bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compounding artefacts with uncertainty, and an amyloid cascade hypothesis that is ‘too big to fail’
Authors: Castellani Rudy J , Smith Mark A 
Published: March 2011

AbstractWith each failure of anti‐amyloid‐β therapy in clinical trials, new trials are initiated with no hint of slowing down. This may be due, in part, to the fact that the amyloid cascade hypothesis has been so modified over time that it is now impossible to confirm or deny. The hypothesis now states, in effect, that invisible molecules target invisible structures. Still relevant, however, are multiple factors that surely cast some doubt but have either been rationalized or overlooked. Among these are the poor correlation between amyloid‐β deposits and disease, the substantial differences between familial and sporadic disease, pathological assessment that indicates the secondary nature of lesions/proteins/cascades, the fact that soluble species are poorly reproducible laboratory phenomena, and the irrelevance of synaptic assessment to pathological interpretation. Although not yet dogma, the premature addition of mild cognitive impairment as the implied in vivo homologue to the soluble toxin‐synapse interaction is also problematic. In either case, the amyloid cascade hypothesis continues to dominate the Alzheimer's disease literature and grant applications. The more the neuroscience community perseverates along these lines in the face of accumulating outcome data to the contrary, the more one is left to wonder whether the hypothesis is too big to fail. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Growth plate regulation and osteochondroma formation: insights from tracing proteoglycans in zebrafish models and human cartilage
Authors: de Andrea Carlos E , Prins Frans A , Wiweger Malgorzata I , Hogendoorn Pancras CW 
Published: March 2011

AbstractProteoglycans are secreted into the extracellular matrix of virtually all cell types and function in several cellular processes. They consist of a core protein onto which glycosaminoglycans (e.g., heparan or chondroitin sulphates), are attached. Proteoglycans are important modulators of gradient formation and signal transduction. Impaired biosynthesis of heparan sulphate glycosaminoglycans causes osteochondroma, the most common bone tumour to occur during adolescence. Cytochemical staining with positively charged dyes (e.g., polyethyleneimine—PEI) allows, visualisation of proteoglycans and provides a detailed description of how proteoglycans are distributed throughout the cartilage matrix. PEI staining was studied by electron and reflection contrast microscopy in human growth plates, osteochondromas and five different proteoglycan‐deficient zebrafish mutants displaying one of the following skeletal phenotypes: dackel (dak/ext2), lacking heparan sulphate and identified as a model for human multiple osteochondromas; hi307 (β3gat3), deficient for most glycosaminoglycans; pinscher (pic/slc35b2), presenting with defective sulphation of glycosaminoglycans; hi954 (uxs1), lacking most glycosaminoglycans; and knypek (kny/gpc4), missing the protein core of the glypican‐4 proteoglycan. The panel of genetically well‐characterized proteoglycan‐deficient zebrafish mutants serves as a convincing and comprehensive study model to investigate proteoglycan distribution and the relation of this distribution to the model mutation status. They also provide insight into the distributions and gradients that can be expected in the human homologue. Human growth plate, wild‐type zebrafish and fish mutants with mild proteoglycan defects (hi307 and kny) displayed proteoglycans distributed in a gradient throughout the matrix. Although the mutants pic and hi954, which had severely impaired proteoglycan biosynthesis, showed no PEI staining, dak mutants demonstrated reduced PEI staining and no gradient formation. Most chondrocytes from human osteochondromas showed normal PEI staining. However, approximately 10% of tumour chondrocytes were similar to those found in the dak mutant (e.g., lack of PEI gradients). The cells in the reduced PEI‐stained areas are likely associated with loss‐of‐function mutations in the EXT genes, and they might contribute to tumour initiation by disrupting the gradients. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
The use of ultrasound in endemic Burkitt lymphoma in Cameroon
Authors: Marjerrison S. , Fernandez C.V. , Price V.E. , Njume E. , Hesseling P. 
Published: March 2011

AbstractBackgroundAs ultrasound (US) has become more widely available in sub‐Saharan Africa, emerging evidence suggests that the prevalence of abdominal disease in endemic Burkitt lymphoma (eBL) is higher than previous estimates. This retrospective chart review was designed to assess: (1) abdominal US utilisation, (2) the incidence of abdominal disease at diagnosis, (3) correlation of extent of disease at diagnosis with overall and event‐free survival (EFS).ProcedureThe charts of 95 consecutive children with eBL diagnosed between April 2006 and 2008 and treated according to the Malawi 2002/03 protocol at the Banso Baptist Hospital in Cameroon were examined for demographics, clinical presentation, diagnostic workup and outcome. Analysis was performed using descriptive statistics, Z‐tests and Student's t‐tests.ResultsFifty of 95 presumptive eBL patients (52.7%) had fine needle aspirate (FNA) confirmation of their tumours. Ninety‐four of 95 had an US at diagnosis. US was superior to clinical exam in demonstrating abdominal disease (P < 0.001). There was no significant difference between the rates of jaw (73%) and abdominal disease (82%) identified by US at diagnosis. EFS among patients whose disease was upgraded by US (64%) was better that of the patients with clinically diagnosed stage 3 disease.ConclusionsWe demonstrate that US provides more accurate staging of eBL than clinical examination. Abdominal involvement is more common than previously reported and appears to be as frequent as disease of the jaw at presentation. Further study should determine if more accurate staging with US is useful in risk‐stratifying treatment. Pediatr Blood Cancer 2012; 58: 352–355. © 2011 Wiley Periodicals, Inc.
Prognostic implications of serum alpha‐fetoprotein response during treatment of hepatoblastoma
Authors: Koh Kyung Nam , Park Meerim , Kim Bo Eun , Bae Keun Wook , Kim Kyung Mo , Im Ho Joon , Seo Jong Jin 
Published: March 2011

AbstractBackgroundWe evaluated the outcomes and prognostic factors, especially serum levels of alpha‐fetoprotein (AFP) and their changes during the treatment of hepatoblastoma (HB).ProcedureWe retrospectively analyzed the medical records of 43 consecutive children with HB treated at a single institution between 1991 and 2010.ResultsOf 43 patients, 5 (12%) underwent primary tumor resection at diagnosis and 38 (88%) received preoperative chemotherapy. Of those 38 patients, 7 (16%) died of progressive disease during preoperative chemotherapy, and 31 (72%) underwent curative operations, including 5 who underwent liver transplantation, after a median 4 cycles of chemotherapy (range, 3–14 cycles). The 5‐year overall survival and disease‐free survival rates were 62.1 ± 8.3% and 65.6 ± 7.6%, respectively. AFP >263,000 ng/mL at diagnosis, a decline of <1 log in AFP levels after the first cycle of chemotherapy, preoperative AFP levels in the highest tertile, and postoperative AFP levels in the highest tertiles were significantly associated with treatment failure. Age younger than 1 year at diagnosis, thrombocytosis at diagnosis, and early PRETEXT (pretreatment extent of disease) stage were significantly associated with better survival outcomes, whereas gender and metastasis were not. Multivariate analysis showed that high level of preoperative AFP was an independent predictor of treatment failure.ConclusionsSerial monitoring of changes in AFP levels during the treatment, especially perioperative changes, may help identify favorable and poor responders to chemotherapy. Alternative treatment, such as liver transplantation, should be considered for poor responders. Pediatr Blood Cancer 2011; 57: 554–560. © 2011 Wiley‐Liss, Inc.
Polycythemia in an infant secondary to granulocyte transfusions
Authors: Adisa Olufolake , Hendrickson Jeanne E. , Hopkins Courtney K. , Katzenstein Howard M. , Josephson Cassandra D. 
Published: March 2011

AbstractGranulocyte transfusions may be useful for neutropenic pediatric patients with refractory bacterial or fungal infections. Many potential adverse sequelae associated with granulocyte transfusions are well recognized, including febrile reactions, fluid overload, alloimmunization, and lung injury. Other potential adverse sequelae, however, are less well known. This case report describes an infant with familial hemophagocytic lymphohistiocytosis who developed polycythemia (hemoglobin 10–17.6 g/dl) following four daily transfusions of 20 ml/kg of apheresis collected, steroid stimulated donor granulocytes. Expanded knowledge of potential risks of transfused granulocytes will allow for rapid recognition of transfusion‐related complications, should they occur. Pediatr Blood Cancer 2011; 57: 1236–1238. © 2011 Wiley Periodicals, Inc.
Structure and mechanism of functional isotactic polypropylene via in situ chlorination graft copolymerization
Authors: Wang Shuang‐Shuang , Zhao Zhi‐Qiang , Wang Na , Zhao Ji‐Ruo , Feng Ying 
Published: March 2011

AbstractThis paper discusses the structure and mechanism of maleic anhydride (MAH) grafted onto isotactic polypropylene (iPP) via in situ chlorination graft copolymerization (ISCGC). The molecular structure of the grafted iPP was characterized using 1H NMR and 13C NMR spectroscopy, viscosity‐average molecular weight and gel content. The structure of un‐grafted MAH present in the reaction system was investigated using Fourier transform infrared spectroscopy in order to explore the grafting of MAH on iPP. The main side‐reactions, including iPP chain scission and crosslinking, during the grafting reaction were explored. From the experimental results obtained, the reason for controlled macromolecular chain degradation and crosslinking of grafted iPP in ISCGC is proposed. Based on the structural characterization of the grafted polymer, the mechanism of grafting onto iPP obtained via ISCGC was deduced. Mechanical properties, both static and dynamic, of grafted iPP were also investigated and the results showed that the properties of the material changed due to grafted MAH. Copyright © 2011 Society of Chemical Industry
Synthesis and performance enhancement of novel polybenzoxazines with low surface free energy
Authors: Chen Kai‐Chi , Li Hsun‐Tien , Huang Shu‐Chen , Chen Wen‐Bin , Sun Kien‐Wen , Chang Feng‐Chih 
Published: March 2011

AbstractA new siloxane‐imide‐containing benzoxazine, BZ‐A6, has been successfully synthesized. The thermal properties of the polybenzoxazine (PBZ) prepared from BZ‐A6 (PBZ‐A6) are superior to those of conventional PBZs lacking siloxane groups. The normally brittle PBZs are toughened significantly as a result of adding siloxane‐imide moieties. Moreover, the thermal and UV stabilities of the surface free energy of PBZ‐A6 are dramatically improved over the conventional bisphenol‐A‐type PBZ. Siloxane‐imide PBZs are more suitable for application as low‐surface‐free‐energy materials that are highly resistant to temperature and UV radiation. PBZ‐A6 may also be useful in weather‐resistant and self‐cleaning coating materials because of its low surface free energy and good thermal and UV resistance. Copyright © 2011 Society of Chemical Industry
Preparation and properties of temperature‐sensitive soy protein/poly(N‐isopropylacrylamide) interpenetrating polymer network hydrogels
Authors: Liu Yong , Cui Yingde 
Published: March 2011

AbstractTemperature‐sensitive interpenetrating polymer network (IPN) hydrogels based on soy protein and poly(N‐isopropylacrylamide) were successfully prepared. The structure and properties were systematically characterized using Fourier transform infrared spectroscopy, scanning electron microscopy, differential scanning calorimetry and thermogravimetric analysis, and the swelling and deswelling behavior was also investigated. It was found that the hydrogels had good miscibility, thermal stability and temperature sensitivity, and the lower critical solution temperature was ca 32 °C. Changing the content of soy protein or crosslinker could be used to control the swelling behavior, water retention and network structure of the IPN hydrogels. The results show that the novel IPN hydrogels may be of potential interest in drug delivery systems. Copyright © 2011 Society of Chemical Industry
Design of recombinant antibody microarrays for membrane protein profiling of cell lysates and tissue extracts
Authors: Dexlin‐Mellby Linda , Sandström Anna , Antberg Linn , Gunnarsson Jenny , Hansson Stefan R. , Borrebaeck Carl A.K. , Wingren Christer 
Published: March 2011

AbstractGenerating global protein expression profiles, including also membrane proteins, will be crucial for our understanding of biological processes in health and disease. In this study, we have expanded our antibody microarray technology platform and designed the first human recombinant antibody microarray for membrane proteins targeting crude cell lysates and tissue extracts. We have optimized all key technological parameters and successfully developed a setup for extracting, labeling and analyzing non‐fractionated membrane proteomes under non‐denaturing conditions. Finally, the platform was also extended and shown to be compatible with simultaneous profiling of both membrane proteins and water‐soluble proteins.
Comparative proteomic analysis of differentially expressed proteins in β‐aminobutyric acid enhanced Arabidopsis thaliana tolerance to simulated acid rain
Authors: Liu Tingwu , Jiang Xinwu , Shi Wuliang , Chen Juan , Pei Zhenming , Zheng Hailei 
Published: March 2011

AbstractAcid rain is a worldwide environmental issue that has seriously destroyed forest ecosystems. As a highly effective and broad‐spectrum plant resistance‐inducing agent, β‐aminobutyric acid could elevate the tolerance of Arabidopsis when subjected to simulated acid rain. Using comparative proteomic strategies, we analyzed 203 significantly varied proteins of which 175 proteins were identified responding to β‐aminobutyric acid in the absence and presence of simulated acid rain. They could be divided into ten groups according to their biological functions. Among them, the majority was cell rescue, development and defense‐related proteins, followed by transcription, protein synthesis, folding, modification and destination‐associated proteins. Our conclusion is β‐aminobutyric acid can lead to a large‐scale primary metabolism change and simultaneously activate antioxidant system and salicylic acid, jasmonic acid, abscisic acid signaling pathways. In addition, β‐aminobutyric acid can reinforce physical barriers to defend simulated acid rain stress.
Reversed‐phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells
Authors: Wang Yuexi , Yang Feng , Gritsenko Marina A. , Wang Yingchun , Clauss Therese , Liu Tao , Shen Yufeng , Monroe Matthew E. , Lopez‐Ferrer Daniel , Reno Theresa , Moore Ronald J. , Klemke Richard L. , Camp David G. , Smith Richard D. 
Published: March 2011

AbstractIn this study, we evaluated a concatenated low pH (pH 3) and high pH (pH 10) reversed‐phase liquid chromatography strategy as a first dimension for two‐dimensional liquid chromatography tandem mass spectrometry (“shotgun”) proteomic analysis of trypsin‐digested human MCF10A cell sample. Compared with the more traditional strong cation exchange method, the use of concatenated high pH reversed‐phase liquid chromatography as a first‐dimension fractionation strategy resulted in 1.8‐ and 1.6‐fold increases in the number of peptide and protein identifications (with two or more unique peptides), respectively. In addition to broader identifications, advantages of the concatenated high pH fractionation approach include improved protein sequence coverage, simplified sample processing, and reduced sample losses. The results demonstrate that the concatenated high pH reversed‐phased strategy is an attractive alternative to strong cation exchange for two‐dimensional shotgun proteomic analysis.
The ABRF Proteomics Research Group Studies: Educational exercises for qualitative and quantitative proteomic analyses
Authors: Friedman David B. , Andacht Tracy M. , Bunger Maureen K. , Chien Allis S. , Hawke David H. , Krijgsveld Jeroen , Lane William S. , Lilley Kathryn S. , MacCoss Michael J. , Moritz Robert L. , Settlage Robert E. , Sherman Nicholas E. , Weintraub Susan T. , Witkowska H. Ewa , Yates Nathan A. , Turck Christoph W. 
Published: March 2011

AbstractResource (core) facilities have played an ever‐increasing role in furnishing the scientific community with specialized instrumentation and expertise for proteomics experiments in a cost‐effective manner. The Proteomics Research Group (PRG) of the Association of Biomolecular Resource Facilities (ABRF) has sponsored a number of research studies designed to enable participants to try new techniques and assess their capabilities relative to other laboratories analyzing the same samples. Presented here are results from three PRG studies representing different samples that are typically analyzed in a core facility, ranging from simple protein identification to targeted analyses, and include intentional challenges to reflect realistic studies. The PRG2008 study compares different strategies for the qualitative characterization of proteins, particularly the utility of complementary methods for characterizing truncated protein forms. The use of different approaches for determining quantitative differences for several target proteins in human plasma was the focus of the PRG2009 study. The PRG2010 study explored different methods for determining specific constituents while identifying unforeseen problems that could account for unanticipated results associated with the different samples, and included 15N‐labeled proteins as an additional challenge. These studies provide a valuable educational resource to research laboratories and core facilities, as well as a mechanism for establishing good laboratory practices.
Structure analysis reveals the flexibility of the ADAMTS‐5 active site
Authors: Shieh Huey‐Sheng , Tomasselli Alfredo G. , Mathis Karl J. , Schnute Mark E. , Woodard Scott S. , Caspers Nicole , Williams Jennifer M. , Kiefer James R. , Munie Grace , Wittwer Arthur , Malfait Anne‐Marie , Tortorella Micky D. 
Published: March 2011

AbstractA ((1S,2R)‐2‐hydroxy‐2,3‐dihydro‐1H‐inden‐1‐yl) succinamide derivative (here referred to as Compound 12) shows significant activity toward many matrix metalloproteinases (MMPs), including MMP‐2, MMP‐8, MMP‐9, and MMP‐13. Modeling studies had predicted that this compound would not bind to ADAMTS‐5 (a disintegrin and metalloproteinase with thrombospondin motifs‐5) due to its shallow S1′ pocket. However, inhibition analysis revealed it to be a nanomolar inhibitor of both ADAMTS‐4 and −5. The observed inconsistency was explained by analysis of crystallographic structures, which showed that Compound 12 in complex with the catalytic domain of ADAMTS‐5 (cataTS5) exhibits an unusual conformation in the S1′ pocket of the protein. This first demonstration that cataTS5 can undergo an induced conformational change in its active site pocket by a molecule like Compound 12 should enable the design of new aggrecanase inhibitors with better potency and selectivity profiles.
Crystal structure of calcium dodecin (Rv0379), from Mycobacterium tuberculosis with a unique calcium‐binding site
Authors: Arockiasamy Arulandu , Aggarwal Anup , Savva Christos G. , Holzenburg Andreas , Sacchettini James C. 
Published: March 2011

AbstractIn eukaryotes, calcium‐binding proteins play a pivotal role in diverse cellular processes, and recent findings suggest similar roles for bacterial proteins at different stages in their life cycle. Here, we report the crystal structure of calcium dodecin, Rv0379, from Mycobacterium tuberculosis with a dodecameric oligomeric assembly and a unique calcium‐binding motif. Structure and sequence analysis were used to identify orthologs of Rv0379 with different ligand‐binding specificity.
Self‐association studies of the bifunctional N‐acetylglucosamine‐1‐phosphate uridyltransferase from Escherichia coli
Authors: Trempe Jean‐François , Shenker Solomon , Kozlov Guennadi , Gehring Kalle 
Published: March 2011

AbstractThe N‐acetylglucosamine‐1‐phosphate uridyltransferase (GlmU) is a key bifunctional enzyme in the biosynthesis of UDP‐GlcNAc, a precursor in the synthesis of cell wall peptidoglycan. Crystal structures of the enzyme from different bacterial strains showed that the polypeptide forms a trimer through a unique parallel left‐handed beta helix domain. Here, we show that the GlmU enzyme from Escherichia coli forms a hexamer in solution. Sedimentation equilibrium analytical ultracentrifugation demonstrated that the enzyme is in a trimer/hexamer equilibrium. Small‐angle X‐ray scattering studies were performed to determine the structure of the hexameric assembly and showed that two trimers assemble through their N‐terminal domains. The interaction is mediated by a loop that undergoes a large conformational change in the uridyl transferase reaction, a feature that may affect the enzymatic activity of GlmU.
A novel chitosan‐poly(lactide) copolymer and its submicron particles as imidacloprid carriers
Authors: Li Min , Huang Qiliang , Wu Yan 
Published: March 2011

AbstractBACKGROUND: The aim of the present work was to synthesise novel amphiphilic chitosan–co‐(D,L‐lactide) (chitosan–PLA) copolymers and to study the formation of pesticide‐loaded polymeric submicron particles. These copolymeric submicron particle systems are expected to be potential candidates for applications in pesticide delivery.RESULTS: The chemical structures of the copolymers were confirmed by Fourier transform infrared spectroscopy (FT‐IR), 1H nuclear magnetic resonance (1H NMR) and thermogravimetric analysis (TGA). Imidacloprid as a lipophilic model pesticide can be incorporated into chitosan–PLA submicron particles by nanoprecipitation and the emulsion/solvent evaporation method. Size, the size distribution, the imidacloprid loading content (LC) and the imidacloprid release behaviour were investigated.CONCLUSION: Conjugation of PLA to chitosan was shown to be an available method for the preparation of submicron particles for lipophilic pesticide delivery. The imidacloprid‐loaded submicron particles showed a sustained release process. As the mass ratio of copolymer to imidacloprid increased, the submicron particles size and LC decreased. The chitosan–PLA submicron particles could be useful as pesticide carriers for imidacloprid delivery systems. Copyright © 2011 Society of Chemical Industry
Differential photoacoustic cell to study the wetting process during porous silicon formation
Authors: Germán Espinosa‐Arbeláez Diego , Velázquez‐Hernández Rubén , Petricioli‐Carranco Julio , Quintero‐Torres Rafael , Rodríguez‐García Mario Enrique 
Published: March 2011

AbstractThis paper shows the in‐situ study of the wetting process in Silicon during anodization process using an electrochemical Differential photoacoustic Cell (DPC). The Photoacoustic amplitude and phase signals were obtained for samples in air, ethanol, ethanol/HF and finally air. According to these results ethanol is responsible for a mechanical contact reducing the superficial tension and ethanol/HF produce the removing of the SiOx and SiO2species on the Silicon surface. It was found that the DPC is a powerful technique to study the wet surface before the formation of the porous silicon layer (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)