bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging
Authors: Holzhauser Carolin , Berndl Sina , Menacher Florian , Breunig Miriam , Göpferich Achim , Wagenknecht Hans‐Achim 
Published: January 2010

AbstractThe chromophore of thiazole orange (TO) and its derivative TO3 were incorporated synthetically as base surrogates into oligonucleotides using automated phosphoramidite chemistry. In comparison to TO, the TO3 chromophore contains an extended carbomethine bridge that shifts the absorption and emission significantly to the red. (S)‐1‐Aminopropane‐2,3‐diol served as an acyclic linker between the phosphodiesters. This linker was attached either to the quinoline or the thiazole nitrogen of the TO and TO3 dyes. The optical properties of TO and TO3 were studied in different DNA base environments and with different opposite bases. Both dyes asfluorescent DNA base substitutions show a brightness that is sufficient for bioanalytic and imaging applications. Additionally the TO3 dyes were combined as interstrand dimers, but in contrast to TO dimers, a red‐shifted fluorescence was not observed. However, TO and TO3 can be combined to an interstrand chromophore pair and a DNA hybridization‐dependent energy transfer process can be obtained between the modifications. As a result, the emission is shifted from the TO‐typical value of 530 nm to 670 nm. This concept can be applied for fluorescence imaging to monitor DNA delivery as well as processing inside living cells by confocal microscopy. In contrast to the non‐covalently binding TO dyes, the TO‐ and TO3‐modified oligonucleotides are cell‐permeable.
Interaction study of a lysozyme‐binding aptamer with mono‐ and divalent cations by ACE
Authors: Girardot Marie , Gareil Pierre , Varenne Anne 
Published: January 2010

AbstractBinding between an aptamer and its target is highly dependent on the conformation of the aptamer molecule, this latter seeming to be affected by a variety of cations. As only a few studies have reported on the interactions of monovalent or divalent cations with aptamers, we describe herein the use of ACE in its mobility shift format for investigating interactions between various monovalent (Na+, K+, Cs+) or divalent (Mg2+, Ca2+, Ba2+) cations and a 30‐mer lysozyme‐binding aptamer. This study was performed in BGEs of different natures (phosphate and MOPS buffers) and ionic strengths. First, the effective charges of the aptamer in 30 mM ionic strength phosphate and MOPS (pH 7.0) were estimated to be 7.4 and 3.6, respectively. Then, corrections for ionic strength and counterion condensation effects were performed for all studies. The effective mobility shift was attributed not only to these effects, but also to a possible interaction with the buffer components (binary or ternary complexes) as well as possible conformational changes of the aptamer. Finally, apparent binding constants were calculated for divalent cations with mathematical linearization methods, and the influence of the nature of the BGE was evidenced.
A comparison of average rates of alluvial erosion between the south‐western and south‐eastern United States
Authors: Jaeger Kristin L. , Wohl Ellen , Simon Andrew 
Published: January 2010

AbstractAlluvial channel bed incision and bank widening have been reported in both the south‐western and south‐eastern US throughout the past century. Distinct regional differences in climate and landscape properties likely influence the rate of erosion. This study discusses regional differences in hydraulic driving forces and substrate resistance and tests the hypothesis that regional differences exist in average rates of channel incision, bank erosion, and knickpoint retreat. Specifically, we hypothesize that erosion rates are higher in south‐western US streams and reason that this is because of greater flood magnitudes and limited substrate resistance. A review of the literature documenting incision, bank erosion, and knickpoint retreat, however, indicates that intra‐regional differences are larger than inter‐regional differences and that average rates in the south‐western US are either statistically similar or less than the rates in parts of the south‐eastern US. This could either be a result of strong intra‐regional hydroclimatic and substrate variability or because average erosion rate may not be an appropriate metric for inter‐regional comparisons because of the variability between case studies associated with the field methods to measure erosion, duration of study period, and time since disturbance to the channel. Nevertheless, these findings provide a basis for future evaluations of the relative importance of different controls on driving and resisting forces in these and other landscapes characterized by rapid channel incision and arroyo formation. Copyright © 2010 John Wiley & Sons, Ltd.
The influence of DEM resolution on simulated solar radiation‐induced glacier melt
Authors: Hopkinson Chris , Chasmer Laura , Munro Scott , Demuth Michael N. 
Published: January 2010

AbstractThe influence of digital elevation model (DEM) resolution to modelled glacier melt during peak melt production was evaluated by performing a clear sky GIS radiation simulation over the Peyto Glacier in the Canadian Rockies. DEMs were generated at eight resolutions ranging from 1 m to 1000 m grid spacing from airborne lidar data. When applied to the planar area (PA) of the terrain, it was found that total melt increased with DEM resolution (r2 = 0·63) by 4% over 3 orders of magnitude. This systematic scaling‐effect was mitigated at the basin scale, however, when the DEM slope variant area (SVA) was used to account for the increased divergence from PA as resolution increases. However, even after the inclusion of SVA in glacier surface melt simulations, localized melt variations with scale were still evident in the ablation and accumulation zone observations. In the ablation zone, there was a systematic increase in simulated melt (∼4%) as resolution decreased from 1 m to 1000 m (r2 = 0·89), with the opposite effect in the accumulation zone (r2 = 0·81). DEM resolution also affected the diurnal melt cycle, such that for the entire glacier there was a tendency for a morning over‐estimation and afternoon underestimation of melt rate with decreasing resolution. For the accumulation zone, there was an increased melt rate at low resolutions occurring in the afternoon, while in the ablation zone there was a tendency for increasing melt rates with decreasing resolution throughout the day. These localized spatio‐temporal variations in simulated melt are largely due to the lowering of ridges and raising of valley floors that occur as resolution decreases. This scale dependence in the representation of terrain morphology directly controls the pattern and relative proportion of direct beam shadowing over actively melting surfaces and thereby has a systematic influence on the grid cell‐level hydrological balance. It is recommended that GIS‐based glacier melt modelling routines take into account the slope area of grid cells, while noting that the choice of DEM scale can have a discernible and systematic influence on modelled runoff magnitude. It is important to note that while higher grid resolutions mitigate the effect of terrain smoothing on spatio‐temporal melt patterns, lower resolutions actually mitigate the systematic error associated with assuming all surface areas are planar. Copyright © 2010 John Wiley & Sons, Ltd and Her Majesty the Queen in right of Canada.
Are transit times useful process‐based tools for flow prediction and classification in ungauged basins in montane regions?
Authors: Soulsby C. , Tetzlaff D. , Hrachowitz M. 
Published: January 2010

AbstractTransit times are being increasingly explored as process‐based tools for conceptualizing hydrological function at a range of scales. Despite this, little effort has been made to relate transit times to conventional hydrometric flow statistics. Rather, the identification of the appropriate transit time distribution (TTD) for a hydrological system and the derivation of metrics such as the mean transit time (MTT) have required quantitative assessment of input–output relationships for conservative tracers using lumped parameter models. This has allowed the main landscape controls to be identified and has facilitated the prediction of MTTs in ungauged basins in particular geomorphic provinces, though relationships with streamflow measures have been unexamined. We used estimated MTTs (with uncertainty) for 16 experimental catchments (0·5–690 km2in area) with contrasting geologic, topographic, pedologic and climatic characteristics in Scotland. The MTT was highly variable ranging from 60 days toca> 1500 days, reflecting differences in catchment soil cover, geomorphic properties and precipitation. The MTT was closely correlated with key hydrometric design statistics such as the mean annual flood (MAF) and percentiles of high (Q5) and low (Q95) flows. Analysis of MTT estimates, in conjunction with geographic information system (GIS)‐based assessment of landscape controls, showed that MTT could be predicted to within 30% for ungauged basins from catchment soil cover and drainage density. Furthermore, hydrometric design statistics for ungauged basins could also be forecast from MTT predictions with median relative errors of 14, 11 and 28% for the MAF, Q5and Q95respectively. We suggest that MTTs—predicted from mapped landscape characteristics—can be useful diagnostic metrics for ungauged montane basins, as well as a useful similarity index for process‐based catchment classification. This is important as montane headwaters are often critical, but data‐poor environments influencing the quantity, quality and ecology of downstream flows. Copyright © 2010 John Wiley & Sons, Ltd.
Osteocalcin gene polymorphisms influence concentration of serum osteocalcin and enhance fracture identification
Authors: McGuigan Fiona , Kumar Jitender , Ivaska Kaisa K , Obrant Karl J , Gerdhem Paul , Åkesson Kristina 
Published: January 2010

Abstract
Osteoporosis is a major health problem affecting more than 75 million people throughout Europe, the United States, and Japan. Epidemiologic studies have determined that both genetic and environmental factors contribute to the pathogenesis of osteoporosis. We have investigated the association between polymorphisms at the osteocalcin locus and variables linked to bone health. Osteocalcin provides a link between bone and energy metabolism, hence its potential importance as an osteoporosis candidate gene. In this study, we included a total of 996 women (all aged 75 years) from the Osteoporosis Prospective Risk Assessment (OPRA) cohort. We sequenced the osteocalcin gene along with flanking regions to search for novel coding polymorphisms. We also analyzed four polymorphisms selected from within and flanking regions of the osteocalcin gene to study their association with serum total osteocalcin levels (S-TotalOC), total-body (TB) bone mineral density (BMD), fracture, TB fat mass, and body mass index (BMI). The promoter polymorphism rs1800247 was significantly associated with S-TotalOC (p = .012) after controlling for BMI and TB BMD. The polymorphism rs1543297 was significantly associated with prospectively occurring fractures (p = .008). In a model taking into account rs1543297 and rs1800247, along with TB BMD, BMI, smoking, and S-TotalOC, the polymorphisms together were able to identify an additional 6% of women who sustained a fracture (p = .02). We found no association between the polymorphisms and TB BMD, BMI, or TB fat mass. In conclusion, polymorphisms in and around the osteocalcin locus are significantly associated with S-TotalOC and fracture. Genotyping at the osteocalcin locus could add valuable information in the identification of women at risk of osteoporosis. © 2010 American Society for Bone and Mineral Research
Similarities and discrepancies in subchondral bone structure in two differently induced canine models of osteoarthritis
Authors: Intema Femke , Sniekers Yvonne H , Weinans Harrie , Vianen Marieke E , Yocum Sue A , Zuurmond Anne-Marie M , DeGroot Jeroen , Lafeber Floris P , Mastbergen Simon C 
Published: January 2010

Abstract
In osteoarthritis (OA), cartilage degradation is accompanied by subchondral bone changes. The pathogenesis and physiology of bone changes in OA are still unclear. The changes in subchondral bone architecture and cartilage damage were compared in differently induced experimental models of OA. Experimental OA was induced bilaterally by anterior cruciate ligament transection (ACLT) or by cartilage trauma (Groove model); bilateral sham surgery served as control. Lysylpyridinoline (LP, bone resorption) and C-telopeptide of type II collagen (CTX-II, cartilage breakdown) were measured over time. At 20 weeks after surgery, the subchondral cortical plate and trabecular bone of the tibia were analyzed by micro–computed tomography (µCT) and cartilage degeneration was analyzed histologically and biochemically. In both models, cartilage degeneration and cortical subchondral plate thinning were present. CTX-II levels were elevated over time in both models. Subchondral trabecular bone changes were observed only in the ACLT model, not in the Groove model. Correspondingly, LP levels were elevated over time in the ACLT model and not in the Groove model. Interestingly, the trabecular bone changes in the ACLT model were extended to the metaphyseal area. The early decrease in plate thickness, present in both models, as was cartilage damage, suggests that plate thinning is a phenomenon that is intrinsic to the process of OA independent of the cause/induction of OA. On the other hand, trabecular changes in subchondral and metaphyseal bone are not part of a common pathway of OA development and may be induced biomechanically in the destabilized and less loaded ACLT joint. © 2010 American Society for Bone and Mineral Research
Local low-dose lovastatin delivery improves the bone-healing defect caused by Nf1 loss of function in osteoblasts
Authors: Wang Weixi , Nyman Jeffry S , Moss Heather E , Gutierrez Gloria , Mundy Gregory R , Yang Xiangli , Elefteriou Florent 
Published: January 2010

Abstract
Postfracture tibial nonunion (pseudoarthrosis) leads to lifelong disability in patients with neurofibromatosis type I (NF1), a disorder caused by mutations in the NF1 gene. To determine the contribution of NF1 in bone healing, we assessed bone healing in the Nf1 ob−/− conditional mouse model lacking Nf1 specifically in osteoblasts. A closed distal tibia fracture protocol and a longitudinal study design were used. During the 21- to 28-day postfracture period, callus volume, as expected, decreased in wild-type but not in Nf1 ob−/− mice, suggesting delayed healing. At these two time points, bone volume (BV/TV) and volumetric bone mineral density (vBMD) measured by 3D micro–computed tomography were decreased in Nf1 ob−/− callus-bridging cortices and trabecular compartments compared with wild-type controls. Histomorphometric analyses revealed the presence of cartilaginous remnants, a high amount of osteoid, and increased osteoclast surfaces in Nf1 ob−/− calluses 21 days after fracture, which was accompanied by increased expression of osteopontin, Rankl, and Tgfβ. Callus strength measured by three-point bending 28 days after fracture was reduced in Nf1 ob−/− versus wild-type calluses. Importantly, from a clinical point of view, this defect of callus maturation and strength could be ameliorated by local delivery of low-dose lovastatin microparticles, which successfully decreased osteoid volume and cartilaginous remnant number and increased callus BV/TV and strength in mutant mice. These results thus indicate that the dysfunctions caused by loss of Nf1 in osteoblasts impair callus maturation and weaken callus mechanical properties and suggest that local delivery of low-dose lovastatin may improve bone healing in NF1 patients. © 2010 American Society for Bone and Mineral Research
Patients with high-bone-mass phenotype owing to Lrp5-T253I mutation have low plasma levels of serotonin
Authors: Frost Morten , Andersen Tom Erenskjold , Yadav Vijay , Brixen Kim , Karsenty Gerard , Kassem Moustapha 
Published: January 2010

Abstract
The Lrp5 gene is a major determinant of bone mass accrual. It has been demonstrated recently to achieve this function by hampering the synthesis of gut-derived serotonin, which is a powerful inhibitor of bone formation. In this study we analyzed plasma serotonin levels in patients with a high-bone-mass (HBM) phenotype owing to gain-of-function mutation of Lrp5 (T253I). A total of 9 HBM patients were compared with 18 sex- and age-matched controls. In HBM patients, the serotonin concentrations in platelet-poor plasma were significantly lower than in the controls (mean ± SEM: 2.16 ± 0.28 ng/mL versus 3.51 ± 0.49 ng/mL, respectively, p &lt; .05). Our data support the hypothesis that circulating serotonin levels mediate the increased bone mass resulting from gain-of-function mutations in Lrp5 in humans. © 2010 American Society for Bone and Mineral Research.
The role of mast cells in parathyroid bone disease
Authors: Turner Russell T , Iwaniec Urszula T , Marley Kevin , Sibonga Jean D 
Published: January 2010

AbstractChronic hyperparathyroidism (HPT) is a common cause of metabolic bone disease. These studies investigated the underlying cellular and molecular mechanisms responsible for the detrimental actions of elevated parathyroid hormone (PTH) on the skeleton. Bone biopsies from hyperparathyroid patients revealed an association between parathyroid bone disease and increased numbers of bone marrow mast cells. We therefore evaluated the role of mast cells in the etiology of parathyroid bone disease in a rat model for chronic HPT. In rats, mature mast cells were preferentially located at sites undergoing bone turnover, and the number of mast cells at the bone–bone marrow interface was greatly increased following treatment with PTH. Time-course studies and studies employing parathyroid hormone–related peptide (PTHrP), as well as inhibitors of platelet-derived growth factor-A (PDGF-A, trapidil), kit (gleevec), and PI3K (wortmannin) signaling revealed that mature mast cell redistribution from bone marrow to bone surfaces precedes and is associated with osteitis fibrosa, a hallmark of parathyroid bone disease. Importantly, mature mast cells were not observed in the bone marrow of mice. Mice, in turn, were resistant to the development of PTH-induced bone marrow fibrosis. These findings suggest that the mast cell may be a novel target for treatment of metabolic bone disease. © 2010 American Society for Bone and Mineral Research
Composition of the air emission from a tobacco factory and development of the biocatalyst for odour control
Authors: Zagustina Natalya A , Krikunova Natalya I , Kulikova Albina K , Misharina Tamara A , Romanov Maxim E , Ruzhitsky Aleksander O , Terenina Margarita B , Veprizky Andrey A , Zhukov Vitaly G , Popov Vladimir O 
Published: January 2010

AbstractBACKGROUND: Tobacco processing facilities produce voluminous air emissions containing a large number of smelly and potentially harmful volatile compounds that require implementation of the efficient odour control techniques. Biofiltration is the proved method for deodorisation of complex multi‐component emissions. The purpose of the present study was to identify substances present in the emission of a typical tobacco industrial facility and demonstrate efficiency of the biotrickling filter for odour control.RESULTS:Composition of volatile compounds of leaf tobacco was investigated by capillary GC–MS. More than 80 individual compounds were identified. For evaluating the odour of individual components a GC‐sniffing analysis was employed. Laboratory‐scale trickling biofilters were used to develop a method for deodorisation of a simulated tobacco emission. Biofilters were operated for 12 months and demonstrated the absence of the ‘tobacco smell’ at the filter outlet and a stable rate of conversion of nicotine exceeding 90%.CONCLUSION:Composition of volatile substances of the leaf tobacco was investigated and compounds responsible for ‘tobacco smell’ were identified. A trickling biofiltration technique was shown to be an efficient method for control of tobacco odours. The results of the study have been scaled up to the pilot level to control emissions of an operating tobacco factory. Copyright © 2010 Society of Chemical Industry
Gum Arabic coated magnetic nanoparticles with affinity ligands specific for antibodies
Authors: Batalha Iris L. , Hussain Abid , Roque A. C. A. 
Published: January 2010

AbstractA novel magnetic support based on gum Arabic (GA) coated iron oxide magnetic nanoparticles (MNP) has been endowed with affinity properties towards immunoglobulin G (IgG) molecules. The success of the in situ triazine ligand synthesis was confirmed by fluorescence assays. Two synthetic ligands previously developed for binding to IgG, named as ligand 22/8 (artificial Protein A) and ligand 8/7 (artificial Protein L) were immobilized on to MNPs coated with GA (MNP_GA). The dimension of the particles core was not affected by the surface functionalization with GA and triazine ligands. The hydrodynamic diameters of the magnetic supports indicate that the coupling of GA leads to the formation of larger agglomerates of particles with about 1 µm, but the introduction of the triazine ligands leads to a decrease on MNPs size. The non‐functionalized MNP_GA bound 28 mg IgG/g, two times less than bare MNP (60 mg IgG/g). MNP_GA modified with ligand 22/8 bound 133 mg IgG/g support, twice higher than the value obtained for ligand 8/7 magnetic adsorbents (65 mg/g). Supports modified with ligand 22/8 were selected to study the adsorption and the elution of IgG. The adsorption of human IgG on this support followed a Langmuir behavior with a Qmáx of 344 mg IgG/g support and Ka of 1.5 × 105 M. The studies on different elution conditions indicated that although the 0.05 M citrate buffer (pH 3) presented good recovery yields (elution 64% of bound protein), there was occurrence of iron leaching at this acidic pH. Therefore, a potential alternative would be to elute bound protein with a 0.05 M glycine‐NaOH (pH 11) buffer. Copyright © 2010 John Wiley & Sons, Ltd.
Quantitative MR in multi‐center clinical trials
Authors: Ashton Edward 
Published: January 2010

AbstractMRI has a wide variety of applications in the clinical trials process. MR has shown particular utility in the early phases of clinical development, when trial sponsors are interested in demonstrating proof of concept and must make decisions about allocation of resources to a particular compound based on the results from a small number of experimental subjects. This utility is largely due to the many different imaging endpoints that can be measured using MR, ranging from structural (tumor burden, hippocampal volume) to functional (blood flow, vascular permeability) to molecular (hepatic fat fraction, glycosaminoglycan content). The unique flexibility of these systems has proven to be both a blessing and a curse to those attempting to deploy MR in multi‐center clinical trials, however, as differences among scanner manufacturers and models in pulse sequence implementation, hardware capabilities, and even terminology make it increasingly difficult to ensure that results obtained at one center are comparable to those at another. These problems are compounded by the differences between the procedures used in clinical trials and those used in routine clinical practice, which make trial‐specific training for site technologists and radiologists a necessity in many cases. This article will briefly review the benefits of including quantitative MR imaging in clinical trials, then explore in detail the challenges presented by the need to develop and deploy a detailed MR protocol that is both effective and implementable across many different MR systems and software versions. J. Magn. Reson. Imaging 2010; 31: 279–288. © 2010 Wiley‐Liss, Inc.