bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of X‐ray tomography to quantify macropore characteristics of loess soil under two perennial plants
Authors: Li T. C. , Shao M. A. , Jia Y. H. 
Published: March 2016

SummaryWith the advent of large‐scale restoration of vegetation in the Loess Plateau, northwest China, there has been an increase in concern about the suitability of loess soil to support permanent vegetation cover. The quantification of soil macropore characteristics could be critical in determining the architecture and hydrological processes of loess soil on the plateau. In this research, we compared the effects of Purple alfalfa (Medicago sativa L.) and Korshinsk peashrub (Caragana korshinskii K.) on the macropore characteristics of a soil profile on the plateau with computed tomography (CT). To achieve this, undisturbed cores of soil were excavated from beneath purple alfalfa (ALF), 22‐year‐old Korshinsk peashrub (KOP22) and 40‐year‐old Korshinsk peashrub (KOP40) vegetation types in the Liudaogou watershed for evaluation. The soil macropore characteristics (including macroporosity, largest pore area, amounts of macropores, circularity, surface area density, branch density, junction density and connectivity) were determined with image analysis software. Soil under KOP22 and KOP40 treatments had approximately the same amounts of macropores (17 per 6359‐mm2 area), which was three times greater than those under ALF plants. Macroporosity ratios of soil under KOP22 and KOP40 plants to that under ALF plants were 2.3 and 3.6, respectively. Compared with KOP22, KOP40 had a larger macroporosity and the largest pore area at the 100–300‐mm soil depth. The KOP plants, in particular KOP40, apparently improved the macropore network structure of the soil more than ALF. However, the macropores under ALF were much rounder at the 100–300‐mm soil depth than those under the other two plants. There was no correlation between macropore characteristics and organic matter content of the soil at 100–400‐mm depth. Nevertheless, macroporosity was strongly correlated with the largest pore area. The findings of this research are critical for developing strategies for the restoration of vegetation in the Loess Plateau through improvement of the hydrological process of loess soil.Highlights
We examined macropore characteristics of loess soil on the Loess Plateau in China.
We determined the effects of different plants on soil macropore characteristics.
Soil under Korshinsk peashrub had better macropore structure than that under Purple alfalfa.
Long‐term recovery of KOP benefits the macropore structure most on the northern Loess Plateau.
Structure of smAKAP and its regulation by PKA‐mediated phosphorylation
Authors: Burgers Pepijn P. , Bruystens Jessica , Burnley Rebecca J. , Nikolaev Viacheslav O. , Keshwani Malik , Wu Jian , Janssen Bert J. C. , Taylor Susan S. , Heck Albert J. R. , Scholten Arjen 
Published: March 2016

The A‐kinase anchoring protein (AKAP) smAKAP has three extraordinary features; it is very small, it is anchored directly to membranes by acyl motifs, and it interacts almost exclusively with the type I regulatory subunits (RI) of cAMP‐dependent kinase (PKA). Here, we determined the crystal structure of smAKAP's A‐kinase binding domain (smAKAP‐AKB) in complex with the dimerization/docking (D/D) domain of RIα which reveals an extended hydrophobic interface with unique interaction pockets that drive smAKAP's high specificity for RI subunits. We also identify a conserved PKA phosphorylation site at Ser66 in the AKB domain which we predict would cause steric clashes and disrupt binding. This correlates with in vivo colocalization and fluorescence polarization studies, where Ser66 AKB phosphorylation ablates RI binding. Hydrogen/deuterium exchange studies confirm that the AKB helix is accessible and dynamic. Furthermore, full‐length smAKAP as well as the unbound AKB is predicted to contain a break at the phosphorylation site, and circular dichroism measurements confirm that the AKB domain loses its helicity following phosphorylation. As the active site of PKA's catalytic subunit does not accommodate α‐helices, we predict that the inherent flexibility of the AKB domain enables its phosphorylation by PKA. This represents a novel mechanism, whereby activation of anchored PKA can terminate its binding to smAKAP affecting the regulation of localized cAMP signaling events.DatabaseStructural data are available in the PDB under accession number 5HVZ.
Rapid finite element evaluation of the averaged strain energy density of mixed‐mode (I + II) crack tip fields including the T‐stress contribution
Authors: Campagnolo A. , Meneghetti G. , Berto F. 
Published: March 2016

AbstractThe strain energy density (SED) averaged over a material dependent control volume has been demonstrated to control fracture and fatigue behaviour of different materials in many engineering design situations. A method to rapidly calculate the averaged SED at the tip of long cracks under in‐plane mixed mode (I + II) loading has been recently proposed. It was based on the peak stresses evaluated from finite element (FE) analyses, according to the peak stress method (PSM). The aim of this work is to extend this FE approach to short cracks. In the present paper short cracks are distinguished from long cracks by considering that the stress fields within the control volume of short cracks are no longer governed solely by the stress intensity factors (SIFs), but the contribution of higher order terms, and primarily the T‐stress, becomes significant to estimate the averaged SED. Therefore the averaged SED is calculated using the linear elastic nodal stresses evaluated by FEM either at the crack tip, to account for the SIF contribution, and at selected FE nodes of the crack free edges, to include the T‐stress contribution. The proposed approach is referred to as nodal stress approach. The advantage of the nodal stress approach is two‐fold: there is no need of mesh refinements in the close neighbourhood of the points of singularity, so that coarse FE meshes can be adopted; moreover, geometrical modelling of the control volume in FE models is no longer necessary. Infinite plates weakened by central small cracks subjected to mixed mode I + II loading and a lap joint geometry have been analysed taking into consideration different crack lengths, mode mixities and average finite element sizes of the employed meshes. A comparison between approximate values of the averaged SED according to the nodal stress approach and those derived directly from the FE strain energy adopting very refined FE meshes has been successfully performed within a range of applicability.
Plastid genome sequencing reveals biogeographical structure and extensive population genetic variation in wild populations of Phalaris arundinacea L. in north‐western Europe
Authors: Perdereau Aude , Klaas Manfred , Barth Susanne , Hodkinson Trevor R. 
Published: March 2016

AbstractNew and comprehensive collections of the perennial rhizomatous reed canary grass (Phalaris arundinacea) were made in NW Europe along north‐to‐south and east‐to‐west clines from Denmark, Germany, Ireland, Poland, Sweden and the United Kingdom. Rhizome, seed and leaf samples were taken for analysis and genetic resource conservation. A subsample covering the geographical range was characterized using plastid genome sequencing and SNP discovery generated using a long‐read PCR and MiSeq sequencing approach. Samples were also subject to flow cytometry and all found to be tetraploid. New sequences were assembled against a Lolium perenne (perennial ryegrass) reference genome, and an average of approximately 60% of each genome was aligned (81 064 bp). Genetic variation was high among the 48 sequenced genotypes with a total of 1793 SNPs, equating to 23 SNPs per kbp. SNPs were subject to principal coordinate and Structure analyses to detect population genetic groupings and to examine phylogeographical pattern. Results indicate substantial genetic variation and population genetic structuring of this allogamous species at a broad geographical scale in NW Europe with plastid genetic diversity organized more across an east‐to‐west than a north‐to‐south cline.
On the Incentive Effects of Sample Size in Monitoring Agents – A Theoretical and Experimental Analysis
Authors: Avrahami Judith , Kareev Yaakov , Uske Tobias , Gueth Werner 
Published: March 2016

AbstractWhen agents compete for a bonus and their productivity in each of several possible occasions depends stochastically on (constant) effort, the number of times this is checked to assign the bonus affects the level of uncertainty in the selection process. Uncertainty, in turn, is expected to increase the effort made by competing agents (Cowen and Glazer, 1996; Dubey and Haimanko, 2003; Dubey and Wu, 2001). Theoretical predictions are derived and experimental evidence is collected for two competing agents, with the bonus awarded to that agent who outperforms the other. Sampling occasions (1 or 3), cost of production (high or low), cost symmetry (asymmetric or symmetric), and piece-rate reward are manipulated factorially to test the robustness of the effects of uncertainty. For control, a single-agent case is included. Results indicate that, for tournaments, greater uncertainty does indeed lead to greater than expected effort and lower average variable costs.
Scripting MODFLOW Model Development Using Python and FloPy
Authors: Bakker M. , Post V. , Langevin C. D. , Hughes J. D. , White J. T. , Starn J. J. , Fienen M. N. 
Published: March 2016

AbstractGraphical user interfaces (GUIs) are commonly used to construct and postprocess numerical groundwater flow and transport models. Scripting model development with the programming language Python is presented here as an alternative approach. One advantage of Python is that there are many packages available to facilitate the model development process, including packages for plotting, array manipulation, optimization, and data analysis. For MODFLOW‐based models, the FloPy package was developed by the authors to construct model input files, run the model, and read and plot simulation results. Use of Python with the available scientific packages and FloPy facilitates data exploration, alternative model evaluations, and model analyses that can be difficult to perform with GUIs. Furthermore, Python scripts are a complete, transparent, and repeatable record of the modeling process. The approach is introduced with a simple FloPy example to create and postprocess a MODFLOW model. A more complicated capture‐fraction analysis with a real‐world model is presented to demonstrate the types of analyses that can be performed using Python and FloPy.
Gleason grade 4 prostate adenocarcinoma patterns: an interobserver agreement study among genitourinary pathologists
Authors: Kweldam Charlotte F , Nieboer Daan , Algaba Ferran , Amin Mahul B , Berney Dan M , Billis Athanase , Bostwick David G , Bubendorf Lukas , Cheng Liang , Compérat Eva , Delahunt Brett , Egevad Lars , Evans Andrew J , Hansel Donna E , Humphrey Peter A , Kristiansen Glen , van der Kwast Theodorus H , Magi‐Galluzzi Cristina , Montironi Rodolfo , Netto George J , Samaratunga Hemamali , Srigley John R , Tan Puay H , Varma Murali , Zhou Ming , van Leenders Geert J L H 
Published: March 2016

AimsTo assess the interobserver reproducibility of individual Gleason grade 4 growth patterns.Methods and resultsTwenty‐three genitourinary pathologists participated in the evaluation of 60 selected high‐magnification photographs. The selection included 10 cases of Gleason grade 3, 40 of Gleason grade 4 (10 per growth pattern), and 10 of Gleason grade 5. Participants were asked to select a single predominant Gleason grade per case (3, 4, or 5), and to indicate the predominant Gleason grade 4 growth pattern, if present. ‘Consensus’ was defined as at least 80% agreement, and ‘favoured’ as 60–80% agreement. Consensus on Gleason grading was reached in 47 of 60 (78%) cases, 35 of which were assigned to grade 4. In the 13 non‐consensus cases, ill‐formed (6/13, 46%) and fused (7/13, 54%) patterns were involved in the disagreement. Among the 20 cases where at least one pathologist assigned the ill‐formed growth pattern, none (0%, 0/20) reached consensus. Consensus for fused, cribriform and glomeruloid glands was reached in 2%, 23% and 38% of cases, respectively. In nine of 35 (26%) consensus Gleason grade 4 cases, participants disagreed on the growth pattern. Six of these were characterized by large epithelial proliferations with delicate intervening fibrovascular cores, which were alternatively given the designation fused or cribriform growth pattern (‘complex fused’).ConclusionsConsensus on Gleason grade 4 growth pattern was predominantly reached on cribriform and glomeruloid patterns, but rarely on ill‐formed and fused glands. The complex fused glands seem to constitute a borderline pattern of unknown prognostic significance on which a consensus could not be reached.
Primary intra‐articular sarcoma: a clinicopathological study of 15 cases
Authors: Chebib Ivan , Rosenberg Andrew E , Fletcher Christopher D M , Rosenthal Daniel I , Hornicek Francis J , Nielsen G Petur 
Published: March 2016

AimsTo assess the clinical and histopathological spectrum of primary intra‐articular sarcomas.Methods and resultsFifteen patients were identified as having primary intra‐articular sarcomas and the clinical and pathological features were evaluated. There were nine males and six females who ranged in age from 16 to 84 (mean 44) years. All tumours originated in the knee joint. The pathological diagnoses included: five synovial sarcoma, three extraskeletal myxoid chondrosarcomas, two high‐grade myxofibrosarcoma (one conventional, one epithelioid), two undifferentiated pleomorphic sarcoma (one with giant cells) and one each myxoinflammatory fibroblastic sarcoma, conventional hyaline chondrosarcoma, and high‐grade myofibroblastic sarcoma. All tumours were treated by segmental resection or amputation. Adjuvant therapy was given in selected cases. Follow‐up ranged from 11 to 150 months. Of patients with follow‐up, two died of disease; one developed pulmonary metastases after 6 years and was then lost to follow‐up. Nine patients were alive and free of disease 12–150 months after diagnosis.ConclusionsPrimary sarcomas of the joints are very rare and most frequently affect the knee. Our experience indicates that synovial sarcoma and extraskeletal myxoid chondrosarcoma are the most common intra‐articular sarcomas.
Changes in liver steatosis evaluated by transient elastography with the controlled attenuation parameter in HIV‐infected patients
Authors: Macías J , Real LM , Rivero‐Juárez A , Merchante N , Camacho A , Neukam K , Rivero A , Mancebo M , Pineda JA 
Published: March 2016

ObjectivesThere are scant data on the progression of hepatic steatosis (HS) in HIV infection. We therefore evaluated changes in HS over time in HIV‐infected patients using the controlled attenuation parameter (CAP).MethodsA prospective cohort of 326 HIV‐infected patients was included in this study. All patients underwent a CAP measurement. Changes in steatosis were evaluated by calculating the median (Q1–Q3) difference between baseline and 12‐month CAP values.ResultsThe median (Q1–Q3) CAP was 221 (196–252) dB/m at baseline and 224 (198–257) dB/m at the 12‐month visit (P = 0.617). Significant steatosis, that is, CAP ≥ 238 dB/m, was observed in 76 individuals (37%) at baseline and in 80 (39%) at the 12‐month visit (P = 0.683). The following variables were associated with ΔCAP: plasma HIV RNA [< 50 vs. ≥ 50 HIV‐1 RNA copies/mL: median (Q1–Q3) ΔCAP, 4 (−21, 27) vs. −21 (−49, 4) dB/m, respectively; P = 0.024]; body mass index (BMI) [no increase vs. increase: −13 (−40, 4) vs. 14 (−6, 32) dB/m, respectively; P < 0.001]; triglycerides [no increase vs. increase: −1 (−30, 22) vs. 15 (−3, 40) dB/m, respectively; P = 0.001]; fasting plasma glucose [not impaired vs. impaired: −4 (−31, 16) vs. 30 (15, 49) dB/m, respectively; P < 0.001]; and raltegravir [no vs. yes: 5 (−20, 29) vs. −11 (−37.5, 15) dB/m, respectively; P = 0.018]. The only factor independently associated with ΔCAP was BMI [B (standard error): 9.03 (1.9); P < 0.001].ConclusionsIncreases in CAP values over a period of 12 months in HIV‐infected patients were strongly associated with elevations in BMI. Other metabolic factors and antiretroviral drugs were not predictors of CAP changes independent of BMI.
High‐level expression of periostin is significantly correlated with tumour angiogenesis and poor prognosis in osteosarcoma
Authors: Hu Fei , Shang Xi‐Fu , Wang Wei , Jiang Wei , Fang Ce , Tan Dong , Zhou Hang‐Cheng 
Published: March 2016

SummaryPeriostin (PN), originally named as osteoblast‐specific factor‐2 (OSF‐2), has been involved in regulating adhesion and differentiation of osteoblasts. Recently many studies have shown that high‐level expression of PN is correlated significantly with tumour angiogenesis and prognosis in many kinds of human cancer. However, whether and how periostin expression influences prognosis in osteosarcoma remains unknown. This study aimed to examine the expression of PN in patients with osteosarcoma and explore the relationship of PN expression with clinicopathologic factors, tumour angiogenesis and prognosis. Immunohistochemistry was performed to determine the expression of PN in osteosarcoma and osteochondroma respectively. Vascular endothelial growth factor (VEGF) and CD34 were also examined in tissues from the osteosarcoma patients mentioned above. The results showed that PN expression was significantly (P < 0.05) higher in osteosarcoma (80.9%) than in osteochondroma (14.7%). Increased PN protein expression was associated with histological subtype (P = 0.000), Enneking stage (P = 0.027) and tumour size (P = 0.009). The result also showed that high expression of PN correlated with VEGF expression (r = 0.285; P = 0.019) and that tumours with PN‐positive expression significantly had higher microvessal density (44.6 ± 13.7 vs. 20.6 ± 6.5; P = 0.000) compared to those in normal bone tissues. Additionally, the expression of PN was found to be an independent prognostic factor in osteosarcoma patients. In conclusion, our findings suggest that PN may have an important role in tumour progression and may be used as a prognostic biomarker for patients with osteosarcoma.
Effects of reaction parameters on generation of volatile compounds from the Maillard reaction between L‐ascorbic acid and glycine
Authors: Li Ya , Yang Yan , Yu Ai‐Nong 
Published: March 2016

SummaryThe formation of volatiles from the reaction between L‐ascorbic acid (ASA) and glycine (Gly) at different reaction parameters, such as temperature, time and pH, were reported and 20 different volatile compounds were identified using solid‐phase microextraction–gas chromatography–mass spectrometry (SPME‐GC‐MS). The results showed that the reaction parameters had the different effects on formation of volatiles, while the effect of pH was the most remarkable. When the initial solution pH was 4.5, the major volatiles were found to be furfural or derivatives of furan; while when pH ranged from 6.8 to 9.5, the major volatiles were found to be derivatives of pyrazines, including 2,5‐dimethyl‐pyrazine, 2‐ethyl‐5‐methyl‐pyrazine, trimethyl‐pyrazine, 3‐ethyl‐2,5‐dimethyl‐pyrazine and 2,3‐diethyl‐5‐methyl‐pyrazine. The quantity of 2,5‐dimethyl‐pyrazine and 2‐ethyl‐5‐methyl‐pyrazine reached the maximum when pH was 8.0. Finally, a possible reaction mechanism of ASA and Gly and the pathway for the formation of the various kinds of volatile products were proposed.
The effects of self‐management intervention among middle‐age adults with knee osteoarthritis
Authors: Kao Mei‐Hua , Tsai Yun‐Fang , Chang Ting‐Kuo , Wang Jong‐Shyan , Chen Chie‐Pein , Chang Yue‐Cune 
Published: March 2016

AbstractAimThe aim of this study was to explore the effects of a self‐management intervention for middle‐aged adults with knee osteoarthritis.BackgroundKnee osteoarthritis is a common cause of lower limb disability in middle‐aged and older adults. Use of self‐management interventions that apply the self‐regulation theory have not been reported for patients with knee osteoarthritis.DesignA quasi‐experimental design was applied.MethodsKnee osteoarthritis patients were recruited from two medical centres in northern Taiwan by convenience sampling between July 2013–May 2014. We developed a self‐management intervention programme for knee osteoarthritis; participants began an individualized programme 4 weeks after recruitment. Effectiveness of the intervention was evaluated using the Knee Injury and Osteoarthritis Outcome Score, Health Care Questionnaire and the Short‐Form Health Survey. A generalized estimating equation compared assessment scores for 105 participants after the intervention (10 and 18 weeks) with scores at 4 weeks.ResultsKnee symptoms and physical function scores significantly improved and quality‐of‐life scores significantly increased while body mass index, unplanned medical consultations and doses of pain medication significantly decreased at 10 and 18 weeks compared with 4 weeks. After adjusting for the effect of time‐ and significant‐related factors, knee symptoms and physical function, body mass index and quality of life significantly improved at 10 and 18 weeks compared with 4 weeks.ConclusionsThe self‐management intervention based on self‐regulation theory, improved participants’ symptoms and functions of knee osteoarthritis, overall health and quality of life. Offering self‐management interventions in clinical practice can be beneficial for patients with knee osteoarthritis.
A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna
Authors: Krehenwinkel Henrik , Graze Maxene , Rödder Dennis , Tanaka Kazuhiro , Baba Yuki G. , Muster Christoph , Uhl Gabriele 
Published: March 2016

AbstractAimThe phylogeographical history of wide‐ranging Palaearctic species is not well understood. Here, we present a range‐wide phylogeographical study of the wasp spider, Argiope bruennichi (Scopoli, 1772), a highly dispersive and widely distributed Palaearctic species. We aim to identify glacial refugia and patterns of interglacial gene flow across the Palaearctic.LocationPalaearctic region, including the Azores, Madeira, Europe, North Africa and Asia.MethodsWe conduct a range‐wide phylogeographical survey. Our study is based on nuclear and mitochondrial DNA markers, as well as morphological characters. We use species distribution models to predict the species’ current range as well as its historical distribution during and shortly after the Last Glacial Maximum (LGM).ResultsAll analysed genetic markers and morphological characters support the divergence of a lineage in eastern Asia from the remainder of the Palaearctic. Within the Western Palaearctic, a less pronounced divergence into an Azorean and a European clade is found. Species distribution models predict a pronounced loss of suitable habitat for Western Palaearctic lineages during the LGM, whereas the range of East Asian populations remained largely unaffected.Main conclusionsOur results highlight the existence of non‐European glacial refugia for Palaearctic species, particularly in East Asia. The current genetic structure is best explained by the recent recolonization of the Western Palaearctic from eastern Asia, or repeated interglacial contact of populations.