bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tidal channel meander formation by depositional rather than erosional processes: examples from the prograding Skagit River Delta (Washington, USA)
Authors: Hood W. Gregory 
Published: February 2010

AbstractChannel meander dynamics in fluvial systems and many tidal systems result from erosion of concave banks coupled with sediment deposition on convex bars. However, geographic information system (GIS) analysis of historical aerial photographs of the Skagit Delta marshes provides examples of an alternative meander forming process in a rapidly prograding river delta: deposition‐dominated tidal channel meander formation through a developmental sequence beginning with sandbar formation at the confluence of a blind tidal channel and delta distributary, proceeding to sandbar colonization and stabilization by marsh vegetation to form a marsh island opposite the blind tidal channel outlet, followed by narrowing of the gap between the island and mainland marsh, closure of one half of the gap to join the marsh island to the mainland, and formation of an approximately right‐angle blind tidal channel meander bend in the remaining half of the gap. Topographic signatures analogous to fluvial meander scroll bars accompany these planform changes. Parallel sequences of marsh ridges and swales indicate locations of historical distributary shoreline levees adjacent to filled former island/mainland gaps. Additionally, the location of marsh islands within delta distributaries is not random; islands are disproportionately associated with blind tidal channel/distributary confluences. Furthermore, blind tidal channel outlet width is positively correlated with the size of the marsh island that forms at the outlet, and the time until island fusion with mainland marsh. These observations suggest confluence hydrodynamics favor sandbar/marsh island development. The transition from confluence sandbar to tidal channel meander can take as little as 10 years, but more typically occurs over several decades. This depositional blind tidal channel meander formation process is part of a larger scale systemic depositional process of delta progradation that includes distributary elongation, gradient reduction, flow‐switching, shoaling, and narrowing. Copyright © 2010 John Wiley & Sons, Ltd.
A comparative study of high‐order variable‐property segregated algorithms for unsteady low Mach number flows
Authors: Knikker R. 
Published: February 2010

AbstractIn this paper, five different algorithms are presented for the simulation of low Mach flows with large temperature variations, based on second‐order central‐difference or fourth‐order compact spatial discretization and a pressure projection‐type method. A semi‐implicit three‐step Runge–Kutta/Crank–Nicolson or second‐order iterative scheme is used for time integration. The different algorithms solve the coupled set of governing scalar equations in a decoupled segregate manner. In the first algorithm, a temperature equation is solved and density is calculated from the equation of state, while the second algorithm advances the density using the differential form of the equation of state. The third algorithm solves the continuity equation and the fourth algorithm solves both the continuity and enthalpy equation in conservative form. An iterative decoupled algorithm is also proposed, which allows the computation of the fully coupled solution. All five algorithms solve the momentum equation in conservative form and use a constant‐ or variable‐coefficient Poisson equation for the pressure. The efficiency of the fourth‐order compact scheme and the performances of the decoupling algorithms are demonstrated in three flow problems with large temperature variations: non‐Boussinesq natural convection, channel flow instability, flame–vortex interaction. Copyright © 2010 John Wiley & Sons, Ltd.
Infrared spectroscopy indicates altered bone turnover and remodeling activity in renal osteodystrophy
Authors: Isaksson Hanna , Turunen Mikael J , Rieppo Lassi , Saarakkala Simo , Tamminen Inari S , Rieppo Jarno , Kröger Heikki , Jurvelin Jukka S 
Published: February 2010

Abstract
Renal osteodystrophy alters metabolic activity and remodeling rate of bone and also may lead to different bone composition. The objective of this study was to characterize the composition of bone in high-turnover renal osteodystrophy patients by means of Fourier transform infrared spectroscopic imaging (FTIRI). Iliac crest biopsies from healthy bone (n = 11) and patients with renal osteodystrophy (ROD, n = 11) were used in this study. The ROD samples were from patients with hyperparathyroid disease. By using FTIRI, phosphate-to-amide I ratio (mineral-to-matrix ratio), carbonate-to-phosphate ratio, and carbonate-to-amide I ratio (turnover rate/remodeling activity), as well as the collagen cross-link ratio (collagen maturity), were quantified. Histomorphometric analyses were conducted for comparison. The ROD samples showed significantly lower carbonate-to-phosphate (p &lt; .01) and carbonate-to-amide I (p &lt; .001) ratios. The spatial variation across the trabeculae highlighted a significantly lower degree of mineralization (p &lt; .05) at the edges of the trabeculae in the ROD samples than in normal bone. Statistically significant linear correlations were found between histomorphometric parameters related to bone-remodeling activity and number of bone cells and FTIRI-calculated parameters based on carbonate-to-phosphate and carbonate-to-amide I ratios. Hence the results suggested that FTIRI parameters related to carbonate may be indicative of turnover and remodeling rate of bone. © 2010 American Society for Bone and Mineral Research
Fracture risk prediction using BMD and clinical risk factors in early postmenopausal women: Sensitivity of the WHO FRAX tool
Authors: Trémollieres Florence A , Pouillès Jean-Michel , Drewniak Nicolas , Laparra Jacques , Ribot Claude A , Dargent-Molina Patricia 
Published: February 2010

Abstract
The aim of this prospective study was (1) to identify significant and independent clinical risk factors (CRFs) for major osteoporotic (OP) fracture among peri- and early postmenopausal women, (2) to assess, in this population, the discriminatory capacity of FRAX and bone mineral density (BMD) for the identification of women at high risk of fracture, and (3) to assess whether adding risk factors to either FRAX or BMD would improve discriminatory capacity. The study population included 2651 peri- and early postmenopausal women [mean age (± SD): 54 ± 4 years] with a mean follow-up period of 13.4 years (±1.4 years). At baseline, a large set of CRFs was recorded, and vertebral BMD was measured (Lunar, DPX) in all women. Femoral neck BMD also was measured in 1399 women in addition to spine BMD. Women with current or past OP treatment for more than 3 months at baseline (n = 454) were excluded from the analyses. Over the follow-up period, 415 women sustained a first low-energy fracture, including 145 major OP fractures (108 wrist, 44 spine, 20 proximal humerus, and 13 hip). In Cox multivariate regression models, only 3 CRFs were significant predictors of a major OP fracture independent of BMD and age: a personal history of fracture, three or more pregnancies, and current postmenopausal hormone therapy. In the subsample of women who had a hip BMD measurement and who were not receiving OP therapy (including hormone-replacement therapy) at baseline, mean FRAX value was 3.8% (±2.4%). The overall discriminative value for fracture, as measured by the area under the Receiver Operating Characteristic (ROC) curve (AUC), was equal to 0.63 [95% confidence interval (CI) 0.56–0.69] and 0.66 (95% CI 0.60–0.73), respectively, for FRAX and hip BMD. Sensitivity of both tools was low (ie, around 50% for 30% of the women classified as the highest risk). Adding parity to the predictive model including FRAX or using a simple risk score based on the best predictive model in our population did not significantly improve the discriminatory capacity over BMD alone. Only a limited number of clinical risk factors were found associated with the risk of major OP fracture in peri- and early postmenopausal women. In this population, the FRAX tool, like other risk scores combining CRFs to either BMD or FRAX, had a poor sensitivity for fracture prediction and did not significantly improve the discriminatory value of hip BMD alone. © 2010 American Society for Bone and Mineral Research
Occupational cadmium exposure and calcium excretion, bone density, and osteoporosis in men
Authors: Nawrot Tim , Geusens Piet , Nulens Tom S , Nemery Benoit 
Published: February 2010

Abstract
Exposure to cadmium has been associated with osteoporosis and fracture risk in women and the elderly, but studies in middle-aged men are lacking. In 83 male (ex)workers (mean age 45 years; range 24 to 64 years) in a radiator factory using cadmium-containing solder, we investigated the association between urinary cadmium excretion (as an index of lifetime body burden); bone mineral density (BMD) in the distal forearm, hip, and lumbar spine (by dual-energy X-ray absorptiometry); and urinary calcium excretion. Geometric mean urinary cadmium concentration was 1.02 µg/g of creatinine (5th to 95th percentile 0.17 to 5.51 µg/g). BMD was negatively correlated with urinary exposure to cadmium. The partial correlation coefficients (r) adjusted for age, body-mass index, and current smoking were −0.30 (p = .008) for BMD in the forearm, −0.27 (p = .017) in the hip, and −0.17 (p = .15) in the spine. Urinary calcium correlated positively (r = 0.23, p = .044) with the urinary cadmium excretion. Adjusted for the same covariates, the risk of osteoporosis (defined as a T-score below −2.5 in at least one measured bone site) increased dose dependently. Compared with the lowest tertile of urinary cadmium, the risks were 4.8- and 9.9-fold higher in the middle and highest tertiles, respectively. Only four (5%) men had evidence of renal tubular dysfunction (β2-microglobulin &gt; 300 µg/g of creatinine). Even in the absence of renal tubular dysfunction, occupational exposure to cadmium is associated in men with lower BMD values, a higher risk of having osteoporosis, and a higher urinary calcium excretion, suggesting a direct osteotoxic effect of cadmium. © 2010 American Society for Bone and Mineral Research
Correlates of trabecular and cortical volumetric bone mineral density of the radius and tibia in older men: The osteoporotic fractures in men study
Authors: Barbour Kamil E , Zmuda Joseph M , Strotmeyer Elsa S , Horwitz Mara J , Boudreau Robert , Evans Rhobert W , Ensrud Kristine E , Petit Moira A , Gordon Christopher L , Cauley Jane A ,   for the Osteoporotic Fractures in Men (MrOS) Research Group
Published: February 2010

Abstract
Quantitative computed tomography (QCT) can estimate volumetric bone mineral density (vBMD) and distinguish trabecular from cortical bone. Few comprehensive studies have examined correlates of vBMD in older men. This study evaluated the impact of demographic, anthropometric, lifestyle, and medical factors on vBMD in 1172 men aged 69 to 97 years and enrolled in the Osteoporotic Fractures in Men Study (MrOS). Peripheral quantitative computed tomography (pQCT) was used to measure vBMD of the radius and tibia. The multivariable linear regression models explained up to 10% of the variance in trabecular vBMD and up to 9% of the variance in cortical vBMD. Age was not correlated with radial trabecular vBMD. Correlates associated with both cortical and trabecular vBMD were age (−), caffeine intake (−), total calcium intake (+), nontrauma fracture (−), and hypertension (+). Higher body weight was related to greater trabecular vBMD and lower cortical vBMD. Height (−), education (+), diabetes with thiazolidinedione (TZD) use (+), rheumatoid arthritis (+), using arms to stand from a chair (−), and antiandrogen use (−) were associated only with trabecular vBMD. Factors associated only with cortical vBMD included clinic site (−), androgen use (+), grip strength (+), past smoker (−), and time to complete five chair stands (−). Certain correlates of trabecular and cortical vBMD differed among older men. An ascertainment of potential risk factors associated with trabecular and cortical vBMD may lead to better understanding and preventive efforts for osteoporosis in men. © 2010 American Society for Bone and Mineral Research
Mechanical stretching induces osteoprotegerin in differentiating C2C12 precursor cells through noncanonical Wnt Pathways
Authors: Yu Hsiao-Chi , Wu Tzu-Chin , Chen Mei-Ru , Liu Shan-Wen , Chen Jen-Hao , Lin Kurt Ming-Chao 
Published: February 2010

Abstract
Mechanical loading is known to be important for maintaining the formation and resorption rates of bone. To study the mechanisms by which mechanical loading regulates osteogenesis, we investigated the role of the Wnt pathway in C2C12 cells committed to osteogenic differentiation in response to cyclic mechanical stretching. Osteoprotegerin (OPG) acts as a decoy receptor for RANKL to inhibit osteoclastogenesis and resorption of bone. Our results demonstrate that stretching leads to a sustained increase in OPG expression in C2C12 cells. The expression of osteogenic marker genes, such as osteocalcin and alkaline phosphatase, was transiently decreased by stretching at 24 hours and returned to control levels at 48 hours. The addition of inhibitors of the canonical Wnt/β-catenin pathways, such as the secreted FZD-related peptide sRFP2, as well as siRNA-mediated knockdown, did not inhibit the effect of stretching on OPG expression. In contrast, treatment with inhibitors of noncanonical Wnt signaling, including KN93, and siRNA for Nemo-like kinase (NLK) blocked most of the mechanical inductive effect on OPG. Furthermore, stretching-induced OPG production in the culture medium was able to inhibit the osteoclast formation of bone marrow macrophages. These results suggest that mechanical stretching may play an important role in bone remodeling through the upregulation of OPG and that the mechanical signaling leading to OPG induction involves the noncanonical Wnt pathway. © 2010 American Society for Bone and Mineral Research
Initiation of telomere‐mediated chromosomal rearrangements in cancer
Authors: Mai Sabine 
Published: February 2010

AbstractTelomeres are the ends of chromosomes and protect them from degradation and fusion. As such, their stability is required for normal cellular function. Telomere dysfunction is found often at the origin of cellular transformation and contributes to the onset of genomic instability, a hallmark of cancer cells. In this article, I discuss current data and concepts on telomere‐mediated chromosomal rearrangements in cancer. J. Cell. Biochem. 109: 1095–1102, 2010. © 2010 Wiley‐Liss, Inc.
A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software
Authors: Schmid Nathan , Bötschi Mathias , Van Gunsteren Wilfred F. 
Published: February 2010

AbstractDuring the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent–solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed‐ups up to a factor of 54 (single‐precision GPU vs. double‐precision CPU) could be achieved. The accuracy of the single‐precision GPU implementation is carefully investigated and does not influence structural, thermodynamic, and dynamic quantities. Therefore, the implementation enables users of the GROMOS software for biomolecular simulation to run the solvent–solvent interaction evaluation on a GPU, and thus, to speed‐up their simulations by a factor 6–9. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
A massively multicore parallelization of the Kohn‐Sham energy gradients
Authors: Brown Philip , Woods Christopher J. , McIntosh‐Smith Simon , Manby Frederick R. 
Published: February 2010

AbstractIn a previous article [Brown et al., J Chem Theory Comput 2009, 4, 1620], we described a quadrature‐based formulation of the Kohn‐Sham Coulomb problem that allows for efficient parallelization over thousands of small processor cores. Here, we present the analytic gradients of this modified Kohn‐Sham scheme, and describe the parallel implementation of the gradients on a numerical accelerator architecture. We demonstrate an order‐of‐magnitude acceleration for the combined energy and gradient calculation over a conventional single‐core implementation. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Perceived barriers to psychological treatments and their relationship to depression
Authors: Mohr David C. , Ho Joyce , Duffecy Jenna , Baron Kelly G. , Lehman Kenneth A. , Jin Ling , Reifler Douglas 
Published: February 2010

AbstractIn spite of repeated calls for research and interventions to overcome individual and systemic barriers to psychological treatments, little is known about the nature of these barriers. To develop a measure of perceived barriers to psychological treatment (PBPT), items derived from 260 participants were administered to 658 primary care patients. Exploratory factor analysis on half the sample resulted in 8 factors, which were supported by confirmatory factor analysis conducted on the other half. Associations generally supported the criterion validity of PBPT scales, with self‐reported concurrent use of psychotherapy and psychotherapy attendance in the year after PBPT administration. Depression was associated with greater endorsement of barriers. These findings suggest that the PBPT may be useful in assessing perceived barriers. © 2010 Wiley Periodicals, Inc. J Clin Psychol 66: 1–16, 2010.
Cell signaling and cancer‐possible targets for therapy
Authors: Wenner Charles E. 
Published: February 2010

AbstractTumor progression involves the acquisition of properties which include growth‐factor independent cell proliferation, failure of inhibition by growth‐inhibitory signals, ability to invade surrounding tissues, and to evade apoptosis, etc. Characterization of the profile or molecular signature of the tumor may permit the development of rational therapies that target the aberrant pathways. Rapidly growing tumor cells are usually associated with a high rates of glycolysis and in these cells, it may be advantageous to exploit this pathway which most likely is required for optimal synthetic needs. Combinatorial therapeutic agents which target the growth factor signal transduction pathways as well as apoptotic signaling pathways provide an opportunity for maximal therapeutic benefit. J. Cell. Physiol. 223: 299–308, 2010. © 2010 Wiley‐Liss, Inc.
A comparison of positive and negative ion collision‐induced dissociation for model heptapeptides with one basic residue
Authors: Pu Dan , Clipston Nigel L. , Cassady Carolyn J. 
Published: February 2010

AbstractThe effects of the identity and position of basic residues on peptide dissociation were explored in the positive and negative modes. Low‐energy collision‐induced dissociation (CID) was performed on singly protonated and deprotonated heptapeptides of the type: XAAAAAA, AAAXAAA, AAAAAXA and AAAAAAX, where X is arginine (R), lysine (K) or histidine (H) residues and A is alanine. For [M + H]+, the CID spectra are dominated by cleavages adjacent to the basic residues and the majority of the product ions contain the basic residues. The order of a basic residue's influence on fragmentation of [M + H]+ is arginine > histidine ≈ lysine, which is also the order of decreasing gas‐phase basicity for these amino acids. These results are consistent with the side chains of basic residues being positive ion charge sites and with the more basic arginine residues having a higher retention (i.e. sequestering) of the positive charge. In contrast, for [M − H]− the identity and position of basic residues has almost no effect on backbone fragmentation. This is consistent with basic residues not being negative mode charge sites. For these peptides, more complete series of backbone fragments, which are important in the sequencing of unknowns, can be found in the negative mode. Spectra at both polarities contain C‐terminal y‐ions, but yn″+ has two more hydrogens than the corresponding yn−. Another major difference is the production of the N‐terminal backbone series bn+ in the positive mode and cn− in the negative mode. Thus, comparison of positive and negative ion spectra with an emphasis on searching for pairs of ions that differ by 2 Da (yn″+ vs yn−) and by 15 Da (bn+ vs cn−) may be a useful method for determining whether a product ion is generated from the C‐terminal or the N‐terminal end of a peptide. In addition, a characteristic elimination of NHCNH from arginine residues is observed for deprotonated peptides. Copyright © 2010 John Wiley & Sons, Ltd.
Structure and composition changes in the cell wall in relation to texture of shiitake mushrooms (Lentinula edodes) stored in modified atmosphere packaging
Authors: Jiang Tianjia , Wang Qiushuang , Xu Shasha , Jahangir Muhammad Muzammil , Ying Tiejin 
Published: February 2010

AbstractBACKGROUND: Firmness in shiitake mushroom (Lentinula edodes) is an important textural attribute affecting consumer attitudes toward freshness and quality. In this study, the effects of modified atmosphere packaging (MAP) treatments on structure and composition changes in cell walls in relation to the texture of mushrooms were investigated.RESULTS: Shiitake mushrooms were packaged in low density polyethylene bags with no holes (M0), two microholes (M1), four macroholes (M2), stored at 4 °C for 16 days with non‐wrapped mushrooms as control. Control mushrooms showed the highest firmness value due to significant increase of cellulose and chitin. All three MAP treatments reduced losses of protein and polysaccharides; the M2 treatment can best preserve the original texture while mushrooms in M0 became soft and deteriorated, possibly due to higher CO2 accumulation, lower cellulose and chitin content. Transmission electron microscopy performed on caps at harvest and after 16 days indicated that disintegration of plasmalemma had been alleviated by M2 treatment, leading to better preservation of the cell wall.CONCLUSION: Our results suggest that differences in firmness of shiitake mushrooms during storage may be due to differences in cellulose and chitin concentrations. M2 treatment may be a useful way of maintaining shiitake mushrooms texture during storage at 4 °C. Copyright © 2010 Society of Chemical Industry
Psychiatric diagnoses among Iraq and Afghanistan war veterans screened for deployment‐related traumatic brain injury
Authors: Carlson Kathleen F. , Nelson David , Orazem Robert J. , Nugent Sean , Cifu David X. , Sayer Nina A. 
Published: February 2010

AbstractThe authors examined psychiatric diagnoses in administrative records for 13,201 United States military veterans who were screened for traumatic brain injury (TBI) in Department of Veterans Affairs facilities. Over 80% of the veterans with positive TBI screens had psychiatric diagnoses. Compared to veterans with negative TBI screens, those with positive screens, but without confirmed TBI status, were three times more likely to have a posttraumatic stress disorder (PTSD) diagnosis and were two times more likely to have depression and substance‐related diagnoses. Among veterans with positive TBI screens, those with clinically confirmed TBI status were more likely than those without confirmed TBI status to have diagnoses for PTSD, anxiety, and adjustment disorders. These findings have implications for health care delivery and provider education.