bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of ALK‐PTPN3 gene fusion from human non‐small cell lung carcinoma cell line using next generation RNA sequencing
Authors: Jung Yeonjoo , Kim Pora , Jung Yeonhwa , Keum Juhee , Kim Soon‐Nam , Choi Yong Soo , Do In‐Gu , Lee Jinseon , Choi So‐Jung , Kim Sujin , Lee Jong‐Eun , Kim Jhingook , Lee Sanghyuk , Kim Jaesang 
Published: February 2012

AbstractAn increasing number of chromosomal aberrations is being identified in solid tumors providing novel biomarkers for various types of cancer and new insights into the mechanisms of carcinogenesis. We applied next generation sequencing technique to analyze the transcriptome of the non‐small cell lung carcinoma (NSCLC) cell line H2228 and discovered a fusion transcript composed of multiple exons of ALK (anaplastic lymphoma receptor tyrosine kinase) and PTPN3 (protein tyrosine phosphatase, nonreceptor Type 3). Detailed analysis of the genomic structure revealed that a portion of genomic region encompassing Exons 10 and 11 of ALK has been translocated into the intronic region between Exons 2 and 3 of PTPN3. The key net result appears to be the null mutation of one allele of PTPN3, a gene with tumor suppressor activity. Consistently, ectopic expression of PTPN3 in NSCLC cell lines led to inhibition of colony formation. Our study confirms the utility of next generation sequencing as a tool for the discovery of somatic mutations and has led to the identification of a novel mutation in NSCLC that may be of diagnostic, prognostic, and therapeutic importance. © 2012 Wiley Periodicals, Inc.
Risk factors for medication nonadherence in older adults with cognitive impairment who live alone
Authors: Thiruchselvam Thulasi , Naglie Gary , Moineddin Rahim , Charles Jocelyn , Orlando Laura , Jaglal Susan , Snow William , Tierney Mary C. 
Published: February 2012

ObjectiveThe aim of this study was to prospectively examine the influence of cognitive, medical, behavioral, and social risk factors on medication nonadherence in community‐dwelling older adults with cognitive impairment.MethodsA sample of 339 elderly participants with cognitive impairment, who lived alone and took at least one medication, underwent baseline assessment which included the five subscales of the Dementia Rating Scale (DRS), number of medications, retrospective medication nonadherence, amount of formal and informal assistance, functional impairment, depression, perception of social resources, comorbidity, and alcohol consumption. The outcome was medication nonadherence during the 12‐month prospective period as reported by the participants' primary care physicians and caregivers at three‐month intervals.ResultsFifty‐nine participants (17.4%) had, at least, one report of medication nonadherence. Logistic regression analyses indicated for every point increase on the DRS Conceptualization subscale (OR = 1.14; 95% CI = 1.02–1.27), there was a 14% increase in the odds of nonadherence. For every point increase on the DRS Memory subscale (OR = 0.89; 95% CI = 0.81–0.97) and DRS Initiation/Perseveration subscale (OR = 0.93; 95% CI = 0.87–1.00), there was an 11% decrease and 7% decrease in the odds, respectively. Having at least one previous occurrence of medication nonadherence (OR = 2.61; 95% CI = 1.18–5.62) and taking at least four medications (OR = 2.58; 95% CI = 1.31–5.29), both increased the odds by over 2.5‐fold.ConclusionsOur unique finding that better conceptualization predicted nonadherence has important implications for healthcare providers' approaches to improve adherence in older adults with cognitive impairment. Replication in future studies is warranted. Copyright © 2012 John Wiley & Sons, Ltd.
REGIONAL VARIATION IN THE PRODUCTIVITY OF THE ENGLISH NATIONAL HEALTH SERVICE
Authors: Bojke Chris , Castelli Adriana , Street Andrew , Ward Padraic , Laudicella Mauro 
Published: February 2012

SUMMARYVariation in the provision of health care has long been a policy concern. We adapt the framework for productivity measurement used in the National Accounts, making it applicable for sub‐national comparisons using cross‐sectional data. We assess the productivity of the National Health Service (NHS) across regions of England, termed Strategic Health Authorities (SHAs). Productivity is calculated by comparing the total amount of healthcare output to total inputs for each region, standardised to the national average. Healthcare output comprises 6500 different categories, capturing the number and type of NHS patients treated and the quality of care received. Healthcare inputs include NHS and agency staff, supplies, equipment and capital. We find that productivity varies from 5% above to 6% below the national average. Productivity is highest in South West SHA and lowest in East Midlands, South Central and Yorkshire and The Humber SHAs. We estimate that if all regions were as productive as the most productive region in England, the NHS could treat the same number of patients with £3.2bn fewer resources each year. The methods developed lend themselves to investigate variations in productivity in other types of healthcare organisations and health systems. Copyright © 2012 John Wiley & Sons, Ltd.
Semi‐automated GIS techniques for detecting floodplain earthworks
Authors: Steinfeld Celine M. M. , Kingsford Richard T. , Laffan Shawn W. 
Published: February 2012

AbstractLevees, channels and water storages built on the world's floodplain wetlands control flows for irrigation, flood mitigation and erosion management. Assessing their distribution and hydrological impacts through time and across broad extents is limited by significant costs and technical challenges. We tested the effectiveness of three new semi‐automated geographic information systems and traditional visual interpretation techniques for detecting earthworks. We used commercially or freely available two‐dimensional and three‐dimensional spatial imagery within 19 quadrats in an agricultural floodplain of the Murray–Darling Basin, southeastern Australia. Semi‐automated digital elevation model (DEM) analysis performed best for spatial accuracy (78% of earthworks correctly predicted within 25 m), overall classification accuracy (97.7%) and kappa (0.64), compared with traditional visual interpretation techniques using Landsat TM (52%, 96.3%, 0.39), SPOT (53%, 95.8%, 0.27) and aerial photography (72%, 97.2%, 0.31). DEM analysis also outperformed semi‐automated image segmentation (16%, 93%, 0.29) and integrated analysis (75%, 96.0%, 0.43) that used spectral information. Semi‐automated techniques were slow (DEM analysis: 27 418 s/km2; integrated analysis: 27 737 s/km2; and image segmentation: 1439 s/km2) compared with visual interpretation (Landsat TM: 109 s/km2; SPOT: 166 s/km2; and aerial photography: 276 s/km2); however, processing speed of semi‐automated techniques can be further increased without compromising accuracy. Semi‐automated techniques also offered operational autonomy following model calibration. High quality, cost‐effective earthwork mapping techniques, particularly the semi‐automated techniques in this study, are critical for understanding and managing ecosystem health, flood risk and water security in developed floodplains worldwide and should be implemented by governing institutions. Copyright © 2012 John Wiley & Sons, Ltd.
Characterizing the hydraulic properties of unsaturated sand considering various porosities and drying‐wetting paths of the retention curve
Authors: Ke Kai‐yuan , Tan Yih‐Chi , Chen Chu‐Hui , Lin Hsien‐Tsung 
Published: February 2012

AbstractPrevious studies have shown that water retention curve (WRC) and the hydraulic conductivity vary because of changes of the void ratio or porosity of soil. However, limited documents pointed out the change of hydraulic properties of soil when compacted to different porosities while considering both of the drying and wetting processes of the WRC. This information is sometimes necessary for research like finger flow analysis or the occurrence of wetting and drying cycles as what would be seen in the field. Therefore, this study aims to examine the change of WRC characteristics with varied porosity considering both of the drying and wetting path in WRC by conducting a sand box experiment. Results show that the same type of sand compacted to various porosities have different hydraulic parameters. Hydraulic conductivities generally decrease with reduced porosities; shape parameter α of the van Genuchten equation (1980) linearly decreases with declining porosity and shape parameter n in a reversal manner for the sands of interest whether in the drying process or wetting process. The unsaturated properties of sand are further characterized by inspecting the variations of moisture content, matric suction and vertical displacement of soil body subject to periodic changes of the water level by another sand box experiment. The outcomes suggest that the saturated water content and residual water content are changing during the wetting–drying process, which can be an implication of the changed properties of WRC. The characteristics of volumetric deformation might be varied as well because of the observation of the dissimilar patterns of the changing vertical displacements among each wetting–drying process. Infiltration patterns of the sands also are identified through numerical modelling by introducing a constant infiltration flux from the surface followed by a no‐influx condition. Results indicate that less water accumulates in the sand near the surface for the sand compacted to higher porosity, but water can move deeper. Hydraulic conductivity is found as the prime factor dominating the evolvement of wetting fronts. However, shape parameters of water retention curves also affect the infiltration pattern to some extent. In addition, different sands with similar porosities can have quite different infiltrating characteristics. Copyright © 2012 John Wiley & Sons, Ltd.
Tumorigenicity of acrylamide and its metabolite glycidamide in the neonatal mouse bioassay
Authors: Von Tungeln Linda S. , Doerge Daniel R. , Gamboa da Costa Gonçalo , Matilde Marques M. , Witt William M. , Koturbash Igor , Pogribny Igor P. , Beland Frederick A. 
Published: February 2012

AbstractAcrylamide is a high‐volume industrial chemical, a component of cigarette smoke, and a product formed in certain foods prepared at high temperatures. Previously, we compared the extent of DNA adduct formation and mutations in B6C3F1/Tk mice treated neonatally with acrylamide or glycidamide to obtain information concerning the mechanism of acrylamide genotoxicity. We have now examined the tumorigenicity of acrylamide and glycidamide in mice treated neonatally. Male B6C3F1 mice were injected intraperitoneally on postnatal days 1, 8 and 15 with 0.0, 0.14 or 0.70 mmol acrylamide or glycidamide per kg body weight per day and the tumorigenicity was assessed after 1 year. Survival in each of the groups was >87%, there were no differences in body weights among the groups, and the only treatment‐related neoplasms involved the liver. The incidence of combined hepatocellular adenoma or carcinoma was 3.8% in the control group, 8.3% in the 0.14 mmol acrylamide and glycidamide per kg body weight groups, 4.2% in the 0.70 mmol acrylamide per kg body weight group and 71.4% in the 0.70 mmol glycidamide per kg body weight group. Analysis of the hepatocellular tumors indicated that the increased incidence observed in mice administered 0.70 mmol glycidamide per kg body weight was associated with A → G and A → T mutations at codon 61 of H‐ras. These results, combined with our previous data on DNA adduct formation and mutation induction, suggest that the carcinogenicity of acrylamide is dependent on its metabolism to glycidamide, a pathway that is deficient in neonatal mice.
Side‐Chain Metallocene‐Containing Polymers by Living and Controlled Polymerizations
Authors: Hardy Christopher G. , Ren Lixia , Zhang Jiuyang , Tang Chuanbing 
Published: February 2012

AbstractThis review summarizes recent work on side‐chain metallocene‐containing polymers prepared by controlled and living polymerizations, which include living anionic polymerization (LAP), ring‐opening metathesis polymerization (ROMP) and controlled radical polymerization (CRP) such as atom transfer radical polymerization (ATRP), reversible addition fragmentation chain transfer polymerization (RAFT), and nitroxide‐mediated polymerization (NMP). The majority of efforts in the field are focused on side‐chain ferrocene‐containing polymers, while cobaltocenium‐containing polymers have recently started to draw attention. Future direction on the development of other metallocene‐containing polymers is discussed.
Interstitial interfaces show marked differences in regenerating tubules, matured tubules, and the renal stem/progenitor cell niche
Authors: Minuth Will W. , Denk Lucia 
Published: February 2012

AbstractStem/progenitor cells are promising candidates for the regeneration of parenchyma in acute and chronic renal failure. After an implantation stem/progenitor cells must migrate through the interstitial space to concentrate at the site of damage. However, information is lacking to what extent the interstitial interface is influencing the development of stem/progenitor cells into nephron structures. In consequence, tubule regeneration within an artificial polyester interstitium was analyzed by electron microscopy in comparison with the interstitial interface of matured tubules and the interstitium within the renal stem/progenitor cell niche. The experiments demonstrate that fixation of specimens with glutaraldehyde (GA) is leading in all cases to inconspicuously looking interstitial interfaces. In contrast, fixation of regenerating tubules in GA containing ruthenium red and tannic acid shows a dense network of fibers lining along the basal lamina. In contrast, matured tubules reveal after ruthenium red label an extremely thickened basal lamina, while only a punctate pattern is obtained after tannic acid treatment. Finally, within the renal stem/progenitor cell niche ruthenium red and tannic acid label reveals large amounts of extracellular matrix spanning through the interstitium. Thus, fixation of tissue in GA containing ruthenium red and tannic acid exhibits an unexpectedly regional heterogeneity of the renal interstitial interface. This fact has to be considered for an optimal therapeutic repair of parenchyma, since contacts between stem/progenitor cells with the interstitial interface influence further development. © 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2012.
Improvement in the colloidal stability of protein kinase‐responsive polyplexes by PEG modification
Authors: Tsuchiya Akira , Naritomi Yuki , Kushio Satoshi , Kang Jeong‐Hun , Murata Masaharu , Hashizume Makoto , Mori Takeshi , Niidome Takuro , Katayama Yoshiki 
Published: February 2012

AbstractWe have reported a disease‐cell specific gene expression system that is responsive to intracellular signaling proteins (e.g., protein kinases and proteases) hyperactivated in diseased cells. For this system, cationic peptide‐grafted polymers were synthesized for polyplex formation with genes. Here, we modified poly(ethylene glycol) (PEG) to a protein kinase A (PKA)‐responsive polymer to improve polyplex stability. PEG modification neutralized the surface charge of the polyplex and successfully increased polyplex stability at physiological conditions. However, PEG modification (PEG contents, 0.6 and 3.3 mol %) showed almost negligible effects on the reactivity of grafted peptides to PKA and the promotion of gene expression responding to PKA activity. Excessive modification of PEG (PEG contents, 6.8 mol %) inhibited polyplex formation. These results indicate that moderate modification of PEG to the enzyme‐responsive polymer improves polyplex stability without inhibiting the reaction with enzymes. © 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2012.
Advanced polymeric matrix for valvular complications
Authors: Acharya Gayathri , Hopkins Richard A. , Lee Chi H. 
Published: February 2012

AbstractPoly(L‐lactic acid) (PLLA) matrix systems incorporated with poly(lactic‐co‐glycolic acid) (PLGA) nanoparticles (NPs) containing nitric oxide (NO) donors (DETA NONOate) were developed for prevention of heart valve complications through sustained and controlled release of NO. PLLA matrices were prepared using the salt leaching method and the properties and drug release profiles were characterized. For assessment of the effects of PLLA systems on the pharmacological responses and cytotoxicity, various factors, such as calcium content, alkaline phosphatase (ALP) activity, cyclic guanosine monophosphate (cGMP) expression, intercellular adhesion molecule (ICAM‐1) expression and cell viability of porcine aortic valve interstitial cells (PAVICs), were evaluated. PLLA matrices embedded with PLGA‐ NPs demonstrated its usefulness in alleviating the calcification rate of the VICs. The cGMP levels under osteoblastic conditions significantly increased, supporting that anticalcification activity of NO is mediated through NO‐cGMP signaling pathway. The level of ICAM‐1 expression in cells exposed to NO was lowered, suggesting that NO has an inhibitory activity against tissue inflammation. NO releases from PLLA matrix embedded with PLGA NPs prevented valvular calcification and inflammation without causing any cytotoxic activities. PLLA matrix system loaded with NPs containing NO donors could provide a new platform for sustained and controlled delivery of NO, significantly reducing valvular complications. © 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2012.
Altering surface characteristics of polypropylene mesh via sodium hydroxide treatment
Authors: Regis Shawn , Jassal Manisha , Mukherjee Nilay , Bayon Yves , Scarborough Nelson , Bhowmick Sankha 
Published: February 2012

AbstractIncisional hernias represent a serious and common complication following laparotomy. The use of synthetic (e.g. polypropylene) meshes to aid repair of these hernias has considerably reduced recurrence rates. While polypropylene is biocompatible and has a long successful clinical history in treating hernias and preventing reherniation, this material may suffer some limitations, particularly in challenging patients at risk of wound failure due to, for example, an exaggerated inflammation reaction, delayed wound healing, and infection. Surface modification of the polypropylene mesh without sacrificing its mechanical properties, critical for hernia repair, represents one way to begin to address these clinical complications. Our hypothesis is treatment of a proprietary polypropylene mesh with sodium hydroxide (NaOH) will increase in vitro NIH/3T3 cell attachment, predictive of earlier and improved cell colonization and tissue integration of polypropylene materials. Our goal is to achieve this altered surface functionality via enhanced removal of chemicals/oils used during material synthesis without compromising the mechanical properties of the mesh. We found that NaOH treatment does not appear to compromise the mechanical strength of the material, despite roughly a 10% decrease in fiber diameter. The treatment increases in vitro NIH/3T3 cell attachment within the first 72 h and this effect is sustained up to 7 days in vitro. This research demonstrates that sodium hydroxide treatment is an efficient way to modify the surface of polypropylene hernia meshes without losing the mechanical integrity of the material. This simple procedure could also allow the attachment of a variety of biomolecules to the polypropylene mesh that may aid in reducing the complications associated with polypropylene meshes today. © 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2012.
Growth, differentiation, and migration of osteoblasts on transparent Ni doped TiO2thin films deposited on borosilicate glass
Authors: Dhayal Marshal , Kapoor Renu , Sistla Pavana Goury , Kant Chander , Pandey Ravi Ranjan , Govind  , Saini Krishan Kumar , Pande Gopal 
Published: February 2012

AbstractA simple and cost effective dip coating method was used to deposit thin films of amorphous (AM) or anatase (AN) titanium dioxide (TiO2) on borosilicate glass substrates, either with or without prior doping of TiO2with nickel (Ni) cations by a specially designed sol gel technique. The objective of the study was to compare the physicochemical and biological properties of these films and assess their use in orthopedic implants or forin vitrocell biological studies. Analytical techniques such as XRD and XPS, in combination with ATR‐FTIR and SEM revealed that only AN films, prepared by controlled heating up to 450°C, irrespective of prior doping with Ni, contained significant crystalline structures of variable morphologies. This observation could be linked to the carbon and oxygen contents and the availability of functional groups in the films. Cell biological studies revealed that Ni doping of TiO2in both AM and AN films improved the adhesion, spreading, proliferation, differentiation, and migration of MC3T3 cells. Our studies provide a new approach to prepare optically transparent metal surfaces, with tunable physicochemical properties, which could be suitable for eliciting optimal osteoinductive cell responses and permit the detailedin vitrocell biological studies of osteoblasts. © 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2012.
Effects of alendronate and risedronate on bone material properties in actively forming trabecular bone surfaces
Authors: Hofstetter Birgit , Gamsjaeger Sonja , Phipps Roger J , Recker Robert R , Ebetino Frank H , Klaushofer Klaus , Paschalis Eleftherios P 
Published: February 2012

Abstract
We used Raman and Fourier transform infrared microspectroscopy (FTIRM) analysis to examine the intrinsic bone material properties at actively bone-forming trabecular surfaces in iliac crest biopsies from women with postmenopausal osteoporosis (PMO) who were treated with either alendronate (ALN) or risedronate (RIS). At eight study sites, women were identified who had postmenopausal osteoporosis (PMO), were at least 5 years postmenopause, and had been on long-term therapy (either 3–5 years or &gt;5 years) with daily or weekly ALN or RIS. Following standard tetracycline labeling, biopsies were collected from 102 women (33 treated with ALN for 3–5 years [ALN-3], 35 with ALN for &gt;5 years [ALN-5], 26 with RIS for 3–5 years [RIS-3], and 8 with RIS for &gt;5 years [RIS-5]) and were analyzed at anatomical areas of similar tissue age in bone-forming areas (within the fluorescent double labels). The following outcomes were monitored and reported: mineral to matrix ratio (corresponding to ash weight), relative proteoglycan content (regulating mineralization commencement), mineral maturity (indicative of the mineral crystallite chemistry and stoichiometry, and having a direct bearing on crystallite shape and size), and the ratio of two of the major enzymatic collagen cross-links (pyridinoline/divalent). In RIS-5 there was a significant decrease in the relative proteoglycan content (−5.83% compared to ALN-5), while in both RIS-3 and RIS-5 there was significantly lower mineral maturity/crystallinity (−6.78% and −13.68% versus ALN-3 and ALN-5, respectively), and pyridinoline/divalent collagen cross-link ratio (−23.09% and −41.85% versus ALN-3 and ALN-5, respectively). The results of the present study indicate that ALN and RIS exert differential effects on the intrinsic bone material properties at actively bone-forming trabecular surfaces. © 2012 American Society for Bone and Mineral Research.