bluuebunny/crossref_metadata_2025 huggingface dataset:
Profiling human brain proteome by multi‐dimensional separations coupled with MS
Authors: Park Young Mok , Kim Jin Young , Kwon Kyung‐Hoon , Lee Sang Kwang , Kim Young Hye , Kim Se‐Young , Park Gun Wook , Lee Jeong Hwa , Lee Bonghee , Yoo Jong Shin
Published: August 2006

In our initial attempt to analyze the human brain proteome, we applied multi‐dimensional protein separation and identification techniques using a combination of sample fractionation, 1‐D SDS‐PAGE, and MS analysis. The complexity of human brain proteome requires multiple fractionation strategies to extend the range and total number of proteins identified. According to the method of Klose (Methods Mol. Biol. 1999, 112, 67), proteins of the temporal lobe of human brain were fractionated into (i) cytoplasmic and nucleoplasmic, (ii) membrane and other structural, and (iii) DNA‐binding proteins. Each fraction was then separated by SDS‐PAGE, and the resulting gel line was cut into approximately 50 bands. After trypsin digestion, the resulting peptides from each band were analyzed by RP‐LC/ESI‐MS/MS using an LTQ spectrometer. The SEQUEST search program, which searched against the IPI database, was used for peptide sequence identification, and peptide sequences were validated by reversed sequence database search and filtered by the Protein Hit Score. Ultimately, 1533 proteins could be detected from the human brain. We classified the identified proteins according to their distribution on cellular components. Among these proteins, 24% were membrane proteins. Our results show that the multiple separation strategy is effective for high‐throughput characterization of proteins from complex proteomic mixtures.
2‐D DIGE as a quantitative tool for investigating the HUPO Brain Proteome Project mouse series
Authors: Föcking Melanie , Boersema Paul J. , O'Donoghue Niaobh , Lubec Gert , Pennington Stephen R. , Cotter David R. , Dunn Michael J.
Published: August 2006

Brain development and aging is a complex process involving proliferation, differentiation and apoptosis. Elucidating proteome changes in these processes can help to understand the mechanisms of brain development and maintenance as well as neurodegenerative diseases. The research reported here is a contribution to the HUPO Brain Proteome Project mouse pilot study. Whole, frozen C57BL/6J mouse brain comprising three different developmental stages (embryonic day 16, postnatal day 7, and postnatal days 54–58) were processed by using 2‐D DIGE. A total of 1999 spots were matched between all gels. Of these, 206 spots were differentially expressed between the different stages: 122 spots were highest in intensity in embryonic stage E16, 26 highest in the juvenile group P7 and 58 spots highest in P56, the adult stage. The results show a pattern of temporal expression. Based on the expression patterns we tentatively suggest that proteins involved in the establishment of primary structures in the brain are expressed highest in the embryonic mouse. Proteins involved in the development of the brain are expressed highest in the juvenile phase and proteins that make utilization of the brain possible by delivering energy are expressed highest in the adult mice.
Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase
Authors: Stephan Christian , Reidegeld Kai A. , Hamacher Michael , van Hall André , Marcus Katrin , Taylor Chris , Jones Philip , Müller Michael , Apweiler Rolf , Martens Lennart , Körting Gerhard , Chamrad Daniel C. , Thiele Herbert , Blüggel Martin , Parkinson David , Binz Pierre‐Alain , Lyall Andrew , Meyer Helmut E.
Published: August 2006

The newly available techniques for sensitive proteome analysis and the resulting amount of data require a new bioinformatics focus on automatic methods for spectrum reprocessing and peptide/protein validation. Manual validation of results in such studies is not feasible and objective enough for quality relevant interpretation. The necessity for tools enabling an automatic quality control is, therefore, important to produce reliable and comparable data in such big consortia as the Human Proteome Organization Brain Proteome Project. Standards and well‐defined processing pipelines are important for these consortia. We show a way for choosing the right database model, through collecting data, processing these with a decoy database and end up with a quality controlled protein list merged from several search engines, including a known false‐positive rate.
HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy
Authors: Hamacher Michael , Apweiler Rolf , Arnold Georg , Becker Albert , Blüggel Martin , Carrette Odile , Colvis Christine , Dunn Michael J. , Fröhlich Thomas , Fountoulakis Michael , van Hall André , Herberg Friedrich , Ji Juango , Kretzschmar Hans , Lewczuk Piotr , Lubec Gert , Marcus Katrin , Martens Lennart , Palacios Bustamante Nadine , Park Young Mok , Pennington Stephen R. , Robben Johan , Stühler Kai , Reidegeld Kai A. , Riederer Peter , Rossier Jean , Sanchez Jean‐Charles , Schrader Michael , Stephan Christian , Tagle Danilo , Thiele Herbert , Wang Jing , Wiltfang Jens , Yoo Jong Shin , Zhang Chenggang , Klose Joachim , Meyer Helmut E.
Published: August 2006

The Human Proteome Organisation (HUPO) initiated several projects focusing on the proteome analysis of distinct human organs. The Brain Proteome Project (BPP) is the initiative dedicated to the brain, its development and correlated diseases. Two pilot studies have been performed aiming at the comparison of techniques, laboratories and approaches. With the help of the results gained, objective data submission, storage and reprocessing workflow have been established. The biological relevance of the data will be drawn from the inter‐laboratory comparisons as well as from the re‐calculation of all data sets submitted by the different groups. In the following, results of the single groups as well as the centralised reprocessing effort will be summarised and compared, showing the added value of this concerted work.
Early events ofBacillus anthracisgermination identified by time‐course quantitative proteomics
Authors: Jagtap Pratik , Michailidis George , Zielke Ryszard , Walker Angela K. , Patel Nishi , Strahler John R. , Driks Adam , Andrews Philip C. , Maddock Janine R.
Published: August 2006

Germination ofBacillus anthracisspores involves rehydration of the spore interior and rapid degradation of several of the protective layers, including the spore coat. Here, we examine the temporal changes that occur duringB. anthracisspore germination using an isobaric tagging system. Over the course of 17 min from the onset of germination, the levels of at least 19 spore proteins significantly decrease. Included are acid‐soluble proteins, several known and predicted coat proteins, and proteins of unknown function. Over half of these proteins are small (less than 100 amino acids) and would have been undetectable by conventional gel‐based analysis. We also identified 20 proteins, whose levels modestly increased at the later time points when metabolism has likely resumed. Taken together, our data show that isobaric labeling of complex mixtures is particularly effective for temporal studies. Furthermore, we describe a rigorous statistical approach to define relevant changes that takes into account the nature of data obtained from multidimensional protein identification technology coupled with the use of isobaric tags. This study provides an expanded list of the proteins that may be involved in germination of theB. anthracisspore and their relative levels during germination.
Cyclocopolymerization of 1,4‐pentadiene with ethene in the presence of group‐4 metallocenes
Authors: Napoli Mariagrazia , Costabile Chiara , Cavallo Gabriella , Longo Pasquale
Published: August 2006

The behaviors ofrac‐[CH2(3‐tert‐butyl‐1‐indenyl)2]ZrCl2(1) and Cp2ZrCl2(2) activated by methylaluminoxane in ethene/1,4‐pentadiene copolymerization are compared. In the presence of1, inserted methylene‐1,3‐cyclobutane units, a large number of crosslinks, and a small number of methylene‐1,3‐cyclohexane units are obtained. Differently, a polyethene containing only 1,3‐cyclohexane rings is achieved with2as the catalytic precursor. Polymer microstructures are compared with those obtained with1and2in ethene/1,6‐heptadiene copolymerization, which leads only to polyethene containing cyclohexane rings. A tentative rationalization of the experimental data is reported. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5525–5532, 2006
Multiarm star nanocarriers containing a poly(ethylene imine) core and polylactide arms
Authors: Adeli M. , Haag R.
Published: August 2006

Star polymers (SPs) containing a hyperbranched poly(ethylene imine) (PEI; number‐average molecular weight = 10,000) core and polylactide arms were synthesized via the ring‐opening polymerization of lactide. PEI was used as a multifunctional macroinitiator for the ring‐opening polymerization of lactide. Different lactide monomer/amino‐functional group (LA/NHn; n = 1 or 2) ratios were used for preparing SPs with different molecular weights. SPs were able to encapsulate small guest molecules such as Rose Bengal; they also transported small, hydrophilic molecules from water to the organic phase. The transport capacity of all the nanocarriers depended on the LA/NHn ratio used for synthesizing the SPs. Nanocarriers with a higher LA/NHn ratio had higher transport capacities. The size of all the nanocarriers depended on the type of solvent. In chloroform, these nanoparticles had several sizes that were related to the self‐assembly of these nanocarriers, but in acetone, they were monodisperse, and their size was smaller than that in chloroform. Also, the transport of polar dyes from water to the chloroform phase was possible. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5740–5749, 2006
Exploring 9‐arylcarbazole moiety as the building block for the synthesis of photoluminescent group 10–12 heavy metal diynes and polyynes with high‐energy triplet states
Authors: Liu Li , Wong Wai‐Yeung , Shi Jian‐Xin , Cheah Kok‐Wai
Published: August 2006

A new series of organic‐soluble and thermally stable group 10 platinum(II) polyyne polymers functionalized with 9‐arylcarbazole moiety trans‐[Pt(PBu3)2CCRCC]n (R = 9‐arylcarbazole‐3,6‐diyl; aryl = phenyl, p‐methylphenyl, p‐fluorophenyl) were prepared in good yields by Hagihara's dehydrohalogenative polymerization of trans‐[PtCl2(PBu3)2] with HCCRCCH under ambient conditions. The regiochemical structures of the polymers were characterized by multinuclear NMR spectroscopy. We discuss the optical spectroscopy of these polymetallaynes and compare the results with their bimetallic molecular model complexes trans‐[Pt(Ph)(PEt3)2CCRCCPt(Ph)(PEt3)2] as well as its group 11 gold(I) and group 12 mercury(II) congeners [(PPh3)AuCCRCCAu(PPh3)] and [MeHgCCRCCHgMe]. The structural properties of several model complexes were studied by X‐ray crystallography. The influence of the heavy metal atom and the 9‐aryl substituent of carbazole on the phosphorescence behavior and the spatial distribution of the lowest singlet (S1) and triplet (T1) excitons in these metalated alkynyl systems are comprehensively elucidated. The present work indicates that the efficiency of organic triplet emissions harnessed through the heavy‐atom effect of group 10–12 transition metals in the main chain generally follows the order Pt > Au > Hg but the optical properties of the materials are relatively insensitive to the nature of the 9‐aryl group on the carbazolyl ring. All of these metallaynyl‐carbazole materials with high‐energy T1 states of 2.68 eV or higher show high phosphorescence efficiencies at low temperatures. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5588–5607, 2006
Synthesis and characterization of novel hyperbranched polybenzimidazoles based on an AB2 monomer containing four amino groups and one carboxylic group
Authors: Li Z. X. , Liu J. H. , Yang S. Y. , Huang S. H. , Lu J. D. , Pu J. L.
Published: August 2006

A new kind of AB2 monomer, 4‐[2,6‐bis(3,4‐diaminophenyl)pyridin‐4‐yl]benzoic acid, was synthesized, and several hyperbranched polybenzimidazoles (HPBIs) were prepared through self‐polymerization followed by modification reactions with end‐capping reagents such as 4‐methyl benzoic acid and 3‐[3,5‐bis(trifluoromethyl)phenoxy] benzoic acid. The HPBIs had good solubility in strongly aprotic solvents, such as N‐methyl‐2‐pyrrolidone, N,N′‐dimethylformamide, N,N′‐dimethylacetamide, and dimethyl sulfoxide. They also exhibited excellent thermal properties, with glass‐transition temperatures of 318–381 °C and 10% weight loss in the range of 338–674 °C in nitrogen and 329–509 °C in air. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5729–5739, 2006
Controlling grafting density and side chain length in poly(n‐butyl acrylate) by ATRP copolymerization of macromonomers
Authors: Ohno Shigeki , Matyjaszewski Krzysztof
Published: August 2006

Atom transfer radical polymerization (ATRP) was used for the preparation and subsequent copolymerization of two acryloyl‐terminated poly(n‐butyl acrylate) macromonomers with different degrees of polymerization (DPnBA = 25 and 42). Homopolymerization of the higher molecular weight macromonomer (MM1; PnBA42‐A, Mn = 5600, DPMM = 42, Mw/Mn = 1.18) resulted in preparation of a densely grafted polymer with a narrow molecular weight distribution (Mw/Mn = 1.14), but with the limited degree of polymerization DP = 12. The ultimate degree of homopolymerization for the lower molecular weight macromonomer (MM2; PnBA25‐A, Mn = 3400, DPMM = 25, Mw/Mn = 1.20) was higher, and DP increased from 12 to 22. The limited DP could be because of progressively increasing steric congestion for macromonomers in approaching the growing chain ends of densely grafted polymers. When MMs were copolymerized with nBA, the reactivity of MM was nearly the same as that of nBA monomer irrespective of the differences in the degree of polymerization of the MMs and the initial molar ratio of nBA to MM. Well‐defined graft polymers with different lengths of backbone and side chains, and different graft density were successfully prepared by “grafting through” ATRP. Tadpole‐shaped and dumbbell‐shaped graft polymers were also synthesized by ATRP. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5454–5467, 2006
Synthesis of poly(n‐hexyl isocyanate‐b‐N‐vinylpyrrolidone) block copolymers by the combination of anionic and nitroxide‐mediated radical polymerizations: Micellization properties in aqueous solutions
Authors: Bilalis Panayiotis , Zorba Georgia , Pitsikalis Marinos , Hadjichristidis Nikos
Published: August 2006

A combination of anionic and nitroxide‐mediated radical polymerizations (dual initiator) was employed for the synthesis of poly(n‐hexyl isocyanate‐b‐N‐vinylpyrrolidone) (PHIC‐b‐PNVP) block copolymers. The samples were characterized with a size exclusion chromatograph equipped with refractive‐index and light scattering detectors as well as 1H NMR spectroscopy. Relatively good control over the molecular weights was achieved. However, rather broad molecular weight distributions were obtained. The micellar properties of the PHIC‐b‐PNVP block copolymers were studied in water, which is a selective solvent for the poly(N‐vinylpyrrolidone) blocks. Static and dynamic light scattering revealed the presence of equilibrium between the micelles and clusters. The clusters partially deaggregated with increasing temperature. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5719–5728, 2006
Synthesis and investigation of the effect of nematic phases on the glass‐transition behavior of novel cycloaliphatic liquid‐crystalline poly(ester amide)s
Authors: Deepa P. , Sona C. , Jayakannan M.
Published: August 2006

We designed and developed novel cycloaliphatic liquid‐crystalline (LC) poly(ester amide)s to investigate the effects of nematic LC phases and hydrogen‐bonding interactions on the glass‐transition behavior. Three series of poly(ester amide)s based on commercially important poly(1,4‐cyclohexanedimethylene terephthalate) were synthesized with two new cycloaliphatic diamines {3,8‐bis(aminomethyl)‐tricyclo [5.2.1.0.(2,6)]decane (tricyclic) and 1,3‐cyclohexane bismethylene amine (monocyclic)} and a linear counterpart (1,6‐hexamethylene diamine). The compositions of the ester/amide units in the copolymers were varied up to 50% by the adjustment of the amounts of the diol and diamine in the feed. The structures of the polymers were confirmed with NMR and Fourier transform infrared, and their inherent viscosities were measured at 30 °C with an Ubbelohde viscometer. Thermal analysis revealed that the poly(ester amide)s having less than 25 mol % amide linkages were thermotropic and LC, and threadlike nematic phases were observed under a polarizing microscope. The introduction of nematic, LC phases drastically affected the glass‐transition temperatures of the copolymers, and a plot of the composition versus the glass‐transition temperature passed through a maximum for lower amide incorporation, regardless of the structural differences of the amide units (cyclic or linear). This nonlinear Flory–Fox trend was correlated to the cooperative effect of the strong alignment of polymer chains in the nematic phases and intermolecular packing induced by the hydrogen bonding in the poly(ester amide)s. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5557–5571, 2006
Synthesis and properties of thermosetting polymers from a phosphorous‐containing fatty acid derivative
Authors: Lligadas G. , Ronda J. C. , Galià M. , Cádiz V.
Published: August 2006

A new phosphorous‐containing fatty acid diepoxide was obtained from 10‐undecenoyl chloride and 10‐(2′,5′‐dihydroxyphenyl)‐9,10‐dihydro‐9‐oxa‐10‐phosphaphenanthrene‐10‐oxide and crosslinked with 4,4′‐diaminodiphenylmethane and bis(m‐aminophenyl)methylphosphine oxide. The properties of the thermosetting materials were evaluated by differential scanning calorimetry, dynamic mechanical thermal analysis, thermogravimetric analysis, and limiting oxygen index (LOI). Thermal and thermooxidative degradation was studied by gas chromatography/mass spectrometry, FTIR, 31P magic angle spinning NMR spectroscopy, and scanning electron microscopy. LOI values indicate good flame‐retardant properties that are related to the formation of a protective phosphorous‐rich layer that slowed down the degradation and prevented it from being total. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5630–5644, 2006
Switchable thin‐film surface prepared via a simple grafting‐to method using a polystyrene‐b‐poly(2‐vinylpyridine) copolymer
Authors: Wang Ying , Zheng Joseph X. , Brittain William J. , Cheng Stephen Z. D.
Published: August 2006

A polystyrene‐b‐poly(2‐vinylpyridine) block copolymer containing a methylhydridosilane linking group was chemically grafted to an 8‐trichlorosilyloctene monolayer via a simple one‐step hydrosilylation reaction. The resulting Y‐shaped thin film exhibited a low grafting density, which was characteristic of the grafting‐to technique. To further reduce the miscibility of the two arms, methyl iodide was reacted with the poly(2‐vinylpyridine) block to produce quaternary ammonium groups. The surfaces before and after quaternization were both solvent‐switchable when subjected to block‐selective solvents. Tensiometry, ellipsometry, attenuated total reflection/Fourier transform infrared, and atomic force microscopy were used to characterize the properties and morphology of both unquaternized and quaternized samples. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5608–5617, 2006
Free‐radical copolymerization of ethyl α‐hydroxymethylacrylate with methyl methacrylate by reversible addition–fragmentation chain transfer
Authors: Cuervo‐Rodríguez R. , Bordegé V. , Sánchez‐Chaves M. , Fernández‐García M.
Published: August 2006

The controlled free‐radical homopolymerization of ethyl α‐hydroxymethylacrylate and copolymerization with methyl methacrylate were performed in chlorobenzene at 70 °C by the reversible addition–fragmentation chain transfer polymerization technique with 2,2′‐azobisisobutyronitrile as the initiator. 2‐Phenylprop‐2‐yl dithiobenzoate and 2‐cyanoprop‐2‐yl dithiobenzoate were used as chain‐transfer agents in the homopolymerization, whereas only the former was used in the copolymerization. All reactions presented pseudolinear kinetics. The effect of the monomer feed ratio on the copolymerization kinetics was examined. The conversion level decreased when the proportion of ethyl α‐hydroxymethylacrylate in the monomer feed was larger. Kinetic studies indicated that the radical polymerizations proceeded with apparent living character according to experiments, demonstrating an increase in the molar mass with the monomer conversion and a relatively narrow molar mass distribution. All copolymers were statistical in chain structure, as confirmed by determinations of the monomer reactivity ratios. The monomer reactivity ratios were determined, and the Mayo–Lewis terminal model provided excellent predictions for the variations of the intermolecular structure over the entire conversion range. Additionally, the chemical modification of poly(ethyl α‐hydroxymethylacrylate) was carried out to introduce glucose pendant groups into the structure. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5618–5629, 2006
Polyketanils. Polymers protonated with Bronsted acid
Authors: Iwan Agnieszka , Kaczmarczyk Bozena , Kasperczyk Janusz , Jurusik Jan , Janeczek Henryk , Sek Danuta , mazurak Zbigniew
Published: August 2006

New luminescent materials—aromatic polyketanils (PKs) containing p‐phenylene and biphenylene linkages in the backbone and electron‐donating, side‐group substitutions—were synthesized via melt polycondensation with the goal of studying the interactions between the polymer chains (PKs), primary dopant [1,2‐(di‐2‐ethylhexyl)ester of 4‐sulfophthalic acid (PSA)], and secondary dopant [m‐cresol (MC)] with 1H NMR, 13C NMR, Fourier transform infrared (FTIR), ultraviolet–visible, and photoluminescence measurements. Spectral changes were observed for the PKs after primary and secondary doping, and they supported ionic‐ and hydrogen‐bond formation between the PKs and the PSA and MC, respectively. This specific interaction of the dopant with the host polymer influenced the PK properties, and the following observations were made: (1) HOMO/LUMO energy gap of the protonated PKs; (2) bathochromic/hypsochromic photoluminescence shifts observed after protonation with PSA; (3) a downfield chemical shift of the labile proton in the protonating agent OH group in the 1H NMR spectra of the protonated polymers; (4) a protonation decrease in the intensity of the CN stretching band in the FTIR spectrum; and (5) a spherulite‐like morphology, detected by atomic force microscopy and polarized optical microscopy. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5645–5660, 2006
Burnout and psychiatric morbidity among physicians engaged in end‐of‐life care for cancer patients: a cross‐sectional nationwide survey in Japan
Authors: Asai Mariko , Morita Tatsuya , Akechi Tatsuo , Sugawara Yuriko , Fujimori Maiko , Akizuki Nobuya , Nakano Tomohito , Uchitomi Yosuke
Published: August 2006

Purpose: To determine the prevalence of burnout and psychiatric morbidity among physicians engaged in end‐of‐life care for cancer patients in Japan and to explore associated factors related to end‐of‐life care.

Methods: Questionnaires were mailed to 1436 Japanese clinical oncologists and palliative care physicians with a request to complete the Maslach Burnout Inventory (MBI), the General Health Questionnaire (GHQ‐12), and to report on individual factors, including confidence in patient care. High levels of burnout and psychiatric morbidity were identified using cut‐off scores of the MBI and GHQ‐12.

Results: A total of 697 physicians returned the questionnaires (response rate, 49.6%). Twenty‐two percent of the respondents had a high level of emotional exhaustion, 11% had a high level of depersonalization, 62% had a low level of personal accomplishment, and 20% had psychiatric morbidity. Clinical oncologists showed a significantly higher psychiatric morbidity than palliative care physicians. Confidence in having sufficient time to communicate with patients was significantly associated with all the burnout subscales.

Conclusions: A low level of personal accomplishment was relatively high among Japanese physicians compared with previous studies. Insufficient confidence in the psychological care of patients was associated with physician burnout rather than involvement in end‐of‐life care. Copyright © 2006 John Wiley & Sons, Ltd.
Screening childhood cancer survivors with the brief symptom inventory‐18: classification agreement with the symptom checklist‐90‐revised
Authors: Recklitis Christopher J. , Rodriguez Paola
Published: August 2006

The Brief Symptom Inventory‐18 (BSI‐18) is an 18‐item symptom checklist used as a brief distress screening in cancer and other medical patients. This study evaluated the validity of the BSI‐18 in a sample of 221 adult survivors of childhood cancers ages 18–55 (median = 26). Validity of the BSI‐18 was compared to the Symptom Checklist‐90‐Revised (SCL‐90‐R). Results indicated the BSI‐18 scales had acceptable internal consistency (alpha >0.80) and were highly correlated with the corresponding SCL‐90‐R subscales (correlations from 0.88 to 0.94). When subjects were classified as case positive (significantly distressed) using the BSI‐18 manual case‐rule, classification agreement with the SCL‐90‐R was poor as evidenced by low sensitivity (41.78%). An alternative BSI‐18 case‐rule previously developed for cancer patients using the General Severity Index (GSI; GSI t‐score ⩾57) demonstrated better sensitivity (83.54%). ROC analysis indicated the BSI‐18 had strong diagnostic utility relative to the SCL‐90‐R (AUC = 0.98) and several possible GSI cut‐off scores were evaluated. The optimal cut‐of score was a t‐score ⩾50 which had a sensitivity of 97.47% and a specificity of 85.21%. Results support use of the BSI‐18 with adult survivors of childhood cancer but indicate an alternative case‐rule must be used. Copyright © 2006 John Wiley & Sons, Ltd.
Behavioral risk factors among Black and White women newly diagnosed with breast cancer
Authors: Tercyak Kenneth P. , Davis Kimberly M. , Loffredo Christopher A.
Published: August 2006

Background: To determine the rates of three behavioral risk factors (depression symptoms, smoking, and drinking) among women newly diagnosed with breast cancer and to examine if the rates under investigation differed between Black and White women.

Method: Subjects were 147 women (47% Black, 53% White) newly diagnosed with breast cancer and participating in an epidemiologic interview study conducted at two metropolitan area cancer centers in the same city. The epidemiologic interview included women's tobacco, alcohol, and drug use history, medical and family history, and depression symptoms.

Results: Among all women in the sample, 33% reported clinically significant depression symptoms, 10% currently smoked cigarettes, and 57% currently drank alcohol. Seventy percent of women reported experiencing one or more behavioral risk factors, and White women were more likely than Black women to do so. After controlling for other demographic variables, White women were 50% more likely to report clinical symptoms of depression (odds ratio=1.55, 95% confidence interval=1.03, 2.30) and over two times more likely to report being current drinkers (odds ratio=2.19, 95% confidence interval=1.45, 3.30) than were Black women (p<0.05).

Conclusions: The results suggest that certain behaviors of Black women may be associated with lower levels of self‐reported distress. These findings also suggest the need for further research to examine behavioral comorbidity among women with breast cancer, and the roles that race, ethnicity, and culture may play in their expression. Copyright © 2006 John Wiley & Sons, Ltd.
Using the theory of planned behavior to understand the determinants of exercise intention in patients diagnosed with primary brain cancer
Authors: Jones Lee W. , Guill Bebe , Keir Stephen T. , Carter Karen , Friedman Henry S. , Bigner Darell D. , Reardon David A.
Published: August 2006

The purpose of the present study was to examine the demographic, medical, and social cognitive determinants of exercise intentions in a institution‐based cohort of primary brain tumor patients. Using a cross‐sectional survey, 100 primary brain tumor patients completed a mailed survey that assessed medical and demographic characteristics, past exercise behavior using the Godin Leisure Time Exercise Questionnaire (GLTEQ), and social cognitive beliefs towards exercise using Aizen's theory of planned behavior (TPB; i.e. intention, perceived behavioral control, subjective norm, affective and instrumental attitude). Descriptive statistics indicated that participants had positive social cognitive beliefs towards exercise. In support of the tenets of the TPB, we found moderate to large (>0.40) positive correlations between the majority of TPB constructs. Moreover, the TPB constructs combined to explain 32% of the variance in exercise intentions with affective attitude (β = 0.24; p = 0.020) and perceived behavioral control (β = 0.36; p<0.001) being the most important determinants. Except past exercise behavior, medical and demographic variables were not consistently correlated with any TPB constructs. Finally, participant's gender and body mass index influenced the association between instrumental attitude and exercise intention with male and overweight/obese patients (⩾25 kg/m2) considering the health benefits of exercise to be more important than their female and normal weight (<25 kg/m2) counterparts. Information gained from this study suggests that the TPB is a useful framework to design and implement theoretically based interventions to promote exercise in primary brain cancer patients. Copyright © 2006 John Wiley & Sons, Ltd.
Current methodological approaches to the study of sleep disturbances and quality of life in adults with cancer: a systematic review
Authors: Berger Ann M. , Sankaranarayanan Jayashri , Watanabe‐Galloway Shinobu
Published: August 2006

In recent years, sleep disturbances and the health‐related quality of life (QOL) experienced by adults with cancer, during and after cancer treatment, have received increasing attention in the scientific literature. The purpose of this paper was to systematically review current methodological approaches to the study of sleep disturbances and QOL in adults with cancer. Databases were searched to identify longitudinal studies of adults with cancer that measured sleep disturbances and QOL in the past 10 years. The review was focused in five primary areas: trends in publication, measurement of sleep and QOL, study design, changes in sleep disturbances and QOL, and the level of this evidence. Of the 40 studies that met the authors' criteria for inclusion, 75% were descriptive in design and 25% were intervention studies. Studies on sleep and QOL among cancer patients have become more common since 2000, include a range of sample sizes and settings, use a variety of measures of sleep and QOL, and examine patients undergoing many types of cancer therapies. No programs of research have been developed in sleep disturbances and QOL in adults with cancer. The ‘evidence’ that can be drawn from such studies is obviously weak. Current approaches usually describe changes over time, but have not described whether a relationship exists between sleep disturbances and QOL in adults with cancer. Directions for future research are suggested. Copyright © 2006 John Wiley & Sons, Ltd.
Comparison of Primary Rat Hepatocyte Attachment to Collagen and Plasma‐Polymerised Allylamine on Glass
Authors: Dehili Chafika , Lee Pauline , Shakesheff Kevin M. , Alexander Morgan R.
Published: August 2006

Summary: Cellular attachment to substrata is a crucial stage in cell culture and tissue engineering. Many cells including hepatocytes attach poorly to synthetic substrata and favour attachment to ECM proteins. Currently, cellular attachment to synthetic materials is often optimised by applying ECM protein coatings such as collagen. In this work, ppAAm was examined as an alternative coating method to collagen type‐I gel to promote attachment of primary rat hepatocytes to glass. XPS analysis was used to quantify the composition of the nitrogen containing ppAAm surfaces where the nitrogen is present in the form of amine, imine and possibly amide functionalities. Phase contrast microscopy and total cellular protein measurements indicated that hepatocyte attachment to glass was significantly improved by coating with ppAAm, collagen type‐I gel or collagen type‐I gel on ppAAm. In addition, cytochrome P450 activity and albumin secretion of hepatocytes cultured on ppAAm were similar to the levels observed in hepatocytes plated on collagen type‐I gel or collagen type‐I gel on ppAAm. In conclusion, the ppAAm coating was shown to improve the attachment of hepatocytes to glass while maintaining similar functionality to cells cultured on collagen type‐I gel.

Phase contrast images of primary rat hepatocytes plated on collagen type‐I gel (top) and plasma polymerised allylamine (bottom) after 24 h in culture.

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Phase contrast images of primary rat hepatocytes plated on collagen type‐I gel (top) and plasma polymerised allylamine (bottom) after 24 h in culture.
Inactivation of Bacteria by the Plasma Pencil
Authors: Laroussi Mounir , Tendero Claire , Lu Xinpei , Alla Sudhakar , Hynes Wayne L.
Published: August 2006

Summary: A device capable of generating a relatively long cold plasma plume has recently been developed. The advantages of this device are: plasma controllability and stability, room temperature and atmospheric pressure operation, and low power consumption. These features are what is required from a plasma source to be used reliably in material processing applications, including the biomedical applications. In this communication we describe the device and we present evidence that it can be used successfully to inactivate Escherechia coli in a targeted fashion. More recent experiments have shown that this device inactivates other bacteria also, but these will be reported in the future.

Photograph of a He plasma plume launched out of the plasma pencil.

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Photograph of a He plasma plume launched out of the plasma pencil.
Long loop prediction using the protein local optimization program
Authors: Zhu Kai , Pincus David L. , Zhao Suwen , Friesner Richard A.
Published: August 2006

We have developed an improved sampling algorithm and energy model for protein loop prediction, the combination of which has yielded the first methodology capable of achieving good results for the prediction of loop backbone conformations of 11 residue length or greater. Applied to our newly constructed test suite of 104 loops ranging from 11 to 13 residues, our method obtains average/median global backbone root‐mean‐square deviations (RMSDs) to the native structure (superimposing the body of the protein, not the loop itself) of 1.00/0.62 Å for 11 residue loops, 1.15/0.60 Å for 12 residue loops, and 1.25/0.76 Å for 13 residue loops. Sampling errors are virtually eliminated, while energy errors leading to large backbone RMSDs are very infrequent compared to any previously reported efforts, including our own previous study. We attribute this success to both an improved sampling algorithm and, more critically, the inclusion of a hydrophobic term, which appears to approximately fix a major flaw in SGB solvation model that we have been employing. A discussion of these results in the context of the general question of the accuracy of continuum solvation models is presented. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge‐based potentials, and clustering
Authors: Zhu Jiang , Xie Li , Honig Barry
Published: August 2006

In this article, we present an iterative, modular optimization (IMO) protocol for the local structure refinement of protein segments containing secondary structure elements (SSEs). The protocol is based on three modules: a torsion‐space local sampling algorithm, a knowledge‐based potential, and a conformational clustering algorithm. Alternative methods are tested for each module in the protocol. For each segment, random initial conformations were constructed by perturbing the native dihedral angles of loops (and SSEs) of the segment to be refined while keeping the protein body fixed. Two refinement procedures based on molecular mechanics force fields — using either energy minimization or molecular dynamics — were also tested but were found to be less successful than the IMO protocol. We found that DFIRE is a particularly effective knowledge‐based potential and that clustering algorithms that are biased by the DFIRE energies improve the overall results. Results were further improved by adding an energy minimization step to the conformations generated with the IMO procedure, suggesting that hybrid strategies that combine both knowledge‐based and physical effective energy functions may prove to be particularly effective in future applications. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein–ligand complexes
Authors: Czodrowski Paul , Dramburg Ingo , Sotriffer Christoph A. , Klebe Gerhard
Published: August 2006

For routine pKa calculations of protein–ligand complexes in drug design, the PEOE method to compute partial charges was modified. The new method is applicable to a large scope of proteins and ligands. The adapted charges were parameterized using experimental free energies of solvation of amino acids and small organic ligands. For a data set of 80 small organic molecules, a correlation coefficient of r2 = 0.78 between calculated and experimental solvation free energies was obtained. Continuum electrostatics pKa calculations based on the Poisson–Boltzmann equation were carried out on a validation set of nine proteins for which 132 experimental pKa values are known. In total, an overall RMSD of 0.88 log units between calculated and experimentally determined data is achieved. In particular, the predictions of significantly shifted pKa values are satisfactory, and reasonable estimates of protonation states in the active sites of lysozyme and xylanase could be obtained. Application of the charge‐assignment and pKa‐calculation procedure to protein–ligand complexes provides clear structural interpretations of experimentally observed changes of protonation states of functional groups upon complex formation. This information is essential for the interpretation of thermodynamic data of protein–ligand complex formation and provides the basis for the reliable factorization of the free energy of binding in enthalpic and entropic contributions. The modified charge‐assignment procedure forms the basis for future automated pKa calculations of protein–ligand complexes. Proteins 2006; © 2006 Wiley‐Liss, Inc.
Impact of EGFR point mutations on the sensitivity to gefitinib: Insights from comparative structural analyses and molecular dynamics simulations
Authors: Liu Bing , Bernard Brandon , Wu Jian Hui
Published: August 2006

Emergence of resistant mutations in drug targets represents a serious problem in the targeted chemotherapy. One challenging issue is to understand the atomic‐detailed effect of the mutation on the target. Another intriguing issue is how to predict specific mutations that would show up in the clinical setting, leading to drug resistance. By computational approaches, we have investigated structural, dynamics and energetic effects of a series of EGFR mutations identified from the lung cancer patients. We demonstrated mutation L858R caused gefitinib move closer to the hinge region, whereas T790M caused the ligand escape from the binding pocket. In particular, the T790M decreased the size of the hydrophobic slot formed by L718 and G796. This suggests that, to be effective against the T790M mutant, the inhibitors should avoid interactions with the hydrophobic slot. Mutations T790M, L858R, and their combinations are found to cause different conformational redistribution and to perturb the electrostatic potential at the ATP‐binding pocket. Normal mode analysis revealed the mutations resulted in changes in the correlated movements in the protein. In an attempt to develop a computational descriptor for predicting the functional effect of EGFR mutations, we have developed a Plarm algorithm, and the Plarm score was found to be an excellent predictor of the functional impact of six clinical relevant mutations in EGFR tyrosine kinase domains, including T790M, L858R, G719C, L861Q, T790M + L858R double mutant, and delL747–P753insS. The Plarm algorithm could be readily extended to investigate other drug targets. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Structure determination of a new protein from backbone‐centered NMR data and NMR‐assisted structure prediction
Authors: Mayer K. L. , Qu Y. , Bansal S. , LeBlond P. D. , Jenney F. E. , Brereton P. S. , Adams M. W. W. , Xu Y. , Prestegard J. H.
Published: August 2006

Targeting of proteins for structure determination in structural genomic programs often includes the use of threading and fold recognition methods to exclude proteins belonging to well‐populated fold families, but such methods can still fail to recognize preexisting folds. The authors illustrate here a method in which limited amounts of structural data are used to improve an initial homology search and the data are subsequently used to produce a structure by data‐constrained refinement of an identified structural template. The data used are primarily NMR‐based residual dipolar couplings, but they also include additional chemical shift and backbone‐nuclear Overhauser effect data. Using this methodology, a backbone structure was efficiently produced for a 10 kDa protein (PF1455) from Pyrococcus furiosus. Its relationship to existing structures and its probable function are discussed. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Identifying cysteines and histidines in transition‐metal‐binding sites using support vector machines and neural networks
Authors: Passerini Andrea , Punta Marco , Ceroni Alessio , Rost Burkhard , Frasconi Paolo
Published: August 2006

Accurate predictions of metal‐binding sites in proteins by using sequence as the only source of information can significantly help in the prediction of protein structure and function, genome annotation, and in the experimental determination of protein structure. Here, we introduce a method for identifying histidines and cysteines that participate in binding of several transition metals and iron complexes. The method predicts histidines as being in either of two states (free or metal bound) and cysteines in either of three states (free, metal bound, or in disulfide bridges). The method uses only sequence information by utilizing position‐specific evolutionary profiles as well as more global descriptors such as protein length and amino acid composition. Our solution is based on a two‐stage machine‐learning approach. The first stage consists of a support vector machine trained to locally classify the binding state of single histidines and cysteines. The second stage consists of a bidirectional recurrent neural network trained to refine local predictions by taking into account dependencies among residues within the same protein. A simple finite state automaton is employed as a postprocessing in the second stage in order to enforce an even number of disulfide‐bonded cysteines. We predict histidines and cysteines in transition‐metal‐binding sites at 73% precision and 61% recall. We observe significant differences in performance depending on the ligand (histidine or cysteine) and on the metal bound. We also predict cysteines participating in disulfide bridges at 86% precision and 87% recall. Results are compared to those that would be obtained by using expert information as represented by PROSITE motifs and, for disulfide bonds, to state‐of‐the‐art methods. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Prediction of flammability speciation for the lower alkanes, carboxylic acids, and esters
Authors: Palucis M. , Glowienka T. , Van Brunt V. , Ervin R. , Chastain W. , Kline R. , Lodal P.
Published: August 2006

A Gibbs energy minimization procedure is used to predict the flammability envelopes of alkanes, carboxylic acids, and acetates. In addition to providing the calculated adiabatic flame temperature (CAFT), the product profiles reveal regions of incomplete combustion products and the onset of methane formation above 0.0001 mole fraction. Temperatures at the predicted onset of methane production appear to be closely related to the temperature at the upper flammability limit (UFL). Although a fixed CAFT value could be related to the lower flammability limit (LFL), it was found that this was not the case with the UFL and only for acetic acid could a single CAFT value of 1200K be used to conservatively predict the flammable region. Rather, in general, a single CAFT value could not conservatively predict the upper flammable region. The predictions also reveal local maxima and minima in the concentrations of reaction products. These maps of incomplete combustion products for the flammability region predict that incomplete combustion products are produced at fuel/oxygen ratios significantly below the fuel/oxygen stoichiometric ratio. This region decreases as the limiting oxygen concentration is approached. © 2006 American Institute of Chemical Engineers Process Saf Prog, 2006
Retracted: Spatial distribution of beetle pests in precision integrated pest management in a food processing mill
Authors: Trematerra Pasquale , Gentile Paolo
Published: August 2006

Retracted: P. Trematerra and P. Gentile. Spatial distribution of beetle pests in precision integrated Pest Management in a food processing mill, Pest Management Science. [DOI: 10.1002/ps.1250].
The above article, published online in EarlyView on 28 June 2006, has been retracted for legal reasons. Copyright © 2006 Society of Chemical Industry