bluuebunny/crossref_metadata_2025 huggingface dataset:
Cytodiagnosis of extra-nasal rhinosporidiosis: A study of 16 cases from endemic area
Authors: Pal Subrata , Chakrabarti Srabani , Biswas Biplab Kr , Sinha Rajani , Rakshit Arindam , Das Purna Chandra
Published: September 2014

Context: Extra-nasal rhinosporidiosis is not uncommon in endemic region like India. Clinical presentations of extra-nasal rhinosporidiosis lesion often lead to diagnostic dilemma. Cytology can help in the preoperative diagnosis of such lesions.

Aims: The aims of our study were to find the clinico-pathological presentation of extra-nasal rhinosporidiosis and to evaluate the role of cytology in diagnosing these lesions preoperatively.

Settings and Design: Fine-needle aspiration cytology is often used for preoperative diagnosis of sub-cutaneous lesions of the head and neck region. This retrospective study was designed to include the cytologically diagnosed cases of rhinosporidiosis and to compare with final histopathology of the lesions.

Materials and Methods: A total of 21 cases of extra-nasal rhinosporidiosis were diagnosed in our study period of 18 months. Cytology was approached in 17 cases and 16 cases were diagnosed as rhinosporidiosis, which were included in the study group. Twelve cases were sampled by fine-needle aspiration and four cases by scrap technique. Histopathological confirmation was possible in all cytologically diagnosed cases.

Results: Head and neck region were involved in 15 cases and only one case was on the skin of right upper arm. Orbital region was the most common extra-nasal site of involvement. Most of the cases (13 cases, 81.25%) belonged to the age group of 11-30 years. All cytologicaly diagnosed cases of rhinosporidiosis were concordant with histopathology. Only one false-negative case was cytologically diagnosed as suppurative inflammatory lesion. Sensitivity and specificity of cytology in diagnosis of extra-nasal rhinosporidiosis were 94.11% and 100% respectively.

Conclusions: Extra-nasal rhinosporidiosis is an important differential diagnosis of nodular, polypoid mass of head-neck-face region. Cytology can be used as an important tool in preoperative diagnosis of extra-nasal rhinosporidiosis.
The Epidemiological Profile of Candidemia at an Indian Trauma Care Center
Authors: Tak Vibhor , Mathur Purva , Varghese Prince , Gunjiyal Jacinta , Xess Immaculata , Misra Mahesh C
Published: September 2014

Purpose: Candida spp. is a common cause of bloodstream infections. Candidemia is a potentially fatal infection that needs urgent intervention to salvage the patients. Trauma patients are relatively young individuals with very few comorbidities, and the epidemiology of candidemia is relatively unknown in this vulnerable and growing population. In this study, we report the epidemiology of candidemia in a tertiary care Trauma Center of India.

Materials and Methods: The study was conducted from January 2009 to July 2012. All patients from whose blood samples a Candida spp. was recovered were included in this study. A detailed history and follow up of the patients was done. The isolates of Candida were identified to the species level. The speciation was done by conventional methods, including morphology on Corn Meal Agar, color development on Triphenyl Tetrazolium Chloride Agar and CHROMagar, and germ tube tests. The VITEK 2 YST ID colorometric card, a fully automated identification system was also used. Antifungal susceptibility was performed using the VITEK 2 system.

Results: A total of 212 isolates of the Candida species were recovered from blood samples of 157 patients over the study period. Candida tropicalis, 82 (39%), was the most common, followed by C. parapsilosis, 43 (20%), C. albicans, 29 (14%), C. glabrata, 24 (11%), C. rugosa, 20 (9%), C. hemulonii,; 6 (3%), C. guilliermondii, 4 (2%), C. famata, 3 (1.5%), and C. lusitaniae 1 (0.5%). Out of all the candidemia patients, 68 (43%) had a fatal outcome. Fluconazole and Amphotericin B resistance was seen in seven (3.3%) and seven (3.3%) of the isolates, respectively.

Conclusion: Candidemia is a significant cause of mortality in trauma patients in our center, with C. tropicalis and C. parapsilosis being the predominant pathogens. Resistance to antifungal drugs is a matter of concern. Better hospital infection control practices and good antibiotic stewardship policies could possibly help in reducing the morbidity and mortality associated with candidemia.
Comparison of Epidemiological and Antibiotic Susceptibility Pattern of Metallo-Beta-Lactamase-Positive and Metallo-Beta-Lactamase-Negative Strains of Pseudomonas Aeruginosa
Authors: Ranjan Shikha , GS Banashankari , Babu PR Sreenivasa
Published: September 2014

Background: The infections caused by metallo-beta-lactamases (MBLs) producing Pseudomonas aeruginosa are associated with higher rates of mortality, morbidity, and overall healthcare costs compared to non-MBL P. aeruginosa infections.

Purpose: To compare the epidemiologic factors and antibiograms of MBL-positive and MBL-negative P. aeruginosa isolates in a tertiary care hospital.

Methods: In an observational study, from January 2011 to December 2012, all non-duplicate P. aeruginosa isolates were subjected to an antimicrobial sensitivity test against 10 antibiotics of five different classes. All P. aeruginosa strains showing resistance to at least one of the carbapenems were subjected to the MBL-E test. Epidemiological features and antibiograms of MBL-positive and MBL-negative strains were compared and statistically analyzed.

Results: Out of 350 isolates (total sample = 5330) of P. aeruginosa, MBL was detected in 58 isolates by the E-test, resulting in a prevalence of 16.57%. Resistance to most of the antibiotics was significantly higher in the MBL-positive strains with 100% resistance to ciprofloxacin, tobramycin, and meropenem, followed by imipenem (93.10%) and gentamicin (89.66%). The prevalence of multidrug-resistant and pandrug-resistant strains was significantly higher among the MBL group as compared to that in the non-MBL group ((55.17 vs. 7.88% (P < 0.0001) and 8.62 vs. 0.68% (P = 0.0006)), respectively.

Conclusions: MBL-positive P. aeruginosa strains showed very high resistance to various antibiotics, as compared to the non-MBL strains. Increasing prevalence of MBL-producing isolates in hospital settings makes it important to perform routine detection of MBL-positive P. aeruginosa strains by in vitro testing before antibiotic use, for the purposes of infection prevention, and control, and for minimizing the adverse outcomes of infections with MBL-producing strains.
A Rare Case of Splenic Littoral Cell Angioma in a Child
Authors: Bedir Recep , Şehitoğlu İbrahim , Calapoğlu Ahmet Salih , Yurdakul Cüneyt
Published: September 2014

Littoral cell angioma (LCA) is a rare, benign primary vascular neoplasm of the spleen. The tumor originates from the littoral cells lining the sinuses of the red pulp of the spleen. Preoperative distinction of this tumor from other benign or malign splenic lesions is difficult. Radiologically most cases present as multiple nodules. Definitive diagnosis can only be made histopathologically and immunohistochemically following splenectomy. This clinical situation can coexist with various malignancies and autoimmune disorders. Even though, it is mostly benign, since it has the potential to become malignant after splenectomy, long-term follow-up is required. We present an LCA case, which appeared as a solitary mass in the spleen of an 11-year-old girl with abdominal pain admitted to our hospital.
Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing
Authors: Bao Riyue , Huang Lei , Andrade Jorge , Tan Wei , Kibbe Warren A. , Jiang Hongmei , Feng Gang
Published: September 2014

The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, preprocessing, alignment, post-processing, and variant analysis (detection, annotation, and prioritization). We evaluate the performance of open-source alignment programs and variant calling tools using simulated and benchmark datasets, and highlight the challenges posed by the lack of concordance among variant detection tools. Based on these results, we recommend adopting multiple tools and resources to reduce false positives and increase the sensitivity of variant calling. In addition, we briefly discuss the current status and solutions for big data management, analysis, and summarization in the field of bioinformatics.
Integrative Bayesian Network Analysis of Genomic Data
Authors: Ni Yang , Stingo Francesco C. , Baladandayuthapani Veerabhadran
Published: September 2014

Rapid development of genome-wide profiling technologies has made it possible to conduct integrative analysis on genomic data from multiple platforms. In this study, we develop a novel integrative Bayesian network approach to investigate the relationships between genetic and epigenetic alterations as well as how these mutations affect a patient's clinical outcome. We take a Bayesian network approach that admits a convenient decomposition of the joint distribution into local distributions. Exploiting the prior biological knowledge about regulatory mechanisms, we model each local distribution as linear regressions. This allows us to analyze multi-platform genome-wide data in a computationally efficient manner. We illustrate the performance of our approach through simulation studies. Our methods are motivated by and applied to a multi-platform glioblastoma dataset, from which we reveal several biologically relevant relationships that have been validated in the literature as well as new genes that could potentially be novel biomarkers for cancer progression.
A Review of Cancer Risk Prediction Models with Genetic Variants
Authors: Wang Xuexia , Oldani Michael J. , Zhao Xingwang , Huang Xiaohui , Qian Dajun
Published: September 2014

Cancer risk prediction models are important in identifying individuals at high risk of developing cancer, which could result in targeted screening and interventions to maximize the treatment benefit and minimize the burden of cancer. The cancer-associated genetic variants identified in genome-wide or candidate gene association studies have been shown to collectively enhance cancer risk prediction, improve our understanding of carcinogenesis, and possibly result in the development of targeted treatments for patients. In this article, we review the cancer risk prediction models that have been developed for popular cancers and assess their applicability, strengths, and weaknesses. We also discuss the factors to be considered for future development and improvement of models for cancer risk prediction.
Chronic Lymphocytic Leukemia with t(14;18)(q32;q21) as a Sole Cytogenetic Abnormality
Authors: Elyamany Ghaleb , Fadalla Kamal , Elghezal Hatem , Alsuhaibani Omar , Osman Hani , Al-Abulaaly Abdulaziz
Published: September 2014

Background

Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults. The chromosomal abnormality t(14;18)(q32;q21) is most commonly associated with neoplasms of a follicular center cell origin. However, t(14;18) has also been reported in rare cases of CLL.

Objective

We describe the clinicopathologic, immunophenotypic, conventional, and molecular cytogenetic features of two rare cases proven to be CLL morphologically and immunologically in which t(14;18) was found as the sole cytogenetic abnormality.

Methods

Morphologic, flow cytometric analysis and molecular cytogenetic of peripheral blood and/or bone marrow samples were analyzed.

Results

Cytomorphologically, the cells were small mature lymphocytes without any findings that had characteristics of follicular lymphoma (FL) such as indented or clefted nuclei. Immunologic findings were characteristic of typical CLL without expression of CD10. A cytogenetic study revealed the two cases of CLL carrying t(14;18)(q32;q21).

Conclusion

We concluded that CLL with t(14;18) is rare and should be differentiated from FL as the therapy is highly diverse between both diseases. Using immunoglobulin heavy chain gene ( IGH) probes are important in the workup of patients with suspected CLL and suggest that the IGH probe should be used routinely in all CLL fluorescence in situ hybridization (FISH) panels.
Global Health Research in Narrative: A Qualitative Look at the FICRS-F Experience
Authors: Bearnot Benjamin , Coria Alexandra , Barnett Brian Scott , Clark Eva H. , Gartland Matthew G. , Jaganath Devan , Mendenhall Emily , Seu Lillian , Worjoloh Ayaba G. , Carothers Catherine Lem , Vermund Sten H. , Heimburger Douglas C.
Published: September 2014

For American professional and graduate health sciences trainees, a mentored fellowship in a low- or middle-income country (LMIC) can be a transformative experience of personal growth and scientific discovery. We invited 86 American trainees in the Fogarty International Clinical Research Scholars and Fellows Program and Fulbright–Fogarty Fellowship 2011–2012 cohorts to contribute personal essays about formative experiences from their fellowships. Nine trainees contributed essays that were analyzed using an inductive approach. The most frequently addressed themes were the strong continuity of research and infrastructure at Fogarty fellowship sites, the time-limited nature of this international fellowship experience, and the ways in which this fellowship period was important for shaping future career planning. Trainees also addressed interaction with host communities vis-à-vis engagement in project implementation. These qualitative essays have contributed insights on how a 1-year mentored LMIC-based research training experience can influence professional development, complementing conventional evaluations. Full text of the essays is available at http://fogartyscholars.org/.
Imported African Histoplasmosis in an Immunocompetent Patient 40 Years after Staying in a Disease-Endemic Area
Authors: Richaud Clémence , Chandesris Marie-Olivia , Lanternier Fanny , Benzaquen-Forner Hélène , Garcia-Hermoso Dea , Picard Capucine , Catherinot Emilie , Bougnoux Marie-Elisabeth , Lortholary Olivier
Published: September 2014

Histoplasmosis caused by Histoplasma capsulatum var. duboisii is a rare disease outside central and western Africa. In Europe, all cases are imported. We report a case of an African histoplasmosis with isolated pulmonary involvement in a non-immunocompromised patient that occurred 40 years after his stay in a disease-endemic area. The patient was given itraconazole. 18F-fluoro-2-deoxy-d-glucose positron emission tomography–computed tomography was used to assess evolution during treatment. The outcome for the patient was favorable.
The Effect of a Health Communication Campaign on Compliance with Mass Drug Administration for Schistosomiasis Control in Western Kenya—The SCORE Project
Authors: Omedo Martin , Ogutu Michael , Awiti Alphonce , Musuva Rosemary , Muchiri Geoffrey , Montgomery Susan P. , Secor W. Evan , Mwinzi Pauline
Published: September 2014

Compliance with mass drug administration (MDA) can be affected by rumors and mistrust about the drug. Communication campaigns are an effective way to influence attitudes and health behaviors in diverse public health contexts, but there is very little documentation about experiences using health communications in schistosomiasis control programs. A qualitative study was conducted with community health workers (CHWs) as informants to explore the effect of a health communication campaign on their experiences during subsequent praziquantel MDA for schistosomiasis. Discussions were audio-recorded, transcribed verbatim, translated into English where applicable, and analyzed thematically using ATLAS.ti software. According to the CHWs, exposure to mass media messages improved awareness of the MDA, which in turn, led to better treatment compliance. Our findings suggest that communication campaigns influence health behaviors and create awareness of schistosomiasis control interventions, which may ultimately improve praziquantel MDA.
Quantitative Evaluation of a Handheld Light Microscope for Field Diagnosis of Soil-Transmitted Helminth Infection
Authors: Bogoch Isaac I. , Andrews Jason R. , Speich Benjamin , Ame Shaali M. , Ali Said M. , Stothard J. Russell , Utzinger Jürg , Keiser Jennifer
Published: September 2014

We evaluated the Newton Nm1, a commercially available handheld light microscope and compared it with conventional light microscopy for the diagnosis of soil-transmitted helminth infections. A total of 91 Kato-Katz thick smears were examined by experienced microscopists and helminth eggs were counted and expressed as eggs per gram of stool (EPG). Mean egg counts were significantly higher with the conventional light microscope (5,190 EPG versus 2,386 EPG for Ascaris lumbricoides; 826 versus 456 for Trichuris trichiura; both P < 0.05). Using regression coefficients and accounting for intensity of infection, we found that the agreement between the two devices was excellent for both species (κ = 0.90, 95% confidence interval = 0.82–0.99 for A. lumbricoides and κ = 0.96, 95% CI = 0.91–1.00 for T. trichiura). The Newton Nm1 microscope may be a useful tool for the detection and quantification of soil-transmitted helminth infection in clinical, epidemiologic, and public health settings.
Summertime tropospheric ozone assessment over the Mediterranean region using the thermal infrared IASI/MetOp sounder and the WRF-Chem model
Authors: Safieddine S. , Boynard A. , Coheur P.-F. , Hurtmans D. , Pfister G. , Quennehen B. , Thomas J. L. , Raut J.-C. , Law K. S. , Klimont Z. , Hadji-Lazaro J. , George M. , Clerbaux C.
Published: September 2014

Abstract. Over the Mediterranean region, elevated tropospheric ozone (O3) values are recorded, especially in summer. We use the thermal Infrared Atmospheric Sounding Interferometer (IASI) and the Weather Research and Forecasting Model with Chemistry (WRF-Chem) to understand and interpret the factors and emission sources responsible for the high O3 concentrations observed in the Mediterranean troposphere. Six years (2008–2013) of IASI data have been analyzed and results show consistent maxima during summer, with an increase of up to 22% in the [0–8] km O3 column in the eastern part of the basin compared to the middle of the basin. We focus on summer 2010 to investigate the processes that contribute to these summer maxima. Using two modeled O3 tracers (inflow to the model domain and local anthropogenic emissions), we show that, between the surface and 2 km, O3 is mostly formed from anthropogenic emissions, while above 4 km it is mostly transported from outside the domain or from stratospheric origins. Evidence of stratosphere-to-troposphere exchange (STE) events in the eastern part of the basin is shown, and corresponds to a low water vapor mixing ratio and high potential vorticity.
Carbon balance of China constrained by CONTRAIL aircraft CO2 measurements
Authors: Jiang F. , Wang H. M. , Chen J. M. , Machida T. , Zhou L. X. , Ju W. M. , Matsueda H. , Sawa Y.
Published: September 2014

Abstract. Terrestrial carbon dioxide (CO2) flux estimates in China using atmospheric inversion method are beset with considerable uncertainties because very few atmospheric CO2 concentration measurements are available. In order to improve these estimates, nested atmospheric CO2 inversion during 2002–2008 is performed in this study using passenger aircraft-based CO2 measurements over Eurasia from the Comprehensive Observation Network for Trace gases by Airliner (CONTRAIL) project. The inversion system includes 43 regions with a focus on China, and is based on the Bayesian synthesis approach and the TM5 transport model. The terrestrial ecosystem carbon flux modeled by the Boreal Ecosystems Productivity Simulator (BEPS) model and the ocean exchange simulated by the OPA-PISCES-T model are considered as the prior fluxes. The impacts of CONTRAIL CO2 data on inverted China terrestrial carbon fluxes are quantified, the improvement of the inverted fluxes after adding CONTRAIL CO2 data are rationed against climate factors and evaluated by comparing the simulated atmospheric CO2 concentrations with three independent surface CO2 measurements in China. Results show that with the addition of CONTRAIL CO2 data, the inverted carbon sink in China increases while those in South and Southeast Asia decrease. Meanwhile, the posterior uncertainties over these regions are all reduced (2–12%). CONTRAIL CO2 data also have a large effect on the inter-annual variation of carbon sinks in China, leading to a better correlation between the carbon sink and the annual mean climate factors. Evaluations against the CO2 measurements at three sites in China also show that the CONTRAIL CO2 measurements may have improved the inversion results.
Aircraft testing of the new Blunt-body Aerosol Sampler (BASE)
Authors: Moharreri A. , Craig L. , Dubey P. , Rogers D. C. , Dhaniyala S.
Published: September 2014

Abstract. There is limited understanding of the role of aerosols in the formation and modification of clouds, partly due to inadequate data on such systems. Aircraft-based aerosol measurements in the presence of cloud particles have proven to be challenging because of the problem of cloud droplet/ice particle shatter and the generation of secondary artifact particles that contaminate aerosol samples. Recently, the design of a new aircraft inlet, called the Blunt-body Aerosol Sampler (BASE), which enables sampling of interstitial aerosol particles, was introduced. Numerical modeling results and laboratory test data suggested that the BASE inlet should sample interstitial particles with minimal shatter particle contamination. Here, the sampling performance of the inlet is established from aircraft-based measurements. Initial aircraft test results obtained during the PLOWS (Profiling of Winter Storms) campaign indicated two problems with the original BASE design: separated flows around the BASE at high altitudes and a significant shatter problem when sampling in drizzle. The test data were used to improve the accuracy of flow and particle trajectory modeling around the inlet, and the results from the improved flow model were used to guide design modifications of the BASE to overcome the problems identified in its initial deployment. The performance of the modified BASE was tested during the ICE–T (Ice in Clouds Experiment – Tropics) campaign, and the inlet was seen to provide near shatter-free measurements in a wide range of cloud conditions. The initial aircraft test results, design modifications, and the performance characteristics of the BASE relative to another interstitial inlet, the submicron aerosol inlet (SMAI), are presented.
Observations of precipitable water vapour over complex topography of Ethiopia from ground-based GPS, FTIR, radiosonde and ERA-Interim reanalysis
Authors: Mengistu Tsidu G. , Blumenstock T. , Hase F.
Published: September 2014

Abstract. Water vapour is one of the most important green house gases. Long-term changes in the amount of water vapour in the atmosphere need to be monitored not only for its direct role as a green house gas but also because of its role in amplifying other feedbacks in general circulation models. In recent decades, monitoring of water vapour on regular and continuous basis is becoming possible as a result of increase in the number of deployed Global Positioning Satellite (GPS) ground-based receivers at a faster pace. However, Horn of Africa region remains a data void region in this regard until recently when some GPS ground-receiver stations have been deployed to monitor tectonic movements in the Great Rift Valley. This study seizes this opportunity and the installation of Fourier Transform Infrared Spectrometer (FTIR) at Addis Ababa to assess the quality and comparability of Precipitable Water Vapour (PWV) from GPS, FTIR, radiosonde and ERA-Interim over Ethiopia. The PWVs from the three instruments and reanalysis show good correlation in the range from 0.83 to 0.92. The radiosonde PWV shows dry bias with respect to other observations and reanalysis. ERA-Interim PWV shows wet bias with respect to all while GPS PWV exhibits wet bias with respect to FTIR. The intercomparison between GPS and ERA-Interim is extended to seven other GPS stations in the country. Despite the sensitivity of GPS PWV to uncertainty in surface pressure in general, observed surface pressure is used only at four GPS stations. The gain obtained from using observed surface pressure in terms of reducing bias and strengthening correlation is significant but shows some variations among the GPS sites. In contrast to comparison at Addis Ababa, the comparison between GPS and ERA-Interim PWVs over seven other GPS stations shows difference in the magnitude and sign of bias of ERA-Interim with respect to GPS PWV from station to station. This variation is also visible across different seasons. The main cause of the variation is linked to variation in ECMWF model skill over different regions and seasons which might be related to poor observational constraint from this part of the globe and sensitivity of model convection scheme to orography. The latter is consistent with observed wet bias over some highland stations and dry bias over few lowland stations. However, there are also exceptions to this inference at few stations suggesting other factors such as proximity to water bodies and vegetations might have a role. The skill of ECMWF in reproducing realistic PWV varies with season showing large bias during warm and wet summer for most of the GPS sites.
Implementation of a soil albedo scheme in the CABLEv1.4b land surface model and evaluation against MODIS estimates over Australia
Authors: Kala J. , Evans J. P. , Pitman A. J. , Schaaf C. B. , Decker M. , Carouge C. , Mocko D. , Sun Q.
Published: September 2014

Abstract. Land surface albedo, the fraction of incoming solar radiation reflected by the land surface, is a key component of the Earth system. This study evaluates snow-free surface albedo simulations by the Community Atmosphere Biosphere Land Exchange (CABLEv1.4b) model with the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Satellite Pour L'Observation de la Terre (SPOT) albedo. We compare results from offline simulations over the Australian continent. The control simulation has prescribed background snow-free and vegetation-free soil albedo derived from MODIS whilst the experiments use a simple parameterisation based on soil moisture and colour, originally from the Biosphere Atmosphere Transfer Scheme (BATS), and adopted in the Common Land Model (CLM). The control simulation, with prescribed soil albedo, shows that CABLE simulates overall albedo over Australia reasonably well, with differences compared to MODIS and SPOT albedos within ±0.1. Application of the original BATS scheme, which uses an eight-class soil classification, resulted in large differences of up to −0.25 for the near-infrared (NIR) albedo over large parts of the desert regions of central Australia. The use of a recalibrated 20-class soil colour classification from the CLM, which includes a higher range for saturated and VIS (visible) and NIR soil albedos, reduced the underestimation of the NIR albedo. However, this soil colour mapping is tuned to CLM soil moisture, a quantity which is not necessarily transferrable between land surface models. We therefore recalibrated the soil color map using CABLE's climatological soil moisture, which further reduced the underestimation of the NIR albedo to within ±0.15 over most of the continent as compared to MODIS and SPOT albedos. Small areas of larger differences of up to −0.25 remained within the central arid parts of the continent during summer; however, the spatial extent of these large differences is substantially reduced as compared to the simulation using the default eight-class uncalibrated soil colour map. It is now possible to use CABLE coupled to atmospheric models to investigate soil-moisture–albedo feedbacks, an important enhancement of the model.
A fully coupled 3-D ice-sheet–sea-level model: algorithm and applications
Authors: de Boer B. , Stocchi P. , van de Wal R. S. W.
Published: September 2014

Abstract. Relative sea-level variations during the late Pleistocene can only be reconstructed with the knowledge of ice-sheet history. On the other hand, the knowledge of regional and global relative sea-level variations is necessary to learn about the changes in ice volume. Overcoming this problem of circularity demands a fully coupled system where ice sheets and sea level vary consistently in space and time and dynamically affect each other. Here we present results for the past 410 000 years (410 kyr) from the coupling of a set of 3-D ice-sheet-shelf models to a global sea-level model, which is based on the solution of the gravitationally self-consistent sea-level equation. The sea-level model incorporates the glacial isostatic adjustment feedbacks for a Maxwell viscoelastic and rotating Earth model with coastal migration. Ice volume is computed with four 3-D ice-sheet-shelf models for North America, Eurasia, Greenland and Antarctica. Using an inverse approach, ice volume and temperature are derived from a benthic δ18O stacked record. The derived surface-air temperature anomaly is added to the present-day climatology to simulate glacial–interglacial changes in temperature and hence ice volume. The ice-sheet thickness variations are then forwarded to the sea-level model to compute the bedrock deformation, the change in sea-surface height and thus the relative sea-level change. The latter is then forwarded to the ice-sheet models. To quantify the impact of relative sea-level variations on ice-volume evolution, we have performed coupled and uncoupled simulations. The largest differences of ice-sheet thickness change occur at the edges of the ice sheets, where relative sea-level change significantly departs from the ocean-averaged sea-level variations.
Effect of year-to-year variability of leaf area index on variable infiltration capacity model performance and simulation of streamflow during drought
Authors: Tesemma Z. K. , Wei Y. , Peel M. C. , Western A. W.
Published: September 2014

Abstract. This study assessed the effect of using observed monthly leaf area index (LAI) on hydrologic model performance and the simulation of streamflow during drought using the variable infiltration capacity (VIC) hydrological model in the Goulburn–Broken catchment of Australia, which has heterogeneous vegetation, soil and climate zones. VIC was calibrated with both observed monthly LAI and long-term mean monthly LAI, which were derived from the Global Land Surface Satellite (GLASS) observed monthly LAI dataset covering the period from 1982 to 2012. The model performance under wet and dry climates for the two different LAI inputs was assessed using three criteria, the classical Nash–Sutcliffe efficiency, the logarithm transformed flow Nash–Sutcliffe efficiency and the percentage bias. Finally, the percentage deviation of the simulated monthly streamflow using the observed monthly LAI from simulated streamflow using long-term mean monthly LAI was computed. The VIC model predicted monthly streamflow in the selected sub-catchments with model efficiencies ranging from 61.5 to 95.9% during calibration (1982–1997) and 59 to 92.4% during validation (1998–2012). Our results suggest systematic improvements from 4 to 25% in the Nash–Sutcliffe efficiency in pasture dominated catchments when the VIC model was calibrated with the observed monthly LAI instead of the long-term mean monthly LAI. There was limited systematic improvement in tree dominated catchments. The results also suggest that the model overestimation or underestimation of streamflow during wet and dry periods can be reduced to some extent by including the year-to-year variability of LAI in the model, thus reflecting the responses of vegetation to fluctuations in climate and other factors. Hence, the year-to-year variability in LAI should not be neglected; rather it should be included in model calibration as well as simulation of monthly water balance.
A framework for assessing hydrological regime sensitivity to climate change in a convective rainfall environment: a case study of two medium-sized eastern Mediterranean catchments, Israel
Authors: Peleg N. , Shamir E. , Georgakakos K. P. , Morin E.
Published: September 2014

Abstract. A modeling framework is formulated and applied to assess the sensitivity of the hydrological regime of two catchments in a convective rainfall environment with respect to projected climate change. The study uses likely rainfall scenarios with high spatiotemporal resolution that are dependent on projected changes in the driving regional meteorological synoptic systems. The framework was applied to a case study in two medium-sized Mediterranean catchments in Israel, affected by convective rainfall, by combining the HiReS-WG rainfall generator and the SAC-SMA hydrological model. The projected climate change impact on the hydrological regime was examined for the RCP4.5 and RCP8.5 emission scenarios, comparing the historical (beginning of the 21st century) and future (mid-21st-century) periods from three General Circulation Models simulations available from CMIP5. Focusing on changes in the occurrence frequency of regional synoptic systems and their impact on rainfall and streamflow patterns, we find that the mean annual rainfall over the catchments is projected to be reduced by 15% (range 2–23%) and 18% (7–25%) for the RCP4.5 sand RCP8.5 emission scenarios, respectively. The mean annual streamflow volumes are projected to be reduced by 45% (10–60%) and 47% (16–66%). The average events' streamflow volumes for a given event rainfall depth are projected to be lower by a factor of 1.4–2.1. Moreover, the streamflow season in these ephemeral streams is projected to be shorter by 22% and 26–28% for the RCP4.5 and RCP8.5, respectively. The amplification in reduction of streamflow volumes relatively to rainfall amounts is related to the projected reduction in soil moisture, as a result of fewer rainfall events and longer dry spells between rainfall events during the wet season. The dominant factors for the projected reduction in rainfall amount were the reduction in occurrence of wet synoptic systems and the shortening of the wet synoptic systems durations. Changes in the occurrence frequency of the two dominant types of the regional wet synoptic systems (Active Red Sea Trough and Mediterranean low) were found to have a minor impact on the total rainfall.
Improving operational flood ensemble prediction by the assimilation of satellite soil moisture: comparison between lumped and semi-distributed schemes
Authors: Alvarez-Garreton C. , Ryu D. , Western A. W. , Su C.-H. , Crow W. T. , Robertson D. E. , Leahy C.
Published: September 2014

Abstract. Assimilation of remotely sensed soil moisture data (SM–DA) to correct soil water stores of rainfall-runoff models has shown skill in improving streamflow prediction. In the case of large and sparsely monitored catchments, SM–DA is a particularly attractive tool. Within this context, we assimilate active and passive satellite soil moisture (SSM) retrievals using an ensemble Kalman filter to improve operational flood prediction within a large semi-arid catchment in Australia (>40 000 km2). We assess the importance of accounting for channel routing and the spatial distribution of forcing data by applying SM–DA to a lumped and a semi-distributed scheme of the probability distributed model (PDM). Our scheme also accounts for model error representation and seasonal biases and errors in the satellite data. Before assimilation, the semi-distributed model provided more accurate streamflow prediction (Nash–Sutcliffe efficiency, NS = 0.77) than the lumped model (NS = 0.67) at the catchment outlet. However, this did not ensure good performance at the "ungauged" inner catchments. After SM–DA, the streamflow ensemble prediction at the outlet was improved in both the lumped and the semi-distributed schemes: the root mean square error of the ensemble was reduced by 27 and 31%, respectively; the NS of the ensemble mean increased by 7 and 38%, respectively; the false alarm ratio was reduced by 15 and 25%, respectively; and the ensemble prediction spread was reduced while its reliability was maintained. Our findings imply that even when rainfall is the main driver of flooding in semi-arid catchments, adequately processed SSM can be used to reduce errors in the model soil moisture, which in turn provides better streamflow ensemble prediction. We demonstrate that SM–DA efficacy is enhanced when the spatial distribution in forcing data and routing processes are accounted for. At ungauged locations, SM–DA is effective at improving streamflow ensemble prediction, however, the updated prediction is still poor since SM–DA does not address systematic errors in the model.
A preliminary investigation of rogue waves off the Jiangsu coast, China
Authors: Wang Y. , Tao A.-F. , Zheng J.-H. , Doong D.-J. , Fan J. , Peng J.
Published: September 2014

Abstract. Due to the potential disasters induced by rogue waves, research in this field has increased rapidly in the last 2 decades. However, there are still a lot of open questions left, including some classic ones, such as whether the rogues waves are just rare events or not. One of the key reasons is that not enough of the observed rogue waves have been investigated. China has a wide sea area, but none of the research has addressed the observed rogue waves. In the present study, 1 year of observed wave data from Jiangsu coastal area, China, are analyzed. It is found that rogue waves are present, although the wave heights are not very large; furthermore, the probability of their occurrence is similar to the Rayleigh distribution prediction, due to the local silty coastal topography. The characteristics of rouge waves are investigated and the results indicate that a new type of rogue wave may exist.
Data interoperability software solution for emergency reaction in the Europe Union
Authors: Casado R. , Rubiera E. , Sacristan M. , Schütte F. , Peters R.
Published: September 2014

Abstract. Emergency management becomes more challenging in international crisis episodes because of cultural, semantic and linguistic differences between all stakeholders, especially first responders. Misunderstandings between first responders makes decision-making slower and more difficult. However, spread and development of networks and IT-based Emergency Management Systems (EMS) has improved emergency responses, becoming more coordinated. Despite improvements made in recent years, EMS have not still solved problems related to cultural, semantic and linguistic differences which are the real cause of slower decision-making. In addition, from a technical perspective, the consolidation of current EMS and the different formats used to exchange information offers another problem to be solved in any solution proposed for information interoperability between heterogeneous EMS surrounded by different contexts. To overcome these problems we present a software solution based on semantic and mediation technologies. EMERGency ELements (EMERGEL) (Fundacion CTIC and AntwortING Ingenieurbüro PartG 2013), a common and modular ontology shared by all the stakeholders, has been defined. It offers the best solution to gather all stakeholders' knowledge in a unique and flexible data model, taking into account different countries cultural linguistic issues. To deal with the diversity of data protocols and formats, we have designed a Service Oriented Architecture for Data Interoperability (named DISASTER) providing a flexible extensible solution to solve the mediation issues. Web Services have been adopted as specific technology to implement such paradigm that has the most significant academic and industrial visibility and attraction. Contributions of this work have been validated through the design and development of a cross-border realistic prototype scenario, actively involving both emergency managers and emergency first responders: the Netherlands–Germany border fire.
Improving the ensemble transform Kalman filter using a second-order Taylor approximation of the nonlinear observation operator
Authors: Wu G. , Yi X. , Wang L. , Liang X. , Zhang S. , Zhang X. , Zheng X.
Published: September 2014

Abstract. The ensemble transform Kalman filter (ETKF) assimilation scheme has recently seen rapid development and wide application. As a specific implementation of the ensemble Kalman filter (EnKF), the ETKF is computationally more efficient than the conventional EnKF. However, the current implementation of the ETKF still has some limitations when the observation operator is strongly nonlinear. One problem in the minimization of a nonlinear objective function similar to 4D-Var is that the nonlinear operator and its tangent-linear operator have to be calculated iteratively if the Hessian is not preconditioned or if the Hessian has to be calculated several times. This may be computationally expensive. Another problem is that it uses the tangent-linear approximation of the observation operator to estimate the multiplicative inflation factor of the forecast errors, which may not be sufficiently accurate. This study attempts to solve these problems. First, we apply the second-order Taylor approximation to the nonlinear observation operator in which the operator, its tangent-linear operator and Hessian are calculated only once. The related computational cost is also discussed. Second, we propose a scheme to estimate the inflation factor when the observation operator is strongly nonlinear. Experimentation with the Lorenz 96 model shows that using the second-order Taylor approximation of the nonlinear observation operator leads to a reduction in the analysis error compared with the traditional linear approximation method. Furthermore, the proposed inflation scheme leads to a reduction in the analysis error compared with the procedure using the traditional inflation scheme.
Effective coastal boundary conditions for tsunami wave run-up over sloping bathymetry
Authors: Kristina W. , Bokhove O. , van Groesen E.
Published: September 2014

Abstract. An effective boundary condition (EBC) is introduced as a novel technique for predicting tsunami wave run-up along the coast, and offshore wave reflections. Numerical modeling of tsunami propagation in the coastal zone has been a daunting task, since high accuracy is needed to capture aspects of wave propagation in the shallower areas. For example, there are complicated interactions between incoming and reflected waves due to the bathymetry and intrinsically nonlinear phenomena of wave propagation. If a fixed wall boundary condition is used at a certain shallow depth contour, the reflection properties can be unrealistic. To alleviate this, we explore a so-called effective boundary condition, developed here in one spatial dimension. From the deep ocean to a seaward boundary, i.e., in the simulation area, we model wave propagation numerically over real bathymetry using either the linear dispersive variational Boussinesq or the shallow water equations. We measure the incoming wave at this seaward boundary, and model the wave dynamics towards the shoreline analytically, based on nonlinear shallow water theory over bathymetry with a constant slope. We calculate the run-up heights at the shore and the reflection caused by the slope. The reflected wave is then influxed back into the simulation area using the EBC. The coupling between the numerical and analytic dynamics in the two areas is handled using variational principles, which leads to (approximate) conservation of the overall energy in both areas. We verify our approach in a series of numerical test cases of increasing complexity, including a case akin to tsunami propagation to the coastline at Aceh, Sumatra, Indonesia.
Diferenciais de rendimentos do trabalho feminino no Sul do Brasil: uma abordagem dual
Authors: Margonato Rita de Cassia Garcia , Souza Solange de Cassia Inforzato de , Nascimento Sidnei Pereira do
Published: September 2014

Este estudo analisa a formação e os diferenciais de rendimentos das mulheres nos setores de atividade econômica da Região Sul do Brasil, no período de 2002 e2009, a partir dos microdados da Pesquisa Nacional por Amostra de Domicílios (PNAD). Para tanto, o procedimento metodológico consiste em estimar as equações de seleção e de rendimento, corrigidas pelo Modelo de Seleção de Heckman (1979), a partir das quais realiza-se a mensuração do diferencial de rendimento das mulheres nos setores de comércio, indústria e serviços domésticos, comparativamente ao rendimento das mulheres no setor de serviços por meio de uma adaptação da Decomposição de Oaxaca-Blinder (1973) feita por Jann (2008). Evidenciou-se a hipótese de que a segmentação setorial ocorre no mercado de trabalho feminino da Região Sul do Brasil, pois os diferenciais de rendimento são explicados não apenas pelos atributos pessoais (produtivos ou não) e pela categoria de emprego, mas também pelas especificidades dos setores (efeito setor)  observados no mercado de trabalho  feminino da Região Sul. Em média, o efeito setor explicou 30% do diferencial salarial observado na indústria, 24% no comércio, e 34% no setor de serviços domésticos, quando comparado ao rendimento obtido no setor de serviços, em vantagem salarial.
A inserção da agricultura do Paraná no mercado internacional entre 2000 e 2011
Authors: Campos Lediany Freitas , Braun Mirian Beatriz Schneider
Published: September 2014

Este trabalho tem por objetivo analisar a inserção da agricultura paranaense no mercado externo, de2000 a2011. Foi utilizado o método estatístico descritivo, a partir de dados secundários, como Alice Web, Comtrade, Ipardes, dentre outros. Constatou-se que o Paraná tem, em média, cerca de 50% das suas exportações baseadas em produtos agrícolas, tendo aumentado para 64,01% em 2011. Doze principais produtos representam em torno de 90% das exportações agrícolas e em 2011 foram responsáveis por 56,42% da exportação total. Quanto aos mercados de destino, a União Europeia perdeu participação para a Ásia, com grande destaque para a China. O produto A – soja em grãos, mesmo triturados - se destaca como o mais importante na pauta de exportação do Estado. A agricultura aumentou a participação nas exportações do Paraná e o Estado perdeu participação na exportação agrícola nacional.
Estrutura etária da população paranaense entre 1970 e 2010
Authors: Pintor Eduardo de , Silva Geisiane Michelle da , Rippel Ricardo
Published: September 2014

A teoria da transição demográfica teve início com esforço de Frank Notestein (1945) para compreender as mudanças demográficas que estavam ocorrendo no ocidente da Europa desde o final do século XIX. A transição demográfica consiste na passagem entre dois cenários de crescimento demográfico, o que altera a estrutura etária da população. As transformações na estrutura etária do Paraná indicam a redução da participação da população jovem e aumento do envelhecimento da população, com crescimento do peso relativo da população idosa. As políticas públicas de educação, saúde, previdência social e mercado de trabalho devem considerar a atual mudança na estrutura etária. Deste modo, o objetivo deste artigo foi analisar a mudança na estrutura etária da população do estado do Paraná. Para isto foram utilizados dados dos Censos Demográficos do Instituto Brasileiro de Geografia e Estatística (IBGE) sobre a distribuição etária da população urbana e rural paranaense e de suas Mesorregiões. Conclui-se que a mudança na estrutura etária ocorre de forma generalizada em todas as Mesorregiões do estado. Entretanto, ocorre de forma desigual entre a população urbana e rural.