cssi/SciSciGPT-SciSciNet huggingface dataset:
Stereochemistry of the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase reaction and the chorismate synthetase reaction.

Abstract (Z)- and (E)-[3-3H]P-enolpyruvate were prepared from [1-3H]glucose and [1-3H]mannose with the glycolytic enzymes and were converted into shikimates tritiated at C-6 with non-labeled erythrose-4-P and cell-free extract of Escherichia coli mutant 83-24. Degradation to malate and analysis by the fumarase reaction showed that (Z)-[3-3H]P-enolpyruvate had produced [6-3H]shikimate of predominantly 6R configuration and the E isomer had given predominantly (6S)-[6-3H]shikimate. The DAHP synthetase reaction therefore is stereospecific with respect of C-3 of P-enolpyruvate, involving si attack at this center. As a consequence, the transient formation of a methyl group at C-3 of P-enolpyruvate as part of the reaction, as proposed by DeLeo and Sprinson ((1968) Biochem. Biophys. Res. Commun., 32, 873), is unlikely. Further conversion of (6R)- and (6S)-[6-3H]shikimate into chorismate showed that the pro-6R hydrogen is eliminated in this process. Thus, the 1,4-conjugate elimination of phosphoric acid in the chorismate synthetase reaction is anti, rendering a concerted (E2') mechanism unlikely.
Shirokov's contracting lifetimes and the interpretation of velocity eigenstates for unstable quantons

This paper is concerned with the interpretation of velocity eigenstates for unstable quantons, their relationship to space-like momentum eigenstates for such quantons and the explanation of Shirokov’s contracting lifetimes for such velocity eigenstates. It is an elaboration of a portion of the authors earlier study.
What Is Next after 40 Years? Part 1: Prior Learning Assessment: 1970–2011

Education practices focused on adult learners, such as prior learning assessment, are becoming more established in the United States (Bamford-Rees, 2008; Hoover, 2010). Initially, prior learning as...
Mechanisms Controlling Cell Size and Shape during Isotropic Cell Spreading

Cell motility is important for many developmental and physiological processes. Motility arises from interactions between physical forces at the cell surface membrane and the biochemical reactions that control the actin cytoskeleton. To computationally analyze how these factors interact, we built a three-dimensional stochastic model of the experimentally observed isotropic spreading phase of mammalian fibroblasts. The multiscale model is composed at the microscopic levels of three actin filament remodeling reactions that occur stochastically in space and time, and these reactions are regulated by the membrane forces due to membrane surface resistance (load) and bending energy. The macroscopic output of the model (isotropic spreading of the whole cell) occurs due to the movement of the leading edge, resulting solely from membrane force-constrained biochemical reactions. Numerical simulations indicate that our model qualitatively captures the experimentally observed isotropic cell-spreading behavior. The model predicts that increasing the capping protein concentration will lead to a proportional decrease in the spread radius of the cell. This prediction was experimentally confirmed with the use of Cytochalasin D, which caps growing actin filaments. Similarly, the predicted effect of actin monomer concentration was experimentally verified by using Latrunculin A. Parameter variation analyses indicate that membrane physical forces control cell shape during spreading, whereas the biochemical reactions underlying actin cytoskeleton dynamics control cell size (i.e., the rate of spreading). Thus, during cell spreading, a balance between the biochemical and biophysical properties determines the cell size and shape. These mechanistic insights can provide a format for understanding how force and chemical signals together modulate cellular regulatory networks to control cell motility.
The pathology and radiology of solitary benign bone tumors

Abstract The more common solitary benign bone tumors have been classified as fibrogenic, chondrogenic, osteogenic, or of unknown origin. Although histopathologic characteristics determine the exact designation of each tumor, the roentgen reflection of the gross pathologic changes provides significant diagnostic evidence in all instances. The roentgenogram is often more revealing than an ill chosen or poorly interpreted microscopic specimen. From the therapeutic standpoint, irradiation is hazardous and is rarely indicated in the management of these processes.
Lung function and airway cytologic profiles in horses with recurrent airway obstruction maintained in low-dust environments.

Background: The effects of long-term environmental management on airway obstruction and inflammation in horses with recurrent airway obstruction (RAO) are unknown. Hypothesis: Horses with RAO maintained in low-dust environments have persistent airway obstruction and neutrophilic inflammation. Animals: Study horses were treated for RAO and then maintained in low-dust environments with no medical management. Horses were classified into 3 groups by years after diagnosis: 1 year (time 1, n = 9), 2–3 years (time 2, n = 7), and 5–6 years (time 3, n = 8). The comparison groups were age-matched healthy horses. Methods: In this cross-sectional study, a clinical examination was performed, and the clinical score was calculated. Standard lung function, forced expiratory maneuvers, and the cytology of bronchoalveolar lavage fluid (BALF) were evaluated. Results: The clinical scores of the RAO horses were higher than those of the non-RAO horses at time 2 (P= .018). Standard lung function data were not different between the groups at any time point. The forced expiratory flow between 75–95% of exhaled vital capacity was lower in RAO horses than in non-RAO horses at all time points (P < .02), indicating persistent peripheral airway obstruction. Cytologic evaluation of BALF revealed no difference in total nucleated cell numbers or differential cell counts between RAO and non-RAO horses at any time point. Conclusions and Clinical Importance: The peripheral airway obstruction detected in horses with RAO maintained in low-dust environments likely is due to irreversible airway remodeling but is not associated with cytologic evidence of airway inflammation.
Molecular-beam studies of Penning ionization

Molecular-beam experiments have exposed a new wealth of detail on the general reaction ${A}^{*}+B\ensuremath{\rightarrow}A+{B}^{+}+{e}^{\ensuremath{-}}$ first suggested by Penning in 1927. The new capabilities not available to traditional swarm techniques include mass and electron spectroscopy on the reaction products and angle-resolved measurements of the scattering of both reagents and products. These new results have stimulated the recent development of both the electronic structure and the dynamical theories necessary for a first-principles description of at least the simplest of these reactions, those involving small atomic and diatomic species $B$. Recent progress in both experiment and interpretation is critically reviewed, and the prospects for attaining a global understanding of Penning ionization in larger systems are assessed.
Electrical conductivity and photoluminescence of diamond films grown by downstream microwave plasma CVD

Electrical conductivity measurements and photoluminescence (PL) were used to study the effects that sample distance from the plasma during growth has on the carrier transport properties of undoped CVD diamond. The films were grown by downstream microwave plasma chemical vapor deposition at distances from 0.5 to 2.0 cm from the edge of plasma glow. Electrical conductivity measurements were performed between room temperature and 1000° C and then complimented with Raman spectroscopy and PL studies in an attempt to gain a better understanding of the CVD growth process and the resulting electrical and optical properties of the diamond films. Room temperature electrical conductivity was found to vary by over 5 orders of magnitude with increasing growth distance from the plasma, while only moderate changes were observed in the luminescence spectra.
Continuum models for static and dynamic analysis of repetitive lattices

A simple, rational approach is presented for developing continuum models for large repetitive lattice structures subjected to static and dynamic loadings. The procedure involves introducing kinematic assumptions to reduce the dimensionality of the lattice, and equating the strain and kinetic energies of the continuum model to those of the original lattice structure. The proposed procedure is applied to obtain effective elastic and dynamic characteristics of continuum plate models for double-layered grids. Numerical results are presented of stress and free vibration problems for two double-layered grids. These problems demonstrate the high accuracy of the continuum plate models developed. Also, an assessment is made of different approximations to these models.
Rapid pulsed field separation of DNA molecules up to 250 kb

Pulsed field gel electrophoresis (PFGE) is capable of resolving a wide size range of DNA molecules which would all co-migrate in conventional agarose gels. We describe pulsed field gel conditions which permit DNA fragments of up to 250 kilobases (kb) to be separated in only 3.5 h. The separations, which employ commercially available gel boxes, are achieved using conditions which deviate significantly from traditional pulsed field conditions. PFGE separations have been thought to require reorientation angles greater than 90 degrees to be effective. However, reorientation angles of 90 degrees and even less will resolve DNA fragments a few hundred kb and smaller approximately 5 x faster than with standard pulsed field conditions. The mobility of DNA fragments separated with 90 degrees reorientation angles is switch time-dependent, as is seen for DNA run with the commonly used reorientation angle of 120 degrees. With DNA fragments of several hundred kb and smaller, higher field strengths may be used, resulting in still greater increases in separation speed. The conditions described allow DNA from large insert bacterial clones, such as those using cosmid, Fosmid, P1, bacterial artificial chromosome (BAC), or P1-derived artificial chromosome (PAC) vectors, to be prepared, digested and analyzed on gels within a single working day.
Existentialism entails anti-haecceitism

Existentialism concerning singular propositions is the thesis that singular propositions ontologically depend on the individuals they are directly about in such a way that necessarily, those propositions exist only if the individuals they are directly about exist. Haecceitism is the thesis that what non-qualitative facts there are fails to supervene on what purely qualitative facts there are. I argue that existentialism concerning singular propositions entails the denial of haecceitism and that this entailment has interesting implications for debates concerning the philosophy of language, the nature of propositions, and the metaphysics of modality.
618. Hydrodynamic Limb Vein-Delivered Xenogeneic Plasmid DNA Cancer Vaccine Effectively Induces Antitumor Protection

We recently developed a clinically relevant approach for intravascular hydrodynamic limb vein (HLV) delivery of nucleic acids that results in high-level transgene expression in myofibers. This novel delivery method is a very effective means to induce a high-titer antibody response against expressed transgene antigens following genetic immunization. Here, we examine the utility of HLV as a method to deliver a genetic cancer vaccine in mice.
Charged-Particle Activation Analysis for Trace Impurities in Water

A charged particle activation technique has been developed to analyze for trace impurities in the ppm range or less in water. Water samples are evaporated onto a tantalum foil and activated in a 15 MeV proton beam in the present work. The gamma ray spectrum from the activated sample is analyzed to quantitatively determine simultaneously trace amounts of boron, bromine, sodium, cadmium, chromium, selenium, and nitrogen. Total irradiation and counting time is less than two minutes. Beam currents are ? 1 ?a.
Geochemical Inputs for Hydrological Models of Deep-Lying Sedimentary Units: Loss of Mineral Hydration Water

Abstract Graf, D.L. and Anderson, D.E., 1981. Geochemical inputs for hydrological models of deep-lying sedimentary units: loss of mineralogical hydration water. In: W. Back and R. Letolle (Guest-Editors), Symposium on Geochemistry of Groundwater — 26th International Geological Congress. J. Hydrol., 54: 297ndash;314. Hydrological models that treat phenomena occurring deep in sedimentary piles, such as petroleum maturation and retention of chemical and radioactive waste, may require time spans of at least several million years. Many input quantities classically treated as constants will be variables on this time scale. Models sophisticated enough to include transport contributions from such processes as chemical diffusion, mineral dehydration and shale membrane behavior require considerable knowledge about regional geological history as well as the pertinent mineralogical and geochemical relationships. Simple dehydrations such as those of gypsum and halloysite occur at sharply-defined temperatures but, as with all mineral dehydration reactions, the equilibrium temperature is strongly dependent on the pore-fluid salinity and degree of overpressuring encountered in the subsurface. The dehydrations of analcime and smectite proceed by reactions involving other sedimentary minerals. The smectite reaction is crystallographically complex, yielding a succession of mixed-layered illite/smectites, and on the U.S.A. Gulf of Mexico coast continues over several million years at a particular stratigraphic interval.
Local density-functional theory of frequency-dependent linear response.

The linear density response of inhomogeneous electronic systems is discussed from a density-functional point of view. We derive a local density approximation for the frequency-dependent exchange-correlation potential which is compared with the ``adiabatic'' expression used in former work.
New Directions in Rifle Marksmanship Research

We propose that future rifle marksmanship research be framed within a phases-of-skill-development model (Ackerman, 1987, 1992; Anderson, 1982; Fitts & Posner, 1967). Prior research on predicting sh...
Human factors and safety in the design of intelligent vehicle-highway systems (IVHS)

Abstract Intelligent Vehicle-Highway Systems (IVHS) have been proposed in the wake of rapid worldwide growth in traffic volume and density. These systems involve the application of advanced sensor, communications, computational, and control technologies to the design of highways and vehicles to improve traffic flow and safety. Similar technologies have been applied in other transportation systems such as aviation and air-traffic control, and it is suggested that the human factors insights derived from these systems can be usefully applied, proactively rather than retroactively, in IVHS design. Several safety and human factors issues relevant to the design of IVHS technologies, both near-term and long-term, are discussed, including: (a) the optimization of driver mental workload in highly-automated “hybrid” systems; (b) the design of in-vehicle navigation aids and the resolution of display conflicts; (c) individual and group differences in driver behavior and their implications for training and licensure; (d) the evolution and integration of IVHS technologies; and (e) traffic management and the regulation of driver trust in IVHS. Successful resolution of these issues and their incorporation in IVHS design will provide for fully functional systems that will serve the twin needs of reducing traffic congestion and improving highway safety.
OpenCL-Based Remote Offloading Framework for Trusted Mobile Cloud Computing

OpenCL has emerged as the open standard for parallel programming for heterogeneous platforms enabling a uniform framework to discover, program, and distribute parallel workloads to the diverse set of compute units in the hardware. For that reason, there have been efforts exploring the advantages of parallelism from the OpenCL framework by offloading GPGPU workloads within an HPC cluster environment. In this paper, we present an OpenCL-based remote offloading framework designed for mobile platforms by shifting the motivation and advantages of using the OpenCL framework for the HPC cluster environment into mobile cloud computing where OpenCL workloads can be exported from a mobile node to the cloud. Furthermore, our offloading framework handles service discovery, access control, and data privacy by building the framework on top of a social peer-to-peer virtual private network, Social VPN. We developed a prototype implementation and deployed it into local- and wide-area environments to evaluate the performance improvement and energy implications of the proposed offloading framework. Our results show that, depending on the complexity of the workload and the amount of data transfer, the proposed architecture can achieve more energy efficient performance by offloading than executing locally.
Gas chromatographic method for determination of 2'-O-methylation in RNA.

Abstract A technique is described for the determination of 2′- O -methylation in RNA using gas chromatography to quantitate the methanol released by perchloric acid cleavage of the 2′-methoxy group. The technique can be used with small samples of RNA and does not require radioactive labeling. It is shown that base methylated compounds do not interfere with the assay and that the method is accurate over widely ranging contents of 2′- O -methylnucleotides.
Chemical speciation and cellular deposition of lead in Sesbania drummondii

The internalized speciation of lead in roots and leaves of Sesbania drummondii, a lead hyperaccumulator, grown in lead nitrate solution was studied using x-ray absorption near-edge structure and extended x-ray absorption fine structure. Lead was predominantly present as lead acetate in both plant tissues. The other dominant forms of accumulation were lead-sulfur compounds. Whereas lead sulfate and sulfide were found in leaves, only lead sulfide was detected in root samples. These observations indicate that S. drummondii is able to biotransform lead nitrate in the nutrient solution to lead acetate and sulfate in its tissues. Complexation with acetate and sulfate may be a lead detoxification strategy in this plant. Transmission-electron microscopy revealed the pattern of lead distribution in and around the cells. Dense distributions of lead grains were detected in root cell walls and plasma membranes, whereas evidence for vacuolar transport of lead was noticed in the stem cells.
Controls on magnesium and strontium uptake in planktonic foraminifera determined by live culturing

Abstract Because strontium and magnesium occur in seawater with nearly constant ratios to calcium, variations in Sr/Ca and Mg/Ca in modern foraminifer shells are due to the influence of environmental parameters on calcification. We have cultured two species of planktonic foraminifera, Globigerina bulloides and Orbulina universa, to establish the influence of temperature, pH, and salinity. Experimental results indicate that temperature is the primary control on shell Mg/Ca and that shell Mg/Ca increases exponentially by about 8 to 10% per °C. The exponential rise in shell Mg with temperature mirrors the results from inorganic precipitation experiments and suggests at least partial thermodynamic control on Mg incorporation. Both seawater pH and salinity are secondary influences on shell Mg/Ca: −6% per 0.1 pH unit increase and +4% per salinity unit increase. Shell Sr/Ca responds far more weakly to environmental parameters, and the small range observed in shell Sr/Ca relative to measurement precision of the ICP-MS method used here limits how well controls on shell Sr can be determined. Higher temperature, salinity, and pH all appear to increase shell Sr/Ca, most likely through the kinetic influence of calcification. Our culturing results demonstrate the potential of Mg/Ca in G. bulloides as a paleothermometer. The culturing results suggest that the standard error of Mg paleothermometry is ±1.1°C, but when the secondary effects of salinity and pH are considered the error increases to ±1.3°C.
Non-initiation of adjuvant hormonal therapy in women with hormone receptor-positive breast cancer: The Breast Cancer Quality of Care Study (BQUAL)

Adjuvant hormonal therapy for non-metastatic hormone receptor (HR)-positive breast cancer decreases risk of breast cancer recurrence and increases survival. However, some women do not initiate this life-saving treatment. We used a prospective cohort design to investigate factors related to non-initiation of hormonal therapy among women with newly diagnosed, non-metastatic HR-positive breast cancer recruited from three U.S. sites. Serial interviews were conducted at baseline and during treatment to examine sociodemographic factors, tumor characteristics, and treatment decision-making factors. Multivariate modeling assessed associations between variables of interest and hormonal therapy initiation. Of 1,050 breast cancer patients recruited, 725 (69 %) had HR-positive breast cancer, of whom 87 (12.0 %) based on self-report and 122 (16.8 %) based on medical record/pharmacy fill rates did not initiate hormonal therapy. In a multivariable analysis, non-initiation of hormonal therapy, defined by medical record/pharmacy, was associated with having greater negative beliefs about efficacy of treatment (OR 1.42, 95 % CI 1.18–1.70). Non-initiation was less likely in those who found the quality of patient/physician communication to be higher (OR 0.96, 95 % CI 0.93–0.99), the hormonal therapy treatment decision an easy one to make (OR 0.45, 95 % CI 0.23–0.90) or neither easy nor difficult (OR 0.34, 95 % CI 0.20–0.58); and had more positive beliefs about hormonal therapy efficacy (OR 0.40, 95 % CI 0.34–0.62). Factors influencing non-initiation of adjuvant hormonal therapy are complex and influenced by patient beliefs regarding treatment efficacy and side effects. Educational interventions to women about the benefits of hormonal therapy may decrease negative beliefs and increase hormone therapy initiation.
Subcellular localization of prostaglandin endoperoxide synthase-2 in murine 3T3 cells.

Polyclonal antisera specific for prostaglandin endoperoxide (PGH) synthases-1 and -2 were used to determine the subcellular locations of each PGH synthase isozyme in detergent-permeabilized mouse 3T3 fibroblasts by indirect immunocytofluorescence. Antiserum to PGH synthase- 1 demonstrated a mottled pattern of cytoplasmic and perinuclear staining of both serum-starved and serum-stimulated 3T3 cells. This pattern of staining is consistent with the results of earlier studies which demonstrated that PGH synthase-1 is associated with the endoplasmic reticulum and nuclear envelope of these cells. As expected, antibodies directed against a peptide unique to PGH synthase-2 failed to stain serum-starved cells, which lack appreciable levels of this second form of the enzyme. However, serum-stimulated 3T3 cells, which do express PGH synthase-2, showed the same pattern of staining with PGH synthase-2 antibodies as was observed with anti-PGH synthase-1 serum-mottled cytoplasmic staining and perinuclear staining. We conclude that the subcellular location of PGH synthase-2 is the same as PGH synthase-1 in murine 3T3 cells. Thus, the notable differences in the primary amino acid sequence-the signal peptide and the additional 18 amino acid C-terminal segment in PGH synthase-2-do not cause a change in localization. Colocalization of PGH synthases-1 and -2 implies that the source of arachidonate substrate, the site of PGH2 and prostanoid formation, and the mechanism of product transport from the inside to the outside of the cell are the same for these isozymes.
Fundamental limits in digital information processing

Computing and information processing are limited by a variety of factors. Some of these, such as the need to dissipate energy, the high voltage requirement, and the difficulty of removing heat are fundamental in that they have a basis in physical theory and in knowledge of the properties of materials. Limits arising from the physics of devices are also in this class. It appears that many of these physical limits could be relaxed by operating circuits at low temperature. Another class of limits is based on the experiences of many independent workers who find that a large amount of communication among various parts of a system is required. The many long interconnections utilized create great complexity and play a dominant role in the power dissipation required in information processing.
EMAST is a Form of Microsatellite Instability That is Initiated by Inflammation and Modulates Colorectal Cancer Progression

DNA mismatch repair (MMR) function is critical for correcting errors coincident with polymerase-driven DNA replication, and its proteins are frequent targets for inactivation (germline or somatic), generating a hypermutable tumor that drives cancer progression. The biomarker for defective DNA MMR is microsatellite instability-high (MSI-H), observed in ~15% of colorectal cancers, and defined by mono- and dinucleotide microsatellite frameshift mutations. MSI-H is highly correlated with loss of MMR protein expression, is commonly diploid, is often located in the right side of the colon, prognosticates good patient outcome, and predicts poor efficacy with 5-fluorouracil treatment. Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) is another form of MSI at tetranucleotide repeats that has been observed in multiple cancers, but its etiology and clinical relevance to patient care has only been recently illuminated. Specifically, EMAST is an acquired somatic defect observed in up to 60% of colorectal cancers and caused by unique dysfunction of the DNA MMR protein MSH3 (and its DNA MMR complex MutSβ, a heterodimer of MSH2-MSH3), and in particular a loss-of-function phenotype due to a reversible shift from its normal nuclear location into the cytosol in response to oxidative stress and the pro-inflammatory cytokine interleukin-6. Tumor hypoxia may also be a contributor. Patients with EMAST colorectal cancers show diminished prognosis compared to patients without the presence of EMAST in their cancer. In addition to defective DNA MMR recognized by tetranucleotide (and di- and tri-nucleotide) frameshifts, loss of MSH3 also contributes to homologous recombination-mediated repair of DNA double stranded breaks, indicating the MSH3 dysfunction is a complex defect for cancer cells that generates not only EMAST but also may contribute to chromosomal instability and aneuploidy. Areas for future investigation for this most common DNA MMR defect among colorectal cancers include relationships between EMAST and chemotherapy response, patient outcome with aneuploid changes in colorectal cancers, target gene mutation analysis, and mechanisms related to inflammation-induced compartmentalization and inactivation for MSH3.
Highlights of the 2011 Mayo Clinic Systems Engineering and Operations Research conference

Abstract In this report, we share highlights of the fourth annual Mayo Clinic Systems Engineering and Operations Research conference. The conference provided a forum for system engineers, operations researchers, clinicians, managers and administrators to share experiences, learning and success stories from their work in applying analytical and modeling tools to a range of problems. This report represents a snapshot of the challenges faced in acute health care, the techniques being deployed and the progress being made by engineers and operations researchers in helping to improve the quality and value of services.
Spatiotemporal Structures and Mechanisms of the Tropospheric Biennial Oscillation in the Indo-Pacific Warm Ocean Regions*

Abstract The observed structure and seasonal evolution characteristics of the tropospheric biennial oscillation (TBO) in the warm ocean areas of the Indo-Pacific region are explored using a seasonal-sequence EOF analysis approach. The major convective activity centers associated with the TBO appear in the southeast Indian Ocean (SEIO) and western North Pacific (WNP), accompanied by anticyclonic (or cyclonic) circulation patterns with a first-baroclinic-mode structure. The convection and circulation anomalies have distinctive life cycles in the SEIO and WNP: the former have a peak phase in northern fall and the latter persist from northern winter to subsequent summer. The mechanisms of the TBO in this region are investigated with a hybrid coupled GCM. Numerical results show that air–sea interaction in the warm ocean alone can support TBO variability that has many observed characteristics. Key processes involved in the TBO include the WNP monsoon variability and associated cross-equatorial flows, convective...
Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex

Human topoisomerase I (top1) is the molecular target of a diverse set of anticancer compounds, including the camptothecins, indolocarbazoles, and indenoisoquinolines. These compounds bind to a transient top1−DNA covalent complex and inhibit the resealing of a single-strand nick that the enzyme creates to relieve superhelical tension in duplex DNA. (Hertzberg, R. P.; et al. Biochem. 1989, 28, 4629−4638. Hsiang, Y. H.; et al. J. Biol. Chem 1985, 260, 14873−14878. Champoux, J. J. Annu. Rev. Biochem. 2001, 70, 369−413. Stewart, L.; et al. Science 1998, 729, 1534−1541.) We report the X-ray crystal structures of the human top1−DNA complex bound with camptothecin and representative members of the indenoisoquinoline and indolocarbazole classes of top1 poisons. The planar nature of all three structurally diverse classes allows them to intercalate between DNA base pairs at the site of single-strand cleavage. All three classes of compounds have a free electron pair near Arg364, a residue that if mutated confers resi...
Measurement of jet shapes in photoproduction at HERA

The shape of jets produced in quasi-real photon-proton collisions at centre-of-mass energies in the range 134–277 GeV has been measured using the hadronic energy flow. The measurement was done with the ZEUS detector at HERA. Jets are identified using a cone algorithm in the \(\eta - \phi\) plane with a cone radius of one unit. Measured jet shapes both in inclusive jet and dijet production with transverse energies \(E^{jet}_T>14\) GeV are presented. The jet shape broadens as the jet pseudorapidity (\(\eta^{jet}\)) increases and narrows as \(E^{jet}_T\) increases. In dijet photoproduction, the jet shapes have been measured separately for samples dominated by resolved and by direct processes. Leading-logarithm parton-shower Monte Carlo calculations of resolved and direct processes describe well the measured jet shapes except for the inclusive production of jets with high \(\eta^{jet}\) and low \(E^{jet}_T\). The observed broadening of the jet shape as \(\eta^{jet}\) increases is consistent with the predicted increase in the fraction of final state gluon jets.
WE-G-217BCD-11: A New Phantom to Study Combined Effects of In-Plane (x,y) and Z Axis Resolution for 3-D Imaging.

Purpose: The aim of this work is to develop phantoms that can be used to sample the radial and 3D properties of a CTimage, including in‐plane (x,y) and z‐axis information. The Phantom is amenable to mathematical analysis of the x, y, and z axis resolution properties separately and combined. Methods: A periodic pattern of a pair of opposed (30°) angled ramps is configured to produce a waveform profile across the CTimage. A perfect CTimage (with no loss of resolution) of the test object would produce a consistent geometric pattern of the intersection of a line with the pair of angled ramps. However, due to the finite resolution (x, y and z), the CT waveform profile will not yield the perfect profile; rather it will be influenced by slice thickness, and in‐plane resolution (PSF, MTF), as well as noise limitations, and other sources of non‐uniformity such as beam hardening etc. Various characteristics of the waveform profile including, amplitude, frequency, and slope (rate of climb) of the peaks, can be studied using mathematical analysis such as the Fourier transform. It will be shown how these performance characteristics are encoded in the wave pattern. Results: The waveform profiles are visually examined and mathematically analyzed, to demonstrate the effect of Slice Thickness (z axis) and changes of In‐Plane (x,y) Resolution and non‐uniformity across the image field; moreover, the harmonic analysis of the waveform is used to predict, either the in‐plane resolution (MTF), or the z‐axis MTF when one of the two is already known. Conclusions: The Wave pattern phantom offers a way to consider 3‐D imaging characteristics of a CT scanner by scanning a single repetitive test object that encodes both in‐plane resolution and z‐axis resolution and also offers a way to study non‐uniformity effects throughout the CT plane (volume). DJG is a consultant to The Phantom Laboratory and Image OWL, Salem, NY. Funding of other authors is supplied by Image OWL Salem, NY.
Metadata mapping and reuse in caBIG.

This paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facilitate the building domain models. This is examined in the context of an existing system, the National Cancer Institute (NCI)'s cancer Biomedical Informatics Grid (caBIG™). The goal is to demonstrate the deployment of open source tools that can be used to effectively map models and enable the reuse of existing information objects and CDEs in the development of new models for translational research applications. This effort is intended to help developers reuse appropriate CDEs to enable interoperability of their systems when developing within the caBIG™ framework or other frameworks that use metadata repositories. The Dice (di-grams) and Dynamic algorithms are compared and both algorithms have similar performance matching UML model class-attributes to CDE class object-property pairs. With algorithms used, the baselines for automatically finding the matches are reasonable for the data models examined. It suggests that automatic mapping of UML models and CDEs is feasible within the caBIG™ framework and potentially any framework that uses a metadata repository. This work opens up the possibility of using mapping algorithms to reduce cost and time required to map local data models to a reference data model such as those used within caBIG™. This effort contributes to facilitating the development of interoperable systems within caBIG™ as well as other metadata frameworks. Such efforts are critical to address the need to develop systems to handle enormous amounts of diverse data that can be leveraged from new biomedical methodologies.
The potential roles of biological soil crusts in dryland hydrologic cycles

Biological soil crusts (BSCs) are the dominant living cover in many drylands of the world. They possess many features that can influence different aspects of local hydrologic cycles, including soil porosity, absorptivity, roughness, aggregate stability, texture, pore formation, and water retention. The influence of biological soil crusts on these factors depends on their internal and external structure, which varies with climate, soil, and disturbance history. This paper presents the different types of biological soil crusts, discusses how crust type likely influences various aspects of the hydrologic cycle, and reviews what is known and not known about the influence of biological crusts on sediment production and water infiltration versus runoff in various drylands around the world. Most studies examining the effect of biological soil crusts on local hydrology are done by comparing undisturbed sites with those recently disturbed by the researchers. Unfortunately, this greatly complicates interpretation of the results. Applied disturbances alter many soil features such as soil texture, roughness, aggregate stability, physical crusting, porosity, and bulk density in ways that would not necessarily be the same if crusts were not naturally present. Combined, these studies show little agreement on how biological crusts affect water infiltration or runoff. However, when studies are separated by biological crust type and utilize naturally occurring differences among these types, results indicate that biological crusts in hyperarid regions reduce infiltration and increase runoff, have mixed effects in arid regions, and increase infiltration and reduce runoff in semiarid cool and cold drylands. However, more studies are needed before broad generalizations can be made on how biological crusts affect infiltration and runoff. We especially need studies that control for sub-surface soil features such as bulk density, micro- and macropores, and biological crust structure. Unlike the mixed effects of biological crusts on infiltration and runoff among regions, almost all studies show that biological crusts reduce sediment production, regardless of crust or dryland type.Copyright © 2006 John Wiley & Sons, Ltd.
Understanding the ‘Heritage’ in Heritage Tourism: Ideological Tool or Economic Tool for a Japanese Hot Springs Resort?

Abstract This study examines the complex relationship between the economic and ideological aspects of heritage, as observed in Kurokawa Onsen, a hot springs resort located on the island of Kyushu, Japan. In the 1980s, this remote village reinvented itself, on the way to becoming a nationally recognized tourist destination that currently attracts around one million visitors a year. The town's success is largely due to its utilization of a nation-wide nostalgia for the country's agricultural past. Through the careful incorporation of elements of the idealized rural village, known as furusato (native place), the resort's business leaders have used the country's rural heritage as a theme in which to situate its own business plan. This study argues that local business leaders use heritage not for ideological reasons, but purely economic ones. In other words, heritage is used as a theme that is profitable and desired by tourists, not because it offers a crucial representation of the past to be maintained at all...
Developmental Expression of Echinonectin, an Endogenous Lectin of the Sea Urchin Embryo

Echinonectin (EN) is a galactose-binding lectin present in eggs and embryos of the sea urchin Lytechinus variegatus. Recent studies have suggested that EN is a hyaline layer protein that may function as a substrate adhesion molecule (SAM) during development. We have used monoclonal and affinity-purified polyclonal antibodies that specifically recognize this protein to determine its spatial and temporal expression during embryogenesis. EN is stored in granules or vesicles in the unfertilized egg. After fertilization, these granules are rapidly redistributed to the apical cytoplasm of the zygote. Our results show that at subsequent stages of development the lectin is expressed by cells of all three germ layers, including cells of the developing gut, coelomic pouches, and ectoderm, and by both primary and secondary mesenchyme cells. In contrast to previous observations based solely upon light level immunofluorescent staining, immunoelectron microscopy demonstrates that EN is localized in intracellular, membrane-bounded vesicles. In epithelial cell types these vesicles have a highly polarized distribution and are found in the apical cortical cytoplasm. In mesenchyme cells the distribution of EN-containing vesicles is not obviously polarized. Steady-state levels of EN protein in the embryo remain almost constant from fertilization to the pluteus larva stage, Metabolic labeling studies show that synthesis of EN in L. variegatus begins immediately after fertilization and continues throughout embryogenesis. Monospecific antibodies raised against L. variegatus EN have also been used to determine whether this lectin is expressed in other echinoid species.
General Issues Influencing Connection Performance

Welded-flange--bolted-web connections were damaged during the 1994 Northridge earthquake. The SAC Steel Project was founded to address the problems associated with this damage. The Connection Performance Team completed research on the behavior of a number of connection types. During this research, some issues were found to influence the behavior of many different connection types. This paper summarizes these general issues and describes their impact on connection performance. These general issues include: process and toughness, web attachment, panel zone yielding, beam depth and frame geometry, yield stress of the steel, geometry and column orientation, effect of composite slabs, local slenderness and unsupported length, and temperature and strain rate.
Goal-directed Ultrasonography for Detecting Traumatic X-ray Missed Fibula Fracture in the Emergency Department

We present the case of a 45-year-old man who presented to the emergency department (ED) for ankle trauma sustained during a football match. Physical examination and X-ray of his ankle were negative for bone fractures. He was discharged from the ED, but returned 3 weeks later with a painful and swelling leg. Compressive ultrasonography of his right lower limb was negative for venous thrombosis, but ultrasound evaluation of the leg clearly showed a fibula fracture. Although the diagnosis of fractures usually relies on X-ray, the literature contains many reports of goal-directed ultrasound diagnosis of long bone fracture in military settings and remote locations. The usefulness of a noninva-sive examination like bedside ultrasonography and goal-directed evaluation of patients in the ED are discussed, with reference to the literature.
Design and Fabrication of Rock-Based Micromodel

A rock-based micromodel was designed using depth averaging with Boise rock digital images obtained from the X-ray micro-computed tomography. Design optimization of 2.5D micromodels was carried out using computational fluid dynamics (CFD) simulations through error analysis of dynamic flow parameters (velocities and permeability), which showed the close dynamic flow match between the actual 3D rock and the optimized 2.5D micromodel. Multiple numbers of polymer micromodels were microfabricated via micromilling of a brass mold insert and hot embossing in polymethylmethacrylate (PMMA). The design optimization and the replication-based microfabrication processes enabled the realistic pore geometry generation, which conforms to the pore dimensions of an actual rock sample but with coarser features in a polymer microfluidic platform. The microfabricated PMMA micromodel was used for fluidic characterization with nanoparticles to compare the flow patterns between the designed micromodel and the microfabricated micromodel. Particle motion paths observed in the particle experiments showed the consistent similarity of stream-traces from the CFD simulations of the designed 2.5D micromodel. Further fluidic investigation on the 2.5D rock-based micromodels will provide better understanding on fluid transport mechanism in porous media.Copyright © 2012 by ASME
Optimal intervention policies for a region facing pollution-induced uncertainty

This paper examines optimal interventions in the presence of externality-induced uncertainty. A regional model of three activities involving polluting, nonpolluting and pollution-abating industries is developed, and a Taylor series technique is utilized to represent a stochastic regional utility function. Optimal intervention policies in the forms of output or input taxes and subsidies are then deduced and analyzed.
Local and global instability properties of separation bubbles

Abstract A family of velocity profiles with reversed flow, typical of those found in separated flows, are examined for their linear instability properties. Specifically, a family of modified Falkner-Skan profiles are analyzed for the onset of absolute instability as the magnitude of the reversed flow increases. The mode of instability associated with the inflection point in the vicinity of the dividing streamline is found to become absolutely unstable as the peak reversed flow approaches about thirty percent of the free stream value. The family of profiles were used to construct generic models of separation bubbles and study the possible onset of global instability in the representative spatially-developing flows.
Factors Affecting Isolation of Protoplasts from Leaves of Grape ( Vitis Vinifera )

A method of isolating grape mesophyll protoplasts was investigated to facilitate the use of genetic engineering techniques to improve this economically important woody plant species. Grape leaves were macerated under aseptic conditions using Cellulysin and Macerase in combination with a variety of different factors known to promote the isolation of protoplasts from herbaceous plants. The effects of several factors influencing protoplast isolation could be evaluated quickly by using leaf disks 1 cm in diameter and known volumes of maceration and wash media. The best yields of mesophyll protoplasts were obtained using medium-sized leaves of well-fertilized grapevines kept in the dark for 24 hr prior to maceration in 1% Cellulysin, 0.5% Macerase, 0.7 M mannitol, 5 ppm 2,4-dichlorophenoxyacetic acid, 0.1 ppm benzylaminopurine, and one-tenth strength Murashige and Skoog medium, then incubated at 22°C in the light (1,000 lux) for 24 hr. Over 5,000 protoplasts per cm2 of leaf were produced using these conditions. This method of screening factors affecting protoplast isolation would be applicable to other species as well.
Use of Internal Thoracic Artery as a Systemic–Pulmonary Artery Shunt

Numerous technical and physiologic problems have been described with conventional systemic-pulmonary artery shunts. We report the case of a 1-year-old girl in whom the internal thoracic artery was used to create a systemic-pulmonary artery shunt after the failure of a previous Blalock-Taussig shunt. The internal thoracic artery as an alternative systemic-pulmonary artery shunt may offer several potential advantages and can be used successfully to improve cyanotic heart disease in selected cases.
Fatigue crack growth behavior of a Zr-Ti-Cu-Ni-Be bulk metallic glass: Role of ambient air environment

The fatigue crack growth behavior of a Zr 44 Ti 11 Ni 10 Cu 10 Be 25 bulk metallic glass (BMG) was measured in an inert dry N 2 environment. When compared to results measured in ambient air, the present results showed a higher fatigue threshold and lower crack growth rates in the near-threshold region. Such results reveal that there is a significant effect of ambient air in accelerating fatigue crack growth for this BMG.
Building partnerships in liberal arts education: library team teaching

The new academic library in the information age will be a teaching library. Teaching students the information literacy skills of how to identify, locate, access and evaluate information has become a fundamental responsibility for academic librarians. This article examines the framework for library bibliographic instruction, analyzes current information literacy initiatives, and reviews efforts of the Olin Library, Rollins College in promoting active learning and critical thinking skills through partnerships with classroom faculty and professionals of information technology and services.