the above process. The effect of the order of addition of PEG4000 and cellulase on lignocellulose saccharification processes, and the interaction between PEG4000 and eocellobiohydrolase I (CBH I) were investigated by DNS, UV absorption spectra and Fourier transform infrared (FTIR) spectroscopy. RESULTS: Results show that different orders of addition of PEG4000 and cellulase have a strong influence on the saccharification process, and both orders of addition can improve the saccharification rate. In particular, the addition of PEG4000 before cellulase can reduce wasteful cellulase adsorption on the lignin, and the saccharification rate of lignocellulose can be significantly improved. Without corn stover (substrate) in the saccharification process, examinations by UV absorption spectra and FTIR demonstrate that the interactions between PEG4000 and CBH I are hydrogen bonds and hydrophobic interaction. In addition, it is found that the activity of CBH I is decreased with increasing interaction time and the amount of the PEG4000 added in the saccharification process. CONCLUSION: The addition of PEG4000 before cellulase to lignocellulose saccharification processes is a reasonable way to improve the saccharification rate of lignocellulose. Copyright © 2010 Society of Chemical Industry
Accelerated repair of cortical bone defects using a synthetic extracellular matrix to deliver human demineralized bone matrix (2006)

Injectable hydrogel and porous sponge formulations of Carbylan-GSX, a crosslinked synthetic extracellular matrix (ECM), were used to deliver human demineralized bone matrix (DBM) in a rat femoral defect model. A cortical, full-thickness 5-mm defect was created in two femurs of each rat. Six rats were assigned to each of five experimental groups (thus, 12 defects per group). The defects were either untreated or filled with Carbylan-GSX hydrogel or sponges with or without 20% (w/v) DBM. Radiographs were obtained on day 1 and at weeks 2, 4, 6, and 8 postsurgery of each femur. Animals were sacrificed at week 8 postsurgery and each femur was fixed, embedded, sectioned, and processed for Masson's Trichrome staining. The bone defects were measured from radiographs and the fraction of bone healing was calculated. The average fractions of bone healing for each group were statistically different among all groups, and all treatment groups were significantly better than the control group. The Carbylan-GSX sponge with DBM was superior to the sponge without DBM and to the hydrogel with DBM. Histology showed that defects treated with the Carbylan-GSX sponge plus DBM were completely filled with newly generated bone tissue with a thickness comparable to native bone. Carbylan-GSX sponge was an optimal delivery vehicle for human DBM to accelerate bone healing.
Vascular integrin alpha(v)beta3: a new prognostic indicator in breast cancer. (1998)

Blood vessel density is a prognostic indicator of multiple tumor types. Recently, it has been established that tumor-associated blood vessels express elevated levels of integrin alpha(v)beta3. In fact, there is evidence that integrin alpha(v)beta3 identifies the most proliferative endothelial cells within human breast carcinomas. Therefore, we evaluated breast cancer tissue in terms of both blood vessel density and alpha(v)beta3 expression. We found that the antibody LM609 to integrin alpha(v)beta3 preferentially stains the blood vessels of small caliber. Furthermore, comparative studies between LM609 and anti-CD31 antibodies on normal breast indicate that very low and weak expression of integrin alpha(v)beta3 was found on vessels within normal tissue, whereas CD31 antigen was expressed in almost all vasculature. Indeed, expression of integrin alpha(v)beta3 was significantly higher in tumors of patients with metastasis than in those without metastasis. In a series of 197 consecutive patients with invasive breast cancer and long follow-up, vascular expression of integrin alpha(v)beta3 in tumor vascular "hot spots" was found to be the most significant prognostic factor predictive of relapse-free survival in both node-negative and node-positive patients. These findings support the contention that angiogenesis plays a critical role in breast cancer progression and suggest that integrin alpha(v)beta3 is an endothelial cell marker with significant prognostic value and potential usefulness as a target for specific antiangiogenic therapy.
Sequence and characterization of the Escherichia coli genome between the ndk and gcpE genes (1994)

The region of the chromosome immediately upstream of the Escherichia coli gene gcpE has been cloned and sequenced. This region contains two functional open reading frames, orf 384 and orf 337, encoding proteins of 43082 and 36189 Da, respectively. Sequencing analysis (this paper) and the isolation of a DNA fragment containing a functional promoter (Talukder, A.A., Yanai, S., and Yamada, M. (1994) Biosci. Biotech. Biochem. 58, 117–120) indicate that orf 337 is in an operon with gcpE. The gene orf 384 is immediately downstream of the gene ndk, which encodes nucleoside diphosphate kinase.
Image-Based Geometrical Characterization of Nodes in Additively Manufactured Lattice Structures (2020)

Additive manufacturing (AM) enables the fabrication of lattice structures with optimal mechanical, fluid, and thermal properties. However, during the AM fabrication process, defects are produced in the strut and node elements, which comprise the lattice structure. This leads to discrepancies between the AM fabricated lattice and its idealized computer-aided design (CAD) model, negatively affecting the ability to predict the mechanical behavior of the fabricated lattice via numerical models. Current research is focused on quantification of geometric uncertainties in the strut elements of the lattice; as-manufactured node geometries remain relatively unexplored on an individual scale, despite their criticality to the mechanical response of the structure. Understanding the geometrical properties of as-manufactured nodes relative to CAD idealizations can be used to improve lattice designs and numerical models. In this research, X-ray microcomputed tomography (μCT) is used to analyze and quantify the as-manufactured nodal geometry, found in face-centered cubic and face-centered cubic with axial struts lattices fabricated via selective laser melting. A custom tool is developed that enables auto-isolation and classification of nodal joints from μCT-derived cross-sectional slices. Geometrical properties are extracted from the isolated nodal cross sections and compared with their idealized CAD model counterpart. Quantification of geometrical defects provides insight into how nodes within an AM lattice structure differ from each other and their idealized design. Overall, this research is an initial step toward developing accurate and efficient numerical models, as well as better node design for AM.
Titanium disilicide formation on heavily doped silicon substrates (1987)

Titanium disilicide formation on heavily doped silicon substrates was investigated with sheet resistance measurements, elemental depth profiling, and transmission electron microscopy. As found in a previous study [H.K. Park, J. Sachitano, M. McPherson, T. Yamaguchi, and G. Lehman, J. Vac. Sci. Technol. A 2, 264 (1984)], the TiSi2 growth rate depended on the dopant concentration. The growth rate was highest on undoped substrates, intermediate on heavily phosphorus-doped substrates, and lowest on heavily arsenic-doped substrates. However, the critical dopant concentration effect reported by Park et al. was not observed. The uniformity of the titanium-silicon reaction was not seriously affected by heavy substrate doping. For heavily arsenic-doped substrates (3.0×1021 As/cm3), TiAs precipitates formed at C49 TiSi2 grain boundaries, and the C49-to-C54 transformation temperature increased to 850 °C. For heavily phosphorus-doped substrates (1.0×1021 P/cm3), no phosphides were unambiguously detected, and the C49-to-C54 transformation temperature remained below 800 °C. Discrete blocking layers at the silicide-silicon interface, such as the native silicon oxide or a dopant-rich phase, did not cause the reduction in silicide growth. Thus, it is concluded that dopant and knock-on oxygen atoms in solid solution in both the silicide and the silicon retard TiSi2 growth.
Children with enuresis (2012)

Many thanks to Dr. Kiddoo for a helpful overview of the diagnostic and therapeutic considerations involved in managing enuresis in children.[1][1] However, the importance of the abdominal examination, in particular the palpation for stool, was somewhat glossed over. The potential for a stool-laden
A novel resistance mechanism against beta-lactams in Streptococcus pneumoniae involves CpoA, a putative glycosyltransferase (1997)

Piperacillin resistance in Streptococcus pneumoniae was mediated by mutations in a novel gene, cpoA, that also confer transformation deficiency and a decrease in penicillin-binding protein la. cpoA is part of an operon located downstream of the primary sigma factor of S. pneumoniae. The deduced protein, CpoA, and the peptide encoded by the adjacent 3' open reading frame contained domains homologous to glycosyltransferases of procaryotes and eucaryotes that act on membrane-associated substrates, such as enzymes functioning in lipopolysaccharide core biosynthesis of gram-negative bacteria, RodD of Bacillus subtilis, which is involved in teichoic acid biosynthesis, and the human PIG-A protein, which is required for early steps of glycosylphosphatidylinositol anchor biosynthesis. This suggests that the cpo operon has a similar function related to cell surface components.
Fully automatic 3D digitization of unknown objects using progressive data bounding box (2012)

The goal of this work is to develop a complete and automatic scanning system with minimum prior information. We aim to establish a methodology for the automation of the 3D digitization process. The paper presents a method based on the evolution of the Bounding Box of the object during the acquisition. The registration of the data is improved through the modeling of the positioning system. The obtained models are analyzed and inspected in order to evaluate the robustness of our method. Tests with real objects have been performed and results of digitization are provided.
Letters (1991)

Emily Toth, Laura S. Levitt, Janette Turner Hospital, Patricia Murphy, Frieda Forman, Cheryl Gaster, Shane Penn, Christina Thompson, Letters, The Women's Review of Books, Vol. 8, No. 12 (Sep., 1991), pp. 4-5
Pharmacokinetics of the Antiviral Agent β- <scp>d</scp> -2′-Deoxy-2′-Fluoro-2′- <i>C</i> -Methylcytidine in Rhesus Monkeys (2007)

beta-D-2'-Deoxy-2'-fluoro-2'-C-methylcytidine (PSI-6130) is an effective inhibitor of hepatitis C virus (HCV) replication in vitro. The purpose of this study was to evaluate the single-dose pharmacokinetics of PSIota-6130 in rhesus monkeys following intravenous (i.v.) and oral administration. Noncompartmental analysis of the serum data obtained following oral and i.v. administration was performed. Pharmacokinetic studies with rhesus monkeys indicated slow and incomplete absorption with a mean absorption time (MAT) of 4.6 h and an oral bioavailability of 24.0% +/- 14.3% (mean +/- standard deviation), with comparable mean apparent half-lives following i.v. (4.54 +/- 3.98 h) and oral (5.64 +/- 1.13 h) administrations. The average percentages of the total dose recovered unchanged and in deaminated form in the urine were 32.9% +/- 12.6% and 18.9% +/- 6.6% (i.v.) and 6.0% +/- 3.9% and 3.9% +/- 1.0% (oral), respectively. The total bioavailability, taking into account the parent drug and its deaminated metabolite 2'-deoxy-2'-fluoro-2'-C-methyluridine (PSI-6206), was 64% +/- 26%. PSI-6130 was present in the cerebrospinal fluid after oral and i.v. dosing. However, no deamination of radiolabeled PSI-6130 was detected after 8 h of incubation in monkey and human whole blood. An N(4)-modified prodrug of PSI-6130 (PSI-6419) was orally administered to monkeys, but it failed to improve the oral bioavailability of PSI-6130. Further studies are warranted to improve the oral bioavailability and reduce the deamination of PSI-6130 in order to explore the potential of this drug for the treatment of HCV-infected individuals.