bluuebunny/crossref_metadata_2025 huggingface dataset:
Mass spectrometry‐based proteomics: The road to lung cancer biomarker discovery
Authors: Indovina Paola , Marcelli Eleonora , Pentimalli Francesca , Tanganelli Piero , Tarro Giulio , Giordano Antonio
Published: July 2012

Lung cancer is the leading cause of cancer death in men and women in Western nations, and is among the deadliest cancers with a 5‐year survival rate of 15%. The high mortality caused by lung cancer is attributable to a late‐stage diagnosis and the lack of effective treatments. So, it is crucial to identify new biomarkers that could function not only to detect lung cancer at an early stage but also to shed light on the molecular mechanisms that underlie cancer development and serve as the basis for the development of novel therapeutic strategies. Considering that DNA‐based biomarkers for lung cancer showed inadequate sensitivity, specificity, and reproducibility, proteomics could represent a better tool for the identification of useful biomarkers and therapeutic targets for this cancer type. Among the proteomics technologies, the most powerful tool is mass spectrometry. In this review, we describe studies that use mass spectrometry‐based proteomics technologies to analyze tumor proteins and peptides, which might represent new diagnostic, prognostic, and predictive markers for lung cancer. We focus in particular on those findings that hold promise to impact significantly on the clinical management of this disease. © 2012 Wiley Periodicals, Inc., Mass Spec Rev 32:129–142, 2013
Per‐subject characterization of bolus width in pulsed arterial spin labeling using bolus turbo sampling
Authors: Villien M. , Chipon E. , Troprès I. , Bouvier J. , Cantin S. , Chechin D. , Le Bas J.‐F. , Krainik A. , Warnking J. M.
Published: July 2012

Quantification of cerebral blood flow using QUIPSSII pulsed arterial spin labeling requires that the QUIPSS saturation delay TI1 is shorter than the natural temporal bolus width. Yet the duration of the bolus of tagged spins entering the region of interest varies during vasoactive stimuli such as gaseous challenges or across subjects due to differences in blood velocity or vessel geometry. A new technique, bolus turbo sampling, to rapidly measure the duration of the inflowing bolus is presented. It allows to optimize the arterial spin labeling acquisition to ensure reliable quantification of perfusion while maximizing the arterial spin labeling signal by avoiding the use of unnecessarily short label durations. The average bolus width measured in the right and left middle cerebral artery territories using the bolus turbo sampling technique has a repeatability coefficient of 75 ms and correlates significantly with the TI1,max determined from a novel multi‐TI1 protocol (R = 0.65, P < 0.05). The possibility to measure the bolus width under hypercapnia is demonstrated. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Progression of experimental lesions of atherosclerosis: Assessment by kinetic modeling of black‐blood dynamic contrast‐enhanced MRI
Authors: Chen Huijun , Ricks Jerry , Rosenfeld Michael , Kerwin William S.
Published: July 2012

Pharmacokinetic modeling of dynamic contrast‐enhanced (DCE) magnetic resonance imaging (MRI) is used to noninvasively characterize neovasculature and inflammation in atherosclerotic vessels by estimating perfusion characteristics, such as fractional plasma volume vp and transfer constant Ktrans. DCE‐MRI has potential to study the evolution of nascent lesions involving early pathological changes. However, currently used bright‐blood DCE‐MRI approaches are difficult to apply to small lesions because of the difficulty in separating the signal in the thin vessel wall from the adjacent lumen. By suppressing the lumen signal, black‐blood DCE‐MRI techniques potentially provide a better tool for early atherosclerotic lesion assessment. However, whether black‐blood DCE‐MRI can detect temporal changes in physiological kinetic parameters has not been investigated for atherosclerosis. This study of balloon‐injured New Zealand White rabbits used a reference‐region‐based pharmacokinetic model of black‐blood DCE‐MRI to evaluate temporal changes in early experimental atherosclerotic lesions of the abdominal aorta. Six rabbits were imaged at 3 and 6 months after injury. Ktrans was found to increase from 0.10 ± 0.03 min−1 to 0.14 ± 0.05 min−1 (P = 0.01). In histological analysis of all twelve rabbits, Ktrans showed a significant correlation with macrophage content (R = 0.70, P =0.01). These results suggest black‐blood DCE‐MRI and a reference‐region kinetic model could be used to study plaque development and therapeutic response in vivo. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
In vivo MRI of fresh stored osteochondral allograft transplantation with delayed gadolinium‐enhanced MRI of cartilage: Protocol considerations and recommendations
Authors: Durkan Michael G. , Szumowski Jerzy , Brown Dawson S. , Foss Erik W. , Crawford Dennis C.
Published: July 2012

The protocol for delayed gadolinium‐enhanced MRI of cartilage (dGEMRIC) was adapted for the evaluation of transplanted osteochondral allograft cartilage. Eight patients with focal grade 4 cartilage defects of the femoral condyle were treated with single cylindrical osteochondral allografts. At 1 and 2 years, dGEMRIC image sequences were acquired and regions of interest (ROIs) were drawn in repair and native control cartilage. Mean T1 values of region of interest were used to calculate established dGEMRIC metrics. The correlation was measured between the ΔR1 and R1‐Post metrics for repair and native cartilage. T1 times were measured in deep and superficial zones of cartilage. A strong correlation was identified between full‐thickness, deep, and superficial ΔR1 and R1‐Post values for native cartilage and repair cartilage for all years (range: 0.893–1.0). The mean T1 times and ΔR1 rate between deep and superficial regions of articular cartilage were statistically different for all regions of the distal femora analyzed at 1 year and 2 years after osteochondral allograft transplantation (P < 0.05). The dGEMRIC pre‐Gadolinium scan is unnecessary when evaluating transplanted osteochondral allograft cartilage. The observation of stratified T1 and ΔR1 values indicates a need to re‐evaluate the methodology behind the placement of region of interest in dGEMRIC. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Fatigue in Ankylosing Spondylitis: Causes, Consequences and Self‐Management
Authors: Farren Wendy , Goodacre Lynne , Stigant Mark
Published: July 2012

Objectives

To explore the perceived causes, consequences and management of fatigue in ankylosing spondylitis (AS).

Methods

In this single‐cohort qualitative study, ten participants completed a seven‐day diary and participated in a semi‐structured interview exploring possible causes, consequences and self‐management of fatigue. Interviews were recorded, transcribed and analysed using ‘framework’ analysis. Ethical approval was obtained.

Results

Three themes emerged: patterns and causes, consequences and management of fatigue. While patients’ descriptions of fatigue were similar, the patterns and perceived causes of fatigue varied between individuals. Fatigue impacted on social life, relationships and work. Two approaches to fatigue management were observed: help and support from others and self‐management, with four participants having sought medical help for fatigue.

Conclusions

The study suggested that fatigue has a negative impact on quality of life in people with AS. Future practice should include a comprehensive fatigue assessment and the development of treatment programmes directed at enhancing self‐management techniques. Copyright © 2012 John Wiley & Sons, Ltd.
Chloride transfer in cement‐based materials. Part 1. Theoretical basis and modelling
Authors: Bourbatache K. , Millet O. , Aït‐Mokhtar A. , Amiri O.
Published: July 2012

In this first part of the work, we develop macroscopic models for migration and diffusion–migration of ionic species in saturated porous media, based on periodic homogenization. The prior application is chloride transport in cementitious materials. The dimensional analysis of Nernst–Planck equation lets appear to dimensionless numbers characterizing the ionic transfer in the porous medium. Using experimental data obtained from electrodiffusion tests on cement‐based materials (Part II), these dimensionless numbers are linked to the perturbation parameter ϵ. For a strong imposed electrical field, the asymptotic expansion of Nernst–Planck equation leads to a macroscopic model where the migration is predominant. For a weak imposed electrical field or in natural diffusion, we obtain a macroscopic model coupling diffusion and migration at the same order. In both models, the expression of the homogenized diffusion tensor is identical and only involves the geometric properties of the material microstructure. Copyright © 2012 John Wiley & Sons, Ltd.
Averaging frameworks for simulation optimization with applications to simulated annealing
Authors: Prudius Andrei A. , Andradóttir Sigrún
Published: July 2012

We present two frameworks for designing random search methods for discrete simulation optimization. One of our frameworks is very broad (in that it includes many random search methods), whereas the other one considers a special class of random search methods called point‐based methods, that move iteratively between points within the feasible region. Our frameworks involve averaging, in that all decisions that require estimates of the objective function values at various feasible solutions are based on the averages of all observations collected at these solutions so far. Also, the methods are adaptive in that they can use information gathered in previous iterations to decide how simulation effort is expended in the current iteration. We show that the methods within our frameworks are almost surely globally convergent under mild conditions. Thus, the generality of our frameworks and associated convergence guarantees makes the frameworks useful to algorithm developers wishing to design efficient and rigorous procedures for simulation optimization. We also present two variants of the simulated annealing (SA) algorithm and provide their convergence analysis as example application of our point‐based framework. Finally, we provide numerical results that demonstrate the empirical effectiveness of averaging and adaptivity in the context of SA. © 2012 Wiley Periodicals, Inc. Naval Research Logistics, 2012
Optimal inventory control policy for periodic‐review inventory systems with inventory‐level‐dependent demand
Authors: Chen Youhua (Frank) , Lu Ye , Xu Minghui
Published: July 2012

We consider a setting in which inventory plays both promotional and service roles; that is, higher inventories not only improve service levels but also stimulate demand by serving as a promotional tool (e.g., as the result of advertising effect by the enhanced product visibility). Specifically, we study the periodic‐review inventory systems in which the demand in each period is uncertain but increases with the inventory level. We investigate the multiperiod model with normal and expediting orders in each period, that is, any shortage will be met through emergency replenishment. Such a model takes the lost sales model as a special case. For the cases without and with fixed order costs, the optimal inventory replenishment policy is shown to be of the base‐stock type and of the (s,S) type, respectively. © 2012 Wiley Periodicals, Inc. Naval Research Logistics, 2012
Two improvements in formulation of nine‐node element MITC9
Authors: Wisniewski K. , Panasz P.
Published: July 2012

The paper concerns a well‐known two‐dimensional nine‐node quadrilateral element MITC9, which is based on two‐level approximations of strains (assumed strain method). The element has good accuracy, but does not pass the patch test.

As the first improvement, we propose a modification of the element's transformations, partly resolving the problem with the patch test. The source of the problem is the use of covariant components in a (local) natural co‐basis, different at each sampling point.

As the second improvement, we use the corrected shape functions of Celia MA, Gray WG. An improved isoparametric transformation for finite element analysis. International Journal for Numerical Methods in Engineering 1984; 20:1447–1459, extending their applicability to the nine‐node element for plane elasticity and the 3 × 3 integration. Originally, they are tested for an eight‐node element for the heat conduction equation and the 4 × 4 integration.

The improved element, designated as MITC9i, is based on the Green strain and derived from the potential energy for the plane stress condition. It is subjected to a range of tests, to confirm that it passes the patch test for several types of mesh distortions, to prove its coarse mesh accuracy and the absence of locking as well as to establish its sensitivity to mesh distortions.

The improved element MITC9i performs substantially better than the MITC9 element, QUAD9** element, and our previous 9‐AS element.Copyright © 2012 John Wiley & Sons, Ltd.
Fetal evaluation of the modified‐myocardial performance index in pregnancies complicated by diabetes
Authors: Figueroa Horacio , Silva Maria Carolna , Kottmann Cristian , Viguera Sebastian , Valenzuela Ignacio , Hernandez‐Andrade Edgar , Gratacos Eduard , Arraztoa Jose Antonio , Illanes Sebastián E.
Published: July 2012

Objective

To evaluate the fetal cardiac function by modified myocardial performance index (Mod‐MPI) in pregnant diabetic patients.

Methods

Modified myocardial performance index was measured in fetuses of patients with diabetes (DM) between 30 and 40 weeks of gestation. The isovolumetric contraction time, isovolumetric relaxation time and ejection time were measured. Mod‐MPI was calculated as (isovolumetric contraction time + isovolumetric relaxation time)/ejection time. Results were analyzed by using one‐way analysis of variance (post hoc Bonferroni correction), Chi‐square and Student's test.

Results

Modified myocardial performance index values of fetuses from DM mothers were significantly higher than controls (0.43 vs 0.37, P < 0.0001), and it was not different between gestational versus pregestational DM (0.42 vs 0.45, P = 0.18). Mod‐MPI was also higher in the presence of polyhydramnios (0.49 vs 0.41, P < 0.0001), insulin use (0.46 vs 0.40, P < 0.05), and large for gestational age fetuses (0.49 vs 0.40, P < 0.0001). There were no significant differences in Mod‐MPI between newborns with versus without neonatal complications such as hypoglycemia or polycythemia.

Conclusions

In fetuses of DM mothers, evaluation of the Mod‐MPI identifies those with worse maternal disease and large fetal size. © 2012 John Wiley & Sons, Ltd.
Project Management Training Curricula at South African Public Universities: Is the Balanced Demand of the Profession Sufficiently Accommodated?
Authors: Louw Thelma , Rwelamila P. D.
Published: July 2012

In March 2004, the British Engineering and Physical Sciences Research Council (EPSRC) commissioned a study that focused on the “rethinking” of project management. The objective of the EPSRC study, commonly known as the EPSRC Network, was first to create a multidisciplinary network of academics, researchers, and practitioners interested in developing project management and the practice thereof in industry and, second, to define and identify a new interdisciplinary research agenda that would allow the field of project management to develop beyond the conceptual foundations that existed at the time—a conceptual base that attracted criticism for its lack of relevance to practice. The core philosophy behind the network was to link theory and practice through an organized process of interaction between academics and practitioners. Research was conducted to determine the extent to which South African universities have extended or adapted their project management curricula to accommodate the issues identified in the findings of the EPSRC study and other relevant research, as it is the norm for South African universities to review their curricula every 3 to 5 years. A way forward is mapped out to ensure that the training of project managers in South Africa sufficiently accommodates the balanced demand of the profession.
Governance of Public Investment Projects in Ethiopia
Authors: Shiferaw Asmamaw Tadege , Klakegg Ole Jonny , Haavaldsen Tore
Published: July 2012

The purpose of this article is to map and review the governance of public investment projects in Ethiopia and to identify the most important front-end challenges of public investment projects in the country. The research focuses on the front-end governance of major construction projects. The findings of the research indicate that the top-down project approach, lack of mandatory control gateways at the front-end project preparation and decision-making stages, and weak links between project stakeholders affected the effectiveness of the project governance system. In additon to this, the most important factors that could affect the relevance and sustainability of public investment projects are identified.
Interaction of Argon, Hydrogen and Oxygen Plasma Early Afterglow with Polyvinyl Chloride (PVC) Materials
Authors: Kregar Zlatko , Bišćan Marijan , Milošević Slobodan , Mozetič Miran , Vesel Alenka
Published: July 2012

Samples of PVC foils are exposed to an early afterglow of gaseous plasma created by an electrode‐less RF discharge in predominant H‐mode using Ar, H2 and O2 gases. Sample temperature is measured with a pyrometer while the presence of reaction products is determined with an optical spectrometer. The temporal evolution of major radiative species is measured. The results show that the samples are rather immune to the Ar afterglow. H2 afterglow causes substantial heating of the sample due to heterogeneous surface recombination of H‐atoms, while O2 plasma treatment results in etching of the material which is substantial already at room temperature. The specific behaviour of reactive species is explained by taking into account spectrometer calibration curves, excitation energies and radiative species lifetimes.

magnified image
Measurement and Analysis of the Burning Rate of HAN‐Based Liquid Propellants
Authors: Pan Yu‐Zhu , Yu Yong‐Gang , Zhou Yan‐Huang , Lu Xin
Published: July 2012

A new device for measuring the linear burning rate of liquid propellants at high pressures is reported. High‐pressure environments were generated by the combustion of solid propellants. The coated propellants, which burn progressively, were introduced to maintain the approximate constant‐pressure environments. By use of ion probe transducers, measurements were made of the spread velocity of the flame surface, i.e. the apparent linear burning rate of the HAN‐based liquid propellant LP1846 (HAN =hydroxylammonium nitrate) was measured quantitatively at pressures from 6 to 28  MPa. The results show that it follows the exponential burning rate law. The burning rate coefficient and exponent were fitted by least‐squares methods. Based on the experiment, a simplified model of the linear burning rate of HAN‐based liquid propellants at high pressures was developed. The numerical simulation is found to be in good agreement with the experimental data.
Light induced degradation in B doped Cz‐Si solar cells
Authors: Carvalho Alexandra , Santos Paulo , Coutinho José , Jones Robert , Rayson Mark J. , Briddon Patrick R.
Published: July 2012

We analyse the formation energy of interstitial boron (Bi) and the properties of the defect resulting from its association with an oxygen dimer (BiO2i) to evaluate the possibility that it may be the slow‐forming centre responsible for the light‐induced degradation of B‐doped Si solar cells. However, we find that the formation energy of Bi is too high, and therefore its concentration is negligible. Moreover, we find that the lowest energy form of BiO2i is a shallow donor, and the deep donor form is high in energy.

magnified image

Lowest energy structure of the BiO2i defect.
In situ fabrication of freestanding single‐walled carbon nanotube rope interconnection
Authors: Kim Taewoo , Kang Tae June , Seo Dong Kyun , Jang Eui Yun , Jin Kyoung Cheol , Choi Ajeong , Kim Dae‐Weon , Park Yung Woo , Jeong Dae Hong , Kim Yong Hyup
Published: July 2012

A single‐walled carbon nanotube rope interconnect is fabricated by utilizing dielectrophoresis and capillary condensation. The rope connects a pair of prefabricated cantilevers with good alignment and outstanding packing density. The diameter and resistance of the rope are readily controlled by adjusting the dielectrophoresis parameters such as applied voltage and frequency. The properties of the rope, including packing density, electron transport, and maximum current density, are investigated. The maximum current density of the rope is measured to be as high as 1 × 107 A/cm2 in vacuum.

magnified image
In Vitro and In Vivo Inhibitory Activities of Four Indian Medicinal Plant Extracts and their Major Components on Rat Aldose Reductase and Generation of Advanced Glycation Endproducts
Authors: Rao Ajmeera Rama , Veeresham Ciddi , Asres Kaleab
Published: July 2012

The polyol enzyme aldose reductase (AR) and advanced glycation endproducts (AGEs) play an important role in diabetic complications such as cataracts. The purpose of this study was to investigate four standardized plant extracts used for the treatment of diabetes and related diseases, and their principal components for AR inhibitory activity and to find out their influence in diabetic complications. Thus, Boswellia serrata Triana & Planch. (Burseraceae), Lagerstroemia speciosa (L.) Pers. (Lythraceae), Ocimum gratissimum (L.) (Lamiaceae) and Syzygium cumin (L.) Skeels. (Myrthaceae) and their respective major constituents, boswellic acid, corosolic acid, ursolic acid and ellagic acid, were studied for their inhibitory activity against rat lens AR, rat kidney AR, human recombinant AR and generation of AGEs. In addition, in vivo inhibition of lens galactitol accumulation by the major constituents of the plants in galactose‐fed rat has been studied. The results revealed that all the tested extracts and their active ingredients possess significant AR inhibitory actions in both in vitro and in vivo assays with urosolic acid showing the most potent effect. Furthermore, the study indicates the potential of the studied plants and their major constituents as possible protective agents against long‐term diabetic complications. Copyright © 2012 John Wiley & Sons, Ltd.
Electronuclear multiconfiguration time‐dependent hartree calculations on the confined H atom with mobile electron and nucleus
Authors: Skouteris Dimitrios , Laganà Antonio
Published: July 2012

A multiconfiguration time‐dependent Hartree method oriented toward calculations of a non‐Born‐Oppenheimer nature has been applied to the calculation of the dynamical properties of a confined H atom. The calculation is fully six‐dimensional and does not take into account constraints arising from linear or angular momentum conservation. The orbital evolution is monitored and the energy level spectrum of the system, as well as the dependence of the results on the decomposition of the Hamiltonian and on the correlation between radial degrees of freedom, is determined. © 2012 Wiley Periodicals, Inc.
Theoretical analysis of correlation between ionization threshold fluence in IR‐MALDI and IR absorption spectrum of matrix molecules
Authors: Hatakeyama Makoto , Mashiko Takako , Hazama Hisanao , Awazu Kunio , Tachikawa Masanori
Published: July 2012

To investigate the correlation between the wavelength dependence of ionization threshold fluence of target molecule in matrix‐assisted laser desorption/ionization by infrared (IR) laser and the IR absorption spectrum of matrix molecule, we have analyzed the IR absorption spectra of four matrix molecules using density functional theory and correlated ab initio molecular orbital method. The calculated IR absorption spectra of the isolated molecules showed more qualitative correlation with the wavelength dependence of ionization threshold fluence than those of the solid state structures. We can consider that a portion of matrix molecules lost the ordered crystal structure and that the transition to the diluted or isolated state occurred at the early process of IR laser irradiation. © 2012 Wiley Periodicals, Inc.
A TD‐DFT basis set and density functional assessment for the calculation of electronic excitation energies of fluorene
Authors: Barboza Cristina Aparecida , Vazquez Pedro Antonio Muniz , Mac‐Leod Carey Desmond , Arratia‐Perez Ramiro
Published: July 2012

Conjugated organic materials are the subject of intensive research for a range of optoelectronic applications. A model for such molecules is fluorene, which consists of rigid planar biphenyl units of C2v symmetry. A low energy experimental absorption spectrum in the gas phase is composed of A1 and B2 transitions. The aim of this work is to evaluate the performance of the basis sets cc‐pVXZ (X = D and T), aug‐cc‐pVDZ, 6‐31G**, 6‐31++G**, 6‐311G**, 6‐311++G**, Sadlej‐pVTZ, Z2Pol, Z3Pol, and pSBKJC and of the functionals B3LYP, B3LYP/CS00, CAM‐B3LYP, PBE0, and LB94 in predicting the electronic transitions obtained taking linear response‐coupled cluster singles and doubles (LR‐CCSD) results as the theoretical reference. Our findings suggest that the time‐dependent density functional theory singles method is not able to correctly assign the predicted spectrum while LR‐CCSD always correctly describes the experimental data. Among the studied density functionals, the best performance was achieved by the CAMB3LYP. For transitions above 5 eV, diffuse functions are required to properly predict the observed transitions. © 2012 Wiley Periodicals, Inc.
Nonlinear model predictive control from data: a set membership approach
Authors: Canale M. , Fagiano L. , Signorile M.C.
Published: July 2012

A new approach to design a Nonlinear Model Predictive Control law that employs an approximate model, derived directly from data, is introduced. The main advantage of using such models lies in the possibility to obtain a finite computable bound on the worst‐case model error. Such a bound can be exploited to analyze the robust convergence of the system trajectories to a neighborhood of the origin. The effectiveness of the proposed approach, named Set Membership Predictive Control, is shown in a vehicle lateral stability control problem, through numerical simulations of harsh maneuvers. Copyright © 2012 John Wiley & Sons, Ltd.
A robust discrete‐time adaptive control approach for systems with almost periodic time‐varying parameters
Authors: Abidi Khalid
Published: July 2012

A periodic adaptive control approach is proposed for a class of nonlinear discrete‐time systems with time‐varying parametric uncertainties which are almost periodic, and the only prior knowledge is the periodicity. The new adaptive controller updates the parameters and the control signal periodically in a pointwise manner over one entire period, in the sequel that achieves a bounded tracking convergence. The result is further extended to scenarios with unknown input gain, higher order dynamics, and tracking. Copyright © 2012 John Wiley & Sons, Ltd.
Misconceptions about “misconceptions”: Preservice secondary science teachers' views on the value and role of student ideas
Authors: Larkin Douglas
Published: July 2012

There remains a lack of agreement in the field of science education as to whether student “misconceptions” ought to be considered obstacles or resources, and this has implications for the ways in which prospective teachers think about the value of their students' ideas. This empirical study examines how 14 preservice secondary science teachers in four different science teacher preparation programs interpreted the rationale for eliciting student ideas. The findings indicate that the preservice teachers in this study showed an increase in recognizing the importance of student ideas, yet not all took the same view of their role and value in teaching, which appeared to be closely connected to beliefs about how learning takes place. Five different orientations to student ideas are described in the findings. These include viewing student ideas as evidence of content coverage, as obstacles to understanding, as tools to prime students thinking, interest, and activity, as elements of a positive classroom environment, and as the raw material of learning. The findings suggest that science teacher educators help focus preservice teachers' attention on student thinking and help them learn to incorporate their students' ideas into their instruction in ways that build upon those ideas. © 2012 Wiley Periodicals, Inc. Sci Ed 96:927–959, 2012
A transition model for quality‐of‐life data with non‐ignorable non‐monotone missing data
Authors: Liao Kaijun , Freres Derek R. , Troxel Andrea B.
Published: July 2012

In this paper, we consider a full likelihood method to analyze continuous longitudinal responses with non‐ignorable non‐monotone missing data. We consider a transition probability model for the missingness mechanism. A first‐order Markov dependence structure is assumed for both the missingness mechanism and observed data. This process fits the natural data structure in the longitudinal framework. Our main interest is in estimating the parameters of the marginal model and evaluating the missing‐at‐random assumption in the Effects of Public Information Study, a cancer‐related study recently conducted at the University of Pennsylvania. We also present a simulation study to assess the performance of the model. Copyright © 2012 John Wiley & Sons, Ltd.
Point source modeling of matched case–control data with multiple disease subtypes
Authors: Li Shi , Mukherjee Bhramar , Batterman Stuart
Published: July 2012

In this paper, we propose nonlinear distance‐odds models investigating elevated odds around point sources of exposure, under a matched case‐control design where there are subtypes within cases. We consider models analogous to the polychotomous logit models and adjacent‐category logit models for categorical outcomes and extend them to the nonlinear distance‐odds context. We consider multiple point sources as well as covariate adjustments. We evaluate maximum likelihood, profile likelihood, iteratively reweighted least squares, and a hierarchical Bayesian approach using Markov chain Monte Carlo techniques under these distance‐odds models. We compare these methods using an extensive simulation study and show that with multiple parameters and a nonlinear model, Bayesian methods have advantages in terms of estimation stability, precision, and interpretation. We illustrate the methods by analyzing Medicaid claims data corresponding to the pediatric asthma population in Detroit, Michigan, from 2004 to 2006. Copyright © 2012 John Wiley & Sons, Ltd.
Analysis of multi‐stage treatments for recurrent diseases
Authors: Huang Xuelin , Ning Jing
Published: July 2012

Patients with a non‐curable disease such as many types of cancer usually go through the process of initial treatment, a various number of disease recurrences and salvage treatments, and eventually death. The analysis of the effects of initial and salvage treatments on overall survival is not trivial. One may try to use disease recurrences and salvage treatments as time‐dependent covariates in a Cox proportional hazards model. However, because disease recurrence is an intermediate outcome between initial treatment and final survival, the interpretation of such an estimation result is awkward. It does not estimate the causal effects of treatments on overall survival. Nevertheless, such causal effect estimates are critical for treatment decision making. Our approach to address this issue is that, at any treatment stage, for each patient, we compute a potential survival time if he or she would receive the optimal subsequent treatments, and use this potential survival time to do comparison between current‐stage treatment groups. This potential survival time is assumed to follow an accelerated failure time model at each treatment stage and calculated by backward induction, starting from the last stage of treatment. By doing that, the effects on survival of different treatments at each stage can be consistently estimated and fairly compared. Under suitable conditions, these estimated effects have a causal interpretation. We evaluated the proposed model and estimation method by simulation studies and illustrated using the motivating, real data set that describes initial and salvage treatments for patients with soft tissue sarcoma. Copyright © 2012 John Wiley & Sons, Ltd.
Integrated program verification tools in education
Authors: de Caso Guido , Garbervetsky Diego , Gorín Daniel
Published: July 2012

Automated software verification is an active field of research, which has made enormous progress both in theoretical and practical aspects. Even if not ready for large‐scale industrial adoption, the technology behind automated program verifiers is now mature enough to gracefully handle the kind of programs that arise in introductory programming courses. This opens exciting new opportunities in teaching the basics of reasoning about program correctness to novice students. However, for these tools to be effective, command‐line‐style user‐interfaces need to be replaced. In this paper, we report on our experience using the verifying compiler for PEST in an introductory programming course as well as in a more advanced course on program analysis. PEST is an extremely basic programming language, but with expressive annotations capabilities and semantics amenable to verification. In particular, we comment on the crucial role played by the integration of this verifying compiler with the Eclipse integrated development environment. Copyright © 2012 John Wiley & Sons, Ltd.
DNA‐based plasmonic nanoarchitectures: from structural design to emerging applications
Authors: Chen Yi , Cheng Wenlong
Published: July 2012

Plasmonic nanoarchitectures refer to the well‐defined groupings of elementary metallic nanoparticle building blocks. Such nanostructures have a plethora of technical applications in diagnostics, energy‐harvesting, and nanophotonic circuits, to name a few. Nevertheless, it remains challenging to construct plasmonic nanoarchitectures at will inexpensively. Bottom‐up self‐assembly is promising to overcome these limitations, but such methods often produce defects and low‐yields. For these purposes, DNA has emerged as a powerful nanomaterial beyond its genetic function in biology to either program or template synthesis of plasmonic nanostructures, or act as a ligand to mediate large‐area self‐assembly. In conjunction with top‐down lithography, DNA‐based strategies can afford excellent control over internal and overall structures of plasmonic nanoarchitectures. In this review, we outline the representative methodologies for building various well‐defined plasmonic nanoarchitectures and cover their recent exciting applications. WIREs Nanomed Nanobiotechnol 2012, 4:587–604. doi: 10.1002/wnan.1184

This article is categorized under:

Diagnostic Tools > Diagnostic Nanodevices

Diagnostic Tools > In Vitro Nanoparticle-Based Sensing

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
A direct comparison of camera‐trapping and sign transects for monitoring wildlife in the Wanglang National Nature Reserve, China
Authors: Li Sheng , McShea William J. , Wang Dajun , Huang Junzhong , Shao Liangkun
Published: July 2012

Wildlife monitoring plays a critical role in evaluating the management and conservation of biodiversity. During monitoring activities in Chinese nature reserves dedicated to giant panda conservation, indirect sign surveys along fixed transects are the standard methodology used to monitor large‐mammal populations. Camera‐trapping has been recently introduced to these reserves as an additional monitoring tool. We present a case study of comparing current sign‐transect monitoring with camera‐trapping in Wanglang National Nature Reserve, China, from September 2004 through October 2005, and we assess the effectiveness of both methods in detecting terrestrial fauna. Camera‐trapping detected 21 mammal species, while sign transects detected 16 species. We found no significant difference in the animal community detected by each method; however, sign transects were weighted toward detecting large‐sized animals. Each survey technique had different strengths; therefore, a combined sampling of camera‐trapping (800 camera‐days) and sign transects (80 km) was sufficient to detect 95% of detectable large, terrestrial mammal species within this 323‐km2 reserve. Our estimate of species richness based on camera‐trapping (39.0 ± 13.6 species) and sign transects (20.0 ± 4.4 species) suggests that camera‐trapping can detect more species when extensive sampling effort is employed by both methods. Camera‐trapping also has the potential for more robust estimates of population parameters than are possible with sign transects. We propose that the giant panda reserves in China can increase their efficiency and range of species monitored by using a system that integrates camera‐trapping with sign transects. © 2012 The Wildlife Society.
The prevailing paradigm as a hindrance to conservation
Authors: Morrison Michael L. , Collier Bret A. , Mathewson Heather A. , Groce Julie E. , Wilkins R. Neal
Published: July 2012

We review the history of population and ecological knowledge of the golden‐cheeked warbler (Setophaga chrysoparia). We highlight how incomplete information on distribution and abundance has led to substantial misunderstanding on species status and associated conservation goals. We discuss how once a paradigm is established, subsequent studies unconsciously fortify accepted understanding regardless of the paradigm's accuracy. For the golden‐cheeked warbler, understanding of the species at the time of listing in 1990 was based on either incorrect or untested assumptions of species distribution within available habitats. Adhering to untested assumptions led to development of priorities for research and management that were well‐intentioned but largely misguided. Ample information on the distribution of the warbler's habitats existed, however, which should have encouraged questions into the basis of population conditions when developing management prescriptions. Current knowledge clearly indicates that a new paradigm for the warbler is needed, that being one of a widely distributed species that is preadapted to occur within a variety of environmental conditions. © 2012 The Wildlife Society.
The contribution of medium-modified color flow to jet quenching
Authors: Beraudo Andrea , Milhano José Guilherme , Wiedemann Urs Achim
Published: July 2012

Abstract

Multiple interactions between parton showers and the surrounding QCD matter are expected to underlie the strong medium-modifications of jet observables in ultra- relativistic heavy ion collisions at RHIC and at the LHC. Here, we note that such jet- medium interactions alter generically and characteristically the color correlations in the parton shower. We characterize these effects in a color-differential calculation of the medium-induced gluon radiation spectrum to first and second order in opacity. By interfacing simple branching histories of medium-modified color flow with the Lund hadronization model, we analyze how the medium modification of color correlations can affect the distribution of hadronic fragments in jets. Importantly, we observe that jet-medium interactions give rise to the medium-induced color decoherence of gluons from the parton shower. Since hadronization respects color flow and since each color singlet in a parton shower is hadronized separately, this medium-induced color decoherence leaves characteristic signatures in the jet fragmentation pattern. In particular, it can contribute to the quenching of leading hadron spectra. Moreover, it can increase strongly the yield of soft hadronic fragments from a jet, while the distribution of more energetic hadrons follows naturally the shape of a vacuum-like fragmentation pattern of lower total energy.
Enigmatic adult overwintering in damselflies: coexistence as weaker intraguild competitors due to niche separation in time
Authors: Harabiš Filip , Dolný Aleš , Šipoš Jan
Published: July 2012

Odonata, like most freshwater invertebrates, tend to overwinter in water due to the thermal properties of a water environment. Winter damselflies (genus Sympecma), however, hibernate as adults in terrestrial habitats. The strategy of adult overwintering combined with high mortality is associated with several unique adaptations to semiarid conditions, but winter damselflies maintain this unique life history throughout almost the entire Palaearctic. We assume that the unique strategy of adult overwintering in temperate zones is indirectly maintained by niche separation in time. We used phenological data from the Czech Republic to compare the seasonal phenology of Sympecma spp. with other coexisting odonate species. Seasonal population growth patterns between S. fusca and other coexisting species representing different life histories were compared using GLMMs and LME. The models showed negative non‐linear dependence between the population growth of S. fusca and the estimated abundance of compared species. We found that the specific strategy of adult overwintering makes it possible to avoid seasonal maxima of competition and predation in adult and larval stages. Adults may benefit from free niches during spring while larvae may benefit from size advantage among intraguild competitors and optimal conditions for development.
Are Genetic Counselors and the Social Service System for People with Intellectual Disability Reaching Rapprochement?
Authors: Simon Elliott W.
Published: July 2012

Recent advances in syndromic identification have resulted in genetic counselors providing services to increasing numbers of people with intellectual disability (ID) and their families. However, from the standpoint of professionals who support people with ID, genetic counselors are on the periphery of the extensive ID social service system. Reasons for this, based on a review of historical circumstances, definitional differences funding and a divergence of approaches, are critically presented and discussed. A model is offered that would allow for a closer working relationship and an integrated team approach that includes genetic counselors.
On the analysis of traveling waves to a nonlinear flux limited reaction–diffusion equation
Authors: Campos Juan , Guerrero Pilar , Sánchez Óscar , Soler Juan
Published: July 2012

In this paper we study the existence and qualitative properties of traveling waves associated with a nonlinear flux limited partial differential equation coupled to a Fisher–Kolmogorov–Petrovskii–Piskunov type reaction term. We prove the existence and uniqueness of finite speed moving fronts of

C^{2}

classical regularity, but also the existence of discontinuous entropy traveling wave solutions.
Structural and functional characterization of the bacterial translocation inhibitor GE82832
Authors: Brandi Letizia , Maffioli Sonia , Donadio Stefano , Quaglia Fabio , Sette Marco , Milón Pohl , Gualerzi Claudio O. , Fabbretti Attilio
Published: July 2012

The structure of GE82832, a translocation inhibitor produced by a soil microorganism, is shown to be highly related to that of dityromycin, a bicyclodecadepsipeptide antibiotic discovered long ago whose characterization had never been pursued beyond its structural elucidation. GE82832 and dityromycin were shown to interfere with both aminoacyl‐tRNA and mRNA movement and with the Pi release occurring after ribosome‐ and EF‐G‐dependent GTP hydrolysis. These findings and the unusual ribosomal localization of GE82832/dityromycin near protein S13 suggest that the mechanism of inhibition entails an interference with the rotation of the 30S subunit “head” which accompanies the ribosome‐unlocking step of translocation.
Annexin A9 is a periplakin interacting partner in membrane‐targeted cytoskeletal linker protein complexes
Authors: Boczonadi Veronika , Määttä Arto
Published: July 2012

Annexin‐9
physically interacts with
Periplakin
by anti bait co‐immunoprecipitation (View interaction)
Periplakin
physically interacts with
Annexin‐9
by anti tag co‐immunoprecipitation (View Interaction: 1, 2)
Periplakin
and
Annexin‐9
colocalize by fluorescence microscopy (View Interaction: 1, 2, 3)
Keratin‐8
and
Periplakin
colocalize by fluorescence microscopy (View interaction)
Morbidity Pattern of the 27th Indian Scientific Expedition to Antarctica
Authors: Bhatia Abhijeet , Pal Ranabir
Published: July 2012

Objective

To evaluate morbidity prototype of 27th Indian Scientific Expedition to Antarctica (ISEA).

Methods

Twenty-six team members of 27th ISEA wintered over at the Indian Antarctic Station, Maitri, from February 2008 to January 2009. The morbidity pattern was sourced from the medical records. Preexisting illnesses were also considered in this analysis.

Results

The team consisted of men between 27 and 59 years of age (mean age, 43 years). Nine team members had preexisting illnesses. A total of 93 illness incidents were recorded during the stay in Antarctica. Most of these (27) were musculoskeletal injuries, bruises, and lacerations. Thirty-two (34%) incidents of illness were noted under the purview of medicine; 26 (28%), surgery; 15 (16%), orthopedics; 9 (10%), otorhinolaryngology; 8 (9%), ophthalmology; 2 (2%), dentistry; and 3 (3%), psychiatry. Oral ulcers were noted in 8 (8%) participants primarily during early wintering.

Conclusions

Injuries continue to be the most common cause of morbidity in Antarctica. Nutritional deficiencies and cold-related injuries are relatively less common.
Soft Tissue Foreign Body Removal Technique Using Portable Ultrasonography
Authors: Paziana Karolina , Fields J. Matthew , Rotte Masashi , Au Arthur , Ku Bon
Published: July 2012

Retained foreign objects account for as much as 2% of soft tissue injuries sustained in the wilderness. Subcutaneously embedded fragments are often missed during the initial medical evaluation and may result in morbidity secondary to delayed removal. Although the utility of ultrasonography in the emergency department for the detection of retained objects is established, the potential use of point-of-care ultrasound to aid with foreign body removal in the field has not been well described. We present 2 case reports that demonstrate the value of ultrasonography in detecting and successfully removing foreign bodies sustained in the wilderness, and outline a procedural technique that minimizes morbidity and uses equipment available in wilderness medical field kits. We propose that with the advent of portable and handheld ultrasound units, foreign body removal in the field has become feasible and may decrease the morbidity of soft tissue injuries, particularly in austere and wilderness environments with limited access to immediate medical care.
Paleowind velocity and paleocurrents of pluvial Lake Manly, Death Valley, USA
Authors: Knott Jeffrey R. , Fantozzi Joanna M. , Ferguson Kelly M. , Keller Summer E. , Nadimi Khadija , Rath Carolyn A. , Tarnowski Jennifer M. , Vitale Michelle L.
Published: July 2012

Pluvial lake deposits are found throughout western North America and are frequently used to reconstruct regional paleoclimate. In Death Valley, California, USA, we apply the beach particle technique (BPT) of Adams (2003), Sedimentology, 50, 565–577 and Adams (2004), Sedimentology, 51, 671–673 to Lake Manly deposits at the Beatty Junction Bar Complex (BJBC), Desolation Canyon, and Manly Terraces and calculate paleowind velocities of 14–27 m/s. These wind velocities are within the range of present-day wind velocities recorded in the surrounding area. Sedimentary structures and clast provenance at Desolation Canyon and the Manly Terraces indicate sediment transport from north to south. Lake level, based on the elevation of constructional features, indicates that the hill west of the BJBC was an island and that the BJBC spits formed during simple lake regression. The data are consistent with the hypothesis that the present wind regime (velocity and direction) formed the pluvial Lake Manly features.