bluuebunny/crossref_metadata_2025_split huggingface dataset:
A rapid flow cytometry test based on histone H2AX phosphorylation for the sensitive and specific diagnosis of ataxia telangiectasia
Authors: Porcedda Paola , Turinetto Valentina , Brusco Alfredo , Cavalieri Simona , Lantelme Erica , Orlando Luca , Ricardi Umberto , Amoroso Antonio , Gregori Dario , Giachino Claudia 
Published: April 2008

AbstractAtaxia telangiectasia (A‐T) is a progressive neurodegenerative disease with onset in early childhood, caused by mutations in the ATM (ataxia‐telangiectasia mutated) gene. Diagnosis relies on laboratory tests showing high levels of serum alphafetoprotein, cell sensitivity to ionizing radiation (IR) and absence or reduced levels of ATM protein. Many tests, however, are not sufficiently sensitive or specific for A‐T, have long turnaround times, or require large blood samples. This prompted us to develop a new flow cytometry method for the diagnosis of A‐T based on the measurement of histone H2AX phosphorylation. We established normal ranges of histone H2AX phosphorylation after 2 Gy IR by testing T‐cell lines, lymphoblastoid cell lines (LCLs) and/or peripheral blood mononuclear cells (PBMCs) or both from 20 genetically proven A‐T and 46 control donors. To further evaluate the specificity and sensitivity of the test, we analyzed cells from 19 patients suspected of having A‐T, and from one Friedreich Ataxia, one Ataxia with Oculomotor Apraxia type 2, and one Nijmegen Breakage Syndrome patients. Phosphorylated histone H2AX mean fluorescence intensity of irradiated A‐T cells was significantly lower than that of healthy donors. The intrastaining, intraassay, and interassay imprecisions were ≤13.22%. Sensitivity and specificity were virtually 100% when the test was performed on PBMCs. Screening of 19 consecutive new patients with suspected A‐T classified 15 patients as non‐A‐T and four as A‐T; diagnosis of the latter four was subsequently confirmed by DNA sequencing to identify ATM mutations. The Friedreich Ataxia patient, the Ataxia with Oculomotor Apraxia type 2 patient and the Nijmegen Breakage Syndrome patient were classified as non‐A‐T. This flow cytometry test is very sensitive, specific and rapid, and requires only 2 ml of blood. It may thus be proposed for the early differential diagnosis of A‐T as an alternative to methods requiring the production of LCLs. © 2008 International Society for Advancement of Cytometry
Growth dynamics of mammalian cells monitored with automated cell cycle staining and flow cytometry
Authors: Sitton Greg , Srienc Friedrich 
Published: April 2008

AbstractTo accurately observe high‐frequency events during transient cell cycle kinetics, we have implemented a single step 15‐min DNA staining protocol using automated flow cytometry. This protocol was used to sample and to analyze a Chinese hamster ovary cell culture for the DNA distribution, viable cell concentration, apoptotic cell concentration, and light scattering properties every 25 min over 4.5 days in response to a nutrient deprivation and a nutrient upshift. After the nutrient deprivation and exposure to fresh growth medium, two populations of cells started proliferating at different times likely corresponding to cells leaving the G0 and G1 cell cycle phases. After a nutrient upshift in late exponential growth, a cell cycle arrest occurred at the G1/S and G2/M boundary. The resulting cell cycle and proliferation kinetics followed damped oscillations that directly reveal the average time cells spend in each cell cycle phase. The observed detailed dynamics of the cell cycle progression is made possible through the high‐frequency sampling enabled by automated flow cytometry. The approach should be useful in studying cell cycle perturbations in response to different environmental conditions resulting from exposure to specific nutrients or to drugs. © 2008 International Society for Advancement of Cytometry
Standardized method to minimize variability in a functional P2X7 flow cytometric assay for a multi‐center clinical trial
Authors: Korpi‐Steiner N. L. , Sheerar D. , Puffer E. B. , Urben C. , Boyd J. , Guadarrama A. , Schell K. , Denlinger L. C. 
Published: April 2008

AbstractBackgroundFlow cytometric analysis of human P2X7 pore activity segregates variant from common P2RX7 genotypes and may serve as a biomarker for cancer, pain, inflammation, and immune responses to infection. Standardization is needed to accommodate variable sample age and instrumentation differences in a multicenter clinical trial.MethodsCD14‐PE‐stained whole blood samples were treated with YO‐PRO‐1 combined with a P2X7 agonist (BzATP) or control, followed by the addition of PI after closure of the P2X7 pore. Recalled instrument settings from previous publications were used to adapt a standardized fluorescent particle‐adjusted set‐up method. Experiments were performed to compare the two methods while evaluating components of systematic variability and facilitating reliable processing of samples with varied ages.ResultsThe median YO‐PRO‐1 fluorescence of BzATP‐treated samples had less variability when collected by the bead‐adjusted method and was less influenced by the compensation strategy used. The average day‐to‐day coefficient of variance for assessments of P2X7 pore activity by this method was 0.11 ± 0.04, and the exclusion of nonviable cells was found to accommodate samples aged up to 4 days after phlebotomy. The bead‐adjusted set‐up method produced measurements differing by only 2.0% ± 1.5% on two analog cytometers, and within similar decades when comparing analog to digital instruments.ConclusionsThese results provide a standardized method for quantitative flow cytometric analysis of P2X7 receptor phenotypes in blood monocytes with minimal intralaboratory variation and potential for interlaboratory comparisons that can greatly facilitate multicenter functional genomic clinical studies. © 2008 Clinical Cytometry Society
Nucleophilic Reactivities of Pyrroles (Eur. J. Org. Chem. 14/2008)
Authors: Nigst Tobias A. , Westermaier Martin , Ofial Armin R. , Mayr Herbert 
Published: April 2008

AbstractThe cover picture is misleading! With the determination of the nucleophilic reactivities of pyrroles, our electrophilicity‐nucleophilicity puzzle, where synthetically useful reactions are found in the green corridor (see: R. Lucius, R. Loos, H. Mayr, Angew. Chem. Int. Ed. 2002, 41, 91–95), is not yet complete. The picture illustrates, however, that the reactions of pyrroles with electrophiles also follow the linear free‐energy relationship log k20°C = s(N + E), where N and s characterize the reactivities of nucleophiles and E describes the reactivities of electrophiles. Alkyl substitution increases the nucleophilicity of pyrrole by a factor of up to 10 million, and from the nucleophilicity parameters reported in this article by H. Mayr et al. on p. 2369 ff, one can derive suitable electrophilic reaction partners for alkyl‐substituted pyrroles.
Fabrication of 3‐D gel microarrays directly with raw polymerase chain reaction products by heat‐directed polymerization
Authors: Pan Zhiqiang , Li Yanqiang , Shan Qun , Hong Xiaohong , Zhou Dongrui , Zhang Minghao , Chen Ping , Xiao Pengfeng , Lu Zuhong 
Published: April 2008

AbstractIn this study, a new method for fabricating 3‐D polyacrylamide gel microarrays was presented. In the method, a 3‐D gel microarray was successfully fabricated by directly heating the slides with arrayed prepolymer at 80°C for 2 min. The prepolymer on the microarray only contained 40% v/v raw/unpurified PCR products, 1.4% ammonium persulfate (APS), 6% acrylamide, and 20% glycerol and the balance H2O but no TEMED. The heat could induce the free radicals from APS to initiate polymerization of the 3‐D gel and allow the incorporation of raw PCR products into the 3‐D gel. The immobilized DNA on the gel microarray had the specificity of hybridization and the ability to distinguish base mismatch. It has been demonstrated that SNP genotyping of both the 194072 loci and the 252944 loci in the β2 subunit gene of γ‐aminobutyric acid A receptor (GABRB2) gene was successfully performed by using the 3‐D gel microarray. This method is efficient, simple, rapid, and easy to control in preparing a 3‐D gel microarray, which would be widely used for various purposes in laboratory research and clinic application.
Exonuclease activity of proofreading DNA polymerases is at the origin of artifacts in molecular profiling studies
Authors: Gury Jerome , Zinger Lucie , Gielly Ludovic , Taberlet Pierre , Geremia Roberto A. 
Published: April 2008

AbstractCE fingerprint methods are commonly used in microbial ecology. We have previously noticed that the position and number of peaks in CE‐SSCP (single‐strand conformation polymorphism) profiles depend on the DNA polymerase used in PCR [1]. Here, we studied the fragments produced by Taq polymerase as well as four commercially available proofreading polymerases, using the V3 region of the Escherichia coli rss gene as a marker. PCR products rendered multiple peaks in denaturing CE; Taq polymerase was observed to produce the longest fragments. Incubation of the fragments with T4 DNA polymerase indicated that the 3′‐ends of the proofreading polymerase amplicons were recessed, while the Taq amplicon was partially +A tailed. Treatment of the PCR product with proofreading DNA polymerase rendered trimmed fragments. This was due to the 3′–5′ exonuclease activity of these enzymes, which is essential for proofreading. The nuclease activity was reduced by increasing the concentration of dNTP. The Platinum® Pfx DNA polymerase generated very few artifacts and could produce 85% of blunted PCR products. Nevertheless, despite the higher error rate, we recommend the use of Taq polymerase rather than proofreading in the framework for molecular fingerprint studies. They are more cost‐effective and therefore ideally suited for high‐throughput analysis; the +A tail artifact rate can be controlled by modifying the PCR primers and the reaction conditions.
High frequency stream bed mobility of a low‐gradient agricultural stream with implications on the hyporheic zone
Authors: Peterson Eric W. , Sickbert Timothy B. , Moore Suzanna L. 
Published: April 2008

AbstractLittle Kickapoo Creek (LKC), a low‐gradient stream, mobilizes its streambed–fundamentally altering its near‐surface hyporheic zone–more frequently than do higher‐gradient mountain and karst streams. LKC streambed mobility was assessed through streambed surveys, sediment sampling, and theoretical calculations comparing basal shear stress (τb) with critical shear stress (τc). Baseflow τb is capable of entraining a d50 particle; bankfull flow could entrain a 51·2 mm particle. No particle that large occurs in the top 30 cm of the substrate, suggesting that the top 30 cm of the substrate is mobilized and redistributed during bankfull events. Bankfull events occur on average every 7·6 months; flows capable of entraining d50 and d85 particles occur on average every 0·85 and 2·1 months, respectively. Streambed surveys verify streambed mobility at conditions below bankfull. While higher gradient streams have higher potential energy than LKC, they achieve streambed‐mobilization thresholds less frequently. Heterogeneous sediment redistribution creates an environment where substrate hydraulic conductivity (K) varies over four orders of magnitude. The frequency and magnitude of the substrate entrainment has implications on hyporheic zone function in fluid, solute and thermal transport models, interpretations of hyporheic zone stability, and understanding of LKC's aquatic ecosystem. Copyright © 2008 John Wiley & Sons, Ltd.
Retracted: Genistein mediated histone acetylation and demethylation activates tumor suppressor genes in prostate cancer cells
Authors: Kikuno Nobuyuki , Shiina Hiroaki , Urakami Shinji , Kawamoto Ken , Hirata Hiroshi , Tanaka Yuichiro , Majid Shahana , Igawa Mikio , Dahiya Rajvir 
Published: April 2008

The above article, published online on 22 April 2008 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal Editor in Chief, Prof. Peter Lichter, and John Wiley & Sons Ltd. The retraction has been agreed due to errors identified in Figs, 3, 4, and 5. The concerns about these figures cannot be resolved because the original data can no longer be retrieved.Reference

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Shiina H,
Urakami S,
Kawamoto K,
Hirata H,
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Majid S,
Igawa M and
Dahiya R. (2008), . Int J Cancer, 123:552–560. DOI: 10.1002/ijc.23590
SU‐8 2000 rendered cytocompatible for neuronal bioMEMS applications
Authors: Vernekar Varadraj N. , Cullen D. Kacy , Fogleman Nick , Choi Yoonsu , García Andrés J. , Allen Mark G. , Brewer Gregory J. , LaPlaca Michelle C. 
Published: April 2008

AbstractMicrofabrication advances have resulted in small, cheap, and precise devices for biological microelectromechanical systems (bioMEMS). SU‐8/SU‐8 2000 is an attractive material for these applications because of its high‐aspect ratio fabrication capability, dielectric properties, and thermochemical stability. Despite these advantages, the potential toxicity of SU‐8 2000 may limit its use in cell‐based applications. We show that <10% of primary neurons survived when cultured adjacent to or on top of untreated SU‐8 2000. We evaluated the efficacy of various detoxification and surface treatments for SU‐8 2000 in neuronal cultures after 7–21 days in vitro. Viability was improved to 45.8% ± 4.5% (mean ± standard error of the mean) following 3‐day heat treatment (150°C) under vacuum, while UV exposure and CO2 supercritical extraction did not improve survival. Furthermore, parylene coating (25 μm), in combination with heat and sonication (in isopropanol) treatments effectively masked the SU‐8 2000 and led to 86.4% ± 1.9% viability. Glow discharge (oxygen plasma) treatment rendered the SU‐8 2000 surface more hydrophilic and improved neuronal viability, possibly through improved cell adhesion. No organic leachants were detected by mass spectrometry before or after heat treatment or after sonication. However, XPS analysis revealed the presence of potentially neurotoxic elements, fluorine and antimony. Strategies to improve the cytocompatibility of SU‐8 2000 with primary neurons will allow longer culture times and have applications for cell‐based microfabrication. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Fabrication of free‐standing albumin‐nanosheets having heterosurfaces
Authors: Okamura Yosuke , Goto Takahiro , Niwa Daisuke , Fukui Yoshihito , Otsuka Masanobu , Motohashi Norikazu , Osaka Tetsuya , Takeoka Shinji 
Published: April 2008

AbstractSheet‐shaped carriers, having both obverse and reverse surfaces and thus a large contact area for targeting a site, have several advantages over spherical‐shaped carriers, which have an extremely small contact area for targeting sites. Here, we proposed a novel method to prepare a free‐standing ultrathin and biocompatible nanosheet having heterosurfaces, by a combination of four processes: (1) specific adsorption of recombinant human serum albumin (rHSA) molecules onto a patterned octadecyltrimethoxysilane self‐assembled monolayer region (ODS‐SAM), (2) preparation of nanosheets of rHSA molecules bearing thiol groups (SH‐rHSA) via two‐dimensionally disulfide crosslinking, (3) surface modification of the resulting nanosheet, and (4) preparation of the free‐standing nanosheet by detachment from the ODS‐SAM. The SH‐rHSA molecules at pH 5.0 and a concentration of 1 μg/mL were specifically adsorbed on the patterned ODS‐SAM regions by hydrophobic interaction, and were two‐dimensionally crosslinked in the presence of copper ion as an oxidant. The rHSA‐nanosheets were then simply detached from the ODS‐SAM by treatment with surfactant. We succeeded in the preparation of rectangular (10 μm × 30 μm) and ultrathin (4.5 ± 1.0 nm) rHSA‐nanosheets on a patterned ODS‐SAM, and could also obtain free‐standing rHSA‐nanosheets having heterosurfaces by surface modification with fluorescent latex beads. Thus, the rHSA‐nanosheets having heterosurfaces could be regarded as a new biomaterial for drug carriers, hemostatic reagents, wound dressing for burn injury, and so forth. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Material properties and bone marrow stromal cells response to In situ crosslinkable RGD‐functionlized lactide‐co‐glycolide scaffolds
Authors: Jabbari Esmaiel , He Xuezhong , Valarmathi Mani T. , Sarvestani Alireza S. , Xu Weijie 
Published: April 2008

AbstractIn situ crosslinkable biomaterials with degradation profiles that can be tailored to a particular application are indispensable for treating irregularly shaped defects and for fabrication of shape‐selective scaffolds. The objective of this work was to synthesize ultra low molecular weight functionalized PLA and PLGA macromers that can be grafted with bioactive peptides and crosslinked in situ to fabricate biodegradable functional scaffolds. In situ crosslinkable lactide‐co‐glycolide macromer (cMLGA; “c” for crosslinkable, “M” for macromer, and “LGA” for lactide‐co‐glycolide) was synthesized by anionic polymerization of lactide and glycolide monomers followed by condensation polymerization with fumaryl chloride. The cMLA (100% L‐lactide) and cMLGA macromers formed porous crosslinked scaffolds with NVP as the crosslinker. The mass loss of the crosslinked cMLA and cMLGA was linear with incubation time in vitro (zero‐order degradation) and the degradation rate depended on the ratio of lactide to glycolide. cMLGA scaffold with 1:1 lactide to glycolide ratio completely degraded after 4 weeks while the cMLA lost less than 40% of its initial mass after 35 weeks. When cMLA scaffold was functionalized with acrylated integrin‐binding Ac‐GRGD amino acid sequence, bone marrow stromal (BMS) cells attached and spread on the cMLA scaffold and exhibited focal‐point cell adhesion. The mRNA expression levels of collagen‐1α, osteonectin, and osteopontin for BMS cells seeded in the scaffolds with 1 and 5% Ac‐GRGD were upregulated compared with those without Ac‐GRGD. cMLGA is attractive as in situ crosslinkable macromer for fabrication of functional scaffolds with degradation characteristics that can be tailored to a particular application. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
The effect of dehydrothermal treatment on the mechanical and structural properties of collagen‐GAG scaffolds
Authors: Haugh Matthew G. , Jaasma Michael J. , O'Brien Fergal J. 
Published: April 2008

AbstractThe mechanical properties of tissue engineering scaffolds are critical for preserving the structural integrity and functionality during both in vivo implantation and long‐term performance. In addition, the mechanical and structural properties of the scaffold can direct cellular activity within a tissue‐engineered construct. In this context, the aim of this study was to investigate the effects of dehydrothermal (DHT) treatment on the mechanical and structural properties of collagen‐glycosaminoglycan (CG) scaffolds. Temperature (105–180°C) and exposure period (24–120 h) of DHT treatment were varied to determine their effect on the mechanical properties, crosslinking density, and denaturation of CG scaffolds. As expected, increasing the temperature and duration of DHT treatment resulted in an increase in the mechanical properties. Compressive properties increased up to twofold, while tensile properties increased up to 3.8‐fold. Crosslink density was found to increase with DHT temperature but not exposure period. Denaturation also increased with DHT temperature and exposure period, ranging from 25% to 60% denaturation. Crosslink density was found to be correlated with compressive modulus, whilst denaturation was found to correlate with tensile modulus. Taken together, these results indicate that DHT treatment is a viable technique for altering the mechanical properties of CG scaffolds. The enhanced mechanical properties of DHT‐treated CG scaffolds improve their suitability for use both in vitro and in vivo. In addition, this work facilitates the investigation of the effects of mechanical properties and denaturation on cell activity in a 3D environment. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Efficacy of a p38 mitogen activated protein kinase inhibitor in mitigating an established inflammatory reaction to polyethylene particles in vivo
Authors: Ma T. , Ren P.‐G. , Larsen D. M. , Suenaga E. , Zilber S. , Genovese M. , Smith R. L. , Goodman S. B. 
Published: April 2008

AbstractThe inhibitor of p38 mitogen‐activated protein kinase (MAPK) is of interest in the nonoperative treatment of periprosthetic osteolysis due to wear particles. Previous studies demonstrated that an oral p38 MAPK inhibitor did not suppress bone formation when given during the initial phase of tissue differentiation. However, the oral p38 MAPK inhibitor also did not curtail the foreign body and chronic inflammatory response to particles when given simultaneously. The purpose of the current study was to examine the efficacy of a p38 MAPK inhibitor, SCIO‐323, on mitigating an established inflammatory reaction that parallels the clinical situation more closely. The Bone Harvest Chamber was implanted in rabbits and submicron polyethylene particles were placed in the chamber for 6 weeks. The contents of the chambers were harvested every 6 weeks. Oral treatment with the SCIO‐323 included delivery for 3 weeks and stopping for 3 weeks, delivery for 3 weeks after an initial 3‐week delay, and delivery for 6 weeks continuously. Administration of the SCIO‐323 continuously for 6 weeks with/without the presence of particles, or for the initial 3 of 6 weeks had minor effects on bone ingrowth. After establishing a particle‐induced chronic inflammatory reaction for 3 weeks, administration of SCIO‐323 for a subsequent 3 weeks suppressed net bone formation. The activity of osteoclast‐like cells remained low among all treatments when compared with the first control. Using the present model, the oral p38 MAPK inhibitor was ineffective in improving bone ingrowth in the presence of polyethylene particles. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Doubly stochastic Poisson distribution of platelet adhesion on material surfaces and its implication on fluorescence image analysis
Authors: Pang Zhengyu , Cawse James N. , Yu Liming , Richards William D. 
Published: April 2008

AbstractAn image based assay has been developed to quantify platelet adhesion on material surfaces. Briefly, citrated platelet rich plasma (PRP) is incubated with materials for 2 h to allow platelet adhesion on the surface, followed by fluorescence labeling of platelets with Celltracker Green™. Multiple images are acquired by an automatic fluorescence microscope, IN Cell Analyzer 1000™. Platelets are identified and counted by an automatic image analysis algorithm. We have observed that the variance of the counts is considerably greater than expected from simple distribution laws. Statistical analysis of that difference shows that these measurements will often follow a doubly stochastic Poisson process in which the variance is inherently very large. To overcome this, multiple images (n ≥ 8 images/well, about 3% of total area) are necessary to achieve accurate counting. This method has been compared to the commonly used enzyme based platelet adhesion assay, lactate dehydrogenase (LDH) assay. It is concluded that the present method is only effective in quantifying adherent platelets when a large number of samples are used. However, this method does provide additional information on platelet morphology and spatial distribution, which is lacking in the LDH assay. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009