bluuebunny/crossref_metadata_2025 huggingface dataset:
Induction of Cyclooxygenase-2 Signaling by Stomatococcus mucilaginosus Highlights the Pathogenic Potential of an Oral Commensal
Authors: Yuan Zhihong , Panchal Dipti , Syed Mansoor Ali , Mehta Hiren , Joo Myungsoo , Hadid Walid , Sadikot Ruxana T.
Published: September 2013

Stomatococcus mucilaginosus is an oral commensal that has been occasionally reported to cause severe infections in immunocompromised patients. There is no information about the pathogenic role of S. mucilaginosus in airway infections. In a cohort of 182 subjects with bronchiectasis, we found that 9% were colonized with S. mucilaginosus in their lower airways by culture growth from bronchoalveolar lavage. To address the pathogenic potential of S.mucilaginosus, we developed a murine model of S. mucilaginosus lung infection. Intratracheal injection of S. mucilaginosus in C57BL/6 mice resulted in a neutrophilic influx with production of proinflammatory cytokines, chemokines, and lipid mediators, mainly PGE2 with induction of cyclooxygenase-2 (COX-2) in the lungs. Presence of TLR2 was necessary for induction of COX-2 and production of PGE2 by S. mucilaginosus. TLR2-deficient mice showed an enhanced clearance of S. mucilaginosus compared with wild-type mice. Administration of PGE2 to TLR2−/− mice resulted in impaired clearance of S. mucilaginosus, suggesting a key role for COX-2–induced PGE2 production in immune response to S. mucilaginosus. Mechanistically, induction of COX-2 in macrophages was dependent on the p38-ERK/MAPK signaling pathway. Furthermore, mice treated with S. mucilaginosus and Pseudomonas aeruginosa showed an increased mortality compared with mice treated with PA103 or S. mucilaginosus alone. Inhibition of COX-2 significantly improved survival in mice infected with PA103 and S. mucilaginosus. These data provide novel insights into the bacteriology and personalized microbiome in patients with bronchiectasis and suggest a pathogenic role for S. mucilaginosus in patients with bronchiectasis.
Osseous Hamartoma Arising from the Eustachian Tube
Authors: Kawamoto Ai , Katori Yukio , Honkura Yohei , Ogura Masaki , Oshima Takeshi , Kobayashi Toshimitsu
Published: September 2013

A fairly quite rare case of osseous tumor arising from the Eustachian tube (ET) is described. A 56-year-old man presented with a smooth bulky mass in the nasopharynx and secretory otitis media in the right ear. Computed tomography and magnetic resonance imaging indicated a solid tumor-like region occupying the nasopharynx with apparent extension to the right ET. Transnasal endoscopic surgery demonstrated that the tumor had originated from the ET, and the tumor was partially removed in the area where it had expanded into the nasopharynx. The pathological diagnosis was an osseous hamartoma consisting of bony tissue, fat cells and fibroblasts. To our knowledge, this is the first reported case of osseous hamartoma arising from the ET in the world literature. The patient presented symptoms of nasal obstruction and unilateral aural fullness. Reduction surgery and tympanostomy tube insertion were useful for accurate diagnosis and resolution of the symptoms.
Alveolar Soft Part Sarcoma: Unusual Etiology of Mediastinal Mass in an Adolescent
Authors: Schenning Ryan , Vajtai Petra , Troxell Megan , Pollock Jeffrey , Hopkins Katharine
Published: September 2013

Alveolar soft part sarcoma (ASPS) is a rare malignancy that usually arises in an extremity. Mediastinal involvement is uncommon, with only two reports of primary mediastinal disease and two reports of metastatic mediastinal disease in the literature, all referencing adult patients. To our knowledge, ours is the first report of ASPS presenting with a mediastinal mass in adolescence. Although ASPS is not generally included in the differential for adolescent mediastinal masses, it should be considered when clinical presentation and imaging appearance are characteristic.
Adenocarcinoma of an Ileostomy in a Case of Hirschprung’s Disease with Retroviral Disease
Authors: Bakhshi Girish , Shenoy Sachin S. , Jadhav Kavita V. , Tayade Mukund B. , Patil Sunil R. , Patel Chintan B.
Published: September 2013

The number of ileostomies created for benign diseases such as familial adenomatous polyposis and ulcerative colitis is increasing. Long-term ileostomies are prone to develop various complications over time. Ileostomy site carcinoma is a well-established complication in ulcerative colitis and familial adenomatous polyposis that have undergone total colectomy. However, no case of ileostomy site carcinoma has been described in a patient with Hirschprung’s disease. We present the first case of adenocarcinoma at an ileostomy site in a patient with Hirschprung’s disease with retroviral disease.
Patients’ Experience of a Regional Allergy Service
Authors: Jones Ray , O'Connor Anita , Kaminski Edward
Published: September 2013

Background

The principle reason for referral to specialist allergy clinics is to establish diagnoses and provide treatment plans to help patients manage their allergy. If patients do not accept, understand, or remember diagnoses or treatment, clinic visits may have been a waste of time. Few specialist allergy clinics follow up patients after diagnosis.

Design and Methods

This was a postal survey to assess patients’ i) perception of usefulness of specialist allergy clinic visits, ii) understanding of their allergy, iii) confidence in managing it, and iv) response to joining a regional online forum. Data for patients with confirmed allergy who attended the Peninsula Allergy Service (PAS) from 1998-2009 were extracted from consultant letters to general practitioners. Postal questionnaires were sent to 933 patients; 39% (336) responded.

Results

Two-thirds (63%) thought their clinic visit useful and resulted in them being more in control of their allergy; 9% thought it useful but they still had problems, 26% thought it had not been much use. One in six (16%, 55) respondents had major differences in their view of their allergy compared to that recorded by PAS. Over half (56%) had had further symptoms since their clinic visit and 120 patients, who were not confident in coping with their allergy, listed aspects of their lives that gave concern.

Conclusions

Specialist clinics need routine feedback from patients if they are to monitor their effectiveness and some better form of follow up for patients is needed to reinforce education and support patients. Public education is important.
Post-Traumatic Stress Disorder in Adolescents in Lebanon as Wars Gained in Ferocity: A Systematic Review
Authors: Shaar Khuzama Hijal
Published: September 2013

For decades, Lebanon was war-torn by civil strife, and occupation and invasion by neighboring countries. In time, these wars have escalated in intensity from sniping, barricading streets and random shelling of residential quarters to the use of rockets, aerial bombing, and heavy artillery. Adverse mental health effects are noted in times of war with post traumatic stress disorder (PTSD) as a main outcome. The aim of this study was to carry out a systematic review of published studies documenting the prevalence of PTSD in the adolescent population of Lebanon, to investigate the increase in these rates with the escalation of war intensity, and to examine PTSD determinants. A search strategy was developed for online databases (PubMed and Google Scholar) between inception to the first week of January 2013. Search terms used were PTSD, adolescents and Lebanon. Eleven studies reporting PTSD in adolescents met the inclusion criteria for a total number of 5965 adolescents. Prevalence rates of PTSD ranged from 8.5% to 14.7% for the civil war, 3.7% for adolescents with sensory disabilities, 21.6% for the Grapes of Wrath War, and 15.4% to 35.0% for the 2006 July War. Some increase in PTSD rates in time is noted. Type of trauma such as bereavement, injury, house destruction, and economic problems, low self efficacy and scholastic impairment were related to PTSD. These findings may help in the development of public health policies for PTSD prevention and treatment for the protection of adolescents from war atrocities and their consequences.
Learning Environments’ Activity Potential for Preschoolers (LEAPP): Study Rationale and Design
Authors: Tucker Patricia , Vanderloo Leigh M. , Newnham-Kanas Courtney , Burke Shauna M. , Irwin Jennifer D. , Johnson Andrew M. , van Zandvoort Melissa M.
Published: September 2013

Background

The purpose of this paper is to provide an overview of the study protocol for the Learning Environments’ Activity Potential for Preschoolers (LEAPP) study, the goal of which is to describe the activity levels of preschoolers attending various early learning venues and explore which attributes of these facilities (e.g. curriculum, policies, equipment, etc.) support activity participation.

Design and Methods

This cross-sectional study aimed to recruit approximately 30 early learning environments requesting participation from preschoolers aged 2.5-5 years. Data collection included: Actical accelerometers (MiniMitter, Oregon, USA) to measure the activity levels of children for five consecutive days (15-second epoch length) while in care; the Environment and Policy Assessment and Observation tool to explore the early learning environment's impact on activity; anthropometric data; the Child Temperament Questionnaire to assess the influence of preschoolers’ temperament on physical activity; and demographic information from parents/guardians and early learning staff. ANOVA and linear regression analyses will be conducted to assess variances in activity levels among preschoolers attending different early learning types and to explore the impact of early learning environments on their activity levels. Independent sample t-tests will be used to examine differences in activity levels based on sex and weight status.

Expected impact of the study for public health

This research will provide the first Canadian data to address environmental influences on preschoolers’ activity levels in differing early learning environments. Additionally, this work will highlight the extent to which activity levels vary among preschoolers enrolled in full-day kindergarten, centre-, and home-based childcare.
Crisis Communication in the Area of Risk Management: The CriCoRM Project
Authors: Scarcella Carmelo , Antonelli Laura , Orizio Grazia , Rossmann Costanze , Ziegler Lena , Meyer Lisa , Garcia-Jimenez Leonarda , Losada Jose Carlos , Correia Joao , Soares Joana , Covolo Loredana , Lirangi Enrico , Gelatti Umberto
Published: September 2013

Background

During the last H1N1 pandemic has emerged the importance of crisis communication as an essential part of health crisis management. The Project aims specifically to improve the understanding of crisis communication dynamics and effective tools and to allow public health institutions to communicate better with the public during health emergencies.

Design and Methods

The Project will perform different activities: i) state of the art review; ii) identification of key stakeholders; iii) communicational analysis performed using data collected on stakeholder communication activities and their outcomes considering the lessons learnt from the analysis of the reasons for differing public reactions during pandemics; iv) improvement of the existing guidelines; v) development of Web 2.0 tools as web-platform and feed service and implementation of impact assessment algorithms; vi) organization of exercises and training on this issues.

Expected impact of the study for public health

In the context of health security policies at an EU level, the project aims to find a common and innovative approach to health crisis communication that was displayed by differing reactions to the H1N1 pandemic policies. The focus on new social media tools aims to enhance the role of e-health, and the project aims to use these tools in the specific field of health institutions and citizens. The development of Web 2.0 tools for health crisis communication will allow an effective two-way exchange of information between public health institutions and citizens. An effective communication strategy will increase population compliance with public health recommendations.
Characterization of a Pollen-Specific and Desiccation-Associated AP2/ERF Type Transcription Factor Gene from Castor Bean (Ricinus communis L.)
Authors: Cipriano Thaís de Moura , Morais Angélica Taveira , Aragão Francisco José Lima
Published: September 2013

DREB transcription factors (TF) belong to the superfamily of AP2/ERF and their involvement in protein-protein interactions and DNA binding has been proposed. AP2/ERF proteins have important functions in the transcriptional regulation of a variety of biological processes related to growth and development, as well as various responses to environmental stimuli, regulating expression of plant biotic and abiotic stress-responsive genes. In this study an AP2/ERF TF gene (named RcDREB1) was isolated from castor bean (Ricinus communis L.) and its expression was analyzed in developing seeds, leaves, ovules, stems and petals of plants cultivated under field conditions. Transcripts were only observed in pollen grains, peaking during anthesis. The RcDREB1 deduced amino acid sequence was compared to other AP2/ERF TF proteins and presented 38–78% identity. Phylogenetic analysis classified it as a member of the CBF/DREB subfamily, rooting with the subgroup A-5. The RcDREB1 promoter was fused to the gus reporter gene and used to transform tobacco. Transgenic plants were exposed to various abiotic stress treatments (low and high tempera- tures, drought, salinity and exogenous ABA) and no detectable GUS expression was observed, suggesting that the RcDREB1 promoter is not active under tested conditions. In silico analyses revealed the presence of three copies of the regulatory late pollen-specific element (AGAAA) in the RcDREB1 5′-region. Interestingly, GUS expression was only observed in pollen grains, starting when the flower opened and initiating the senescence process; at this point, desiccated mature pollen grains are released from anthers. In addition, dehydrated developing pollen grains also expressed the gus gene. This is the first study on a DREB gene presenting pollen-specific expression.
Seed Extracts Impede Germination in Brassica rapa Plants
Authors: Barnum Kimberly , Franks Steven J.
Published: September 2013

Allelopathy is an important mechanism of interference competition in some plants, but little is known about whether compounds exuded from seeds influence the germination of neighbors. We treated seeds of multiple lines of Brassica rapa (field mustard) with aqueous extracts of Brassica rapa Fast Plant seeds and extracts of seeds of the invasive, allelopathic plant Alliaria petiolata (garlic mustard). Germination patterns differed significantly among populations, with Fast Plants germinating earliest. As predicted, Alliaria seed extracts significantly delayed germination compared to controls. Surprisingly, Fast Plant extracts reduced germination probability and delayed germination more than both controls and Alliaria extract-treated seeds. These results suggest that compounds in the seeds of both species appear to be allelopathic, and indicate a potentially important and unrecognized role for allelopathy in intra- and inter- specific competition at the seed stage.
Correlation of stroke Volume Measurement between sonosite portable Echocardiogram and Edwards Flotrac sensor-Vigileo Monitor in an Intensive care Unit
Authors: Behnia Mehrdad , Powell Sherry , Fallen Linda , Tamaddon Houman , Behnia Masud
Published: September 2013

Purpose

Stroke volume (SV) is a parameter that is being recognized as an endpoint in fluid resuscitation algorithms. Its role is now being realized as an important variable in hemodynamic assessment in various clinical scenarios such as septic and cardiogenic shocks. Direct measurement of stroke volume (SV) and its novel corollary, stroke volume variation (SVV) derived by proprietary software, are preferred over mean cardiac output (CO) measurements because they render a more accurate reflection of hemodynamic status independent of heart rate. Flotrac-Vigileo monitor (FTV) (Edwards Lifesciences, Irvine, CA, USA) is a system that uses a complex algorithm analyzing arterial waveform to calculate SV, SVV, and CO. We assessed the feasibility of obtaining SV measurements with a portable echocardiogram and validated its accuracy with the FTV system in mechanically ventilated patients in our intensive care unit (ICU). Furthermore, we emphasized the importance of hemodynamic measurements and familiarity with critical care echocardiography for the intensivists.

Methods

Ten patients who were on mechanical ventilation were studied. A femoral arterial line was connected to the FTV system monitoring SV and CO. A portable echocardiogram (M-Turbo; Sonosite, Bothell, WA) was used to measure SV. CO was calculated by multiplying SV by heart rate. No patient had arrhythmia. We used biplane Simpson's method of discs to calculate SV in which subtraction of end-systolic volume from end-diastolic volume yields the SV

Results

The comparison of simultaneous SV and CO measurements by echocardiography with FTV showed a strong correlation between the 2. (For SV, y = 0.9545x + 3.3, R2 = 0.98 and for CO, y = 0.9104x + 7.7074, R2 = 0.97).

Conclusions

In our small cohort, the SV and CO measured by a portable echocardiogram (Sonosite M-Turbo) appears to be closely correlated with their respective values measured by FTV. Portable echocardiography is a reliable noninvasive tool for the hemodynamic assessment of the critically ill. Its results need further validation with gold standard measures in a larger cohort of patients. However, our results suggest portable echocardiography could be an attractive tool in assessment of different hemodynamic scenarios in the critically ill.
Mathematical Modelling of Malaria with Treatment
Authors: Ghosh Mini
Published: September 2013

This paper proposes a Susceptible-Infective-Susceptible (SIS) model to study the malaria transmission with treatment by considering logistic growth of mosquito population. In this work, it is assumed that the treatment rate is proportional to the number of infectives below the capacity and is constant when the number of infectives is greater than the capacity. We find that the system exhibits backward bifurcation if the capacity is small and it gives bi-stable equilibria which makes the system more sensitive to the initial conditions. The existence and stability of the equilibria of the model are discussed in-detail and numerical simulations are presented to illustrate the numerical results.
A Solver for Helmholtz System Generated by the Discretization of Wave Shape Functions
Authors: Yuan Long , Hu Qiya
Published: September 2013

An interesting discretization method for Helmholtz equations was introduced in B. Després [1]. This method is based on the ultra weak variational formulation (UWVF) and the wave shape functions, which are exact solutions of the governing Helmholtz equation. In this paper we are concerned with fast solver for the system generated by the method in [1]. We propose a new preconditioner for such system, which can be viewed as a combination between a coarse solver and the block diagonal preconditioner introduced in [13]. In our numerical experiments, this preconditioner is applied to solve both two-dimensional and three-dimensional Helmholtz equations, and the numerical results illustrate that the new preconditioner is much more efficient than the original block diagonal preconditioner.
Analyses of the Dispersion Overshoot and Inverse Dissipation of the High-Order Finite Difference Scheme
Authors: Li Qin , Guo Qilong , Zhang Hanxin
Published: September 2013

Analyses were performed on the dispersion overshoot and inverse dissipation of the high-order finite difference scheme using Fourier and precision analysis. Schemes under discussion included the pointwise- and staggered-grid type, and were presented in weighted form using candidate schemes with third-order accuracy and three-point stencil. All of these were commonly used in the construction of difference schemes. Criteria for the dispersion overshoot were presented and their critical states were discussed. Two kinds of instabilities were studied due to inverse dissipation, especially those that occur at lower wave numbers. Criteria for the occurrence were presented and the relationship of the two instabilities was discussed. Comparisons were made between the analytical results and the dispersion/dissipation relations by Fourier transformation of typical schemes. As an example, an application of the criteria was given for the remedy of inverse dissipation in Weirs & Martín’s third-order scheme.
A Meshless Regularization Method for a Two-Dimensional Two-Phase Linear Inverse Stefan Problem
Authors: Tomas Johansson B. , Lesnic Daniel , Reeve Thomas
Published: September 2013

In this paper, a meshless regularization method of fundamental solutions is proposed for a two-dimensional, two-phase linear inverse Stefan problem. The numerical implementation and analysis are challenging since one needs to handle composite materials in higher dimensions. Furthermore, the inverse Stefan problem is ill-posed since small errors in the input data cause large errors in the desired output solution. Therefore, regularization is necessary in order to obtain a stable solution. Numerical results for several benchmark test examples are presented and discussed.
A Constrained Cauchy-Born Elasticity Accelerated Multigrid Method for Nanoindentation
Authors: Chen Jingrun , Ming Pingbing , Yang Jerry Zhijian
Published: September 2013

We introduce a new multigrid method to study the lattice statics model arising from nanoindentation. A constrained Cauchy-Born elasticity model is used as the coarse-grid operator. This method accelerates the relaxation process and considerably reduces the computational cost. In particular, it saves quite a bit when dislocations nucleate and move, as demonstrated by the simulation results.
An Entropic Scheme for an Angular Moment Model for the Classical Fokker-Planck-Landau Equation of Electrons
Authors: Mallet Jessy , Brull Stéphane , Dubroca Bruno
Published: September 2013

In plasma physics domain, the electron transport is described with the Fokker-Planck-Landau equation. The direct numerical solution of the kinetic equation is usually intractable due to the large number of independent variables. That is why we propose in this paper a new model whose derivation is based on an angular closure in the phase space and retains only the energy of particles as kinetic dimension. To find a solution compatible with physics conditions, the closure of the moment system is obtained under a minimum entropy principle. This model is proved to satisfy the fundamental properties like a H theorem. Moreover an entropic discretization in the velocity variable is proposed on the semi-discrete model. Finally, we validate on numerical test cases the fundamental properties of the full discrete model.
A Survey on Parallel Computing and its Applications in Data-Parallel Problems Using GPU Architectures
Authors: Navarro Cristóbal A. , Hitschfeld-Kahler Nancy , Mateu Luis
Published: September 2013

Parallel computing has become an important subject in the field of computer science and has proven to be critical when researching high performance solutions. The evolution of computer architectures (multi-coreandmany-core) towards a higher number of cores can only confirm that parallelism is the method of choice for speeding up an algorithm. In the last decade, the graphics processing unit, or GPU, has gained an important place in the field of high performance computing (HPC) because of its low cost and massive parallel processing power. Super-computing has become, for the first time, available to anyone at the price of a desktop computer. In this paper, we survey the concept of parallel computing and especially GPU computing. Achieving efficient parallel algorithms for the GPU is not a trivial task, there are several technical restrictions that must be satisfied in order to achieve the expected performance. Some of these limitations are consequences of the underlying architecture of the GPU and the theoretical models behind it. Our goal is to present a set of theoretical and technical concepts that are often required to understand the GPU and itsmassive parallelismmodel. In particular, we show how this new technology can help the field ofcomputational physics,especially when the problem isdata-parallel.We present four examples of computational physics problems;n-body, collision detection, Potts modelandcellular automatasimulations. These examples well represent the kind of problems that are suitable for GPU computing. By understanding the GPU architecture and its massive parallelism programming model, one can overcome many of the technical limitations found along the way, design better GPU-based algorithms for computational physics problems and achieve speedups that can reach up to two orders of magnitude when compared to sequential implementations.
A Multi-Material CCALE-MOF Approach in Cylindrical Geometry
Authors: Friess Marie Billaud , Breil Jérôme , Maire Pierre-Henri , Shashkov Mikhail
Published: September 2013

In this paper we present recent developments concerning a Cell-Centered Arbitrary Lagrangian Eulerian (CCALE) strategy using the Moment Of Fluid (MOF) interface reconstruction for the numerical simulation of multi-material compressible fluid flows on unstructured grids in cylindrical geometries. Especially, our attention is focused here on the following points. First, we propose a new formulation of the scheme used during the Lagrangian phase in the particular case of axisymmetric geometries. Then, the MOF method is considered for multi-interface reconstruction in cylindrical geometry. Subsequently, a method devoted to the rezoning of polar meshes is detailed. Finally, a generalization of the hybrid remapping to cylindrical geometries is presented. These explorations are validated by mean of several test cases using unstructured grid that clearly illustrate the robustness and accuracy of the new method.
A Parallel Adaptive Treecode Algorithm for Evolution of Elastically Stressed Solids
Authors: Feng Hualong , Barua Amlan , Li Shuwang , Li Xiaofan
Published: September 2013

The evolution of precipitates in stressed solids is modeled by coupling a quasi-steady diffusion equation and a linear elasticity equation with dynamic boundary conditions. The governing equations are solved numerically using a boundary integral method (BIM). A critical step in applying BIM is to develop fast algorithms to reduce the arithmetic operation count of matrix-vector multiplications. In this paper, we develop a fast adaptive treecode algorithm for the diffusion and elasticity problems in two dimensions (2D). We present a novel source dividing strategy to parallelize the treecode. Numerical results show that the speedup factor is nearly perfect up to a moderate number of processors. This approach of parallelization can be readily implemented in other treecodes using either uniform or non-uniform point distribution. We demonstrate the effectiveness of the treecode by computing the long-time evolution of a complicated microstructure in elastic media, which would be extremely difficult with a direct summation method due to CPU time constraint. The treecode speeds up computations dramatically while fulfilling the stringent precision requirement dictated by the spectrally accurate BIM.
A Coupled Immersed Interface and Level Set Method for Three-Dimensional Interfacial Flows with Insoluble Surfactant
Authors: Xu Jian-Jun , Huang Yunqing , Lai Ming-Chih , Li Zhilin
Published: September 2013

In this paper, a numerical method is presented for simulating the 3D interfacial flows with insoluble surfactant. The numerical scheme consists of a 3D immersed interface method (IIM) for solving Stokes equations with jumps across the interface and a 3D level-set method for solving the surfactant convection-diffusion equation along a moving and deforming interface. The 3D IIM Poisson solver modifies the one in the literature by assuming that the jump conditions of the solution and the flux are implicitly given at the grid points in a small neighborhood of the interface. This assumption is convenient in conjunction with the level-set techniques. It allows standard Lagrangian interpolation for quantities at the projection points on the interface. The interface jump relations are re-derived accordingly. A novel rotational procedure is given to generate smooth local coordinate systems and make effective interpolation. Numerical examples demonstrate that the IIM Poisson solver and the Stokes solver achieve second-order accuracy. A 3D drop with insoluble surfactant under shear flow is investigated numerically by studying the influences of different physical parameters on the drop deformation.
Population Vulnerability to Biannual Cholera Outbreaks and Associated Macro-Scale Drivers in the Bengal Delta
Authors: Akanda Ali Shafqat , Jutla Antarpreet S. , Gute David M. , Sack R. Bradley , Alam Munirul , Huq Anwar , Colwell Rita R. , Islam Shafiqul
Published: September 2013

The highly populated floodplains of the Bengal Delta have a long history of endemic and epidemic cholera outbreaks, both coastal and inland. Previous studies have not addressed the spatio-temporal dynamics of population vulnerability related to the influence of underlying large-scale processes. We analyzed spatial and temporal variability of cholera incidence across six surveillance sites in the Bengal Delta and their association with regional hydroclimatic and environmental drivers. More specifically, we use salinity and flood inundation modeling across the vulnerable districts of Bangladesh to test earlier proposed hypotheses on the role of these environmental variables. Our results show strong influence of seasonal and interannual variability in estuarine salinity on spring outbreaks and inland flooding on fall outbreaks. A large segment of the population in the Bengal Delta floodplains remain vulnerable to these biannual cholera transmission mechanisms that provide ecologic and environmental conditions for outbreaks over large geographic regions.
Modeling Risk Categories to Predict the Longitudinal Prevalence of Childhood Diarrhea in Indonesia
Authors: Sima Laura C. , Ng Reuben , Elimelech Menachem
Published: September 2013

We present an innovative approach for analyzing diarrheal prevalence data that uses latent variables to model the relationships between multiple, interdependent environmental risk factors, and socioeconomic mediators. This strategy was applied to elucidate diarrheal longitudinal prevalence risk factors in children 1–4 years of age in low-income areas of Jakarta, Indonesia. Through a prospective cohort study, we identified 257 children who had at least one episode of diarrhea. At the onset of the study, we collected responses to 44 indicators, covering a wide range of previously identified diarrhea risk factors, including demographic and socioeconomic factors. We used exploratory factor analysis to uncover four latent categories of risk factors and their respective indicators from the initial pool of 44 indicators. Thereafter, we used structural equation modeling to model the relationships between the four risk categories and diarrheal longitudinal prevalence, controlling for socioeconomic and demographic covariates. Our final model elucidated several pathways to longitudinal diarrheal prevalence. Most notably, poverty exerts its effect on increased diarrheal prevalence via dual pathways: poor household hygiene and food quality, controlling for covariates. Implications of this and other findings for disease control in Jakarta are discussed.
Density-Dependent Blood Stage Plasmodium falciparum Suppresses Malaria Super-Infection in a Malaria Holoendemic Population
Authors: Pinkevych Mykola , Petravic Janka , Chelimo Kiprotich , Vulule John , Kazura James W. , Moormann Ann M. , Davenport Miles P.
Published: September 2013

Recent studies of Plasmodium berghei malaria in mice show that high blood-stage parasitemia levels inhibit the development of subsequent liver-stage infections. Whether a similar inhibitory effect on liver-stage Plasmodium falciparum by blood-stage infection occurs in humans is unknown. We have analyzed data from a treatment-time-to-infection cohort of children < 10 years of age residing in a malaria holoendemic area of Kenya where people experience a new blood-stage infection approximately every 2 weeks. We hypothesized that if high parasitemia blocked the liver stage, then high levels of parasitemia should be followed by a “skipped” peak of parasitemia. Statistical analysis of “natural infection” field data and stochastic simulation of infection dynamics show that the data are consistent with high P. falciparum parasitemia inhibiting liver-stage parasite development in humans.
Comparison of the Mosquito Inoculation Technique and Quantitative Real Time Polymerase Chain Reaction to Measure Dengue Virus Concentration
Authors: Choy Milly M. , Ellis Brett R. , Ellis Esther M. , Gubler Duane J.
Published: September 2013

An accurate measure of infectious dengue virus in human and mosquito tissues is critical to fully understand virus–host relationships, disease severity, viral fitness, and pathogenesis. In recent years, RNA copy number measured by quantitative real time-polymerase chain reaction has been used to measure dengue virus concentration in vitro and in vivo. In this study, we detail important differences in the measurement of viral growth kinetics in Vero and C6/36 tissue cultures, in Aedes aegypti mosquitoes, and in viremic human sera using RNA genomic equivalents and mosquito infectious dose 50 (MID50). Although there was reasonably good correlation between the two methods, RNA copy number was 2 to 5 logs greater than infectious virus titers. These differences varied significantly depending on virus strain, viral platform, infectious virus assay, and viral growth phase. The results have important implications for the correct interpretation of biological and epidemiological data from experimental and clinical studies, and show that genomic equivalents should be interpreted with caution when used as a proxy for infectious virus in such studies.
Trends in Antimalarial Drug Use in Africa
Authors: Flegg Jennifer A. , Metcalf Charlotte J. E. , Gharbi Myriam , Venkatesan Meera , Shewchuk Tanya , Hopkins Sibley Carol , Guerin Philippe J.
Published: September 2013

Resistance to chloroquine (CQ) and sulphadoxine-pyrimethamine (SP) led the World Health Organization (WHO) to recommend changes in national drug policies. The time between policy changes and their implementation profoundly affects program impact. We developed a model based on data on antimalarial treatments, extracted from household surveys and national antimalarial policy information from the literature. Drug use in each country during the time period 1999–2011 and the trend in reduction of CQ use after policy change were estimated. The SP use estimates were correlated with the prevalence of a molecular marker associated with SP resistance. There was no spatial pattern in the country-level rate of reduction of CQ use, after policy change. In East Africa SP drug use was strongly correlated to resistance. If artemisinin resistance spreads to, or emerges in, Africa this methodology will be a valuable tool to estimate actual drug use and its impact on changes in drug efficacy.
The Impact of a School-Based Hygiene, Water Quality and Sanitation Intervention on Soil-Transmitted Helminth Reinfection: A Cluster-Randomized Trial
Authors: Freeman Matthew C. , Clasen Thomas , Brooker Simon J. , Akoko Daniel O. , Rheingans Richard
Published: September 2013

We conducted a cluster-randomized trial to assess the impact of a school-based water treatment, hygiene, and sanitation program on reducing infection with soil-transmitted helminths (STHs) after school-based deworming. We assessed infection with STHs at baseline and then at two follow-up rounds 8 and 10 months after deworming. Forty government primary schools in Nyanza Province, Kenya were randomly selected and assigned to intervention or control arms. The intervention reduced reinfection prevalence (odds ratio [OR] 0.56, 95% confidence interval [CI] 0.31–1.00) and egg count (rate ratio [RR] 0.34, CI 0.15–0.75) of Ascaris lumbricoides. We found no evidence of significant intervention effects on the overall prevalence and intensity of Trichuris trichiura, hookworm, or Schistosoma mansoni reinfection. Provision of school-based sanitation, water quality, and hygiene improvements may reduce reinfection of STHs after school-based deworming, but the magnitude of the effects may be sex- and helminth species-specific.
Evaluation of Chemical Preparation on Insect Wing Shape for Geometric Morphometrics
Authors: Lorenz Camila , Suesdek Lincoln
Published: September 2013

Geometric morphometrics is an approach that has been increasingly applied in studies with insects. A limiting factor of this technique is that some mosquitoes have wings with dark spots or many scales, which jeopardizes the visualization of landmarks for morphometric analysis. Recently, in some studies, chemically treatment (staining) of the wings was used to improve the viewing of landmarks. In this study, we evaluated whether this method causes deformation of the wing veins and tested whether it facilitates the visualization of the most problematic landmarks. In addition, we tested whether mechanical removal of the scales was sufficient for this purpose. The results showed that the physical and chemical treatments are equally effective in improving visualization of the landmarks. The chemical method did not cause deformation of the wing. Thus, some of these treatments should be performed before beginning geometric morphometric analysis to avoid erroneous landmark digitizing.
Regional inversion of CO2 ecosystem fluxes from atmospheric measurements: reliability of the uncertainty estimates
Authors: Broquet G. , Chevallier F. , Bréon F.-M. , Kadygrov N. , Alemanno M. , Apadula F. , Hammer S. , Haszpra L. , Meinhardt F. , Morguí J. A. , Necki J. , Piacentino S. , Ramonet M. , Schmidt M. , Thompson R. L. , Vermeulen A. T. , Yver C. , Ciais P.
Published: September 2013

Abstract. The Bayesian framework of CO2 flux inversions permits estimates of the retrieved flux uncertainties. Here, the reliability of these theoretical estimates is studied through a comparison against the misfits between the inverted fluxes and independent measurements of the CO2 Net Ecosystem Exchange (NEE) made by the eddy covariance technique at local (few hectares) scale. Regional inversions at 0.5° resolution are applied for the western European domain where ~ 50 eddy covariance sites are operated. These inversions are conducted for the period 2002–2007. They use a mesoscale atmospheric transport model, a prior estimate of the NEE from a terrestrial ecosystem model and rely on the variational assimilation of in situ continuous measurements of CO2 atmospheric mole fractions. Averaged over monthly periods and over the whole domain, the misfits are in good agreement with the theoretical uncertainties for prior and inverted NEE, and pass the chi-square test for the variance at the 30% and 5% significance levels respectively, despite the scale mismatch and the independence between the prior (respectively inverted) NEE and the flux measurements. The theoretical uncertainty reduction for the monthly NEE at the measurement sites is 53% while the inversion decreases the standard deviation of the misfits by 38%. These results build confidence in the NEE estimates at the European/monthly scales and in their theoretical uncertainty from the regional inverse modelling system. However, the uncertainties at the monthly (respectively annual) scale remain larger than the amplitude of the inter-annual variability of monthly (respectively annual) fluxes, so that this study does not engender confidence in the inter-annual variations. The uncertainties at the monthly scale are significantly smaller than the seasonal variations. The seasonal cycle of the inverted fluxes is thus reliable. In particular, the CO2 sink period over the European continent likely ends later than represented by the prior ecosystem model.
Laboratory studies of immersion and deposition mode ice nucleation of ozone aged mineral dust particles
Authors: Kanji Z. A. , Welti A. , Chou C. , Stetzer O. , Lohmann U.
Published: September 2013

Abstract. Ice nucleation in the atmosphere is central to the understanding the microphysical properties of mixed-phase and cirrus clouds. Ambient conditions such as temperature (T) and relative humidity (RH), as well as aerosol properties such as chemical composition and mixing state play an important role in predicting ice formation in the troposphere. Previous field studies have reported the absence of sulfate and organic compounds on mineral dust ice crystal residuals sampled at mountain top stations or aircraft based measurements despite the long-range transport mineral dust is subjected to. We present laboratory studies of ice nucleation for immersion and deposition mode on ozone aged mineral dust particles for 233 < T < 263 K. Heterogeneous ice nucleation of untreated kaolinite (Ka) and Arizona Test Dust (ATD) particles is compared to corresponding aged particles that are subjected to ozone concentrations of 0.4–4.3 ppmv in a stainless steel aerosol tank. The portable ice nucleation counter (PINC) and immersion chamber combined with the Zurich ice nucleation chamber (IMCA-ZINC) are used to conduct deposition and immersion mode measurements, respectively. Ice active fractions as well as ice active surface site densities (ns) are reported and observed to increase as a function of decreasing temperature. We present first results that demonstrate enhancement of the ice nucleation ability of aged mineral dust particles in both the deposition and immersion mode due to ageing. We also present the first results to show a suppression of heterogeneous ice nucleation activity without the condensation of a coating of (in)organic material. In immersion mode, low ozone exposed Ka particles showed enhanced ice activity requiring a median freezing temperature of 1.5 K warmer than that of untreated Ka, whereas high ozone exposed ATD particles showed suppressed ice nucleation requiring a median freezing temperature of 3 K colder than that of untreated ATD. In deposition mode, low exposure Ka had ice active fractions of an order of magnitude higher than untreated Ka, whereas high ozone exposed ATD had ice active fractions up to a factor of 4 lower than untreated ATD. From our results, we derive and present parameterizations in terms of ns(T) that can be used in models to predict ice nuclei concentrations based on available aerosol surface area.
Influence of surface morphology on the immersion mode ice nucleation efficiency of hematite particles
Authors: Hiranuma N. , Hoffmann N. , Kiselev A. , Dreyer A. , Zhang K. , Kulkarni G. , Koop T. , Möhler O.
Published: September 2013

Abstract. In this paper, the effect of the morphological modification of aerosol particles with respect to heterogeneous ice nucleation is comprehensively investigated for laboratory-generated hematite particles as a model substrate for atmospheric dust particles. The surface area-scaled ice nucleation efficiencies of monodisperse cubic hematite particles and milled hematite particles were measured with a series of expansion cooling experiments using the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) cloud simulation chamber. Complementary off-line characterization of physico-chemical properties of both hematite subsets were also carried out with scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, dynamic light scattering (DLS), and an electro-kinetic particle charge detector to further constrain droplet-freezing measurements of hematite particles. Additionally, an empirical parameterization derived from our laboratory measurements was implemented in the single-column version of the Community Atmospheric Model version 5 (CAM5) to investigate the model sensitivity in simulated ice crystal number concentration on different ice nucleation efficiencies. From an experimental perspective, our results show that the immersion mode ice nucleation efficiency of milled hematite particles is almost an order of magnitude higher at −35.2 °C < T < −33.5 °C than that of the cubic hematite particles, indicating a substantial effect of morphological irregularities on immersion mode freezing. Our modeling results similarly show that the increased droplet-freezing rates of milled hematite particles lead to about one order magnitude higher ice crystal number in the upper troposphere than cubic hematite particles. Overall, our results suggest that the surface irregularities and associated active sites lead to greater ice activation through droplet-freezing.
Antecedent flow conditions and nitrate concentrations in the Mississippi River Basin
Authors: Murphy J. C. , Hirsch R. M. , Sprague L. A.
Published: September 2013

Abstract. The influence of antecedent flow conditions on nitrate concentrations was explored at eight sites in the Mississippi River Basin, USA. Antecedent moisture conditions have been shown to influence nutrient export from small, relatively homogenous basins, but this influence has not been observed at a regional or continental scale. Antecedent flow conditions were quantified as the ratio between the mean daily flow of the previous year and the mean daily flow from the period of record (Q ratio), and the Q ratio was statistically related to nitrate anomalies (the unexplained variability in nitrate concentration after filtering out season, long-term trend, and contemporaneous flow effects) at each site. Nitrate anomaly and Q ratio were negatively related at three of the four major tributary sites and upstream in the Mississippi River, indicating that when the previous year was drier than average, at these sites, nitrate concentrations were higher than expected. The strength of these relationships increased when data were subdivided by contemporaneous flow conditions. Five of the eight sites had significant negative relationships (p ≤ 0.05) at high or moderately high contemporaneous flows, suggesting nitrate that accumulates in these basins during a drought is flushed during subsequent storm events. At half of the sites, when flow during the previous year was 50% drier than average, nitrate concentration can be from 9 and 27% higher than nitrate concentrations that follow a year with average daily flow. Conversely, nitrate concentration can be from 8 and 21% lower than expected when the previous year was 50% wetter than average. These relationships between nitrate concentration and Q ratio serve as the basis for future studies that can better define specific hydrologic processes occurring during and after a drought, which influence nitrate concentration, such as the duration or magnitude of low flows, and the timing of low and high flows.