bluuebunny/crossref_metadata_2025 huggingface dataset:
Innovative Procedures to Assess Seismic Behaviour of Existing Structures by Means of Non Linear Static Analysis: Polar Spectrum and Capacity Domains
Authors: Petti Luigi , Marino Ivana
Published: July 2012

In the last few years, the need to evaluate the seismic performances of buildings on sustaining strong motion has encouraged the development of simplified non-linear static analyses. Several procedures are available today to assess the behavior of plane-frame systems or plan-regular framed buildings suitable for engineering purposes. Less accurate procedures are instead available for irregular structures. This study introduces new tools to assess the seismic performance of irregular structures by using capacity domains and polar spectra. In particular, the capacity domains, plotted in terms of base shear and node control displacements and obtained by means of static non-linear analyses, lead to the evaluation of the direction of least seismic capacity of the investigated structure. The polar spectrum, instead, leads to taking into account the directivity and site effects of seismic events. In particular, the polar spectrum represents the spectral seismic response evaluated for different in-plan directions.
Automated Quantitative Analysis of p53, Cyclin D1, Ki67 and pERK Expression in Breast Carcinoma Does Not Differ from Expert Pathologist Scoring and Correlates with Clinico-Pathological Characteristics
Authors: Cass Jamaica D. , Varma Sonal , Day Andrew G. , Sangrar Waheed , Rajput Ashish B. , Raptis Leda H. , Squire Jeremy , Madarnas Yolanda , SenGupta Sandip K. , Elliott Bruce E.
Published: July 2012

There is critical need for improved biomarker assessment platforms which integrate traditional pathological parameters (TNM stage, grade and ER/PR/HER2 status) with molecular profiling, to better define prognostic subgroups or systemic treatment response. One roadblock is the lack of semi-quantitative methods which reliably measure biomarker expression. Our study assesses reliability of automated immunohistochemistry (IHC) scoring compared to manual scoring of five selected biomarkers in a tissue microarray (TMA) of 63 human breast cancer cases, and correlates these markers with clinico-pathological data. TMA slides were scanned into an Ariol Imaging System, and histologic (H) scores (% positive tumor area x staining intensity 0–3) were calculated using trained algorithms. H scores for all five biomarkers concurred with pathologists’ scores, based on Pearson correlation coefficients (0.80–0.90) for continuous data and Kappa statistics (0.55–0.92) for positive vs. negative stain. Using continuous data, significant association of pERK expression with absence of LVI (p = 0.005) and lymph node negativity (p = 0.002) was observed. p53 over-expression, characteristic of dysfunctional p53 in cancer, and Ki67 were associated with high grade (p = 0.032 and 0.0007, respectively). Cyclin D1 correlated inversely with ER/PR/HER2-ve (triple negative) tumors (p = 0.0002). Thus automated quantitation of immunostaining concurs with pathologists’ scoring, and provides meaningful associations with clinico-pathological data.
REGEN: Ancestral Genome Reconstruction for Bacteria
Authors: Yang Kuan , Heath Lenwood S. , Setubal João C.
Published: July 2012

Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.
Antioxidant Property Enhancement of Sweet Potato Flour under Simulated Gastrointestinal pH
Authors: Chan Kim Wei , Khong Nicholas M. H. , Iqbal Shahid , Umar Imam Mustapha , Ismail Maznah
Published: July 2012

Sweet potato is known to be rich in healthful antioxidants, but the stability of its antioxidant properties under gastrointestinal pH is very much unknown. Hence, this study aimed to evaluate the changes in antioxidant properties (total contents of phenolics and flavonoids as well as antioxidant activity) of sweet potato flour (SPF) under simulated gastrointestinal pH conditions. It was found that the yield of SPF crude phenolic extract increased from 0.29 to 3.22 g/100 g SPF upon subjection to gastrointestinal pH conditions (p < 0.05). Also elevated significantly were the total phenolic content (TPC), total flavonoid content (TFC) and antioxidant activity of SPF (p < 0.05). In summary, the antioxidant properties of SPF were enhanced under gastrointestinal pH conditions, suggesting that SPF might possess a considerable amount of bound phenolic and other antioxidative compounds. The antioxidant properties of SPF are largely influenced by pH and thus might be enhanced during the in vivo digestive process.
Hepatoprotective Effects of Berberis vulgaris L. Extract/β Cyclodextrin on Carbon Tetrachloride–Induced Acute Toxicity in Mice
Authors: Hermenean Anca , Popescu Cristina , Ardelean Aurel , Stan Miruna , Hadaruga Nicoleta , Mihali Ciprian-Valentin , Costache Marieta , Dinischiotu Anca
Published: July 2012

The present study investigated the capacity of formulated Berberis vulgaris extract/β-cyclodextrin to protect liver against CCl4-induced hepatotoxicity in mice. Formulated and non-formulated extracts were given orally (50 mg/kg/day) to mice for 7 days and were then intra-peritoneally injected with 1.0 mL/kg CCl4 on the 8th day. After 24 h of CCl4 administration, an increase in the levels of apartate-amino-transferase (AST), alanine-amino-transferase (ALT) and malondialdehyde (MDA) was found and a significant decrease in superoxide-dismutase (SOD), catalase (CAT), glutathione (GSH) and glutathione-peroxidase (GPx) levels could be detected. This was accompanied by extended centrilobular necrosis, steatosis, fibrosis and an altered ultrastructure of hepatocytes. Pre-treatment with formulated or non-formulated extract suppressed the increase in ALT, AST and MDA levels and restored the level of antioxidant enzymes at normal values. Histopathological and electron-microscopic examination showed milder liver damage in both pre-treated groups and the protective effect was more pronounced after the formulated extract was administered. Internucleosomal DNA fragmentation induced by CCl4 was reduced in the group which received non-formulated extract and absent in the group which received formulated extract. Taken together, our results suggest that Berberis vulgaris/β-cyclodextrin treatment prevents hepatic injury induced by CCl4 and can be considered for further nutraceutical studies.
2-Methoxy-5-{4-oxo-2-[(E)-2-(4-sulfamoylphenyl)ethenyl-3,4-dihydroquinazolin-3-yl]benzene-1-sulfonamide
Authors: Hayun  , Hanafi Muhammad , Yanuar Arry , Hudiyono Sumi
Published: July 2012

The title compound, 2-methoxy-5-{4-oxo-2-[(E)-2-(4-sulfamoylphenyl) ethenyl-3, 4-dihydroquinazolin-3-yl] benzene-1-sulfonamide 2 has been synthesized by the reaction of 3-(4-methoxyphenyl)-2-styryl-4(3H)-quinazolinone 1 with an excess of chlorosulfonic acid, followed by amidation of the sulfonyl chloride product with ammonia gas. The structure of the synthesized compound was confirmed on the basis of IR, 1H-NMR, 13C-NMR and mass spectral data.
Molecularly Imprinted Membranes
Authors: Trotta Francesco , Biasizzo Miriam , Caldera Fabrizio
Published: July 2012

Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films) that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed.
Metabolism of Tanshinone IIA, Cryptotanshinone and Tanshinone I from Radix Salvia Miltiorrhiza in Zebrafish
Authors: Wei Yingjie , Li Ping , Wang Changmei , Peng Yunru , Shu Luan , Jia Xiaobin , Ma Wenquan , Wang Bing
Published: July 2012

The study aimed to investigate the potential of zebrafish in imitating mammal phase I metabolism of natural compounds. Three diterpenoid quinones from Radix Salvia miltiorrhiza, namely tanshinone IIA (TIIA), cryptotanshinone (Cry) and tanshinone I (TI) were selected as model compounds, and their metabolites mediated by zebrafish were characterized using a high-performance liquid chromatography coupled ion-trap mass spectrometry (HPLC/IT-MSn) method with electrospray ionization in positive mode. The separation was performed with a Zorbax C-18 column using a binary gradient elution of 0.05% formic acid acetonitrile/0.05% formic acid water. According to the MS spectra and after comparison with reference standards and literature reports, hydroxylation, dehydrogenation or D-ring hydrolysis metabolites of TIIA and Cry but not of TI were characterized, which coincided with those reported using regular in vivo or in vitro metabolic analysis methods, thus verifying that zebrafish can successfully imitate mammalian phase I metabolism which instills further confidence in using zebrafish as a novel and prospective metabolism model.
Analysis of the Scaling Effects in the Area-Averaged Fraction of Vegetation Cover Retrieved Using an NDVI-Isoline-Based Linear Mixture Model
Authors: Obata Kenta , Miura Tomoaki , Yoshioka Hiroki
Published: July 2012

The spectral unmixing of a linear mixture model (LMM) with Normalized Difference Vegetation Index (NDVI) constraints was performed to estimate the fraction of vegetation cover (FVC) over the earth’s surface in an effort to facilitate long-term surface vegetation monitoring using a set of environmental satellites. Although the integrated use of multiple sensors improves the spatial and temporal quality of the data sets, area-averaged FVC values obtained using an LMM-based algorithm suffer from systematic biases caused by differences in the spatial resolutions of the sensors, known as scaling effects. The objective of this study is to investigate the scaling effects in area-averaged FVC values using analytical approaches by focusing on the monotonic behavior of the scaling effects as a function of the spatial resolution. The analysis was conducted based on a resolution transformation model introduced recently by the authors in the accompanying paper (Obata et al., 2012). The maximum value of the scaling effects present in FVC values was derived analytically and validated numerically. A series of derivations identified the error bounds (inherent uncertainties) of the averaged FVC values caused by the scaling effect. The results indicate a fundamental difference between the NDVI and the retrieved FVC from NDVI, which should be noted for accuracy improvement of long-term observation datasets.
A Formula to Estimate the Optimal Dosage of Ribavirin for the Treatment of Chronic Hepatitis C: Influence of Itpa Polymorphisms
Authors: Krishnan Sheeja M , Dixit Narendra M
Published: July 2012

Background

Greater cumulative exposure to ribavirin increases response to interferon–ribavirin combination therapy for hepatitis C but also induces more severe anaemia. Polymorphisms in the ITPA gene protect against ribavirin-induced anaemia. The maximum dosage of ribavirin that can be tolerated by patients with different ITPA polymorphisms remains unknown.

Methods

We developed a mathematical model of haemoglobin (Hb) decline in patients undergoing combination therapy. Using it to analyse published patient data, we estimated the average erythrocyte lifespan in patients with different ITPA polymorphisms. Coupled with a previous population pharmacokinetic study, we derived a formula for predicting the optimal ribavirin dosage, Dopt, above which anaemia becomes intolerable (Hb<10 g/dl).

Results

Our model provided good fits to patient data of ribavirin accumulation in erythrocytes and the ensuing Hb decline during therapy. With the current treatment protocol, the average erythrocyte lifespan was approximately 36 days in patients with wild-type ITPA activity, and approximately 43 days and 55 days, respectively, in patients with mild and moderate ITPA deficiency. Our model yielded a facile formula for estimating Dopt given a patient's weight, creatinine clearance, pretreatment Hb and ITPA polymorphism. Patients with moderate ITPA deficiency are predicted to tolerate twice the ribavirin dosage as patients with wild-type ITPA.

Conclusions

Our formula for Dopt presents an avenue for personalizing ribavirin dosage. By keeping anaemia tolerable, the predicted optimal dosage may improve adherence, reduce the need for drug monitoring, and increase response rates. Response rates may be increased further by the higher dosages recommended for patients with ITPA deficiency.
Immune Suppression and Resistance Mediated by Constitutive Activation of Wnt/β-Catenin Signaling in Human Melanoma Cells
Authors: Yaguchi Tomonori , Goto Yasufumi , Kido Kenji , Mochimaru Hiroshi , Sakurai Toshiharu , Tsukamoto Nobuo , Kudo-Saito Chie , Fujita Tomonobu , Sumimoto Hidetoshi , Kawakami Yutaka
Published: July 2012

Cancer-induced immunosuppression is a major problem reducing antitumor effects of immunotherapies, but its molecular mechanism has not been well understood. We evaluated immunosuppressive roles of activated Wnt/β-catenin pathways in human melanoma for dendritic cells (DCs) and CTLs. IL-10 expression was associated with β-catenin accumulation in human melanoma cell lines and tissues and was induced by direct β-catenin/TCF binding to the IL-10 promoter. Culture supernatants from β-catenin–accumulated melanoma have activities to impair DC maturation and to induce possible regulatory DCs. Those immunosuppressive culture supernatant activities were reduced by knocking down β-catenin in melanoma cells, partly owing to downregulation of IL-10. Murine splenic and tumor-infiltrating DCs obtained from nude mice implanted with human mutant β-catenin–overexpressed melanoma cells had less ability to activate T cells than did DCs from mice with control melanoma cells, showing in vivo suppression of DCs by activated Wnt/β-catenin signaling in human melanoma. This in vivo DC suppression was restored by the administration of a β-catenin inhibitor, PKF115-584. β-catenin–overexpressed melanoma inhibited IFN-γ production by melanoma-specific CTLs in an IL-10–independent manner and is more resistant to CTL lysis in vitro and in vivo. These results indicate that Wnt/β-catenin pathways in human melanoma may be involved in immunosuppression and immunoresistance in both induction and effector phases of antitumor immunoresponses partly through IL-10 production, and they may be attractive targets for restoring immunocompetence in patients with Wnt/β-catenin–activated melanoma.
Neutrophil Expression of Fas Ligand and Perforin Directs Effector CD8 T Cell Infiltration into Antigen-Challenged Skin
Authors: Kish Danielle D. , Gorbachev Anton V. , Parameswaran Neetha , Gupta Neetu , Fairchild Robert L.
Published: July 2012

Contact hypersensitivity (CHS) is a T cell response to hapten skin challenge of sensitized individuals proposed to be mediated by hapten-primed CD8 cytolytic T cells. Effector CD8 T cell recruitment into hapten challenge sites to elicit CHS requires prior CXCL1- and CXCL2-mediated neutrophil infiltration into the site. We investigated whether neutrophil activities directing hapten-primed CD8 T cell skin infiltration in response to 2,4-dinitro-1-fluorobenzene (DNFB) required Fas ligand (FasL) and perforin expression. Although DNFB sensitization of gld/perforin−/− mice induced hapten-specific CD8 T cells producing IFN-γ and IL-17, these T cells did not infiltrate the DNFB challenge site to elicit CHS but did infiltrate the challenge site and elicit CHS when transferred to hapten-challenged naive wild-type recipients. Hapten-primed wild-type CD8 T cells, however, did not elicit CHS when transferred to naive gld/perforin−/− recipients. Wild-type bone marrow neutrophils expressed FasL and perforin, and when transferred to sensitized gld/perforin−/− mice, they restored hapten-primed CD8 T cell infiltration into the challenge site and CHS. The FasL/perforin-mediated activity of wild-type neutrophils induced the expression of T cell chemoattractants, CCL1, CCL2, and CCL5, within the hapten-challenged skin. These results indicate FasL/perforin-independent functions of hapten-primed CD8 T cells in CHS and identify new functions for neutrophils in regulating effector CD8 T cell recruitment and immune responses in the skin.
The 3BP2 Adapter Protein Is Required for Chemoattractant-Mediated Neutrophil Activation
Authors: Chen Grace , Dimitriou Ioannis , Milne Laura , Lang Karl S. , Lang Philipp A. , Fine Noah , Ohashi Pamela S. , Kubes Paul , Rottapel Robert
Published: July 2012

3BP2 is a pleckstrin homology and Src homology 2 domain-containing adapter protein mutated in cherubism, a rare autosomal-dominant human bone disorder. Previously, we have demonstrated a functional role for 3BP2 in peripheral B cell development and in peritoneal B1 and splenic marginal zone B cell-mediated Ab responses. In this study, we show that 3BP2 is required for G protein-coupled receptor-mediated neutrophil functions. Neutrophils derived from 3BP2-deficient (Sh3bp2−/−) mice failed to polarize their actin cytoskeleton or migrate in response to a gradient of chemotactic peptide, fMLF. Sh3bp2−/− neutrophils failed to adhere, crawl, and emigrate out of the vasculature in response to fMLF superfusion. 3BP2 is required for optimal activation of Src family kinases, small GTPase Rac2, neutrophil superoxide anion production, and for Listeria monocytogenes bacterial clearance in vivo. The functional defects observed in Sh3bp2−/− neutrophils may partially be explained by the failure to fully activate Vav1 guanine nucleotide exchange factor and properly localize P-Rex1 guanine nucleotide exchange factor at the leading edge of migrating cells. Our results reveal an obligate requirement for the adapter protein 3BP2 in G protein-coupled receptor-mediated neutrophil function.
FDG PET/CT in Detection of Metastatic Involvement of Heart and Treatment Monitoring in Non-Hodgkin′s Lymphoma
Authors: Agrawal Kanhaiyalal , Mittal Bhagwant , Manohar Kuruva , Kashyap Raghava , Bhattacharya Anish , Varma Subhash
Published: July 2012

Cardiac metastasis occurs in up to a quarter of patients with metastatic cancer and is seen most commonly in melanoma and lymphoma. Metastatic involvement of the heart and pericardium may go unrecognized until autopsy. We describe a patient of non-Hodgkin′s lymphoma detected to have involvement of right atrium on F-18 FDG PET/CT and monitoring of response to chemotherapy.
Pneumocephalus after surgical evacuation of chronic subdural hematoma: Is it a serious complication?
Authors: Ihab Zidan
Published: July 2012

Background: Pneumocephalus is commonly encountered after surgical evacuation of chronic subdural hematoma (CSDH). This study was done to study the incidence, clinical presentation, and management of patients who developed pneumocephalus after surgical evacuation of CSDH. Materials and Methods: This prospective study was carried out on consecutive 50 patients who had received surgical treatment for CSDH. All the patients included were followed-up postoperatively with regular clinical and computed tomography (CT) examinations immediately postoperatively, before discharge, and 2 months after surgery. Pneumocephalus was classified into simple and tension, based upon the clinical and radiological criteria. The neurologic grading system of Markwalder et al was used to evaluate the surgical results. Results: The immediate postoperative CT scan showed pneumocephalus in 22 patients (44%). Tension pneumocephalus was found in two patients who did not require any further surgery. There was statistically significant increase in the incidence of pneumocephalus (immediate and postoperative) in the patients aged over 60 years as well as those presenting with a midline shift more than 5 mm in their CT scan. With regard to the 22 cases of pneumocephalus, good postoperative results were found in 16 patients (73%), while bad results were found in 6 patients (27%). No statistically significant difference in the outcome between patients who had pneumocephalus after surgery and those who had not.
Conclusion: Pneumocephalus after surgical evacuation of CSDH is a common finding in the immediate CT scan as well as at time of discharge. Tension pneumocephalus may not require surgical intervention and simple aspiration of air using a syringe may be sufficient.
Smoking Prevalence and the Association between Smoking and Sociodemographic Factors Using the Korea National Health and Nutrition Examination Survey Data, 2008 to 2010
Authors: Kim Sungroul
Published: July 2012

Using data from the Korea National Health and Nutrition Examination Survey collected from 2008 to 2010, smoking prevalence for Korean adults (n = 11,681) by gender and age group and the association between smoking and sociodemographic factors were evaluated.

Smoking prevalence was 42.3% for men and 5.6% for women. Young adult (YA) males, ie, 19 to 24 and 25 to 34 years old, were 2.45 (95% CI: 1.60, 3.73) and 5.05 (95% CI: 3.83, 6.66) times more likely to smoke compared to male adults aged 65 and above (31.6%) after controlling for sociodemographic factors. The association between smoking and marital status was different by gender.

In South Korea, the high smoking prevalence among young adults is a troubling pattern. The high smoking prevalence among widowed or divorced women is also concern.
Authentic leadership and feedback-seeking behaviour: An examination of the cultural context of mediating processes in China
Authors: Qian Jing , Lin Xiaosong , Chen George Zhen-Xiong
Published: July 2012

Despite an increasing number of studies that show a positive relationship between the supportiveness of the feedback source and feedback seeking, little is known about the role that supervisors play in promoting employee feedback-seeking behaviour when they serve as feedback sources. The present article developed a model to fill this void and tested it with data from a sample of 237 supervisor–subordinate dyads. We hypothesized and found that authentic leadership was positively related to feedback-seeking behaviour mediated by both perceived instrumental value and image cost of feedback seeking. The results also demonstrated that employees' individual cultural value of power distance moderated the relationships between authentic leadership and the perceived instrumental value and image cost of feedback seeking.
Work–family interface: Effect of enrichment and conflict on job performance of Korean workers
Authors: Lim Doo Hun , Song Ji Hoon , Choi Myungweon
Published: July 2012

Many studies conducted in Western societies indicated that work–family enrichment (WFE) and conflict influence employees' work performance positively and/or negatively. However, few studies have been conducted in collectivist, rapidly growing societies like Korea. The purpose of this study was to identify the extent to which those work–family interface variables influence the work performance of employees within the Korean organizational context. We performed forward and backward translation procedure to develop the Korean language versions of the WFE scale, work–family conflict (WFC) scale, and other scales assessing life satisfaction and job performance. Data were collected from a sample of 425 workers from various for-profit firms and universities in Korea. For data analysis, basic descriptive analyses, item reliability and construct validity tests, and a two-step structural equation modeling (SEM) approach were employed to identify influential relationships among WFE/WFC, life satisfaction, and job performance. Results indicated that WFE was a significant factor influencing Korean workers' life satisfaction (WLS) and job performance, whereas WFC was not. Implications of the study findings, including the strategies for improving employee well-being within the Korean cultural context, were presented.
The role of legitimacy for the survival of new firms
Authors: Brown Richard S
Published: July 2012

Using a content analysis on a sample of 77 internet companies that went public in the late 1990s, this paper tested the factors surrounding the legitimacy of new firms in a turbulent environment. Support was found for most of the hypotheses as to which factors were legitimating and which had the opposite effect. Legitimating factors included CEO Duality and Alliance inclusion while delegitimating factors included Capital Raising, Acquisitions, Restructuring, Delisting and Geographic Diversification. This paper adds to the theoretical issues surrounding legitimacy as a precursor to reputation. At the same time, this work fills a gap in the literature which currently lacks empirical testing of the notion of legitimacy.
Isoprene emissions in Africa inferred from OMI observations of formaldehyde columns
Authors: Marais E. A. , Jacob D. J. , Kurosu T. P. , Chance K. , Murphy J. G. , Reeves C. , Mills G. , Casadio S. , Millet D. B. , Barkley M. P. , Paulot F. , Mao J.
Published: July 2012

Abstract. We use 2005–2009 satellite observations of formaldehyde (HCHO) columns from the OMI instrument to infer biogenic isoprene emissions at monthly 1 × 1° resolution over the African continent. Our work includes new approaches to remove biomass burning influences using OMI absorbing aerosol optical depth data (to account for transport of fire plumes) and anthropogenic influences using AATSR satellite data for persistent small-flame fires (gas flaring). The resulting biogenic HCHO columns (ΩHCHO) from OMI follow closely the distribution of vegetation patterns in Africa. We infer isoprene emission (EISOP) from the local sensitivity S = ΔΩHCHO / ΔEISOP derived with the GEOS-Chem chemical transport model using two alternate isoprene oxidation mechanisms, and verify the validity of this approach using AMMA aircraft observations over West Africa and a longitudinal transect across central Africa. Displacement error (smearing) is diagnosed by anomalously high values of S and the corresponding data are removed. We find significant sensitivity of S to NOx under low-NOx conditions that we fit to a linear function of tropospheric column NO2. We estimate a 40% error in our inferred isoprene emissions under high-NOx conditions and 40–90% under low-NOx conditions. Our results suggest that isoprene emission from the central African rainforest is much lower than estimated by the state-of-the-science MEGAN inventory.
Transport of short-lived species into the Tropical Tropopause Layer
Authors: Ashfold M. J. , Harris N. R. P. , Atlas E. L. , Manning A. J. , Pyle J. A.
Published: July 2012

Abstract. We use NAME, a trajectory model, to investigate the routes and timescales over which air parcels reach the tropical tropopause layer (TTL). Our aim is to assist the planning of aircraft campaigns focussed on improving knowledge of such transport. We focus on Southeast Asia and the Western Pacific which appears to be a particularly important source of air that enters the TTL. We first study the TTL above Borneo in November 2008, under neutral El Niño/Southern Oscillation (ENSO) conditions. Air parcels (trajectories) arriving in the lower TTL (below ~15 km) are most likely to have travelled from the boundary layer (BL; <1 km) above the West Pacific. Few air parcels found above ~16 km travelled from the BL in the previous 15 days. We then perform similar calculations for moderate El Niño (2006) and La Niña (2007) conditions and find year-to-year variability consistent with the phase of ENSO. Under El Niño conditions fewer air parcels travel from the BL to the TTL above Borneo. During the La Niña year, more air parcels travel from the BL to the mid and upper TTL (above ~15 km) than in the ENSO-neutral year, and again they do so from the BL above the West Pacific. We also find intra-month variability in all years, with day-to-day differences of up to an order of magnitude in the fraction of an idealised short-lived tracer travelling from the BL to the TTL above Borneo. These calculations were performed as a prelude to the SHIVA field campaign, which took place in Borneo during November 2011. So finally, to validate our approach, we consider measurements made in two previous campaigns. The features of vertical profiles of short-lived species observed in the TTL during CR-AVE and TC4 are in broad agreement with calculated vertical profiles of idealised short-lived tracers. It will require large numbers of observations to fully describe the statistical distribution of short-lived species in the TTL. This modelling approach should prove valuable in planning flights for the long-duration aircraft now capable of making such measurements.
Analysis of global methane changes after the 1991 Pinatubo volcanic eruption
Authors: Bândă N. , Krol M. , van Weele M. , van Noije T. , Röckmann T.
Published: July 2012

Abstract. The global methane growth rate showed large variations after the eruption of Mount Pinatubo in June 1991. Both sources and sinks of tropospheric methane were altered following the eruption, by feedback processes between climate and photo-chemistry. Such processes include Ultra Violet (UV) radiative changes due to the presence of volcanic sulfur dioxide (SO2) and sulphate aerosols in the stratosphere, and due to stratospheric ozone depletion. Changes in temperature and water vapour in the following years caused changes in the tropospheric chemistry, as well as in natural emissions. We quantify the effects that these processes had on methane concentrations using a one-dimensional chemistry model representative for the global tropospheric column. To infer the changes in UV radiative fluxes, we couple the chemistry model to a radiative transfer model. We find that the overall effect of the eruption on the methane growth rate is dominated by the effect of stratospheric ozone depletion. However, all the other processes are found to have non-negligible effects, and should therefore be taken into account in order to obtain a good estimate of methane concentrations after the eruption. We find that the overall effect was a small initial increase in the methane growth rate after the eruption, then a decrease by about 8 ppb yr−1 by mid-1993. When changes in anthropogenic emissions are employed according to emission inventories, an additional decrease of about 5 ppb yr−1 in the methane growth rate is obtained between the years 1991 and 1993.
Satellite retrieval of the liquid water fraction in tropical clouds between −20 and −38 °C
Authors: Mitchell D. L. , d'Entremont R. P.
Published: July 2012

Abstract. This study describes a satellite remote sensing method for directly retrieving the liquid water fraction in mixed phase clouds, and appears unique in this respect. The method uses MODIS split-window channels for retrieving the liquid fraction from cold clouds where the liquid water fraction is less than 50% of the total condensate. This makes use of the observation that clouds only containing ice exhibit effective 12-to-11 μm absorption optical thickness ratios (βeff) that are quasi-constant with retrieved cloud temperature T. This observation was made possible by using two CO2 channels to retrieve T and then using the 12 and 11 μm channels to retrieve emissivities and βeff. Thus for T < −40 °C, βeff is constant, but for T > −40 °C, βeff slowly increases due to the presence of liquid water, revealing mean liquid fractions of ~ 10% around −22 °C from tropical clouds identified as cirrus by the cloud mask. However, the uncertainties for these retrievals are large, and extensive in situ measurements are needed to refine and validate these retrievals. Such liquid levels are shown to reduce the cloud effective diameter De such that cloud optical thickness will increase by more than 50% for a given water path, relative to De corresponding to pure ice clouds. Such retrieval information is needed for validation of the cloud microphysics in climate models. Since low levels of liquid water can dominate cloud optical properties, tropical clouds between −25 and −20 °C may be susceptible to the first aerosol indirect effect.
On-line determination of ammonia at low pptv mixing ratios in the CLOUD chamber
Authors: Bianchi F. , Dommen J. , Mathot S. , Baltensperger U.
Published: July 2012

Abstract. A new instrument for the on-line determination of ammonia was developed. Since ammonia is a rather sticky compound, sampling losses were minimised with a new sampling device where the ammonia was transferred to the liquid phase only 5 mm after the inlet tip. The liquid phase was then analyzed by long pathlength absorption spectrophotometry using the Berthelot reaction with phenol and hypochlorite as reagents. The measurements were made during the CLOUD3 campaign at CERN where the influence of ammonia on the nucleation rate was studied. At stable conditions the detection limit reached with this instrument was 35 pptv (air flow rate of 2 l min−1, liquid flow rate of 0.3 ml min−1), although occasionally the instrument was affected by background problems. The range of mixing ratios during this campaign was varied from the background contamination (<35 pptv) up to around 2 ppbv. The measured ammonia concentration was correlated with the rate of ammonia injected into the chamber, but with a response time of several hours due to the high tendency of ammonia to adsorb to or to desorb from surfaces. Since it was found that ammonia strongly increases the nucleation rate already at the lowest measured concentration, future work will focus on further decreasing the detection limit of the instrument.
Assessment of two aerosol optical thickness retrieval algorithms applied to MODIS Aqua and Terra measurements in Europe
Authors: Glantz P. , Tesche M.
Published: July 2012

Abstract. The aim of the present study is to validate AOT (aerosol optical thickness) and Ångström exponent (α), obtained from MODIS (MODerate resolution Imaging Spectroradiometer) Aqua and Terra calibrated level 1 data (1 km horizontal resolution at ground) with the SAER (Satellite AErosol Retrieval) algorithm and with MODIS Collection 5 (c005) standard product retrievals (10 km horizontal resolution), against AERONET (AErosol RObotic NETwork) sun photometer observations over land surfaces in Europe. An inter-comparison of AOT at 0.469 nm obtained with the two algorithms has also been performed. The time periods investigated were chosen to enable a validation of the findings of the two algorithms for a maximal possible variation in sun elevation. The satellite retrievals were also performed with a significant variation in the satellite-viewing geometry, since Aqua and Terra passed the investigation area twice a day for several of the cases analyzed. The validation with AERONET shows that the AOT at 0.469 and 0.555 nm obtained with MODIS c005 is within the expected uncertainty of one standard deviation of the MODIS c005 retrievals (ΔAOT = ± 0.05 ± 0.15 · AOT). The AOT at 0.443 nm retrieved with SAER, but with a much finer spatial resolution, also agreed reasonably well with AERONET measurements. The majority of the SAER AOT values are within the MODIS c005 expected uncertainty range, although somewhat larger average absolute deviation occurs compared to the results obtained with the MODIS c005 algorithm. The discrepancy between AOT from SAER and AERONET is, however, substantially larger for the wavelength 488 nm. This means that the values are, to a larger extent, outside of the expected MODIS uncertainty range. In addition, both satellite retrieval algorithms are unable to estimate α accurately, although the MODIS c005 algorithm performs better. Based on the inter-comparison of the SAER and MODIS c005 algorithms, it was found that SAER on the whole is able to obtain results within the expected uncertainty range of MODIS Aqua and Terra observations.
Monitoring and quantifying future climate projections of dryness and wetness extremes: SPI bias
Authors: Sienz F. , Bothe O. , Fraedrich K.
Published: July 2012

Abstract. The adequacy of the gamma distribution (GD) for monthly precipitation totals is reconsidered. The motivation for this study is the observation that the GD fails to represent precipitation in considerable areas of global observed and simulated data. This misrepresentation may lead to erroneous estimates of the Standardised Precipitation Index (SPI), evaluations of models, and assessments of climate change. In this study, the GD is compared to the Weibull (WD), Burr Type III (BD), exponentiated Weibull (EWD) and generalised gamma (GGD) distribution. These distributions extend the GD in terms of possible shapes (skewness and kurtosis) and the behaviour for large arguments. The comparison is based on the Akaike information criterion, which maximises information entropy and reveals a trade-off between deviation and the numbers of parameters used. We use monthly sums of observed and simulated precipitation for 12 calendar months of the year. Assessing observed and simulated data, (i) the Weibull type distributions give distinctly improved fits compared to the GD and (ii) the SPI resulting from the GD overestimates (underestimates) extreme dryness (wetness).
A mechanistic description of the formation and evolution of vegetation patterns
Authors: Foti R. , Ramírez J. A.
Published: July 2012

Abstract. Vegetation patterns are a common and well-defined characteristic of many landscapes. In this paper we explore some of the physical mechanisms responsible for the establishment of self-organized, non-random vegetation patterns that arise at the hillslope scale in many areas of the world, especially in arid and semi-arid regions. In doing so, we provide a fundamental mechanistic understanding of the dynamics of vegetation pattern formation and development. Reciprocal effects of vegetation on the hillslope thermodynamics, runoff production and run-on infiltration, root density, surface albedo and soil moisture content are analyzed. In particular, we: (1) present a physically based mechanistic description of processes leading to vegetation pattern formation; (2) quantify the relative impact of each process on pattern formation; and (3) describe the relationships between vegetation patterns and the climatic, hydraulic and topographic characteristics of the system. We validate the model by comparing simulations with observed natural patterns in the areas of Niger near Niamey and Somalia near Garoowe. Our analyses suggest that the phenomenon of pattern formation is primarily driven by run-on infiltration and mechanisms of facilitation/inhibition among adjacent vegetation groups mediated by vegetation effects on soil properties and controls on soil moisture and albedo. Nonetheless, even in presence of those mechanisms, patterns arise only when the climatic conditions, particularly annual precipitation and net radiation, are favorable.
Assimilation of sea-ice concentration in a global climate model – physical and statistical aspects
Authors: Tietsche S. , Notz D. , Jungclaus J. H. , Marotzke J.
Published: July 2012

Abstract. We investigate the initialization of Northern-hemisphere sea ice in the global climate model ECHAM5/MPI-OM by assimilating sea-ice concentration data. The analysis updates for concentration are given by Newtonian relaxation, and we discuss different ways of specifying the analysis updates for mean thickness. Because the conservation of mean ice thickness or actual ice thickness in the analysis updates leads to poor assimilation performance, we introduce a proportional dependence between concentration and mean thickness analysis updates. Assimilation with these proportional mean-thickness analysis updates significantly reduces assimilation error both in identical-twin experiments and when assimilating sea-ice observations, reducing the concentration error by a factor of four to six, and the thickness error by a factor of two. To understand the physical aspects of assimilation errors, we construct a simple prognostic model of the sea-ice thermodynamics, and analyse its response to the assimilation. We find that the strong dependence of thermodynamic ice growth on ice concentration necessitates an adjustment of mean ice thickness in the analysis update. To understand the statistical aspects of assimilation errors, we study the model background error covariance between ice concentration and ice thickness. We find that the spatial structure of covariances is best represented by the proportional mean-thickness analysis updates. Both physical and statistical evidence supports the experimental finding that proportional mean-thickness updates are superior to the other two methods considered and enable us to assimilate sea ice in a global climate model using simple Newtonian relaxation.
Three-dimensional thermal structure of subduction zones: effects of obliquity and curvature
Authors: Bengtson A. K. , van Keken P. E.
Published: July 2012

Abstract. Quantifying the precise thermal structure of subduction zones is essential for understanding the nature of metamorphic dehydration reactions, arc volcanism, and intermediate depth seismicity. High resolution two-dimensional (2-D) models have shown that the rheology of the mantle wedge plays a critical role and establishes strong temperature gradients in the slab. The influence of three-dimensional (3-D) subduction zone geometry on thermal structure is however not yet well characterized. A common assumption for 2-D models is that the cross-section is taken normal to the strike of the trench with a corresponding velocity reduction in the case of oblique subduction, rather than taken parallel to velocity. A comparison between a full 3-D Cartesian model with oblique subduction and selected 2-D cross-sections demonstrates that the trench-normal cross-section provides a better reproduction of the slab thermal structure than the velocity-parallel cross-section. An exception is found in the case of strongly curved subduction, such as in the Marianas, where strong 3-D flow in the mantle wedge is generated. In this case it is shown that the full 3-D model should be evaluated for an accurate prediction of the slab thermal structure.
A recent bifurcation in Arctic sea-ice cover
Authors: Livina V. N. , Lenton T. M.
Published: July 2012

Abstract. There is ongoing debate over whether Arctic sea-ice has already passed a "tipping point", or whether it will do so in future, with several recent studies arguing that the loss of summer sea ice does not involve a bifurcation because it is highly reversible in models. Recently developed methods can detect and sometimes forewarn of bifurcations in time-series data, hence we applied them to satellite data for Arctic sea-ice cover. Here we show that a new low ice cover state has appeared from 2007 onwards, which is distinct from the normal state of seasonal sea ice variation, suggesting a bifurcation has occurred from one attractor to two. There was no robust early warning signal of critical slowing down prior to this bifurcation, consistent with it representing the appearance of a new ice cover state rather than the loss of stability of the existing state. The new low ice cover state has been sampled predominantly in summer-autumn and seasonal forcing combined with internal climate variability are likely responsible for triggering recent transitions between the two ice cover states. However, all early warning indicators show destabilization of the summer-autumn sea-ice since 2007. This suggests the new low ice cover state may be a transient feature and further abrupt changes in summer-autumn Arctic sea-ice cover could lie ahead; either reversion to the normal state or a yet larger ice loss.
Climate Change Mitigation Activities and Determinants in the Rural Guinea Savannah of Nigeria
Authors: Abraham Falola , Bamidele Fakayode Segun , Adebola Akangbe Jones , Kobe Ibrahim Hussein
Published: July 2012

Nigeria loses about $750 million annually to the depletion of its 350 000 hectares of land by direct human activities and climate change. Consequently, the Sahara Desert has been moving southwards by 600 metres annually. 10 000 farming families have already been forced to move off the degraded land that has become barren. In the light of this, this study examined climate mitigation activities and determinants in Nigeria. Specifically, the study examined climate change knowledge/perception, cost implications and mitigation practices of rural households as well as factors responsible for the level of mitigation activities. 120 household respondents were selected across 8 communities in the Guinea Savannah of Kwara State, Nigeria. Study analytical tools used were descriptive statistics, principal component and Tobit analysis. Results showed that households perceived the effects of increased temperatures, reduced rainfall, desertification, flooding and increased crop pest and disease infestations. Crop harvest losses due to changing climate were large and worrisome. Principal component analysis PCA results implied that prevalent practices undertaken to combat climate change were crude and non-radical. These activities were inorganic and organic fertilizers use, mulching, bush fallow and crude agro-forestry practices. Factors determining the extent of mitigation activities were found to include educational status, type of farming activities and farm size. The study therefore calls for radical efforts at educating the rural masses on climate change devastations and the need for mitigating climate change, use of early maturing crop varieties. Green zone/forest should be developed while tree planting and afforestation should be encouraged and possibly enforced.
Assessment of Fertilizer Policy, Farmers’ Perceptions and Implications for Future Agricultural Development in Nepal
Authors: Raut Nani , Sitaula Bishal K.
Published: July 2012

This paper assesses the origins of and changes to fertilizer policy in Nepal over a period of time. It assesses farmers’ awareness of the recent changes to the subsidy policy and examines their perceptions of the extension services. This paper looks at the environmental implications of the concentrated application of chemical fertilizer, particularly as far as food security is concerned. Questionnaire surveys, group discussions, a workshop, soil analyses and archival materials were used to collect data for this study. Changes in fertilizer policy have occurred in four different phases: (i) without subsidy; (ii) with subsidy; (iii) with deregulation of fertilizer trade; and (iv) the current phase of subsidies for fertilizer. However, timely and effective fertilizer distribution by the government has always been a problem. Only few farmers (12 %) know about recent changes in the fertilizer policy; most of them (44 %) were satisfied with the new subsidy scheme. Valid proof of land ownership is a requirement for qualifying for subsidized fertilizer, and this makes it difficult for some small farmers who are tenant. The soil analysis indicated a significant decrease in the soil pH as a result of intensified agriculture. One reason is due to the intensive use of chemical fertilizers and the declining use of farmyard manure. The ineffectiveness of the extension services also influences farmers’ use of fertilizer as they are not aware of which fertilizer and how much to use. The use of fertilizer may increase yields in the short term, but in the longer term, it may worsen the food insecurity in the country.