bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase composition and tribomechanical properties of Ti–B–C nanocomposite coatings prepared by magnetron sputtering
Authors: Sánchez-López J C , Abad M D , Justo A , Gago R , Endrino J L , García-Luis A , Brizuela M 
Published: August 2012

Abstract
Protective nanocomposite coatings based on hard ceramic phases (TiC, TiB2) combined with amorphous carbon (a-C) are of interest because of their adequate balance between mechanical and tribological performances. In this work, Ti–B–C nanocomposite coatings were prepared by co-sputtering of graphite and TiB2 targets. Varying the discharge power ratio applied to the graphite and TiB2 targets from 0 to 2, the a-C content in the coatings could be tuned from 0 to 60%, as observed by means of Raman and x-ray photoelectron spectroscopy (XPS). The microstructural characterization demonstrated a progressive decrease in crystallinity from an initial nanocrystalline (nc) TiB2-like structure to a distorted TiB
x
C
y
ternary compound with increasing C concentration. X-ray absorption near-edge structure measurements on the B K-edge helped to determine a hexagonal arrangement around the B atoms in the ternary TiB
x
C
y
phase. A fitting analysis of the C 1s XPS peak allowed us to evaluate the relative amount of a-C and TiB
x
C
y
components. A drastic change in hardness (from 52 to 13 GPa) and friction coefficient values (from 0.8 to 0.2) is noticed when moving from nc-TiB2 to TiBC/a-C nanocomposites. The fraction of a-C necessary to decrease the friction below 0.2 was found to be 45%. Raman observation of the wear tracks determined the presence of disordered sp2-bonded carbon phase associated with the diminution of the friction level.
Alfvén eigenmode structure during off-axis neutral beam injection
Authors: Tobias B. , Bass E.M. , Classen I.G.J. , Domier C.W. , Grierson B.A. , Heidbrink W.W. , Luhmann N.C. , Nazikian R. , Park H.K. , Spong D.A. , Zeeland M.A. Van 
Published: August 2012

Abstract
The spatial structure of Alfvén eigenmodes on the DIII-D tokamak is compared for contrasting fast ion deposition profiles resulting from on- and off-axis neutral beam injection (NBI). In both cases, poloidal mode rotation and eigenmode twist, or radial phase variation, are correlated with the direction of the normal ion diamagnetic flow and readily inverted with a reversal of toroidal magnetic field, B
T. While off-axis NBI results in weakly driven reversed shear induced Alfvén eigenmodes due to reduced fast ion pressure gradient, ∇β
fast, in the region of the mode, these marginally unstable modes exhibit a 2D phase structure that is indistinguishable from that observed during on-axis injection. This result is consistent with recent explorations using the non-perturbative codes Gyro and TAEFL that show a weak dependence of eigenmode structure on drive when fast ion density is uniformly reduced by a scalar multiplier. These codes also obtain unstable, counter-propagating modes with the inverted 2D phase structure when B
T is kept constant and the diamagnetic flow direction is reversed by making ∇β
fast sufficiently positive for an isotropic population of fast ions. While measurements of the spatial profile of fast ion D-α light from the recently upgraded charge exchange recombination diagnostic on DIII-D suggest a strong modification of fast ion pressure towards this limit, no counter-propagating modes have yet been observed in experiment.
The unified effect of counter-toroidal rotation and power across separatrix on type-I ELMs in JT-60U
Authors: Urano H. , Oyama N. , Kamiya K. , Aiba N. , Kamada Y. , Fujita T. 
Published: August 2012

Abstract
By conducting power scan experiments using perpendicular neutral beams (NBs) after the injection of tangential NBs in directions co-, balanced and counter to the plasma current, the unified effect of counter-toroidal rotation and heating power on type-I edge-localized modes (ELMs) was investigated in a JT-60U tokamak. ELM frequency f
ELM increased monotonically together with the power across the separatrix P
sep for all the cases of tangential NBs. However, dependence of f
ELM on P
sep was explicitly stronger than a simple proportionality when perpendicular NBs were injected. The toroidal rotation velocity at the H-mode pedestal

shifted continuously in the counter-direction when perpendicular NBs were applied. At fixed values of

, f
ELM increased clearly in proportion to P
sep. In addition, this proportionality between f
ELM and P
sep holds regardless of the mixture of datasets of the toroidal momentum inputs. The proportional coefficient decreased as

shifted in the co-direction.
Occurrence Of Viruses Infecting Watermelon, Other Cucurbits, and Weeds in the Parts of Southern United States
Authors: Ali Akhtar , Abdalla Osama , Bruton Benny , Fish Wayne , Sikora Edward , Zhang Shouan , Taylor Merritt 
Published: August 2012

Field surveys were conducted to determine the distribution and frequency of viruses infecting watermelon and other cucurbits in the southern US in 2010 and 2011. Leaf samples were collected from 715 symptomatic plants from 10 states and were tested by dot-immunobinding assays or reverse transcriptionpolymerase chain reaction for 17 viruses that included Alfalfa mosaic virus (AMV), Bean pod mottle virus (BPMV), Cucurbit aphid born yellows virus (CABYV), Cucurbit yellow stunting disorder virus (CYSDV), Cucumber green mottle mosaic virus (CGMMV), Cucumber mosaic virus (CMV), Melon necrotic spot virus (MNSV), Papaya ringspot virus-W (PRSV-W), Squash leaf curl virus (SLCuV), Soybean mosaic virus (SMV), Squash mosaic virus (SqMV), Squash vein yellowing virus (SqVYV), Tobacco ringspot virus (TRSV), Watermelon mosaic virus (WMV), Watermelon silver mottle virus (WSMoV), Zucchini yellow mosaic virus (ZYMV), and Zucchini green mottle mosaic virus (ZGMMV). Thirteen out of 17 viruses were detected in this study. The distribution of detected viruses varied with the highest average frequency for WMV (30.6%), followed by PRSV-W (24.7%), ZYMV (13.9%), TRSV (5.7%), SqMV (3.5%), and MNSV (2.6%). The percent frequency of the remaining viruses was less than 2%. Seven viruses (AMV, BPMV, CMV, SqMV, TRSV, PRSV-W, and ZYMV) were also detected either from nearby agricultural crops or weeds species. Mixed infections were also recorded for some viruses with potyviruses being the most common. There is limited information on frequency and distribution of viruses that occur on watermelon and other cucurbits. These results indicate that potyviruses, particularly PRSV-W, WMV, and ZYMV, are frequently present in infected watermelon and other cucurbits in the southern US. Accepted for publication 30 July 2012. Published 24 August 2012.
Arabidopsis ECERIFERUM2 Is a Component of the Fatty Acid Elongation Machinery Required for Fatty Acid Extension to Exceptional Lengths
Authors: Haslam Tegan M. , Mañas-Fernández Aurora , Zhao Lifang , Kunst Ljerka 
Published: August 2012

Abstract
Primary aerial surfaces of land plants are coated by a lipidic cuticle, which forms a barrier against transpirational water loss and protects the plant from diverse stresses. Four enzymes of a fatty acid elongase complex are required for the synthesis of very-long-chain fatty acid (VLCFA) precursors of cuticular waxes. Fatty acid elongase substrate specificity is determined by a condensing enzyme that catalyzes the first reaction carried out by the complex. In Arabidopsis (Arabidopsis thaliana), characterized condensing enzymes involved in wax synthesis can only elongate VLCFAs up to 28 carbons (C28) in length, despite the predominance of C29 to C31 monomers in Arabidopsis stem wax. This suggests additional proteins are required for elongation beyond C28. The wax-deficient mutant eceriferum2 (cer2) lacks waxes longer than C28, implying that CER2, a putative BAHD acyltransferase, is required for C28 elongation. Here, we characterize the cer2 mutant and demonstrate that green fluorescent protein-tagged CER2 localizes to the endoplasmic reticulum, the site of VLCFA biosynthesis. We use site-directed mutagenesis to show that the classification of CER2 as a BAHD acyltransferase based on sequence homology does not fit with CER2 catalytic activity. Finally, we provide evidence for the function of CER2 in C28 elongation by an assay in yeast (Saccharomyces cerevisiae).
Carbon Deprivation-Driven Transcriptome Reprogramming in Detached Developmentally Arresting Arabidopsis Inflorescences
Authors: Trivellini Alice , Jibran Rubina , Watson Lyn M. , O’Donoghue Erin M. , Ferrante Antonio , Sullivan Kerry L. , Dijkwel Paul P. , Hunter Donald A. 
Published: August 2012

AbstractSenescence is genetically controlled and activated in mature tissues during aging. However, immature plant tissues also display senescence-like symptoms when continuously exposed to adverse energy-depleting conditions. We used detached dark-held immature inflorescences of Arabidopsis (Arabidopsis thaliana) to understand the metabolic reprogramming occurring in immature tissues transitioning from rapid growth to precocious senescence. Macroscopic growth of the detached inflorescences rapidly ceased upon placement in water in the dark at 21°C. Inflorescences were completely degreened by 120 h of dark incubation and by 24 h had already lost 24% of their chlorophyll and 34% of their protein content. Comparative transcriptome profiling at 24 h revealed that inflorescence response at 24 h had a large carbon-deprivation component. Genes that positively regulate developmental senescence (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN92) and shade-avoidance syndrome (PHYTOCHROME INTERACTING FACTOR4 [PIF4] and PIF5) were up-regulated within 24 h. Mutations in these genes delayed degreening of the inflorescences. Their up-regulation was suppressed in dark-held inflorescences by glucose treatment, which promoted macroscopic growth and development and inhibited degreening of the inflorescences. Detached inflorescences held in the dark for 4 d were still able to reinitiate development to produce siliques upon being brought out to the light, indicating that the transcriptional reprogramming at 24 h was adaptive and reversible. Our results suggest that the response of detached immature tissues to dark storage involves interactions between carbohydrate status sensing and light deprivation signaling and that the dark-adaptive response of the tissues appears to utilize some of the same key regulators as developmental senescence.
The simple fool's guide to population genomics via RNA‐Seq: an introduction to high‐throughput sequencing data analysis
Authors: De Wit Pierre , Pespeni Melissa H. , Ladner Jason T. , Barshis Daniel J. , Seneca François , Jaris Hannah , Therkildsen Nina Overgaard , Morikawa Megan , Palumbi Stephen R. 
Published: August 2012

AbstractHigh‐throughput sequencing technologies are currently revolutionizing the field of biology and medicine, yet bioinformatic challenges in analysing very large data sets have slowed the adoption of these technologies by the community of population biologists. We introduce the ‘Simple Fool's Guide to Population Genomics via RNA‐seq’ (SFG), a document intended to serve as an easy‐to‐follow protocol, walking a user through one example of high‐throughput sequencing data analysis of nonmodel organisms. It is by no means an exhaustive protocol, but rather serves as an introduction to the bioinformatic methods used in population genomics, enabling a user to gain familiarity with basic analysis steps. The SFG consists of two parts. This document summarizes the steps needed and lays out the basic themes for each and a simple approach to follow. The second document is the full SFG, publicly available at http://sfg.stanford.edu, that includes detailed protocols for data processing and analysis, along with a repository of custom‐made scripts and sample files. Steps included in the SFG range from tissue collection to de novo assembly, blast annotation, alignment, gene expression, functional enrichment, SNP detection, principal components and FST outlier analyses. Although the technical aspects of population genomics are changing very quickly, our hope is that this document will help population biologists with little to no background in high‐throughput sequencing and bioinformatics to more quickly adopt these new techniques.
Positive crosstalk between arginase‐II and S6K1 in vascular endothelial inflammation and aging
Authors: Yepuri Gautham , Velagapudi Srividya , Xiong Yuyan , Rajapakse Angana G. , Montani Jean‐Pierre , Ming Xiu‐Fen , Yang Zhihong 
Published: August 2012

SummaryAugmented activities of both arginase and S6K1 are involved in endothelial dysfunction in aging. This study was to investigate whether or not there is a crosstalk between arginase and S6K1 in endothelial inflammation and aging in senescent human umbilical vein endothelial cells and in aging mouse models. We show increased arginase‐II (Arg‐II) expression/activity in senescent endothelial cells. Silencing Arg‐II in senescent cells suppresses eNOS‐uncoupling, several senescence markers such as senescence‐associated‐β‐galactosidase activity, p53‐S15, p21, and expression of vascular adhesion molecule‐1 (VCAM1) and intercellular adhesion molecule‐1 (ICAM1). Conversely, overexpressing Arg‐II in nonsenescent cells promotes eNOS‐uncoupling, endothelial senescence, and enhances VCAM1/ICAM1 levels and monocyte adhesion, which are inhibited by co‐expressing superoxide dismutase‐1. Moreover, overexpressing S6K1 in nonsenescent cells increases, whereas silencing S6K1 in senescent cells decreases Arg‐II gene expression/activity through regulation of Arg‐II mRNA stability. Furthermore, S6K1 overexpression exerts the same effects as Arg‐II on endothelial senescence and inflammation responses, which are prevented by silencing Arg‐II, demonstrating a role of Arg‐II as the mediator of S6K1‐induced endothelial aging. Interestingly, mice that are deficient in Arg‐II gene (Arg‐II−/−) are not only protected from age‐associated increase in Arg‐II, VCAM1/ICAM1, aging markers, and eNOS‐uncoupling in the aortas but also reveal a decrease in S6K1 activity. Similarly, silencing Arg‐II in senescent cells decreases S6K1 activity, demonstrating that Arg‐II also stimulates S6K1 in aging. Our study reveals a novel mechanism of mutual positive regulation between S6K1 and Arg‐II in endothelial inflammation and aging. Targeting S6K1 and/or Arg‐II may decelerate vascular aging and age‐associated cardiovascular disease development.
Detection of infliximab levels and anti‐infliximab antibodies: a comparison of three different assays
Authors: Vande Casteele N. , Buurman D. J. , Sturkenboom M. G. G. , Kleibeuker J. H. , Vermeire S. , Rispens T. , van der Kleij D. , Gils A. , Dijkstra G. 
Published: August 2012

SummaryBackgroundFormation of antibodies to infliximab (ATI) inversely correlates with functional drug levels and clinical outcome. Comparison of drug levels and anti‐drug antibody monitoring is hampered by lack of standardisation.AimTo determine the correlation between three different assays for measuring infliximab and ATI.MethodsSerum samples and spiked controls (total 62) were evaluated in a blinded way in infliximab and ATI assays developed by Sanquin Amsterdam, Netherlands (A), Laboratory for Pharmaceutical Biology, KU Leuven, Belgium (B) and a commercially available kit from Biomedical Diagnostics (BMD), Paris, France (C) performed by the University Medical Center Groningen (UMCG), Netherlands.ResultsAll infliximab assays showed a linear quantitative correlation (Pearson r = 0.91 for A vs. B, 0.83 for A vs. C and 0.73 for B vs. C). Assay C detected infliximab in 11 samples (18%) not detected by A and B, including samples containing only ATI. All ATI assays showed a good linear correlation (Pearson r = 0.95 for A vs. B, 0.99 for A vs. C and 0.97 for B vs. C). Assay A detected ATI in five samples with low ATI that were not detected by assays B and C. Assay B did not detect ATI in three patient samples with low ATI according to assays A and C.ConclusionsThere is a good correlation of infliximab and antibodies to infliximab measurements between these assays. Nevertheless, the Biomedical Diagnostics kit detected false positive infliximab levels in 18% of the samples.
Reactive gastropathy is associated with inflammatory conditions throughout the gastrointestinal tract
Authors: Maguilnik I. , Neumann W. L. , Sonnenberg A , Genta R. M. 
Published: August 2012

SummaryBackgroundThe epidemiology of reactive gastropathy and its relationship with other conditions of the gastrointestinal tract associated with NSAID use have not been evaluated.AimsTo test the hypothesis that if reactive gastropathy shares common aetiological factors with these conditions, the analysis of a large cohort would unveil associations.MethodsWe queried a national pathology database for subjects with a diagnosis of reactive gastropathy; controls were patients with normal gastric biopsies. We also extracted diagnoses of H. pylori infection, intestinal metaplasia, duodenal lymphocytosis, duodenitis, ileitis, microscopic colitis and focal colitis.ResultsOf 504 011 patients with gastric biopsies, 69 101 had oesophageal, 166 134 duodenal, 13 010 ileal and 83 334 colonic biopsies. Reactive gastropathy was diagnosed in 15.6% of patients, H. pylori infection in 10.3% and normal gastric mucosa in 16.3%. Reactive gastropathy was evenly distributed across the US and increased from 2.0% in the first decade of life to >20% in octogenarians. Compared with controls, reactive gastropathy was significantly associated with Barrett's mucosa (OR 1.21 95% CI 1.16–129); duodenitis (OR 1.36; 95% CI 1.28–1.44); duodenal intraepithelial lymphocytosis (OR 1.25; 95% CI 1.13–1.39); active ileitis (OR 1.88; 95% CI 1.47–2.40); focal active colitis (OR 1.57; 95% CI 1.33–1.86); and collagenous colitis (OR 1.50; 95% CI 1.12–2.03).ConclusionsReactive gastropathy, a common histopathological feature of the stomach, shows an age‐dependent rise and is associated with changes of the digestive tract believed to be caused by NSAID use or duodenogastric reflux. However, a large fraction of reactive gastropathy remains unexplained; its frequent occurrence merits further efforts at elucidating its aetiology.
Expression of p16 alone does not differentiate between Spitz nevi and Spitzoid melanoma
Authors: Mason Ashley , Wititsuwannakul Jade , Klump Vincent R. , Lott Jason , Lazova Rossitza 
Published: August 2012

BackgroundSpitz nevi and Spitzoid melanomas show overlapping histopathologic features, often making the diagnosis challenging. The p16 protein functions as a tumor suppressor and loss of its expression may be seen in some melanomas.MethodsWe evaluated 18 Spitz nevi and 19 Spitzoid melanomas from the Yale Spitzoid Neoplasm Repository for p16 expression. A staining intensity score (SIS) was calculated by multiplying a score for the percentage of stained cells (0–3) by a score for staining intensity (0–3).ResultsStaining with p16 was positive in 15/18 (83%) Spitz nevi and 15/19 (79%) Spitzoid melanomas (p = 0.73). Both Spitz nevi and Spitzoid melanomas had a similar SISs, 4.9 and 3.8, respectively (p = 0.057). All 19 patients with Spitzoid melanomas had poor outcome with either death (6 patients) or metastases (13 patients) at a median (3 years) and mean (5.4 years) follow up. In contrast, all 18 patients with Spitz nevi had a benign course with no adverse events at a median (4 years) and mean (4 years) follow up.ConclusionsWe found no significant difference in p16 staining in Spitz nevi and Spitzoid melanomas. We conclude that p16 does not appear to be a useful immunohistochemical marker in distinguishing between Spitz nevi and Spitzoid melanomas.
Incidence of dieback disease following fungal inoculations of sexually and asexually propagated shisham (Dalbergia sissoo)
Authors: Ahmad By I. , Khan R. A. , Siddiqui M. T. 
Published: August 2012

SummaryShisham (Dalbergia sissoo) is an important multipurpose tree with great economic importance, but this tree has been devastated by dieback disease. Seedlings and asexually propagated (cuttings) plants were artificially inoculated with four fungi (Fusarium solani, Botryodiplodia theobromae, Curvularia lunata and Ganoderma lucidum) to evaluate the potential role of these fungi in shisham dieback disease. Results at 2 years revealed that highest disease was caused by inoculation of F. solani (31.39%), followed by B. theobromae (19.042%) and C. lunata (12.22%), but no dieback disease was caused by G. lucidum. During both years, seedlings exhibited greater susceptibility to disease (17.24%) compared to cuttings (7.83%). In particular, F. solani caused more disease in seedlings (46.18%) compared to cuttings (16.61%). With the F. solani inoculations, maximum disease rate was observed at 8 weeks post‐inoculation both in seedlings (77%) and in cuttings (31%), but the maximum disease increase was observed at 4–5 weeks post‐inoculation. Analysis of variance showed significant differences among the different fungi and also between seedlings and cuttings. F. solani can be considered as a major fungal pathogen contributing to dieback disease of shisham, and asexual propagation can reduce the severity of dieback.
Scale‐dependent longitudinal patterns in mussel communities
Authors: ATKINSON CARLA L. , JULIAN JASON P. , VAUGHN CARYN C. 
Published: August 2012

Summary1. Species richness and assemblage patterns of organisms are dictated by numerous factors, probably operating at multiple scales. Freshwater mussels (Unionidae) are an endangered, speciose faunal group, making them an interesting model system to study the influence of landscape features on organisms. In addition, landscape features that influence species distributions and the scale at which the factors have the greatest impact are important issues that need to be answered to conserve freshwater mussels.2. In this study, we quantified freshwater mussel communities at 16 sites along three mid‐sized rivers in the south‐central United States. We addressed the following questions: (i) Are there predictable longitudinal changes in mussel community composition? (ii) What landscape variables best explain shifts in community composition? and (iii) At what scale do landscape variables best predict mussel community composition?3. After controlling for the influence of longitudinal position along the stream, we compared mussel distributions to a suite of hypothesised explanatory landscape variables across multiple scales – catchment scale (entire drainage area), buffer scale (100‐m riparian buffer of the entire catchment) and reach scale (100‐m riparian buffer extending 1 km upstream from the sampling site).4. We found a significant and consistent longitudinal shift in dominant mussel species across all three rivers, with community composition strongly related to distance from the headwaters, which is highly correlated with stream size. After accounting for stream size, variables at the buffer scale were the best predictors of mussel community composition. After accounting for catchment position, mean channel slope was the best explanatory variable of community composition and appeared in all top candidate models at the catchment and buffer scales. Coverage of wetland and urban area were also correlated with community composition at the catchment and buffer scales.5. Our results suggest that landscape‐scale habitat factors influence mussel community composition. Landscape features at the buffer scale performed best at determining community composition after accounting for position in the catchment; thus, further protection of riparian buffers will help to conserve mussel communities.