bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sixty years of change in the macrophyte vegetation of north‐west German running waters: a community‐ and landscape‐level analysis
Authors: Steffen Kristina , Leuschner Christoph 
Published: June 2015

AbstractLong‐term change in the macrophyte assemblages of 70 streams and rivers in four regions of north‐west Germany was examined with a semi‐permanent plot design based on 337 historical vegetation relevés from the 1950s that were repeated in 2010/2011. Plant assemblages were classified with two alternative phytosociological approaches based on character species and dominant species. Over the ∼60 years, the structure and composition of the vegetation changed profoundly in all four regions, even though local differences in vegetation dynamics existed. In general, stands assignable to the alliances Ranunculion (Batrachion) and Potamogetonion (assemblages dominated by submerged rooted plants) decreased greatly in frequency, while Nymphaeion stands (dominated by floating‐leaved rooted plants) increased. Communities weakly characterized by diagnostic species increased, revealing losses of specialist taxa and homogenization of the assemblages; macrophyte community diversity at the landscape level decreased. Eutrophication, hydraulic engineering and regular maintenance works in the water courses are discussed as likely causes of the vegetation change. We conclude that decade‐long human impact on river hydraulics and chemistry has significantly reduced community diversity at the landscape level, profoundly altering the relative abundance of the assemblages.The nomenclature follows Buttler & Thieme (2011) for vascular plants, Koperski et al. (2000) for bryophytes and Preising et al. (1990) or Chytrý (2011) for vegetation units. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A New subspecies of Cassiope fastigiata (Wall.) D. Don (Ericaceae) from Sikkim Himalaya
Authors: Maity Debabrata 
Published: June 2015

AbstractCassiope fastigiata (Wall.) D. Don subsp. sennikovii D. Maity, subsp. nov. (Ericaceae) is described from Sikkim Himalaya. It differs from the previously known typical Cassiope fastigiata (Wall.) D. Don subsp. fastigiata by its funnel‐shaped or narrowly campanulate corolla and larger corolla lobes, sepals, stamens and anther awns. This new taxon is described and illustrated. PCA (Principal Component Analysis) and UP‐GMA (unweighted pair‐group method with arithmetic averages) cluster analysis are used to test the identity of Cassiope taxa found in this region. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Evaluating the importance of characterizing soil structure and horizons in parameterizing a hydrologic process model
Authors: Mirus Benjamin B. 
Published: June 2015

AbstractIncorporating the influence of soil structure and horizons into parameterizations of distributed surface water/groundwater models remains a challenge. Often, only a single soil unit is employed, and soil‐hydraulic properties are assigned based on textural classification, without evaluating the potential impact of these simplifications. This study uses a distributed physics‐based model to assess the influence of soil horizons and structure on effective parameterization. This paper tests the viability of two established and widely used hydrogeologic methods for simulating runoff and variably saturated flow through layered soils: (1) accounting for vertical heterogeneity by combining hydrostratigraphic units with contrasting hydraulic properties into homogeneous, anisotropic units and (2) use of established pedotransfer functions based on soil texture alone to estimate water retention and conductivity, without accounting for the influence of pedon structures and hysteresis. The viability of this latter method for capturing the seasonal transition from runoff‐dominated to evapotranspiration‐dominated regimes is also tested here. For cases tested here, event‐based simulations using simplified vertical heterogeneity did not capture the state‐dependent anisotropy and complex combinations of runoff generation mechanisms resulting from permeability contrasts in layered hillslopes with complex topography. Continuous simulations using pedotransfer functions that do not account for the influence of soil structure and hysteresis generally over‐predicted runoff, leading to propagation of substantial water balance errors. Analysis suggests that identifying a dominant hydropedological unit provides the most acceptable simplification of subsurface layering and that modified pedotransfer functions with steeper soil‐water retention curves might adequately capture the influence of soil structure and hysteresis on hydrologic response in headwater catchments. Published 2015. This article is a U.S. Government work and is in the public domain in the USA
Simulating high‐resolution soil moisture patterns in the Shale Hills watershed using a land surface hydrologic model
Authors: Shi Yuning , Baldwin Douglas C. , Davis Kenneth J. , Yu Xuan , Duffy Christopher J. , Lin Henry 
Published: June 2015

AbstractSoil moisture is a critical variable in the water and energy cycles. The prediction of soil moisture patterns, especially at high spatial resolution, is challenging. This study tests the ability of a land surface hydrologic model (Flux‐PIHM) to simulate high‐resolution soil moisture patterns in the Shale Hills watershed (0.08 km2) in central Pennsylvania. Locally measured variables including a soil map, soil parameters, a tree map, and lidar topographic data, all have been synthesized into Flux‐PIHM to provide model inputs. The predicted 10‐cm soil moisture patterns for 15 individual days encompassing seven months in 2009 are compared with the observations from 61 soil moisture monitoring sites. Calibrated using only watershed‐scale and a few point‐based measurements, and driven by spatially uniform meteorological forcing, Flux‐PIHM is able to simulate the observed macro spatial pattern of soil moisture at ~10‐m resolution (spatial correlation coefficient ~ 0.6) and the day‐to‐day variation of this soil moisture pattern, although it underestimates the amplitude of the spatial variability and the mean soil moisture. Results show that the spatial distribution of soil hydraulic parameters has the dominant effect on the soil moisture spatial pattern. The surface topography and depth to bedrock also affect the soil moisture patterns in this watershed. Using the National Land Cover Database (NLCD) in place of a local tree survey map makes a negligible difference. Field measured soil type maps and soil type‐specific hydraulic parameters significantly improve the predicted soil moisture pattern as compared to the most detailed national soils database (Soil Survey Geographic Database, or SSURGO, 30‐m resolution). Copyright © 2015 John Wiley & Sons, Ltd.
Hitting Restart
Authors: Altura Gerard J. , Curwood Jen Scott 
Published: June 2015

AbstractResearch suggests that video games can foster deep engagement, critical thinking, and collaborative learning. To highlight how video games promote student achievement, we focus on a year 9 elective class in Australia. Our findings suggest that this games‐based class encouraged student learning and motivated students to develop advanced literacy skills, including critical analysis, creative writing, and programming.
Density Gradient Centrifugation for the Isolation of Cells of Multiple Lineages
Authors: Yamamoto Yumiko , Itoh Shousaku , Yamauchi Yukako , Matsushita Kenta , Ikeda Shun , Naruse Haruna , Hayashi Mikako 
Published: June 2015

ABSTRACTWe recently developed a simple strategy for the enrichment of mesenchymal stem cells (MSCs) with the capacity for osteoblast, chondrocyte, and adipocyte differentiation. On transplantation, the progenitor‐enriched fraction can regenerate bone with multiple lineages of donor origin. Although comprising multiple precursor cell types, the population is enriched >100‐fold in osteoprogenitors, hence the name “highly purified osteoprogenitors” (HipOPs). To establish a new modified method of purifying pure MSCs, it is useful to know the expression patterns of surface markers on heterogeneous MSCs and committed cells such as osteoblasts, adipocytes, and chondrocytes. However, calcium deposition by osteoblasts is a critical obstacle in visualizing the expression patterns of surface markers. We now report a new method of separating differentiated osteoblastic HipOPs (OB‐HipOPs) from calcium deposits using the Percoll density gradient centrifugation technique. After centrifuge separation, calcium deposits were observed at the bottom of the centrifuge tube, and living OB‐HipOPs were harvested from the 10–70% fractions. However, there were no living cells in the 70–80% fraction. We concluded that living OB‐HipOPs are separated by one 10–70% Percoll gradient. Furthermore, we analyzed the expression patterns of putative MSC markers on differentiated HipOPs. FACS analysis revealed that Sca‐1, CD44, CD73, CD105, and CD106 were decreased in OB‐HipOPs. In adipogenic‐ and chondrogenic‐HipOPs, Sca‐1, CD73, CD105, and CD106 were decreased. This new technique is a helpful tool to identify MSC surface markers and to clarify in more detail the differentiation stages of osteoblasts. J. Cell. Biochem. 116: 2709–2714, 2015. © 2015 Wiley Periodicals, Inc.
Large‐scale Modeling of Soil Erosion with RUSLE for Conservationist Planning of Degraded Cultivated Brazilian Pastures
Authors: Galdino Sergio , Sano Edson E. , Andrade Ricardo G. , Grego Celia R. , Nogueira Sandra F. , Bragantini Claudio , Flosi Ana H. G. 
Published: June 2015

AbstractPasture degradation is one of the major environmental and economic problems of Brazilian livestock production. Based on the estimates of soil loss in 140,297 km2 pasturelands of Goiás State and the Federal District, the effects of land use and management and conservation practices on soil erosion by water were evaluated. Soil loss was estimated with the empirical revised universal soil loss equation model under four scenarios of land use and management of pastures and the implementation of terraces. The effects of converting hilly areas into permanently preserved areas were also evaluated. Well‐managed pastures planted in terraces and highly sloped areas with native vegetation featured a reduction of 709% in the rate of soil erosion by water in comparison with poorly managed pastures without soil conservation practices. The environmental consequences of pasture degradation become particularly important when they are associated with land use in the Amazon and Cerrado biomes because farmers in these regions are forced to open new natural areas. In addition, the high indices of bare soil in degraded pastures contribute significantly to sediment deposition in rivers and dams. The modeling of soil loss is demonstrated to be an important tool for land use planning and supporting public policies focused on the sustainable use of natural resources. The results of these simulations demonstrate the importance of actions to recover degraded pastures, such as the Federal Government's program known as ABC (Low Carbon Agriculture). Copyright © 2015 John Wiley & Sons, Ltd.
Reconstruction of maxillary defect with musculo‐adipose rectus free flap
Authors: Low Tsu‐Hui (Hubert) , Lindsay Andrew , Clark Jonathan , Chai Francis , Lewis Richard 
Published: June 2015

BackgroundThe rectus myocutaneous free flap (RMFF) is used for medium to large maxillectomy defects. However, in patients with central obesity the inset could be difficult due to the bulk from excessive layer of adipose tissue. We describe a modification of the RMFF for patients with excessive central obesity with a flap consisting of adipose tissue with minimal rectus muscle; the musculo‐adipose rectus free flap (MARF).MethodsFive cases of MARF reconstruction were performed between 2003 and 2013, with patients’ body mass indexes ranging from 29.0 to 41.2 kg/m2. All patients had sinonasal tumor, of which three were adenoid cystic carcinoma, one squamous cell carcinoma, and one melanoma. Four patients had Codeiro IIIb defects and one had Codeiro II defect. Using the MARF technique, the maxillectomy defect was obliterated with vascularized adipose tissue overlying the rectus muscle and was trimmed to fit the maxillectomy defect. The adipose tissue was allowed to granulate and mucosalize.ResultsThe volume of adipose tissue harvested was between 120 and 160 mL. All flaps survived with no requirement for re‐exploration. Complete oro‐nasal separation was achieved in all patients. The time to commencement of oral intake ranges from 5 to 15 days. One patient developed seroma and one developed wound breakdown on the donor site. The length of stay at the hospital ranges from 9 to 22 days. On follow‐up ranging 7.5–32.8 months, two patients died from their malignancies. The other three patients were able to tolerate oral soft diet.ConclusionThe MARF may be considered as an alternative to myocutaneous rectus free flap particularly for the reconstruction of maxillary defects in patients with central obesity. © 2015 Wiley Periodicals, Inc. Microsurgery 37:137–141, 2017.
Calebin‐A inhibits adipogenesis and hepatic steatosis in high‐fat diet‐induced obesity via activation of AMPK signaling
Authors: Lai Ching‐Shu , Liao Sih‐Ning , Tsai Mei‐Ling , Kalyanam Nagabhushanam , Majeed Muhammed , Majeed Anju , Ho Chi‐Tang , Pan Min‐Hsiung 
Published: June 2015

ScopeDiet‐induced obesity and associated nonalcoholic fatty liver disease have increased and become a major health problem worldwide. This study was conducted to investigate the chemopreventive effects of dietary Calebin‐A, a curcuminoid, on differentiation of 3T3‐L1 adipocytes and high‐fat diet (HFD) induced obesity and hepatic steatosis. Potential mechanisms contributing to these effects were also elucidated.Methods and resultsCalebin‐A effectively and dose dependently suppressed accumulation of lipid droplets in adipocytes through the suppression of adipogenic specific factor peroxisome proliferator‐activated receptor (PPAR) γ and fatty acid synthase and activated acetyl‐CoA carboxylase. Dietary Calebin‐A effectively decreased weight gain and relative perigonadal, retroperitoneal, and mesenteric fat weight in HFD‐fed mice. Furthermore, Calebin‐A markedly reduced hepatic steatosis and the serum levels of glutamate oxaloacetate transaminase, glutamate pyruvate transaminase, total cholesterol, and triacylglycerol. These effects were associated with the downregulation of PPARγ, sterol regulatory element‐binding protein‐1, and particularly the activation of AMP‐activated protein kinase α signaling found in both adipocytes and liver tissues.ConclusionTaken together, these results demonstrated for the first time that Calebin‐A suppressed adipocyte differentiation, prevented HFD‐induced obesity, and improved hepatic steatosis, suggesting a novel application for the prevention and treatment of obesity and associated nonalcoholic fatty liver disease.
Analysis of autophagic flux in response to sulforaphane in metastatic prostate cancer cells
Authors: Watson Gregory W. , Wickramasekara Samanthi , Fang Yufeng , Palomera‐Sanchez Zoraya , Maier Claudia S. , Williams David E. , Dashwood Roderick H. , Perez Viviana I. , Ho Emily 
Published: June 2015

ScopeThe phytochemical sulforaphane (SF) has been shown to decrease prostate cancer metastases in a genetic mouse model of prostate carcinogenesis, though the mechanism of action is not fully known. SF has been reported to stimulate autophagy, and modulation of autophagy has been proposed to influence SF cytotoxicity; however, no conclusions about autophagy can be drawn without assessing autophagic flux, which has not been characterized in prostate cancer cells following SF treatment.Methods and resultsWe conducted an investigation to assess the impact of SF on autophagic flux in two metastatic prostate cancer cell lines at a concentration shown to decrease metastasis in vivo. Autophagic flux was assessed by multiple autophagy related proteins and substrates. We found that SF can stimulate autophagic flux and cell death only at high concentrations, above what has been observed in vivo.ConclusionThese results suggest that SF does not directly stimulate autophagy or cell death in metastatic prostate cancer cells under physiologically relevant conditions, but instead supports the involvement of in vivo factors as important effectors of SF‐mediated prostate cancer suppression.
Borderline personality features and associated difficulty in emotion perception: An examination of accuracy and bias
Authors: Meyer Justin K. , Morey Leslie C. 
Published: June 2015

ABSTRACTResearch on borderline personality disorder (BPD) has consistently found that those with the disorder often experience volatile interpersonal interactions, and several areas of research have been dedicated to the understanding of the mechanisms behind these interpersonal struggles. One of the most common theories is that the emotional dysregulation that is characteristic of BPD may adversely impact these interpersonal interactions, perhaps through a resulting misperception of emotional states in others. The purpose of the current study was to examine perception of negative affect in those with borderline personality features using a signal detection paradigm, a modified version of the Reading the Mind in the Eyes Task. Results support the hypothesis of atypical perception of negative emotions in BPD, but with disinhibitory aspects of the disorder demonstrating the largest potential influence. This finding was obtained even after controlling for gender differences that were also observed on this task. These results suggest that an examination of trait components of BPD may be necessary for a complete understanding of the emotion perception abilities of those with the disorder. Copyright © 2015 John Wiley & Sons, Ltd.
Effect of single point mutations in a form of systemic amyloidosis
Authors: Bhavaraju Manikanthan , Hansmann Ulrich H.E. 
Published: June 2015

AbstractAmyloid deposits of light‐chain proteins are associated with the most common form of systemic amyloidosis. We have studied the effects of single point mutations on amyloid formation of these proteins using explicit solvent model molecular dynamics simulations. For this purpose, we compare the stability of the wild‐type immunoglobulin light‐chain protein REI in its native and amyloid forms with that of four mutants: R61N, G68D, D82I, and A84T. We argue that the experimentally observed differences in the propensity for amyloid formation result from two effects. First, the mutant dimers have a lower stability than the wild‐type dimer due to increase exposure of certain hydrophobic residues. The second effect is a shift in equilibrium between monomers with amyloid‐like structure and such with native structures. Hence, when developing drugs against light‐chain associated systemic amyloidosis, one should look for components that either stabilize the dimer by binding to the dimer interface or reduce for the monomers the probability of the amyloid form.
Computational study of the W260A activating mutant of Src tyrosine kinase
Authors: Meng Yilin , Roux Benoît 
Published: June 2015

AbstractTyrosine kinases are enzymes playing a critical role in cellular signaling. Mutations causing increased in kinase activity are often associated with cancer and various pathologies. One example in Src tyrosine kinases is offered by the substitution of the highly conserved tryptophan 260 by an alanine (W260A), which has been shown to cause an increase in activity. Here, molecular dynamics simulations based on atomic models are carried out to characterize the conformational changes in the linker region and the catalytic (kinase) domain of Src kinase to elucidate the impact of the W260A mutation. Umbrella sampling calculations show that the conformation of the linker observed in the assembled down‐regulated state of the kinase is most favored when the kinase domain is in the inactive state, whereas the conformation of the linker observed in the re‐assembled up‐regulated state of the kinase is favored when the kinase domain is in the unphosphorylated active‐like state. The calculations further indicate that there are only small differences between the WT and W260A mutant. In both cases, the intermediates states are very similar and the down‐regulated inactive conformation is the most stable state. However, the calculations also show that the free energy cost to reach the unphosphorylated active‐like conformation is slightly smaller for the W260A mutant compared with WT. A simple kinetic model is developed and submitted to a Bayesian Monte Carlo analysis to illustrate how such small differences can contribute to accelerate the trans‐autophosphorylation reaction and yield a large increase in the activity of the mutant as observed experimentally.
Engineering trypsin for inhibitor resistance
Authors: Batt Anna R. , St. Germain Commodore P. , Gokey Trevor , Guliaev Anton B. , Baird Teaster 
Published: June 2015

AbstractThe development of effective protease therapeutics requires that the proteases be more resistant to naturally occurring inhibitors while maintaining catalytic activity. A key step in developing inhibitor resistance is the identification of key residues in protease‐inhibitor interaction. Given that majority of the protease therapeutics currently in use are trypsin‐fold, trypsin itself serves as an ideal model for studying protease‐inhibitor interaction. To test the importance of several trypsin‐inhibitor interactions on the prime‐side binding interface, we created four trypsin single variants Y39A, Y39F, K60A, and K60V and report biochemical sensitivity against bovine pancreatic trypsin inhibitor (BPTI) and M84R ecotin. All variants retained catalytic activity against small, commercially available peptide substrates [kcat/KM = (1.2 ± 0.3) × 107 M−1 s−1. Compared with wild‐type, the K60A and K60V variants showed increased sensitivity to BPTI but less sensitivity to ecotin. The Y39A variant was less sensitive to BPTI and ecotin while the Y39F variant was more sensitive to both. The relative binding free energies between BPTI complexes with WT, Y39F, and Y39A were calculated based on 3.5 µs combined explicit solvent molecular dynamics simulations. The BPTI:Y39F complex resulted in the lowest binding energy, while BPTI:Y39A resulted in the highest. Simulations of Y39F revealed increased conformational rearrangement of F39, which allowed formation of a new hydrogen bond between BPTI R17 and H40 of the variant. All together, these data suggest that positions 39 and 60 are key for inhibitor binding to trypsin, and likely more trypsin‐fold proteases.
Covalent docking using autodock: Two‐point attractor and flexible side chain methods
Authors: Bianco Giulia , Forli Stefano , Goodsell David S. , Olson Arthur J. 
Published: June 2015

AbstractWe describe two methods of automated covalent docking using Autodock4: the two‐point attractor method and the flexible side chain method. Both methods were applied to a training set of 20 diverse protein–ligand covalent complexes, evaluating their reliability in predicting the crystallographic pose of the ligands. The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested. Both methods are freely available at the AutoDock website (http://autodock.scripps.edu).