bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human cystatin C: A new biomarker of idiopathic pulmonary fibrosis?
Authors: Kasabova Mariana , Joulin‐Giet Alix , Lecaille Fabien , Saidi Ahlame , Marchand‐Adam Sylvain , Lalmanach Gilles 
Published: November 2013

PurposeHuman idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disorder with a poor prognosis. The identification of a new and specific biomarker in bronchoalveolar lavage fluids (BALFs) may assist in the diagnosis of the disease.Experimental designCharacterization of cysteine Cats and their endogenous inhibitor, cystatin C, was conducted by immunochemical analysis and measurement of endopeptidase activity of control (n = 11) and IPF (n = 25) BALFs (normalized conditions, 20 μg protein/assay).ResultsCathepsin (Cat) B was detected as proform and mature enzyme for both control and IPF samples, while Cats K, L, and S were found as zymogens with a strengthened staining in IPF BALFs. The overall endopeptidase activity related mainly to Cat B and did not vary significantly between control and IPF samples. Conversely a significant increase of immunoreactive cystatin C was measured in BALFs for each of three IPF grades.Conclusions and clinical relevanceAn excessive deposition of extracellular matrix proteins is the hallmark of fibrotic disorders. Cats are potent collagenases and might be essential for lung homeostasis. Taken together, increase of cystatin C in IPF BALFs may reflect abnormal regulation of proteolytic activity of Cats in lung, which in turn can promote the development of fibrosis.
Seed and feeder use by birds in the United States and Canada
Authors: Horn David J. , Johansen Stacey M. , Wilcoxen Travis E. 
Published: November 2013

ABSTRACTMore people feed birds and other wildlife than hunt and fish combined. Despite its popularity, many bird‐feeding traditions lack scientific data. We examined seed and feeder use by wild birds in the United States and Canada, and how seed use may change by season and geographic region. Between 2005 and 2008, 173 individuals from 38 states and 3 provinces in Canada made 20,077, 45‐minute observations at bird feeders, recording 106 species and 1,282,424 bird visits. Of the 10 seed types most commonly used in bird seed blends, 3 are most attractive to birds: black‐oil sunflower, medium sunflower chips, and white proso millet. Other seeds such as red milo are less attractive. Chickadees (Poecile spp.), nuthatches (Sitta spp.), and larger finches (Carpodacus spp.) were most abundant at black‐oil sunflower, smaller finches (Carduelis spp.) were most abundant at Nyjer® (Wild Bird Feeding Institute, Chicago, IL) and sunflower chips, and sparrows (Spizella spp.) were most abundant at white proso millet. Bird‐feeding traditions have been widely reported in books, magazines, newspaper articles, and websites. These traditions are often conflicting and have not been verified empirically. Studies such as this can be used to develop scientifically based recommendations that can lead to a better bird‐feeding experience and that attract fewer species with known negative ecological consequences. © 2013 The Wildlife Society.
The aqueous extract from Toona sinensis leaves inhibits microglia‐mediated neuroinflammation
Authors: Wang Chao‐Chuan , Tsai Yee‐Jean , Hsieh Ya‐Ching , Lin Rong‐Jyh , Lin Chih‐Lung 
Published: November 2013

AbstractThe leaves of Toona sinensis, a well‐known traditional oriental medicine, have been prescribed for the treatment of enteritis and infection. Recently, aqueous extracts of Toona sinensis leaves (TSL‐1) have demonstrated many biological effects both in vitro and in vivo. In the central nervous system, microglial activation and their proinflammatory responses are considered an important therapeutic strategy for neuroinflammatory disorders such as cerebral ischemia, Alzheimer's disease, and Parkinson's disease. The present study attempted to validate the effect of TSL‐1 on microglia‐mediated neuroinflammation stimulated by lipopolysaccharide (LPS). As inflammatory parameters, the production of nitric oxide (NO), inducible NO synthase, and tumor necrosis factor‐α were evaluated. Our results demonstrate that TSL‐1 suppresses LPS‐induced NO production, tumor necrosis factor‐α secretion, and inducible NO synthase protein expression in a concentration‐dependent manner, without causing cytotoxicity. In addition, the inhibitory effects of TSL‐1 in LPS‐stimulated BV‐2 microglia were extended to post‐treatment suggesting the therapeutic potential of TSL‐1. Therefore, this work provides the future evaluation of the role of TSL‐1 in the treatment of neurodegenerative diseases by inhibition of inflammatory mediator production in activated microglia.
Unifying binary fluid diffuse-interface models in the sharp-interface limit
Authors: Sibley David N. , Nold Andreas , Kalliadasis Serafim 
Published: November 2013

AbstractRecent results published by Gugenberger et al. on surface diffusion (Phys. Rev. E, vol. 78, 2008, 016703), show that the sharp-interface limit of the phase field models often adopted in the literature fails to produce the appropriate boundary conditions. With this knowledge, we consider the sharp-interface limit of phase field models for binary fluids, obtained carefully, where hydrodynamic equations are coupled to phase field evolution based on Cahn–Hilliard or Allen–Cahn theories, in a variety of guises, and unify and contrast their forms and behaviours in the sharp-interface limit. In particular, a tensorial mobility model is analysed, which allows the bulk fluids in the outer region to satisfy classical Navier–Stokes type equations to all orders in the Cahn number.
Inertial instability of flows on the inside or outside of a rotating horizontal cylinder
Authors: Benilov E. S. , Lapin V. N. 
Published: November 2013

AbstractWe consider thin liquid films on the inside (rimming flows) or outside (coating flows) of a cylinder with horizontal axis, rotating about this axis. If the liquid’s net volume is small, such films are known to evolve towards a steady state with a smooth surface, whereas, for larger amounts, the flow develops a ‘shock’ similar to a tidal bore. In this work, smooth films are shown to be unstable. Since the strongest instability occurs at wavelengths comparable to the film’s thickness, our analysis is based on the full Navier–Stokes equations, not on the lubrication approximation (which has been traditionally used in this problem). It is also shown that, for cylinders of sufficiently small radii, the instability can be suppressed by surface tension.
Instability regimes in the primary breakup region of planar coflowing sheets
Authors: Fuster D. , Matas J.-P. , Marty S. , Popinet S. , Hoepffner J. , Cartellier A. , Zaleski S. 
Published: November 2013

AbstractThis article investigates the appearance of instabilities in two planar coflowing fluid sheets with different densities and viscosities via experiments, numerical simulation and linear stability analysis. At low dynamic pressure ratios a convective instability is shown to appear for which the frequency of the waves in the primary atomization region is influenced by both liquid and gas velocities. For large dynamic pressure ratios an asymptotic regime is obtained in which frequency is solely controlled by gas velocity and the instability becomes absolute. The transition from convective to absolute is shown to be influenced by the velocity defect induced by the presence of the separator plate. We show that in this regime the splitter plate thickness can also affect the nature of the instability if it is larger than the gas vorticity thickness. Computational and experimental results are in agreement with the predictions of a spatio-temporal stability analysis.
TaqIB polymorphism in the cholesteryl ester transfer protein (CETP) gene influences lipid responses to the consumption of kiwifruit in hypercholesterolaemic men
Authors: Gammon Cheryl S. , Minihane Anne M. , Kruger Rozanne , Conlon Cathryn A. , von Hurst Pamela R. , Jones Beatrix , Stonehouse Welma 
Published: November 2013

Fruit and vegetables are key elements of a cardioprotective diet, but benefits on plasma lipids, especially HDL-cholesterol (HDL-C), are inconsistent both within and between studies. In the present study, we investigated whether four selected HDL-C-related polymorphisms (cholesteryl ester transfer protein (CETP) Taq1B, APOA1 − 75G/A, hepatic lipase (LIPC) − 514C → T, and endothelial lipase (LIPG) I24582) modulate the plasma lipid response to a kiwifruit intervention. This is a retrospective analysis of data collected during a 12-week randomised controlled cross-over trial. A total of eighty-five hypercholesterolaemic men completed a 4-week healthy diet run-in period before being randomised to one of two 4-week intervention sequences of two green kiwifruit/d plus healthy diet (kiwifruit intervention) or healthy diet alone (control intervention). The measurement of anthropometric parameters and collection of fasting blood samples were carried out at baseline 1 and after the run-in (baseline 2) and intervention periods. At baseline 2, B1/B1 homozygotes of the CETPTaq1B gene had significantly higher total cholesterol:HDL-C, TAG:HDL-C, and apoB:apoA1 ratios and small-dense LDL concentrations than B2 carriers. A significant CETP Taq1B genotype × intervention interaction was observed for the TAG:HDL-C ratio (P= 0·03). B1/B1 homozygotes had a significantly lower TAG:HDL-C ( − 0·23 (sd 0·58) mmol/l; P= 0·03) ratio after the kiwifruit intervention than after the control intervention, whereas the ratio of B2 carriers was not affected. The lipid response was not affected by other gene polymorphisms. In conclusion, the significant decrease in the TAG:HDL-C ratio in B1/B1 homozygotes suggests that regular inclusion of green kiwifruit as part of a healthy diet may improve the lipid profiles of hypercholesterolaemic men with this genotype.
Risk factors for susceptibility to varicella in newly arrived adult migrants in Canada
Authors: GREENAWAY C. , BOIVIN J. F. , CNOSSEN S. , ROSSI C. , TAPIERO B. , SCHWARTZMAN K. , OLSON S. , MILLER M. 
Published: November 2013

SUMMARYVaricella occurs at an older age in tropical compared to cold climates. Migrants from tropical countries provide the opportunity to gain insights into observed global differences in varicella epidemiology. Severity of varicella increases with age thus, description of risk factors for varicella susceptibility will identify those who would benefit most from vaccination. A total of 1480 migrants, with a mean age of 32 years, were recruited in the pre-vaccination period (2002–2004) in Montreal, Canada. A questionnaire was administered and serum varicella antibodies were measured. Overall 6% were susceptible and ranged from 0·8% to 14·1% in subgroups. Risk factors for susceptibility were younger age, recent arrival, and originating from a tropical country. This could be modified by conditions that increased the probability of person-to-person spread of varicella through direct contact in source countries such as larger community size or household crowding. Many new young adult migrants would benefit from targeted varicella vaccination programmes.
Identifying the public health benefits of livestock-dependent, agro-ecosystems under climate change
Authors: Gillette Shana 
Published: November 2013

AbstractAs the demand for meat continues to grow in South Asia and Africa and access to communal sources of water and forage shrinks, intensification of small-scale livestock systems in peri-urban areas is expected to expand. In South East Asia, smallholder transition to livestock intensification has been transformative, increasing economic opportunities while also introducing new disease risks. While we have an understanding of the emerging disease burden from livestock intensification; we have just begun to understand the possible public health benefits of sustainable landscapes and the potential health savings accrued from disease avoidance. To date, few studies have attempted to quantify the health benefits attributable to sustainable agro-ecosystems, especially in regard to livestock systems. In this paper, I will examine what is needed to measure and communicate the public health benefits and cost-savings (from disease avoidance) of sustainable agro-ecosystems.
The cytokine-induced conformational switch of nuclear factor κB p65 is mediated by p65 phosphorylation
Authors: Milanovic Maja , Kracht Michael , Schmitz M. Lienhard 
Published: November 2013

The transcription factor NF-κB (nuclear factor κB) serves to up-regulate gene expression in response to precarious signals such as the pro-inflammatory cytokines TNF (tumour necrosis factor) and IL-1 (interleukin 1). In the present study we show that stimulation of cells with TNF or IL-1 results in a profound conformational switch of the NF-κB subunit p65, as revealed by limited proteolysis assays. We also describe the identification of a conformation-specific monoclonal antibody that preferentially immunoprecipitates the inducibly refolded p65 protein. The cytokine-triggered reconfiguration of p65 mainly occurs for p65 contained in the nuclear fraction. Phosphorylations serve as the central driving force for the inducible reconfiguration of p65. Accordingly, mutation of single phosphorylation sites in the C-terminal transactivation domain led to large conformational changes which result in strongly decreased ubiquitination and also in differential protein–protein interactions. Induced conformational changes of p65 thus increase the intramolecular flexibility and therefore expand and specify the repertoire of possible protein–protein interactions. Constitutively bound chaperones of the Hsp (heat-shock protein)/Hsc70 (heat-shock cognate protein, 73 kDa) family are not important for the cytokine-induced conformational switch, but rather control the fidelity of protein rearrangement. Accordingly, pharmacological inhibition of Hsp/Hsc70 interferes with p65-triggered gene expression.
Prediction and early diagnosis of complex diseases by edge-network
Authors: Yu Xiangtian , Li Guojun , Chen Luonan 
Published: November 2013

Abstract
Motivation: In this article, we develop a novel edge-based network i.e. edge-network, to detect early signals of diseases by identifying the corresponding edge-biomarkers with their dynamical network biomarker score from dynamical network biomarkers. Specifically, we derive an edge-network based on the second-order statistics representation of gene expression profiles, which is able to accurately represent the stochastic dynamics of the original biological system (with Gaussian distribution assumption) by combining with the traditional node-network, which is based only on the first-order statistics representation of the noisy data. In other words, we show that the stochastic network of a biological system can be described by the integration of its node-network and its edge-network in an accurate manner.
Results: By applying edge-network analysis to gene expressions of healthy adults within live influenza experiment sampling at time points before the appearance of infection symptoms, we identified the edge-biomarkers (80 edges with 22 densely connected genes) discovered in edge-networks corresponding to symptomatic adults, which were used to predict the subsequent outcomes of influenza infection. In particular, we not only correctly predict the final infection outcome of each individual at an early time point before his/her clinic symptom but also reveal the key molecules during the disease progression. The prediction accuracy achieves ∼90% under the leave-one-out cross-validation. Furthermore, we demonstrate the superiority of our method on disease classification and predication by comparing with the conventional node-biomarkers. Our edge-network analysis not only opens a new way to understand pathogenesis at a network level due to the new representation for a stochastic network, but also provides a powerful tool to make the early diagnosis of diseases.
Contact: lnchen@sibs.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
The functional therapeutic chemical classification system
Authors: Croset Samuel , Overington John P. , Rebholz-Schuhmann Dietrich 
Published: November 2013

Abstract
Motivation: Drug repositioning is the discovery of new indications for compounds that have already been approved and used in a clinical setting. Recently, some computational approaches have been suggested to unveil new opportunities in a systematic fashion, by taking into consideration gene expression signatures or chemical features for instance. We present here a novel method based on knowledge integration using semantic technologies, to capture the functional role of approved chemical compounds.
Results: In order to computationally generate repositioning hypotheses, we used the Web Ontology Language to formally define the semantics of over 20 000 terms with axioms to correctly denote various modes of action (MoA). Based on an integration of public data, we have automatically assigned over a thousand of approved drugs into these MoA categories. The resulting new resource is called the Functional Therapeutic Chemical Classification System and was further evaluated against the content of the traditional Anatomical Therapeutic Chemical Classification System. We illustrate how the new classification can be used to generate drug repurposing hypotheses, using Alzheimers disease as a use-case.
Availability: https://www.ebi.ac.uk/chembl/ftc; https://github.com/loopasam/ftc.
Contact: croset@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Effect of a High Tunnel, Organic Cropping System on Lettuce Diseases in Western Washington
Authors: Powell Marianne , Cowan Jeremy , Miles Carol , Inglis Debra Ann 
Published: November 2013

Incidence of gray mold and lettuce drop, and yield of six cultivars representing market classes Boston/Crisphead, Leaf, and Romaine, were evaluated in open ended high tunnel and open field organic production systems near Mount Vernon, WA from 2010 to 2012. Each year seedlings were transplanted in April and heads harvested in June/July. In 2010, Romaine types had significantly (P < 0.0001) greater incidence of gray mold (caused by Botrytis cinerea) than other types. In 2011, incidence of gray mold was significantly (P = 0.004) greater in high tunnel than open field plots, and greatest in high tunnels when fog persisted. All cultivars were equally susceptible to lettuce drop (caused by Sclerotinia sclerotiorum), although in 2012, incidence was significantly (P < 0.0001) greater in high tunnel than open field plots. ‘Green Star’ (Leaf type) had reduced incidence of gray mold and lettuce drop in 2010 and 2011. Incidence of tipburn was significantly (P = 0.032 and P = 0.001, respectively) greater in the high tunnels in 2011 and 2012 compared to the open field. Total yield (kg) was greater in the open field in 2012, but not in 2011 and 2010. Accepted for publication 8 July 2013. Published 22 September 2013.
When Do Foliar Pyraclostrobin Fungicide Applications Produce Profitable Soybean Yield Responses?
Authors: Kyveryga Peter M. , Blackmer Tracy M. , Mueller Daren S. 
Published: November 2013

From 2005 through 2009, 282 on-farm evaluation trials were conducted in soybean fields across Iowa to identify when a foliar application of pyraclostrobin produced profitable yield responses. Because of a delay in plant maturity, 218 trials exhibited a fungicide-induced “greening effect” documented using the late-season color infrared (CIR) digital aerial imagery of the soybean canopy. These 218 trials were approximately 35% more likely to produce profitable yield responses (65% vs 30%) than those without “the greening effect.” In addition, greater yield responses were observed in trials that received more than 12 inches of cumulative March through May rainfall. Potentially, site-specific observations of spring rainfall could be used to identify fields that are or are not likely to produce above break-even yield responses, and therefore, help farmers avoid unnecessary foliar fungicide applications on soybean. Accepted for publication 30 July 2013. Published 28 September 2013.
First Report of Geosmithia morbida and Pityophthorus juglandis Causing Thousand Cankers Disease in Butternut
Authors: Serdani Maryna , Vlach Joshua J. , Wallis Kelly L. , Zerillo Marcelo , McCleary Tim , Romero-Severson Jeanne , Tisserat Ned A. 
Published: November 2013

To our knowledge, this is the first report of natural infection of butternut by G. morbida and P. juglandis. Accepted for publication 15 October 2013. Published 18 October 2013.
Fungicide Management of Brown Patch of Tall Turf-type Fescue in the Residential Landscape in Oklahoma
Authors: Smith Damon L. , Walker Nathan R. 
Published: November 2013

In the transition zone of the USA, cool-season grasses such as tall fescue are often planted in shaded areas, where warm-season grasses are less adapted. The most damaging disease of tall fescue is brown patch, caused by Rhizoctonia solani. Fungicide applications and cultural practices are often used to manage brown patch in this region. A three-year study was implemented in Oklahoma to evaluate ready-to-use fungicides available to residential lawn owners and compare these to several common commercial fungicide formulations used by professional lawn care applicators. A selection of fungicides representing products commonly available to the residential market and commercial standards were applied to small plots of tall fescue or tall fescue/Kentucky bluegrass mixtures from 2008 to 2010. All products tested, with the exception of azoxystrobin, provided limited or inconsistent control of brown patch and resulted in lower turfgrass quality in all years. Further examination of carrier type (granular vs. liquid) and timing (preventive vs. curative) did not result in strong differences in the level of brown patch control or overall quality. These studies suggest that control of brown patch in tall fescue in the transition zone should focus on integrated disease management principals and not only on applications of fungicides directed at the residential market. Accepted for publication 5 August 2013. Published 22 October 2013.
Streptomycin Resistance of Erwinia amylovora Isolated from Apple (Malus domesticus) in Utah
Authors: Nischwitz Claudia , Dhiman Christine 
Published: November 2013

Fire blight, caused by the bacterium Erwinia amylovora, causes devastating losses in multiple fruit and ornamental crops worldwide. It is the most important disease for apple and pear growers in Utah. Currently, the only effective management strategy is the application of streptomycin. In 2006, isolates resistant to streptomycin were detected in an apple orchard in central Utah for the first time. To determine the distribution of resistant isolates and the level of resistance, isolates of E. amylovora were collected between 2006 and 2012 from apple trees across the state and tested for resistance to streptomycin. Each isolate was initially screened against 0, 50, 100, and 1,000 ppm of streptomycin. Selected isolates resistant to 1,000 ppm were exposed to higher concentrations of streptomycin. The majority of resistant isolates were found in Utah Co., the largest apple and pear production area in the state. Resistant isolates tolerated up to 200,000 ppm of streptomycin. The resistance mechanism in all isolates obtained in Utah was identified as a mutation of codon 43 found in the rpsL gene. Accepted for publication 15 August 2013. Published 25 October 2013.