bluuebunny/crossref_metadata_2025 huggingface dataset:
Screen‐printed Emitter‐Wrap‐Through solar cell with single step side selective emitter with 18.8% efficiency
Authors: Mingirulli N. , Stüwe D. , Specht J. , Fallisch A. , Biro D.
Published: August 2010

A fabrication process for Emitter‐Wrap‐Through solar cells on monocrystalline material with high quality gap passivation by wet thermal silicon dioxide is investigated. Masking and structuring steps are performed by screen‐printing technology. Via‐holes are created by an industrially applicable high‐speed laser drilling process. The cell structure features a selective emitter structure fabricated in a single high temperature step: a highly doped emitter at the via‐holes and the rear side, allowing for a low via‐hole resistivity as well as a low resistivity contact to screen‐printed pastes, and a moderately doped front side emitter exhibiting high quantum efficiency in the low wavelength range. Therefore a novel approach is applied depositing either doped or undoped PECVD silicon dioxide layers on the front side. It is shown that doping profiles advantageous for the EWT‐cell structure can be achieved. The screen‐printed aluminum paste is found to penetrate the underlying thermal dioxide layer at appropriate contact firing conditions leading to a zone of high recombination in the overlap region of aluminum and silicon dioxide. It is shown that conventional PECVD‐anti‐reflection silicon nitride acts as effective protection layer reducing the recombination in this region. Designated area conversion efficiencies up to 18.8% on FZ material are obtained applying the single step side selective emitter fabrication technique. Copyright © 2010 John Wiley & Sons, Ltd.
Numerical analysis of J–V characteristics of a polymer solar cell
Authors: Mitroi Mihai Razvan , Iancu Vladimir , Fara Laurentiu , Ciurea Magdalena Lidia
Published: August 2010

A numerical method to determine the cell parameters from the analysis of the J–V characteristics of a polymer solar cell is proposed. This method uses the equations given by the diode model, experimental data from the literature, and an adequate fitting procedure with seven fit parameters. Different aspects of the obtained results are discussed. Information concerning cell design optimization is also obtained. The method is of general application in the field of polymer solar cells, as well as to any kind of diode‐like cell. Copyright © 2010 John Wiley & Sons, Ltd.
Real‐time reliability test for a CPV module based on a power degradation model
Authors: González J.R. , Vázquez M. , Algora C. , Núñez N.
Published: August 2010

Models based on degradation are powerful and useful tools to evaluate the reliability of those devices in which failure happens because of degradation in the performance parameters. This paper presents a procedure for assessing the reliability of concentrator photovoltaic (CPV) modules operating outdoors in real‐time conditions. With this model, the main reliability functions are predicted. This model has been applied to a real case with a module composed of GaAs single‐junction solar cells and total internal reflection (TIR) optics. Copyright © 2010 John Wiley & Sons, Ltd.
Combined therapy versus usual care for the treatment of depression in oncologic patients: a randomized controlled trial
Authors: Rodríguez Vega B. , Palao A. , Torres G. , Hospital A. , Benito G. , Pérez E. , Dieguez M. , Castelo B. , Bayón C.
Published: August 2010

Objective: To compare narrative therapy (NT) plus escitalopram versus escitalopram plus usual care on quality of life and depressive symptomatology of depressed patients with oncologic disease.

Methods: A total of 72 subjects (mean age 54.6 years), predominantly female with non‐metastatic breast, lung and colon cancer and depressive disorder (DSM‐IV‐TR) were randomized to receive treatment with NT plus escitalopram (n=39) or escitalopram (10–20 mg QD) plus usual care (n=33). Main endpoints were improvement in dimensions of quality of life measured by the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire C‐30 and reduction of depressive symptoms using the Hospital Anxiety and Depression Scale at weeks 12 and 24.

Results: The combined therapy group showed significantly greater improvement in all the functioning dimensions (p<0.01), pain scale (p=0.02), global health (p=0.02), and global quality of life (p=0.007) at weeks 12 and 24. There were no statistically significant differences in depressive symptomatology between the groups. From week 12 to week 24 study retention was higher in the combined treatment group (p=0.01).

Conclusions: Brief NT in combination with escitalopram was superior to usual care and escitalopram in improving functioning dimensions of quality life. Copyright © 2010 John Wiley & Sons, Ltd.
Identification of patient‐reported distress by clinical nurse specialists in routine oncology practice: a multicentre UK study
Authors: Mitchell Alex J. , Hussain Nadia , Grainger Lorraine , Symonds Paul
Published: August 2010

Background: There is uncertainty regarding how well clinical nurse specialists are able to identify distress in cancer settings.

Methods: We examined recognition of patient‐reported distress by nurse specialists across three sites in the East Midlands (UK). Clinicians were asked to report on their clinical opinion regarding the presence of distress or any mental health complication after routine assessment of 401 mixed cancer patients. Patient‐reported distress was defined by the distress thermometer at a cut‐off of 4 or higher.

Results: We found that the prevalence of patient‐reported distress was 45.4%. The rates for mild, moderate and severe distress were: 23.4, 13.7 and 8.2, respectively. When looking for distress (or any mental health complication) nurse practitioners had a detection sensitivity of 50.5% and specificity 80.0%. Cohen's kappa suggested fair agreement between staff and patients. Examining predictors of distress, clinicians were better able to recognise higher severities of distress (adjusted R2=0.87 P=0.001). There was lower sensitivity in palliative stages but no differences according to the type of cancer. There was also higher sensitivity but lower specificity in those clinicians with high self‐rated confidence.

Conclusions: Nurses working in cancer settings have difficulty identifying distress using their routine clinical judgement and tend to make more false‐negative than false‐positive errors. Evidence‐based strategies that improve detection of mild and moderate distress are required in routine cancer care. Copyright © 2010 John Wiley & Sons, Ltd.
Can health beliefs help in explaining attendance to follow‐up care? The Swiss Childhood Cancer Survivor Study
Authors: Michel Gisela , Kuehni Claudia E. , Rebholz Cornelia E. , Zimmermann Karin , Eiser Christine , Rueegg Corina S. , von der Weid Nicolas X. ,   for the Swiss Paediatric Oncology Group (SPOG)
Published: August 2010

Objective: Improved treatment has increased the survival of childhood cancer patients in recent decades, but follow‐up care is recommended to detect and treat late effects. We investigated relationships between health beliefs and follow‐up attendance in adult childhood cancer survivors.

Methods: Childhood cancer survivors aged younger than 16 years when diagnosed between 1976 and 2003, who had survived for more than 5 years and were currently aged 20+ years, received a postal questionnaire. We asked survivors whether they attended follow‐up in the past year. Concepts from the Health Belief Model (perceived susceptibility and severity of future late effects, potential benefits and barriers to follow‐up, general health value and cues to action) were assessed. Medical information was extracted from the Swiss Childhood Cancer Registry.

Results: Of 1075 survivors (response rate 72.3%), 250 (23.3%) still attended regular follow‐up care. In unadjusted analyses, all health belief concepts were significantly associated with follow‐up (p<0.05). Adjusting for other health beliefs, demographic, and medical variables, only barriers (OR=0.59; 95%CI: 0.43–0.82) remained significant. Younger survivors, those with lower educational background, diagnosed at an older age, treated with chemotherapy, radiotherapy, or bone marrow transplantation and with a relapse were more likely to attend follow‐up care.

Conclusions: Our study showed that more survivors at high risk of cancer‐ and treatment‐related late effects attend follow‐up care in Switzerland. Patient‐perceived barriers hinder attendance even after accounting for medical variables. Information about the potential effectiveness and value of follow‐up needs to be available to increase the attendance among childhood cancer survivors. Copyright © 2010 John Wiley & Sons, Ltd.
Etiologies of spontaneous pneumomediastinum in children in middle Taiwan
Authors: Lee Chia‐Ying , Wu Chou‐Chieh , Lin Ching‐Yuang
Published: August 2010

Introduction

Spontaneous pneumomediastinum (SPM), while rare, is probably underestimated in children. Treatment targets on the underlying disease and trigger factors. The study aimed in analysis different etiology in different age groups.

Patients and Methods

Total 37 children with SPM were analyzed from two medical centers in middle Taiwan from 1994 to 2007.

Results

Incidence of SPM in children was 1:11,726 patients at Department of Pediatric Emergency in middle Taiwan. Bimodal peak in incidence occurred in those under 7 and in those aged 15–18 years old. The Characteristic symptoms were dyspnea (64.9%), followed by chest pain (62.2%) and neck pain (40.5%); common specific physical signs were subcutaneous emphysema (SCE) (67.6%) and Hammer's sign (13.5%). Trigger factors were infection (43.2%), asthma (21.0%), esophageal rupture (5.4%), foreign body aspiration (2.7%), and diabetic ketoacidosis (2.7%). Idiopathic SPM accounted for 35.1% of patients with mean age 14.1 years. In age distribution, preschoolers (<7 years old) got SPM mostly due to lower respiratory tract infection. In adolescents, the most common etiologies were asthma and upper respiratory tract infection. Mean hospitalization was 6.4 days. Although 17 (46.0%) patients needed intensive care, nearly all had complete resolution in chest radiography before discharge.

Conclusion

Clinician should keep alert to incidence of SPM from these symptoms. Etiologies varied with age and treatment must target on factors and underlying disease. Pediatr. Pulmonol. 2010; 45:869–873. © 2010 Wiley‐Liss, Inc.
Influence of heat treatment on the vacancy content at the B‐site in the ABO3 manganites La0.6Sr0.1MnO3−δ
Authors: Liu S. P. , Zhang Y. G. , Tang G. D. , Qi W. H. , Ji D. H. , Li Y. F. , Liu G. H. , Xie Y. , Chen W. , Hou D. L.
Published: August 2010

The effects of heat‐treatment temperature, THT, and heat‐treatment time, tHT, on the structural and magnetic properties of manganites with a nominal composition La0.6Sr0.1MnO3−δ, prepared by the sol–gel method, were investigated. The XRD spectra indicate that the samples have two phases with the $R\overline {3} c$ perovskite being the dominant phase and Mn3O4 being the second phase. It was found that the Curie temperature of the samples varies as THT and tHT are changed. Calculation of the ion content ratios at the A, B, and O sites in the ABO3 perovskite phase on the basis of the thermal equilibrium theory of crystal defects, and Rietveld fitting of X‐ray powder diffraction data lead us to believe that the origin of this variation is due to the fact that the vacancy content, z, at B‐sites in the ABO3 perovskite phase increases as THT and tHT increase. The calculations also show that the samples are double‐phase compositions of La0.6Sr0.1Mn1−yO1.5(1.7‐y+z)/(Mn3O4)y/3.
Robotic‐assisted minimally invasive surgery; a useful tool in resident training—the Peoria experience, 2002–2009
Authors: Huettner Franziska , Dynda Danuta , Ryan Michael , Doubet Jamie , Crawford David L.
Published: August 2010

Background

The purpose of this study was to review the use of robotic‐assisted general surgery at our institution. We evaluated the 8 year experience of one minimally invasive surgery (MIS) fellowship‐trained surgeon in Peoria, IL, performing 240 cases of foregut, colon, solid organ and biliary surgery using the da Vinci system, with resident assistance. Foregut and colon procedures are the fifth and sixth most commonly performed procedures of the senior author annually.

Methods

An IRB‐approved retrospective review of prospectively collected data representing 124 foregut and 102 colon operations was performed. Data analysed were procedure performed and indications for surgery, gender, age, body mass index (BMI), estimated blood loss (EBL), port set‐up time (PST), robot operating time (ROT), total case time (TCT), length of stay (LOS), complications, conversions and resident involvement were recorded. Fourteen cases were excluded from the data review. Statistical analysis using the ANOVA test was applied. A specific review of resident participation was performed.

Results

Times for 226 foregut and colon cases were: PST 31.2 ± 9.4 (range 10–64) min, ROT 119.3 ± 41.5 (range 12–306) min, and TCT 194.8 ± 50.3 (range 50–380) min. The EBL was 48.6 ± 55.0 (range 5–500) ml, BMI 28.5 ± 4.7 (range 15.4–46.8) kg/m2, and median LOS 2.0 (range 0–27) days. The overall complication rate was 13.3%. No deaths occurred. Over the 8 year study period the number of cases participated in by residents was 0, 16, 22, 15, 29, 26, 28 and 10 (as of June 2009), respectively.

Conclusion

This series demonstrates the technical feasibility and safety of robotic surgery for the foregut and colon in a clinical setting where the surgeon does far more of other types of MIS. This series compares favorably with the literature. Incorporation of robotic training in the curriculum has allowed residents to learn robotic techniques in an effective manner. Copyright © 2010 John Wiley & Sons, Ltd.
Improving autonomy and control of autonomous surface vehicles in port protection and mine countermeasure scenarios
Authors: Pastore Thomas , Djapic Vladimir
Published: August 2010

Recent experimentation with autonomous surface vehicles (ASVs) has focused on the use of such platforms to perform tasks of classification or identification of objects first discovered by another sensor. The ASV generally carries small sensors capable of high‐resolution imaging, but only at relatively short ranges. Reacquisition of a contact is inherent in the problem of classification and involves positioning of the surface vehicle with good precision such that the object of interest is in the field of view of the sensors aboard the ASV. This critical task of positioning the vehicle such that the classification sensors can be effectively brought to bear is the primary goal of our autonomy development. Experimental results from a variety of sensors are presented, but the most important in our present work has been a high‐resolution multibeam imaging sonar operating at 450 kHz. This sensor has been successfully used to image divers and bottom objects, with telemetry data sent back to shore via wireless LAN. Although classification was done by a human operator ashore, the vehicle has the capability to keep an object in view of the sensor, representing an important operational advantage of the autonomy. Future work could expand the role of the unmanned platform to deployment of effectors—warning devices or entanglement devices in the case of harbor protection missions or neutralization devices in the case of countermine operations. © 2010 Wiley Periodicals, Inc.
Airborne vision‐based collision‐detection system
Authors: Lai John , Mejias Luis , Ford Jason J.
Published: August 2010

Machine vision represents a particularly attractive solution for sensing and detecting potential collision‐course targets due to the relatively low cost, size, weight, and power requirements of vision sensors (as opposed to radar and Traffic Alert and Collision Avoidance System). This paper describes the development and evaluation of a real‐time, vision‐based collision‐detection system suitable for fixed‐wing aerial robotics. Using two fixed‐wing unmanned aerial vehicles (UAVs) to recreate various collision‐course scenarios, we were able to capture highly realistic vision (from an onboard camera perspective) of the moments leading up to a collision. This type of image data is extremely scarce and was invaluable in evaluating the detection performance of two candidate target detection approaches. Based on the collected data, our detection approaches were able to detect targets at distances ranging from 400 to about 900 m. These distances (with some assumptions about closing speeds and aircraft trajectories) translate to an advance warning of between 8 and 10 s ahead of impact, which approaches the 12.5‐s response time recommended for human pilots. We overcame the challenge of achieving real‐time computational speeds by exploiting the parallel processing architectures of graphics processing units (GPUs) found on commercial‐off‐the‐shelf graphics devices. Our chosen GPU device suitable for integration onto UAV platforms can be expected to handle real‐time processing of 1,024 × 768 pixel image frames at a rate of approximately 30 Hz. Flight trials using manned Cessna aircraft in which all processing is performed onboard will be conducted in the near future, followed by further experiments with fully autonomous UAV platforms. © 2010 Wiley Periodicals, Inc.
Nonparametric sequential monitoring of longitudinal trials
Authors: Bogowicz P. , Gombay E. , Heo G.
Published: August 2010

This paper considers the sequential monitoring of multi‐armed longitudinal clinical trials. We describe an approach that is relatively simple and accessible. Sequential ranks are used to form partial sum statistics, yielding processes that have independent increments, and hence can be approximated by Brownian motions. Three monitoring procedures are proposed. The first two are asymptotic, continuous analogues of the well‐known Pocock and O'Brien–Fleming group sequential procedures, whereas the third procedure is exact. Performance of the procedures is assessed using Monte Carlo simulations. Data from an orthodontic clinical trial is used to illustrate the proposed methods, for the comparison of three treatment groups. Copyright © 2010 John Wiley & Sons, Ltd.
What can go wrong when ignoring correlation bounds in the use of generalized estimating equations
Authors: Sabo R. T. , Chaganty N. R.
Published: August 2010

The analysis of repeated measure or clustered data is often complicated by the presence of correlation. Further complications arise for discrete responses, where the marginal probability‐dependent Fr'echet bounds impose feasibility limits on the correlation that are often more restrictive than the positive definite range. Some popular statistical methods, such as generalized estimating equations (GEE), ignore these bounds, and as such can generate erroneous estimates and lead to incorrect inferential results. In this paper, we discuss two alternative strategies: (i) using QIC to select a data‐driven correlation value within the Fréchet bounds, and (ii) the use of likelihood‐based latent variable modeling, such as multivariate probit, to get around the problem all together. We provide two examples of the repercussions of incorrectly using existing GEE software in the presence of correlated binary responses. Copyright © 2010 John Wiley & Sons, Ltd.
Propinquity in global software engineering: examining perceived distance in globally distributed project teams
Authors: Prikladnicki Rafael
Published: August 2010

In social psychology, propinquity refers to the physical (objective) or psychological (subjective) proximity between people. In this paper, we explore the psychological dimension of propinquity by examining the phenomenon of feeling distant from geographically distributed people, in the context of distributed software teams. The perceived distance is an important challenge faced by distributed teams, and it is frequently based on factors beyond the physical distance, such as communication and cultural differences. The purpose of this paper is to present a model to assess and make more visible the construct of ‘perceived distance’ among members of global software engineering teams. The model was applied in three real‐world cases to assess its effectiveness in uncovering hidden and useful information during the project lifecycle. The practical experience lived with the quantification of perceived distance gave us good indication that this data can benefit the practice of global software engineering. In most of the projects evaluated, project managers were not expecting the results found. We present the model, details of its applications, analysis of the results, lessons learned and practical implications for the management of distributed software projects and teams. Copyright © 2010 John Wiley & Sons, Ltd.
Methodology for process improvement through basic components and focusing on the resistance to change
Authors: Calvo‐Manzano Jose A. , Cuevas Gonzalo , Gómez Gerzón , Mejia Jezreel , Muñoz Mirna , San Feliu Tomás
Published: August 2010

This paper describes a multi‐model methodology that implements a smooth and continuous process improvement, depending on the organization's business goals and allowing users to establish their improvement implementation pace. The methodology focuses on basic process components known as ‘best practices’. Besides, it covers following the topics: knowledge management and change management. The methodology description and the results of a case study on project management process are included. Copyright © 2010 John Wiley & Sons, Ltd.
Performance analysis and comparison of burst transmission schemes in unsaturated 802.11e WLANs
Authors: Hu Jia , Min Geyong , Woodward Mike E.
Published: August 2010

Contention free bursting (CFB) and block acknowledgement (BACK) are two innovative burst transmission schemes specified in the IEEE 802.11e standard for reducing the contention overheads and further improving the channel utilization of wireless local area networks (WLANs). Existing studies on performance analysis of the CFB and BACK schemes have been primarily focused on the system throughput and have not taken into account the realistic factors, such as unsaturated traffic loads and finite buffer capacity. To fill this gap, this paper proposes a new and comprehensive analytical model for evaluating the Quality‐of‐Service (QoS) metrics including throughput, end‐to‐end delay, and frame loss probability of both burst transmission schemes under unsaturated traffic conditions. The proposed model is validated through extensive simulation experiments and then is used to conduct performance analysis and comparison of the burst transmission schemes under various working conditions. The analytical results reveal that (1) both CFB and BACK schemes can substantially improve the QoS performance; (2) BACK scheme outperforms the CFB scheme when the transmission opportunity (TXOP) limit exceeds a threshold; (3) the analytical model can be used to identify the optimal configuration of system parameters for the burst transmission schemes subject to QoS constraints. Copyright © 2010 John Wiley & Sons, Ltd.
Collaboration and competition between DNA double‐strand break repair pathways
Authors: Kass Elizabeth M. , Jasin Maria
Published: August 2010

DNA double‐strand breaks resulting from normal cellular processes including replication and exogenous sources such as ionizing radiation pose a serious risk to genome stability, and cells have evolved different mechanisms for their efficient repair. The two major pathways involved in the repair of double‐strand breaks in eukaryotic cells are non‐homologous end joining and homologous recombination. Numerous factors affect the decision to repair a double‐strand break via these pathways, and accumulating evidence suggests these major repair pathways both cooperate and compete with each other at double‐strand break sites to facilitate efficient repair and promote genomic integrity.
Provenance of freshwater pulses in the Gulf of Mexico during the last deglaciation
Authors: Sionneau T. , Bout-Roumazeilles V. , Flower B.P. , Bory A. , Tribovillard N. , Kissel C. , Van Vliet-Lanoë B. , Montero Serrano J.C.
Published: August 2010

During the last deglaciation, the decaying Laurentide Ice Sheet (LIS) delivered huge volumes of meltwater toward the Gulf of Mexico. The present investigation of clay mineralogy and grain-size characteristics of terrigenous sediments deposited in the Orca Basin (Gulf of Mexico) offers a unique opportunity to link the marine record of these meltwater floods with the reconstructed continental glacial history and the modeled drainage patterns. Five peculiar sedimentary levels, characterized by high smectite content and low CaCO3 content, were identified and occurred simultaneously with major meltwater floods. According to recently published clay mineral distribution maps for North America, these results help to pinpoint the southwestern margin of the LIS as a main contributor to most of the meltwater discharges. In addition, the peculiar mineralogical composition (illite and chlorite-rich) of the sediments characterizing the meltwater episode associated with Heinrich event 1 suggests a provenance from the Great Lakes area, supporting the interpretation of destabilization of the LIS southeastern margin during this event. Decreased terrigenous contribution associated with changing provenance of sediments after 12.9 cal ka BP suggests strong modifications of the continental hydrography in relation to Lake Agassiz history and changes in the morphology of Mississippi delta due to rising sea level.
The Most Redundant Sequences in Human CpG Island Library Are Derived from Mitochondrial Genome
Authors: He Ximiao , Tao Shu , Jin Jing , Hu Songnian , Yu Jun
Published: August 2010

An altered pattern of epigenetic modifications, such as DNA methylation and histone modification, is critical to many common human diseases, including cancer. Recently, mitochondrial DNA (mtDNA) was reported to be associated with tumorigenesis through epigenetic regulation of methylation patterns. One of the promising approaches to study DNA methylation and CpG islands (CGIs) is sequencing and analysis of clones derived from the physical library generated by methyl-CpG-binding domain proteins and restriction enzyme MseI. In this study, we observed that the most redundant sequences of 349 clones in a human CGI library were all generated from the human mitochondrial genome. Further analysis indicated that there was a 5,845-bp DNA transfer from mtDNA to chromosome 1, and all the clones should be the products of a 510-bp MseI fragment, which contained a putative CGI of 270 bp. The 510-bp fragment was annotated as part of cytochrome c oxidase subunit II (COXII), and phylogenetic analysis of homologous sequences containing COXII showed three DNA transfer events from mtDNA to nuclear genome, one of which underwent secondary transfer events between different chromosomes. These results may further our understanding of how the mtDNA regulates DNA methylation in the nucleus.
Sequence Signatures of Nucleosome Positioning in Caenorhabditis Elegans
Authors: Chen Kaifu , Wang Lei , Yang Meng , Liu Jiucheng , Xin Chengqi , Hu Songnian , Yu Jun
Published: August 2010

Our recent investigation in the protist Trichomonas vaginalis suggested a DNA sequence periodicity with a unit length of 120.9 nt, which represents a sequence signature for nucleosome positioning. We now extended our observation in higher eukaryotes and identified a similar periodicity of 175 nt in length in Caenorhabditis elegans. In the process of defining the sequence compositional characteristics, we found that the 10.5-nt periodicity, the sequence signature of DNA double helix, may not be sufficient for cross-nucleosome positioning but provides essential guiding rails to facilitate positioning. We further dissected nucleosome-protected sequences and identified a strong positive purine (AG) gradient from the 5′-end to the 3′-end, and also learnt that the nucleosome-enriched regions are GC-rich as compared to the nucleosome-free sequences as purine content is positively correlated with GC content. Sequence characterization allowed us to develop a hidden Markov model (HMM) algorithm for decoding nucleosome positioning computationally, and based on a set of training data from the fifth chromosome of C. elegans, our algorithm predicted 60%-70% of the well-positioned nucleosomes, which is 15%-20% higher than random positioning. We concluded that nucleosomes are not randomly positioned on DNA sequences and yet bind to different genome regions with variable stability, well-positioned nucleosomes leave sequence signatures on DNA, and statistical positioning of nucleosomes across genome can be decoded computationally based on these sequence signatures.
Genome-Wide Survey and Evolutionary Analysis of Trypsin Proteases in Apicomplexan Parasites
Authors: Arenas Aylan Farid , Osorio-Méndez Juan Felipe , Gutierrez Andres Julian , Gomez-Marin Jorge E.
Published: August 2010

Apicomplexa are an extremely diverse group of unicellular organisms that infect humans and other animals. Despite the great advances in combating infectious diseases over the past century, these parasites still have a tremendous social and economic burden on human societies, particularly in tropical and subtropical regions of the world. Proteases from apicomplexa have been characterized at the molecular and cellular levels, and central roles have been proposed for proteases in diverse processes. In this work, 16 new genes encoding for trypsin proteases are identified in 8 apicomplexan genomes by a genome-wide survey. Phylogenetic analysis suggests that these genes were gained through both intracellular gene transfer and vertical gene transfer. Identification, characterization and understanding of the evolutionary origin of protease-mediated processes are crucial to increase the knowledge and improve the strategies for the development of novel chemotherapeutic agents and vaccines.
BiDiBlast: Comparative Genomics Pipeline for the PC
Authors: de Almeida João M.G.C.F.
Published: August 2010

Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http://moodle.fct.unl.pt/course/view.php?id=2079 or https://sourceforge.net/projects/bidiblast/ under the GNU GPL license.
Transitivity in spaces of vector-valued functions
Authors: Sánchez Félix Cabello
Published: August 2010

We exhibit a real Banach space M such that C(K,M) is almost transitive if K is the Cantor set, the growth of the integers in its Stone–Čech compactification or the maximal ideal space of L∞. For finite K, the space C(K,M) = M|K| is even transitive.
Characterizing Jordan maps on C*-algebras through zero products
Authors: Alaminos J. , Brešar J. M. , Extremera J. , Villena A. R.
Published: August 2010

Let A and B be C*-algebras, let X be an essential Banach A-bimodule and let T : A → B and S : A → X be continuous linear maps with T surjective. Suppose that T(a)T(b) + T(b)T(a) = 0 and S(a)b + bS(a) + aS(b) + S(b)a = 0 whenever a, b ε A are such that ab = ba = 0. We prove that then T = wΦ and S = D + Ψ, where w lies in the centre of the multiplier algebra of B, Φ: A → B is a Jordan epimorphism, D: A → X is a derivation and Ψ: A → X is a bimodule homomorphism.
Experimental study of a tip leakage flow: wavelet analysis of pressure fluctuations
Authors: CAMUSSI R. , GRILLIAT J. , CAPUTI-GENNARO G. , JACOB M. C.
Published: August 2010

A wavelet-based conditional analysis of unsteady flow and sound signals highlights the role of intermittent perturbations both in the sound generation and the unsteady field of an aerofoil tip leakage flow experiment. It is shown how the most probable flow perturbations generated at the pressure side tip edge are convected through the gap and swept downstream along the suction side past the trailing edge tip corner, where they radiate sound. The nascent sound sources are identified and localized in the clearance between 40% and 60% of the chord. It is also found that the time dependence of the averaged intermittent structures scales with the inverse of the square root of the mean velocity and a physical interpretation based on a simple potential vortex model is proposed. The data are retrieved from an experiment that has been carried out at low Mach number (Ma < 0.3) in an anechoic test facility. A single motionless instrumented NACA 5510 aerofoil was mounted into the potential core of an open rectangular jet between two plates with an adjustable clearance. The tip leakage flow was ensured by the 5% camber and a 15° angle of attack. A large database obtained by a variety of measurement techniques is thus available for the present analysis. More specifically, the conditional approach is applied to joint far field, wall pressure and particle image velocimetry (PIV) measurements. The wall pressure probes are located along the suction side tip edge and on the tip inside the gap, whereas the PIV plane is parallel to the mid-gap plane. Additional joint wall pressure and single hot-wire anemometry (HWA) measurements are also analysed with a hot-wire probe located near the trailing edge tip corner. The conditional averaging is triggered by high-energy wavelet events selected in a reference signal by setting a threshold to the so-called local intermittency measure.
Helical-wave decomposition and applications to channel turbulence with streamwise rotation
Authors: YANG Y.-T. , SU W.-D. , WU J.-Z.
Published: August 2010

Using helical-wave decomposition (HWD), a solenoidal vector field can be decomposed into helical modes with different wavenumbers and polarities. Here, we first review the general formulation of HWD in an arbitrary single-connected domain, along with some new development. We then apply the theory to a viscous incompressible turbulent channel flow with system rotation, including a derivation of helical bases for a channel domain. By these helical bases, we construct the inviscid inertial-wave (IW) solutions in a rotating channel and derive their existing condition. The condition determines the specific wavenumber and polarity of the IW. For a set of channel turbulent flows rotating about a streamwise axis, this channel-domain HWD is used to decompose the flow data obtained by direct numerical simulation. The numerical results indicate that the streamwise rotation induces a polarity-asymmetry and concentrates the fluctuating energy to particular helical modes. At large rotation rates, the energy spectra of opposite polarities exhibit different scaling laws. The nonlinear energy transfer between different helical modes is also discussed. Further investigation reveals that the IWs do exist when the streamwise rotation is strong enough, for which the theoretical predictions and numerical results are in perfect agreement in the core region. The wavenumber and polarity of the IW coincide with that of the most energetic helical modes in the energy spectra. The flow visualizations show that away from the channel walls, the small vortical structures are clustered to form very long columns, which move in the wall-parallel plane and serve as the carrier of the IW. These discoveries also help clarify certain puzzling problems raised in previous studies of streamwise-rotating channel turbulence.
Schmidt’s game, fractals, and orbits of toral endomorphisms
Authors: BRODERICK RYAN , FISHMAN LIOR , KLEINBOCK DMITRY
Published: August 2010

Given an integer matrix M∈GLn(ℝ) and a point y∈ℝn/ℤn, consider the set S. G. Dani showed in 1988 that whenever M is semisimple and y∈ℚn/ℤn, the set $ \tilde E(M,y)$ has full Hausdorff dimension. In this paper we strengthen this result, extending it to arbitrary M∈GLn(ℝ)∩Mn×n(ℤ) and y∈ℝn/ℤn, and in fact replacing the sequence of powers of M by any lacunary sequence of (not necessarily integer) m×n matrices. Furthermore, we show that sets of the form $ \tilde E(M,y)$ and their generalizations always intersect with ‘sufficiently regular’ fractal subsets of ℝn. As an application, we give an alternative proof of a recent result [M. Einsiedler and J. Tseng. Badly approximable systems of affine forms, fractals, and Schmidt games. Preprint, arXiv:0912.2445] on badly approximable systems of affine forms.
On the Suitability of SIFT Technique to Deal with Image Modifications Specific to Confocal Scanning Laser Microscopy
Authors: Stanciu Stefan G. , Hristu Radu , Boriga Radu , Stanciu George A.
Published: August 2010

Computer vision tasks such as recognition and classification of objects and structures or image registration and retrieval can provide significant information when applied to microscopy images. Recently developed techniques for the detection and description of local features make the extraction and description of local image features that are invariant to various changes possible. The invariance and robustness of feature detection and description techniques play a key role in the design and implementation of object recognition, image registration, or image mosaicing applications. The scale-invariant feature transform (SIFT) technique is a widely used method for the detection, description, and matching of image features. In this article we present the results of our experiments regarding the repeatability of SIFT features, and to the precision of the SIFT feature matching, under image modifications specific to confocal scanning laser microscopy (CSLM). We have analyzed the behavior of SIFT while changing the pinhole aperture, photomultiplier gain, laser beam power, and electronic zoom. Our experiments, conducted on CSLM images, show that the SIFT technique is able to match detected key points between images acquired at different values of the acquisition parameters with good precision and represents a consistent tool for computer vision applications in CSLM.
Feeding a protein-restricted diet during pregnancy induces altered epigenetic regulation of peroxisomal proliferator-activated receptor-α in the heart of the offspring
Authors: Slater-Jefferies J. L. , Lillycrop K. A. , Townsend P. A. , Torrens C. , Hoile S. P. , Hanson M. A. , Burdge G. C.
Published: August 2010

Impaired flexibility in the use of substrates for energy production in the heart is implicated in cardiomyopathy. We investigated the effect of maternal protein restriction during pregnancy in rats on the transcription of key genes in cardiac lipid and carbohydrate metabolism in the offspring. Rats were fed protein-sufficient or protein-restricted (PR) diets during pregnancy. Triacylglycerol concentration in adult (day 105) heart was altered by maternal protein intake contingent on post-weaning fat intake and sex. mRNA expression of peroxisomal proliferator-activated receptor (PPAR)-α and carnitine palmitoyltransferase-1 was increased by the maternal PR diet in adult, but not neonatal, offspring. PPARα promoter methylation was lower in adult and neonatal heart from PR offspring. These findings suggest that prenatal nutrition alters the future transcriptional regulation of cardiac energy metabolism in the offspring through changes in epigenetic regulation of specific genes. However, changes in gene functional changes may not be apparent in early life.
Arecibo's thermospheric gravity waves and the case for an ocean source
Authors: Djuth F. T. , Zhang L. D. , Livneh D. J. , Seker I. , Smith S. M. , Sulzer M. P. , Mathews J. D. , Walterscheid R. L.
Published: August 2010

Wave‐like disturbances in electron density ne have been observed in the thermosphere above Arecibo Observatory, Puerto Rico throughout its 45 year history. However, only recently has it become evident that these waves are continuously present in the Arecibo thermosphere. The wave characteristics are fairly constant between day and night and from season to season. High‐resolution electron density measurements obtained by applying the coded long‐pulse radar technique to photoelectron‐enhanced Langmuir waves are presented. These new observations strongly suggest that the perturbations in electron density are the result of internal acoustic‐gravity waves (AGWs) propagating through the Arecibo thermosphere. The AGWs appear to be broadbanded in wave number space. The downward phase trajectories of Δne/ne between 400 and 120 km combined with the low horizontal phase velocities obtained from airglow measurements support the idea that the AGWs are not ducted but rather are locally produced. In addition, the altitudes at which major peaks in Δne/ne are observed follow theoretical estimates for nonducted waves. The nominal period of the AGWs is ∼60 min at 250 km altitude, but periods of ∼20 min are also evident at lower attitudes. Classic sources of AGWs do not appear to be consistent with the Arecibo observations of a continuous flux of background AGWs. Ray tracing of the AGWs combined with 630.0 nm airglow observations point to a source location in the Atlantic Ocean that is roughly 2100 km east northeast of Arecibo. Internal ocean waves generated in response to the internal tide at the mid‐Atlantic Ridge are the most likely source of Arecibo's thermospheric AGWs.
Synthesis of vector wave envelopes on the free surface of a random medium for the vertical incidence of a plane wavelet based on the Markov approximation
Authors: Emoto Kentaro , Sato Haruo , Nishimura Takeshi
Published: August 2010

In short‐period seismograms of earthquakes, we often observe the broadening of apparent duration of P and/or S waves and the excitation of the transverse component especially for P waves as travel distance increases. Such phenomena are well explained by scattering caused by random velocity fluctuation in the lithosphere. The Markov approximation is known as one of the powerful stochastic methods for the direct synthesis of wave envelopes. We extend the method to synthesize vector wave envelopes on the free surface of a random medium since seismic observation is usually done on the ground surface. We evaluate the mean square (MS) envelope on the free surface by multiplying the amplification factor on the free surface to the angular spectrum in an infinite random medium. We synthesize MS envelopes for the vertical incidence of an impulsive plane P or S wavelet into a 3‐D random medium characterized by a Gaussian autocorrelation function with typical parameters of the lithosphere. As a result, the vertical and horizontal component MS envelopes show different amplification rates on the free surface; however, we may say that “a factor of 4” is a good approximation for the amplification rate for both components. Finally, we numerically confirm the validity of our direct envelope syntheses by the comparison with finite difference simulations of waves in 2‐D random media. The Markov approximation is accurate when the wavelength is shorter than the correlation distance and the fractional fluctuation is much smaller than the ratio of the correlation distance to the propagation distance.
Exploiting diurnal variations to evaluate the ISCCP‐FD flux calculations and radiative‐flux‐analysis‐processed surface observations from BSRN, ARM, and SURFRAD
Authors: Zhang Yuanchong , Long Charles N. , Rossow William B. , Dutton Ellsworth G.
Published: August 2010

Using a meteorological similarity comparison method (MSCM), we performed a mutual and simultaneous evaluation of the surface radiative flux datasets from the International Satellite Cloud Climatology Project‐FD and the new radiative‐flux‐analysis‐processed surface observations (RFA‐PSO). For downward shortwave (SW), diffuse (Dif), and direct (Dir) fluxes, matching cloud fraction (CF) reduces the flux difference between FD and RFA‐PSO by up to a factor of 2. Decreasing the aerosol optical depth values used in the FD calculations accounts for much of the remaining difference. For downward longwave (LW) flux, matching either surface air temperature or CF reduces the flux difference to nearly zero. For the total downward SW diurnal variations, there is excellent agreement for both clear and cloudy sky, but less good agreement for the Dif and Dir components. The latter agree much better for clear sky when the FD aerosol optical depth is reduced and for cloudy sky when matching CF and cloud optical depth jointly. For LW diurnal variations, the agreement is best for clear sky, but FD has a larger amplitude by 3–7 W/m2 for cloudy sky because of differing sensitivities to cirrus and low clouds in the two datasets. These results confirm that the source of the FD surface flux uncertainty of ∼10–15 W/m2 is the input quantities, not the radiative transfer model. An important limitation of the RFA‐PSO cloud parameters (not the fluxes) is the inhomogeneous diurnal sampling and the retrieval difficulties with broken clouds (SW) and cirrus clouds (LW).
Lightning‐generated NOx seen by the Ozone Monitoring Instrument during NASA's Tropical Composition, Cloud and Climate Coupling Experiment (TC4)
Authors: Bucsela Eric J. , Pickering Kenneth E. , Huntemann Tabitha L. , Cohen Ronald C. , Perring Anne , Gleason James F. , Blakeslee Richard J. , Albrecht Rachel I. , Holzworth Robert , Cipriani James P. , Vargas‐Navarro Dylana , Mora‐Segura Ileana , Pacheco‐Hernández Alexia , Laporte‐Molina Sadí
Published: August 2010

We present case studies identifying lightning‐generated upper tropospheric NOx (LNOx) observed during NASA's Tropical Composition, Cloud and Climate Coupling Experiment (TC4) in July and August 2007. In the campaign, DC‐8 aircraft missions, flown from Costa Rica, recorded in situ NO2 profiles near active storms and in relatively quiet areas. We combine these TC4 DC‐8 data with satellite data from the Ozone Monitoring Instrument (OMI) to estimate the lightning‐generated NO2 (LNO2), above background levels, in the observed OMI NO2 fields. We employ improved off‐line processing techniques to customize the OMI retrieval for LNO2. Information on lightning flashes (primarily cloud‐to‐ground) observed by the Costa Rica Lightning Detection Network operated by the Instituto Costarricense de Electricidad and the World Wide Lightning Location Network were examined over storms upwind of regions where OMI indicates enhanced LNO2. These flash data are compared with Tropical Rainfall Measuring Mission/Lightning Imaging Sensor satellite data to estimate total flashes. Finally, using [NOx]/[NO2] ratios from NASA's Global Modeling Initiative model, we estimate LNOx production per flash for four cases and obtain rates of ∼100‐250 mol/flash. These are consistent with rates derived from previous studies of tropical and subtropical storms and below those from modeling of observed midlatitude storms. In our study, environments with stronger anvil‐level winds were associated with higher production rates. LIS flash footprint data for one of the low‐LNOx production cases with weak upper tropospheric winds suggest below‐average flash lengths for this storm. LNOx enhancements over background determined from the OMI data were in less than, but roughly proportional to, aircraft estimates.