bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attempt to manage after‐effects of beaver impounding activities in drainage systems: One trial assay
Authors: Lamsodis Romanas 
Published: May 2010

AbstractWhen there is a high population density of beavers, they readily occupy open drains. By impounding these drains, the animals also dam up the subsurface drainage systems that empty into them. This paper provides the results from a trial conducted in a beaver‐obstructed stretch of the open drain, Žiedupis, and its environs in the Nevėžis River basin in Lithuania. Studies were carried out on the functioning of pond drains installed in beaver dams, the behaviour of beavers in reacting to the lowered water levels, the condition of the tile drain pipes operating under damming, and the hydrological conditions of the soils drained by these drains. The trial was conducted in soils with a light texture. The weather conditions were generally rather drier than average. It was found that pond drains were able to maintain water in ponds at the desirable levels that benefit the functioning of subsurface drainage systems. However, they did not prevent beavers from building new dams, and did not encourage the animals to abandon the beaver site. Possible reasons for beaver expansion into open drains, as well as ways to avoid or mitigate the harm from their damming of drainage systems, are also discussed in the paper. Copyright © 2010 John Wiley & Sons, Ltd.
The Kennedy pathway—De novo synthesis of phosphatidylethanolamine and phosphatidylcholine
Authors: Gibellini Federica , Smith Terry K. 
Published: May 2010

AbstractThe glycerophospholipids phosphatidylcholine (PC) and phosphatidylethanolamine (PE) account for greater than 50% of the total phospholipid species in eukaryotic membranes and thus play major roles in the structure and function of those membranes. In most eukaryotic cells, PC and PE are synthesized by an aminoalcoholphosphotransferase reaction, which uses sn‐1,2‐diradylglycerol and either CDP‐choline or CDP‐ethanolamine, respectively. This is the last step in a biosynthetic pathway known as the Kennedy pathway, so named after Eugene Kennedy who elucidated it over 50years ago. This review will cover various aspects of the Kennedy pathway including: each of the biosynthetic steps, the functions androles of the phospholipid products PC and PE, and how the Kennedy pathway has the potential of being a chemotherapeutic target against cancer and various infectious diseases. © 2010 IUBMB IUBMB Life, 62(6): 414–428, 2010
Single point vs. mapping approach for spectral cytopathology (SCP)
Authors: Schubert Jennifer M. , Mazur Antonella I. , Bird Benjamin , Miljković Milosˇ , Diem Max 
Published: May 2010

AbstractIn this paper we describe the advantages of collecting infrared microspectral data in imaging mode opposed to point mode. Imaging data are processed using the PapMap algorithm, which co‐adds pixel spectra that have been scrutinized for R‐Mie scattering effects as well as other constraints. The signal‐to‐noise quality of PapMap spectra will be compared to point spectra for oral mucosa cells deposited onto low‐e slides. Also the effects of software atmospheric correction will be discussed. Combined with the PapMap algorithm, data collection in imaging mode proves to be a superior method for spectral cytopathology. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Bioconversion of soysterols to androstenedione by Mycobacterium fortuitum subsp. fortuitum NCIM 5239, a mutant derived from total sterol degrader strain
Authors: Gulla Vrushali , Banerjee Tushar , Patil Shridhar 
Published: May 2010

AbstractBACKGROUND: The bioconversion of soysterols to androstenedione (AD) by microbial cleavage of C‐17 side chain is of practical interest since AD serves as the starting compound for the production of the majority of pharmaceutically active steroids. A total soysterols degrader strain was subjected to combined mitomycin C and UV treatments and a mutant designated Mycobacterium fortuitum subsp. fortuitum NCIM 5239 was isolated that accumulated AD as major bioconversion product.RESULTS: The maximum bioconversion of soysterols to AD (71.3 mol %) was obtained at 30 °C, pH 5, 15% inoculum grown for 48 h, glycerol (12.68 g L−1) and urea (1.06 g L−1) as carbon and nitrogen sources, respectively, at C:N ratio of 10, the use of 10% polypropylene glycol‐400 (PPG‐400) as soysterols carrier solvent and 3 mg mL−1 concentration of soysterols after 240 h incubation period in shake flask culture. In a laboratory scale fermentor, a maximum of 64.8 mol % bioconversion of soysterols to AD was recorded after 99 h.CONCLUSION: The mutant Mycobacterium fortuitum subsp. fortuitum NCIM 5239 possesses high potential for industrial production of AD from soysterols. Copyright © 2010 Society of Chemical Industry
Effect of pH on the uptake of arsenate and vanadate by hydrotalcites in alkaline solutions: a Raman spectroscopic study
Authors: Palmer Sara J. , Frost Ray L. 
Published: May 2010

AbstractHydrotalcites have been synthesised using solutions of three different pH values to assess the effect of pH on the uptake of arsenate and vanadate. The ability of these hydrotalcites to remove vanadate and arsenate from solution has been determined by inductively coupled optical emission spectroscopy. Raman spectroscopy was used to monitor changes in the anionic species for hydrotalcites synthesised at different pH values. The results show a reduction in the concentration of arsenate and vanadate anions that are removed in extremely alkaline solutions. Hydrotalcites containing arsenate and vanadate are stable in solutions up to pH 10. Exposure of these hydrotalcites to higher pH values results in the removal of large percentages of arsenate and vanadate from the hydrotalcite interlayer. Copyright © 2010 John Wiley & Sons, Ltd.
Predictive factors of carcinoma in 279 patients with Hürthle cell neoplasm of the thyroid gland
Authors: Strazisar Branka , Petric Rok , Sesek Manja , Zgajnar Janez , Hocevar Marko , Besic Nikola 
Published: May 2010

AbstractBackground and ObjectivesEstimation of the risk of malignancy in a Hürthle cell (HC) neoplasm is important for optimum extent of thyroid surgical treatment. The aim of this retrospective study was to find predictive factors of carcinoma in patients with HC neoplasm.MethodsA total of 279 patients (241 females, 38 males; median age 55 years, range 15–86 years) with HC neoplasm in whom carcinoma was only suspected and who were surgically treated at our Institute in the period 1990–2007, were included in this study. Risk factors for malignancy were identified by the chi‐squared test and logistic regression.ResultsThe histopatological diagnoses were carcinoma, benign goiter and adenoma in 71 (25%), 68 (25%) and 140 (50%) patients, respectively. Predictive factors for carcinoma, shown by chi‐square test, were: age of patients, tumor diameter, thyroid volume and Tg concentration. The independent predictors of malignancy as shown by multivariate logistic regression were age of patients and pre‐operative Tg concentration. Carcinoma was more common in the patients older than 65 years of age and with Tg concentration over 1,000 ng/ml.ConclusionsThe independent predictors of malignancy in HC neoplasm were age of patients and pre‐operative Tg concentration. J. Surg. Oncol. 2010; 101:582–586. © 2010 Wiley‐Liss, Inc.
Gene expression profiling of formalin‐fixed, paraffin‐embedded familial breast tumours using the whole genome‐DASL assay
Authors: Waddell Nic , Cocciardi Sibylle , Johnson Julie , Healey Sue , Marsh Anna , Riley Joan , Silva Leonard da , Vargas Ana Cristina , Reid Lynne , Simpson Peter T , Lakhani Sunil R , Chenevix‐Trench Georgia 
Published: May 2010

AbstractTissue sample acquisition is a limiting step in many studies. There are many thousands of formalin‐fixed, paraffin‐embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumour banks. Once samples are fixed in formalin, the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study, we have evaluated the ability of the whole genome DASL (cDNA‐mediated Annealing, Selection, extension, and Ligation) assay from Illumina to perform transcriptomic analysis of archived breast tumour tissue in formalin‐fixed, paraffin‐embedded (FFPE) blocks. We profiled 76 familial breast tumours from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non‐BRCA1/2 families. We found that replicate samples correlated well with each other (r2 = 0.9–0.98). In 12/15 cases, the matched formalin‐fixed and frozen samples predicted the same tumour molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterization of many diseases. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Low‐dose ultraviolet radiation selectively degrades chromophore‐rich extracellular matrix components
Authors: Sherratt Michael J , Bayley Christopher P , Reilly Siobhan M , Gibbs Neil K , Griffiths Christopher EM , Watson Rachel EB 
Published: May 2010

AbstractPhotoageing of human skin due to chronic exposure to ultraviolet radiation (UVR) is characterized histologically by extensive remodelling of the dermal elastic fibre system. Whilst enzymatic pathways are thought to play a major role in mediating extracellular matrix (ECM) degeneration in UV‐exposed skin, the substrate specificity of UVR‐up‐regulated and activated matrix metalloproteinases (MMPs) is low. It is unclear, therefore, how such cell‐mediated mechanisms alone could be responsible for the reported selective degradation of elastic fibre components such as fibrillin‐1 and fibulin‐5 during the early stages of photoageing. Here we use atomic force microscopy (AFM) and scanning transmission electron microscopy (STEM) to demonstrate that physiologically attainable doses (20–100 mJ/cm2) of direct UV‐B radiation can induce profound, dose‐dependent, changes in the structure of, and mass distribution within, isolated fibrillin microfibrils. Furthermore, using reducing and native PAGE in combination with AFM, we show that, whilst exposure to low‐dose UV‐B radiation significantly alters the macromolecular and quaternary structures of both UV chromophore (Cys, His, Phe, Trp and Tyr)‐rich fibrillin microfibrils (fibrillin‐1, 21.0%) and fibronectin dimers (fibronectin, 12.9%), similar doses have no detectable effect on UV chromophore‐poor type I collagen monomers (2.2%). Analysis of the published primary amino acid sequences of 49 dermal ECM components demonstrates that most elastic fibre‐associated proteins, but crucially neither elastin nor members of the collagen family, are rich in UV chromophores. We suggest, therefore, that the amino acid composition of elastic fibre‐associated proteins [including the fibrillins, fibulins, latent TGFβ binding proteins (LTBPs) and the lysyl oxidase family of enzymes (LOK/LOXLs)] may predispose them to direct degradation by UVR. As a consequence, this selective acellular photochemical pathway may play an important role in initiating and/or exacerbating cell‐mediated ECM remodelling in UVR‐exposed skin. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Cystoscopy assisted transvesical biopsy of prostatic rhabdomyosarcoma
Authors: England Richard J. , Al‐Adnani Mudher , Cohen Marta C. , Godbole Prasad P. , Marven Sean S. 
Published: May 2010

AbstractThe treatment of prostatic rhabdomyosarcoma (RMS) depends on tumour stratification based on site and histology. An increasing range of cytogenetic, molecular, and immunohistochemistry studies are required. This is difficult to achieve using standard cystoscopic biopsies alone. We present a 5‐year‐old male, diagnosed with a prostatic RMS. He underwent cystoscopy to confirm the diagnosis and at the same time tissue was obtained for histology using laparoscopic graspers via a STEP™ Port inserted percutaneously into the apex of his bladder. Histology and cytogenetics confirmed an embryonal botryoid RMS for which he received chemotherapy followed by a radical prostatectomy for residual disease. Pediatr Blood Cancer. 2010;55:583–586. © 2010 Wiley‐Liss, Inc.
Investigation of the thermal, mechanical and morphological properties of poly(vinyl chloride)/polyhedral oligomeric silsesquioxane nanocomposites
Authors: Silva Rodrigo , Salles Cléia , Mauler Raquel , Oliveira Ricardo 
Published: May 2010

AbstractResearch into organic–inorganic nanocomposites has recently become popular, particularly the development of new polymer nanocomposites. Compared to pristine polymers or conventional composites, these nanocomposites exhibit improved properties. The storage modulus of a poly(vinyl chloride) (PVC)/polyhedral oligomeric silsesquioxane (POSS) nanocomposite slightly decreased with POSS content, but had a higher modulus from 50 to 100 °C. Some of the material appeared to be aggregated with 1 wt% POSS in the polymeric matrix. Conversely, with a POSS content of 5 wt%, a better dispersion of the nanoparticles was observed. The presence of POSS in the plasticised PVC compound had little influence on the final properties of the nanocomposites, showing weaker interactions between the POSS and the plasticised PVC compound. Copyright © 2010 Society of Chemical Industry
Long‐term effects of birth order and age at diagnosis in cystic fibrosis: A sibling cohort study
Authors: Slieker M.G. , van den Berg J.M.W. , Kouwenberg J. , van Berkhout F. Teding , Heijerman H.G.M. , van der Ent C.K. 
Published: May 2010

AbstractBackgroundSiblings with cystic fibrosis (CF) share many genetic and environmental factors but may present different phenotypes. Younger sibs are mostly earlier diagnosed with CF than their older sibs, but might be at risk for an earlier colonization with Pseudomonas aeruginosa (PA) than their older counterparts due to cross‐infection within families.AimsTo analyze the effects of birth order and age at diagnosis on lung function, PA colonization, nutritional status, and survival during the first two decades of life in siblings with CF.MethodsA retrospective cohort study of 52 sibling pairs was performed in two Dutch CF centers. Data were analyzed both cross‐sectionally and longitudinally using Kaplan–Meier curves and modified log‐rank tests.ResultsMedian age at diagnosis was significantly higher in the older sib compared with the younger sib (3.0 and 0.2 years, respectively, P < 0.0001). At the age of 5, 10, and 15 years no difference in lung function was found. However, at the age of 20 years, forced expiratory volume in 1 sec (FEV1) in older sibs was 19.4% (95% CI: 5.9–32.9%, P = 0.007) lower than in younger sibs. In the younger sibs group, FEV1 at age 20 years was significantly better in those who had a diagnosis before the age of 6 months (difference 22.9%, 95% CI: 0.1–45.8%, P < 0.05). In the first 10 years of life the younger sibs tended to be earlier colonized with PA than their older counterparts. No differences in nutritional status and survival were observed.ConclusionIn this sibling cohort study, an early diagnosis of CF was associated with better lung function after two decades of life. Although younger siblings tended to be colonized with PA at an earlier age, they showed better lung function outcomes. This underscores the importance of early diagnosis with newborn screening and early referral to a specialized center in the prevention of long‐term deleterious effects on lung function. Pediatr Pulmonol. 2010; 45:601–607. © 2010 Wiley‐Liss, Inc.
GaN nanorods and LED structures grown on patterned Si and AlN/Si substrates by selective area growth
Authors: Li Shunfeng , Fündling Sönke , Sökmen Ünsal , Neumann Richard , Merzsch Stephan , Hinze Peter , Weimann Thomas , Jahn Uwe , Trampert Achim , Riechert Henning , Peiner Erwin , Wehmann Hergo‐Heinrich , Waag Andreas 
Published: May 2010

AbstractGaN nanorods (NRs) show promising applications in high‐efficiency light emitting diodes, monolithic white light emission and optical interconnection due to their superior properties. In this work, we performed GaN nanostructures growth by pre‐patterning the Si and AlN/Si substrates. The pattern was transferred to Si and AlN/Si substrates by photolithography and inductively‐coupled plasma etching. GaN NRs were grown on these templates by metal‐organic vapour phase epitaxy (MOVPE). GaN grown on Si pillar templates show a truncated pyramidal structure. Transmission electron microscopy measurements demonstrated clearly that the threading dislocations bend to the side facets of the GaN nanostructures and terminate. GaN growth can also be observed on the sidewalls and bottom surface between the Si pillars. A simple phenomenological model is proposed to explain the GaN nanostructure growth on Si pillar templates. Based on this model, we developed another growth method, by which we grow GaN rod structures on pre‐patterned AlN/Si templates. By in‐situ nitridation and decreasing of the V/III ratio, we found that GaN rods only grew on the patterned AlN/Si dots with an aspect ratio of about 1.5 ‐ 2. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Affective personality type, post‐traumatic stress disorder symptom severity and post‐traumatic growth in victims of violence
Authors: Kunst Maarten Jacob J. 
Published: May 2010

AbstractThe current study explored the differential association between affective personality type, post‐traumatic stress disorder (PTSD) symptom severity, and post‐traumatic growth (PTG) in victims of violence (N = 113). Relying on previous research, median cut off‐scores on the Positive and Negative Affect Schedule Short Form were used to classify participants as high affective [i.e. high positive affectivity (PA) and high negative affectivity (NA)], self‐actualizing (i.e. high PA and low NA), self‐destructive (i.e. low PA and high NA) and low affective (i.e. low PA and low NA). Results indicated that the self‐destructive and high affective personality styles were strongly associated with increased PTSD symptoms severity. High affective personality type was found to be the only significant predictor of PTG. Results, study limitations and directions for future research were discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Mitochondrial Reactive Oxygen Species Mediate Cardiomyocyte Formation from Embryonic Stem Cells in High Glucose
Authors: Crespo Francisco Luna , Sobrado Veronica R. , Gomez Laura , Cervera Ana M. , McCreath Kenneth J. 
Published: May 2010

Abstract
Accumulating evidence points to reactive oxygen species (ROS) as important signaling molecules for cardiomyocyte differentiation in embryonic stem (ES) cells. Given that ES cells are normally maintained and differentiated in medium containing supraphysiological levels of glucose (25 mM), a condition which is known to result in enhanced cellular ROS formation, we questioned whether this high glucose concentration was necessary for cardiomyocyte lineage potential. We show here that ES cells cultured in physiological glucose (5 mM), maintained their general stemness qualities but displayed an altered mitochondrial metabolism, which resulted in decreased ROS production. Furthermore, ES and induced pluripotent stem (iPS) cells differentiated in lower glucose concentrations failed to generate cardiomyocyte structures; an effect mimicked with antioxidant treatments using catalase, N-acetyl cysteine and mitoubiquinone, under high glucose conditions in ES cells. Molecular analysis revealed that ES cells differentiated in 5 mM glucose had reduced expression of the pro-cardiac NOX4 gene and diminished phosphorylation of p38 mitogen-activated protein kinase (MAPK), together with specific changes in the cardiac transcriptional network. These outcomes could be reversed by supplementation of low glucose cultures with ascorbic acid, paradoxically acting as a pro-oxidant. Furthermore, forced expression of an upstream p38 MAPK kinase (MKK6) could bypass the requirement for ROS during differentiation to cardiomyocytes under low glucose conditions, illustrating a key role for p38 in the cardiac differentiation program. Together these data demonstrate that endogenous ROS control is important for cardiomyocyte formation from ES cells, and furthermore that supraphysiological glucose, by supplying ROS, is absolutely required.
Regulation of mRNA decapping
Authors: Li You , Kiledjian Megerditch 
Published: May 2010

AbstractDecapping is a critical step in the control of mRNA stability and the regulation of gene expression. Two major decapping enzymes involved in mRNA turnover have been identified, each functioning in one of the two exonucleolytic mRNA decay pathways in eukaryotic cells. The Dcp2 protein cleaves capped mRNA and initiates 5′ to 3′ degradation; the scavenger decapping enzyme, DcpS, hydrolyzes the cap structure generated by the 3′ to 5′ decay pathway. Consistent with the important role of decapping in gene expression, cap hydrolysis is exquisitely controlled by multiple regulators that influence association with the cap and the catalytic step. In this review, we will discuss the functions of the two different decapping enzymes, their regulation by cis‐elements and trans‐factors, and the potential role of the decapping enzymes in human neurological disorders. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms
RNA Turnover and Surveillance > Regulation of RNA Stability
No‐go decay: a quality control mechanism for RNA in translation
Authors: Harigaya Yuriko , Parker Roy 
Published: May 2010

AbstractEukaryotic cells have evolved multiple quality control mechanisms that recognize and eliminate defective mRNA during the process of translation. One mechanism, referred to as No‐go decay (NGD), targets mRNAs with elongation stalls for degradation initiated by endonucleolytic cleavage in the vicinity of the stalled ribosome. NGD is promoted by the evolutionarily conserved Dom34 and Hbs1 proteins, which are related to the translation termination factors eRF1 and eRF3, respectively. NGD is likely to occur by Dom34/Hbs1 interacting with the A site in the ribosome leading to release of the peptide or peptidyl‐tRNA. The process of NGD and/or the function of Dom34/Hbs1 appear to be important in several different biological contexts. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms
RNA Turnover and Surveillance > Regulation of RNA Stability
The role of KSRP in mRNA decay and microRNA precursor maturation
Authors: Gherzi Roberto , Chen Ching‐Yi , Trabucchi Michele , Ramos Andres , Briata Paola 
Published: May 2010

AbstractKH‐type splicing regulatory protein (KSRP)/FBP2, a single‐strand nucleic acid binding protein originally identified as both an RNA‐binding protein and a transcription factor, affects RNA fates at multiple levels. In this review we will discuss the ability of KSRP to (1) promote decay of labile mRNAs by interacting with some components of the mRNA decay machinery and (2) favor the maturation of a select group of microRNA precursors. We also discuss how its peculiar modular structure allows KSRP to specifically interact with a wide spectrum of RNA sequences and how post‐translational modifications influence KSRP functions in cell proliferation and differentiation. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

RNA Evolution and Genomics > Ribonomics
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
RNA Turnover and Surveillance > Regulation of RNA Stability