bluuebunny/crossref_metadata_2025_split huggingface dataset:
Working memory in survivors of childhood acute lymphocytic Leukemia: Functional neuroimaging analyses
Authors: Robinson Kristen E. , Livesay Katherine L. , Campbell Laura K. , Scaduto Mary , Cannistraci Christopher J. , Anderson Adam W. , Whitlock James A. , Compas Bruce E. 
Published: December 2009

AbstractBackgroundResearch on the physical and psychological late effects of treatment of childhood cancer has led to the identification of significant long‐term neurocognitive deficits experienced by some survivors, particularly in the areas of memory and executive functioning. Despite indications of deficits based on cognitive assessment, the identification of specific mechanisms of neurocognitive deficits using neuroimaging techniques has yet to be adequately considered.ProcedureThis study used functional neuroimaging techniques to examine working memory and executive functioning deficits of survivors of childhood acute lymphocytic leukemia (ALL), as compared to age‐ and gender‐matched healthy controls.ResultsThere was a trend for ALL survivors to perform more poorly on a working memory task in terms of overall accuracy. Additionally, survivors displayed significantly greater activation in areas underlying working memory (dorsolateral and ventrolateral prefrontal cortex) and error monitoring (dorsal and ventral anterior cingulate cortex).ConclusionsThese results support the theory of compensatory activation in necessary brain regions in order to complete tasks in pediatric ALL survivors, similar to that observed in multiple sclerosis patients. Concurrent examination of testing and brain imaging enables the connection of behavioral observations with underlying neurological characteristics of deficits in survivors and may help provide insight into mechanisms through which deficits appear. Pediatr Blood Cancer 2010;54:585–590. © 2009 Wiley‐Liss, Inc.
Media attention and the influence on the reporting odds ratio in disproportionality analysis: an example of patient reporting of statins
Authors: van Hunsel Florence , van Puijenbroek Eugène , de Jong‐ van den Berg Lolkje , van Grootheest Kees 
Published: December 2009

AbstractAimTo study the influence of media attention about statins and ADRs on the level of disproportionality, expressed as the reporting odds ratio (ROR) for statins in the Lareb database, based on patients' reports.MethodsPatient reports about statins, before and after the broadcast of a consumer programme about statins, were compared. In order to calculate the correlation between the ROR for patient‐statin reports between the period before and after the broadcast a Pearson correlation‐coefficient (r) was calculated. The type of reported ADRs associated with statins before and after the broadcast was compared both on the level of system organ class (SOC) and preferred terms (PT).ResultsPearson's Correlation‐coefficient for the comparison of RORs before and after the broadcast was 0.83. In respect to specific ADRs, no differences were found in reporting on SOC level before and after the broadcast, except for the SOCMusculoskeletal and connective tissue disorders. For ADRs that were specifically mentioned during the broadcast, no differences were found except for an increased number of myalgia and arthralgia reports.ConclusionOur study demonstrates that media attention does not necessarily influence the relative reporting by patients expressed as RORs in the national ADR database. On SOC level only inMusculoskeletal and connective tissue disordersthe relative reporting increased. For myalgia and arthralgia, there was a proportional increase of reporting within the statin class but not for the other ADRs that were explicitly mentioned in the TV programme about statins. Copyright © 2009 John Wiley & Sons, Ltd.
Comparative analysis of the secretory proteome of human adipose stromal vascular fraction cells during adipogenesis
Authors: Kim Jaeyoon , Choi Yoon Sup , Lim Seyoung , Yea Kyungmoo , Yoon Jong Hyuk , Jun Dong‐Jae , Ha Sang Hoon , Kim Jung‐Wook , Kim Jae Ho , Suh Pann‐Ghill , Ryu Sung Ho , Lee Taehoon G. 
Published: December 2009

AbstractAdipogenesis is a complex process that is accompanied by a number of molecular events. In this study, a proteomic approach was adopted to identify secretory factors associated with adipogenesis. A label‐free shotgun proteomic strategy was implemented to analyze proteins secreted by human adipose stromal vascular fraction cells and differentiated adipocytes. A total of 474 proteins were finally identified and classified according to quantitative changes and statistical significances. Briefly, 177 proteins were significantly upregulated during adipogenesis (Class I), whereas 60 proteins were significantly downregulated (Class II). Changes in the expressions of several proteins were confirmed by quantitative RT‐PCR and immunoblotting. One obvious finding based on proteomic data was that the amounts of several extracellular modulators of Wnt and transforming growth factor‐β (TGF‐β) signaling changed during adipogenesis. The expressions of secreted frizzled‐related proteins, dickkopf‐related proteins, and latent TGF‐β‐binding proteins were found to be altered during adipogenesis, which suggests that they participate in the fine regulation of Wnt and TGF‐β signaling. This study provides useful tools and important clues regarding the roles of secretory factors during adipogenic differentiation, and provides information related to obesity and obesity‐related metabolic diseases.
Environmental proteomics: Analysis of structure and function of microbial communities
Authors: Schneider Thomas , Riedel Kathrin 
Published: December 2009

AbstractProkaryotic and eukaryotic microorganisms make a vital contribution to biogeochemical cycles by decomposing virtually all natural compounds and thereby exert a lasting effect on biosphere and climate. The rapidly growing number of metagenomic sequences together with revolutionary advances in bioinformatics and protein analyses have opened completely new horizons to investigate the molecular basis of such complex processes. Proteomics has contributed substantially to our understanding of individual organisms at the cellular level as it offers excellent possibilities to probe many protein functions and responses simultaneously. However, it has not yet been widely applied in microbial ecology, although most proteins have an intrinsic metabolic function which can be used to relate microbial activities to the identity of defined organisms in multispecies communities. Albeit still in its infancy, environmental proteomics enables simple protein cataloging, comparative and semi‐quantitative proteomics, analyses of protein localization, discovery of post‐translational modifications, and even determination of amino‐acid sequences and genotypes by strain‐resolved proteogenomics. This review traces the historical development of environmental proteomics and summarizes milestone publications in the field. In conclusion, we briefly discuss current limitations of microbial community proteomics but also the potential of emerging technologies to shape the future of metaproteome analyses.
De novo sequencing of peptides by MS/MS
Authors: Seidler Joerg , Zinn Nico , Boehm Martin E. , Lehmann Wolf D. 
Published: December 2009

AbstractThe current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS spectra. The relation between peptide structure and observed fragment ion series is discussed and the exhaustive extraction of sequence information from CID spectra of protonated peptide ions is described. The partial redundancy of the extracted sequence information and a high mass accuracy are recognized as key parameters for dependable de novo sequencing by MS. In addition, the benefits of special techniques enhancing the generation of long uninterrupted fragment ion series for de novo peptide sequencing are highlighted. Among these are terminal 18O labeling, MSn of sodiated peptide ions, N‐terminal derivatization, the use of special proteases, and time‐delayed fragmentation. The emerging electron transfer dissociation technique and the recent progress of MALDI techniques for intact protein sequencing are covered. Finally, the integration of bioinformatic tools into peptide de novo sequencing is demonstrated.
Contribution of proteomics toward solving the fascinating mysteries of the biogenesis of the envelope of Escherichia coli
Authors: Leverrier Pauline , Vertommen Didier , Collet Jean‐François 
Published: December 2009

AbstractThe cell envelope of Gram‐negative bacteria is a complex macromolecular structure that is essential for their viability. Little is known on how the proteins which are secreted to the envelope fold into their unique three‐dimensional structure. Several folding factors, including chaperones and protein folding catalysts involved in disulfide bond formation, have been identified in the periplasm. The characterization of these proteins has advanced our understanding of envelope biogenesis, although many fundamental questions remain unanswered. In particular, we still do not know how β‐barrel proteins are transported through the periplasm and inserted into the outer membrane. Here, we discuss the recent discoveries that have shed new light on the mechanisms that ensure the correct folding of envelope proteins. We have paid particular attention to the significant contribution of proteomic studies.
Cell‐free synthesis‐based protein microarrays and their applications
Authors: Chandra Harini , Srivastava Sanjeeva 
Published: December 2009

AbstractThe entire complement of proteins expressed by the genome of an organism under a set of defined conditions represents the proteome. The need for rapid, efficient, and high‐throughput technologies to understand the proteome of organisms have resulted in the development of protein microarrays. Traditional, cell‐based technologies for the generation of protein arrays involve laborious and protracted procedures, which also pose several other technical problems. These limitations have been suitably overcome by cell‐free expression systems that carry out rapid, in situ synthesis of proteins from their corresponding DNA templates. This article provides an overview of commonly used cell‐free systems that have been used for the generation of protein microarrays, with special emphasis on the diverse applications of cell‐free synthesis‐based protein microarrays.
Peptide and protein quantification: A map of the minefield
Authors: Vaudel Marc , Sickmann Albert , Martens Lennart 
Published: December 2009

AbstractThe increasing popularity of gel‐free proteomics technologies has created a strong demand for compatible quantitative analysis methods. As a result, a plethora of different techniques has been proposed to perform gel‐free quantitative analysis of proteomics samples. Each of these methods comes with certain strengths and shortcomings, and they often are dedicated to a specific purpose. This review will present a brief overview of the main methods, organized by their underlying concepts, and will discuss the issues they raise with a focus on data processing. Finally, we will list the available software that can help with the data processing from quantitative experiments. We hope that this review will thus enable researchers to find the most appropriate method available for their research objectives, and can also serve as a basis for creating a reliable data processing strategy.
Nanobiocatalysis for protein digestion in proteomic analysis
Authors: Kim Jungbae , Kim Byoung Chan , Lopez‐Ferrer Daniel , Petritis Konstantinos , Smith Richard D. 
Published: December 2009

AbstractThe process of protein digestion is a critical step for successful protein identification in bottom‐up proteomic analyses. To substitute the present practice of in‐solution protein digestion, which is long, tedious, and difficult to automate, many efforts have been dedicated for the development of a rapid, recyclable and automated digestion system. Recent advances of nanobiocatalytic approaches have improved the performance of protein digestion by using various nanomaterials such as nanoporous materials, magnetic nanoparticles, and polymer nanofibers. Especially, the unprecedented success of trypsin stabilization in the form of trypsin‐coated nanofibers, showing no activity decrease under repeated uses for 1 year and retaining good resistance to proteolysis, has demonstrated its great potential to be employed in the development of automated, high‐throughput, and on‐line digestion systems. This review discusses recent developments of nanobiocatalytic approaches for the improved performance of protein digestion in speed, detection sensitivity, recyclability, and trypsin stability. In addition, we also introduce approaches for protein digestion under unconventional energy input for protein denaturation and the development of microfluidic enzyme reactors that can benefit from recent successes of these nanobiocatalytic approaches.
Analysis of proteomic changes associated with sperm capacitation through the combined use of IPG‐strip pre‐fractionation followed by RP chromatography LC‐MS/MS analysis
Authors: Baker Mark A. , Reeves Gabi , Hetherington Louise , Aitken R. John 
Published: November 2009

AbstractFollowing ejaculation, mammalian spermatozoa undergo an obligatory process known as capacitation, which enables these cells to bind to and fertilize an oocyte. Since spermatozoa are transcriptionally and translationally silent, the functional metamorphosis of these cells during capacitation is accomplished entirely by PTMs. Despite the importance of this process, very few studies have attempted to define the precise nature of the proteomic changes that allow spermatozoa to attain a capacitated state. Here we report the use of an IPG‐strip pre‐fractionation approach to isolate and purify tryptic peptides derived from mouse spermatozoa exhibiting varying degrees of capacitation. Following focusing, the strips were cut into 1 cm segments, the peptides extracted and run into a mass spectrometer. Label‐free, quantitative analysis of proteomic changes associated with capacitation was then performed. In total, we found 210 significant peptide changes. Of these, we could conclusively interpret the tandem mass spectra of 71 peptides, corresponding to 52 protein changes during capacitation. Many proteins including VDAC2, Fascin‐3 and sorbitol dehydrogenase (SORD) have not previously been implicated in this process. To validate our data, we were able to show significant upregulation of SORD activity during capacitation, suggesting that the polyol pathway is activated during this process.
Characterization of Low‐Temperature Microwave Plasma Treatment With and Without UV Light for Disinfection
Authors: Shimizu Tetsuji , Nosenko Tetyana , Morfill Gregor Eugen , Sato Takehiko , Schmidt Hans‐Ulrich , Urayama Takuya 
Published: December 2009

AbstractChemical characteristics and bactericidal properties of two low‐temperature atmospheric‐pressure Ar plasma devices are investigated: one of them with UV and the other with almost no UV on treated samples. The control of the UV radiation is achieved by two nozzles. One has a straight shape, and the other has a 90°‐bent. The bent nozzle blocks the light produced inside the torch, whilst allowing the plasma gas to reach the samples. The use of the straight nozzle allows the treatment by both the plasma gas and UV. We demonstrate that even an almost UV‐free plasma treatment has bactericidal properties. Our measurements suggest that reactive species represent the main bactericidal factor of our low‐temperature plasma.magnified image
Effects of airway pressure release ventilation on blood pressure and urine output in children
Authors: Kamath Sameer S. , Super Dennis M. , Mhanna Maroun J. 
Published: December 2009

AbstractObjectiveIncreased intrathoracic pressures during airway pressure release ventilation (APRV) may compromise systemic venous return resulting in decreased cardiac output and renal perfusion. We sought to study the short‐term effect of APRV on blood pressure (BP) and urine output (UO) in children with acute lung injury (ALI) or acute respiratory distress syndrome (ARDS).DesignRetrospective cohort study.PatientsAll patients with ALI/ARDS who were admitted to our Pediatric Intensive Care Unit (PICU) between 1/00 and 06/04, and who were ventilated with APRV (for at least 12 hr) for worsening oxygenation while on conventional ventilation (CV).Measurements and ResultsMedical records were reviewed for patients' demographics, Pediatric Risk of Mortality (PRISM III) score, admitting diagnosis, ventilator settings, gas exchange data, heart rate (HR), central venous pressure (CVP), blood pressure (BP), UO, and use of other therapies [sedatives, pressors, inotropes, and intravenous fluid (IVF)]. Eleven patients met our inclusion and exclusion criteria with a mean age of 6.2 ± 4.8 years (range: 1–15 years), a weight of 35.5 ± 29.5 kg (range: 12–90 kg), and a PRISM score of 18.4 ± 9.6 (range: 2–36). Within 10 hrs of APRV, patients' mean airway pressure (Paw) increased from 16.1 ± 6.6 to 21.1 ± 5.5 cm of H2O (P = 0.04). Despite a higher Paw there were no differences in HR, CVP, BP, UO, IVF and use of other therapies while on CV or APRV (P > 0.10).ConclusionIn children with ALI/ARDS, despite a higher Paw, APRV does not affect BP or UO. Pediatr Pulmonol. 2010; 45:48–54. © 2009 Wiley‐Liss, Inc.
Costs of Treating Children With Complicated Pneumonia: A Comparison of Primary Video‐Assisted Thoracoscopic Surgery and Chest Tube Placement
Authors: Shah Samir S. , Ten Have Thomas R. , Metlay Joshua P. 
Published: December 2009

AbstractObjectivesTo describe charges associated with primary video‐assisted thoracoscopic surgery (VATS) and primary chest tube placement in a multicenter cohort of children with empyema and to determine whether pleural fluid drainage by primary VATS was associated with cost‐savings compared with primary chest tube placement.Study DesignRetrospective cohort study.Setting and ParticipantsAdministrative database containing inpatient resource utilization data from 27 tertiary care children's hospitals. Patients between 12 months and 18 years of age diagnosed with complicated pneumonia were eligible if they were discharged between 2001 and 2005 and underwent early (within 2 days of index hospitalization) pleural fluid drainage.Main ExposureMethod of pleural fluid drainage, categorized as VATS or chest tube placement.ResultsPleural drainage in the 764 patients was performed by VATS (n = 50) or chest tube placement (n = 714). There were 521 (54%) males. Median hospital charges were $36,320 [interquartile range (IQR), $24,814–$62,269]. The median pharmacy and radiologic imaging charges were $5,884 (IQR, $3,142–$11,357) and $2,875 (IQR, $1,703–$4,950), respectively. Adjusting for propensity score matching, patients undergoing primary VATS did not have higher charges than patients undergoing primary chest tube placement.ConclusionsIn this multicenter study, we found that the charges incurred in caring for children with empyema were substantial. However, primary VATS was not associated with higher total or pharmacy charges than primary chest tube placement, suggesting that the additional costs of performing VATS are offset by reductions in length of stay (LOS) and requirement for additional procedures. Pediatr Pulmonol. 2010; 45:71–77. © 2009 Wiley‐Liss, Inc.
Cost‐effectiveness modelling in osteoporosis: alternatives to NICE
Authors: Brown Pam 
Published: December 2009

AbstractThe cost‐effectiveness modelling used by NICE in its 2008 guidance on the prevention of osteoporotic fracture in postmenopausal women has recently been challenged. Here, the author presents alternative cost‐effectiveness analyses and discusses the disparities with that published by NICE. Copyright © 2009 Wiley Interface Ltd
Antithrombotic failure and aspirin and clopidogrel resistance
Authors: Waller James , Waller Derek 
Published: December 2009

AbstractDespite antiplatelet therapy for the secondary prevention of cardiovascular events, many patients will still experience clinical events – in some cases this may be due to drug resistance. Here, the authors discuss the mechanism of platelet inhibition and the relationship between laboratory resistance and clinical events. Copyright © 2009 Wiley Interface Ltd
Control of interface between HfO2 and air‐exposed InGaAs by ultrathin Si interface control layer
Authors: Akazawa Masamichi , Hasegawa H. 
Published: December 2009

AbstractThis paper attempts to control the interface between the air‐exposed InGaAs wafer and a high‐k dielectric by the Si interface control layer (ICL) technique. As the high‐k insulator, HfO2 film was formed by atomic layer deposition (ALD). Prior to a molecular beam epitaxy (MBE) growth of the Si ICL, efforts were made to minimize native oxide components from the InGaAs surface by various wet surface treatment. After the growth of the Si ICL, an ultrathin SiNx layer was formed by in‐situ partial nitridation of the Si ICL to prevent a subcutaneous oxidation during the sample transfer in air to the ALD chamber. Surface/interface properties were characterized by in‐situ X‐ray photoelectron spectroscopy (XPS) at each step of interface formation. By using HF‐based cleaning, interface bonding configurations similar to those obtained by in‐situ UHV process was realized with no trace of native oxide components. As compared with the ALD HfO2/InGaAs metal‐insulator‐semiconductor (MIS) structure which showed existence of strong Fermi level pinning, insertion of the Si ICL achieved large reduction of interface state density, Dit, giving a minimum value of 2x1011 eV‐1cm‐2. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
SXPS study of model GaAs(100)/electrolyte interface
Authors: Lebedev Mikhail V. , Mankel Eric , Mayer Thomas , Jaegermann Wolfram 
Published: December 2009

AbstractModel GaAs(100)/electrolyte interfaces are prepared in vacuum by co‐adsorption of Cl2 and 2‐propanol molecules at LN2 temperature. On adsorption of Cl2 molecules gallium chlorides, elemental arsenic and arsenic chlorides are formed. Co‐adsorption of 2‐propanol causes formation of additional GaCl3 and AsCl, as well as soluble/volatile As‐based complexes, which are released from the surface depleting the sur‐ face by arsenic. Comparison of the As 3d and Ga 3d spectra obtained after heating the model interface to room temperature with the corresponding spectra obtained after emersion of the GaAs(100) surface from HCl/2‐propanol solution allows to conclude that in HCl solution Cl– ions attack gallium sites and H+ ions mostly attack arsenic sites. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Platinum nanoparticles deposited on wide‐bandgap semiconductor surfaces for catalytic applications
Authors: Schäfer Susanne , Wyrzgol Sonja A. , Wang Yizhen , Lercher Johannes A. , Stutzmann Martin 
Published: December 2009

AbstractWith the aim of the electronic control of catalytic processes, nano‐sized Schottky diodes were fabricated by physical vapour deposition (PVD) as well as spincoating of platinum nanoparticles to n‐GaN surfaces. Both methods were suitable to achieve defined coverages, which were in the range of 45% to 95% for PVD particles and 1% to multilayers for spin‐coated particles, as investigated by atomic force microscopy. A catalytic conversion of 1% was observed for PVD samples for the hydrogenation of ethene to ethane. The surface properties were investigated by X‐ray photoelectron spectroscopy (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)