bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of single‐base mutations using 1‐D microfluidic beads array
Authors: Zhang He , Yang Xiaohai , Wang Kemin , Tan Weihong , Zhou Leiji , Zuo Xinbing , Wen Jianhui , Chen Yunqing 
Published: December 2007

AbstractThe application of a 1‐D microfluidic beads array that is composed of individually addressable functionalized SiO2 beads has been demonstrated for detection of single‐base mutations based on “sandwich” hybridization assay without additional sample labeling and PCR amplification. We concentrated on detection of mutations in the human p53 tumor suppressor gene with more than 50% mutation frequency in the known human cancers. Using a microinjection system, functionalized beads could be selectively and linearly arrayed in a single microfluidic channel comprising many periodic chambers. This 1‐D microfluidic beads array was sufficiently sensitive to identify single‐nucleotide mutations in 40 pM quantities of DNA targets and could discriminate the mutated alleles in an excess of nonmutated alleles at a level of one mutant in 100 wild‐type sequences. The surface of beads was regenerated and rehybridized up to six times without obvious loss of signal. The entire reaction process was done at room temperature within minutes, and only 2–10 μL sample solution was needed to complete the whole detection process. The p53 genotypes of A549, CNE2, and SKBr‐3 cell lines were also correctly evaluated by using mRNA extracts as target without need for sample labeling and amplification. Thus, this platform enabled rapid and exact discrimination of gene mutations with the advantages of reusability, simple handling of liquid, low cost, and little reagent consumption.
Channel wall coating on a poly‐(methyl methacrylate) CE microchip by thermal immobilization of a cellulose derivative for size‐based protein separation
Authors: Okada Hiroki , Kaji Noritada , Tokeshi Manabu , Baba Yoshinobu 
Published: December 2007

AbstractWe demonstrate channel wall coating using a cellulose derivative on a poly‐(methyl methacrylate) (PMMA) CE microchip to eliminate EOF disturbing protein separation. The channel walls were modified by preconditioning with a solution containing the cellulose derivative and then thermally evaporating the solution to produce hydrophilic channel walls which prevent adsorption of analytes via a hydrophobic interaction. When the PMMA substrate was coated with the cellulose derivative hydroxypropylmethylcellulose (HPMC) 90SH, the water contact angle on the coated substrate was decreased (up to 15°) and EOF was significantly suppressed (up to 4.0×10−6 cm2⋅V–1⋅s–1). Three proteins (20.5, 68.0, and 114.6 kDa) were successfully separated on the 0.15% HPMC 90SH‐coated channel walls with good reproducibility of migration time (RSD <1.75%) and high efficiency (theoretical plate number per meter: 2.62×105).
Floating resistivity detector for microchip electrophoresis
Authors: Tay Elaine Teng Teng , Law Wai Siang , Sim Steven Poh Chuen , Feng Huatao , Zhao Jian Hong , Li Sam Fong Yau 
Published: December 2007

AbstractA newly developed conductivity detector, the floating resistivity detector (FRD), for microchip electrophoresis was introduced in this work. The detector design permits decoupling of the detection circuit from the high separation voltage without compromising separation efficiency. This greatly simplifies the integration of microchip electrophoresis systems. Its method of detection relies on platinum electrodes being dipped in two buffer‐filled branched detection probe reservoirs on the microchip device. In this way, analytes passing through the detection window will not pass through and subsequently adsorb onto the electrodes, alleviating problems of electrode fouling due to analyte contamination and surface reactions. A customized microchip design was proposed and optimized stepwise for the new FRD system. Each branched detection probe was determined to be 4.50 mm long with a 0.075 mm detection window gap between them. The distance between the detection window and buffer waste reservoir was determined to be 1.50 mm. The optimized microchip design was subsequently used in the analysis of four groups of analytes – inorganic cations, amino acids, aminoglycosides antibiotics, and biomarkers. Based on the preliminary results obtained, the detection limits were in the range of 0.4–0.7 mg/L for the inorganic cations and 1.5–15 mg/L for the amino compounds.
Faster and improved microchip electrophoresis using a capillary bundle
Authors: Sun Yi , Kwok Yien Chian , Nguyen Nam Trung 
Published: December 2007

AbstractJoule heating generated in CE microchips is known to affect temperature gradient, electrophoretic mobility, diffusion of analytes, and ultimately the efficiency and reproducibility of the separation. One way of reducing the effect of Joule heating is to decrease the cross‐section area of microchannels. Currently, due to the limit of fabrication technique and detection apparatus, the typical dimensions of CE microchannels are in the range of 50–200 μm. In this paper, we propose a novel approach of performing microchip CE in a bundle of extremely narrow channels by using photonic crystal fiber (PCF) as separation column. The PCF was simply encapsulated in a poly(methyl methacrylate) (PMMA) microchannel right after a T‐shaped injector. CE was simultaneously but independently carried out in 54 narrow capillaries, each capillary with diameter of 3.7 μm. The capillary bundle could sustain high electric field strength up to 1000 V/cm due to efficient heat dissipation, thus faster and enhanced separation was attained.
Real‐time monitoring of intracellular calcium dynamic mobilization of a single cardiomyocyte in a microfluidic chip pertaining to drug discovery
Authors: Li Xiujun , Huang Jingbo , Tibbits Glen F , Li Paul C.H. 
Published: December 2007

AbstractA microfluidic method for real‐time quantitative measurement of cellular response pertaining to drug discovery is reported. This method is capable of multiple‐step liquid delivery for measuring the drug response of a single cardiomyocyte, due to the improved cell retention by a newly designed chip. The chip, which consists of a cell‐retention chamber with a weir structure, was fabricated just by a one‐photomask microfabrication procedure followed by on‐chip etching. This method differs from the conventional method, which uses two‐mask photolithography to fabricate the microchannel (deep etch) and the weir structure (shallow etch). The dimensions of the weir structure have been predicted by a mathematical model, and confirmed by confocal microscopy. Using this microfluidic method, the dynamic [Ca2+]i mobilization in a single cardiomyocyte during its spontaneous contraction was quantified. Furthermore, we measured the cellular response of a cardiomyocyte on (i) a known cardiotonic agent (caffeine), (ii) a cardiotoxic chemotherapeutic drug (daunorubicin), and (iii) an herbal anticancer drug candidate – isoliquiritigenin (IQ) based on the fluorescent calcium measurement. It was found that IQ had produced a less pronounced effect on calcium mobilization of the cardiomyocytes whereas caffeine and daunorubicin had much stronger effects on the cells. These three experiments on cardiomyocytes pertaining to drug discovery were only possible after the improved cell retention provided by the new chip design (MV2) required for multiple‐step real‐time cellular analysis on a microchip, as compared with our old chip design (MV1).
SU‐8 as a structural material for labs‐on‐chips and microelectromechanical systems
Authors: Abgrall Patrick , Conedera Veronique , Camon Henri , Gue Anne‐Marie , Nguyen Nam‐Trung 
Published: December 2007

AbstractSince its introduction in the nineties, the negative resist SU‐8 has been increasingly used in micro‐ and nanotechnologies. SU‐8 has made the fabrication of high‐aspect ratio structures accessible to labs with no high‐end facilities such as X‐ray lithography systems or deep reactive ion etching systems. These low‐cost techniques have been applied not only in the fabrication of metallic parts or molds, but also in numerous other micromachining processes. Its ease of use has made SU‐8 to be used in many applications, even when high‐aspect ratios are not required. Beyond these pattern transfer applications, SU‐8 has been used directly as a structural material for microelectromechanical systems and microfluidics due to its properties such as its excellent chemical resistance or the low Young modulus. In contrast to conventional resists, which are used temporally, SU‐8 has been used as a permanent building material to fabricate microcomponents such as cantilevers, membranes, and microchannels. SU‐8‐based techniques have led to new low‐temperature processes suitable for the fabrication of a wide range of objects, from the single component to the complete lab‐on‐chip. First, this article aims to review the different techniques and provides guidelines to the use of SU‐8 as a structural material. Second, practical examples from our respective labs are presented.
Microfluidic platform with mass spectrometry detection for the analysis of phosphoproteins
Authors: Dawoud Abdulilah A. , Sarvaiya Hetal A. , Lazar Iulia M. 
Published: December 2007

AbstractThe development of novel and reliable technologies for the analysis of proteins and their post‐translational modifications, in particular, has recently received much attention and interest. The implementation of a fully integrated microfluidic device interfaced with MS detection for the analysis of phosphoproteins is presented in this paper. The microfluidic platform (3′′×1.5′′) comprises two individual sample processing systems: one for performing direct sample infusion and one for performing microfluidic LC separations. Various MS detection strategies, specific for the study of post‐translational modifications, were conducted using α‐casein as a model protein. Neutral loss ion mapping, data‐dependent triple‐play and neutral loss analysis, and in situ dephosphorylation followed by LC separation and MS detection were performed. Consistent results in identifying phosphopeptides with conventional and microfluidic instrumentation have been obtained. Unlike with conventional instrumentation, however, the microfluidic device enabled the completion of each analysis from only a few microliters of sample, in ∼10–15 min, and on a bioanalytical platform that facilitates multiplexing and disposability, and thus high‐throughput, contamination‐free analysis.
Stability analysis of SDOF real‐time hybrid testing systems with explicit integration algorithms and actuator delay
Authors: Chen Cheng , Ricles James M. 
Published: December 2007

AbstractReal‐time hybrid testing is a method that combines experimental substructure(s) representing component(s) of a structure with a numerical model of the remaining part of the structure. These substructures are combined with the integration algorithm for the test and the servo‐hydraulic actuator to form the real‐time hybrid testing system. The inherent dynamics of the servo‐hydraulic actuator used in real‐time hybrid testing will give rise to a time delay, which may result in a degradation of accuracy of the test, and possibly render the system to become unstable. To acquire a better understanding of the stability of a real‐time hybrid test with actuator delay, a stability analysis procedure for single‐degree‐of‐freedom structures is presented that includes both the actuator delay and an explicit integration algorithm. The actuator delay is modeled by a discrete transfer function and combined with a discrete transfer function representing the integration algorithm to form a closed‐loop transfer function for the real‐time hybrid testing system. The stability of the system is investigated by examining the poles of the closed‐loop transfer function. The effect of actuator delay on the stability of a real‐time hybrid test is shown to be dependent on the structural parameters as well as the form of the integration algorithm. The stability analysis results can have a significant difference compared with the solution from the delay differential equation, thereby illustrating the need to include the integration algorithm in the stability analysis of a real‐time hybrid testing system. Copyright © 2007 John Wiley & Sons, Ltd.
Genomic gains of COL1A1‐PDFGB occur in the histologic evolution of giant cell fibroblastoma into dermatofibrosarcoma protuberans
Authors: Macarenco Ricardo S. , Zamolyi Renata , Franco Marcello F. , Nascimento Antonio G. , Abott Jared J. , Wang Xiaoke , Erickson‐Johnson Michele R. , Oliveira Andre M. 
Published: December 2007

AbstractGiant cell fibroblastoma (GCF) is a subcutaneous mesenchymal neoplasm characterized by the chromosomal t(17;22), which results in the formation of the fusion gene COL1A1‐PDGFB. This same fusion gene is also seen in the supernumerary ring chromosome of dermatofibrosarcoma protuberans (DFSP). Several studies have addressed the molecular genetics of DFSP but molecular cytogenetic characterization of individual areas and cell components in pure GCF and GCF/DFSP hybrids have not been performed. Herein, we studied the frequency and genomic copy number of COL1A1‐PDGFB in pure GCF and GCF/DFSP hybrids, and identified the molecular cytogenetic signatures in individual cells in each component. Four pure GCF and nine GCF/DFSP hybrids were studied. All tumors exhibited classical histological features and CD34 expression. COL1A1 and PDGFB rearrangements were evaluated by fluorescence in situ hybridization (FISH) using probes for COL1A1 and PDGFB on paraffin‐embedded thin tissue sections. All GCF and GCF/DFSP hybrids showed unbalanced rearrangements of COL1A1‐PDGFB at the molecular cytogenetic level. Genomic gains of COL1A1‐PDGFB were found predominantly in the DFSP component of GCF/DFSP hybrids but in none of the pure GCF, suggesting that these gains are associated with the histologic evolution of GCF into DFSP. The molecular cytogenetic abnormalities were found not only in the spindle/stellated cells but also in individual nuclei of the multinucleated giant cells, suggesting that these cells may result from the fusion of individual neoplastic cells. © 2007 Wiley‐Liss, Inc.
Myelin‐phagocytosing macrophages in isolated sciatic and optic nerves reveal a unique reactive phenotype
Authors: van Rossum Denise , Hilbert Sören , Straßenburg Silke , Hanisch Uwe‐karsten , Brück Wolfgang 
Published: December 2007

AbstractMacrophages are key effectors in demyelinating diseases of the central and peripheral nervous system by phagocytosing myelin and releasing immunoregulatory mediators. Here, we report on a distinct, a priori anti‐inflammatory reaction of macrophages phagocytosing myelin upon contact with damaged nerve tissue. Macrophages rapidly invaded peripheral (sciatic) and central (optic) nerve tissues in vitro, readily incorporated myelin and expressed high levels of phagocytosis‐associated molecules (e.g., Fc and scavenger receptors). In contrast, factors involved in antigen presentation (MHC class‐II, CD80, CD86) revealed only a restricted expression. In parallel, a highly ordered appearance of cytokines and chemokines was detected. IL‐10, IL‐6, CCL22, and CXCL1 were immediately but transiently induced, whereas CCL2, CCL11, and TGFβ revealed more persisting levels. Such a profile would attract neutrophils, monocytes/macrophages, and Th2 cells as well as bias for a Th2‐supporting environment. Importantly, proinflammatory/Th1‐supporting factors, such as TNFα, IL‐12p70, CCL3, and CCL5, were not induced. Still the simultaneous presence of TGFβ and IL‐6 could assist Th17 development, further depending on yet not present IL‐23. The release pattern was clearly distinct from reactive phenotypes induced in isolated macrophages and microglia upon treatment with IL‐4, IL‐13, bacterial lipopolysaccharide, IFNγ, or purified myelin. Nerve‐exposed macrophages thus commit to a unique functional orientation. © 2007 Wiley‐Liss, Inc.
The significance of dyslexia screening for the assessment of dementia in older people
Authors: Metzler‐Baddeley Claudia , Salter Amanda , Jones Roy W. 
Published: December 2007

AbstractDyslexia and Dementia are disorders that share cognitive impairments in attention, language, and working memory. It is therefore possible that the presence of dyslexia may influence the assessment of the severity of dementia and potentially lead to the development of atypical forms of dementia. The present study investigated the prevalence of problems suggestive of dyslexia with a brief self‐report questionnaire in a sample of 195 older adults referred to a Memory Clinic for dementia assessment. Ten percent reported problems suggestive of dyslexia consistent with the estimated prevalence in the general population. This group performed significantly lower in a number of attention and language related tests but not in other cognitive domains. These results highlight the importance of dyslexia screening for the assessment of dementia, not least because the choice of treatment is guided by the outcome of the assessment of the severity and the type of dementia. Copyright © 2007 John Wiley & Sons, Ltd.
Abnormal diffusion of cerebral white matter in early blindness
Authors: Shu Ni , Li Jun , Li Kuncheng , Yu Chunshui , Jiang Tianzi 
Published: December 2007

AbstractEarly visual deprivation may lead to both abnormal and plastic changes in the visual and other systems of the brain. Such secondary changes in the gray matter of the early blind have been well studied, but not so well in the cerebral white matter whose subtle changes may be revealed by diffusion tensor imaging. The first purpose of this study is to explore the possible changed white matter regions of the early blind in whole brain manners, using voxel‐based analysis (VBA) and tract‐based spatial statistics (TBSS) methods. The second purpose is to investigate the changes of diffusion eigenvalues in the abnormal white matter fiber tracts using tractography based group mapping analysis. From VBA of fractional anisotropy (FA) images, the significant changed white matter regions were the geniculocalcarine tract (GCT) and its adjacent regions. This finding was validated by TBSS method. Then we studied the changes of mean diffusivity (MD), FA, primary (λ1) and transverse diffusivities (λ23) in the GCT using tractography based group mapping analysis. We found the early blind had significantly lower FA (P < 0.0001), higher MD (P = 0.001) and λ23 (P < 0.0001) in the GCT. This pattern of diffusion changes is similar to findings seen in immaturity or axonal degeneration. Thus, we suggest that transneuronal degeneration and/or immaturity may account for the abnormal diffusion changes in the GCT of the early blind. Hum Brain Mapp 2009. © 2007 Wiley‐Liss, Inc.
MC1R variants associated susceptibility to basal cell carcinoma of skin: Interaction with host factors and XRCC3 polymorphism
Authors: Scherer Dominique , Bermejo Justo Lorenzo , Rudnai Peter , Gurzau Eugene , Koppova Kvetoslava , Hemminki Kari , Kumar Rajiv 
Published: December 2007

AbstractThe variants within the human melanocortin 1 receptor (MC1R) gene are associated with an increased risk of different skin cancers. In this study, we genotyped by direct sequencing, 529 cases of basal cell carcinoma of the skin (BCC) and 533 healthy controls for polymorphisms in the entire MC1R gene. In addition to 10 common polymorphisms, we detected 23 rare variants in the gene. The presence of any nonsynonymous MC1R variant was associated with an increased risk in the carriers (odds ratio OR 1.66, 95% confidence interval CI 1.28–2.14) corresponding to a population attributable fraction of about 27%. The odds ratio for the risk in the carriers of 2 MC1R variants was 2.69 (95% CI 1.77–4.08). The risk of BCC in the carriers of MC1R variants with fair complexion was almost twice as much as in the corresponding noncarriers. The carriers of the R163Q variant with a medium skin complexion were at a 3‐fold higher risk than the noncarrier counterparts. The interaction, of effect on the BCC risk, between the MC1R variants and types of skin response to sun exposure was greater than multiplicative. We also observed a multiplicative interaction of risk due to the MC1R variants and the common allele (high risk) of the T241M polymorphism in the XRCC3 gene. Our data confirmed the status of the nonsynonymous MC1R variants as independent genetic risk factors for BCC. However, the mechanism through which the variants influence the risk likely involves complex interactions with other genetic and host risk factors. © 2007 Wiley‐Liss, Inc.
Regulatory roles of tumor‐suppressor proteins and noncoding RNA in cancer and normal cell functions
Authors: Garen Alan , Song Xu 
Published: December 2007

AbstractWe describe a mechanism for reversible regulation of gene transcription, mediated by a family of tumor‐suppressor proteins (TSP) containing a DNA‐binding domain (DBD) that binds to a gene and represses transcription, and RNA‐binding domains (RBDs) that bind RNA, usually a noncoding RNA (ncRNA), forming a TSP/RNA complex that releases the TSP from a gene and reverses repression. This mechanism appears to be involved in the regulation of embryogenesis, oncogenesis, and steroidogenesis. Embryonic cells express high levels of RNA that bind to a TSP and prevent repression of proto‐oncogenes that drive cell proliferation. The level of the RNA subsequently decreases in most differentiating cells, enabling a TSP to repress proto‐oncogenes and stop cell proliferation. Oncogenesis can result when the level of the RNA fails to decrease in a proliferating cell or increases in a differentiated cell. This mechanism also regulates transcription of P450scc, the first gene in the steroidogenic pathway. © 2007 Wiley‐Liss, Inc.
Determining the drainable pore space through field tests in Konya plain, Turkey
Authors: Bahçeci İdris 
Published: December 2007

AbstractDrainable pore space (µ) is known as one of the main criteria when designing subsurface drainage systems under unsteady‐state flow conditions. Determining µ is both a difficult and time‐consuming process. An easy and exact method for determining µ could provide researchers with a considerably valuable advantage in decision‐making stages. This parameter is influenced by the soil moisture condition at a certain position and time. When groundwater tables are relatively shallow, the parameter value is highly variable in time and space. Because of this, one should be cautious when using this parameter to design subsurface drainage systems. This paper describes a field experiment to determine the drainable pore space as a function of groundwater table depth and drain discharge and some hydraulic parameters of soil to verify our point of view. Copyright © 2007 John Wiley & Sons, Ltd.