bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of perpetrator similarity in reactions toward innocent victims
Authors: Bal Michèlle , van den Bos Kees 
Published: July 2009

AbstractBuilding and extending on just world theory, this paper studies people's negative reactions to innocent victims of rape or sexual assault. Specifically, we focus on an as yet unexplored variable that may help to explain these reactions, namely whether the perpetrator of the crime was similar or dissimilar to people who observed what happened to the victim. Perpetrator similarity refers to whether the perpetrator belongs to the personal world of the observer or not, and in accordance with predictions derived from just world theory, findings of three studies reveal that especially men take more physical distance from an innocent victim (Study 1) and blame (Study 2) and derogate (Study 3) an innocent victim more when the perpetrator is similar to them as opposed to when the perpetrator is different from them. Implications are discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Detection of autoantibodies against cyclophilin A and triosephosphate isomerase in sera from breast cancer patients by proteomic analysis
Authors: Tamesa Michiko Sato , Kuramitsu Yasuhiro , Fujimoto Masanori , Maeda Noriko , Nagashima Yukiko , Tanaka Toshiyuki , Yamamoto Shigeru , Oka Masaaki , Nakamura Kazuyuki 
Published: July 2009

AbstractMuch interest is presently being shown toward identifying markers for the detection of breast cancer. To detect autoantibodies that could represent diagnostic markers for breast cancer, we comprehensively analyzed serum autoantibodies showing immunoreactivity to proteins in tumor tissues of breast cancer. Tumor tissues were obtained from 40 patients with breast cancer, along with sera from 30 other patients with breast cancer and 22 healthy donors. Proteins from tumor tissues were separated by 2‐DE. After blotting onto PVDF membranes, tissue proteins were immunoblotted with sera from patients or healthy donors. By comparing each immunoblot pattern, three immunoreactive spots displayed stronger staining intensity with patient sera than with sera from healthy donors. The matched protein spots on 2‐DE gels were digested and used for LC‐MS/MS analysis, and identified as cyclophilin A (peptidyl‐prolylcis‐transisomerase A), triosephosphate isomerase and ubiquitin‐conjugating enzyme E2N. Immunoblot analysis was then performed using commercially available purified proteins, confirming the specificity of anti‐cyclophilin A and anti‐triosephosphate isomerase antibodies in sera from patients.
Rapid recovery of DNA from agarose gel slices by coupling electroelution with monolithic SPE
Authors: Yu Shengbing , Yang Shuixian , Zhou Ping , Zhou Ke , Wang Jing , Chen Xiangdong 
Published: July 2009

AbstractAn amino silica monolithic column prepared by in situ polymerization of tetraethoxysilane and N‐(β‐aminoethyl)‐γ‐aminopropyltriethoxysilane was firstly applied to recover DNA from agarose gel slices by coupling electroelution with monolithic SPE. DNA was electroeluted from the agarose gel slices onto the amino silica monolithic column. The DNA adsorbed on this monolithic column was then recovered using sodium phosphate solution at pH 10. The whole recovery procedure could be completed within 10 min because the use of amino silica monolithic column accelerated the DNA capture and facilitated the DNA release. Electroelution conditions, such as buffer pH, buffer concentration and applied voltage, were online optimized. The average yield for herring sperm DNA, pBR 322 DNA and λDNA recovered from 1.0% w/v agarose gel slices were 55±4, 50±6 and 42±7% (n=3), respectively. The polymerase chain reaction performance of pGM plasmid recovered from agarose gel slices demonstrated that the method could provide high‐quality DNA for downstream processes. The combination of electroelution with monolithic SPE allows a rapid, simple and efficient DNA recovery method. This technique is especially useful for applications that need to purify small starting amounts of DNA.
Separation of acidic and basic proteins by CE with CTAB additive and its applications in peptide and protein profiling
Authors: Liu Qian , Yang Yanmin , Huang Yan , Pan Chunfeng , Nie Zhou , Yao Shouzhuo 
Published: July 2009

AbstractIn this paper, we report a very simple but efficient cationic micellar CE method for protein analysis in complex samples without any modification for the capillary wall. It was found that increased concentration (≥2 mM) of CTAB additive in electrophoretic buffer can effectively suppress the wall adsorption of both acidic and basic proteins. The separation was improved with buffer pH decreasing from 6.0 to 3.0. By using a buffer containing 2 mM CTAB at pH 3.0, nine proteins with a wide range of pI values (4.7–11.0) were separated within 9 min with high efficiencies (>6×105 plates per meter) and good reproducibility (RSDs of migration time <0.8% for run‐to‐run assays) and recoveries (91.6–119.0%). This method was successfully applied to the analysis of complex biological samples, including plasma and red blood cells. Most importantly, we demonstrate the proteomic applications of the proposed method, including the analysis of tryptic digests of BSA and crude protein extracts from Escherichia coli cells. With simplicity, high efficiency, and good reproducibility, this method is promising for protein analysis in complex samples and may find its place in the future proteomic research.
Proteomic signature of reversine‐treated murine fibroblasts by 2‐D difference gel electrophoresis and MS: Possible associations with cell signalling networks
Authors: Fania Chiara , Anastasia Luigi , Vasso Michele , Papini Nadia , Capitanio Daniele , Venerando Bruno , Gelfi Cecilia 
Published: July 2009

AbstractRecent advances in stem cell biology have demonstrated that terminally differentiated adult cells can be induced to de‐differentiate into progenitor cells (induced stem cells) upon proper stimuli. This has been achieved by the induced expression of key regulatory genes by retro‐ or lenti‐viral systems. On the other hand, synthetic “small molecules” can also induce de‐differentiation and may represent a potentially safer approach as compared with genetic manipulation. Along this line, a synthetic purine called “reversine” has been shown to induce the de‐differentiation of fibroblasts into mesenchymal stem‐cell‐like progenitors, which can be successively induced to differentiate into skeletal muscle, smooth muscle and bone cells. The mechanism whereby reversine is able to achieve de‐differentiation has yet to be clarified. In this context, we defined the protein changes induced by reversine treatment in murine fibroblasts by 2‐D difference gel electrophoresis, coupled with MS. Proteins involved in cytoskeletal and cell shape remodeling, RNA export, degradation, folding, stress control and ATP production were found to be remarkably changed after reversine treatment. Ingenuity pathway analysis (IPA) predicted that these protein pattern changes enabled to propose that about 40 proteins might be associated to several biological functional networks, including cellular assembly, cell signaling and cell death. Altogether our data confirm the intrinsic complexity of the de‐differentiation process induced by reversine and suggest more selected approaches to investigate the action mechanism of this small molecule.
Protein attachment onto silica surfaces – a survey of molecular fundamentals, resulting effects and novel preventive strategies in CE
Authors: Stutz Hanno 
Published: July 2009

AbstractThis review addresses the fundamentals governing the adsorption of individual protein molecules onto the surface of fused‐silica capillaries, the protein aggregation to adsorbate clusters and their final accretion to monolayers with subsequent stratification to protein multilayers. The attention in CE protein separation has primarily been focused on (i) tuning the BGE including the buffer type, ionic strength, pH and additives, (ii) tailored post‐rinse procedures to detach adhered protein residues and (iii) the optimization of capillary wall shielding in order to reduce protein attachment. Improvements in protein separation as well as related adverse effects are mainly discussed on the basis of parameters known to become deteriorated in case of protein adhesion, e.g. repeatability of the EOF and of migration times, peak width, theoretical plate numbers, resolution and asymmetry factor. However, knowledge of the molecular principles controlling protein adsorption onto silica surfaces is indispensable for separation optimization. Furthermore, it facilitates troubleshooting and the interpretation of undesired concomitant phenomena. This review comprehensively discusses protein adsorption models derived from surface chemistry primarily in terms of their relevance for CE, clearly showing that the adsorption process in its complexity is only partially revealed by models, which address single or binary protein solutions. In a further section theoretical concepts and surface models are related to surface phenomena encountered in CE. The final part of the review surveys recent concepts for prevention of protein adhesion, thereby addressing capillary treatment, favorable buffer types, dynamic and adhesive semi‐permanent coating strategies covering the literature from 2000–2008.
Complete sequencing of GABAAreceptor subunit β3 by a rapid technique following in‐gel digestion of the protein
Authors: Kang Sung Ung , Lubec Gert 
Published: July 2009

AbstractKnowledge on complete sequences is pivotal to identify splice variants, generate specific antibodies and predict conformation. A simple analytical approach to obtain 100% sequence coverage, however, is currently not available. Recombinant gamma‐aminobutyric acid A receptor subunits were from insect SF9 cells that were co‐transfected with rat α1 and His‐tag β3. The complex of these two subunits was run on blue‐native PAGE, followed by multidimensional electrophoretic steps. Spots resolved at the third electrophoretic step were in‐gel digested with trypsin, chymotrypsin and Asp‐N. In‐gel modification of lysines by acetylation was carried out to increase sequence coverage. Subsequently, peptides were analyzed by nano‐ESI‐LC‐MS/MS using both, collision‐induced dissociation and electron transfer dissociation principles. When results from trypsin, chymotrypsin and Asp‐N digestion were combined, a single peptide [424 KKTHLRRRSSQL 435] was still not identified. In‐gel lysine acetylation leads to unambiguous identification of this peptide by the use of MASCOT v2.2. The use of the Modiro™software along with MASCOT, however, was able to provide 100% sequence coverage even without the use of in‐gel lysine acetylation. It was observed that the use of trypsin, chymotrypsin and Asp‐N with bioinformatic handling by the MASCOT and Modiro™software is sufficient to obtain complete sequencing of a highly hydrophobic membrane protein.
Simple method for determination of cocaine and main metabolites in urine by CE coupled to MS
Authors: da Costa José Luiz , Tonin Fernando Gustavo , Zanolli Luiz Antonio , da Matta Chasin Alice Aparecida , Tavares Marina Franco Maggi 
Published: July 2009

AbstractIn this work, a simple method for the simultaneous determination of cocaine (COC) and five COC metabolites (benzoylecgonine, cocaethylene (CET), anhydroecgonine, anhydroecgonine methyl ester and ecgonine methyl ester) in human urine using CE coupled to MS via electrospray ionization (CE‐ESI‐MS) was developed and validated. Formic acid at 1 mol/L concentration was used as electrolyte whereas formic acid at 0.05 mol/L concentration in 1:1 methanol:water composed the coaxial sheath liquid at the ESI nozzle. The developed method presented good linearity in the dynamic range from 250 ng/mL to 5000 ng/mL (coefficient of determination greater than 0.98 for all compounds). LODs (signal‐to‐noise ratio of 3) were 100 ng/mL for COC and CET and 250 ng/mL for the other studied metabolites whereas LOQ's (signal‐to‐noise ratio of 10) were 250 ng/mL for COC and CET and 500 ng/mL for all other compounds. Intra‐day precision and recovery tests estimated at three different concentration levels (500, 1500 and 5000 ng/mL) provided RSD lower than 10% (except anhydroecgonine, 18% RSD) and recoveries from 83–109% for all analytes. The method was successfully applied to real cases. For the positive urine samples, the presence of COC and its metabolites was further confirmed by MS/MS experiments.
Fabrication of a microfluidic enzyme reactor utilizing magnetic beads
Authors: Liu Xiaojun , Lo Roger C. , Gomez Frank A. 
Published: July 2009

AbstractAn enzyme‐catalyzed microfluidic assay using magnetic micro‐beads is described. Here, diaphorase (DI) (E.C. 1.6.99) is covalently attached to the magnetic micro‐beads (2.7 μm) and integrated into a short section of a microchip fabricated from PDMS. DI converts non‐fluorescent resazurin to fluorescent resorufin in the presence of nicotinamide adenine dinucleotide phosphate (NADH). In this work, an embedded magnet holds the micro‐beads in place within the microchannel while a solution of resazurin and NADH in buffer is flowed through the beads. Incorporation of the micro‐beads into the microchannel requires only a few minutes and offers well‐defined spatial resolution and reproducibility. At a flow rate of 41.2 μL/h, a stable state for the enzyme reaction in the microfluidic format was achieved within 50 s. The maximum conversion of the reaction was obtained at a concentration of 1.25 mM NADH. The reaction yield is affected by ZnCl2 and at concentrations in excess of 90.0 mM, the activity of DI was almost double without ZnCl2. At 5.2 mM potassium chloride, the activity of DI reached its maximum value. Overall, the conversion of resazurin in microfluidic format was more than twice than that in a batch assay.
Introducing the CPL/MUW proteome database: Interpretation of human liver and liver cancer proteome profiles by referring to isolated primary cells
Authors: Wimmer Helge , Gundacker Nina C. , Griss Johannes , Haudek Verena J. , Stättner Stefan , Mohr Thomas , Zwickl Hannes , Paulitschke Verena , Baron David M. , Trittner Wolfgang , Kubicek Markus , Bayer Editha , Slany Astrid , Gerner Christopher 
Published: July 2009

AbstractInterpretation of proteome data with a focus on biomarker discovery largely relies on comparative proteome analyses. Here, we introduce a database‐assisted interpretation strategy based on proteome profiles of primary cells. Both 2‐D‐PAGE and shotgun proteomics are applied. We obtain high data concordance with these two different techniques. When applying mass analysis of tryptic spot digests from 2‐D gels of cytoplasmic fractions, we typically identify several hundred proteins. Using the same protein fractions, we usually identify more than thousand proteins by shotgun proteomics. The data consistency obtained when comparing these independent data sets exceeds 99% of the proteins identified in the 2‐D gels. Many characteristic differences in protein expression of different cells can thus be independently confirmed. Our self‐designed SQL database (CPL/MUW – database of the Clinical Proteomics Laboratories at the Medical University of Vienna accessible via www.meduniwien.ac.at/proteomics/database) facilitates (i) quality management of protein identification data, which are based on MS, (ii) the detection of cell type‐specific proteins and (iii) of molecular signatures of specific functional cell states. Here, we demonstrate, how the interpretation of proteome profiles obtained from human liver tissue and hepatocellular carcinoma tissue is assisted by the Clinical Proteomics Laboratories at the Medical University of Vienna‐database. Therefore, we suggest that the use of reference experiments supported by a tailored database may substantially facilitate data interpretation of proteome profiling experiments.
Nanostructured pillars based on vertically aligned carbon nanotubes as the stationary phase in micro‐CEC
Authors: Wu Ren‐Guei , Yang Chung‐Shi , Wang Pen‐Cheng , Tseng Fan‐Gang 
Published: July 2009

AbstractWe present a micro‐CEC chip carrying out a highly efficient separation of dsDNA fragments through vertically aligned multi‐wall carbon nanotubes (MWCNTs) in a microchannel. The vertically aligned MWCNTs were grown directly in the microchannel to form straight nanopillar arrays as ordered and directional chromatographic supports. 1‐Pyrenedodecanoic acid was employed for the surface modification of the MWCNTs' stationary phase to adsorb analytes by hydrophobic interactions. This device was used for separating dsDNA fragments of three different lengths (254, 360, and 572 bp), and fluorescence detection was employed to verify the electrokinetic transport in the MWCNT array. The micro‐CEC separation of the three compounds was achieved in less than 300 s at a field strength of 66 V/cm due to superior laminar flow patterns and a lower flow resistance resulting from the vertically aligned MWCNTs being used as the stationary phase medium. In addition, a fivefold reduction of band broadening was obtained when the analyte was separated by the chromatographic MWCNT array channel instead of the CE channel. From all of the results, we suggest that an in situ grown and directional MWCNT array can potentially be useful for preparing more diversified forms of stationary phases for vertically efficient chip‐based electrochromatography.
Visualizing disease associations: graphic analysis of frequency distributions as a function of age using moving average plots (MAP) with application to Alzheimer's and Parkinson's disease
Authors: Payami Haydeh , Kay Denise M. , Zabetian Cyrus P. , Schellenberg Gerard D. , Factor Stewart A. , McCulloch Colin C. 
Published: July 2009

AbstractAge‐related variation in marker frequency can be a confounder in association studies, leading to both false‐positive and false‐negative findings and subsequently to inconsistent reproducibility. We have developed a simple method, based on a novel extension of moving average plots (MAP), which allows investigators to inspect the frequency data for hidden age‐related variations. MAP uses the standard case‐control association data and generates a birds‐eye view of the frequency distributions across the age spectrum; a picture in which one can see if, how, and when the marker frequencies in cases differ from that in controls. The marker can be specified as an allele, genotype, haplotype, or environmental factor; and age can be age‐at‐onset, age when subject was last known to be unaffected, or duration of exposure. Signature patterns that emerge can help distinguish true disease associations from spurious associations due to age effects, age‐varying associations from associations that are uniform across all ages, and associations with risk from associations with age‐at‐onset. Utility of MAP is illustrated by application to genetic and epidemiological association data for Alzheimer's and Parkinson's disease. MAP is intended as a descriptive method, to complement standard statistical techniques. Although originally developed for age patterns, MAP is equally useful for visualizing any quantitative trait. Genet. Epidemiol. 34:92–99, 2010. © 2009 Wiley‐Liss, Inc.
Methods for detecting interactions between genetic polymorphisms and prenatal environment exposure with a mother‐child design
Authors: Wang Shuang , Zheng Tian , Chanock Stephen , Jedrychowski Wieslaw , Perera Frederica P. 
Published: July 2009

AbstractPrenatal exposures such as polycyclic aromatic hydrocarbons and early postnatal environmental exposures are of particular concern because of the heightened susceptibility of the fetus and infant to diverse environmental pollutants. Marked inter‐individual variation in response to the same level of exposure was observed in both mothers and their newborns, indicating that susceptibility might be due to genetic factors. With the mother‐child pair design, existing methods developed for parent‐child trio data or random sample data are either not applicable or not designed to optimally use the information. To take full advantage of this unique design, which provides partial information on genetic transmission and has both maternal and newborn outcome status collected, we developed a likelihood‐based method that uses both the maternal and the newborn information together and jointly models gene‐environment interactions on maternal and newborn outcomes. Through intensive simulation studies, the proposed method has demonstrated much improved power in detecting gene‐environment interactions. The application on a real mother‐child pair data from a study conducted in Krakow, Poland, suggested four significant gene‐environment interactions after multiple comparisons adjustment. Genet. Epidemiol. 34: 125–132, 2010. © 2009 Wiley‐Liss, Inc.
Quality of life analysis in patients with anterior skull base neoplasms
Authors: Palme Carsten E. , Irish Jonathan C. , Gullane Patrick J. , Katz Mark R. , Devins Gerald M. , Bachar Gideon 
Published: July 2009

AbstractBackground.Significant morbidity is associated with management of anterior skull base neoplasms. The aim of this study was to evaluate the posttreatment patient's quality of life (QOL).Methods.A retrospective chart review identified 27 patients. QOL tools included the Functional Assessment of Cancer Therapy–Head & Neck, Centre for Epidemiologic Studies Depression Scale (CES‐D), Atkinson Life Happiness Rating (ALHR), and Midface Dysfunction Scale (MDS).Results.Postoperative radiotherapy and chemotherapy was required in 16 and 2 patients, respectively. The median FACT, ALHR, and CES‐D scores were 118 ± 21, 9 ± 2, and 17 ± 8, respectively. Smell and nasal crusting disturbance was reported by 69% and 61%, respectively. CES‐D > 16 and patients with recurrent disease correlated with a lower Total‐FACT score. Adjuvant radiotherapy correlated with a lower FACT‐H&N score. Patient sex, marital‐status, pathology, surgical technique, or complication rate did not correlate with worse QOL.Conclusion.Anterior skull base neoplasms survivors have an overall acceptable QOL. Most complaints relate to MDS. Recurrence, adjuvant radiotherapy, and MDS had lower QOL scores. © 2009 Wiley Periodicals, Inc. Head Neck, 2009
Spurious hypercalcitoninemia in patients with nodular thyroid disease induced by heterophilic antibodies
Authors: Kim Jung Min , Chung Ki‐Wook , Kim Seok Won , Choi Seon Hyeong , Min Hye Sook , Kim Ji‐na , Won Woo‐jae , Kim Seok Ki , Lee Ji In , Chung Jae Hoon , Kim Sun Wook 
Published: July 2009

AbstractBackgroundSerum calcitonin is the most useful tumor marker for the diagnosis and follow‐up of medullary thyroid carcinoma (MTC). Spurious hypercalcitoninemia caused by heterophilic antibody interference (HAI) is rarely found in patients without MTC.MethodsWe studied 2 patients with hypercalcitoninemia and thyroid nodules, but no evidence of MTC on fine‐needle aspiration cytology. We performed calcium stimulation tests, measured serum calcitonin with another calcitonin kit, performed dilution tests, and remeasured serum calcitonin after applying heterophilic blocking tubes.ResultsIn a 31‐year‐old woman with no response to the calcium stimulation test, serum calcitonin was <5 pg/mL using another kit. After we applied heterophilic blocking tubes, the serum calcitonin level decreased to normal range. We concluded that patient had spurious hypercalcitoninemia. In a 63‐year‐old woman, all tests revealed that the patient had true hypercalcitoninemia. The patient underwent total thyroidectomy that revealed MTC.ConclusionsWe suggest that patients suspected for spurious hypercalcitoninemia should undergo further investigation due to HAI. © 2009 Wiley Periodicals, Inc. Head Neck, 2010