bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ligase detection reaction for the analysis of point mutations using free‐solution conjugate electrophoresis in a polymer microfluidic device
Authors: Sinville Rondedrick , Coyne Jennifer , Meagher Robert J. , Cheng Yu‐Wei , Barany Francis , Barron Annelise , Soper Steven A. 
Published: December 2008

AbstractWe have developed a new method for the analysis of low abundant point mutations in genomic DNA using a combination of an allele‐specific ligase detection reaction (LDR) with free‐solution conjugate electrophoresis (FSCE) to generate and analyze the genetic products. FSCE eliminates the need for a polymer sieving matrix by conjugating chemically synthesized polyamide “drag‐tags” onto the LDR primers. The additional drag of the charge‐neutral drag‐tag breaks the linear scaling of the charge‐to‐friction ratio of DNA and enables size‐based separations of DNA in free solution using electrophoresis with no sieving matrix. We successfully demonstrate the conjugation of polyamide drag‐tags onto a set of four LDR primers designed to probe the K‐ras oncogene for mutations highly associated with colorectal cancer, the simultaneous generation of fluorescently labeled LDR/drag‐tag conjugate (LDR‐dt) products in a multiplexed, single‐tube format with mutant:WT ratios as low as 1:100, respectively, and the single‐base, high‐resolution separation of all four LDR‐dt products. Separations were conducted in free solution with no polymer network using both a commercial capillary array electrophoresis (CAE) system and a PMMA microchip replicated via hot‐embossing with only a Tris‐based running buffer containing additives to suppress the EOF. Typical analysis times for LDR‐dt were 11 min using the CAE system and as low as 85 s for the PMMA microchips. With resolution comparable to traditional gel‐based CAE, FSCE along with microchip electrophoresis decreased the separation time by more than a factor of 40.
Transverse imaging and simulation of dsDNA electrophoresis in microfabricated glass channels
Authors: Zeitoun Ramsey I. , Chen Zheng , Burns Mark A. 
Published: December 2008

AbstractWe have observed the non‐uniform distribution of DNA molecules during PAGE in a microfabricated system. Confocal laser scanning microscopy was used to visualize fluorescently labeled DNA during electrophoretic migration. The distribution of double‐stranded DNA larger than 100 bp is observed to transition from a center‐biased motion on the transverse plane 1 cm downstream from injection to an edge‐biased motion 2 cm downstream. Although this distribution increased with increasing dsDNA size in a cross‐linked gel, no similar distribution was found with the same dsDNA molecules in a linear polyacrylamide solution (6%). Simulations of DNA distribution in gels suggest that DNA distribution non‐uniformities may be caused by biased electrophoretic migration resulting from motion in an inhomogeneous gel system.
Hydrophobically modified polyacrylamide block copolymers for fast, high‐resolution DNA sequencing in microfluidic chips
Authors: Forster Ryan E. , Chiesl Thomas N. , Fredlake Christopher P. , White Corin V. , Barron Annelise E. 
Published: December 2008

AbstractBy using a microfluidic electrophoresis platform to perform DNA sequencing, genomic information can be obtained more quickly and affordably than the currently employed capillary array electrophoresis instruments. Previous research in our group has shown that physically cross‐linked, hydrophobically modified polyacrylamide matrices separate dsDNA more effectively than linear polyacrylamide (LPA) solutions. Expanding upon this work, we have synthesized a series of LPA‐co‐dihexylacrylamide block copolymers specifically designed to electrophoretically sequence ssDNA quickly and efficiently on a microfluidic device. By incorporating very small amounts of N,N‐dihexylacrylamide, a hydrophobic monomer, these copolymer solutions achieved up to ∼10% increases in average DNA sequencing read length over LPA homopolymer solutions of matched molar mass. Additionally, the inclusion of the small amount of hydrophobe does not significantly increase the polymer solution viscosities, relative to LPA solutions, so that channel loading times between the copolymers and the homopolymers are similar. The resulting polymer solutions are capable of providing enhanced sequencing separations in a short period of time without compromising the ability to rapidly load and unload the matrix from a microfluidic device.
Thermoresponsive N‐alkoxyalkylacrylamide polymers as a sieving matrix for high‐resolution DNA separations on a microfluidic chip
Authors: Root Brian E. , Hammock Mallory L. , Barron Annelise E. 
Published: December 2008

AbstractIn recent years, there has been an increasing demand for a wide range of DNA separations that require the development of materials to meet the needs of high resolution and high throughput. Here, we demonstrate the use of thermoresponsive N‐alkoxyalkylacrylamide polymers as a sieving matrix for DNA separations on a microfluidic chip. The viscosities of the N‐alkoxyalkylacrylamide polymers are more than an order of magnitude lower than that of a linear polyacrylamide (LPA) of corresponding molecular weight, allowing rapid loading of the microchip. At 25°C, N‐alkoxyalkylacrylamide polymers can provide improved DNA separations compared with LPA in terms of reduced separation time and increased separation efficiency, particularly for the larger DNA fragments. The improved separation efficiency in N‐alkoxyalkylacrylamide polymers is attributed to the peak widths increasing only slightly with DNA fragment size, while the peak widths increase appreciably above 150 bp using an LPA matrix. Upon elevating the temperature to 50°C, the increase in viscosity of the N‐alkoxyalkylacrylamide solutions is dependent upon their overall degree of hydrophobicity. The most hydrophobic polymers exhibit a lower critical solution temperature below 50°C, undergoing a coil‐to‐globule transition followed by chain aggregation. DNA separation efficiency at 50°C therefore decreases significantly with increasing hydrophobic character of the polymers, and no separations were possible with solutions with a lower critical solution temperature below 50°C. The work reported here demonstrates the potential for this class of polymers to be used for applications such as PCR product and RFLP sizing, and provides insight into the effect of polymer hydrophobicity on DNA separations.
Alternative non‐linear demand estimation methods for probability‐based seismic assessments
Authors: Jalayer F. , Cornell C. A. 
Published: December 2008

AbstractAlternative non‐linear dynamic analysis procedures, using real ground motion records, can be used to make probability‐based seismic assessments. These procedures can be used both to obtain parameter estimates for specific probabilistic assessment criteria such as demand and capacity factored design and also to make direct probabilistic performance assessments using numerical methods. Multiple‐stripe analysis is a non‐linear dynamic analysis method that can be used for performance‐based assessments for a wide range of ground motion intensities and multiple performance objectives from onset of damage through global collapse. Alternatively, the amount of analysis effort needed in the performance assessments can be reduced by performing the structural analyses and estimating the main parameters in the region of ground motion intensity levels of interest. In particular, single‐stripe and double‐stripe analysis can provide local probabilistic demand assessments using minimal number of structural analyses (around 20 to 40). As a case study, the displacement‐based seismic performance of an older reinforced concrete frame structure, which is known to have suffered shear failure in its columns during the 1994 Northridge Earthquake, is evaluated. Copyright © 2008 John Wiley & Sons, Ltd.
Disruption of laminin in the peripheral nervous system impedes nonmyelinating Schwann cell development and impairs nociceptive sensory function
Authors: Yu Wei‐Ming , Yu Huaxu , Chen Zu‐Lin , Strickland Sidney 
Published: December 2008

AbstractThe mechanisms controlling the differentiation of immature Schwann cells (SCs) into nonmyelinating SCs is not known. Laminins are extracellular matrix proteins critical for myelinating SC differentiation, but their roles in nonmyelinating SC development have not been established. Here, we show that the peripheral nerves of mutant mice with laminin‐deficient SCs do not form Remak bundles, which consist of a single nonmyelinating SC interacting with multiple unmyelinated axons. These mutant nerves show aberrant L1 and neural cell adhesion molecule (N‐CAM) expression pattern during development. The homophilic and heterophilic interactions of N‐CAM are also impaired in the mutant nerves. Other molecular markers for nonmyelinating SCs, including Egr‐1, glial fibrillary acidic protein, and AN2/NG2, are all absent in adult mutant nerves. Analysis of expression of SC lineage markers demonstrates that nonmyelinating SCs do not develop in mutant nerves. Additionally, mutant mice are insensitive to heat stimuli and show a decreased number of C‐fiber sensory neurons, indicating reduced nociceptive sensory function. These results show that laminin participates in nonmyelinating SC development and Remak bundle formation and suggest a possible role for laminin deficiency in peripheral sensory neuropathies. © 2008 Wiley‐Liss, Inc.
Chemokines in the immunopathogenesis of hepatitis C infection #
Authors: Heydtmann Mathis , Adams David H. 
Published: December 2008

Abstract
Chronic infection with the hepatitis C virus, a noncytopathic hepatotropic RNA virus, affects over 170 million people worldwide. In the majority of cases, neither the early innate immune response nor the later adaptive immune response succeeds in clearing the virus, and the infection becomes chronic. Furthermore, in many patients, the ineffective inflammatory response drives fibrogenesis and the development of cirrhosis. It is critical to understand this immune pathology if preventative and curative therapies are to be developed. Chemokines are a superfamily of small proteins that promote leukocyte migration and orchestrate the immune response to viruses, including hepatitis C virus. Chemokines are crucial for viral elimination, but inappropriate persistence of expression in chronic hepatitis C infection can drive tissue damage and inflammation. Here we review the role of chemokines and their receptors in hepatitis C virus infection. (Hepatology 2009;49:676–688.)
Prediction of pool boiling heat transfer coefficient in ammonia/water mixtures
Authors: Inoue Toshiaki , Monde Masanori 
Published: December 2008

AbstractA correlation of nucleate pool boiling heat transfer coefficients in ammonia/water mixtures was proposed on the basis of measured heat transfer data on a horizontal heated wire. The correlation was derived using both the fraction difference between vapor and liquid, y1−x1, and the temperature difference between dew and bubble points, ΔTE. It can predict the heat transfer coefficients of the mixtures during pool boiling within an accuracy of ±20% over the entire fraction range for heat fluxes below 1000 kW/m2, which corresponds to the experimental range performed by Inoue et al. [1]. It was clarified that the coefficients more strongly depend on y1−x1 than on ΔTE for ammonia/water mixtures, while the heat transfer coefficients mainly depend on ΔTE for Freon (DuPont's trade name) mixtures. © 2008 Wiley Periodicals, Inc. Heat Trans Asian Res; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20234
Study on the hydrological conditions for the conservation of the nesting habitat of the Red‐crowned Crane in Xianghai Wetlands, China
Authors: He Chunguang , Ishikawa Tadaharu , Sheng Lianxi , Irie Mitsuteru 
Published: December 2008

AbstractThe hydrological condition of the Xianghai National Natural Reserve (XNNR) in China was studied in relation to the conservation of the breeding habitat of the Red‐crowned crane, an endangered waterfowl species. In recent years, the condition of the cranes' habitat in XNNR has deteriorated due to shrinking of the wetlands caused by the increase of uncontrolled intake of river water. Because XNNR is located in a remote rural area, the condition of the cranes' habitat was not surveyed in detail, therefore, basic information about the wetlands such as, topographic and hydrological data were not fully available. As a result, a large amount of time is required to frame a detailed plan for the allocation of water resources for the conservation of the cranes. In order to progress, the ‘precautionary approach’ must be applied even without full scientific certainty (The Ramsar Convention on Wetlands, Resolution VIII.1, 2002), based on the information available at present, and in order to reach an agreement among stakeholders. For this purpose, the study took the following four steps. Firstly, field observations conducted over a period of seven years clarified that reed communities surrounded by a shallow water body were the favourable conditions for nesting. Secondly, Landsat‐TM data analysis showed that the number of nests became stable when the reed area developed to some extent, and also that the reed area has a high correlation with the total water area in the XNNR. Thirdly, the variation of the total water area over 20 years were estimated from 143 analog images of Landsat data and its correlations with some basic hydrological factors were obtained by regression analyses. The final step involved combining the above mentioned results, which was then used to develop a practical guideline for the use of river water by the local community that is balanced with the conservation of the Red‐crowned cranes. Copyright © 2008 John Wiley & Sons, Ltd.
Transglutaminase 3 as a prognostic biomarker in esophageal cancer revealed by proteomics
Authors: Uemura Norihisa , Nakanishi Yukihiro , Kato Hoichi , Saito Shigeru , Nagino Masato , Hirohashi Setsuo , Kondo Tadashi 
Published: December 2008

AbstractTo develop a prognostic biomarker for esophageal squamous cell carcinoma (ESCC), we examined the proteomic profile of ESCC using two‐dimensional difference gel electrophoresis (2D‐DIGE), and identified proteins associated with prognosis by mass spectrometry. The prognostic performance of the identified proteins was examined by immunohistochemistry in additional cases. We identified 22 protein spots whose intensity was statistically different between ESCC cases with good (N = 9; survived more than 5 years without evidence of recurrence) and poor (N = 24; died within 2 years postsurgery) prognosis, within the patient group that had two or more lymph node metastases. Mass spectrometric protein identification resulted in 18 distinct gene products from the 22 protein spots. Transglutaminase 3 (TGM3) was inversely correlated with shorter patient survival. The prognostic performance of TGM3 was further examined by immunohistochemistry in 76 ESCC cases. The 5‐year disease‐specific survival rate was 64.5% and 32.1% for patients with TGM3‐positive and TGM3‐negative tumors, respectively (p = 0.0033). Univariate and multivariate analyses revealed that TGM3 expression was an independent prognostic factor among the clinicopathologic variables examined. It is noteworthy that the prognostic value of TGM3 was shown to be higher than those of the lymph node metastasis, intramural metastasis and vascular invasion status. These results establish TGM3 as a novel prognostic biomarker for ESCC for the first time. Examination of TGM3 expression may provide novel therapeutic strategies to prevent recurrence of ESCC. © 2008 Wiley‐Liss, Inc.
He–Ne laser (632.8 nm) pre‐irradiation gives protection against DNA damage induced by a near‐infrared trapping beam
Authors: Sahu Khageswar , Mohanty Samarendra Kumar , Gupta Pradeep Kumar 
Published: December 2008

AbstractWe report the results of a study carried out to investigate the effect of He–Ne laser (632.8 nm) pre‐irradiation on DNA damage induced by continuous wave 1064 nm trapping beam exposure in MCF‐7 cells. A significant decrease in % tail DNA (p < 0.05) was observed in MCF‐7 cells pre‐exposed to He–Ne laser beam. The dependence of the induced protection against 1064 nm trapping beam irradiation induced DNA damage on the time interval between the two irradiations as well as the He–Ne laser pre‐irradiation parameters is presented. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spreading of an anchorage‐dependent cell on a selectively ligand‐coated substrate mediated by receptor‐ligand binding
Authors: Liu Ping , Zhang Yong W. , Yu Hanry , Zhang Xin , Cheng Qian H. , Lu Chun , Bonfield William 
Published: December 2008

AbstractA continuum model was proposed to simulate a biological cell adhering to a substrate surface domain with selectively coated ligands. Cell adhesion was modeled by a traction‐separation law depending on the receptor‐ligand distance and their densities. It was found that the obtained spreading patterns are consistent with published experimental data and that adhesion requires a nonuniform distribution of receptors at the spreading front with convex fronts requiring a much higher receptor density than concave fronts. Adhesion strength was also found to be more influential than adhesion energy on the spreading kinetics. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Pathogenic Vibrio harveyi, in contrast to non‐pathogenic strains, intervenes with the p38 MAPK pathway to avoid an abalone haemocyte immune response
Authors: Travers Marie‐Agnès , Le Bouffant Ronan , Friedman Carolyn S. , Buzin Florence , Cougard Bertrand , Huchette Sylvain , Koken Marcel , Paillard Christine 
Published: December 2008

AbstractVibrio harveyi is a marine bacterial pathogen responsible for episodic abalone epidemics associated with massive mortalities in France, Japan, and Australia. The aim of this study was the understanding of a possible role of the p38 MAPK in abalone haemocyte responses towards this bacterium. First, the pathogenicity of different V. harveyi strains was compared in both immersion and injection trials, and clear differences were detected. The three strains, ORM4, 04/092, and 05/053, all isolated from moribund abalone, induced up to 80% mortalities in immersion or injection challenges (LD50 (ORM4) = 2.5 × 102 CFU animal−1). The two strains, LMG 4044T and LMG 7890 were non‐pathogenic towards abalone in immersion trials, and needed very high numbers for killing by intramuscular injections (LD50 = 8.9 × 104 and 1.6 × 105 CFU animal−1, respectively). To start unraveling the mechanism explaining these differences, the p38‐MAPK, a keyplayer in antimicrobial immune response, was studied. The non‐pathogenic strain, LMG 7890 can be eliminated by abalone haemocytes and induces haemocyte phagocytosis and high ROS production. With different concentrations of a p38‐specific inhibitor, SB203580, p38 implication was shown. This inhibitor reduced phagocytosis and ROS induction leading to LMG 7890 proliferation. In the case of the pathogenic ORM4 which can not be eliminated by abalone haemocytes, no phagocytosis and ROS production was induced, and a retarded p38 activation was observed. Taken together, our results suggest that p38 MAPK modulation may be one of the ways of virulent V. harveyi to attack its host and escape abalone immune response. J. Cell. Biochem. 106: 152–160, 2009. © 2008 Wiley‐Liss, Inc.
Predicting responsiveness to a depressive mood induction procedure
Authors: Scherrer Martin C. , Dobson Keith S. 
Published: December 2008

AbstractInducing various mood states—sad or depressed mood in particular—has become a widely employed and accepted means of experimentally examining the link between emotion and cognition, particularly with research on cognitive theory and depression. Using various criteria, studies utilizing mood induction procedures (MIPs) have reported successful induction of the desired mood in participants at rates ranging from 50 to 75%, clearly reflecting substantial individual variation. Individual differences in response to MIPs, however, have received little attention. Drawing on both theory and previous research, the present study identified and examined a range of possible predictors of response to depressive mood induction in a sample of 100 undergraduate students. Results indicated that of the examined predictors, experience with recent negative events prior to the mood induction and participant mood state, including self‐reported symptoms of anxiety, significantly predicted reported mood state following the MIP. The implications of these results for models of vulnerability and resilience to negative mood states are discussed, and future research directions are provided © 2008 Wiley Periodicals, Inc. J Clin Psychol 65:1–16, 2009.
DNA aptamers developed against a soman derivative cross‐react with the methylphosphonic acid core but not with flanking hydrophobic groups
Authors: Bruno John G. , Carrillo Maria P. , Cadieux C. Linn , Lenz David E. , Cerasoli Douglas M. , Phillips Taylor 
Published: December 2008

AbstractTwelve rounds of systematic evolution of ligands by exponential enrichment (SELEX) were conducted against a magnetic bead conjugate of thepara‐aminophenylpinacolylmethylphosphonate (PAPMP) derivative of the organophosphorus (OP) nerve agent soman (GD). The goal was to develop DNA aptamers that could scavenge GDin vivo, thereby reducing or eliminating the toxic effects of this dangerous compound. Aptamers were sequenced and screened in peroxidase‐based colorimetric plate assays after rounds 8 and 12 of SELEX. The aptamer candidate sequences exhibiting the highest affinity for the GD derivative from round 8 also reappeared in several clones from round 12. Each of the highest affinity PAPMP‐binding aptamers also bound methylphosphonic acid (MPA). In addition, the aptamer with the highest overall affinity for PAPMP carried a sequence motif (TTTAGT) thought to bind MPA based on previously published data (J. Fluoresc 18: 867–876, 2008). This sequence motif was found in several other relatively high affinity PAPMP aptamer candidates as well. In studies with the nerve agent GD, pre‐incubation of a large molar excess of aptamer candidates failed to protect human butyrylcholinesterase (BuChE) from inhibition. With the aid of three‐dimensional molecular modeling of the GD derivative it appears that a hydrophilic cleft sandwiched between the pinacolyl group and thep‐aminophenyl ring might channel nucleotide interactions to the phosphonate portion of the immobilized GD derivative. However,bona fideGD free in solution may be repulsed by the negative phosphate backbone of aptamers and rotate its phosphonate and fluorine moieties away from the aptamer to avoid being bound. Future attempts to develop aptamers to GD might benefit from immobilizing the pinacolyl group ofbona fideGD to enhance exposure of the phosphonate and fluorine to the random DNA library. Copyright © 2008 John Wiley & Sons, Ltd.