bluuebunny/crossref_metadata_2025 huggingface dataset:
A Significant Fraction of 21-Nucleotide Small RNA Originates from Phased Degradation of Resistance Genes in Several Perennial Species
Authors: Källman Thomas , Chen Jun , Gyllenstrand Niclas , Lagercrantz Ulf
Published: April 2013

Small RNAs (sRNAs), including microRNA (miRNA) and short-interfering RNA (siRNA), are important in the regulation of diverse biological processes. Comparative studies of sRNAs from plants have mainly focused on miRNA, even though they constitute a mere fraction of the total sRNA diversity. In this study, we report results from an in-depth analysis of the sRNA population from the conifer spruce (Picea abies) and compared the results with those of a range of plant species. The vast majority of sRNA sequences in spruce can be assigned to 21-nucleotide-long siRNA sequences, of which a large fraction originate from the degradation of transcribed sequences related to nucleotide-binding site-leucine-rich repeat-type resistance genes. Over 90% of all genes predicted to contain either a Toll/interleukin-1 receptor or nucleotide-binding site domain showed evidence of siRNA degradation. The data further suggest that this phased degradation of resistance-related genes is initiated from miRNA-guided cleavage, often by an abundant 22-nucleotide miRNA. Comparative analysis over a range of plant species revealed a huge variation in the abundance of this phenomenon. The process seemed to be virtually absent in several species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and nonvascular plants, while particularly high frequencies were observed in spruce, grape (Vitis vinifera), and poplar (Populus trichocarpa). This divergent pattern might reflect a mechanism to limit runaway transcription of these genes in species with rapidly expanding nucleotide-binding site-leucine-rich repeat gene families. Alternatively, it might reflect variation in a counter-counter defense mechanism between plant species.
A Guanine Nucleotide Exchange Factor for Rab5 Proteins Is Essential for Intracellular Transport of the Proglutelin from the Golgi Apparatus to the Protein Storage Vacuole in Rice Endosperm
Authors: Fukuda Masako , Wen Liuying , Satoh-Cruz Mio , Kawagoe Yasushi , Nagamura Yoshiaki , Okita Thomas W. , Washida Haruhiko , Sugino Aya , Ishino Sonoko , Ishino Yoshizumi , Ogawa Masahiro , Sunada Mariko , Ueda Takashi , Kumamaru Toshihiro
Published: April 2013

Rice (Oryza sativa) glutelins are synthesized on the endoplasmic reticulum as a precursor, which are then transported via the Golgi to protein storage vacuoles (PSVs), where they are proteolytically processed into acidic and basic subunits. The glutelin precursor mutant6 (glup6) accumulates abnormally large amounts of proglutelin. Map-base cloning studies showed that glup6 was a loss-of-function mutant of guanine nucleotide exchange factor (GEF), which activates Rab GTPase, a key regulator of membrane trafficking. Immunofluorescence studies showed that the transport of proglutelins and α-globulins to PSV was disrupted in glup6 endosperm. Secreted granules of glutelin and α-globulin were readily observed in young glup6 endosperm, followed by the formation of large dilated paramural bodies (PMBs) containing both proteins as the endosperm matures. The PMBs also contained membrane biomarkers for the Golgi and prevacuolar compartment as well as the cell wall component, β-glucan. Direct evidence was gathered showing that GLUP6/GEF activated in vitro GLUP4/Rab5 as well as several Arabidopsis (Arabidopsis thaliana) Rab5 isoforms to the GTP-bound form. Therefore, loss-of-function mutations in GEF or Rab5 disrupt the normal transport of proglutelin from the Golgi to PSVs, resulting in the initial extracellular secretion of these proteins followed, in turn, by the formation of PMBs. Overall, our results indicate that GLUP6/GEF is the activator of Rab5 GTPase and that the cycling of GTP- and GDP-bound forms of this regulatory protein is essential for the intracellular transport of proglutelin and α-globulin from the Golgi to PSVs and in the maintenance of the general structural organization of the endomembrane system in rice seeds.
Predicting the development of acute kidney injury in liver cirrhosis – an analysis of glomerular filtration rate, proteinuria and kidney injury biomarkers
Authors: Slack A. J. , McPhail M. J. W. , Ostermann M. , Bruce M. , Sherwood R. , Musto R. , Dew T. , Auzinger G. , Bernal W. , O'Grady J. , Heneghan M. A. , Moore K. , Wendon J. A.
Published: April 2013

Background

The timely diagnosis of acute kidney injury (AKI) in liver cirrhosis is challenging.

Aim

To evaluate whether quantification of glomerular filtration rate (GFR), proteinuria and kidney injury biomarkers can accurately predict the development of AKI.

Methods

A prospective cohort analysis of patients with cirrhosis was performed. Measures of baseline kidney function included serum creatinine, iohexol clearance and urine protein:creatinine ratio. Blood and urine samples were collected daily. A retrospective analysis of cystatin C GFR and neutrophil gelatinase‐associated lipocalin (NGAL) measured 48 h prior to the diagnosis of AKI was undertaken to evaluate their ability to predict the development of AKI.

Results

Eighteen of the 34 cirrhosis patients studied developed AKI. A GFR <60 mL/min/1.73 m2 was identified in 56% with Iohexol clearance compared to 8% using the four‐variable modified diet in renal disease formula (P < 0.0001). Prediction of AKI, 48 h prior to the development of AKI with cystatin C GFR and serum NGAL concentration were similar; area under the receiver operating curve (AUROC) values 0.74 (0.51–0.97), P = 0.04 and 0.72 (0.52–0.92), P = 0.02 respectively. The development of AKI was strongly predicted by urine protein:creatinine ratio above the cut‐off of >30 (equivalent to 300 mg/day of proteinuria) sensitivity 82% (57–96) and specificity 80% (52–96), AUROC 0.86 (0.73–0.98), P ≤ 0.0001. [OR 21 (3–133), P ≤ 0.002].

Conclusions

In patients with liver cirrhosis a urine protein:creatinine ratio >30 predicts AKI. Iohexol clearance and cystatin C formulae identify a greater proportion of patients with a GFR <60 mL/min/1.73 m2, which also predicts the development of AKI.
Comparison of pollinators and natural enemies: a meta‐analysis of landscape and local effects on abundance and richness in crops
Authors: Shackelford Gorm , Steward Peter R. , Benton Tim G. , Kunin William E. , Potts Simon G. , Biesmeijer Jacobus C. , Sait Steven M.
Published: April 2013

To manage agroecosystems for multiple ecosystem services, we need to know whether the management of one service has positive, negative, or no effects on other services. We do not yet have data on the interactions between pollination and pest‐control services. However, we do have data on the distributions of pollinators and natural enemies in agroecosystems. Therefore, we compared these two groups of ecosystem service providers, to see if the management of farms and agricultural landscapes might have similar effects on the abundance and richness of both. In a meta‐analysis, we compared 46 studies that sampled bees, predatory beetles, parasitic wasps, and spiders in fields, orchards, or vineyards of food crops. These studies used the proximity or proportion of non‐crop or natural habitats in the landscapes surrounding these crops (a measure of landscape complexity), or the proximity or diversity of non‐crop plants in the margins of these crops (a measure of local complexity), to explain the abundance or richness of these beneficial arthropods. Compositional complexity at both landscape and local scales had positive effects on both pollinators and natural enemies, but different effects on different taxa. Effects on bees and spiders were significantly positive, but effects on parasitoids and predatory beetles (mostly Carabidae and Staphylinidae) were inconclusive. Landscape complexity had significantly stronger effects on bees than it did on predatory beetles and significantly stronger effects in non‐woody rather than in woody crops. Effects on richness were significantly stronger than effects on abundance, but possibly only for spiders. This abundance‐richness difference might be caused by differences between generalists and specialists, or between arthropods that depend on non‐crop habitats (ecotone species and dispersers) and those that do not (cultural species). We call this the ‘specialist‐generalist’ or ‘cultural difference’ mechanism. If complexity has stronger effects on richness than abundance, it might have stronger effects on the stability than the magnitude of these arthropod‐mediated ecosystem services. We conclude that some pollinators and natural enemies seem to have compatible responses to complexity, and it might be possible to manage agroecosystems for the benefit of both. However, too few studies have compared the two, and so we cannot yet conclude that there are no negative interactions between pollinators and natural enemies, and no trade‐offs between pollination and pest‐control services. Therefore, we suggest a framework for future research to bridge these gaps in our knowledge.
Ketamine as a Fast Acting Antidepressant: Current Knowledge and Open Questions
Authors: Salvadore Giacomo , Singh Jaskaran B.
Published: April 2013

Several recent studies have shown that a single intravenous subanesthetic dose of ketamine, a NMDA receptor antagonist, exerts rapid antidepressant effects in patients with treatment refractory mood disorders and reduces suicidal ideation. Those insights have fueled tremendous excitement in the efforts to elucidate the mechanism underlying ketamine's antidepressant properties in animal models of depression, as well as in humans through the use of brain imaging as well as peripheral blood measurements. For example, there is emerging evidence that ketamine's antidepressant properties rely on increasing AMPA signaling and rapidly inducing synaptogenesis. While pilot clinical studies are promising, a number of critical questions still remain unanswered. They relate to the safe and effective use of ketamine in patients with mood disorders regarding the optimal dose range, modality and method of administration for acute and long‐term maintenance of effect, and the biomarkers associated with response/nonresponse. In this review article, we first summarize the clinical evidence about the use of ketamine in mood disorders, as well as preclinical and humans studies which investigated the mechanisms of action of ketamine, and predictors of antidepressant response in clinical populations. We then provide a critical overview of the knowledge gaps about the use of ketamine in depression and suggest some future research directions for the investigation of ketamine as a promising tool to develop novel more effective and fast acting antidepressants.
Inhaled fluticasone furoate/vilanterol does not affect hypothalamic‐pituitary‐adrenal axis function in adolescent and adult asthma: randomised, double‐blind, placebo‐controlled study
Authors: Allen Ann , Schenkenberger Isabelle , Trivedi Roopa , Cole Jeremy , Hicks Wesley , Gul Nadeem , Jacques Loretta
Published: April 2013

Introduction

Fluticasone furoate (FF) is a novel inhaled corticosteroid with 24‐h activity. FF is in development as a once‐daily treatment for asthma as monotherapy and in combination with vilanterol (VI), a long‐acting β2 agonist. Corticosteroids can have systemic effects on hypothalamic‐pituitary‐adrenal (HPA) axis function, potentially resulting in cortisol suppression.

Objectives

To assess the effect of FF/VI compared with placebo on the HPA axis by evaluating 24‐h weighted mean serum cortisol levels in adolescent and adult patients with persistent asthma.

Methods

One hundred eighty‐five patients with >12 weeks history of asthma were randomised in a 4:4:4:1 ratio to one of two once‐daily FF/VI treatments (100/25 μg or 200/25 μg), placebo or an active control group that received inhaled placebo plus one prednisolone 10 mg capsule daily for the last 7 days of the study. Twenty‐four‐hour serum and urinary cortisol was measured at baseline and on day 42.

Results

Non‐inferiority in 24‐h weighted mean serum cortisol after 6 weeks of treatment with once‐daily FF/VI at either strength was shown. Treatment ratios [95% confidence interval (CI)] to placebo for FF/VI 100/25 μg [0.99 (0.87–1.12)] or FF/VI 200/25 μg [0.97 (0.86–1.10)] indicated non‐inferiority of both FF/VI doses to placebo as the lower limit of the 95% CI was greater than the predefined 0.8. Prednisolone substantially reduced 24‐h weighted mean serum cortisol [treatment ratio to placebo 0.34 (0.28–0.41)]. FF/VI was well‐tolerated, and no safety concerns were identified.

Conclusions

FF/VI was found to be non‐inferior to placebo on HPA axis function, with no indication of significant cortisol suppression after 42 days.
Profile likelihood in systems biology
Authors: Kreutz Clemens , Raue Andreas , Kaschek Daniel , Timmer Jens
Published: April 2013

Inferring knowledge about biological processes by a mathematical description is a major characteristic of Systems Biology. To understand and predict system's behavior the available experimental information is translated into a mathematical model. Since the availability of experimental data is often limited and measurements contain noise, it is essential to appropriately translate experimental uncertainty to model parameters as well as to model predictions. This is especially important in Systems Biology because typically large and complex models are applied and therefore the limited experimental knowledge might yield weakly specified model components. Likelihood profiles have been recently suggested and applied in the Systems Biology for assessing parameter and prediction uncertainty. In this article, the profile likelihood concept is reviewed and the potential of the approach is demonstrated for a model of the erythropoietin (EPO) receptor.
Assessing nitrate leaching during the three‐first years of Miscanthus × giganteus from on‐farm measurements and modeling
Authors: Lesur Claire , Bazot Mathieu , Bio‐Beri Fadel , Mary Bruno , Jeuffroy Marie‐Hélène , Loyce Chantal
Published: April 2013

Miscanthus × giganteus is often regarded as one of the most promising crops to produce sustainable bioenergy. This perennial crop, renowned for its high productivity associated with low input requirements, in particular regarding fertilizers, is thought to have low environmental impacts, but few data are available to confirm this. Our study aimed at assessing nitrate leaching from Miscanthus × giganteus crops in farmers' fields, thus including a wide range of soil and cropping system conditions. We focused on the first years of growth after planting as experimental studies have suggested that Miscanthus × giganteus, once established, results in low nitrate leaching. We combined on‐farm measurements and modeling to estimate drainage, leached nitrogen, and nitrate concentration in drainage water in 38 fields located in Center‐East France during two winters (November 2010 to March 2011, November 2011 to March 2012).

Nitrate leaching and nitrate concentration in drainage water were on average very low. Nitrate leaching averaged 6 kg N ha−1 whereas nitrate concentration averaged 12 mg l−1. These low values are attributable to the low estimates of drainage water (mean = 166 mm) but also to the low soil mineral nitrogen contents measured at the beginning of winter (mean = 37 kg N ha−1). Our results were, however, very variable, mainly due to the crop age: nitrate leaching and nitrate concentration were critically higher during the winter following the first growth year of Miscanthus × giganteus, reflecting the low development of the crop. This variability was also explained by the range of soil and cropping conditions explored in the on‐farm design: shallow and/or sandy soils as well as fields where establishment failed had a higher risk of nitrate leaching.
Combinatorial Composition Films and Dielectric Properties of BaxSr1‐xTiO3 Grown on Two‐Inch p‐Si using PLD Process
Authors: Abdel‐Motaleb Ibrahim M. , Navuduri Praveen , Yoo Young‐Zo , Chmaissem Omar , Song Jeong‐Hwan
Published: April 2013

Combinatorial composition films of BaxSr1‐xTiO3 were grown on two‐inch p‐Si by pulsed laser deposition. Large areas of six different combinatorial composition films were grown on the same wafer using three primary target materials. Consequently, the deposition of Ba0.5Sr0.5TiO3 films was obtained from targets BaTiO3 and SrTiO3, the deposition of Ba0.3Sr0.7TiO3 films was obtained from targets SrTiO3 and Ba0.6Sr0.4TiO3, and the Ba0.8Sr0.2TiO3 film was obtained from targets Ba0.6Sr0.4TiO3 and BaTiO3. The results indicate that the deposited materials are perovskite structures with high dielectric constants ranging from 49.4 to 193.2 and leakage current densities as low as 1.25 × 10−7 A/cm2 at −2V.
Pathophysiology of asthma: lessons from genetic research with particular focus on severe asthma
Authors: Melén E. , Pershagen G.
Published: April 2013

Abstract.  Melén E, Pershagen G (Institute of Environmental Medicine and Centre for Allergy Research, Karolinska Institutet; Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden). Pathophysiology of asthma: lessons from genetic research with particular focus on severe asthma (Reveiw). J Intern Med 2012; 272: 108–120.

There is good evidence that both inherited and environmental factors influence the risk of developing asthma. Only recently, large well‐designed studies have been undertaken with the power to identify the genetic causes for asthma, and methods developed in parallel with the Human Genome Project, such as gene expression and epigenetic studies, have made large‐scale analyses of functional genetics possible. In this review, we discuss the recent findings from genetic and genomic research studies of asthma, particularly severe asthma, and highlight specific genes for which there are multiple lines of evidence for involvement in asthma pathogenesis. Bio‐ontologic enrichment analyses of the most recently identified asthma‐related genes point to attributes such as ‘molecular and signal transducer activity’ and ‘immune system processes’, which indicates the importance of immunoregulation and inflammatory response in the pathogenesis of asthma. Finally, we discuss how genetic and environmental factors jointly influence asthma susceptibility and summarize how the results may increase understanding of the pathophysiology of asthma‐related diseases.
Allergen‐specific immunotherapy: from therapeutic vaccines to prophylactic approaches
Authors: Valenta R. , Campana R. , Marth K. , van Hage M.
Published: April 2013

Abstract.  Valenta R, Campana R, Marth K, van Hage M (Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna; Christian Doppler Laboratory for Allergy Research, Medical University of Vienna, Vienna, Austria; and Department of Medicine, Clinical Immunology and Allergy Unit, Karolinska Institutet and University Hospital, Stockholm, Sweden) Allergen‐specific immunotherapy: from therapeutic vaccines to prophylactic approaches (Review). J Intern Med 2012; 272: 144–157.

Immunoglobulin E‐mediated allergies affect more than 25% of the population. Allergen exposure induces a variety of symptoms in allergic patients, which include rhinitis, conjunctivitis, asthma, dermatitis, food allergy and life‐threatening systemic anaphylaxis. At present, allergen‐specific immunotherapy (SIT), which is based on the administration of the disease‐causing allergens, is the only disease‐modifying treatment for allergy. Current therapeutic allergy vaccines are still prepared from relatively poorly defined allergen extracts. However, with the availability of the structures of the most common allergen molecules, it has become possible to produce well‐defined recombinant and synthetic allergy vaccines that allow specific targeting of the mechanisms of allergic disease. Here we provide a summary of the development and mechanisms of SIT, and then review new forms of therapeutic vaccines that are based on recombinant and synthetic molecules. Finally, we discuss possible allergen‐specific strategies for prevention of allergic disease.
Soluble urokinase‐type plasminogen activator receptor in patients with suspected infection in the emergency room: a prospective cohort study
Authors: Uusitalo‐Seppälä R. , Huttunen R. , Tarkka M. , Aittoniemi J. , Koskinen P. , Leino A. , Vahlberg T. , Rintala E. M.
Published: April 2013

Objectives

The soluble form of urokinase‐type plasminogen activator (suPAR) was evaluated as an early prognostic marker of sepsis in patients with suspected infection.

Design

A single‐centre prospective cohort study.

Methods

The cohort comprised 539 patients in the emergency department with suspected infection: 59 without systemic inflammatory response syndrome (SIRS) and without bacterial infection (group 1), 68 with bacterial infection and withoutSIRS(group 2), 54 withSIRSand without bacterial infection (group 3), 309 with sepsis (SIRSand bacterial infection) and without organ failure (group 4) and 49 with severe sepsis (SIRS, bacterial infection and organ failure) (group 5). suPARwas measured on admission using a commercial solid‐phase enzyme‐linked immunosorbent assay.

Results

The median soluble form of the receptor (suPAR) concentrations in groups 1–5 were 4.7, 5.0, 4.4, 4.8 and 7.9 ng mL−1, respectively (P < 0.001). The levels were significantly higher in nonsurvivors compared with survivors (8.3 vs. 4.9 ng mL−1,P < 0.001) and in patients with severe sepsis (group 5) compared with those in the other groups (7.9 vs. 4.8 ng mL−1,P < 0.001). Area under the receiver operating characteristics curve (AUCROC) for the prediction of case fatality was 0.79 (95% confidence interval [CI]: 0.72–0.86,P < 0.0001) and 0.75 for severe sepsis (95%CI: 0.68–0.81,P < 0.0001). At a cut‐off level of 6.4 ng mL−1, suPARhad 76% sensitivity and 69% specificity for fatal disease; at a cut‐off level of 6.6 ng mL−1, the sensitivity and specificity for severe sepsis were 67% and 72%, respectively. In multivariate models, high suPARremained an independent predictor of case fatality and severe sepsis after adjusting for potential confounders.

Conclusions

A high suPARlevel predicts case fatality and severe sepsis in patients with suspected infection.
Vitamin B6 status and interferon‐γ‐mediated immune activation in primary hyperparathyroidism
Authors: Christensen M. H. E. , Pedersen E. K. R. , Nordbø Y. , Varhaug J. E. , Midttun Ø. , Ueland P. M. , Nygård O. K. , Mellgren G. , Lien E. A.
Published: April 2013

Objectives

Primary hyperparathyroidism (PHPT) has been associated with low‐grade inflammation and elevated risk of cardiovascular disease (CVD). In inflammatory conditions, interferon‐γ (IFN‐γ) activity is enhanced and a decreased circulating concentration of vitamin B6 is often observed. Such changes in IFN‐γ activity or vitamin B6 levels have been associated with increased incidence of CVD. The aim of the study was to investigate systemic markers of IFN‐γ‐mediated immune activation, such as neopterin, the kynurenine‐to‐tryptophan ratio (KTR) and kynurenine pathway metabolites, as well as B6 vitamers in patients with PHPT.

Design/subjects

A total of 57 patients with PHPT and a control group of 20 healthy blood donors were included in this study. PHPT patients who responded positively to parathyroidectomy were followed for 6 months. Forty‐three patients participated in the longitudinal study in which blood samples were taken at inclusion and 1, 3 and 6 months after surgery.

Results

Plasma concentrations of the B6 vitamers pyridoxal 5′‐phosphate (PLP) (P = 0.007) and pyridoxal (P = 0.013) were significantly lower in the patient group compared to healthy control subjects. An increase in the KTR indicated that the kynurenine pathway of tryptophan metabolism was altered in PHPT patients (P = 0.015). During the initial 6 months after surgery, levels of PLP (P < 0.001) and anthranilic acid (P < 0.001) increased significantly, whereas neopterin decreased (P = 0.018).

Conclusions

The results of this study demonstrate altered levels of vitamin B6 and the KTR in PHPT patients, both of which may reflect cellular immune activation. These abnormalities should be considered in relation to the increased risk of CVD previously observed in patients with PHPT.
Deaths Among Children, Adolescents, and Young Adults with Down Syndrome
Authors: Miodrag, Nancy , Silverberg, Sophie E. , Urbano Richard C. , Hodapp Robert M.
Published: April 2013

Background

Although life expectancies in Down syndrome (DS) have doubled over the past 3–4 decades, there continue to be many early deaths. Yet, most research focuses on infant mortality or later adult deaths.

Materials and Methods

In this US study, hospital discharge and death records from the state of Tennessee were linked to examine 2046 hospitalized individuals with DS (85 died) in three age groups: children (1–9), adolescents (10–19) and young adults (20–29).

Results

Most deaths occurred to young adults, while children had the most hospitalizations. Leading causes of death were cardiovascular and pulmonary conditions, and patients who died had longer hospital stays. Proportions of female deaths rose in young adulthood, and disproportionately more African Americans died at each age period.

Conclusion

Mortality is high among young adults with DS. Special vigilance is needed for individuals with DS who are female, African American and in their 20s.
Nanoscale characterization of gold nanoparticles created by in situ reduction at a polymeric surface
Authors: DUTTA A. , CLUKAY C.J. , GRABILL C.N. , FREPPON D.J. , BHATTACHARYA A. , KUEBLER S.M. , HEINRICH H.
Published: April 2013

Transmission Electron Microscopy is used as a quantitative method to measure the shapes, sizes and volumes of gold nanoparticles created at a polymeric surface by three different in situ synthesis methods. The atomic number contrast (Z‐contrast) imaging technique reveals nanoparticles which are formed on the surface of the polymer. However, with certain reducing agents, the gold nanoparticles are additionally found up to 20 nm below the polymer surface. In addition, plan‐view high‐angle annular dark‐field scanning transmission electron microscopy images were statistically analyzed on one sample to measure the volume, height and effective diameter of the gold nanoparticles and their size distributions. Depth analysis from high‐angle annular dark‐field scanning transmission electron microscopy micrographs also gives information on the dominant shape of the nanoparticles.
How our gut microbes influence our behaviour
Authors: Louis Petra , Flint Harry J
Published: April 2013

It is well established that gut bacteria help to maintain a healthy intestine by providing nutrients and guarding against pathogens. Recent evidence however suggests that their actions reach beyond the gut, as they appear to influence various aspects of host physiology, ranging from the regulation of food intake to behaviour and mood. Bacteria and their metabolites can interact with the host via routes involving the immune, nervous and endocrine system.
WHAT'S TO KNOW ABOUT THE CREDIBILITY OF EMPIRICAL ECONOMICS?
Authors: Ioannidis John , Doucouliagos Chris
Published: April 2013

The scientific credibility of economics is itself a scientific question that can be addressed with both theoretical speculations and empirical data. In this review, we examine the major parameters that are expected to affect the credibility of empirical economics: sample size, magnitude of pursued effects, number and pre‐selection of tested relationships, flexibility and lack of standardization in designs, definitions, outcomes and analyses, financial and other interests and prejudices, and the multiplicity and fragmentation of efforts. We summarize and discuss the empirical evidence on the lack of a robust reproducibility culture in economics and business research, the prevalence of potential publication and other selective reporting biases, and other failures and biases in the market of scientific information. Overall, the credibility of the economics literature is likely to be modest or even low.
Private and Public Merger Waves
Authors: MAKSIMOVIC VOJISLAV , PHILLIPS GORDON , YANG LIU
Published: April 2013

We document that public firms participate more than private firms as buyers and sellers of assets in merger waves and their participation is affected more by credit spreads and aggregate market valuation. Public firm acquisitions realize higher gains in productivity, particularly for on‐the‐wave acquisitions and when the acquirer's stock is liquid and highly valued. Our results are not driven solely by public firms' better access to capital. Using productivity data from early in the firm's life, we find that better private firms subsequently select to become public. Initial size and productivity predict asset purchases and sales 10 and more years later.
High‐sensitivity cardiac troponin T for detection of subtle abnormalities of cardiac phenotype in a general population of elderly individuals
Authors: Masson S. , Latini R. , Mureddu G. F. , Agabiti N. , Miceli M. , Cesaroni G. , Forastiere F. , Wienhues‐Thelen U.‐H. , Block D. , Zaugg C. , Vago T. , Boccanelli A. ,   on behalf of the investigators of the PREDICTOR study
Published: April 2013

Objective

To investigate the association between circulating cardiac biomarkers and minor abnormalities in cardiac phenotype [left ventricular (LV) mass and midwall fractional shortening (MFS)] in elderly individuals in a general population sample.

Design and setting

We examined the relationship between plasma concentrations of high‐sensitivity cardiac troponin T (hs‐cTnT) or N‐terminal probrain natriuretic peptide (NT‐proBNP) and elevated LV mass (LV mass/body surface area >95 g m−2 for women and 115 g m−2 for men), reduced MFS (<15%) or isolated LV diastolic dysfunction in 1973 elderly subjects (mean age 73 ± 5 years, range 65–84) resident in the Lazio region of Italy and enrolled in the PREDICTOR study.

Results

Overall, 24.8% of subjects had elevated LV mass, and 30.4% had reduced MFS. Median [quartile 1–3] plasma concentrations of hs‐cTnT and NT‐proBNP were higher in individuals with elevated than those with normal LV mass: 6.6 [3.5–11.6] and 147 [64–296] ng L−1 vs. 4.6 [3.0–8.1] and 79 [41–151] ng L−1 respectively (P < 0.001). There was a graded increase in median hs‐cTnT concentrations across clinical categories of LV hypertrophy: 4.6 [3.0–8.1], 5.8 [3.1–10.2], 7.6 [3.8–13.7] and 8.4 [3.8–17.6] ng L−1 for subjects with normal LV mass and mild, moderate or severe LV hypertrophy respectively (P < 0.0001); hs‐cTnT also increased with increasing quartiles of MFS or grades of isolated LV diastolic dysfunction.

Conclusions

Within an extremely low range of concentrations, increased hs‐cTnT amongst community‐dwelling elderly subjects is associated with subtle alterations in cardiac phenotype, suggesting that minor injury to cardiac myocytes and subsequent release of troponin reflect subclinical pathophysiological LV deterioration in this population.
Syncope in patients with structural heart disease
Authors: Arnar David O.
Published: April 2013

Syncope is a common condition. It is frequently due to a benign cause, but may occasionally be due to a potentially life‐threatening disorder. The presence of structural heart disease in patients with syncope is associated with a poor prognosis and may be a predictor of sudden cardiac death. In patients who present with syncope, the presence of structural heart disease and primary electrophysiological disorders should be considered and further cardiac evaluation performed as indicated by the clinical history, physical examination and electrocardiographic findings.
Role of IL28B and inosine triphosphatase polymorphisms in the treatment of chronic hepatitis C virus genotype 6 infection
Authors: Seto W.‐K. , Tsang O. T.‐Y. , Liu K. , Chan J. M.‐C. , Wong D. K.‐H. , Fung J. , Lai C.‐L. , Yuen M.‐F.
Published: April 2013

IL28B and inosine triphosphatase (ITPA) polymorphisms are able to predict treatment response and degree of ribavirin‐related anaemia, respectively, in the treatment of chronic hepatitis C virus (HCV) infection. However, their roles in the treatment of chronic HCV genotype 6 remain undetermined. Sixty patients who were infected with HCV genotype 6 were commenced on 48 weeks of combination pegylated interferon and ribavirin therapy. Response to therapy, profiles of haemoglobin changes and platelet counts during therapy and their associations with IL28B rs8099917 and ITPA rs1127354 polymorphisms were analysed. The overall sustained virologic response (SVR) rate was 91.7%. 18 patients (30.0%) required a reduction in ribavirin dosage. The distribution of IL28B rs8099917 TT/TG genotypes and ITPA rs1127354 CC/CA genotypes were in Hardy–Weinberg equilibrium. IL28B rs8099917 TT genotype, when compared to TG genotype, was significantly associated with an increased SVR rate (96.2% and 62.5%, respectively) and was the only clinical parameter that predicted SVR (P = 0.014). The same significant association was observed when analysing allelic frequencies (T vs G, P = 0.001). ITPA rs1127354 CA genotype, when compared to CC genotype, was associated with lesser degree of anaemia throughout therapy (P < 0.05 for all time points). ITPA polymorphisms showed no association with changes in platelet count throughout therapy (P > 0.05 for all time points) and was not associated with SVR (P = 0.640). In chronic HCV genotype 6 infection, IL28B polymorphisms were associated with response to therapy. ITPA polymorphisms influenced the degree of anaemia but not thrombocytopenia during therapy.
Bounded ranges of variation as a framework for future conservation and fire management
Authors: Moritz Max A. , Hurteau Matthew D. , Suding Katharine N. , D'Antonio Carla M.
Published: April 2013

Alterations in natural fire patterns have negatively affected fire‐prone ecosystems in many ways. The historical range of variability (HRV) concept evolved as a management target for natural vegetation composition and fire regimes in fire‐prone ecosystems. HRV‐based management inherently assumes that ecosystem resilience is reflected in observed ranges of past vegetation and fire dynamics, typically without knowledge of where thresholds exist beyond these dynamics. Given uncertainty in future conditions, some have argued that HRV may not adequately reflect ecosystem resilience to future fire activity. We suggest a refinement that includes concepts from the thresholds of potential concern (TPC) framework, which emphasizes tipping points at the extremes of ecosystem dynamics and other socially unacceptable outcomes. We propose bounded ranges of variation (BRV), an approach focused on building resilience by using historical information, but also by identifying socio‐ecological thresholds to avoid and associated management action triggers. Here, we examine nonnative species and carbon sequestration as examples of how the BRV framework could be used in the context of conservation and fire management.
QUANTITATIVE AND QUALITATIVE COMPUTED TOMOGRAPHIC CHARACTERISTICS OF BRONCHIECTASIS IN 12 DOGS
Authors: Cannon Matthew S. , Johnson Lynelle R. , Pesavento Patricia A. , Kass Philip H. , Wisner Erik R.
Published: April 2013

Bronchiectasis is an irreversible dilatation of the bronchi resulting from chronic airway inflammation. In people, computed tomography (CT) has been described as the noninvasive gold standard for diagnosing bronchiectasis. In dogs, normal CT bronchoarterial ratios have been described as <2.0. The purpose of this retrospective study was to describe quantitative and qualitative CT characteristics of bronchiectasis in a cohort of dogs with confirmed disease. Inclusion criteria for the study were thoracic radiography, thoracic CT, and a diagnosis of bronchiectasis based on bronchoscopy and/or histopathology. For each included dog, a single observer measured CT bronchoarterial ratios at 6 lobar locations. Qualitative thoracic radiography and CT characteristics were recorded by consensus opinion of two board‐certified veterinary radiologists. Twelve dogs met inclusion criteria. The mean bronchoarterial ratio from 28 bronchiectatic lung lobes was 2.71 ± 0.80 (range 1.4 to 4.33), and 23/28 measurements were >2.0. Averaged bronchoarterial ratios from bronchiectatic lung lobes were significantly larger (P < 0.01) than averaged ratios from nonbronchiectatic lung lobes. Qualitative CT characteristics of bronchiectasis included lack of peripheral airway tapering (12/12), lobar consolidation (11/12), bronchial wall thickening (7/12), and bronchial lumen occlusion (4/12). Radiographs detected lack of airway tapering in 7/12 dogs. In conclusion, the most common CT characteristics of bronchiectasis were dilatation, a lack of peripheral airway tapering, and lobar consolidation. Lack of peripheral airway tapering was not visible in thoracic radiographs for some dogs. For some affected dogs, bronchoarterial ratios were less than published normal values.
Genome Sequence of a Novel Reassortant H3N2 Avian Influenza Virus from Domestic Mallard Ducks in Eastern China
Authors: Li Qunhui , Zhao Qingqing , Gu Min , Zhu Jie , Gu Xiaobing , Zhao Guo , Liu Qingtao , Wang Xiaoquan , Liu Xiaowen , Liu Xiufan
Published: April 2013

The H3 subtype avian influenza virus (AIV) can provide genes for human influenza virus through gene reassortment, which raises great concerns in terms of its potentia threat to human health. Here, we report the complete genome sequence of a novel H3N2 AIV isolated from domestic ducks in the Jiangsu province of eastern China in 2004, which is a natural recombinant virus whose genes are derived from H3N8, H5N1, H5N2, H11N2, H4N6, and H1N1 AIVs. This genome will help to understand the epidemiology and molecular characteristics of H3N2 influenza virus in eastern China.
EXACT SOLUTIONS OF A FLAT FULL CAUSAL BULK VISCOUS FRW COSMOLOGICAL MODEL THROUGH FACTORIZATION
Authors: CORNEJO-PÉREZ O. , BELINCHÓN J. A.
Published: April 2013

We study the classical flat full causal bulk viscous Friedmann–Robertson–Walker (FRW) cosmological model through the factorization method. The method shows that there exists a relationship between the viscosity parameter s and the parameter γ entering the equations of state of the model. Also, the factorization method allows to find some new exact parametric solutions for different values of the viscous parameter s. Special attention is given to the well-known case s = 1/2, for which the cosmological model admits scaling symmetries. Furthermore, some exact parametric solutions for s = 1/2 are obtained through the Lie group method.
NOVEL APPROACHES FOR THE TRANSFORMATION OF FUZZY MEMBERSHIP FUNCTION INTO BASIC PROBABILITY ASSIGNMENT BASED ON UNCERTAINTY OPTIMIZATION
Authors: HAN DEQIANG , HAN CHONGZHAO , DENG YONG
Published: April 2013

With the development of uncertainty reasoning and information fusion, there have emerged several theories including fuzzy set theory, Dempster-Shafer evidence theory, probability theory and rough set theory, etc., for representing and dealing with the uncertain information. When the fusion of the uncertain information originated from different sources is needed, how to construct a general framework for different theories of uncertainty or how to establish the connection between different theoretical frameworks has become a crucial problem. Particularly, to combine two kinds of information represented respectively by the BPA and the FMF, this paper proposes two transformations of an FMF into a BPA by solving a constrained maximization or minimization optimization problem. The objective function is the uncertainty degree of the body of evidence (BOE) and the corresponding constraints are established based on the given FMF. In fact the transformation of an FMF into a BPA is the transformation of fuzzy sets into random sets, which is currently accepted as a unified framework for several theories of uncertainty. Our proposed approaches have no predefinition of focal elements and they can be used as the general transformations of fuzzy sets into random sets. Some examples and analyses are provided to illustrate and justify the rationality and effectiveness of the proposed approaches.
Synthesis of C60-Antenna Nanostructure-Based Fullerosome Vesicles for Ultrafast Nonlinear Photonic Applications
Authors: Wang Min , Canteenwala Taizoon , Nalla Venkatram , Tan Loon-Seng , Ji Wei , Chiang Long
Published: April 2013

We designed and synthesized amphiphilic oligo(ethylene glycolated) C60-(light-harvesting fluorene antenna) nanostructures C60(>DPAF-EG12C1) by incorporating a donor–acceptor antenna

component of C60–DPAF with highly hydrophilic oligo(ethylene glycol) (EGn) side-chains to increase the amphiphilicity of the molecule. The chain length of EGn arms was selected to match with the overall molecular radius and to achieve a balance between the hydrophobicity and hydrophilicity of resulting molecules Molecular self-assembly of C60(>DPAF-EG12C1) forming bilayered fullerosome nanovesicles led to the observation of ultrafast femtosecond nonlinear optical (NLO) absorption characteristics. Two-photon absorption phenomena were found to be the dominating photophysical events showing a large molar concentration-insensitive 2PA cross-section value equivalent to 8500 GM in a form of vesicles, on average, at the estimated effective nanovesicle concentration as low as 5.5 × 10−8 MV (molecular molar concentration of 5.0 × 10−4 M) in H2O.
Planting of Carbon Nanotubes on Nano-Textured and Micro-Structured Silicon Substrates
Authors: Taak Serveh , Rajabali Shima , Darbari Sara , Poudineh Mahla , Sanaee Zeinab , Mohajerzadeh Shams
Published: April 2013

In this work we have developed a novel method to place previously grown CNTs on desired nano-textured and micro-machined substrates. Once the desired structures are created on a given substrate (silicon here) the already grown nanotubes are planted on the created holes either by a mechanical rubbing or solution dispersing approach. The main idea of this work is to plant partially vertical nanostructures on textured substrates.
Photoelectrochemical Hydrogen Generation: Effect of Photocatalyst Dispersion
Authors: Bruce David , Wilkinson David P.
Published: April 2013

Distributed 3-D films were compared with equivalent planar 2-D films of composite conductive polymer-titania for photocathode use in PEM based hydrogen generation devices. The films were also analyzed for changes in electrochemical performance when placed directly against the N117 membrane or when faced away from the triple phase interface. Electrochemical results indicate that due to resistive losses the films operated most efficiently when placed directly against the membrane. Solar performance of the device benefitted from a 3-D distributed structure, extending the performance improvement from irradiation to higher current densities.
Stress and Microstructure in Electrodeposited Copper Nanofilms and the Effect of Chloride and Polyethylene Glycol (PEG)
Authors: O'Grady Michael , Lenihan Catherine , Buckley Denis Noel
Published: April 2013

Both atomic force microscopy (AFM) imaging and stress measurements were carried out in situ during potentiostatic electrodeposition of copper on gold in 0.05 mol dm-3 CuSO4 in 0.1 mol dm-3 H2SO4 with and without chloride ion (Cl-) and polyethylene glycol (PEG) additives. Our in-situ stress measurement technique allowed us to develop an accurate and reliable method of determining local stress in newly deposited copper films. Stress increases in the tensile direction with thickness and eventually reaches a plateau value. We attribute the initial increase in tension to the coalescence of previously isolated islands and the associated formation of grain boundaries. Stress was observed to be higher at higher overpotentials. The addition of 3 ppm Cl- reduced stress significantly but had very little effect on deposition rate. The addition of 5 ppm PEG with the Cl- enhanced stress reduction.
In Situ Measurement of Stress Evolution and Ion Dynamics in Conducting Polymers
Authors: Sen Sujat , Kim Sungyeol , Jin Shenghua , Palmore Lia R. , Jadhav Nitin , Chason Eric , Palmore G. Tayhas R.
Published: April 2013

Voltage-induced ion motion in conducting polymers (CPs) and the associated stress that evolves play an important role in determining the performance and lifetime of devices fabricated from these materials. In this work, a multi-beam optical stress sensor (MOSS) coupled with potential cycling was used to study films of polypyrrole (pPy) doped with indigo carmine (IC), a redox-active anion. We observe different magnitudes of stress in these films in different electrolytes (NaCl vs. HCl) due to the pH-dependent redox activity of IC. These results indicate that the redox activity of a dopant introduces an additional mode by which stress develops in films of CPs, which in turn could impact device performance.
Effect of Surface Hydrophilicity on the Formation of Nafion Thin Films Inside PEMFC Catalyst Layers: A Computational Study
Authors: Damasceno Borges Daiane , Malek Koursosh , Mossa Stefano , Gebel Gerard , Franco Alejandro A.
Published: April 2013

Structure of Nafion inside Polymer Electrolyte Membrane Fuel Cells (PEMFC) catalyst layers is suspected to have a significant impact on the electrochemical activity and transport phenomena that determine the overall cell performances. In those regions, Nafion can be found as an ultra-thin film, coating the catalyst and the catalyst support surfaces. The impact of the hydrophilic character of these surfaces on the structural formation of the films has not been explored in details yet. Here, we report about our Molecular Dynamic computer simulations studies of the formation of Nafion thin films in contact with unstructured continuous surfaces, characterized by their global wetting properties only. We investigate changes of morphology and nanostructure of the perfluorosulfonic acid polymer as a result of water and polymer-surface affinities. Charge and water distributions are also analyzed. Possible impact of Nafion thin film self-assembly on the actual activity properties of realistic catalysts layers is shortly discussed.
Redox Switching and Oxygen Evolution at Hydrous Nickel Oxide Films in Aqueous Alkaline Solution
Authors: O'Brien Maria , Russell Lisa , Godwin Ian , Doyle Richard L. , Lyons Michael E.G.
Published: April 2013

The redox switching reaction and the oxygen evolution reaction at multi-cycled nickel oxy-hydroxide films in aqueous alkaline solution are discussed. The hydrous oxide is considered as a porous assembly of interlinked octahedrally coordinated anionic metal oxyhydroxide surfaquo complexes which form an open network structure. The latter contains considerable quantities of water molecules which facilitate hydroxide ion discharge at the metal site during active oxygen evolution. The dynamics of redox switching has been quantified in terms of a diffusive frequency using the Laviron-Aoki diffusion model. Steady state Tafel plot analysis has been used to elucidate the kinetics and mechanism of oxygen evolution with slopes of ca. 60 mVdec-1 and ca. 120 mVdec-1 at low and high overpotentials respectively, whereas the reaction order with respect to hydroxide ion activity remains invariant at ca. 1.0 as the potential is increased. These observations are rationalized in terms of a kinetic scheme involving surfaquo groups.