bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum and classical vibrational relaxation dynamics of N‐methylacetamide on ab initio potential energy surfaces
Authors: Fujisaki Hiroshi , Yagi Kiyoshi , Straub John E. , Stock Gerhard
Published: March 2009

Employing extensive quantum‐chemical calculations at the DFT/B3LYP and MP2 level, quartic force fields of isolated N‐methylacetamide are constructed. Taking into account 24 vibrational degrees of freedom, the model is employed to perform numerically exact vibrational configuration interaction calculations of the vibrational energy relaxation of the amide I mode. It is found that the energy transfer pathways may sensitively depend on details of the theoretical description. Moreover, the exact reference calculations were used to study the applicability and accuracy of (i) the quasiclassical trajectory method, (ii) time‐dependent second‐order perturbation theory, and (iii) the instantaneous normal mode description of frequency fluctuations. Based on the results, several strategies to describe vibrational energy relaxation in biomolecular systems are discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Efficient parallel algorithm of second‐order Møller–Plesset perturbation theory with resolution‐of‐identity approximation (RI‐MP2)
Authors: Katouda Michio , Nagase Shigeru
Published: March 2009

An efficient parallel algorithm is developed for second‐order Møller–Plesset perturbation theory with the resolution‐of‐identity approximation of two‐electron repulsion integrals (RI‐MP2) to perform MP2 energy calculations of large molecules on distributed memory processors. Benchmark calculations are carried out for taxol (C47H51NO14), valinomycin (C54H90N6O18), and two‐layer nanographene sheets (C96H24)2, which show the high parallel efficiency of the developed algorithm. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
On the construction of Kramers paired double group symmetry functions
Authors: Peng Daoling , Ma Jianyi , Liu Wenjian
Published: March 2009

Relativistic quantum chemical calculations on molecular systems can greatly be expedited by making use of the full molecular symmetry, including both double point group and time‐reversal symmetry. A simple yet general scheme is proposed here to make double point group symmetry functions also form Kramers pairs such that the resulting operator matrices have the desired structure (i.e., quaternion, complex, or real). The key idea is to insert appropriate phase factors into the symmetry functions or make a suitable unitary transformation of them. Arbitrary finite double point groups can be handled in the same way. As for a product basis, the same symmetrization can be achieved by simple modifications of the vector coupling (Clebsch–Gordan) coefficients. This is especially of interest to, e.g., time‐dependent relativistic density functional linear response theory or relativistic two‐electron repulsion integral evaluations in general. Several examples are provided to illustrate the algorithm and its efficiency. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
How does the free complement wave function become accurate and exact finally for the hydrogen atom starting from the Slater and Gaussian initial functions and for the helium atom on the cusp conditions?
Authors: Nakatsuji Hiroshi , Nakashima Hiroyuki
Published: March 2009

The free complement (FC) method, or the free iterative‐complement‐interaction (ICI) method, for generating the exact wave function from an approximate initial wave function has been applied to the hydrogen atom starting from the Slater and Gaussian functions for comparison. The process of improvement was followed by checking the wave function itself and other quantities that have definite exact values. Because the exact wave function is simple in this case, we could make clear analyses for many aspects of the wave function. We examined the energy, the wave function itself, the wave function error, the H‐square error, the local energy near the nucleus, and the cusp. Both the Slater and Gaussian functions gave similar convergence rates to the exact function with respect to the order of the FC method, but the number of complement functions at a particular order is three times larger for the Gaussian case than for the Slater case. Although the cusp value of the Gaussian initial function is zero, it grows as the FC calculation proceeds and finally becomes essentially exact at convergence. The same was true for all the quantities studied here, irrespective of the type of the initial wave function. For the helium atom, the cusp conditions including the electron–electron cusp were also examined with the FC wave function calculated before and shown to converge to the exact values. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Dual‐level hierarchical scheme for linear‐scaling divide‐and‐conquer correlation theory
Authors: Kobayashi Masato , Nakai Hiromi
Published: March 2009

A dual‐level hierarchical scheme for the linear‐scaling divide‐and‐conquer (DC)‐based correlation theory is presented as a combination of dual‐buffer and dual‐basis approaches. Although the dual‐basis approach has been well developed, the dual‐buffer approach is specific for the DC correlation method and based on the different interaction lengths between the Hartree–Fock and correlation methods. This study performs numerical assessments of the dual‐buffer DC‐MP2 (second‐order Møller–Plesset perturbation) systematically. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Ab initio QM/MM excited‐state molecular dynamics study of coumarin 151 in water solution
Authors: Kina Daisuke , Arora Pooja , Nakayama Akira , Noro Takeshi , Gordon Mark S. , Taketsugu Tetsuya
Published: March 2009

Ab initio molecular dynamics (AIMD) simulations are performed to investigate the excited state dynamics of coumarin 151 (C151) in the gas phase and in water solution at the CASSCF level of theory with segmented DZP basis sets, where in the latter case effective fragment potentials (EFP) are used. The dipole moment of an isolated C151 molecule increases considerably upon electronic vertical excitation, from 5.0 D (S0 state) to 11.1 D (S1 state). Two equilibrium structures have been identified in the S1 state, i.e., a charge‐transfer state with a planar amino group and a deformed structure of the six‐membered ring with the carbonyl group, and a structure that is similar to the S0 equilibrium structure. In AIMD simulations for an isolated C151 molecule (presumably similar to dynamics in nonpolar solvents), C151 decays from S1 to S0 via a crossing point of the charge‐transfer state in some trajectories, while in the AIMD simulations for C151‐EFP (including solvent), the S1 and S0 energies show an almost parallel energy variation with structural changes, and no crossing point is observed. This result is in good agreement with the experimental observation. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Mass spectrometric study of peptides secreted by the skin glands of the brown frog Rana arvalis from the Moscow region
Authors: Samgina T. Yu. , Artemenko K. A. , Gorshkov V. A. , Ogourtsov S. V. , Zubarev R. A. , Lebedev A. T.
Published: March 2009

A high‐performance liquid chromatography nano‐electrospray ionization Fourier transform mass spectrometry (HPLC/nanoESI‐FTMS) approach involving recording of collision‐activated dissociation (CAD) and electron‐capture dissociation (ECD) spectra of an intact sample and two its modifications after performic oxidation and reduction followed by carboxamidomethylation helps to establish peptide profiles in the crude secretion of frog species at mid‐throughput level, including de novo sequencing. The proposed derivatization procedures allow increasing of the general sequence coverage in the backbone, providing complementary information and, what is more important, reveal the amino acid sequence in the cystine ring (‘rana box’). Thus purely mass spectrometric efficient sequencing becomes possible for longer than usual proteolytic peptides.

Seventeen peptides belonging to four known families were identified in the secretion of the European brown frog Rana arvalis inhabiting the Moscow region in Russia. Ranatuerins, considered previously a unique feature of the North American species, as well as a new melittin‐related peptide, are worth special mention. The developed approach was previously successfully used for the identification of peptides in the skin secretion of the Caucasian green frog Rana ridibunda. Copyright © 2009 John Wiley & Sons, Ltd.
Importance of using highly pure internal standards for successful liquid chromatography/tandem mass spectrometric bioanalytical assays
Authors: Bergeron Annik , Furtado Milton , Garofolo Fabio
Published: March 2009

Internal standards (IS) with similar physicochemical properties to the analyte provide multiple advantages in liquid chromatography/tandem mass spectrometric (LC/MS/MS) bioanalytical methods such as: reduction of the analysis run time, improvement in the intra‐injection reproducibility, impact reduction of matrix and ionization effects. However, it is important to evaluate the purity of the IS prior to their use. Indeed, a minor impurity in the IS may lead to an important issue during bioanalytical method development. Stable labelled internal standards are usually appropriate IS for bioanalysis. The use of oxycodone‐D3, ursodiol‐D5 and atovaquone‐D4 as internal standards in three different bioanalytical methods was evaluated. During oxycodone, oxymorphone and noroxycodone simultaneous quantification method development, oxymorphone was identified as a contaminant in oxycodone‐D3. Since the limit of quantification for oxymorphone was very low (10 pg/mL), the presence of an even low percentage of oxymorphone in oxycodone‐D3 leads to the change of the stable labelled IS for an analogue, ethylmorphine. 23‐Nordeoxycholic acid was preferred to ursodiol‐D5 as internal standard for the ursodiol, tauroursodiol and glycoursodiol simultaneous quantification method. Indeed, more than 7% of ursodiol was identified in the ursodiol‐D5 which could not be bypassed by decreasing the IS concentration without compromising the linearity. An atovaquone‐D4 reference standard revealed the non‐negligible presence of atovaquone‐D5 to atovaquone‐D8 that has a large impact on the method validation. Therefore, atovaquone‐D4 was sent for recertification since its isotopic purity was found to be much less than the isotopic purity mentioned on its certificate of analysis. Consequently, during bioanalytical method development, the purity of the IS should be scrutinized. Copyright © 2009 John Wiley & Sons, Ltd.
Assessment of in situ thermal treatment for chlorinated organic source zones
Authors: Truex Michael J. , Gillie James M. , Powers Jefferey G. , Lynch Kira P.
Published: March 2009

The East Gate Disposal Yard (EGDY) at Fort Lewis is the source of a large trichloroethene (TCE) plume at this military installation. Source reduction using thermal treatment was applied using electrical resistance heating. A total of about 5,800 kg of TCE‐equivalent volatile organic compounds (VOCs; TCE and dichloroethene) was extracted during thermal treatment of the three zones selected for source reduction. Pretreatment groundwater TCE concentrations were measured up to 100 ppm. Posttreatment groundwater TCE concentrations within the treatment zones averaged less than 100 ppb. Posttreatment soil TCE concentrations decreased by over 96 percent compared to pretreatment soil concentrations. The overall contaminant flux from EGDY was reduced by an estimated 60 to 90 percent by the source reduction effort. The traditional and new techniques for site characterization and remediation performance monitoring applied at EGDY provide insight for installing, operating, monitoring, and assessing thermal treatment. © 2009 Wiley Periodicals, Inc.
Performing contaminant mass balances for remedy assessments
Authors: Gibbs James T. , Santillan Javier
Published: March 2009

Contaminant mass‐balance assessments are useful tools to help quantify various mass transport and removal mechanisms that may be active in a remedial system setting. This article presents the basics of performing a mass balance and illustrates the utility of using the information derived to support project management decisions. It is important to understand the partitioning of contaminant mass into various environmental media and physical forms, as well as the relationships among the partitions. Contaminant partitioning tends toward an equilibrium state, so natural or engineered mass transfer into or out of one partition will affect the others. Mass balances are exercises that quantify, to the extent possible, the contaminant mass in the various environmental partitions and the transfer and transformation processes that affect contaminant distribution. Understanding mass partitioning and transfer mechanisms helps remediation practitioners to engineer and optimize those mechanisms that contribute to risk reduction at a contaminated site. Such knowledge can inform risk managers when natural mechanisms may dominate engineered approaches and help identify uncertainties in contaminant fate and transport. © 2009 Wiley Periodicals, Inc.
Investigation of NAPL transport through a model sand cap during ebullition
Authors: McLinn Eugene L. , Stolzenburg Thomas R.
Published: March 2009

Nonaqueous‐phase liquid (NAPL) migration from sediments to the surface of water bodies has been reported frequently at sites with sediments contaminated with NAPLs, such as coal tar and creosote. Commonly, transport of NAPL from sediment is facilitated by gas ebullition caused by anaerobic biodegradation of organic matter in the sediment. A remedy often specified for these sites is a sand cap, and sand caps amended with sorbent materials (such as organoclays) are being pilot‐tested. This article discusses a laboratory study to assess the effectiveness of a sand layer for controlling NAPL migration. The study used a test column composed of a Plexiglas tube containing a tar source that was buried beneath a 30‐cm‐thick layer of fine sand. Water was added to the column until 5 cm of standing water covered the sand layer. To simulate ebullition, air was injected into the base of the sand column at approximately 200 mL/min. It was observed that the gas and NAPL migrated primarily through channels and fractures in the sand, and was not filtered through a network of stable pores. Tar migrated through the sand layer in 12 hours and accumulated on the water surface for several hours before losing its buoyancy and settling back down to the sand surface. After ending the tar migration experiment, the test column was frozen to preserve structures in the sand. The study showed that the tar migrated through the simulated sand cap in small (2‐mm) channels only a few sand grains thick. The results of this laboratory work call into question the effectiveness of sand caps for controlling NAPL migration from sediment in the presence of ebullition. © 2009 Wiley Periodicals, Inc.
Passive to active tie‐in for soil gas surveys: Improved technique for source‐area, spatial variability, remediation‐monitoring, and vapor‐intrusion assessment
Authors: Odencrantz Joseph E. , O'Neill Harry
Published: March 2009

The mass‐to‐concentration tie‐in (MtoC Tie‐In) correlates passive soil gas (PSG) data in mass to active soil gas data in concentration determined by the US EPA Method TO‐17 or TO‐15. Passive soil gas surveys consist of rapid deployment of hydrophobic sorbents (dozens to several hundred locations typically installed in one day) to a depth of six inches to three feet in a grid pattern with exposure in the field from three days to two weeks to target a wide variety of organic compounds. A power function is used on a compound‐to‐compound basis to correlate spatially varying mass (nanograms) from selected locations within a passive soil gas survey to concentration (µg/m3) at those same locations. The correlation from selected PSG locations is applied to the remainder of the PSG grid. The MtoC Tie‐In correlations provide added value to a PSG survey, with the PSG data then used to estimate risk throughout the limits of the investigation for quantitative assessment.

The results from a site in northern California show the MtoC Tie‐In correlations for both benzene and total petroleum hydrocarbons (TPH). The correlations are applied on a compound‐to‐compound basis to the remaining locations in the PSG grid to provide an estimate of concentration that can be used for comparison to risk/screening levels or fate‐and‐transport diagnostic tools (partitioning equations, solubility laws, etc.). An example of how the correlations are applied is presented in tabular form. The results from a chlorinated solvent survey show the MtoC Tie‐In correlation from a site in Maryland for tetrachloroethene (PCE). In this instance, there was a near‐perfect relationship between the PSG mass and the active soil gas concentration (R2 value of 1). The concentration estimated throughout a PSG grid enables a vast new realm of interpretive power at sites. Several other sites are discussed, including an example application for groundwater. © 2009 Wiley Periodicals, Inc.
LEHR superfund stormwater runoff and putah creek mercury issues
Authors: Lee G. Fred , Jones‐Lee Anne
Published: March 2009

Stormwater runoff from the University of California, Davis/U.S. Department of Energy Laboratory for Energy‐Related Health Research (UCD/US DOE LEHR) Superfund site located on the University of California campus in Davis, California, has been found to contain over 500 ng/L of total recoverable mercury, which is about ten times the California Toxics Rule criterion. This stormwater runoff is discharged to Putah Creek, which is Clean Water Act Section 303(d) listed as impaired for excessive mercury bioaccumulation in edible fish. A discussion is presented on the potential impact of the mercury in stormwater runoff from LEHR leading to excessive bioaccumulation of mercury in Putah Creek fish. The mercury in the stormwater runoff is derived from former flooding of the soils near the creek, which contains mercury derived from abandoned upstream mercury mines located in the Coast Range Vaca Hills to the west of LEHR. The implications of this situation for implementing a Total Maximum Daily Load (TMDL) to control mercury in stormwater runoff to Putah Creek are presented. © 2009 Wiley Periodicals, Inc.
New statistical approaches for anomaly detection
Authors: Callegari Christian , Giordano Stefano , Pagano Michele
Published: March 2009

Computer security is a growing problem. Over the last years, the number and variety of security attacks in IP‐ based network infrastructures have increasingly grown, leading to the need of developing new security architectures. In this scenario, the use of intrusion detection systems (IDSs) has emerged as a key element, since it permits to tackle security threats by masquerader, misfeasor, and clandestine users. In this paper, we address the problem considering some new statistical techniques for detecting network anomalies. In more detail, the paper discusses the use of several statistical models to characterize the normal behavior of the network traffic running over TCP, so that anomalies can be revealed as significant deviations from such behavior. Namely, our proposal is based on the use of Markov chains, co‐ occurrence matrices, and compression algorithms, for modeling the TCP connections, in terms of statistical analysis of some of the packet header fields. The performance analysis, presented in this paper, demonstrates the effectiveness of the proposed methods. Copyright © 2009 John Wiley & Sons, Ltd.
Regulatory focus and new venture performance: A study of entrepreneurial opportunity exploitation under conditions of risk versus uncertainty
Authors: Hmieleski Keith M. , Baron Robert A.
Published: March 2009

Research on cognitive fit suggests that entrepreneurs will be most successful at leading their firms when approaching the entrepreneurial process through the self‐regulatory mode that most closely matches the requirements of their environment and its accompanying perspective on the nature of entrepreneurial opportunities. Consistent with the discovery view of entrepreneurial opportunities, it is suggested that a prevention focus will be the most effective self‐regulatory mode for entrepreneurs leading their firms within stable industry environments, which are characterized by risk. Building from the creation view of entrepreneurial opportunities, it is argued that a promotion focus will be the most effective self‐regulatory mode for entrepreneurs leading their firms within dynamic industry environments, which are characterized by uncertainty. These arguments are tested using a national (United States) random sample of 201 lead entrepreneurs. The findings indicate that in dynamic environments, entrepreneurs' promotion focus is positively associated with venture performance (i.e., lagged measures of revenue and employment growth), while entrepreneurs' prevention focus is negatively related to performance in such environments. In both cases, these effects are found to be fully mediated by deviation from firms' original business concepts. In stable environments, however, no significant relationships between entrepreneurs' promotion or prevention focus and new venture performance were observed. These results suggest that low cognitive fit (a mismatch between entrepreneurs' mode of self‐regulation and the decision‐making context in which they operate) is more damaging in dynamic environments (i.e., a context of uncertainty) than in stable environments (i.e., a context of risk). Copyright © 2009 Strategic Management Society.
Niche construction: The process of opportunity creation in the environment
Authors: Luksha Pavel
Published: March 2009

This article contributes to the emerging theory of opportunity creation by examining how organizations (including entrepreneurial ones) create and transform their niches. Using insights from contemporary evolutionary theory, the article classifies types of niche construction activities along dimensions of governance and the nature of the strategic actor. It then focuses on mechanisms of niche construction governed by the focal organization or entrepreneur to explain how competitive imperfections can be induced within industries and markets. The central role of communicative strategies in niche construction is emphasized. Copyright © 2009 Strategic Management Society.
Factor payments, resource‐based bargaining, and the creation of firm wealth in technology‐based ventures
Authors: Townsend David M. , Busenitz Lowell W.
Published: March 2009

A central tenet of resource‐based logic is that undervalued resources utilized by firms organized to exploit them will produce superior economic performance over the long run. Yet when young technology‐based ventures pursuing new opportunities do not possess full property over these resources, input providers retain the right to bid up factor prices to match each resource's marginal productivity. In response to these limitations in extant resource‐based logic, we apply and extend Lippman and Rumelt's full payments and bargaining perspectives and propose an alternative method by which entrepreneurs can generate firm wealth through the unique bundling of cospecialized resources. Both theoretical implications and directions for future research are discussed as well. Copyright © 2009 Strategic Management Society.
Exercising entrepreneurial opportunities: The role of information‐gathering and information‐processing capabilities of the firm
Authors: Sleptsov Alexander , Anand Jaideep
Published: March 2009

In this article, we study two capabilities that influence firms' effectiveness in exercising entrepreneurial opportunities: information‐gathering and information‐processing capability. We argue that their effects are not always positive or symmetrical. When the firm's information‐processing capability is low, high levels of its information‐gathering capability may result in lower effectiveness because of managerial cognitive overload. The effects of high information‐processing capability are more nuanced and depend on whether the firm's information processing has experiential or cognitive character. Our analysis offers a counterintuitive insight: the firm may fail to exercise entrepreneurial opportunities effectively not only when it has low levels of information capabilities, but also when its levels are high but unbalanced. Copyright © 2009 Strategic Management Society.
A Bayesian approach to joint analysis of longitudinal measurements and competing risks failure time data
Authors: Hu Wenhua , Li Gang , Li Ning
Published: March 2009

In this paper, we develop a Bayesian method for joint analysis of longitudinal measurements and competing risks failure time data. The model allows one to analyze the longitudinal outcome with nonignorable missing data induced by multiple types of events, to analyze survival data with dependent censoring for the key event, and to draw inferences on multiple endpoints simultaneously. Compared with the likelihood approach, the Bayesian method has several advantages. It is computationally more tractable for high‐dimensional random effects. It is also convenient to draw inference. Moreover, it provides a means to incorporate prior information that may help to improve estimation accuracy. An illustration is given using a clinical trial data of scleroderma lung disease. The performance of our method is evaluated by simulation studies. Copyright © 2009 John Wiley & Sons, Ltd.
A multivariate CAR model for improving the estimation of relative risks
Authors: Greco Fedele P. , Trivisano Carlo
Published: March 2009

Disease mapping studies have been widely performed at univariate level, that is considering only one disease in the estimated models. Nonetheless, simultaneous modelling of different diseases can be a valuable tool both from the epidemiological and from the statistical point of view. In this paper we propose a model for multivariate disease mapping that generalizes the univariate conditional auto‐regressive distribution. The proposed model is proven to be an effective alternative to existing multivariate models, mainly because it overcome some restrictive hypotheses underlying models previously proposed in this context. Model performances are checked via a simulation study and via application to a case study. Copyright © 2009 John Wiley & Sons, Ltd.
Colloidal Gold and Silver Triangular Nanoprisms
Authors: Millstone Jill E. , Hurst Sarah J. , Métraux Gabriella S. , Cutler Joshua I. , Mirkin Chad A.
Published: March 2009

It is now well‐known that the size, shape, and composition of nanomaterials can dramatically affect their physical and chemical properties, and that technologies based on nanoscale materials have the potential to revolutionize fields ranging from catalysis to medicine. Among these materials, anisotropic particles are particularly interesting because the decreased symmetry of such particles often leads to new and unusual chemical and physical behavior. Within this class of particles, triangular Au and Ag nanoprisms stand out due to their structure‐ and environment‐dependent optical features, their anisotropic surface energetics, and the emergence of reliable synthetic methods for producing them in bulk quantities with control over their edge lengths and thickness. This Review will describe a variety of solution‐based methods for synthesizing Au and Ag triangular prismatic structures, and will address and discuss proposed mechanisms for their formation.

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Achieving high and consistent rendering performance of Java AWT/Swing on multiple platforms
Authors: Wang Yi‐Hsien , Wu I‐Chen
Published: March 2009

Wang et al. (Softw. Pract. Exper. 2007; 37(7):727–745) observed a phenomenon of performance inconsistency in the graphics of Java Abstract Window Toolkit (AWT)/Swing among different Java runtime environments (JREs) on Windows XP. This phenomenon makes it difficult to predict the performance of Java game applications. Therefore, they proposed a portable AWT/Swing architecture, called CYC Window Toolkit (CWT), to provide programmers with high and consistent rendering performance for Java game development among different JREs. They implemented a DirectX version to demonstrate the feasibility of the architecture. This paper extends the above research to other environments in two aspects. First, we evaluate the rendering performance of the original Java AWT with different combinations of JREs, image application programming interfaces, system properties and operating systems (OSs), including Windows XP, Windows Vista, Fedora and Mac OS X. The evaluation results indicate that the performance inconsistency of Java AWT also exists among the four OSs, even if the same hardware configuration is used. Second, we design an OpenGL version of CWT, named CWT‐GL, to take advantage of modern 3D graphics cards, and compare the rendering performance of CWT with Java AWT/Swing. The results show that CWT‐GL achieves more consistent and higher rendering performance in JREs 1.4 to 1.6 on the four OSs. The results also hint at two approaches: (a) decouple the rendering pipelines of Java AWT/Swing from the JREs for faster upgrading and supporting old JREs and (b) use other graphics libraries, such as CWT, instead of Java AWT/Swing to develop cross‐platform Java games with higher and more consistent rendering performance. Copyright © 2009 John Wiley & Sons, Ltd.
Automated dynamic detection of busy–wait synchronizations
Authors: Tian Chen , Nagarajan Vijay , Gupta Rajiv , Tallam Sriraman
Published: March 2009

With the advent of multicores, multithreaded programming has acquired increased importance. In order to obtain good performance, the synchronization constructs in multithreaded programs need to be carefully implemented. These implementations can be broadly classified into two categories: busy–wait and schedule‐based. For shared memory architectures, busy–wait synchronizations are preferred over schedule‐based synchronizations because they can achieve lower wakeup latency, especially when the expected wait time is much shorter than the scheduling time. While busy–wait synchronizations can improve the performance of multithreaded programs running on multicore machines, they create a challenge in program debugging, especially in detecting and identifying the causes of data races. Although significant research has been done on data race detection, prior works rely on one important assumption—the debuggers are aware of all the synchronization operations performed during a program run. This assumption is a significant limitation as multithreaded programs, including the popular SPLASH‐2 benchmark have busy–wait synchronizations such as barriers and flag synchronizations implemented in the user code. We show that the lack of knowledge of these synchronization operations leads to unnecessary reporting of numerous races. To tackle this problem, we propose a dynamic technique for identifying user‐defined synchronizations that are performed during a program run. Both software and hardware implementations are presented. Furthermore, our technique can be easily exploited by a record/replay system to significantly speedup the replay. It can also be leveraged by a transactional memory system to effectively resolve a livelock situation. Our evaluation confirms that our synchronization detector is highly accurate with no false negatives and very few false positives. We further observe that the knowledge of synchronization operations results in 23% reduction in replay time. Finally, we show that using synchronization knowledge livelocks can be efficiently avoided during runtime monitoring of programs. Copyright © 2009 John Wiley & Sons, Ltd.
An approach to aid understanding emerging research fields—the case of knowledge management
Authors: Nie Kun , Ma Tieju , Nakamori Yoshiteru
Published: March 2009

Emerging research fields bring confusion to many people. This paper puts forward an approach, based on domain analysis and journal mining, to aiding people to get an overview of an emerging research field. The approach extends the traditional domain analysis method by adding two additional aspects: objectives and applications, and explores six essential issues regarding a research field, which include: why the research field is necessary, what enables its birth or triggers actions on it, what it deals with, how to implement it, how to support it, and where it has been applied. After introducing the approach, this paper gives a case study of applying it to explore the knowledge management (KM) field. Copyright © 2009 John Wiley & Sons, Ltd.
Human Fetal Auditory Stem Cells Can Be Expanded In Vitro and Differentiate Into Functional Auditory Neurons and Hair Cell-Like Cells
Authors: Chen Wei , Johnson Stuart L. , Marcotti Walter , Andrews Peter W. , Moore Harry D. , Rivolta Marcelo N.
Published: March 2009

In the quest to develop the tools necessary for a cell-based therapy for deafness, a critical step is to identify a suitable stem cell population. Moreover, the lack of a self-renovating model system for the study of cell fate determination in the human cochlea has impaired our understanding of the molecular events involved in normal human auditory development. We describe here the identification and isolation of a population of SOX2+OCT4+ human auditory stem cells from 9-week-old to 11-week-old fetal cochleae (hFASCs). These cells underwent long-term expansion in vitro and retained their capacity to differentiate into sensory hair cells and neurons, whose functional and electrophysiological properties closely resembled their in vivo counterparts during development. hFASCs, and the differentiating protocols defined here, could be used to study developing human cochlear neurons and hair cells, as models for drug screening and toxicity and may facilitate the development of cell-based therapies for deafness.

Disclosure of potential conflicts of interest is found at the end of this article.
Use of ultrasound to distinguish between fetal hyperthyroidism and hypothyroidism on discovery of a goiter
Authors: Huel C. , Guibourdenche J. , Vuillard E. , Ouahba J. , Piketty M. , Oury J. F. , Luton D.
Published: March 2009

Objectives

To determine whether sonography can be used to distinguish hyperthyroidism from hypothyroidism in pregnancies with fetal goiter.

Methods

This was a retrospective study of 39 cases of fetal goiter. The majority of the mothers had Graves' disease. Fetuses were scanned for the existence of a hypertrophic thyroid gland (goiter) beginning at 22 gestational weeks. Once a goiter was diagnosed, different echographic features were analyzed and the effect of chosen treatment on fetal thyroid development was monitored.

Results

On color Doppler, 68.8% of hypothyroid goiters had a peripheral vascular pattern vs. 20% in cases of fetal hyperthyroidism (P = 0.0574). No hypothyroid goiter presented central vascularization whereas half the hyperthyroid goiters did (P = 0.0013). Fetal tachycardia was a good indicator of hyperthyroidism (57.1% v.s 6.3%; P = 0.0055). Delayed bone maturation was seen in hypothyroid goiters (46.9% vs. 0%; P = 0.0307), while advanced bone maturity was specific to hyperthyroid goiters (85.7% vs. 0%; P < 0.0001). Lastly, an increase in fetal movement was observed in cases of fetal hypothyroidism (43.8% vs. 0%; P = 0.0364).

Conclusion

Based on the color Doppler pattern of goiter, fetal heart rate, bone maturation and fetal mobility, we established an ultrasound score to predict fetal thyroid function in cases of fetal goiter. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Ultrasonographic measurement of thymus size in IUGR fetuses: a marker of the fetal immunoendocrine response to malnutrition
Authors: Cromi A. , Ghezzi F. , Raffaelli R. , Bergamini V. , Siesto G. , Bolis P.
Published: March 2009

Objective

To test the hypothesis that intrauterine growth restriction (IUGR) is associated with decreased thymus size in the human fetus.

Methods

The thymus perimeter was measured in 60 consecutive IUGR fetuses at prenatal ultrasound examination. IUGR was defined as an abdominal circumference (AC) <5th centile. Sixty controls were identified by selection of the next consecutive appropriately grown fetus of similar gestational age (±1 week). To exclude fetal size effects, ratios between thymus perimeter and fetal biometry measurements including biparietal diameter (BPD), AC and femur length (FL), as well as estimated fetal weight (EFW) were compared between IUGR fetuses and controls.

Results

The proportion of fetuses with thymus perimeter <5th centile for gestation was significantly higher in IUGR fetuses than in controls (58/60 vs. 7/60, P < 0.0001). The mean thymus perimeter/BPD ratio (0.87 ± 0.20 vs. 1.13 ± 0.13, P < 0.0001), thymus perimeter/AC ratio (0.28 ± 0.06 vs. 0.35 ± 0.03, P < 0.0001), thymus perimeter/FL ratio (1.18 ± 0.26 vs. 1.51 ± 0.19, P < 0.001) and thymus perimeter/EFW ratio (0.05 ± 0.01 vs. 0.06 ± 0.01, P = 0.02) were significantly lower in IUGR fetuses than in controls. There was a significant positive correlation between the observed‐to‐expected mean for gestation thymus perimeter ratio and the enrolment‐to‐delivery interval (r = 0.44, P < 0.001).

Conclusion

IUGR is associated with a disproportionately small thymus. This supports the hypothesis that thymic involution may be part of the fetal neuroendocrine response to intrauterine starvation. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Association between ultrasound findings and extent of trophoblastic invasion into the tubal wall in ampullary pregnancy
Authors: Pereira P. P. , Cabar F. R. , Schultz R. , Zugaib M.
Published: March 2009

Objective

Predictive factors of damage to the Fallopian tube may guide the treatment of patients with tubal pregnancy. The aim of the present study was to investigate the association between the depth of trophoblastic invasion into the tubal wall, assessed on postoperative histological examination, with the findings obtained on transvaginal sonography (TVS) in women with ampullary pregnancy.

Methods

Women with ampullary pregnancy undergoing salpingectomy were enrolled into the study. Only women with a finding of either an embryo with cardiac activity or a tubal ring on TVS were included in the analysis, a total of 85 patients. Trophoblastic invasion was assessed postoperatively and was histologically classified as Stage I when limited to the tubal mucosa, Stage II when extending to the muscle layer and Stage III in the case of complete tubal wall infiltration. The association between findings on TVS and the stage of trophoblastic invasion was evaluated.

Results

There was a significant association between the findings on TVS and the depth of trophoblastic invasion (P < 0.001). All patients in whom an embryo with cardiac activity had been identified were found to have Stage II (17.9%) or Stage III (82.1%) invasion, whereas in those patients who showed a tubal ring on TVS, Stage I invasion was the most frequent finding (41.3%).

Conclusions

In ampullary pregnancy, the finding on TVS of an embryo with cardiac activity is associated with deeper penetration of trophoblastic tissue into the tubal wall than is the finding of a tubal ring. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Determination of the real transmission of an x‐ray lens for micro‐focus XRF at the SEM by coupling measurement with calculation of scatter spectra
Authors: Hodoroaba V.‐D. , Procop M.
Published: March 2009

The accurate knowledge of the x‐ray excitation spectrum is a prerequisite for the x‐ray fluorescence analysis (XRFA), particularly when a standardless algorithm is applied. For micro‐focus XRFA the excitation spectrum is the x‐ray tube spectrum multiplied with the transmission of the x‐ray lens. The tube spectrum is usually calculated by fundamental equations. The transmission function is conventionally determined by measuring two scatter spectra, with and without lens, and dividing them by each other. The measurement without lens is costly, requiring a calibrated collimator to be interchanged with the lens.

The alternative to the measurement of the scatter spectrum without lens is its calculation. A rather simple scatter model can be applied for the calculation of the transmission when scatter spectra are calculated for two different tube voltages and measured with lens at the same voltages. The procedure was verified with an iMOXS x‐ray source attached to the scanning electron microscope (SEM). The SEM was equipped with an efficiency calibrated energy dispersive x‐ray (EDX) spectrometer to enable the comparison between measured and calculated spectra. The transmission obtained was in good agreement with that resulted from two measured scatter spectra.

The procedure is especially recommended after an exchange of the x‐ray tube. This will likely modify the alignment of the lens relative to the x‐ray spot on the tube target. Because the transmission of the lens is quite sensitive to this alignment, the real transmission has to be calculated. Additionally, the procedure is sensitive to the effect of possible degradation of the tube target or window. Copyright © 2009 John Wiley & Sons, Ltd.
Strontium depth distribution in human bone measured by micro‐PIXE
Authors: Zamburlini M. , Campbell J. L., , de Silveira G., , Butler R., , Pejović‐Milić A., , Chettle D. R.,
Published: March 2009

Strontium is naturally present in human bone, where it may exert beneficial or detrimental health effects depending on its concentration. The way strontium influences bone health and the concentrations at which the beneficial/detrimental health effects of strontium become important are still unknown, due partly to the difficulty of assessing the bone strontium concentration in vivo non‐invasively. An x‐ray fluorescence (XRF) system was developed, which is capable of measuring normal bone strontium levels in vivo non‐invasively and therefore has the potential of becoming an important tool to understand bone strontium health effects. This technique, however, has the limitation that it relies on assumptions about bone strontium distribution to obtain a quantitative strontium measurement. To understand, to which degree, if any, the bone strontium distribution in bone changes from person to person, the bone strontium depth distribution was explored using micro‐PIXE in five ex vivo cadaver fingers, taken from normal people exposed to strontium only through diet. We found that, in the measured samples, strontium was uniformly distributed across the cortical and trabecular bone, and therefore corrections do not need to be applied to in vivo strontium XRF data to correct for strontium depth distribution. Copyright © 2009 John Wiley & Sons, Ltd.
Peer‐Reviewed, Evidence‐Based Analysis of Vitamin D and Primary Hyperparathyroidism
Authors: Weaver Storm , Doherty David B. , Jimenez Camilo , Perrier Nancy D.
Published: March 2009

Background

Research into the actions of vitamin D on the human body has been increasing at an exponential rate, as has understanding of the impact of vitamin D on various aspects of the endocrine system. Primary hyperparathyroidism (PHPT) is a disease of the endocrine system that can result in debility if not diagnosed. New understanding about the effect of vitamin D on parathyroid hormone regulation may provide an opportunity to better understand the coexistence of PHPT and vitamin D deficiency.

Methods

An evidence‐based literature review was based on a PubMed search for research involving vitamin D and primary hyperparathyroidism, and evaluating existing research on vitamin D. The PubMed search included English‐language articles published between 1977 and 2008, with a focus on research and analysis completed between 2005 and the present. This study examined recent developments in understanding the relationship between vitamin D and PHPT. This review of existing literature examined the impact of vitamin D insufficiency and deficiency, including the impact on diagnosis of vitamin D insufficiency/deficiency, diagnosis and management of PHPT, and the impact on overall health. The level of evidence was determined according to criteria proposed by Sackett et al. and the grade of recommendation according to the criteria proposed by Heinrich et al.

Results

Level III and level IV evidence predominates the vitamin D/PHPT based literature, with several notable Heinrich grade A, B, and C studies available. Additional evaluation of studies’ review is provided by reference and by section.

Conclusions

Vitamin D metabolism plays an important role in PHPT etiology, diagnosis, and management. Care of both conditions may have an important impact on overall health in humans.
Intraoperative Blood Loss is a Critical Risk Factor for Peritoneal Recurrence After Curative Resection of Advanced Gastric Cancer
Authors: Kamei Takao , Kitayama Joji , Yamashita Hiroharu , Nagawa Hirokazu
Published: March 2009

Background

Perioperative blood transfusion has been shown to be associated with poor outcome in various types of malignancy. However, the relationship between the amount of blood loss and specific types of cancer recurrence has not been documented.

Methods

We retrospectively examined the amount of intraoperative blood loss and the recurrence pattern in 146 patients who underwent curative gastrectomy for advanced gastric cancer and assessed the possible correlation between intraoperative blood loss and peritoneal, locoregional, and hematogenous recurrences.

Results

The amount of intraoperative blood loss in patients who developed peritoneal recurrence was significantly greater than that in patients without peritoneal recurrence, irrespective of blood transfusion. In contrast, the blood loss was not associated with nodal or hematogenous recurrence. Multivariate analysis demonstrated that large blood loss as well as operative curability B and adjuvant chemotherapy were independent risk factors for peritoneal recurrence and a worse outcome in advanced gastric cancer.

Conclusions

Intraoperative blood loss in curative gastrectomy for advanced gastric cancer may have a specific association with the development of peritoneal recurrence. Surgeons must remember that clean and dry surgery may lessen not only 30‐day mortality and morbidity but long‐term peritoneal recurrence in gastric cancer.
Postmortem studies on a patient with mucopolysaccharidosis type I: Histopathological findings after one year of enzyme replacement therapy
Authors: Yano S. , Moseley K. , Pavlova Z.
Published: March 2009

Deficiency of lysosomal α‐l‐iduronidase results in systemic accumulation of glycosaminoglycans (GAGs). Cardiac lesions due to accumulation of GAGs include hypertrophic cardiomyopathy, valvular insufficiency/stenosis, and coronary artery stenosis due to intimal proliferation. Cardiac dysfunction is one of the most common causes of death in patients with mucopolysaccharidosis type I (MPS I). Enzyme replacement therapy (ERT) with laronidase has shown clear effects in reduction of hepatomegaly and it has been unclear whether ERT could improve or prevent the cardiac lesions. Postmortem findings in a 3 1/2‐year‐old boy diagnosed with MPS I at age 2 years are described. He received ERT with laronidase at 100 U/kg/week for one year. He suddenly developed cardiorespiratory failure and died the next day after C2–3 spinal surgery for instability. Postmortem examination showed hypertrophic cardiomyopathy, severe aortic valve and mitral valve thickening with shortened chordae, and endocardial fibroelastosis. Histology of the cardiac tissue revealed increased perivascular and interstitial connective tissue in the myocardium and intimal thickening causing stenosis in the cardiac vessels. Electron‐microscopic (EM) studies of the thickened endocardium revealed numerous histiocytes with enlarged lysosomes. EM examination of the liver and the cardiac muscle revealed no accumulation of GAGs. ERT with laronidase showed clear effects in removing GAGs from the liver and the cardiac muscle. However, it did not show a clear effect on the thickened endocardium, myocardial perivascular and interstitial connective tissue or intimal thickening in the epicardial vessels.