cssi/SciSciGPT-SciSciNet huggingface dataset:
Nodular fasciitis in the pediatric population: A single center experience

Abstract Purpose To describe our experience with nodular fasciitis in the pediatric population, in an attempt to contribute additional information that may be used to develop a more comprehensive characterization of the disease. Methods A twenty-year retrospective chart review of patients 18years or younger diagnosed with nodular fasciitis at a single, large, academic institution. Results Five patients were treated for nodular fasciitis during the study period. The majority (60%) were male and all presented with rapidly enlarging masses that were excised surgically. The median age at presentation was 14years. Most (60%) lesions were located in the upper extremities and 80% had no related symptomatology or disability. All lesions were less than 3cm in greatest dimension and 4 patients had no signs of recurrence (one patient was lost to follow-up). Pathologic, immunohistochemical, and long-term follow-up data were lacking in our cohort. Conclusion The characteristics of nodular fasciitis in children at our institution are slightly different than those which have been reported thus far based on no patients with head and neck disease or antecedent trauma to the affected area. Due to variability in clinical presentation and histologic findings, additional studies are necessary to provide more practical, consistent and effective management strategies.
Investigation of the Effects of Inlet Swirl on Compressor Performance and Operability Using a Modified Parallel Compressor Model

Serpentine ducts used by both military and commercial aircraft can generate significant flow angularity and total pressure distortion at the engine face. Most low by-pass ratio turbofan engines with mixed exhaust are equipped with inlet guide vanes (IGV) which can reduce the effect of moderate inlet distortion. High by-pass ratio and some low by-pass ratio turbofan engines are not equipped with IGVs, and swirl can in effect change the angle of attack of the fan blades. Swirl and total pressure distortion at the engine inlet will impact engine performance, operability, and durability. The impact on the engine performance and operability must be quantified to ensure safe operation of the aircraft and propulsion system. Testing is performed at a limited number of discrete points inside the propulsion system flight envelope where it is believed the engine is most sensitive to the inlet distortion in order to quantify these effects. Turbine engine compressor models are based on the limited amount of experimental data collected during testing. These models can be used as an analysis tool to improve the effectiveness of engine testing and to improve understanding of engine response to inlet distortion. The Dynamic Turbine Engine Compressor Code (DYNTECC) utilizes parallel compressor theory and quasi-one-dimensional Euler equations to determine compressor performance. In its standard form, DYNTECC uses user supplied characteristic stage maps in order to calculate stage forces and shaft work for use in the momentum and energy equations. These maps were typically developed using experimental data or created using characteristic codes such as the 1-D Mean Line Code (MLC) or the 2-D Streamline Curvature Code. The MLC was created to calculate the performance of individual compressor stages and requires less computational effort than the 2-D and 3-D models. To improve efficiency and accuracy, the MLC has been incorporated into DYNTECC as a subroutine. Rather than independently developing stage maps using the MLC and then importing these maps into DYNTECC, DYNTECC can now use the MLC to develop the required stage characteristic for the desired operating point. This will reduce time and complexity required to analyze the effects of inlet swirl on compressor performance. The combined DYNTECC/MLC was used in the past to model total pressure distortion. This paper presents the result obtained using the combined DYNTECC/MLC to model the effects of various types of inlet swirl on F109 fan performance and operability for the first time.© 2011 ASME
Post Hoc Quantile Test for One-Way Analysis of Variance Using a Double Bootstrap Method

Comparing samples from two or more populations is among the most common statistical tasks that engineers and scientists perform. Typically a t-test or one-way or two-way analysis of variance is used to compare the means of different populations. Although these tests are useful for describing differences in means for various populations, they are of limited use for comparison of other population parameters, such as quantiles (i.e., percentiles). Quantile comparisons are useful for examining the changes that occur to portions of the population away from the median. Comparison of speed percentiles is especially important to the traffic engineering profession to determine the effect of various treatments on speeds of faster drivers (e.g., 85th percentile speeds). Simply testing the mean speed values does not indicate whether the differences occur because of slower traffic driving more slowly, faster traffic driving more slowly, or both. Furthermore, are positive effects on faster drivers being masked by contr...
In defense of the realm: understanding the threats to information security

The popular press is replete with information about attacks on information systems. Viruses, worms, hackers, and employee abuse and misuse have created a dramatic need for understanding and implementing quality information security. In order to accomplish this, an organization must begin with the identification and prioritization of the threats it faces, as well as the vulnerabilities inherent in the systems and methods within the organization. This study seeks to identify and rank current threats to information security, and to present current perceptions of the level of severity these threats present. It also seeks to provide information on the frequency of attacks from these threats and the prioritization for expenditures organizations are placing in order to protect against them. The study then will compare these findings with those of previous surveys.
Apoptosis by Par-4 in cancer and neurodegenerative diseases.

Abstract Prostate apoptosis response-4 ( par-4 ) is a pro-apoptotic gene identified in prostate cancer cells undergoing apoptosis. Par-4 protein, which contains a leucine zipper domain at the carboxy-terminus, functions as a transcriptional repressor in the nucleus. Par-4 selectively induces apoptosis in androgen-independent prostate cancer cells and Ras-transformed cells but not in androgen-dependent prostate cancer cells or normal cells. Cells that are resistant to apoptosis by Par-4 alone, however, are greatly sensitized by Par-4 to the action of other pro-apoptotic insults such as growth factor withdrawal, tumor necrosis factor, ionizing radiation, intracellular calcium elevation, or those involved in neurodegenerative diseases such as Alzheimer’s, Parkinson’s, Huntington’s, and stroke. Apoptosis induction by Par-4 involves a complex mechanism that requires activation of the Fas death receptor signaling pathway and coparallel inhibition of cell survival NF-κB transcription activity. The unique ability of Par-4 to induce apoptosis in cancer cells but not normal cells and the ability of Par-4 antisense or dominant-negative mutant to abrogate apoptosis in neurodegenerative disease paradigms makes it an appealing candidate for molecular therapy of cancer and neuronal diseases.
Early survival of single-tooth implants in the esthetic zone may be predictable despite timing of implant placement or loading.

Article Title and Bibliographic Information Treatment outcome of immediate, early and conventional single-tooth implants in the esthetic zone: a systematic review to survival, bone level, soft-tissue, aesthetics and patient satisfaction. den Hartog L, Huddleston Slater JJR, Vissink A, Meijer HJA, Raghoebar GM, J Clin Periodontol 2008;35:1073-1086. Reviewer Kent L. Knoernschild, DMD, MS Purpose/Question What are outcomes for single-implant restorations in the esthetic zone when immediate/early or conventional implant placement approaches are used with immediate/early or conventional loading? Source of Funding Authors stated that “no external funding was obtained.” Type of Study/Design Systematic review with meta-analysis of data Level of Evidence Level 2: Limited-quality, patient-oriented evidence Strength of Recommendation Grade Grade B: Inconsistent or limited-quality patient-oriented evidence
Decreasing absolute risk aversion, prudence and increased downside risk aversion

Downside risk increases have previously been characterized as changes preferred by all decision makers u(x) with u′′′(x) > 0. For risk averse decision makers, u′′′(x) > 0 also defines prudence. This paper finds that downside risk increases can also be characterized as changes preferred by all decision makers displaying decreasing absolute risk aversion (DARA) since those changes involve random variables that have equal means. Building on these findings, the paper proposes using “more decreasingly absolute risk averse” or “more prudent” as alternative definitions of increased downside risk aversion. These alternative definitions generate a transitive ordering, while the existing definition based on a transformation function with a positive third derivative does not. Other properties of the new definitions of increased downside risk aversion are also presented.
Developing a tokenizer and morphological parser for English text in C

This paper summarizes the development of a relatively simple tokenizer and morphological analyzer for English-language texts, developed in the C# programming language.
Three-Dimensional Subwavelength Imaging by a Photonic-Crystal Flat Lens Using Negative Refraction at Microwave Frequencies

We experimentally demonstrate subwavelength resolution imaging at microwave frequencies by a three-dimensional (3D) photonic-crystal flat lens using full 3D negative refraction. The photonic crystal was fabricated in a layer-by-layer process. A subwavelength pinhole source and a dipole detector were employed for the measurement. By point-by-point scanning, we obtained the image of the pinhole source shown in both amplitude and phase, which demonstrated the imaging mechanism and subwavelength feature size in all three dimensions. An image of two pinhole sources with subwavelength spacing showed two resolved spots, which further verified subwavelength resolution.
The interplay between experiment and theory in charge-density analysis.

The comparison of theory and experiment remains a cornerstone of scientific inquiry. Various levels of such comparison applicable to charge-density analysis are discussed, including static and dynamic electron densities, topological properties, d-orbital occupancies and electrostatic moments. The advantages and drawbacks of the pseudoatom multipole are discussed, as are the experimentally constrained wavefunctions introduced by Jayatilaka and co-workers, which combine energy minimization with the requirement to provide a reasonable fit to the X-ray structure factors. The transferability of atomic densities can be exploited through construction of a pseudoatom databank, which may be based on analysis of ab initio molecular electron densities, and can be used to evaluate a host of physical properties. Partitioning of theoretical energies with the Morokuma–Ziegler energy decomposition scheme allows direct comparison with electrostatic interaction energies obtained from electron densities represented by the pseudoatom formalism. Compared with the Buckingham expression for the interaction between non-overlapping densities, the agreement with theory is much improved when a newly developed hybrid EP/MM (exact potential/multipole model) method is employed.
Structural, spectroscopic, and electrochemical properties of nonheme Fe(II)-hydroquinonate complexes: synthetic models of hydroquinone dioxygenases.

Using the tris(3,5-diphenylpyrazol-1-yl)borate (Ph2Tp) supporting ligand, a series of mono- and dinuclear ferrous complexes containing hydroquinonate (HQate) ligands have been prepared and structurally characterized with X-ray crystallography. The monoiron(II) complexes serve as faithful mimics of the substrate-bound form of hydroquinone dioxygenases (HQDOs) – a family of nonheme Fe enzymes that catalyze the oxidative cleavage of 1,4-dihydroxybenzene units. Reflecting the variety of HQDO substrates, the synthetic complexes feature both mono- and bidentate HQate ligands. The bidentate HQates cleanly provide five-coordinate, high-spin Fe(II) complexes with the general formula [Fe(Ph2Tp)(HLX)] (1X), where HLX is a HQate(1-) ligand substituted at the 2-position with a benzimidazolyl (1A), acetyl (1B and 1C), or methoxy (1D) group. In contrast, the monodentate ligand 2,6-dimethylhydroquinone (H2LF) exhibited a greater tendency to bridge between two Fe(II) centers, resulting in formation of [Fe2(Ph2Tp)2(μ-LF)(MeCN)]·[2F(MeCN)]. However, addition of one equivalent of “free” pyrazole (Ph2pz) ligand provided the mononuclear complex, [Fe(Ph2Tp)(HLF)(Ph2pz)]·[1F(Ph2pz)], which is stabilized by an intramolecular hydrogen bond between the HLF and Ph2pz donors. Complex 1F(Ph2pz) represents the first crystallographically-characterized example of a monoiron complex bound to an untethered HQate ligand. The geometric and electronic structures of the Fe/HQate complexes were further probed with spectroscopic (UV-vis absorption, 1H NMR) and electrochemical methods. Cyclic voltammograms of complexes in the 1X series revealed an Fe-based oxidation between 0 and −300 mV (vs. Fc+/0), in addition to irreversible oxidation(s) of the HQate ligand at higher potentials. The one-electron oxidized species (1Xoxox) were examined with UV-vis absorption and electron paramagnetic resonance (EPR) spectroscopies.
Histone variant macroH2A contains two distinct macrochromatin domains capable of directing macroH2A to the inactive X chromosome

Chromatin on the inactive X chromosome (Xi) of female mammals is enriched for the histone variant macroH2A that can be detected at interphase as a distinct nuclear structure referred to as a macro chromatin body (MCB). Green fluorescent protein-tagged and Myc epitope-tagged macroH2A readily form an MCB in the nuclei of transfected female, but not male, cells. Using targeted disruptions, we have identified two macrochromatin domains within macroH2A that are independently capable of MCB formation and association with the Xi. Complete removal of the non-histone C-terminal tail does not reduce the efficiency of association of the variant histone domain of macroH2A with the Xi, indicating that the histone portion alone can target the Xi. The non-histone domain by itself is incapable of MCB formation. However, when directed to the nucleosome by fusion to core histone H2A or H2B, the non-histone tail forms an MCB that appears identical to that of the endogenous protein. Mutagenesis of the non-histone portion of macroH2A localized the region required for MCB formation and targeting to the Xi to an approximately 190 amino acid region.
Supporting monolayer Pt on W(110) and C/W(110): Modification effects on the reaction pathways of cyclohexene

Abstract The decomposition, dehydrogenation, self-hydrogenation, and hydrogenation of cyclohexene were used as probe reactions to determine the effects of supporting monolayer Pt on W(110) and C/W(110) surfaces. The reaction pathways were studied using temperature-programmed desorption (TPD) and high-resolution electron energy loss spectroscopy (HREELS). On the clean and carbon-modified W(110) surfaces, the dominant reaction pathway of cyclohexene is the complete decomposition to produce hydrogen and atomic carbon. Monolayer Pt-modification of the W(110) and C/W(110) surfaces reduces the complete decomposition and enhances the selectivity toward the dehydrogenation of cyclohexene to produce gas phase benzene. More importantly, unlike previous studies of supporting monolayer Pt on Ni and Co surfaces, neither self-hydrogenation of cyclohexene nor hydrogenation of cyclohexene with coadsorbed hydrogen is detected on the monolayer Pt-modified W(110) and C/W(110) surfaces. The comparison is consistent with our previous density functional theory (DFT) modeling of monolayer Pt on different substrates, confirming that the chemical properties of supported Pt vary significantly on different substrates.
Increased hepatic efflux of glutathione after chronic ethanol feeding

Abstract Chronic ethanol feeding increases hepatotoxicity of drugs, such as acetaminophen, which form electrophilic metabolites. Availability of glutathione (GSH) is important in preventing liver damage from reactive metabolites. Chronic ethanol feeding has been reported to increase turnover of hepatic GSH in rats. The results of the present study show that the total hepatic efflux of GSH was increased from 5.95 ± 0.42 nmoles/min/g liver (control) to 9.96 ± 0.57 nmoles/min/g (P nmoles / min / g (P
Exploiting spatial parallelism for software-only video effects processing

ABSTRACT Video effects play an important role in adding production value to video programs. The use of video effects with Internet Video sources, however, is still uncommon because traditional hardware-based solutions are poorly suited tothe Internet environment. In previous work, we described a parallel, software-only video effects system designed for Internet Video and explored the use of temporal parallelism. This paper explores the use of spatial parallelism. In particular, an intermediate semicompressed video format is desribed that was designed to exploit spatial parallelism, and performance measurements are reported on the use of this representation.Keywords: Multimedia systems, video processing, parallel processing, video effects 1. INTRODUCTION Experience from the television, video, and film industries shows that visual effects are an important tool for corn-municating and maintaining audience interest." Titling, for example, is used to identify speakers and topics in avideo presentation. Compositing effects that combine two or more video images into one image are used to present
Evidence for the adsorption upon erythrocytes of urokinase and other components of the fibrinolytic system.

Abstract Erythrocytes can adsorb urokinase, a urinary activator of plasma profibrinolysin, and protect it from plasma inhibitors. Adsorption of components of the plasma fibrinolytic system is affected by the fibrinolytic status of the animal from which the erythrocytes and plasma are obtained. The findings suggest that erythrocytes may play a role, heretofore unrecognized, in the development of fibrinolytic activity in vivo .
Foreign metallothionein-I expression by transient transfection in MT-I and MT-II null astrocytes confers increased protection against acute methylmercury cytotoxicity

Abstract The mechanisms associated with metallothionein (MT) gene regulation are complex and poorly understood. Only a modest increase in brain MT expression levels is attained by exposure to metals, MT gene transfection, and MT gene knock-in techniques. Accordingly, in the present study, MT null astrocytes isolated from transgenic mice deficient in MT-I and MT-II genes were introduced as a zero background model of MT expression. MT protein levels were determined by western blot analysis. MT proteins in MT-I and MT-II null astrocytes were undetectable. Transient MT-I gene transfection increased the levels of foreign MT expression in MT-I and MT-II null astrocytes by 2.3-fold above basal levels in wild-type astrocytes. Intracellular Na 2 51 CrO 4 efflux and d -[2,3- 3 H ]aspartate uptake were studied as indices of acute methylmercury (MeHg) (5 μM) cytotoxicity. In MT-I and MT-II knockout astrocytes MeHg led to significant (p Na 2 51 CrO 4 efflux and a significant (p d -[2,3- 3 H ]aspartate uptake compared to MT-I and MT-II knockout controls. Transfection of the MT-I gene in MT-I and MT-II null mice significantly (p Na 2 51 CrO 4 efflux in MT null, as well as wild-type astrocytes. MT-I gene transfection in MT-I and MT-II null astrocytes reversed the inhibitory effect of MeHg on d -[2,3- 3 H ]aspartate uptake, such that initial rates of uptake in MT-I transfected cells in the presence and absence of MeHg (5 μM) were indistinguishable. These results demonstrate that: (1) astrocytes lacking MTs are more sensitive to MeHg than those with basal MT protein levels, (2) the MT-I gene can be overexpressed in MT-I and MT-II null astrocytes by transient MT-I gene transfection, and (3) that foreign MT expression endows astrocytes with increased resistance to MeHg.
Demonstration of a roving-host wireless sensor network for rapid assessment monitoring of structural health

A major challenge impeding the deployment of wireless sensor networks for structural health monitoring (SHM) is developing means to supply power to the sensor nodes in a cost-effective manner. In this work an initial test of a roving-host wireless sensor network was performed on a bridge near Truth or Consequences, NM in August of 2007. The roving-host wireless sensor network features a radio controlled helicopter responsible for wirelessly delivering energy to sensor nodes on an "as-needed" basis. In addition, the helicopter also serves as a central data repository and processing center for the information collected by the sensor network. The sensor nodes used on the bridge were developed for measuring the peak displacement of the bridge, as well as measuring the preload of some of the bolted joints in the bridge. These sensors and sensor nodes were specifically designed to be able to operate from energy supplied wirelessly from the helicopter. The ultimate goal of this research is to ease the requirement for battery power supplies in wireless sensor networks.
Expression and activation of the membrane-cytoskeleton protein ezrin during the normal endometrial cycle

Objective To examine total ezrin expression (ezrin and phospho-ezrin) through the normal endometrial cycle and to correlate ezrin activation and localization with cytologic changes. Design Experimental laboratory study. Setting University medical centers. Patient(s) Reproductive-age women. Intervention(s) A total of 36 samples of normal early, mid-, and late proliferative- and secretory-phase endometrium were studied for immunoreactive total ezrin (ir-T-ezrin) and phospho-ezrin (ir-p-ezrin) expression by histology, immunohistochemistry, and Western blotting. Main Outcome Measure(s) Total ezrin and phospho-ezrin expressions through the normal endometrial cycle. Result(s) Throughout the cycle ir-T-ezrin is present in the epithelium. The intensity and localization of both ir-ezrin and ir-p-ezrin vary greatly throughout the cycle. The main findings include the following: lateral localization of ir-ezrin/ir-p-ezrin in association with membrane specializations; dense staining around secretory vacuoles (secretory phase); dense staining of the apical surfaces, including microvilli and pinopodes of epithelial cells, especially during the mid- to late secretory phases; and the presence of ezrin in the glandular secretions. Immunoreactive total ezrin and ir-p-ezrin were not expressed by stromal fibroblasts. Conclusion(s) Ezrin is a prominent protein in the cycling endometrium. The most striking findings were the gravitation of ir-ezrin/ir-p-ezrin to the periphery of secretory vacuoles, localization on apical surfaces of the luminal epithelium, dense ezrin staining in secretory-phase epithelial cell plumes, and the presence of ir-ezrin/ir-p-ezrin in secretory-phase luminal secretions. These findings may have functional implications, especially for implantation biology.
Demonstration of Copper and Acid Phosphatase Activity in Hepatocyte Lysosomes in Experimental Copper Toxicity

EXCESSIVE amounts of copper accumulate within the tissues in Wilson's disease (hepatolenticular degeneration). Cirrhosis is believed to be an inevitable consequence of chronic copper toxicity1. Attempts to produce equivalent hepatic dysfunction and cirrhosis in experimental animals by copper poisoning have been unsuccessful, however2.
Surgical Management of Anomalous Aortic Origin of a Coronary Artery

Background Anomalous aortic origin of a coronary artery (AAOCA) from the opposite sinus traveling between the aorta and pulmonary artery is associated with ischemia and sudden death. Methods A retrospective review of 36 patients (23 male) who underwent operation between October 1992 and August 2008 for AAOCA was performed. Median age was 47 years (range, 13 to 82 years). Angina, shortness of breath, or syncope was present in 29 (81%), and 9 of 21 (43%) had an abnormal stress test. Coronary or computed tomographic angiography demonstrated an anomalous left main coronary artery arising from the right sinus in 13 (36%), right coronary artery arising from the left sinus in 21 (58%), and left anterior descending artery arising from the right sinus traveling between the aorta and pulmonary artery in 2 (5%). An intramural course was identified on preoperative imaging in 34 (94%). Although no patients had significant associated atherosclerotic coronary artery disease, 5 (14%) had previous acute myocardial infarction related to the AAOCA. Results Operation included coronary artery bypass grafting in 14 patients and unroofing in 22; 6 patients had associated cardiac procedures performed. There were no early deaths. There was one late death secondary to a subdural bleed. At follow-up (mean 1.1 years; maximum 14 years), chest pain recurred in 1 patient who had coronary artery bypass grafting. No recurrent symptoms were noted in the unroofing group. Conclusions Unroofing of an anomalous coronary artery can be performed safely with excellent results in the majority of patients. When concomitant atherosclerotic coronary artery disease is present, coronary artery bypass grafting is an appropriate alternative.
Empirical Methods for Artificial Intelligence

Empirical research exploratory data analysis basic issues in experiment design hypothesis testing and estimation computer-intensive statistical methods performance assessment explaining performance - interactions and dependencies modelling tactics for generalization.
Joint Confirmatory Factor Analysis of the Differential Ability Scales and the Woodcock-Johnson Tests of Cognitive Abilities-Third Edition.

This study examined the underlying constructs measured by the Differential Ability Scales (DAS; C.D. Elliott, 1990a) as they relate to the Cattell-Horn-Carroll (CHC) Theory (K.S. McGrew, 1997) of cognitive abilities. The DAS and Woodcock-Johnson Tests of Cognitive Abilities (WJ-III COG; R.W. Woodcock, K.S. McGrew, & N. Mather, 2001) were administered to 131 children in grades 3 through 5 who took part in a concurrent validity study included in the Woodcock-Johnson Tests of Cognitive Abilities, Third Edition, technical manual (K.S. McGrew & R.W. Woodcock, 2001). Confirmatory factor analyses using maximum likelihood estimation were conducted with the AMOS 5.0 (J.L. Arbuckle, 2001) statistical program to evaluate three models of increasing complexity, to compare how well each fit the data set, and to identify the one that best described the underlying constructs measured by the DAS. Results suggested that the synthesized Three-Stratum CHC Model provided the most parsimonious representation among the three models tested. © 2007 Wiley Periodicals, Inc. Psychol Schs 44: 119–138, 2007.
Irrepresentability by multiple intersection, or why the interval number is unbounded

Abstract We consider the following question: Given a family of sets, is there a positive integer, t, so that every graph is the intersection graph of sets each of which is the union of t sets from the given family? We show that the answer is ‘no’ precisely when some bipartite graph fails to be the intersection graph of sets from the given family. We are especially interested in the case where the given family of sets generalizes the family of real intervals. We extend our results to uniform hypergraphs and simplicial complexes.
On the B to A conformation change of the double helix

We have investigated the B to A conformation change of DNA double helices by a new method “soft-mode analysis.” We find theoretically that a mode does soften when the vibration normal modes are perturbed by increasing the electrostatic interaction between the unbalanced charges on atoms in the double helix. The same mode also softens for enhanced van der Waals interactions. The mode softening indicates the onset of conformation change. The enhancing of the electrostatic and van der Waals interaction mimic the effect of decreasing the polar nature of the solvent or water of hydration associated with the B conformation DNA. We discuss qualitatively the concept of soft modes and their relation to conformation change as well as their applicability to macromolecules. We discuss previous work in which the normal vibrational modes have been calculated. We also discuss the displacement which comes from the soft mode and show that it correlates very well with that expected for the B to A conformation charge.
The contribution of bacteria to the total adenosine triphosphate extracted from the microbiota in the water of a salt-marsh creek☆

The contribution of bacteria to the total adenosine 5-triphosphate (ATP) measured in estuarine samples was investigated. A portion of the bacterial population present in samples was separated from other biological materials by filtration through a 1.0-μm filter (Nucleopore). The quantification of ATP and the enumeration of bacteria (by epifluorescence microscopy) was performed on filtered and unfiltered portions of each sample as well as on cultured organisms. The values of ATP per cell averaged 1.48 × 10−15 g/cell from laboratory cultures and generally two orders-of-magnitude lower in bacteria from the natural system with values ranging from 0.24 to 28.8 × 10−17 g/cell. In bacteria collected from the marsh waters, the higher values of ATP per cell were observed in samples collected during the warmer months. When samples were obtained from areas of the marsh influenced by oceanic waters, the highest values of ATP per cell were observed at low tide. The nucleotide levels in bacterial cells in the high marsh were not markedly influenced by the tides. Bacterial ATP contributed from < 1–83% of the ATP measured in the total microbiota; the average content was 25% of the total. Generally, waters from the high marsh i.e., water influenced strongly by sediment microbes, contained a greater percentage of bacterial ATP.
Computational fluid dynamics endpoints to characterize obstructive sleep apnea syndrome in children

Computational fluid dynamics (CFD) analysis may quantify the severity of anatomical airway restriction in obstructive sleep apnea syndrome (OSAS) better than anatomical measurements alone. However,...
The Solar Dynamics Observatory (SDO)

The Solar Dynamics Observatory (SDO) was launched on 11 February 2010 at 15:23 UT from Kennedy Space Center aboard an Atlas V 401 (AV-021) launch vehicle. A series of apogee-motor firings lifted SDO from an initial geosynchronous transfer orbit into a circular geosynchronous orbit inclined by 28° about the longitude of the SDO-dedicated ground station in New Mexico. SDO began returning science data on 1 May 2010. SDO is the first space-weather mission in NASA’s Living With a Star (LWS) Program. SDO’s main goal is to understand, driving toward a predictive capability, those solar variations that influence life on Earth and humanity’s technological systems. The SDO science investigations will determine how the Sun’s magnetic field is generated and structured, how this stored magnetic energy is released into the heliosphere and geospace as the solar wind, energetic particles, and variations in the solar irradiance. Insights gained from SDO investigations will also lead to an increased understanding of the role that solar variability plays in changes in Earth’s atmospheric chemistry and climate. The SDO mission includes three scientific investigations (the Atmospheric Imaging Assembly (AIA), Extreme Ultraviolet Variability Experiment (EVE), and Helioseismic and Magnetic Imager (HMI)), a spacecraft bus, and a dedicated ground station to handle the telemetry. The Goddard Space Flight Center built and will operate the spacecraft during its planned five-year mission life; this includes: commanding the spacecraft, receiving the science data, and forwarding that data to the science teams. The science investigations teams at Stanford University, Lockheed Martin Solar Astrophysics Laboratory (LMSAL), and University of Colorado Laboratory for Atmospheric and Space Physics (LASP) will process, analyze, distribute, and archive the science data. We will describe the building of SDO and the science that it will provide to NASA.
The preparation of organolithium compounds by the transmetalation reaction part VIII. β-styryllithium☆

Abstract trans -β-Styryllithium can be prepared conveniently by the transmetalation reaction occurring between trans -β-styryltin compounds and organolithium reagents. This procedure is superior to others previously used, since neither acetylenic by-products nor 1,4-diphenylbutadiene are formed. The preparation and characterization of the cis and trans isomers of β-styryltrimethylsilane and -tin are described.
Multivariate Longitudinal Methods for Studying Developmental Relationships between Depression and Academic Achievement.

Recent advances in methods and computer software for longitudinal data analysis have pushed researchers to more critically examine developmental theories. In turn, researchers have also begun to push longitudinal methods by asking more complex developmental questions. One such question involves the relationships between two developmental processes. In this situation, choosing a longitudinal method is not obvious and should depend on specific hypotheses and research questions. This article outlines three common bivariate longitudinal models, including the bivariate latent growth curve model, the latent growth curve with a time-varying covariate, and the bivariate dual change score growth model, and illustrates their use by modeling how the development of depression is related to the development of achievement. Each longitudinal model is fitted to repeated measurements of children's depression and achievement from the National Longitudinal Survey of Youth (NLSY) data set in order to examine differing develo...
The Energetics of Hydrogen-Vacancy Clusters in BCC Iron

We present a general method for investigating the energetics of small impurity-vacancy clusters in crystalline materials. We use a combination of molecular dynamics and Monte Carlo methods to locate low energy configurations of the bubbles, from which the binding energies of various point defects can be determined. This method is applied to case of hydrogen bubbles in alpha-iron. Clusters with ratios of up to 10 hydrogen atoms to a vacancy are studied. We find that hydrogen does help to stabilize voids in alpha-iron, but that hydrogen is quite weakly bound to these voids. Ratios of up to approximately 4 can be supported at low temperatures.
Synthetic aperture radar imaging of ocean waves during the marineland experiment

X - and L -band simultaneously obtained synthetic aperture radar (SAR) data of ocean gravity waves collected during the Marineland Experiment were analyzed using wave contrast measurements. The Marineland data collected in 1975 represents a unique historical data set for testing still-evolving theoretical models of the SAR ocean wave imaging process. The wave contrast measurements referred to are direct measurements of the backscatter variation between wave crests and troughs. These modulation depth measurements, which are indicators of wave detectability, were made as a function of: a) the settings used in processing the SAR signal histories to partially account for wave motion; b) wave propagation direction with respect to radar look direction for both X - and L -band SAR data; c) SAR resolution; and d) number of coherent looks. The contrast measurements indicated that ocean waves imaged by a SAR are most discernible when X -band frequency is used (as compared to L -band), and when the ocean waves are traveling in the range direction. Ocean waves can be detected by both X - and L -band SAR, provided that the radar surface resolution is small compared to the ocean wavelength (at least 1/4 of the ocean wavelength is indicated by this work). Finally, wave detection with L -band SAR can be improved by adjusting the focal distance and rotation of the cylindrical telescope in the SAR optical processor to account for wave motion. The latter adjustments are found to be proportional to a value that is near the wave phase velocity.
A BAYESIAN INTEGRATION MODEL OF HIGH-THROUGHPUT PROTEOMICS AND METABOLOMICS DATA FOR IMPROVED EARLY DETECTION OF MICROBIAL INFECTIONS

High-throughput (HTP) technologies offer the capability to evaluate the genome, proteome, and metabolome of an organism at a global scale. This opens up new opportunities to define complex signatures of disease that involve signals from multiple types of biomolecules. However, integrating these data types is difficult due to the heterogeneity of the data. We present a Bayesian approach to integration that uses posterior probabilities to assign class memberships to samples using individual and multiple data sources; these probabilities are based on lower-level likelihood functions derived from standard statistical learning algorithms. We demonstrate this approach on microbial infections of mice, where the bronchial alveolar lavage fluid was analyzed by three HTP technologies, two proteomic and one metabolomic. We demonstrate that integration of the three datasets improves classification accuracy to approximately 89% from the best individual dataset at approximately 83%. In addition, we present a new visualization tool called Visual Integration for Bayesian Evaluation (VIBE) that allows the user to observe classification accuracies at the class level and evaluate classification accuracies on any subset of available data types based on the posterior probability models defined for the individual and integrated data.
The Biochemistry of Memory Consolidation: A Model System for the Philosophy of Mind

This paper argues that the biochemistry of memory consolidation provides valuable model systems for exploring the multiple realization of psychological states.
Zinc partitions insulin-like growth factors (IGFs) from soluble IGF binding protein (IGFBP)-5 to the cell surface receptors of BC3H-1 muscle cells.

Zinc (Zn 2 + ) is a multifunctional micronutrient. The list of functions for this micronutrient expanded with the recent discovery that Zn 2 + retains insulin-like growth factors binding proteins (IGFBPs) on the surface ofcultured cells, lowers the affinity of cell-associated IGFBPs, and increases the affinity of the cell surface insulin-like growth factor (IGF)-type 1 receptor (IGF-1R). However, currently there is no information concerning the effect of Zn 2 + on soluble IGFBPs. In the current study, the soluble IGFBP-5 secreted by BC 3 H-1 cells is shown to bind approximately 50% more [ 1 2 5 I]-IGF-II than [ 1 2 5 I]-IGF-I at pH 7.4. Zn 2 + is shown to depress the binding of both IGF-I and IGF-II to soluble secreted IGFBP-5; [ 1 2 5 I]-IGF-I binding is affected more so than [ 1 2 5 I]-IGF-II binding. Zn 2 + acts by lowering the affinity (K a ) of IGFBP-5 for the IGFs. Scatchard plots are non-linear indicating the presence of high and low affinity binding sites; Zn 2 + affects only binding to the high affinity site. In contrast, Zn 2 + increases the affinity by which either [ 1 2 5 I]-IGF-I or [ 1 2 5 I]-R 3 -IGF-I binds to the IGF-1 R, but depresses [ 1 2 5 I-IGF-II binding to the IGF-type 2 receptor (IGF-2R) on BC 3 H-1 cells. By depressing the association of the IGFs with soluble IGFBPs, Zn 2 + is shown to repartition either [ 1 2 5 I]-IGF-I or [ 1 2 5 I]-IGF-II from soluble IGFBP-5 onto cell surface IGF receptors. Zn 2 + was active at physiological doses depressing IGF binding to IGFBP-5 and the IGF-2R at 15-20 pM. Hence, a novel mechanism is further characterized by which the trace micronutrient Zn 2 + could regulate IGF activity.
Mixed modeling and sample size calculations for identifying housekeeping genes

Normalization of gene expression data using internal control genes that have biologically stable expression levels is an important process for analyzing reverse transcription polymerase chain reaction data. We propose a three-way linear mixed-effects model to select optimal housekeeping genes. The mixed-effects model can accommodate multiple continuous and/or categorical variables with sample random effects, gene fixed effects, systematic effects, and gene by systematic effect interactions. We propose using the intraclass correlation coefficient among gene expression levels as the stability measure to select housekeeping genes that have low within-sample variation. Global hypothesis testing is proposed to ensure that selected housekeeping genes are free of systematic effects or gene by systematic effect interactions. A gene combination with the highest lower bound of 95% confidence interval for intraclass correlation coefficient and no significant systematic effects is selected for normalization. Sample size calculation based on the estimation accuracy of the stability measure is offered to help practitioners design experiments to identify housekeeping genes. We compare our methods with geNorm and NormFinder by using three case studies. A free software package written in SAS (Cary, NC, U.S.A.) is available at http://d.web.umkc.edu/daih under software tab.
Novel DNA repair alkyltransferase from Caenorhabditis elegans

O6-Alkylguanine DNA-alkyltransferase (AGT) is a widely distributed DNA repair protein that protects living organisms from endogenous and exogenous alkylation damage to DNA at the O6-position of guanine. The search of the C. elegans genome database for an AGT protein revealed the presence of a protein (cAGT-2) with some similarity to known AGTs in addition to the easily recognized cAGT-1 protein. The predicted protein sequence of cAGT-2 contains the amino acid sequence –ProCysHisPro– at the presumed active site of the protein, whereas all other known AGTs have –ProCysHisArg–. A truncated version of the cAGT-2 protein was expressed in E. coli. This purified recombinant protein was able to repair O6-methylguanine and O4-methylthymine adducts in DNA in vitro and also reacted with the bulky benzyl adduct in O6-benzylguanine. This fragment of cAGT-2 (104 amino acids) is the smallest protein possessing AGT activity yet described. The full-length cAGT-2 protein (274 amino acids) totally lacks the N-terminal domain present in all other known AGTs but has a long C-terminal extension that has significant homology to histone 1C. Expression of cAGT-2 in an E. coli strain lacking endogenous AGT activity provided modest but statistically significant resistance to the toxicity of N-methyl-N′-nitro-N-nitrosoguanidine, confirming that cAGT-2 is an alkyltransferase. Environ. Mol. Mutagen. 38:235–243, 2001. © 2001 Wiley-Liss, Inc.
Persistence length and stochastic fragmentation of supramolecular nanotubes under mechanical force.

Cyclic peptide nanotubes (CPNs) exhibit impressive structural, mechanical and chemical properties in resemblance to beta-sheet proteins found in silks and amyloids, and show potential as supramolecular nanotubes that can be utilized to generate novel nanocomposites and nanoporous thin films. Quantifying the persistence length and thermomechanical fragmentation of CPNs is of great importance for establishing a theoretical basis of how to generate rectilinear nanostructures with controlled aspect ratio and rigidity. However, factors governing the elasticity and dynamical breaking of these supramolecular nanostructures remain to be fully understood. Here we present a statistical analysis of the Young’s modulus and persistence length of CPNs using fully-atomistic molecular dynamic simulations in explicit solvent. We show that the measured properties exhibit a dependence on the magnitude of the shear force applied, and extrapolation to the quasi-static deformation case yields 0.46 m for the persistence length and 7.8 GPa for the Young’s modulus, in agreement with our experimental observations from TEM images. We establish a theoretical model for the spatial and temporal distribution of stochastic fracture, which we use to explain the simulation-based observations of spontaneous fragmentation under an applied shear force. Our methodology, blending theory, simulation and experiments provide a framework that can be utilized to investigate the mechanical behavior of self-assembling protein materials, paving the way for their design towards biological and industrial applications. (Some figures may appear in colour only in the online journal)
The Death Penalty in the Legislature - Some Thoughts About Money, Myth, and Morality

For more than a decade, Kansans have debated whether the state should adopt a system of capital punishment. In 1987 and 1989, after particularly stormy debates, the legislature narrowly defeated efforts to reinstate the death penalty. In political terms, these decisions were stunning. The newly elected Governor had made the imposition of capital punishment one of his top campaign issues. He had majorities of his party in both houses of the legislature. According to public opinion polls, his position was supported by the majority of citizens of the state. Moreover, bills reinstating capital punishment had passed in previous legislative sessions, only to be vetoed by the former Governor. Given the presumed popularity of capital punishment, it was difficult to understand why legislators would defy the wishes of their constituents or invite the wrath of the governor.
Oral Human Papillomavirus (HPV) Infection in HPV-Positive Patients With Oropharyngeal Cancer and Their Partners

Purpose To better understand oral human papillomavirus (HPV) infection and cancer risk among long-term sexual partners of patients with HPV-positive oropharyngeal cancer (HPV-OPC). Patients and Methods An oral rinse sample, risk factor survey, cancer history, and oral examination (partners only) were collected from patients with HPV-OPC and their partners. Oral rinse samples were evaluated for 36 types of HPV DNA using PGMY 09/11 primers and line-blot hybridization and HPV16 copy number using quantitative polymerase chain reaction. Oral HPV prevalence was compared with infection among those age 45 to 65 years using National Health and Nutrition Examination Survey (NHANES) 2009-2010. Results A total of 164 patients with HPV-OPC and 93 of their partners were enrolled. Patients were primarily men (90%), were never-smokers (51%), and had performed oral sex (97%), with a median age of 56 years; they had a high prevalence of oncogenic oral HPV DNA (61%) and oral HPV16 DNA (54%) at enrollment. Female partners ha...
Spontaneous closure of the ventricular component of an atrioventricular septal defect.

Abstract It is well recognized that perimembranous ventricular septal defects close or diminish in size spontaneously due to the development of fibrous tissue tags, which are usually termed “aneurysms of the membranous septum.” Morphologic examination, however, has shown conclusively that they are almost always derived from the leaflets of the tricuspid valve. 1 Equally well described, although certainly less well recognized, are the “aneurysmal-like” structures that may be derived from the bridging leaflets in the setting of an atrioventricular (AV) septal defect. The angiomorphologic correlation study of Kudo et al 2 established the frequent existence of such pouches in the setting of so-called “ostium primum” defects, but suggested that they did not exist with common AV valve orifice. We now report a patient with AV septal defect and common orifice in whom ventricular shunting was virtually abolished concomitant with the development of pouches from the bridging leaflets that blocked the septal defect. This report illustrates the angiographic findings in this patient together with the morphologic features of a heart specimen exhibiting a similar malformation.